Artykuły w czasopismach na temat „Local search taxonomy”

Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and ScalaBLAST. In our best case, MPI-blastn was able to run 408 times faster in 384 cores. Our evaluations demonstrated that NCBI-TaxCollector is able to perform taxonomic attachments 125 times faster and needs 120 times less RAM than the previous TaxCollector. Through our optimizations, a multiple sequence search that currently takes 37 hours can be performed in less than 6 min and a post processing with NCBI taxonomic data attachment, which takes 48 hours, now is able to run in 23 min.

Between 1998 and 2004, the planning community has seen vast progress in terms of the sizes of benchmark examples that domain-independent planners can tackle successfully. The key technique behind this progress is the use of heuristic functions based on relaxing the planning task at hand, where the relaxation is to assume that all delete lists are empty. The unprecedented success of such methods, in many commonly used benchmark examples, calls for an understanding of what classes of domains these methods are well suited for. In the investigation at hand, we derive a formal background to such an understanding. We perform a case study covering a range of 30 commonly used STRIPS and ADL benchmark domains, including all examples used in the first four international planning competitions. We *prove* connections between domain structure and local search topology -- heuristic cost surface properties -- under an idealized version of the heuristic functions used in modern planners. The idealized heuristic function is called h^+, and differs from the practically used functions in that it returns the length of an *optimal* relaxed plan, which is NP-hard to compute. We identify several key characteristics of the topology under h^+, concerning the existence/non-existence of unrecognized dead ends, as well as the existence/non-existence of constant upper bounds on the difficulty of escaping local minima and benches. These distinctions divide the (set of all) planning domains into a taxonomy of classes of varying h^+ topology. As it turns out, many of the 30 investigated domains lie in classes with a relatively easy topology. Most particularly, 12 of the domains lie in classes where FF's search algorithm, provided with h^+, is a polynomial solving mechanism. We also present results relating h^+ to its approximation as implemented in FF. The behavior regarding dead ends is provably the same. We summarize the results of an empirical investigation showing that, in many domains, the topological qualities of h^+ are largely inherited by the approximation. The overall investigation gives a rare example of a successful analysis of the connections between typical-case problem structure, and search performance. The theoretical investigation also gives hints on how the topological phenomena might be automatically recognizable by domain analysis techniques. We outline some preliminary steps we made into that direction.

Understanding the relationship between a search algorithm and the space of problems is a fundamental issue in the optimization field. In this paper, we lay the foundations to elaborate taxonomies of problems under estimation of distribution algorithms (EDAs). By using an infinite population model and assuming that the selection operator is based on the rank of the solutions, we group optimization problems according to the behavior of the EDA. Throughout the definition of an equivalence relation between functions it is possible to partition the space of problems in equivalence classes in which the algorithm has the same behavior. We show that only the probabilistic model is able to generate different partitions of the set of possible problems and hence, it predetermines the number of different behaviors that the algorithm can exhibit. As a natural consequence of our definitions, all the objective functions are in the same equivalence class when the algorithm does not impose restrictions to the probabilistic model. The taxonomy of problems, which is also valid for finite populations, is studied in depth for a simple EDA that considers independence among the variables of the problem. We provide the sufficient and necessary condition to decide the equivalence between functions and then we develop the operators to describe and count the members of a class. In addition, we show the intrinsic relation between univariate EDAs and the neighborhood system induced by the Hamming distance by proving that all the functions in the same class have the same number of local optima and that they are in the same ranking positions. Finally, we carry out numerical simulations in order to analyze the different behaviors that the algorithm can exhibit for the functions defined over the search space [Formula: see text].

Detecting the communicative intent behind user queries is critically required by search engines to understand a user’s search goal and retrieve the desired results. Due to increased web searching in local languages, there is an emerging need to support the language understanding for languages other than English. This article presents a distinctive, capsule neural network architecture for intent detection from search queries in Urdu, a widely spoken South Asian language. The proposed two-tiered capsule network utilizes LSTM cells and an iterative routing mechanism between the capsules to effectively discriminate diversely expressed search intents. Since no Urdu queries dataset is available, a benchmark intent-annotated dataset of 11,751 queries was developed, incorporating 11 query domains and annotated with Broder’s intent taxonomy (i.e., navigational, transactional and informational intents). Through rigorous experimentation, the proposed model attained the state of the art accuracy of 91.12%, significantly improving upon several alternate classification techniques and strong baselines. An error analysis revealed systematic error patterns owing to a class imbalance and large lexical variability in Urdu web queries.

Straipsnis skiriamas euristinių optimizavimo algoritmų, kurie jau kelis dešimtmečius traukia kompiuterių mokslo specialistų dėmesį, klasifikavimo klausimų aptarčiai. Jame apibrėžiami euristinių algoritmų tikslai, paskirtis, jų principiniai skiriamieji faktoriai, savybės. Apžvelgiamos svarbesnių euristinių optimizavimo algoritmų (tokių kaip atkaitinimo modeliavimas, tabu paieška, genetiniai algoritmai ir pan.) klasifikavimo schemos (metodikos). Nagrinėjamas universalios algoritmų sudedamųjų komponentų matricos – substancinių konceptų sistemos – naudojimas klasifikuojant euristinius algoritmus. Pabaigoje pateikiamos apibendrinamosios išvados.Reikšminiai žodžiai: algoritmai, algoritmų klasės, euristiniai ir metaeuristiniai algoritmai, algoritmų klasifikavimas.On the classification of heuristic algorithmsAlfonsas Misevičius, Vytautas Bukšnaitis, Jonas Blonskis SummaryIn this paper, the issues related to the classification (taxonomy) of heuristic optimization algorithms are discussed. Firstly, the main goals and features of heuristic techniques are introduced. Further, we outline some important classification schemes (templates) for the classical and modern heuristic algorithms such as (descent) local search, simulated annealing, tabu search, genetic (evolutionary) algorithms, ant colony optimization, etc. We also analyze the basic aspects of a universal classification template based on a set of so-called substantial concepts, i.e. the fundamental structural components of the algorithms. The paper is completed with concluding remarks. Key words: algorithms, heuristic and metaheuristic algorithms, classification of algorithms.

This article presents a novel algorithm based on the cluster first-route second method, which executes a solution through K-means and Optics clustering techniques and Nearest Neighbor and Local Search 2-opt heuristics, for the solution of a vehicle routing problem with time windows (VRPTW). The objective of the problem focuses on reducing distances, supported by the variables of demand, delivery points, capacities, time windows and type of fleet in synergy with the model's taxonomy, based on data referring to deliveries made by a logistics operator in Colombia. As a result, good solutions are generated in minimum time periods after fulfilling the agreed constraints, providing high performance in route generation and solutions for large customer instances. Similarly, the algorithm demonstrates efficiency and competitiveness compared to other methods detailed in the literature, after being benchmarked with the Solomon instance data set, exporting even better results.

Abstract The distribution of the highly diversified and species-rich snake genus Atractus was assessed in search for endemism areas. The dataset of 6000 museum specimens was used to run an Endemicity Analyses in order to identify areas of biogeographic relevance for the genus Atractus. By using distinct methodological approaches and modifying the size and shape of grid cells we obtained a better adjustment to each species range, taking into account species distributed along the Andean and Atlantic Forest mountain ranges or certain vegetation constraints. Three scales of endemism were observed: micro endemic areas, represented by three different regions; intermediate sized endemic areas, represented by nine different regions; and macro-endemic areas, represented by four different provinces. Although most assessed regions corroborate well-defined biogeographic units according to the scientific literature, some, mainly located in the Colombian Andes, are not regularly considered in biogeographic syntheses carried out for vertebrates. Methodological approaches, along with a well curated database and taxonomic accuracy, may significantly influence the recovery of endemism areas, mainly considering mountain topography and local niche structure. The results present herein highlight the relevance of three Colombian Cordilleras, in order to completely understand Neotropical biota patterns of distribution. It is important to note that a well-resolved taxonomy represents both the framework and the first step toward a comprehensive biographical synthesis reducing Wallacean shortfalls in biodiversity.

Nocardiosis is a neglected tropical disease. It has varied geographical presence and a spectrum of clinical presentations. This review aims to focus on the epidemiology of nocardial infections with a systematic approach to their diagnosis and treatment. <i>Nocardia</i>causes chronic infections and ailments, and may remain cryptic but progressive in its course. Unless suspected, diagnosis can be easily missed resulting in increased morbidity and mortality. Thorough knowledge of local epidemiology, demography, clinical course and presentation, diagnostic modalities, and antibiotic susceptibility patterns of the prevalent <i>Nocardia</i> species is essential to curb spread of this infection. This is a systematic review in which internet search has been done for citation indices (Embase, PubMed, Ovid, and other individual journals) till March 2020 utilizing the following key words “Nocardia,” “taxonomy,” “prevalence,” “clinical features,” “diagnosis,” “treatment,” and “susceptibility.” We selected a total of 87 review articles, case series, and case reports all in English language.

Zamiaceae, a family of the ancient order Cycadales, is distributed throughout the tropical and subtropical regions of both the Old and New Worlds. Here, we present a systematic review of Zamiaceae with emphasis on Zamia species from South America. We aim to (a) establish the current knowledge, (b) identify research gaps, and (c) indicate directions for future studies, discussing ecology and conservation of South America species. The search recovered 508 papers, further classified into 11 research topics: taxonomy and systematics, morphology, biochemistry, genetics, phylogeography, population ecology, reproductive biology, ecological interactions, plant propagation, conservation, and reviews. The number of publications doubled in the 21st century, mostly focusing on genetics ( n = 60), taxonomy and systematics ( n = 52), morphology ( n = 36), ecological interactions ( n = 30), and an increasing interest in population ecology ( n = 29) and conservation ( n = 32). Studies are concentrated in North and Central America (54% of all studies) with just 6% (29) addressing South America species of Zamia. Overall, studies point out the key role of pollinators in promoting gene flow through pollen dispersal among populations of Zamiaceae. Therefore, investigate natural history, ecology, reproductive biology, genetic, and phylogeography, especially for South America species, are needed. Moreover, the implementation of in situ and ex situ collections and germplasm banks linked to botanical gardens are essential for the conservation and reestablishment of local populations of critically endangered Zamia species in South America. Concomitantly, we suggest studies modeling the distribution of Zamia species in future climate change scenarios.

