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Journal articles on the topic 'Chemo taxonomy'
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Auling, Georg, Andreas Probst, and Reiner M. Kroppenstedt. "Chemo- and Molecular Taxonomy of D(−)-Tartrate-Utilizing Pseudomonads." Systematic and Applied Microbiology 8, no. 1-2 (July 1986): 114–20. http://dx.doi.org/10.1016/s0723-2020(86)80158-8.
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Guillem, R. M., F. P. Drijfhout, and S. J. Martin. "Using chemo-taxonomy of host ants to help conserve the large blue butterfly." Biological Conservation 148, no. 1 (April 2012): 39–43. http://dx.doi.org/10.1016/j.biocon.2012.01.066.
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Delgado-Tiburcio, Eugenia Elisa, Jorge Cadena-Iñiguez, Edelmiro Santiago-Osorio, Lucero del Mar Ruiz-Posadas, Israel Castillo-Juárez, Itzen Aguiñiga-Sánchez, and Marcos Soto-Hernández. "Pharmacokinetics and Biological Activity of Cucurbitacins." Pharmaceuticals 15, no. 11 (October 26, 2022): 1325. http://dx.doi.org/10.3390/ph15111325.
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Cucurbitacins are a class of secondary metabolites initially isolated from the Cucurbitaceae family. They are important for their analgesic, anti-inflammatory, antimicrobial, antiviral, and anticancer biological actions. This review addresses pharmacokinetic parameters recently reported, including absorption, metabolism, distribution, and elimination phases of cucurbitacins. It includes recent studies of the molecular mechanisms of the biological activity of the most studied cucurbitacins and some derivatives, especially their anticancer capacity, to propose the integration of the pharmacokinetic profiles of cucurbitacins and the possibilities of their use. The main botanical genera and species of American origin that have been studied, and others whose chemo taxonomy makes them essential sources for the extraction of these metabolites, are summarized.
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Guillem, R. M. "Corrigendum to “Using chemo-taxonomy of host ants to help conserve the large blue butterfly” [Biol. Conserv. 148 (2012) 39–43]." Biological Conservation 152 (August 2012): 297. http://dx.doi.org/10.1016/j.biocon.2012.03.033.
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Ewas, Mohamed. "SYSTEMATIC REVISION OF CAPPARIS SPINOSA L. VAR. (CANESCENS, DESERTI, INERMIS), THE ENDEMIC VARIETIES AMONG EGYPTIAN FLORA BASED ON MOLECULAR AND CHEMO-TAXONOMY." Egyptian Journal of Desert Research 73, no. 1 (June 1, 2023): 131–56. http://dx.doi.org/10.21608/ejdr.2023.207924.1141.
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Yang, Yong, Heng-Lin Cui, Pei-Jin Zhou, and Shuang-Jiang Liu. "Halobacterium jilantaiense sp. nov., a halophilic archaeon isolated from a saline lake in Inner Mongolia, China." International Journal of Systematic and Evolutionary Microbiology 56, no. 10 (October 1, 2006): 2353–55. http://dx.doi.org/10.1099/ijs.0.64437-0.
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A novel halophilic archaeon, NG4T, was isolated from Jilantai salt lake in Inner Mongolia, China. The taxonomy of strain NG4T was studied by polyphasic methods. Strain NG4T grew at pH 5.5–8.5 and at a temperature of 22–55 °C. It was chemo-organotrophic, aerobic and required concentrations of 2.7–5.2 M NaCl and 0.05–0.3 M Mg2+ for growth. Cells were Gram-negative, slender rods. Colonies on agar plates containing 25 % (w/v) total salts were red, elevated and round. According to 16S rRNA gene sequence similarity, strain NG4T was phylogenetically related to Halobacterium salinarum DSM 3754T (98.2 %) and Halobacterium noricense A1T (97.3 %). The DNA G+C content was 64.2 mol%. DNA–DNA relatedness values with Hbt. salinarum DSM 3754T and Hbt. noricense A1T were 47 and 35 %, respectively. The polar lipids of strain NG4T consisted of phosphatidylglycerol, methylated phosphatidylglycerol phosphate, phosphatidylglycerol sulfate, triglycosyl diether, sulfated triglycosyl diether and sulfated tetraglycosyl diether. It was concluded that strain NG4T represents a novel species of the genus Halobacterium, for which the name Halobacterium jilantaiense sp. nov. is proposed. The type strain is NG4T (=CGMCC 1.5337T=JCM 13558T).
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Kamiya, Takahiro. "Differences between the sensory organs of phytal and bottom-dwelling <i>Loxoconcha</i> (Ostracoda, Crustacea)." Journal of Micropalaeontology 8, no. 1 (June 1, 1989): 37–47. http://dx.doi.org/10.1144/jm.8.1.37.
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Abstract. The morphology and distribution patterns of pores with a bristle were studied on two Loxoconcha species living in adjacent but different habitats: the phytal species L. japonica and the bottom-dwelling species L. uranouchiensis. Both species have only one kind of pore – sieve-pore – from which either of two kinds of bristles emerges. The two types of bristles are here called the “smooth”– and the “twisted”–type according to their morphological features. The sieve-pore orifice of the phytal Loxoconcha remains completely open, whereas that of the bottom-dwelling species has a special morphology both in the sieve-plate and the basal part of the bristle to cope with the adhesion of dirt. The number and distribution pattern of “twisted”-type bristles (chemo-receptors?) are the same in both species. The “smooth”-type bristles (mechano-receptors?), however, are distributed more densely in the ventral area of the bottom-dwelling species compared with those of the phytal species. This difference seems to be related to the mode of life, specifically the difference in the manner of ventral contact with substrata. Some adaptive characters of ostracod pores are clarified and their significance to ostracod taxonomy and palaeocology is discussed.
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Cotton, Laura J., Wolfgang Eder, and James Floyd. "Larger foraminifera of the Devil's Den and Blue Hole sinkholes, Florida." Journal of Micropalaeontology 37, no. 1 (March 23, 2018): 347–56. http://dx.doi.org/10.5194/jm-37-347-2018.
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Abstract. Shallow-water carbonate deposits are well-known from the Eocene of the US Gulf Coast and Caribbean. These deposits frequently contain abundant larger benthic foraminifera (LBF). However, whilst integrated stratigraphic studies have helped to refine the timing of LBF overturning events within the Tethys and Indo-Pacific regions with respect to global bio- and chemo-stratigraphic records, little recent work has been carried out in the Americas. The American LBF assemblages are distinctly different from those of Europe and the Indo-Pacific. It is therefore essential that the American bio-province is included in studies of LBF evolution, biodiversity and climate events to understand these processes on a global scale. Here we present the LBF ranges from two previously unpublished sections spanning 35 and 29 m of the upper Eocene Ocala limestone, as the early stages of a larger project addressing the taxonomy and biostratigraphy of the LBF of Florida. The study indicates that the lower member of the Ocala limestone may be Bartonian rather than Priabonian in age, with implications for the biostratigraphy of the region. In addition, the study highlights the need for multiple sites to assess the LBF assemblages and fully constrain ranges across Florida and the US Gulf and suggests potential LBF events for future integrated stratigraphic study.