Purpose: to determine the dependence of the development of local relapse depending on the chosen tactics of surgical treatment with different biological subtypes of breast cancer. Materials and methods: molecular taxonomy of breast cancer may improve the prognosis of regional regional recurrence (MPR) and has a great potential for improving decisionmaking regarding local treatment for breast cancer. The review of the world literature, reflecting prospective and retrospective studies on the biological characteristics of breast cancer, is reviewed. The studies reflect such parameters as the degree of malignancy, the age of the patients, the biological subtype of the tumor, and the treatment performed. The development of local and regional regional relapse was assessed depending on the choice of surgical treatment tactics: radical mastectomy and organ-preserving treatment + radiotherapy. The search was limited to 2001, when biological subtypes of breast cancer were identified. Prospective and retrospective studies were evaluated in patients with early operable breast cancer. Conclusions: young age, tumor malignancy, tumor node size, presence of lymphovascular invasion or lymph node involvement and unfavorable tumor subtypes such as Her2 /neu and triple-negative tumors can be considered as the main predictors of relapse in breast cancer. Tumors having a triple-negative nature have the most aggressive course, this concerns both local, regional relapse, and distant metastasis. Advances in modern neoadjuvant therapy have reduced the overall number of local relapses for all subgroups. Radiation therapy also helps to reduce the risk of local and regional recurrence. At present, there is no single-valued data on the choice of surgical treatment tactics for various biological subtypes, however effective systemic therapy as well as radiotherapy reduces the frequency of local recurrences after performing organ-preserving surgeries in unfavorable tumor subtypes and according to the results of studies, the total and disease-free survival is comparable, as and during mastectomy.

Abstract Species of the genus Microascus are uncommon agents of human diseases despite their ubiquitous presence in the environment. In this communication, the first case of white grain eumycetoma caused by the fungus Microascus gracilis is reported. The patient was initially misdiagnosed as having actinomycetoma based on the grains morphological and cytological features and was treated with antimicrobial therapy with no clinical improvement. She underwent wide local surgical excision to improve the response to medical treatment and further grain cultural, molecular and taxonomy techniques were conducted and the diagnosis of mycetoma due to M. gracilis was established. The antifungal susceptibilities of this isolate to nine drugs were tested in vitro and they showed poor activity. Combination therapy with surgery and itraconazole led to complete recovery. A medical literature search revealed no previous report on M. gracilis as a causative agent of eumycetoma and hence we are reporting this new causative agent of human eumycetoma. Also, the difficulty in the management of this patient emphasizes the need for accurate and appropriate diagnostic tests for the identification of mycetoma-causative organisms and thus proper management.

Crosstalk between the gut microbiome and the host plays an important role in animal development and health. Small compounds are key mediators in this host–gut microbiome dialogue. For instance, tryptophan metabolites, generated by biotransformation of tryptophan through complex host–microbiome co-metabolism can trigger immune, metabolic, and neuronal effects at local and distant sites. However, the origin of tryptophan metabolites and the underlying tryptophan metabolic pathway(s) are not well characterized in the current literature. A large number of the microbial contributors of tryptophan metabolism remain unknown, and there is a growing interest in predicting tryptophan metabolites for a given microbiome. Here, we introduce TrpNet, a comprehensive database and analytics platform dedicated to tryptophan metabolism within the context of host (human and mouse) and gut microbiome interactions. TrpNet contains data on tryptophan metabolism involving 130 reactions, 108 metabolites and 91 enzymes across 1246 human gut bacterial species and 88 mouse gut bacterial species. Users can browse, search, and highlight the tryptophan metabolic pathway, as well as predict tryptophan metabolites on the basis of a given taxonomy profile using a Bayesian logistic regression model. We validated our approach using two gut microbiome metabolomics studies and demonstrated that TrpNet was able to better predict alterations in in indole derivatives compared to other established methods.

Sargassum is a well-known genus of brown algae in Indonesia that has long been investigated due to its economic importance. To support its biological research, it is important to identify and classify the species studied. Morphological identification had greatly contributed to taxonomy, however, it cannot distinguish Sargassum species accurately due to its plasticity. The current study aims to identify Lombok Sargassum molecularly using an ITS2 DNA barcode. Fresh algae were collected from Ekas Bay (EB) and Aan Cape (AC) in Lombok. DNA was first purified, and then its gene product was amplified using ITS2 primers. DNA sequences were examined and traced using the Basic Local Alignment Search Tool (BLAST). DNA sequences were processed in MEGA-X to reconstruct the phylogenetic tree and estimate the genetic distance. Three species were identified based on the BLAST results: Sargassum cf granuliferum, Sargassum polycystum, and Sargassum oligocystum. The base length obtained ranged from 521 to 637 bp, with a similarity percentage of 99.25 to 100%. The phylogenetic tree exhibited each recognized Sargassum species was clustered with the same species from the gene bank. Interspecies genetic distance was 0,000-0,0039, while amongst Sargassum species it's 0,0136-0,2395. The genetic distance between Sargassum and Ulva adherens (outgroup) was >1. Sargassum species found in Lombok were closely related to other similar species in the GenBank.

AbstractPhenotypic, chemotaxonomic and genotypic data from 12 strains ofEscherichia coli werecollected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems forE. coliand to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing ofE. colito species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification ofE. coli. The results showed that identification ofE. colistrains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.

Abstract The platform economy and its leading firms, such as Amazon, Facebook and Google, are reorganising the geography of value creation and capture on both a local and global scale. This article argues that economic geographers have underappreciated the implications of the platform on space. First, we demonstrate the concentration of platform giants in terms of location on the US West Coast and in terms of their market share in various services, such as search, maps and online sales. Platforms are simultaneously intermediaries, two-sided markets, data aggregators and leading users of artificial intelligence (AI). Second, we use a labour taxonomy to demonstrate the extensive reach of these platforms in terms of the labour markets that they serve and shape. To illustrate these changes in the geography of value creation, we present case studies of Amazon and Google Maps to show their effects on the location of economic activity. Third, we elaborate on our contention that platforms are at once intermediaries and data hubs. AI is likely to reinforce the power of these platform leaders because they have the largest data sets, the most computational power, enormous teams of the best AI researchers and vast reservoirs of capital that they can use to make acquisitions. We conclude by identifying areas for future research and calling upon economic geographers to consider the implications of the platform economy in reshaping the space of economic activity.

A wireless sensor network (WSN) is defined as a set of spatially distributed and interconnected sensor nodes. WSNs allow one to monitor and recognize environmental phenomena such as soil moisture, air pollution, and health data. Because of the very limited resources available in sensors, the collected data from WSNs are often characterized as unreliable or uncertain. However, applications using WSNs demand precise readings, and uncertainty in data reading can cause serious damage (e.g., health monitoring data). Therefore, an efficient local/distributed data processing algorithm is needed to ensure: (1) the extraction of precise and reliable values from noisy readings; (2) the detection of anomalies from data reported by sensors; and (3) the identification of outlier sensors in a WSN. Several works have been conducted to achieve these objectives using several techniques such as machine learning algorithms, mathematical modeling, and clustering. The purpose of this paper is to conduct a systematic literature review to report the available works on outlier and anomaly detection in WSNs. The paper highlights works conducted from January 2004 to October 2018. A total of 3520 papers are reviewed in the initial search process. Later, these papers are filtered by title, abstract, and contents, and a total of 117 papers are selected. These papers are examined to answer the defined research questions. The current paper presents an improved taxonomy of outlier detection techniques. This will help researchers and practitioners to find the most relevant and recent studies related to outlier detection in WSNs. Finally, the paper identifies existing gaps that future studies can fill.

Background: Primary palliative care (PPC) education programs have arisen in response to the recognition that all clinicians need to have a basic set of knowledge and skills to provide excellent care to all patients. PPC education programs appear to vary widely, making it difficult for potential learners to find the right program to fit their needs. We have cataloged and categorized a snapshot of PPC education programs across the United States to serve as a resource for those seeking training, and for educators interested in starting or optimizing such programs. Methods: Medical and commercial search engines (MSEs and CSEs, respectively) were used to generate a list of PPC education programs in the United States. Programs were contacted to supplement information available online, and then categorized based on intended learner, certification/degree conferred upon completion, and other characteristics. Results: There was little overlap between the PPC education programs found through MSEs and CSEs. Programs found via CSEs varied with respect to intended learners, pedagogy, content, and cost. Among the minority of programs that confer a certification/degree upon completion, there is no consensus as to what these signify. Conclusions: The wide variety of PPC education programs is both a challenge to and strength of the field. We hope that this report will serve as a call to develop a standard PPC education taxonomy to help define essential components of all PPC programs, while also leaving sufficient room for programs to serve the unique needs of their local learners and patient populations.

Mordellidae (tumbling flower beetles) is a globally distributed family of Coleoptera; it is among the most species-rich families (containing 115 genera and 2308 species described). It is important because of its agroforestry significance and its ecosystem-sustaining attributes. However, the past and current status of Mordellidae research remains unclear. A comprehensive literature review of Mordellidae articles published over the period of 1864–2013 based on the Zoological Record was conducted for the first time. A total of 863 articles were used for analysis after a strict literature search using screening protocols. These articles were then assigned to four categories based on the year of publication, topics/themes, primary authors, and frequently utilized journals for publication of Mordellidae-related articles. The results reveal that: (1) there are three prosperous research periods (1876–1898, 1922–1957, and 1977–2012) for Mordellidae during 1864–2013 that are associated with the active period of three generations of the main taxonomists. However, it is unfortunate that it also demonstrates there is a lack of upcoming researchers to continue the work after the retirement of the current generation, thus action should be taken immediately to promote research on Mordellidae; (2) on average, each primary author published 3.1 papers, but ~35% of the Mordellidae articles were published by less than 3% of the primary authors; (3) researchers tended to mostly publish their articles in local journals of their home countries; (4) more than 90% of the articles pertain to traditional taxonomy, with those of early times generally containing only simple descriptions of the species and the holotypes chosen are sparsely deposited with the researchers or amateurs around the world, thus making them difficult to be checked; (5) nearly half of the studies described Mordellidae species from Palaearctic realm, about one-third of the studies described species in other areas rather than in the fauna in which the authors lived, and about two-fifths of the studies described species from countries outside of the authors’ country of origin. Therefore, the in-depth systematic study of worldwide Mordellidae is required to reconstruct Mordellidae phylogeny and a revision of its classification system with modern methods of comparative morphology, molecular biology, zoogeography, and cladistics. In order to better understand the life stages and biology of Mordellidae insects, more work on Mordellidae ecology should be undertaken to develop strategies for pest control. We hope that this review will provide information to the novice and expert alike in Mordellidae research pertaining to its past and current status, possible future research areas, and attract more attention from the scientific world and renew an interest in Mordellidae research.

The present study focuses on the status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae). The internal transcribed spacer (ITS) region of nuclear ribosomal DNA and chloroplast trnL-F gene of the questioned species were sequenced. The Basic Local Alignment Search Tool (BLAST) search showed maximum identity with R. stenostachya. The parsimony analysis of ITS, trnL-F and combined sequences data analyses revealed grouping of Reseda species consistent with established taxonomic sections of the genus, R. pentagyna showed proximity with R. stenostachya (100% bootstrap support), nested within the clade of section Reseda.DOI: http://dx.doi.org/10.3329/bjpt.v20i2.17397Bangladesh J. Plant Taxon. 20(2): 233-238, 2013

Background This study sought to investigate the occurrence of taxonomic patterns between semi-arid and humid regions, verifying how the taxonomic affiliation can influence the selection of plants for medicinal purposes and act as a selection criterion. Methods The relationship between the taxonomic affiliation and the selection of medicinal plants with four different communities was analyzed; two of them associated with a seasonally dry tropical forest and the other two associated with a tropical rain forest. We used the Utilitarian Equivalence Model (transposing the concept of ecological equivalence, proposed by Odum, for ethnobotany) to test the hypothesis that species that have the same taxonomic affiliation tend to have the same therapeutic applications in different environments (utilitarian equivalence). In addition, we used the Utilitarian Redundancy Model to verify whether, within the same medical system, plants of the same taxonomic affiliation tend to be redundant (treating the same diseases). Results We found that a pair of plants of the same genus were 9.25 times more likely to be equivalent than a different genus pair (OR = 9.25, CI [1.68–51.02], p < 0.05). When we analyzed the species used by the same population, the chances of a pair having similar therapeutic uses (utilitarian redundancy) increased when they were species of the same family (OR = 1.94, CI [1.06−3.53]; p < 0.05). Conclusions These findings confirm the hypothesis that there is an influence of taxonomic affiliation, in terms of genera and family, on the selection of medicinal plants in semi-arid and humid areas in Northeast Brazil. In addition, our Utilitarian Equivalence Model can be an important tool in the search for more common selection criteria, in order to identify the shared characteristics among the equivalent pairs and consequently the main types of perceptions or stimuli that led to the inclusion of such species in local pharmacopoeias.

Les poils épidermiques et les types stomatiques chez les morphotypes de karité (Vitellaria paradoxa C.F. Gaertn subsp. paradoxa) ont été étudiés au Tchad en 2010, de Juillet à Septembre. L’objectif est la recherche des caractères micro morphologiques discriminants susceptibles d’améliorer l’identification des morphotypes de cette espèce. En fait, des morphotypes de karité ont été décrits et nommés par les ruraux dans la province du Mandoul au Tchad. Les amandes de karité sont transformées en beurre, ce qui lui confère une importance sur le plan socio-économique. Des fragments de bourgeon apical prélevés sur des jeunes plantes issues de la germination des graines des cinq (5) morphotypes ont permis d’observer les types de poils épidermiques. Aussi, des échantillons de feuilles prélevés distinctement de chaque morphotype ont été préparés selon la méthode de Barfod (1988). Cette méthode a été privilégiée car l’épiderme de la feuille de karité n’est pas facilement détachable. Elle consiste à bouillir les échantillons de feuilles dans de l’eau distillée pendant 10 minutes puis ils sont trempés dans l’acide nitrique à 40% pendant 16 à 20 heures. Cette opération a permis de ramollir le mésophyle et facilite la desquamation de la cuticule. La surface du fragment de la feuille ramollie placée sur une lame de microscope dans une goutte d'eau est grattée délicatement et progressivement à l’aide du bord de ciseaux jusqu'à ce qu'un fragment d'épiderme transparent apparaisse. Les épidermes foliaires ainsi obtenus sont placés dans du Lugol pendant 10 minutes puis montés après rinçage entre lame et lamelle dans la gélatine glycérinée et observés au microscope optique de type MOTIC. Au total 30 dénombrements ont été effectués sur les deux faces soit en moyenne 6 observations par morphotype. Ces dénombrements ont permis de calculer la densité stomatique et l’indice stomatique de chaque morphotype. La densité stomatique est la moyenne des 6 dénombrements par unité de surface (mm²). Les résultats ont montré 4 groupes de morphotypes : 1- des poils épidermiques simples longs observés chez le morphotype A, appelé localement « Bogrombaye » ; 2- des poils simples courts observés Djekota et al., 2020 Journal of Animal & Plant Sciences (J.Anim.Plant Sci. ISSN 2071-7024) Vol.45 (1): 7758-7770 https://doi.org/10.35759/JAnmPlSci.v45-1.1 7759 chez les morphotypes C, E et F « Komane, Mbabète, Ngoïtokoro » ; 3- des poils glanduleux longs observés chez le morphotype D « Meingré » et ; 4- des poils glanduleux courts observés chez le morphotype B « Kiankos ». De plus, des stomates de type anomocytique périgène à subsidiaire dicyclique sont observés chez tous les morphotypes étudiés. La densité stomatique évaluée est 362±5 st/mm² et l’indice stomatique varie de 45,1±0,7% chez les morphotypes de karité étudiés. Ces connaissances pourraient améliorer la systématique des morphotypes et fournir une base pour la sélection du matériel végétal approprié pour les programmes locaux de reboisement et/ou pour la production agronomique, car le beurre de cette espèce est de plus en plus sollicité. Epidermal hair, stomatal types and taxonomy in shea morphotypes (Vitellaria paradoxa C.F. Gaertn subsp. Paradoxa) ABSTRACT Epidermal hair and stomatal types in shea morphotypes (Vitellaria paradoxa C.F. Gaertn subsp. paradoxa) were studied in Chad in 2010, from July to September. The objective is the search for discriminating micro morphological characters likely to improve the identification of the morphotypes of this species. In fact, shea morphotypes have been described and named by rural people in the province of Mandoul in Chad. Shea kernels are transformed into butter, which gives it socio-economic importance. Fragments of the apical bud taken from young plants from the germination of the seeds of the five (5) morphotypes made it possible to observe the types of epidermal hair. Also, leaf samples taken separately from each morphotype were prepared according to the method of Barfod (1988). This method was preferred because the epidermis of the shea leaf is not easily detachable. It involves boiling the leaf samples in distilled water for 10 minutes and then soaking them in 40% nitric acid for 16-20 hours. This operation allowed to soften the mesophyle and facilitates the scaling of the cuticle. The surface of the fragment of the softened leaf placed on a microscope slide in a drop of water is gently and gradually scraped off using the edge of the scissors until a transparent epidermis fragment appears. The leaf epidermis thus obtained are placed in Lugol for 10 minutes and then mounted after rinsing between slide and coverslip in glycerol gelatin and observed under an optical microscope of the MOTIC type. A total of 30 counts were made on both sides, an average of 6 observations per morphotype. These counts made it possible to calculate the stomatal density and the stomatic index of each morphotype. The stomatal density is the average of the 6 counts per unit area (mm²). The results showed 4 groups of morphotypes: 1- long single epidermal hairs observed in morphotype A, locally called "Bogrombaye"; 2- short simple hairs observed in morphotypes C, E and F "Komane, Mbabète, Ngoïtokoro"; 3- long glandular hairs observed in the morphotype D "Meingré" and; 4- short glandular hairs observed in morphotype B "Kiankos". In addition, stomata of the perigenic anomocytic type with dicyclic subsidiary are observed in all the morphotypes studied. The stomatal density evaluated is 362 ± 5 st / mm² and the stomatic index varies from 45.1 ± 0.7% in the shea morphotypes studied. This knowledge could improve the system of morphotypes and provide a basis for the selection of appropriate plant material for local reforestation programs and / or for agronomic production, as butter from this species is in increasing demand.

Local efforts to record fungal species in China were first motivated by the search for agricultural plant pathogens in the 1910s. Regional surveys of fungal diversity emerged in the early 1920s and led to the development of taxonomic mycology in the 1930s. Deng Shuqun (Teng Shu-ch’ün) (1902–1970), who studied at Cornell University from 1923 into 1928, contributed significantly. His papers published in the 1930s reported on more than 2,500 Chinese fungal species and varieties, while a mycological monograph published in 1939 portrayed more than 1,400 taxa. These publications, all written in English, helped to make China's fungal diversity known to the global scientific community. The circulation and distribution of Deng's publications and collections of fungi reflected the inter-war international network within which scientific specimens and information were being shared

<p>Correct identification of fish larvae from East Plawangan is very difficult to be done due to undefined of their morphology, while correct name is an important information for management of that area as spawning and nersery ground. Therefore, so far no scientific report on what species that utilize East Plawangan as their spawning and nursery ground. Cytochrome c oxidase 1 gene provide a precise tool for correct larvae identification. This study aims to test the accuracy of the cytochrome c oxidase 1 gene on fish larvae identification. The COI gene were amplified and sequenced. The homology of sequences were checked using <em>Basic Local Alignment Search Tool</em> (BLAST). Genetic distances were calculated with the help of MEGA 6 software. Taxonomic tree was reconstructed using neighbor-joining and maximum parsimony methods with 1000 bootstraps repeats. A sum of 24 morphotypes were identified, indicating high diversity of fish that utilize East Plawangan as their spawning and nursery ground. BLAST result showed that seven morphotypes were convincingly identified into species level, while three remaining morphotypes could only be identified at generic level. Taxonomic tree shows clear discrimination among morphotypes. This proved that cytochrome c oxidase 1 gene showed high accuracy on larval species discrimination.</p>

The taxonomic status of Anguilla species' in river watershed that empties into Segara Anakan Cilacap is uncertain, thereby making it difficult for further studies to be carried out to determine its genetic in that area. Therefore, this study evaluates Anguilla's taxonomic status and population genetic in Cibeureum and Sapuregel River watersheds. Data were obtained from molecular characterization study using cytochrome c oxidase 1, with fourteen Anguilla specimens collected from two sequenced watersheds. Taxonomic status was determined based on homology and divergence values and monophyly of the samples to the reference species. Meanwhile, genetic divergences among samples to the reference species were calculated based on the Juke-Cantor substitution model in DnaSP6. A homology test was performed using a basic local alignment search tool, with monophyly inferred from the cladogram, which was developed using neighbor-joining and maximum likelihood algorithms in MEGAX with 1000 pseudoreplicates and out-group comparison. Furthermore, population genetic was analyzed through polymorphism, haplotype, nucleotide diversity within the population, divergence, and genetic differences. All calculations conducted in Arlequin 3.5 had Anguilla samples comprising of high (99.23% to 99.84%) to low genetic divergences (0.224% to 1.127%). The result shows that cladogram with all Anguilla samples formed a monophyletic clade with A. bicolor, separated from their taxa. Furthermore, Anguilla samples from both watersheds have low genetic polymorphisms with medium to high haplotype and nucleotide diversity. The population's comparison proved that both populations have low genetic divergence, and no genetic difference based on variance analysis (p=0761). Therefore, Anguilla resources in river watersheds that empty into Segara Anakan are a single genetic conservation unit.