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Raghav, Kanwal Pratap Singh, Wenting Wang, Michael J. Overman, and Scott Kopetz. "MET overexpression as a hallmark of the epithelial-mesenchymal transition (EMT) phenotype in colorectal cancer." Journal of Clinical Oncology 31, no. 4_suppl (February 1, 2013): 334. http://dx.doi.org/10.1200/jco.2013.31.4_suppl.334.
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334 Background: Dysregulation of the proto-oncogene MET (mesenchymal-epithelial transition factor gene) has been implicated in tumorigenesis and correlates with worse survival and chemo/radio-resistance in colorectal cancer (CRC). EMT has been identified as a dominant molecular characteristic of a subset of CRC tumors and represents a key feature in the developing colorectal taxonomy. The purpose of this study was to compare protein expression of MET with protein/gene expression of EMT markers and other clinicopathological characteristics, and to evaluate its impact on overall survival (OS). Methods: We performed an exploratory analysis of 590 CRC samples using data from The Cancer Genome Atlas. Fisher-exact test and Pearson’s method was used to determine the relationship between MET protein expression, clinicopathological characteristics and EMT marker protein expression by reverse-phase protein array (RPPA) and EMT-associated gene expression by RNA-sequencing. Regression tree method was applied to find the best cutoff point for MET using patients with available survival data. Overall survival (OS) was estimated non-parametrically using Kaplan-Meier curve and log-rank test was used to evaluate hazard ratio. Results: MET expression by RPPA did not correlate with traditional clinicopathologic characteristics. MET was overexpressed in 17% of CRC tumors and was significantly associated with OS (HR 2.92; 95% CI: 1.45 - 5.92). Correlation analysis of MET levels with gene expression of EMT markers AXL, CDH1, FGFR1, SNAIL, TWIST1/2, VIM, SLUG, ZEB1/2, FN1 demonstrated that the highest quartile of MET protein expression was associated with a 1.5 fold increase in ZEB1 (p = 0.002), a 1.4 fold increase in AXL (p = 0.005) and ZEB2 (p = 0.008), and a 1.3 fold increase in VIM (p = 0.02). MET expression also correlated strongly with protein expressions of SNAIL (transcription factor for EMT) (r = 0.96) and ERCC1 (r = 0.83) (a marker for oxaliplatin chemo-resistance). Conclusions: Increased MET protein expression is seen in 17% of CRC tumors and strongly correlates with a molecular EMT phenotype and poor survival in patients with CRC. MET protein expression may be a surrogate biomarker for this unique subset of CRC.
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Ng, Terry, Bader Alshamsan, Thanh Nguyen, James Butcher, Carol Stober, Lisa Vandermeer, Garth Nicholas, Alain Stintzi, and Vimoj Nair. "BIOM-40. THERABIOME-GBM: THERAPEUTIC OUTCOMES RELATED TO GUT MICROBIOME IN GLIOBLASTOMA (GBM) PATIENTS RECEIVING CHEMO-RADIATION: A PROSPECTIVE OBSERVATIONAL STUDY." Neuro-Oncology 25, Supplement_5 (November 1, 2023): v13. http://dx.doi.org/10.1093/neuonc/noad179.0051.
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Abstract PURPOSE A major barrier to improving outcomes in glioblastoma multiforme (GBM) is overcoming a heavily immunosuppressed tumor and systemic environment, as demonstrated by several negative phase III randomized studies of nivolumab in both newly diagnosed and recurrent GBM. In several mouse avatar and human studies across several tumor cohorts including in a humanized microbiome GBM model, re-establishing a new gut microbiome (GM) via fecal transplantation led to tumor responses to PD-1/PD-L1 inhibition. A recent scoping review confirmed a paucity of GM clinical data of a uniform GBM cohort with adequate longitudinal GM sample collection. We are conducting a single-center prospective observational study to establish the feasibility of collecting stool samples throughout the time course of GBM treatment and upon recurrence, and to understand the gut microbiome dynamics of newly diagnosed IDH-wild type (WT) GBM patients. METHODS Patients with newly diagnosed unifocal IDH-1 R132H WT WHO grade 4 GBM, ECOG 0-2, at least 70% tumor resected with plan to receive temozolomide-radiation (TMZ-RT) and adjuvant TMZ +/- Tumor Treating Fields are eligible. Stool samples will be collected prior to TMZ-RT, 4 weeks after TMZ-RT, after adjuvant TMZ, and upon recurrence. The primary endpoint is feasibility, defined as stool sample obtained pre-RT, post-RT (pre-adjuvant TMZ), and at time of recurrence in ≥ 70% of enrolled participants, 75% of target sample size enrolled within 2 years, and stool sample volume and quality sufficient for analysis in ≥ 75% of collected samples. Secondary endpoints include progression-free survival (PFS) in pre-defined GM subgroups, GM taxonomy and diversity in late vs. early progressors, and GM differences in patients with and without post-RT necrosis. Age, sex, race, concurrent medication, corticosteroid use, and diet will be carefully accounted for. Patient reported outcomes using EORTC-QLQ-BN20 and QLQ-C30 will be collected at baseline, 3-, 6-, 9-, and 12-months.
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Brendler, Thomas. "From Bush Medicine to Modern Phytopharmaceutical: A Bibliographic Review of Devil’s Claw (Harpagophytum spp.)." Pharmaceuticals 14, no. 8 (July 27, 2021): 726. http://dx.doi.org/10.3390/ph14080726.
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Devil’s claw (Harpagophytum spp., Pedaliaceae) is one of the best-documented phytomedicines. Its mode of action is largely elucidated, and its efficacy and excellent safety profile have been demonstrated in a long list of clinical investigations. The author conducted a bibliographic review which not only included peer-reviewed papers published in scientific journals but also a vast amount of grey literature, such as theses and reports initiated by governmental as well as non-governmental organizations, thus allowing for a more holistic presentation of the available evidence. Close to 700 sources published over the course of two centuries were identified, confirmed, and cataloged. The purpose of the review is three-fold: to trace the historical milestones in devil’s claw becoming a modern herbal medicine, to point out gaps in the seemingly all-encompassing body of research, and to provide the reader with a reliable and comprehensive bibliography. The review covers aspects of ethnobotany, taxonomy, history of product development and commercialization, chemistry, pharmacology, toxicology, as well as clinical efficacy and safety. It is concluded that three areas stand out in need of further investigation. The taxonomical assessment of the genus is outdated and lacking. A revision is needed to account for intra- and inter-specific, geographical, and chemo-taxonomical variation, including variation in composition. Further research is needed to conclusively elucidate the active compound(s). Confounded by early substitution, intermixture, and blending, it has yet to be demonstrated beyond a reasonable doubt that both (or all) Harpagophytum spp. are equally (and interchangeably) safe and efficacious in clinical practice.
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Åkerlund, Emma, Greta Gudoityte, Elisabeth Moussaud Lamodiere, Joseph Carlson, Emelie Wallin, Josefin Fernebro, Olli Kallioniemi, Päivi Östling, Ulrika Joneborg, and Brinton Seashore-Ludlow. "Abstract 1890: Development of the drug efficacy testing in ex vivo 3D cultures (DETECT) platform and its application to functional precision medicine in ovarian cancer." Cancer Research 82, no. 12_Supplement (June 15, 2022): 1890. http://dx.doi.org/10.1158/1538-7445.am2022-1890.
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Abstract Many ovarian cancer (OC) patients receiving chemotherapy relapse with acquired resistance, hence novel treatment allocation strategies are urgently needed. 3D cell culture models and organoid technologies have emerged as exciting tools to study cancer. Despite the advances, there is a need for protocols that can quickly generate patient-relevant 3D models for high-throughput drug screening and for diagnostic drug sensitivity testing. Ideally, such methods should be cost-effective, provide multi-parametric data to reveal distinct phenotypes, have single cell resolution to reveal heterogeneity and cell interactions, meet diagnostic timeframes and be miniaturized to allow the analysis of many drugs and combinations with small numbers of primary tumor cells. Here, we aimed to develop a robust technology for high-throughput ex vivo drug sensitivity testing for functional precision medicine using OC tissue and ascites samples (mostly high-grade serous carcinoma) from patients. We present a scalable drug screening platform: DETECT (Drug Efficacy Testing in Ex-vivo 3D Cultures), where tumor-derived patient cells can be rapidly screened within one week from sampling. Using this information patient-specific drug combinations are subsequently designed and tested with these data available within 9 days. This is much faster than with most screening protocols for organoids and PDC models where many weeks or months are required for establishment of the models and expansion of the required numbers of cells. We have currently tested the efficacy of 58 selected chemo- and targeted drugs in 5 doses using high content imaging and then a complete dose-matrix of 3 combinations at step 2. We report robust drug screening data in 15 out of 18 OC patient samples, which has resulted in a functional taxonomy of patient samples and a taxonomy of drugs based on their efficacy across patient samples. Some of the most common responses were seen for the BCL-XL inhibitor A-1331852 (9/15 patients), Topotecan (7), Dactinomycin (7), Omipalisib (6) and Omacetaxine (6). All but 2 drugs showed efficacy in at least one OC sample, suggesting heterogeneity and opportunities to make use of unique drug response patterns. Combination screening revealed that Carboplatin and A-1331852, a BCL-XL inhibitor, showed increased efficacy in 3 of the 5 tested patient samples. In conclusion, our 3D HT-drug testing assay DETECT with a combination screening capability could in the future be useful for guiding individualized treatment in a clinical setting as well as for identifying existing and emerging drugs and drug combinations for repurposing in OC. Citation Format: Emma Åkerlund, Greta Gudoityte, Elisabeth Moussaud Lamodiere, Joseph Carlson, Emelie Wallin, Josefin Fernebro, Olli Kallioniemi, Päivi Östling, Ulrika Joneborg, Brinton Seashore-Ludlow. Development of the drug efficacy testing in ex vivo 3D cultures (DETECT) platform and its application to functional precision medicine in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1890.
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Maier, Ingo, Dieter G. Müller, Günter Gassmann, Wilhelm Boland, and Lothar Jaenicke. "Sexual Pheromones and Related Egg Secretions in Laminariales (Phaeophyta)." Zeitschrift für Naturforschung C 42, no. 7-8 (August 1, 1987): 948–54. http://dx.doi.org/10.1515/znc-1987-7-836.
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Volatile egg secretions of 15 species belonging to 5 families of the brown algal order Laminariales have been analyzed by high resolution glass capillary gas chromatography. 16 components have been identified and partially determined quantitatively. The composition of the pheromone bouquets and pheromone specificity for induction of spermatozoid-release and -chemotaxis are discussed in respect to ecophysiological functions and significance as chemo- taxonomic markers.
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Barandouzi, Zahra, Tony Eng, Namita Khanna, Joseph Shelton, Pretesh Patel, Isabelle Scott, Rebecca Meador, and Deborah Bruner. "Abstract 3214: Associations of socioeconomic status and gut microbiome with psychoneurological symptom cluster in gynecologic cancer patients." Cancer Research 83, no. 7_Supplement (April 4, 2023): 3214. http://dx.doi.org/10.1158/1538-7445.am2023-3214.
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Abstract Introduction: Emerging evidence highlights the role of socioeconomic status (SES) in symptom burden related to cancer treatments. However, its underlying biological mechanisms are not fully understood. Thus, the present study aimed to evaluate the associations between patients’ education, as an indicator of SES, and the gut microbiome with psychoneurological symptoms (PNS) cluster in gynecologic cancer patients over time. Methods: Nineteen women with cervical and endometrial cancers treated with radiotherapy or chemo-radiotherapy were followed at pre-treatment, 6-8 weeks, and 6 months post-treatment. Functional assessment of cancer therapy-general (FACT-G) and patient health questionnaire-9 (PHQ-9) were used to measure symptoms. An average Z score of at least three out of five symptoms was computed as the PNS cluster total score. Patients’ SES was evaluated using data on education. Rectal swabs were also collected at the same time points and sequenced using 16S rRNA V4 regions. The Kruskal-Wallis and permutational multivariable analysis of variance tests were used to compare α-diversity (within one sample) and β-diversity (between samples) between patients with high and low PNS cluster as well as patients with “below college” and “college or above” level education. The linear discriminant analysis effect size (LEfSe) tested taxa differences between study groups. Also, the linear mixed effect model was used to evaluate the association of the gut microbiome, education, and the PNS cluster over cancer treatment. Results: The patients’ mean age was 58 years, 47% were Black, and 66% had college or above education. Among the participants, 63% had endometrial cancer with stage I disease (63%). There was a different taxonomy profile between patients with high and low PNS as well as patients with “below college” and “college or above” levels of education. Patients with high PNS had a lower α-diversity compared to patients with low PNS (Shannon, p=0.03, Evenness, p=0.03). Also, patients with below college-level education had a lower α-diversity trend after treatment (higher diversity is seen in the “normal” gut) but did not reach significant results. The mixed effects model results showed that low α-diversity, below college-level education, and low abundance of Fusicatenibacter and Ruminococcus were associated with high PNS cluster over cancer treatment. Conclusions: The present study demonstrated alteration in the gut microbiome composition between patients with high and low PNS cluster as well as patients with high and low education. The associations between the gut microbiome and education with the PNS cluster suggest the role of educational level and biological factors in developing PNS cluster. More studies using a larger sample size are required to evaluate the interactions of the gut microbiome and SES to shed light on their role in symptom development. Citation Format: Zahra Barandouzi, Tony Eng, Namita Khanna, Joseph Shelton, Pretesh Patel, Isabelle Scott, Rebecca Meador, Deborah Bruner. Associations of socioeconomic status and gut microbiome with psychoneurological symptom cluster in gynecologic cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3214.