The Republican Collection of Microorganisms (RCM) is a depository of industrial microorganisms intended for research and analytical work, for the organization of biotechnological production.The Biobank of industrial microorganisms of the RCM stores more than 700 strains from various taxonomic groups (bacteria, actinomycetes, yeast, mycelial fungi). In Kazakhstan, there is no single annotated database (DB) of collectible strains of industrial microorganisms, including information about their- and genotypic characteristics.In this regard, the VRCM is working on the creation of a database, containing the genetic characteristics of deposited strains of industrial microorganisms.To compare genomes, the BLAST+ software package (Basic Local Alignment Search Tool) is used according to the instructions of the National Center for Biotechnology Information (NCBI).The creation of a database of genomic sequences of microorganisms based on the BLAST computer program (nucleotide group) and the storage of information in the Biobank of industrial microorganisms of the RCM will contribute to improving the quality of service function and safety of collection cultures.

This work presents currently available knowledge on alien species (AS) found in the inland waters of Morocco. The objective is to provide an updated list of alien species and identify the main introduction pathways and possible threats to native biodiversity. The dataset was built from an extensive literature search supplemented by our own research work (published or in progress). The main areas harboring xenodiversity in Moroccan freshwaters correspond to protected areas (e.g., Ramsar Site and SIBE). These areas are currently home to 41 confirmed AS belonging to different taxonomic groups. Fish are the most abundant taxonomic group with 21 species, followed by molluscs (7 species) and arthropods (7 species). The presence of 15 more species was also noticed but considered doubtful. Almost half of these AS were introduced intentionally. They correspond to restocking programs and are likely the most serious threat to native biodiversity through predation, competition, and hybridization. Commercial activities around aquarium and ornamental species appear as the second source favoring colonization by AS. Implementing protective regulations regarding the import of exotic species in Morocco appears very urgent to protect local native diversity. In addition, detecting and monitoring the expansion of AS within the colonized areas and studies improving biological and ecological knowledge seem crucial to mitigate their possible impacts on native communities and preserve Moroccan freshwater ecosystems.

Biodiversity loss—one of the most prominent forms of modern environmental change—has been heavily driven by terrestrial habitat loss and, in particular, the spread and intensification of agriculture. Expanding agricultural land-use has led to the search for strong conservation strategies, with some suggesting that biodiversity conservation in agriculture is best maximized by reducing local management intensity, such as fertilizer and pesticide application. Others highlight the importance of landscape-level approaches that incorporate natural or semi-natural areas in landscapes surrounding farms. Here, we show that both of these practices are valuable to the conservation of biodiversity, and that either local or landscape factors can be most crucial to conservation planning depending on which types of organisms one wishes to save. We performed a quantitative review of 266 observations taken from 31 studies that compared the impacts of localized (within farm) management strategies and landscape complexity (around farms) on the richness and abundance of plant, invertebrate and vertebrate species in agro-ecosystems. While both factors significantly impacted species richness, the richness of sessile plants increased with less-intensive local management, but did not significantly respond to landscape complexity. By contrast, the richness of mobile vertebrates increased with landscape complexity, but did not significantly increase with less-intensive local management. Invertebrate richness and abundance responded to both factors. Our analyses point to clear differences in how various groups of organisms respond to differing scales of management, and suggest that preservation of multiple taxonomic groups will require multiple scales of conservation.

Introduction: The horse (Equus caballus) is an adaptable large herbivore distributed in a wide range of terrestrial biomes that negatively affects ecosystems around the world. Most research on horse–ecosystems interactions have been focused on plants and soils, whereas horse effects on vertebrate species are poorly understanded. Objective: We aimed to synthesize, at a global scale, the effects of free-roaming horses on wild mammals. Methods: We conducted a systematic literature review that included these words; "feral horses + competition ", "feral horses + interactions", "feral horses + impacts", "feral horses + effects", based on the “Web of Science” internet search engine. Results: We located 366 articles in our search, but only 14 peer-reviewed documents described the effects of horses on local wild mammals. Most studies were published in the last decade (64%), and were located in United States (64%). Additional information showed most studies used correlational approaches while experimental approaches were used less. The effect of horses on mammal taxonomic groups varied significantly, suggesting changes on habitat structure mostly affects vertebrate species such as small rodents. Nevertheless, large ungulates exhibited interference competition derived from presence of free-roaming horses. Conclusion: This review identified patterns and gaps in our current knowledge about the effect of horse presence on wild mammals, and can help to readdress further research. Therefore, we recommend careful monitoring of horses and their potential effects on wildlife by using species proxies such as ungulates and rodents to determine if the presence of horses in protected areas affects conservation objectives

Twenty-five marine cyanobacteria isolated from Irish coasts were characterized based on their morphological characters and 16S rRNA gene sequence analysis. In addition, superoxide dismutase (SOD) and malate dehydrogenase (MDH) isoenzyme banding patterns were used to differentiate two morphologically ambiguous isolates. In this study, six new cyanobacteria-specific primers were designed, and a 16S rRNA gene of twenty-five morphologically diverse cyanobacteria was successfully PCR amplified (1198–1396 bps). Assembled 16S rRNA sequences were used both for a basic local alignment search tool (BLAST) analysis for genus-level identification and to generate a phylogenetic tree, which yielded two major clusters: One with morphologically homogenous cyanobacteria and the other with morphologically very diverse cyanobacteria. Kamptonema okenii and Tychonema decoloratum were isolated from a single field sample of Ballybunion and were originally identified as the same ‘Oscillatoria sp.’ based on preliminary morphological observations. However, an alignment of 16S rRNA gene sequences and SOD and MDH isoenzyme banding pattern analyses helped in differentiating the morphologically-indistinguishable ‘Oscillatoria sp.’. Finally, after a re-evaluation of their morphological characters using modern taxonomic publications, the originally identified ‘Oscillatoria sp.’ were re-identified as Kamptonema okenii and Tychonema decoloratum, thus supporting the polyphasic approach of cyanobacteria characterization.

Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

ABSTRACT Genes of Salmonella enterica serovar Typhimurium LT2 expected to be specifically present in Salmonella were selected using the Basic Local Alignment Search Tool (BLAST) program. The 152 selected genes were compared with 11 genomic sequences of Salmonella serovars, including Salmonella enterica subsp. I and IIIb and Salmonella bongori (V), and were clustered into 17 groups by their comparison patterns. A total of 38 primer pairs were constructed to represent each of the 17 groups, and PCR was performed with various Salmonella subspecies including Salmonella enterica subsp. I, II, IIIa, IIIb, IV, VI, and V to evaluate a comprehensive DNA-based scheme for identification of Salmonella subspecies and the major disease-causing Salmonella serovars. Analysis of PCR results showed that Salmonella enterica subsp. I was critically divided from other subspecies, and Salmonella strains belonging to S. enterica subsp. I were clustered based on their serovars. In addition, genotypic relationships within S. enterica subsp. I by PCR results were investigated. Also, Salmonella signature genes, Salmonella enterica serovar Typhimurium signature genes, and Salmonella enterica subsp. I signature genes were demonstrated based on their PCR results. The described PCR method suggests a rapid and convenient method for identification of Salmonella serovars that can be used by nonspecialized laboratories. Genome sequence comparison can be a useful tool in epidemiologic and taxonomic studies of Salmonella.

Modern biology builds upon the historic exploration of the natural world. Recognizing the origin of a species’ name is one path to honor the historic exploration and description of the natural world and the indigenous peoples that lived closely with organisms prior to their description. While digitization of historic papers catalogued in databases such as the Biodiversity Heritage Library (BHL) allows for searching of the first use and origin of names, the rapid pace of taxonomic publishing can occlude a thorough search for etymologies. The etymological origin of the genus name Ameiva is one such case; while unattributed in multiple recent works, it is of Tupí language origin. The first description was in the Historiae Rerum Naturalium Brasiliae by George Marcgrave (1648). Ameiva was the name used by Marcgrave’s Amerindian hosts in 17th century Dutch Brazil, where local people spoke the now extinct language Tupí. The Tupí origin was not lost, however, until as recently as the 2000s. Herein, the pre- and post-Linnaean use of the name Ameiva is traced and when the name is attributed to the Tupí language and to Marcgrave through time it is noted. The opportunity to discover and/or recover etymological origins, especially names from extinct and indigenous languages, provides insight into the early Western sciences. Careful study of etymology by naturalists is consistent with the idea that science is an evolving process with many predecessors to appreciate.

Modern biology builds upon the historic exploration of the natural world. Recognizing the origin of a species’ name is one path to honor the historic exploration and description of the natural world and the indigenous peoples that lived closely with organisms prior to their description. While digitization of historic papers catalogued in databases such as the Biodiversity Heritage Library (BHL) allows for searching of the first use and origin of names, the rapid pace of taxonomic publishing can occlude a thorough search for etymologies. The etymological origin of the genus name Ameiva is one such case; while unattributed in multiple recent works, it is of Tupí language origin. The first description was in the Historiae Rerum Naturalium Brasiliae by George Marcgrave (1648). Ameiva was the name used by Marcgrave’s Amerindian hosts in 17th century Dutch Brazil, where local people spoke the now extinct language Tupí. The Tupí origin was not lost, however, until as recently as the 2000s. Herein, the pre- and post-Linnaean use of the name Ameiva is traced and when the name is attributed to the Tupí language and to Marcgrave through time it is noted. The opportunity to discover and/or recover etymological origins, especially names from extinct and indigenous languages, provides insight into the early Western sciences. Careful study of etymology by naturalists is consistent with the idea that science is an evolving process with many predecessors to appreciate.