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Park, Hyunchang, and Dongwhan Lee. "Ligand Taxonomy for Bioinorganic Modeling of Dioxygen‐Activating Non‐Heme Iron Enzymes." Chemistry – A European Journal 26, no. 27 (March 17, 2020): 5916–26. http://dx.doi.org/10.1002/chem.201904975.
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Greenaway, W., S. English, F. R. Whatley, and S. B. Rood. "Interrelationships of poplars in a hybrid swarm as studied by gas chromatography – mass spectrometry." Canadian Journal of Botany 69, no. 1 (January 1, 1991): 203–8. http://dx.doi.org/10.1139/b91-028.
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Analysis of bud exudate by gas chromatography-mass spectrometry (GC–MS) of 14 clones belonging to a natural hybrid swarm involving Populus angustifolia, P. balsamifera, and P. deltoides produced results consistent with those obtained by previous analysis of leaf characteristics. Specimens that had leaves most characteristic of a pure species also produced bud exudate GC–MS profiles which were characteristic of those species. GC–MS profiles of interspecific hybrid clones were intermediate between the parental species. This demonstrates the usefulness of GC–MS analysis of bud exudate as a chemo-taxonomic method for the study of intersecific poplar hybrids and also supports the accuracy of analysis of foliar morphology for taxonomic assessment. Key words: Populus, bud exudate, gas chromatography – mass spectrometry.
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Bhagawati, Sudhansu, Badal Bhattacharyya, Binoy K. Medhi, Snigdha Bhattacharjee, and Himangshu Mishra. "Diversity of Soil Dwelling Collembola in a Forest, Vegetable and Tea Ecosystems of Assam, India." Sustainability 13, no. 22 (November 16, 2021): 12628. http://dx.doi.org/10.3390/su132212628.
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Land use change has a great impact in determining the diversity patterns of soil fauna. Adoption of any land use pattern significantly affects the soil structure and its physico-chemical characteristics, which often leads to the loss of biodiversity. Considering the collembolans as the key organism in the indicator shopping basket of soil environment, the response of Collembola communities under three different land uses represented by forest, vegetable and tea ecosystems was studied. Collembolans were sampled at monthly intervals using Tullgren funnel and identified by standard taxonomic keys. Diversity analysis and soil chemo-edaphic factors were studied to establish the impact of different land uses on Collembola communities. Five genera of Collembola viz., Cyphoderus, Entomobrya, Isotoma, Folsomia and Hypogastrura were recorded from the forest ecosystem whereas Folsomia was completely absent in vegetable ecosystem and the tea ecosystem soil was devoid of both Folsomia and Hypogastrura. Seasonal diversity and density of Collembola were recorded to be higher in the forest ecosystem indicating the presence of relatively stable habitats as compared to vegetable and tea ecosystems showing relatively disturbed habitats. Correlation studies between different chemo-edaphic factors and collembolan population revealed that the moisture and organic carbon content of soil had significant positive correlation during all the four seasons in all the ecosystems studied. Higher adoption of mechanical and chemo-centric agriculture depletes the available resources of the soil and makes it less habitable and conducive for the growth and sustenance of collembolans in vegetable and tea ecosystem as compared to forest. Appropriate landscape planning, land management strategies and developing proper methods of land use practices may pave the way for the improvement of collembolan diversity at landscape level.
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Hà, Nguyễn Thị Hoài, Phạm Thị Bích Đào, and Nguyễn Đình Tuấn. "Taxonomic characterization of ten Thraustochytrids strains isolated from mangrove Xuan Thuy, Nam Dinh." Vietnam Journal of Biotechnology 14, no. 2 (June 30, 2016): 377–84. http://dx.doi.org/10.15625/1811-4989/14/2/9364.
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Thraustochytrids have become of considerable industrial and scientific interest in the past decade due to their health benefits. Thraustochytrids are found in a wide variety of marine habitats such as the coastal, mangrove and sediments including the deep sea. Thraustochytrids are extremely common on the detritus, macroalgae and decaying leaf, they play an important role as organic matter-degrading microorganisms Thraustochytrids are unicellular, eukaryotic, chemo-organotrophic organisms. Ten thraustochytrids strains PT269, PT270, PT273, PT274, PT279, PT284, PT285, PT287, PT81, PT84 were isolated from four locations in Xuan Thuy mangroves, Nam Dinh. In this report, classification is based on morphology and 18S rDNA sequences. Ten Thraustochytrid strains could be classified into three types of colony and four types of cell morphology. Molecular phylogenetic analysis of 18S rDNA sequences showed homology score to be 99-100% and these strains belonged to four genera in the family Thraustochytriaceae. PT269, PT279, PT284 and PT287 strains belong to Aurantiochytrium genus, they produce amoeboid cells and occur successive binary division. PT273 and PT285 strains belong to Thraustochytrium genus, thallus directly develop and cleave into sporangium. PT274 strain belong to Aplanochytrium genus with two distinct development, amoeboid cells are found, they rapidly round up and become sporangium; and successive binary cell division. PT270, PT81 and PT84 strains belong to genus Schizochytrium, they have successive binary cell division, zoospores release.
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Najar, Ishfaq Nabi, and Nagendra Thakur. "A systematic review of the genera Geobacillus and Parageobacillus: their evolution, current taxonomic status and major applications." Microbiology 166, no. 9 (September 1, 2020): 800–816. http://dx.doi.org/10.1099/mic.0.000945.
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The genus Geobacillus , belonging to the phylum Firmicutes, is one of the most important genera and comprises thermophilic bacteria. The genus Geobacillus was erected with the taxonomic reclassification of various Bacillus species. Taxonomic studies of Geobacillus remain in progress. However, there is no comprehensive review of the characteristic features, taxonomic status and study of various applications of this interesting genus. The main aim of this review is to give a comprehensive account of the genus Geobacillus . At present the genus acomprises 25 taxa, 14 validly published (with correct name), nine validly published (with synonyms) and two not validly published species. We describe only validly published species of the genera Geobacillus and Parageobacillus . Vegetative cells of Geobacillus species are Gram-strain-positive or -variable, rod-shaped, motile, endospore-forming, aerobic or facultatively anaerobic, obligately thermophilic and chemo-organotrophic. Growth occurs in the pH range 6.08.5 and a temperature of 37–75 °C. The major cellular fatty acids are iso-C15:o, iso-C16:0 and iso-C17:o. The main menaquinone type is MK-7. The G+C content of the DNA ranges between 48.2 and 58 mol%. The genus Geobacillus is widely distributed in nature, being mostly found in many extreme locations such as hot springs, hydrothermal vents, marine trenches, hay composts, etc. Geobacillus species have been widely exploited in various industrial and biotechnological applications, and thus are promising candidates for further studies in the future.
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KOCK, S. "Investigations of intermediate host specificity help to elucidate the taxonomic status of Trichobilharzia ocellata (Digenea: Schistosomatidae)." Parasitology 123, no. 1 (July 2001): 67–70. http://dx.doi.org/10.1017/s0031182001008101.
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The avian schistosomatid Trichobilharzia ocellata plays an important role as causative agent of cercarial dermatitis of humans in Europe. In order to improve the taxonomic knowledge on this parasite, studies of miracidial chemo-orientation as well as experimental infections of different snail species were conducted using strains of T. ocellata and T. franki. Both schistosomes exhibited a high intermediate host specificity. The miracidia clearly preferred the SCW (snail-conditioned water) of the respective natural intermediate host to SCW of other sympatric snail species. T. ocellata proved to be capable of infecting Lymnaea stagnalis and Stagnicola palustris, but could not develop in Radix ovata or R. auricularia. T. franki established an infection in specimens of R. auricularia and R. ovata, but not in L. stagnalis or S. palustris. The results imply that the intermediate host spectrum of T. ocellata is limited to L. stagnalis and S. palustris. Findings of T. ocellata (or Cercaria ocellata) that originated from snails of the genus Radix are likely to have actually belonged to species such as T. franki or T. regenti. The assumption that T. szidati is synonymous to T. ocellata is also discussed.
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Geier, Benedikt, Janina Oetjen, Bernhard Ruthensteiner, Maxim Polikarpov, Harald R. Gruber-Vodicka, and Manuel Liebeke. "Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography." Proceedings of the National Academy of Sciences 118, no. 27 (June 28, 2021): e2023773118. http://dx.doi.org/10.1073/pnas.2023773118.
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Our understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metabolites to the same animal’s three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridization for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning.
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Trigui, Yesmine, Daniel Wolf, Lilit Sahakyan, Hayk Hovakimyan, Kristina Sahakyan, Roland Zech, Markus Fuchs, Tilmann Wolpert, Michael Zech, and Dominik Faust. "First Calibration and Application of Leaf Wax n-Alkane Biomarkers in Loess-Paleosol Sequences and Modern Plants and Soils in Armenia." Geosciences 9, no. 6 (June 17, 2019): 263. http://dx.doi.org/10.3390/geosciences9060263.
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Interpreting paleoenvironmental conditions by means of n-alkane biomarker analyses is challenging because results depend on different influencing factors. Thus, regional calibration of n-alkane patterns is needed because of different plant chemo-taxonomic behavior. We investigated for the first-time leaf wax-derived n-alkane biomarkers from modern plants, litter, top soils, and two recently discovered loess-paleosol sequences (LPSs) in Armenia (Lesser Caucasus). Our results on modern samples show a promising discrimination power based on n-alkane chain length nC33 (probably nC31)) for grasses and herbs versus nC29 for deciduous trees, despite the large interplant variability within vegetation groups. In contrast with other Loess records in Europe, where Late Pleistocene environments are ranging from tundra-like (glacial) to deciduous forest habitats (interglacial), our results from two Armenian LPSs suggest a transition from humid-steppe biome or forest-steppe vegetation dominating during interglacial periods, to semi-desert shrubs species more adapted to the enhanced aridity during glacial periods.
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Nogi, Yuichi, Masaki Yoshizumi, and Masayuki Miyazaki. "Thalassospira povalilytica sp. nov., a polyvinyl-alcohol-degrading marine bacterium." International Journal of Systematic and Evolutionary Microbiology 64, Pt_4 (April 1, 2014): 1149–53. http://dx.doi.org/10.1099/ijs.0.058321-0.
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A polyvinyl-alcohol-degrading marine bacterium was isolated from plastic rope litter found in Tokyo Bay, Japan. The isolated strain, Zumi 95T, was a Gram-reaction-negative, non-spore-forming and facultatively anaerobic chemo-organotroph. The major respiratory quinone was Q-10. The predominant fatty acids were C18 : 1ω7c and C16 : 0. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Thalassospira in the class Alphaproteobacteria . The DNA G+C content of the novel strain was 55.1 mol%. The hybridization values for DNA–DNA relatedness between this strain and four reference strains representing species of the genus Thalassospira were significantly lower than that accepted as the phylogenetic definition of a species. On the basis of differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Thalassospira for which the name Thalassospira povalilytica sp. nov. (type strain Zumi 95T = JCM 18746T = DSM 26719T) is proposed.
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Baba, Atsushi, Masayuki Miyazaki, Takahiko Nagahama, and Yuichi Nogi. "Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests." International Journal of Systematic and Evolutionary Microbiology 61, no. 9 (September 1, 2011): 2215–20. http://dx.doi.org/10.1099/ijs.0.024158-0.
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Three chitin-degrading strains representing two novel species were isolated from mangrove forests in Okinawa, Japan. The isolates, ABABA23T, ABABA211 and ABABA212T, were Gram-negative, non-spore-forming, strictly aerobic chemo-organotrophs. The novel strains produced Q-8 as the major isoprenoid quinone component. The predominant fatty acids were iso-C15 : 0 and C16 : 0. On the basis of 16S rRNA gene sequence analysis, the isolates were closely affiliated with members of the genus Microbulbifer. The DNA G+C contents of strains ABABA23T and ABABA212T were 57.8 and 60.2 mol%, respectively. DNA–DNA relatedness values between these two strains and Microbulbifer reference strains were significantly lower than 70 %, the generally accepted threshold level below which strains are considered to belong to separate species. Based on differences in taxonomic characteristics, the three isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer chitinilyticus sp. nov. (type strain, ABABA212T = JCM 16148T = NCIMB 14577T) and Microbulbifer okinawensis sp. nov. (type strain, ABABA23T = JCM 16147T = NCIMB 14576T; reference strain, ABABA211) are proposed.
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Umoh, Romanus A., Imoh I. Johnny, Emmanuel R. Idio, Nsima A. Andy, Goodnews E. Charles, Anwanabasi E. Udoh, Daniel A. Owineng, and TiyoAbasi A. Udom. "Studies on Various Taxonomic, Pharmacognostic and Phytochemical Properties of Sanchezia speciosa Leonard Acanthaceae." Asian Journal of Biochemistry, Genetics and Molecular Biology 16, no. 6 (May 9, 2024): 70–80. http://dx.doi.org/10.9734/ajbgmb/2024/v16i6384.