Gnetum africanum is a twisted woody climbing wild plant i.e.liana found growing naturally in dense equatorial rainforest but currently domesticated in tropical areas of the world. There has been taxonomic confusion in classifying this liana due to its observable diverse morphological characters. Indeed, morphological characterization alone has not offered the needed solution. However, there is dearth of information on the molecular characterization of Gnetum africanum. Morphological and molecular descriptors, could help offers the needed phenotypic and genotypic characterization of this plant much better. This study is aimed at characterizing Gnetum africanum land races to identify species that could be used for the development of high yielding hybrids. Three different land races or accessions of Gnetum africanum was collected from different locations in Nigeria. High quality genomic DNA was isolated from the different samples; it was checked for purity and quantified as appropriate. The DNA samples were subjected to PCR amplification and DNA barcoding studies (chloroplast large subunit of ribulose -1, 5-bisphophate carboxylase rbcL gene). The amplicons were gel eluted, sequenced and checked for homology by using Basic local alignment search tool -BLAST. Identification was obtained from the top similar outcomes of the samples. For Ekim Fig. 1b sample, the forward blast showed 95% similarity with Basella alba voucherID: NC041293.1 and the reverse had 88% similarity with Talinum fruticosum cultivar ID: MK598685.1. For Etinan Fig. 1a sample, the forward blast had 86% similarity with Rhabdothamnussolandri voucher ID: JQ933464.1 and for reverse, there was no similarity founded.

Determination of species from wildlife specimens is one of the prime goals of forensic laboratories analyzing samples involved in wildlife crimes. The conviction rate in wildlife crimes is often low due to a lack of evidential support in identification of the species involved in crime. When species identification by application of morphological techniques fails due to sample autolysis or lack of anatomical markers in wildlife specimens, DNA analysis provides the vital, foolproof cue. Sequences generated from mitochondrial DNA regions are used to determine the species by matching against a known reference sequence, either using the global GenBank database or using references created locally. The present study employed species identification by DNA analysis using wildlife samples received from the Forest Department across Tamil Nadu, India. The study demonstrates the utility of partial Cytb and 12S rRNAgenes for determination of species from 18 samples without recognizable morphological features, including tissue, hair and blood. The species of the collected specimens were correctly identified by sequence similarity search with 99 to 100% match and taxonomic classification using phylogenetic tree reconstruction. Of the 18 samples analyzed, accurate species identification using 12S rRNA gene was possible for all the samples, while Cytbgene-based identification was successful for 16 samples. Sequences generated from the study could also serve as a local genetic databank for the State Forest Department to match against sequences from wildlife forensic samples referred to the Institute for ascertaining species involved in wildlife trade. The sequences will also be useful to bridge gaps in genetic data on species native to Tamil Nadu.

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java. This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.

Inclusion of fermentable fibres in the diet can have an impact on the hindgut microbiome and provide numerous health benefits to the host. Potato fibre (PF), a co-product of potato starch isolation, has a favourable chemical composition of pectins, resistant and digestible starch, cellulose, and hemicelluloses. The objective of the present study was to evaluate the effect of increasing dietary PF concentrations on the faecal microbiome of healthy adult dogs. Fresh faecal samples were collected from ten female dogs with hound bloodlines (6·13 (sem 0·17) years; 22·0 (sem 2·1) kg) fed five test diets containing graded concentrations of PF (0, 1·5, 3, 4·5 or 6 % as-fed; Roquette Frères) in a replicated 5 × 5 Latin square design. Extraction of DNA was followed by amplification of the V4–V6 variable region of the 16S rRNA gene using barcoded primers. Sequences were classified into taxonomic levels using Basic Local Alignment Search Tool (BLASTn) against a curated GreenGenes database. Inclusion of PF increased (P< 0·05) the faecal proportions of Firmicutes, while those of Fusobacteria decreased (P< 0·05). Similar shifts were observed at the genus level and were confirmed by quantitative PCR (qPCR) analysis. With increasing concentrations of PF, faecal proportions of Faecalibacterium increased (P< 0·05). Post hoc Pearson's correlation analysis showed positive (P< 0·05) correlations with Bifidobacterium spp. and butyrate production and Lactobacillus spp. concentrations. Overall, increases in the proportion of Faecalibacterium (not Lactobacillus/Bifidobacterium, as confirmed by qPCR analysis) and faecal SCFA concentrations with increasing dietary PF concentrations suggest that PF is a possible prebiotic fibre.

This review identifies successful approaches to collating and using biodiversity data in spatial planning and impact assessment, the barriers to obtaining and using existing data sources, and the key data gaps that hinder effective implementation. The analysis is a contribution to the EU BON project funded by the European Commission FP7 research programme, which aimed to identify and pilot new approaches to overcome gaps in biodiversity data in conservation policy at European and national levels. The consideration of biodiversity in impact assessments and spatial planning requires spatially explicit biodiversity data of various types. Where spatial plans take account of biodiversity, there are opportunities through Strategic Environmental Assessment (SEA) of development plans and Environmental Impact Assessment (EIA) of individual development proposals to ensure that consented activities are consistent with no net loss of biodiversity or even a net gain, and help to maintain or develop coherent ecological networks. However, biodiversity components of SEAs and EIAs have often been found to be of insufficient quality due to the lack of data or the inadequate use of existing data. Key obstacles to providing access to biodiversity data include the need for data standardisation and data quality governance and systems, licensing approaches to increase data access, and lack of resources to target gaps in data coverage and to develop and advertise policy-relevant data products. Existing data platforms differ in the degree to which they successfully provide a service to spatial planners and impact assessment practitioners. Some local governments, for example Somerset County Council in the UK and the Bremen federal state in Germany, have invested in integrated data collection and management systems that now provide intensively used tools for spatial planning and impact assessment informed by local data collection and monitoring. The EU BON biodiversity data portal aims to provide a platform that is an access point to datasets relevant to essential biodiversity variables on species, habitats and ecosystems. The EU BON taxonomic backbone provides an integrated search function for species and taxa according to different classifications, and also provides a range of tools for data analysis and decision-support. This will increase the accessibility of the vast range of biodiversity data available in different sources and allow the targeting of future data collection to address current gaps.

Background: The study of microbial diversity and community structures heavily relies on the analyses of sequence data, predominantly taxonomic marker genes like the small subunit of the ribosomal RNA (SSU rRNA) amplified from environmental samples. Until recently, the "gold standard" for this strategy was the cloning and Sanger sequencing of amplified target genes, usually restricted to a few hundred sequences per sample due to relatively high costs and labor intensity. The recent introduction of massive parallel tag sequencing strategies like pyrosequencing (454 sequencing) has opened a new window into microbial biodiversity research. Due to its swift nature and relatively low expense, this strategy produces millions of environmental SSU rDNA sequences granting the opportunity to gain deep insights into the true diversity and complexity of microbial communities. The bottleneck, however, is the computational processing of these massive sequence data, without which, biologists are hardly able to exploit the full information included in these sequence data. Results: The freely available standalone software package JAGUC implements a broad regime of different functions, allowing for efficient and convenient processing of a huge number of sequence tags, including importing custom-made reference data bases for basic local alignment searches, user-defined quality and search filters for analyses of specific sets of sequences, pairwise alignment-based sequence similarity calculations and clustering as well as sampling saturation and rank abundance analyses. In initial applications, JAGUC successfully analyzed hundreds of thousands of sequence data (eukaryote SSU rRNA genes) from aquatic samples and also was applied for quality assessments of different pyrosequencing platforms. Conclusions: The new program package JAGUC is a tool that bridges the gap between computational and biological sciences. It enables biologists to process large sequence data sets in order to infer biological meaning from hundreds of thousands of raw sequence data. JAGUC offers advantages over available tools which are further discussed in this manuscript.

Actuality of research theme. Assessing the competitiveness of an enterprise is a complex multifactorial task, which boils down to identifying the most significant numerical indicators of competitiveness and their integration. The need to aggregate all indicators is due to the fact that the object of modeling (the effective functioning of the enterprise) requires not only generalizing characteristics, but also the ordering of its individual elements according to certain properties and principles. The problem of forming a sound corporate culture as a basis for increasing competitiveness of the enterprise becomes especially acute. Problem statement. Nowadays conditions business environment require introduction of a sound system for assessing the effectiveness of corporate culture and establishing a close relationship with the competitiveness of the enterprise. Analysis of the last researches and publications. Almost all researchers of the theory of assessment and management of competitiveness are engaged in the search for a capable management system that would facilitate the rapid response of the business entity to change the external and internal business environment, adaptation to new conditions. Despite considerable work, there remain problems requiring particular scientific analysis. In particular, insufficient attention is paid to exploring the soundness of corporate culture as a basis for increasing competitiveness of the enterprises of all forms of ownership. Uninvestigated parts of general matters defining. Not enough-researched and unpublished parts in periodicals issues remain related optimal methodological approach to assess the level of competitiveness of the enterprise, taking into account the formed corporate culture and the level of competitiveness of labor resources. The primary purpose of the study comprises to identify the peculiarities of corporate culture formation as a basis for increasing competitiveness of the enterprises of all forms of ownership. The methodological basis of the research was the scientific works of Ukrainian and foreign scientists, leading experts, statistical and analytical materials of state authorities. Results. The peculiarities of definition and formation of corporate culture are investigated. The level of corporate culture at the enterprise is assessmented. It has been revealed that the lack of a sound methodological approach to employee rating and appropriate means of motivation for professional development can lead to the loss of existing intellectual potential and competitive positions in the market services in general. The expediency of using the methodology of assessment of the efficiency of management of the enterprise based on the use of taxonomic analysis is substantiated. The expediency of forming an effective corporate culture as a basis for increasing competitiveness of the enterprises of all forms of ownership is substantiated. The field of application of results. The results of the study can be used by all stakeholders, including public authorities and local self-government, leading enterprises in the region. Conclusions. The leadership of domestic enterprises should ensure the formation and implementation of an effective corporate culture with a certain set of material and spiritual values, rules of behavior of employees.