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Sanchezia speciosa Leonard, Acanthaceae is used as ornamental plant. It used in folklore medicine in the management of pain, anti-microbial and insecticide. An investigation was carried out to evaluate the various taxonomic, pharmacognostic and phytochemical standards to ensure the identity, purity, safety and efficacy of the medicinal plant, S. speciosa. Various observations were recorded which included microscopy, micromeritics, fluorescence, chemomicroscopy, soluble extractive values, moisture contents and phytochemical analysis. The results indicated that the epidermal shapes were both polygonal on the adaxial and abaxial surfaces. Stomatal distribution was amphistomatic with anisocytic and diacytic stomata on the adaxial and abaxial surface, respectively. Stomatal index was 21.47% on the adaxial surface and 15.43% on the abaxial surface. Micromeritics results for the leaf powder were bulk volume of 25.33± 0.408, tapped volume of 19.00± 0.00, bulk density of 0.40± 0.006, tapped density of 0.53± 0.021, Hausner’s ratio of 1.34± 0.037, Carr’s index of 25.00± 2.550 and angle of repose of 43.07°. The micromeritics indicated a passable flow. The chemo microscopy indicated presence of lignin, mucilage and starch. Fluorescence properties showed different colours under different ultraviolet lights. The water-soluble, methanol-soluble, ethanol-soluble extractive values were 14.7% w/w, 4.3% w/w and 5.0% w/w, respectively. Moisture content was 8.5% w/w. Total ash, acid-insoluble and water-soluble ash values were 20.0 % w/w, 2.0% w/w and 4.2% w/w, respectively. GC-MS of methanol extract revealed the total of 39 phytochemicals with over 5 prominent peaks having higher area% which include hexadecanoic acid methyl ester (2.64%), 9,12,15-octadecatrienoic acid methyl ester (4.77%), phytol (9.98%), 9,12,15 octadecatrienoic acid (12.97%), Stigmasterol (2.00%) and Squalene (28.16%). Other compounds are glycerin (5.83%), n-hexadecanoic acid (2.85%) and 9 octadecenamide (2.18%). Many of them possess good pharmacological properties. The data generated from the present study would help to authenticate S. speciosa and also affirm its folklore use in traditional medicine which has potential for further development into drug product.
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VAUGHAN, DAVID B., KEVIN W. CHRISTISON, HAAKON HANSEN, and STEPHEN A. BULLARD. "Species of Hexabothriidae (Monogenea) may have extensive distribution ranges reflecting multiple host species: evidence from three new South African records." Zootaxa 5254, no. 2 (March 10, 2023): 151–80. http://dx.doi.org/10.11646/zootaxa.5254.2.1.
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Many hexabothriid genera require renewed taxonomic attention to provide additional detailed comparative data from new material to resolve existing species quandaries. Our current study describes and provides additional museum material for three hexabothriid species from three genera from South Africa: Erpocotyle catenulata (Guberlet), which is confirmed as a valid species, Heteronchocotyle gymnurae Neifar, Euzet and Ben Hassine, and Hypanocotyle bullardi Chero, Cruces, Sáez, Carolina, Camargo, Portes Santos and Luque. Evidence of these three hexabothriid species from South Africa suggests that hexabothriids have more globally widespread distributions, and that they are less host-specific than previously considered. A detailed summary of hexabothriids reported from the triakid hosts, Galeorhinus galeus and Mustelus mustelus is provided, and the host-specificity of hexabothriids is discussed.
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Vukićević, Dušan R., Dragana D. Stevanović, Marija S. Genčić, Polina D. Blagojević, and Niko S. Radulović. "Essential-Oil Constituents and Alkanes ofCephalaria ambrosioidesRoem. & Schult. (Family Caprifoliaceae, Subfamily Dipsacaceae) and (Chemo)taxonomic Discernment of the Subfamilies Dipsacaceae and Morinaceae." Chemistry & Biodiversity 13, no. 2 (February 2016): 198–209. http://dx.doi.org/10.1002/cbdv.201500050.
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Nogi, Yuichi, Kozue Mori, Hiromi Uchida, and Yuji Hatada. "Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment." International Journal of Systematic and Evolutionary Microbiology 65, Pt_9 (September 1, 2015): 2786–90. http://dx.doi.org/10.1099/ijs.0.000333.
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A novel marine bacterial strain designated JAMH 011T was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Shimia in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, Shimia haliotis WM35T, was 98.1 %. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA–DNA relatedness between strain JAMH 011T and reference strains belonging to the genus Shimia were less than 9.4 ± 0.7 %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Shimia, for which the name Shimia sagamensis sp. nov. is proposed. The type strain is JAMH 011T ( = JCM 30583T = DSM 29734T)
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Lee, Hae-Won, Hong-Shan Yu, Qing-mei Liu, Hae-Min Jung, Dong-Shan An, Wan-Taek Im, Feng-Xie Jin, and Sung-Taik Lee. "Kaistia granuli sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor." International Journal of Systematic and Evolutionary Microbiology 57, no. 10 (October 1, 2007): 2280–83. http://dx.doi.org/10.1099/ijs.0.65023-0.
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A Gram-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (designated strain Ko04T) was isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor, and was investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ko04T belongs to the order Rhizobiales in the Alphaproteobacteria. Comparative 16S rRNA gene sequence analysis showed that strain Ko04T was most closely related to Kaistia adipata (97.5 %) and that sequence similarities with other species of Rhizobiales with validly published names were less than 92.5 %. The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1 ω7c/ω9t/ω12t, C19 : 0 cyclo ω8c and C18 : 0. The G+C content of the genomic DNA of strain Ko04T was 67.8 mol%. The level of DNA–DNA relatedness with K. adipata Chj404T was 15 %. The results of the genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Ko04T represents a novel species within the genus Kaistia, for which the name Kaistia granuli sp. nov. is proposed. The type strain is Ko04T (=KCTC 12575T=LMG 23410T).
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Xu, Ping, Wen-Jun Li, Shu-Kun Tang, Yu-Qin Zhang, Guo-Zhong Chen, Hua-Hong Chen, Li-Hua Xu, and Cheng-Lin Jiang. "Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China." International Journal of Systematic and Evolutionary Microbiology 55, no. 3 (May 1, 2005): 1149–53. http://dx.doi.org/10.1099/ijs.0.63407-0.
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A taxonomic study was performed on strain YIM 31775T, which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 °C and 6·5 to 12·0, respectively; the optimum growth temperature and pH were 28–37 °C and 7·0–9·0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C16 : 1 ω7c (42·4 %) and C16 : 0 (28·1 %). The DNA G+C content was 62·4±0·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775T should be placed within the family ‘Oxalobacteraceae’, in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775T should be classified as representing a novel member of the family ‘Oxalobacteraceae’, for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775T (=CCTCC AA 204003T=KCTC 12194T).
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Ravin, Nikolai V., Simona Rossetti, Alexey V. Beletsky, Vitaly V. Kadnikov, Tatyana S. Rudenko, Dmitry D. Smolyakov, Marina I. Moskvitina, Maria V. Gureeva, Andrey V. Mardanov, and Margarita Yu Grabovich. "Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov." Microorganisms 10, no. 7 (June 27, 2022): 1300. http://dx.doi.org/10.3390/microorganisms10071300.