London planetrees (Platanus × acerifolia, syn. P. × hispanica), American sycamores (P. occidentalis), and oriental planes (P. orientalis) are widely planted as urban shade trees throughout Greece and many other countries. In June 2012, typical symptoms of a powdery mildew were detected on all sycamores (10 trees) along a central avenue of Heraklion (Crete, Greece), with the disease affecting approximately 80% of the leaves of all infected trees. In August 2013, similar symptoms were observed on 20% of the leaves of all three London planes in a small grove in the Vrysses area of Lasithi (Crete, Greece). In both cases, the disease was severe, with white superficial colonies developing amphigenously on leaves, twigs, floral peduncles, inflorescences, and fruits. The colonies were initially distinct and circular but gradually enlarged and often coalesced to cover the entire leaf blade. Young leaves appeared curled and chlorotic, occasionally leading to defoliation. For the morphological description of the pathogen, samples from seven infected P. occidentalis and three P. × acerifolia trees were microscopically characterized. In all samples, the pathogen's mycelium was branched, septate, and hyaline, with lobed appressoria; conidiophores were erect, cylindrical, unbranched, and consisted of three to four (to five) cells; and conidia were single or in short chains (two to four), ellipsoid or doliiform, with a truncated base and rounded apex. Their dimensions were 24.3 to 48.6 × 15.8 to 27.9 μm (averaging 39.2 × 21.2 μm; n = 100), and their surfaces appeared reticulate. The teleomorph was never observed. Total fungal DNA was extracted from conidia harvested from affected leaves of one infected plant of each of P. occidentalis and P. × acerifolia planes, and the ITS1-5.8S-ITS2 region was PCR-amplified with universal primers 18S-ITS1 and 28S-ITS2 (2) and sequenced (GenBank Accession Nos. KM068123 and KM068124, respectively). A BLASTn search of GenBank revealed 100% identity of both samples to Erysiphe platani strains described on P. orientalis in Greece (JQ365943) and P. occidentalis in Brazil (KF499270). Based on the morphological and molecular analyses, the pathogen was identified as E. platani (Howe) U. Braun & S. Takam. (formerly known as Microsphaera platani Howe) (1). To prove pathogenicity and fulfill Koch's postulates, 10 1-year-old seedlings of each of P. occidentalis and P. × acerifolia hosts were artificially inoculated with conidia obtained from naturally infected plants of the corresponding species, with two methods: (i) five plants of each host were dusted with conidia from diseased leaves, and (ii) the remaining five seedlings of each plane were sprayed with a conidial suspension of the fungus (107 conidia ml−1), while five additional control plants of each species were treated only with sterile distilled water. All plants were maintained in the greenhouse at 25 ± 3°C, with 90% humidity. Powdery mildew symptoms, which appeared 9 and 15 days after inoculation on all dusted and sprayed plants, respectively, were similar to those observed on naturally infected trees, whereas no symptoms were observed on control plants. Although E. platani is known to infect plane species in several parts of the world (1), including oriental planes (P. orientalis and P. orientalis var. cretica) in Greece (3), this is the first report of E. platani causing disease of P. occidentalis and P. × acerifolia in Greece, underlining the need for appropriate control measures to prevent significant losses to the local ornamental industry. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11. CBS, Utrecht, 2012. (2) I. A. Papaioannou et al. Eur. J. Plant Pathol. 136:577, 2013. (3) D. J. Vakalounakis and E. Klironomou. EPPO Bull. 25:463, 1995.