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The metagenome of foulings from sulfidic spring “Serovodorodny” (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, ‘Candidatus Thiothrix sulfatifontis’ sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate.
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Castilho, RO, and MAC Kaplan. "Chemosystematics of the Rosiflorae." Brazilian Journal of Biology 68, no. 3 (August 2008): 633–40. http://dx.doi.org/10.1590/s1519-69842008000300022.
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The superorder Rosiflorae (sensu Dahlgren, 1980) belongs to the Angiospermae. It comprises twelve orders and thirty-eight families formed of species with varied habits widely distributed in temperate regions. The chemistry of Rosiflorae species is highly diversified; nevertheless it shows clearly phylogenetic affinity among the orders, except for Buxales. Flavonoids and triterpenoids are the real taxonomic markers for the superorder, due not only to the great number of occurrences, but also to the high structural diversity. On the other hand, the alkaloids are suitable as chemical markers only for the order Buxales. For orders and families of Rosiflorae, analysis of correlations among chemical parameters based on flavonoids and triterpenoids, with themselves and with the morphological and chemo-morphological parameters, showed evolutionary gradients among these taxa in which Trochodendrales occupy a primitive position while Saxifragales have the outpost. According to the types of flavonoids found in the superorder, there is clearly a higher incidence of flavonols than flavones, suggesting a primitive status of the Rosiflorae. Evolutionary advancement parameters relative to flavonoid hydroxyl protection show preferential protection mechanisms of glycosylation against methylation as well as a high percentage of free hydroxyl groups. The order Buxales has an isolated position in the superorder Rosiflorae with a high alkaloid production, which is quite exclusive to this taxon.
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Jung, Hae-Min, Jung-Sook Lee, Heon-Meen Bae, Tae-Hoo Yi, Se-Young Kim, Sung-Taik Lee, and Wan-Taek Im. "Inquilinus ginsengisoli sp. nov., isolated from soil of a ginseng field." International Journal of Systematic and Evolutionary Microbiology 61, no. 1 (January 1, 2011): 201–4. http://dx.doi.org/10.1099/ijs.0.018689-0.
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A Gram-reaction-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (strain Gsoil 080T) was isolated from soil collected in a ginseng field in Pocheon Province, South Korea, and was investigated by using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 080T was related most closely to Inquilinus limosus strains AU0476T and AU1979 (98.9 % similarity to both). Strain Gsoil 080T shared ≤91.3 % 16S rRNA gene sequence similarity with the type strains of other recognized species examined. The genus Inquilinus belongs to the family Rhodospirillaceae in the order Rhodospirillales, class Alphaproteobacteria. The predominant ubiquinone was Q-10 and the major fatty acids were summed feature 7 (C18 : 1 ω9c/ω12t/ω7c) and C19 : 0 cyclo ω8c. The G+C content of the genomic DNA of strain Gsoil 080T was 69.9 mol%. The level of DNA–DNA relatedness between strain Gsoil 080T and I. limosus LMG 20952T was 12 %. The results of genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Gsoil 080T represents a novel species of the genus Inquilinus, for which the name Inquilinus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 080T (=KCTC 12574T =LMG 23638T).
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Vieira, Selma, Javier Pascual, Christian Boedeker, Alicia Geppert, Thomas Riedel, Manfred Rohde, and Jörg Overmann. "Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil." International Journal of Systematic and Evolutionary Microbiology 70, no. 9 (September 1, 2020): 4966–77. http://dx.doi.org/10.1099/ijsem.0.004367.
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The family Caulobacteraceae comprises prosthecate bacteria with a dimorphic cell cycle and also non-prosthecate bacteria. Cells of all described species divide by binary fission. Strain 0127_4T was isolated from forest soil in Baden Württemberg (Germany) and determined to be the first representative of the family Caulobacteraceae which divided by budding. Cells of strain 0127_4T were Gram-negative, rod-shaped, prosthecate, motile by means of a polar flagellum, non-spore-forming and non-capsulated. The strain formed small white colonies and grew aerobically and chemo-organotrophically utilizing organic acids, amino acids and proteinaceous substrates. 16S rRNA gene sequence analysis indicated that this bacterium was related to Aquidulcibacter paucihalophilus TH1-2T and Asprobacter aquaticus DRW22-8T with 91.3 and 89.7% sequence similarity, respectively. Four unidentified glycolipids were detected as the major polar lipids and, unlike all described members of the family Caulobacteraceae , phosphatidylglycerol was absent. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c/C16 : 0 10-methyl), C16 : 0 and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). The major respiratory quinone was Q-10. The G+C content of the genomic DNA was 63.5 %. Based on the present taxonomic characterization, strain 0127_4T represents a novel species of a new genus, Terricaulis silvestris gen. nov., sp. nov. The type strain of Terricaulis silvestris is 0127_4T (=DSM 104635T=CECT 9243T).
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Barbeyron, Tristan, Yannick Lerat, Jean-François Sassi, Sophie Le Panse, William Helbert, and Pi Nyvall Collén. "Persicivirga ulvanivorans sp. nov., a marine member of the family Flavobacteriaceae that degrades ulvan from green algae." International Journal of Systematic and Evolutionary Microbiology 61, no. 8 (August 1, 2011): 1899–905. http://dx.doi.org/10.1099/ijs.0.024489-0.
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A rod shaped, Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, non-gliding bacterium, designated strain PLRT, was isolated from faeces of the mollusc Aplysia punctata (Mollusca, Gastropoda) that had been fed with green algae belonging to the genus Ulva. The novel strain was able to degrade ulvan, a polysaccharide extracted from green algae (Chlorophyta, Ulvophyceae). The taxonomic position of strain PLRT was investigated by using a polyphasic approach. Strain PLRT was dark orange, oxidase-positive, catalase-positive and grew optimally at 25 °C, at pH 7.5 and in the presence of 2.5 % (w/v) NaCl with an oxidative metabolism using oxygen as the electron acceptor. Nitrate could not be used as the electron acceptor. Strain PLRT had a Chargaff’s coefficient (DNA G+C content) of 35.3 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene placed the novel strain in the family Flavobacteriaceae (phylum ‘Bacteroidetes’), within a clade comprising Stenothermobacter spongiae, Nonlabens tegetincola, Sandarakinotalea sediminis, Persicivirga xylanidelens and Persicivirga dokdonensis. The closest neighbours of strain PLRT were P. xylanidelens and P. dokdonensis, sharing 95.2 and 95.5 % 16S rRNA gene sequence similarity, respectively. Phylogenetic inference and differential phenotypic characteristics demonstrated that strain PLRT represents a novel species of the genus Persicivirga, for which the name Persicivirga ulvanivorans sp. nov. is proposed. The type strain is PLRT ( = CIP 110082T = DSM 22727T).