Introduction: There are numerous methods of isolating and detecting organisms that are similar and closely related; one of the most reliable method is molecular typing of 16S rRNA. Apart from being omnipresent as a multigene family, or operons; it is evolutionarily stable; the 16S rRNA gene (1,500 bp) is large enough for informatics purposes. Materials and Method: This study employed molecular sequencing of 16S rRNA by Sanger method to reveal the specific organisms’ nucleotides and blasting (BLASTn) to show the similarities between the resulting organisms and existing organisms. The 16S rRNA remains the best choice of identification process for bacteria because of its distinguishing sizes and evolutionary stability. Results: All isolates were Gram positive rods and were positive in Biochemical tests such as oxidase, catalase, citrate, and protease but were in turn negative in coagulase and indole test tests. On sensitivity test; 80% of all the isolates were resistant to common antibiotics except ciprofloxacin and ceftriaxone. Based on the sequence difference in the variable region (V1) of 16S rRNA as observed from the molecular sequencing results; four isolates out of ten were identified. Six were different strains of B cereus. Others isolates include: wiedmannii, thuringensis, toyonensis and pseudomycoides. Sequence analysis of the primer annealing sites showed that there is no clear‐cut difference in the conserved region of 16S rRNA, and in the gyrB gene, between B. cereus and B. thuringiensis strains. Phylogenetic analysis showed that four isolates showed high similarity to each other; hence the limited number of deletions when subjected to alignments by maximum neighborhood joining parsimony using MEGA X software. B. toyonensis, B. wiedmannii and thuringensis were distantly related. Introduction Authors Pathogens cause illness and death in some countries and it also causes infections and gastrointestinal diseases in other countries thereby causing public health concern. Pathogens are organisms capable of causing diseases. Reliable methods are needed for the detection of pathogens due to pathogen evolution as a result of new human habits or new industrial practices. Microbial classification of organisms ranges from genus to specie level depending upon the technique used either phenotypic or genotypic. Presently, molecular methods now obtain advances to allow utilization in microbiology [1]. There are numerous molecular methods which are of fast and simple application to the detection of pathogen. Among the pathogens involved in human health, Bacillus cereus is interesting due to their ability to survive in various habitats [2]. The genus Bacillus is aerobic or facultative anaerobic bacteria, gram positive spore forming rod shaped bacteria. Which can be characterized by two morphological forms, the vegetative cell which range from 1.02 to 1.2 um in width and from 3.0 to 5.0 in length, it can be straight or slightly curve, motile or non-motile, and the endospore (the non-swelling sporangium). The genus Bacillus is been characterized by the presence of endospore, which is not more than one per cell and they are resistant to many adverse environmental conditions such as heat, radiation, cold and disinfectants. It can also respire either in the presence or absence of oxygen [3]. Cell diameter of Bacillus cereus, sporangium and catalase test do not allow differentiation, where as important in differentiation among B. anthracis, B. cereus, B. thuringiensis can be considered by parasporal crystals and the presence of capsule. [4] Showed a B. thuringiensis strain capable of producing a capsule resembling that of B. anthracis. Most species of the genus display a great kind in physiological characteristics such as degradation of cellulose, starch, pectin, agar, hydrocarbons, production of enzymes and antibiotics and other characteristic such as acidophile, alkalinophile, psychrophile, and thermophile's which allows them to adapt to various environmental conditions [5]. In differentiating between species of the genus Bacillus it was difficult at early attempts when endospore formation and aerobic respiration were the main character used for classification. As reported by many authors that at molecular method level, the differentiation between B. thuringiensis and B. cereus is also very difficult. cereus can survive at the temperature between 4°c and 55°c. The mesophile strains can grow between the temperature of 10°c and 42°c, while psychotropic strains can survive at 4°c, whereas other strains are able to grow at 52 to 55°c. B. cereus vegetative cells grow at pH between 1.0 and 5.2. Heat resistant strain can survive and multiply in wet low acid foods in temperature ranging from 5 to 52°c. The survivability of B. cereus spores at 95°c decreases when the pH level decreases from 6.2 to 4.7 [6]. B. cereus can grow in the presence of salt with concentration up to 7.5% depending on the pH value. thuringiensis possesses a protein crystal that is toxic to insects. This toxin protein was first known as parasporal crystalline inclusion but was later referred to as π - endotoxin or in other ways known as insecticidal crystal protein [7]. Strains of B. thuringiensis bacteria possess a wide range of specificity in various orders of insects such as Lepidoptera, dipteral, coleoptera. These strains of bacteria produce crystalline proteins known as cry protein during sporulation. When B. thuringiensis infects an insects, it will cause the insect to loose appetite, enhances slow movement and over time the insect will die due to crystals of proteins that have been dissolved in the insect's stomach. In the cultivation of vegetable crops, the plant can be attack by many types of pests. Hence, in overcoming pest attacks farmers often use pesticides that contain active synthetic materials. Many negative effects arise from the folly use of chemical pesticides. Among the negative effect is the increase of pest population, resistance, death of natural enemy population and increase in residue level on Agricultural product which makes it unsafe for public consumption [8]. Therefore, it is necessary to find an alternative method in the control of crop pest. The best alternative that can be done is to replace the chemical insecticide with biological control which involves the use of living things in the form of microorganisms. In these profiling microbial communities, the main objective is to identify which bacteria and how much they are present in the environments. Most microbial profiling methods focus on the identification and quantification of bacteria with already sequenced genomes. Further, most methods utilize information obtained from entire genomes. Homology-based methods such as [1–4] classify sequences by detecting homology in reads belonging to either an entire genome or only a small set of marker genes. Composition-based methods generally use conserved compositional features of genomes for classification and as such they utilize less computational resources.Using the 16S rRNA gene instead of whole genome information is not only computational efficient but also economical; Illumina indicated that targeted sequencing of a focused region of interest reduces sequencing costs and enables deep sequencing, compared to whole-genome sequencing. On the other hand, as observed by [8], by focusing exclusively on one gene, one might lose essential information for advanced analyses. We, however, will provide an analysis that demonstrates that at least in the context of oral microbial communities, the 16S rRNA gene retains sufficient information to allow us detect unknown bacteria [9, 10]. This study aimed at employing 16S rRNA as an instrument of identification of seemingly close Bacillus species. Abbreviations BLAST, Basic Local Alignment sequence Tools; PCR, Polymerase Chains reactions; rRNA, ribosomal RNA; Material and methods T Sample collection. Soil samples were collected from three sources from Rice, Sugar Cane, vegetables and abandoned farmland in January 2019. The samples were labeled serially from Sample 1 to Sample 10 (S1 to S10). Bacterial culture: A serial dilution of 10 folds was performed. Bacterial suspension was diluted (10-10) with saline water and 100 μl of bacterial suspension werespread on Nutrient Agar plate and incubated for 24 hours. Bacterial colonies were isolated and grown in Nutrient Broth and nutrient agar. Other microbiological solid agar used include: Chocolate, Blood Agar, EMB, MacConkey, Simon citrate, MRS Agar. Bacteria were characterized by conventional technique by the use of morphological appearance and performance on biochemical analysis [11]. Identification of bacteria:The identification of bacteria was based on morphological characteristics and biochemical tests carried out on the isolates. Morphological characteristics observed for each bacteria colony after 24 h of growth included colony appearance; cell shape, color, optical characteristics, consistency, colonial appearance and pigmentation. Biochemical characterizations were performed according to the method of [12] Catalase test: A small quantity of 24 h old culture was transferred into a drop of 3% Hydrogen peroxide solution on a clean slide with the aid of sterile inoculating loop. Gas seen as white froth indicates the presence of catalase enzyme [13] on the isolates. DNA Extraction Processes The extraction processes was in four phase which are: Collection of cell, lyses of cell, Collection of DNA by phenol, Concentration and purification of DNA. Collection of cell: the pure colonyof the bacteria culture was inoculated into a prepared sterile nutrient broth. After growth is confirmed by the turbidity of the culture, 1.5ml of the culture was taken into a centrifuge tube and was centrifuge at 5000 rpm for 5 minutes; the supernatant layer was discarded leaving the sediment. Lyses of cell: 400 microns of lyses buffer is added to the sediment and was mixed thoroughly and allow to stand for five minutes at room temperature (25°c). 200 microns of Sodium Dodecyl Sulfate (SDS) solution was added for protein lyses and was mixed gently and incubated at 65°c for 10 minutes. Collection of DNA by phenol; 500 microns of phenol chloroform was added to the solution for the separation of DNA, it was mixed completely and centrifuge at 10,000 rpm for 10 minutes. The white pallet seen at the top of the tube after centrifugation is separated into another sterile tube and 1micron of Isopropanol is added and incubated for 1hour at -20°c for precipitation of DNA. The DNA is seen as a colorless liquid in the solution. Concentration and purification of DNA: the solution was centrifuge at 10,000 rpm for 10 minutes. The supernatant layer was discarded and the remaining DNA pellets was washed with 1micron of 17% ethanol, mixed and centrifuge at 10,000 rpm for 10 minutes. The supernatant layer was discarded and air dried. 60 micron TE. Buffer was added for further dissolving of the DNA which was later stored at -40°c until it was required for use [14]. PCR Amplification This requires the use of primers (Forward and Reverse), polymerase enzyme, a template DNA and the d pieces which includedddATP, ddGTP and ddTTP, ddNTP. All this are called the master mix. The PCR reactions consist of three main cycles. The DNA sample was heated at 940c to separate the two template of the DNA strand which was bonded by a hydrogen bond. Once both strand are separated the temperature is reduced to 570c (Annealing temperature). This temperature allows the binding of the forward and reverse primers to the template DNA. After binding the temperature is raised back to 720c which leads to the activation of polymerase enzyme and its start adding d NTPs to the DNA leading to the synthesize of new strands. The cycles were repeated several times in order to obtain millions of the copies of the target DNA [15]. Preparation of Agarose Gel One gram (1 g) of agarose for DNA was measured or 2 g of agarose powdered will be measured for PCR analysis. This done by mixing the agarose powder with 100 ml 1×TAE in a microwaveable flask and microwaved for 1-3 minutes until the agarose is completely dissolved (do not over boil the solution as some of the buffer will evaporate) and thus alter the final percentage of the agarose in the gel. Allow the agarose solution to cool down to about 50°c then after five minutes 10µL was added to EZ vision DNA stain. EZ vision binds to the DNA and allows one to easily visualize the DNA under ultra violet (UV) light. The agarose was poured into the gel tray with the well comb firmly in place and this was placed in newly poured gel at 4°c for 10-15 mins or it sit at room temperature for 20-30 mins, until it has completely solidified[16]. Loading and Running of samples on Agarose gel The agarose gel was placed into the chamber, and the process of electrophoresis commenced with running buffer introduced into the reservoir at the end of the chamber until it the buffer covered at least 2millimeter of the gel. It is advisable to place samples to be loaded in the correct order according to the lanes they are assigned to be running. When loading the samples keep the pipette tip perpendicular to the row of the wells as by supporting your accustomed hand with the second hand; this will reduce the risk of accidentally puncturing the wells with the tip. Lower the tip of the pipette until it breaks the surface of the buffer and is located just above the well. Once all the samples have been loaded it is advised to always avoid any movement of the gel chamber. This might result in the sample spilling into adjacent well. Place the lid on the gel chamber with the terminal correctly positioned to the matching electrodes on the gel chamber black to black and red to red. Remember that DNA is negatively charged hence the movement of the electric current from negatively charged to the positively charged depending on the bandwidth in Kilobytes. Once the electrode is connected to the power supply, switch ON the power supply then set the correct constant voltage (100) and stopwatch for proper time. Press the start button to begin the flow of current that will separate the DNA fragment.After few minutes the samples begins to migrate from the wells into the gel. As the DNA runs, the diaphragm moves from the negative electrode towards the positive electrode [17]. PCR mix Components and Sanger Sequencing This is made up of primers which is both Forward and Reverse, the polymerase enzyme (Taq), a template DNA and the pieces of nucleotides which include: ddNTP, ddATP, ddGTP and ddTTP. Note that the specific Primer’s sequences for bacterial identification is: 785F 5' (GGA TTA GAT ACC CTG GTA) 3', 27F 5' (AGA GTT TGA TCM TGG CTC AG) 3', 907R 5' (CCG TCA ATT CMT TTR AGT TT) 3', 1492R 5' (TAC GGY TAC CTT GTT ACG ACT T) 3' in Sanger Sequencing techniques. BLAST The resulting genomic sequence were assembled and submitted in GenBank at NCBI for assignment of accession numbers. The resultant assertion numbers were subjected to homology search by using Basic Local Alignment Search Tool (BLAST) as NCBI with the assertion number MW362290, MW362291, MW362292, MW362293, MW362294 and MW362295 respectively. Whereas, the other isolates’ accession numbers were retrieved from NCBI GenBank which are:AB 738796.1, JH792136.1, MW 015768.1 and MG745385.1.MEGA 5.2 software was used for the construction of phylogenetic tree and phylogenetic analysis. All the organisms possess 100% identities, 0% gaps and 0.0% E.value which indicated that the organisms are closely related to the existing organisms. The use of 16S rRNA is the best identification process for bacteria because 16S rRNA gene has a distinguishing size of about 500 bases until 1500bp. Rather than using 23S rRNA which is of higher variation, The 16S rRNA is adopted in prokaryotes. 18S rRNA is used for identification in Eukaryotes Results The results of both the conventional morphological and cultural identification was correlated with the molecular sequencing results. Six isolates were confirmed B. cereus species while the other four isolates were. B. wiedmannii, B. thuringiensis, B. toyonensis and B. pseudomycoides.The 16S rRNA sequence of six isolates MW 362290.1- MW362295.1 were assigned accession numbers and deposited in the GenBank while the other four sequences were aligned to those available in the NCBI database. The alignment results showed closely relatedness to LT844650.1with an identity of 100% to 92.2% as above. The six isolates of Bacillus cereus great evolutionary relatedness as shown in the phylogenetic tree constructed using MEGA X software. Results The results of both the conventional morphological and cultural identification was correlated with the molecular sequencing results. Six isolates were confirmed B. cereus species while the other four isolates were. B. wiedmannii, B. thuringiensis, B. toyonensis and B. pseudomycoides.The 16S rRNA sequence of six isolates MW 362290.1- MW362295.1 were assigned accession numbers and deposited in the GenBank while the other four sequences were aligned to those available in the NCBI database. The alignment results showed closely relatedness to LT844650.1with an identity of 100% to 92.2% as above. The six isolates of Bacillus cereus great evolutionary relatedness as shown in the phylogenetic treeconstructed using MEGA X software. Discussion The results obtained in this study is consistent with the previous studies in other countries22,23 The results of the phylogenetic analysis of the 16S rRNA isolate of in this study was similar to the housekeeping genes proposed by [18, 19]. In comparing this study with the earlier study, B. cereus group comprising other species of Bacillus was hypothesized to be considered to form a single species with different ecotypes and pathotype. This study was able to phenotypically differentiated B. thuringiensis, B. pseudomycoides, B. toyonensis, B. wiedmannii and B. cereus sensu strito. Despite differences at the colonial appearance level, the 16S rRNA sequences have homology ranging from 100% to 92% providing insufficient resolution at the species level [6, 7, 18].After analysis through various methods, the strain was identified as Gram-positive bacteria of Bacillus cereus with a homology of 99.4%. Cohan [20] demonstrated that 95–99% of the similarity of 16S rRNA gene sequence between two bacteria hints towards a similar species while >99% indicates the same bacteria.The phylogenetic tree showed that B. toyonensis, B. thuringiensis and B. wiedmanniiare the outgroups of B. cereus group while B. pseudomycoides are most closely related to B. cereus group [19, 21, 22]. Conclusion In the area of molecular epidemiology, genotypic typing method has greatly increased our ability to differentiate between micro-organisms at the intra and interspecies levels and have become an essential and powerful tool. Phenotypic method will still remain important in diagnostic microbiology and genotypic method will become increasingly popular. After analysis through various methods, the strain was identified as Gram-positive bacteria of Bacillus cereus with a homology of between 100% and 92.3%. Acknowledgments Collate acknowledgments in a separate section at the end of the article before the references, not as a footnote to the title. Use the unnumbered Acknowledgements Head style for the Acknowledgments heading. List here those individuals who provided help during the research. Conflicts of interest The Authors declare that there is no conflict of interest. References: Simpkins Meyer F.; Paarmann D.; D’Souza M.; Olson R.; Glass EM.; Kubal M.; Paczian T.; Rodriguez A.; Stevens R. Wilke A The metagenomics rast server–a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008, 9(1), 386. Segata N.; Waldron L.; Ballarini A.; Narasimhan V.; Jousson O.; Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature methods. 2012, 9(8), 811–814. Brady A.; Salzberg SL. Phymm and phymmbl: metagenomic phylogenetic classification with interpolated markov models. Nature Methods. 2009, 6(9), 673–676. Lindner MS.; Renard BY. Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res. 2013, 41(1), 10–10. Wang A.; Ash G.J. Whole genome phylogeny of Bacillus by feature frequency profiles (FFP). Sci Rep. 2015, 5, 13644. Caroll L.M.; Kovac J.; Miller R.A.; Wiedmann M. Rapid, high-throughput identification of anthrax-causing and emetic Bacillus cereus group genome assemblies’ cereus group isolates using nucleotides sequencing data. Appli. Environ. 2017, 83: e01096-e01017 Liu Y.; Lai Q. L.; Goker M.; Meier-Kolthoff J. P.; Wang M.; Sun Y. M.; Wang L.S.; Shao Z. Genomic insights into the taxonomic status of the Bacillus cereus group. Rep. 2015, 5, 14082. Lindner MS.; Renard BY. Metagenomic profiling of known and unknown microbes with microbegps. PloS ONE. 2015, 10(2), 0117711. Versalovic J.; Schneider M.; de Bruijn FJ.; Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). 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DNA Extraction from a bacterial cell. A video on Experimental Biotechnology. 2020. Quick biochemistry. A YouTube video on polymerase chain reaction. 2018. Bio-Rad laboratories. A YouTube video on loading and running of samples on Agarose gel. 2012. Saitou N. and Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Biol. Evol. 1987, 4, 406-425. Doi: 101093/oxfordjournals. Lazarte N.J.; Lopez R.P.; Ghiringhelli P.D.; Beron C.M. Bacillus wiedmannii biovar thuringiensis: A specialized Mosquitocidal pathogen with plasmid from diverse origins Genome. Evol. 2018, 10(10), 2823-2833. Doi.1093/gbe/evy211 Cohan, F.M. What are bacterial species? Rev. Microbiol. 2002, 56, 457-487 Abiola C.; Oyetayo V.O. Isolation and Biochemical Characterization of Microorganisms Associated with the Fermentation of Kersting’s Groundnut (Macrotyloma geocarpum). Research Journal of Microbiology, 2016, 11: 47- 55.DOI:10.3923/jm.2016.47.55 Adeoti O.M.; Usman T.A. 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Background: The increasing trend in unnecessary caesarean sections has caused maternal and neonatal health concerns worldwide. Various medical and non-medical interventions have been designed and implemented to reduce caesarean sections overuse. However, their efficacy is questionable. Aims: This study aimed to identify and classify effective interventions to reduce unnecessary caesarean sections. Methods: We searched EMBASE, MEDLINE, Web of Knowledge and Scopus databases for articles, using appropriate search strategies, up to 2 June 2020. Overall, 7951 identified articles were screened and assessed using a valid quality assessment checklist. Finally, 109 eligible studies were included in this review. Thematic content analysis was used to identify and classify the effective interventions. Results: Overall, 188 effective caesarean section reduction measures were identified. They were categorized into 45 actions, 16 intervention groups and 6 WHO building blocks, including “governance and leadership”, “financing”, “health workforce”, “medical products and technologies”, “information” and “service delivery”. Using qualified and competent staff, intra-partum services, and oversight were the most commonly applied interventions to reduce unnecessary caesarean sections. Conclusions: A taxonomy of effective strategies to reduce unnecessary caesarean sections was developed in this study. A holistic approach is crucial to addressing the new epidemic of unnecessary caesarean section. Multiple interventions based on the underlying causes of caesarean section overuse should be designed and implemented at local and global levels.

Abstract Background The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. Results The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.

The genus Artemisia belongs to family Asteraceae and commonly used for ailments of multiple lethal diseases. Twenty-nine species of the genus have been identified from Pakistan which are widely used as pharmaceutical, agricultural, cosmetics, sanitary, perfumes and food industries. In this review we studied the medicinal uses, taxonomy, essential oils as well as phytochemistry were compiled. Data was collected from the original research articles, texts books and review papers including globally accepted search engines i.e. PubMed, ScienceDirect, Scopus, Google Scholar and Web of Science. Species found of Artemisia in Pakistan with their medicinal properties and phytochemicals were recorded. The present review highlights the geographical distribution, morphological features and medicinal importance of different Artemisia species. Species of the genus are used in different traditional treatments by the local communities of Pakistan and worldwide. The essential oils and some other important derivatives such as artemisinin are commonly used to cure malaria, cancer, stomach, kidney, liver, and spleen other bacterial, fungal, helminthic diseases and much more. These species also possess some important extract such as lignans, polyphenols and flavonoids that help in activation of certain pathways. Majority of work on the taxonomic validation of the species are showing confusion in its morphology, for the correct identification of the species in the present review special focus has been made on its morphological characteristics, along with their traditional uses, pharmacology and phytochemical constituents. This review will provide baseline information for further research on the genus and as well as at species level on different aspects. The aim of this study is to provide comprehensive overview of Genus Artemisia specifically the species of the genus from Pakistan.

The members of the family Iridoviridae are large, double-stranded DNA viruses that infect various hosts, including both vertebrates and invertebrates. Although great progress has been made in genomic and phylogenetic analyses, the adequacy of the existing criteria for classification within the Iridoviridae family remains unknown. In this study, we redetermined 23 Iridoviridae core genes by re-annotation, core-pan analysis and local BLASTN search. The phylogenetic tree based on the 23 re-annotated core genes (Maximum Likelihood, ML-Tree) and amino acid sequences (composition vector, CV-Tree) were found to be consistent with previous reports. Furthermore, the information provided by synteny analysis and codon usage preference (relative synonymous codon usage, correspondence analysis, ENC-plot and Neutrality plot) also supports the phylogenetic relationship. Collectively, our results will be conducive to understanding the genera demarcation within the Iridoviridae family based on genomic synteny and component (codon usage preference) and contribute to the existing taxonomy methods for the Iridoviridae family.

Abstract Background Practice guidelines can reduce variations in nursing practice and improve patient care. However, implementation of guidelines is complex and inconsistent in practice. It is unclear which strategies are effective at implementing guidelines in nursing. This review aimed to describe the use and effects of implementation strategies to facilitate the uptake of guidelines focused on nursing care. Methods We conducted a systematic review of five electronic databases in addition to the Cochrane Effective Practice and Organization of Care (EPOC) Group specialized registry. Studies were included if implementation of a practice guideline in nursing and process or outcome of care provided by nurses were reported. Two reviewers independently screened studies, assessed study quality, extracted data, and coded data using the EPOC taxonomy of implementation strategies. For those strategies not included in the EPOC taxonomy, we inductively categorized these strategies and generated additional categories. We conducted a narrative synthesis to analyze results. Results The search identified 46 papers reporting on 41 studies. Thirty-six studies used a combination of educational materials and educational meetings. Review findings show that multicomponent implementation strategies that include educational meetings, in combination with other educational strategies, report positive effects on professional practice outcomes, professional knowledge outcomes, patient health status outcomes, and resource use/expenditures. Twenty-three of the 41 studies employed implementation strategies not listed within the EPOC taxonomy, including adaptation of practice guidelines to local context (n = 9), external facilitation (n = 14), and changes to organizational policy (n = 3). These implementation strategies also corresponded with positive trends in patient, provider, and health system outcomes. Conclusions Nursing guideline implementation may benefit from using the identified implementation strategies described in this review, including participatory approaches such as facilitation, adaptation of guidelines, and organizational policy changes. Further research is needed to understand how different implementation strategy components work in a nursing context and to what effect. As the field is still emerging, future reviews should also explore guideline implementation strategies in nursing in quasi or non-experimental research designs and qualitative research studies.

Worldwide, global databases on fishes lack fish diversity information at regional scale of a country, which has fascinated many fishery workers to know the regional scale fish diversity. Databases are essential part of the biodiversity science and have been used widely in the biological research. The present study discusses development, services and utility of the database application (UPFBase) providing information on the freshwater fish biodiversity of Uttar Pradesh. To develop UPFBase, data on the fish biodiversity of this region was compiled from different sources that include primary data generated from different projects and secondary data from published literatures. The collected data were screened and then digitized. Microsoft ACCESS relational database and Visual Basic language technologies were used for designing and implementing the standalone database application with the data management capability. Presently, UPFBase provides taxonomy, synonyms, local name, common name, morphology, biology, distribution, habitat, economic importance, conservation status and other fishery information on 129 fishes belonging to 11 orders and 27 families. UPFBase is user friendly and provides ease in working through search, query and action command button tools. It can easily be deployed on the mobile storages devices like CD-ROM, Pen drive, PCMCIA etc and can be installed on any Windows based Intel x86 machines. This version of UPFBase was built for countries, where computational hardware and software resources are in scare and it is expected that it might play imperious role in knowing and managing the indigenous fish diversity for decision making and posterity.

Thrombotic thrombocytopenic purpura (TTP) is one of the two classic thrombotic microangiopathy (TMA) diseases which could be induced by infections. To the best of our knowledge, this is the first report of an acquired immunodeficiency syndrome (AIDS) patient with acquired TTP induced by infection with Salmonella enterica serovar Typhimurium (hereafter, S. Typhimurium) isolate, S. Typhimurium_zhang, which was confirmed by serology and genetic taxonomy. The literature review identified 17 TMA-related genes encoding the candidate triggers, which were searched in the annotated genome sequence of S. Typhimurium_zhang. Anaerobic nitric oxide reductase flavorubredoxin (FlRd), encoded by norV which is related to another TMA, haemolytic uraemic syndrome (HUS), was found in S. Typhimurium_zhang. Basic local alignment search tool (BLAST) analysis revealed that norV and FlRd in S. Typhimurium_zhang, as well as eight S. Typhimurium type strains, have high identity with HUS-related Escherichia coli O157:H7 strain TW14359. Similar results were obtained from the BLAST analysis of 73 S. enterica isolates for congenital TTP which was also previously reported to be triggered by S. enterica. Phylogenetic analysis and amino acid sequence alignment revealed that FlRd was functional and highly conservative on 69 Enterobacteriaceae, including S. Typimurium_zhang and TW14359. In brief, we found norV in the genome of a S. Typhimurium clinical isolate that induced TTP in an AIDS patient. FlRd, the protein encoded by norV, probably triggered the TTP and was highly conservative, functional, and widespread in S. enterica and Enterobacteriaceae. More in vitro and in vivo studies are required to confirm our findings and determine the underlying mechanism.

The microbial symbiotic community in the digestive tract of termites is reportedly influenced by the taxonomy and feeding habit of the host. Both factors are strongly correlated with the nest type. This study aimed to isolate the cellulolytic bacteria from termite’s digestive tract on different nest types and characterize and identify the potential isolates. The research methods included termite sampling conducted in Bukit Baka Bukit Raya National Park (BBBRNP), Melawi, West Kalimantan, isolation of cellulolytic bacteria from termites’ gut, endoglucanase activity test, biochemical characterization, and DNA analysis based on the amplification of 16S rRNA gene. Thirty isolates from 6 different species of termites on three different nest types were successfully isolated. Sixteen potential endoglucanase bacterial isolates were tested in terms of their endoglucanase activity. The cellulolytic index measured from those isolates ranged from 1.162 - 4.894. Three isolates (MRH.13.S, MRH.13.AF, and MRH.13.O2) with the highest cellulolytic index on each nest type were identified. The analysis of 16S rRNA gene using BLAST (Basic Local Alignment Search Tool for Nucleotides) revealed that isolate MRH.13.S had the closest relationship with Bacillus tequilensis (99 % homology). Based on biochemical characterization, MRH.13.AF and MRH.13.O2 isolates were related to Bacillus spp. HIGHLIGHTS Potential cellulolytic bacteria from termite intestinal tract from different nests (i.e., soil, wood, and arboreal) were isolated and compared Termites were obtained from a lowland dipterocarp primary forest ecosystem in Bukit Baka Bukit Raya National Park, West Kalimantan Province, Indonesia Termite species collected were Termes comis, Dicuspiditermes garthwaitei, Synhamitermes quadriceps, Havilanditermes proatripennis, Bulbitermes borneensis, and Bulbitermes parapusillus Potential cellulolytic bacteria acquired were closely related with Bacillus tequilensis and Bacillus spp GRAPHICAL ABSTRACT