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Bereded, Negash Kabtimer, Manuel Curto, Konrad J. Domig, Getachew Beneberu Abebe, Solomon Workneh Fanta, Herwig Waidbacher, and Harald Meimberg. "Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia." Microorganisms 8, no. 7 (July 13, 2020): 1040. http://dx.doi.org/10.3390/microorganisms8071040.
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The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.
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Vázquez-Madrigal, Ana Sofía, Alejandra Barbachano-Torres, Melchor Arellano-Plaza, Manuel Reinhart Kirchmayr, Ilaria Finore, Annarita Poli, Barbara Nicolaus, Susana De la Torre Zavala, and Rosa María Camacho-Ruiz. "Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico." Microorganisms 9, no. 5 (May 20, 2021): 1096. http://dx.doi.org/10.3390/microorganisms9051096.
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The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.
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Ajah, Virginia N., Chukwubuikem Okolo, Ugochukwu Okezie, Cletus Ukwubile, Anita Kelechi Asekunowo, Blessing Umeokoli, and Festus Okoye. "Secondary metabolites of mangrove-derived endophytic fungus, Pseudopestalotiopsis species investigated for antimicrobial and antioxidant activities." Journal of Current Biomedical Research 3, no. 5, September-October (October 31, 2023): 1197–218. http://dx.doi.org/10.54117/jcbr.v3i5.2.
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Attention is being diverted toward the bioprospecting of newer bioactive compounds from marine endophytic fungi. This is because marine fungi have shown a large chemo-diversity of untapped important secondary metabolites needed for drug development. In the present study, the secondary metabolites of a mangrove-derived endophytic fungus Pseudopestalotiopsis species isolated from the root of Rhizophora racemosa were investigated for antimicrobial and antioxidant activities. The fungal isolation, taxonomic identification, fermentation, extraction, and isolation of the fungal secondary metabolites were carried out using standard techniques. The fermentation product was subjected to fractionation. The crude extract and its fractions were screened for antimicrobial and antioxidant assays. The active extracts and fractions exhibited good antimicrobial activities against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas oleaginous, and Candida albicans with MIC values that ranged between 0.06 to 1 mg/mL. The Gram negatives were the most susceptible bacteria while C. albicans was the most susceptible fungi. Moderately low antioxidant activities were recorded in the DPPH and FRAP assays. The chromatographic separation and HPLC analysis of the fungal secondary metabolites yielded compounds: Palitantin (A), Cytosporin D (B), Cytosporin K (C), and Fusarielin (D). These compounds have been previously reported to possess varying pharmacological activities which include antimicrobial and antioxidant activities. Thus, The results of this study show that these compounds may, in part, account for the anti-microbial and antioxidant effect of the root of Rhizophora racemosa ethno medically.
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Zimin, G. V. "TYPES AND STRUCTURE OF LANDSCAPES OF VITICULTURAL RIGIONS ON THE RIGHT BANK OF THE RIVER DON FOR IDENTIFICATION OF MICROZONES FOR HIGH-QUALITY WINEMAKING." Russian Vine 17 (November 2021): 14–22. http://dx.doi.org/10.32904/2712-8245-2021-17-14-22.
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The characteristic of the entire diversity of land-scapes of the right bank of the Lower Don and its tributaries from the city of Konstantinovsk to the city of Tsimlyansk, corresponding taxonomic levels that differ qualitatively from each other by landscape-forming factors, taking into account the degree of influence of these individual fac-tors and their different ratios among themselves on the growth of the grape plant, the yield of grapes, the quality of grapes and products ob-tained from it. The object of the research is the landscapes of the right bank of the Don River from the city Konstantinovka to the city Tsim-lyansk, its main tributaries at the mesorelief level and landscape-forming factors – geography, re-lief, soil and groundwater. The research method is the study of historical and literary data on vit-iculture on the Right Bank of the Lower Don, obtaining the necessary landscape-forming data by drilling wells to a depth of up to 10 m with a morphological description of their soil, geologi-cal and hydrogeological profile, with the selec-tion of soil and groundwater samples for chemi-cal analysis.
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Sanjay, Vaishampayan. "Study of the taxonomic distribution of insect fauna collected in light trap with different light sources during Rabi season at Jabalpur (M.P.)." International Journal of Chemical Studies 9, no. 1 (January 1, 2021): 1911–16. http://dx.doi.org/10.22271/chemi.2021.v9.i1aa.11501.
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Sheu, Shih-Yi, Nian-Tsz Cho, A. B. Arun, and Wen-Ming Chen. "Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli." International Journal of Systematic and Evolutionary Microbiology 61, no. 9 (September 1, 2011): 2284–91. http://dx.doi.org/10.1099/ijs.0.023010-0.
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A bacterial strain designated NAA16T was isolated from a freshwater spring in Taiwan and was characterized using a polyphasic taxonomic approach. Strain NAA16T was aerobic, Gram-staining-negative, rod-shaped, non-spore-forming and motile by means of a single polar flagellum. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–8.0 (optimum, pH 7.5) and with up to 1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain NAA16T were Singularimonas variicoloris MN28T, Sinobacter flavus CW-KD 4T and Solimonas soli DCY12T, with respective sequence similarities of 96.7, 96.6 and 96.2 %. Phylogenetic trees reconstructed from 16S rRNA gene or rpoB sequences (encoding the β-subunit of the RNA polymerase) revealed that the novel strain NAA16T and these three closest relatives formed an independent phylogenetic clade within the Gammaproteobacteria. Strain NAA16T contained C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as predominant fatty acids and possessed phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids. The major isoprenoid quinone was Q-8. The DNA G+C content of strain NAA16T was 66.2 mol%. The taxonomic relationship of strain NAA16T, Singularimonas variicoloris DSM 15731T, Sinobacter flavus DSM 18980T and Solimonas soli LMG 24014T was clarified by means of a direct experimental comparison. Based on phenotypic, chemotaxonomic and phylogenetic data, the descriptions of the genus Solimonas and its type species Solimonas soli are emended. Members of the genus are Gram-negative, oxidase- and catalase-positive, aerobic or facultatively anaerobic and chemo-organotrophic. Chemotaxonomically, members of the genus Solimonas possess Q-8 as the major respiratory quinone, C16 : 0 and C18 : 1ω7c as predominant fatty acids and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids; the DNA G+C content is 64.9–68.4 mol%. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, allowed us to assign strain NAA16T to the genus Solimonas within the novel species Solimonas aquatica sp. nov. (type strain NAA16T = BCRC 17835T = LMG 24500T). The reclassification of Sinobacter flavus as Solimonas flava comb. nov. (type strain CW-KD 4T = DSM 18980T = KCTC 12881T = CCTCC AB 206145T) and Singularimonas variicoloris as Solimonas variicoloris comb. nov. (type strain MN28T = DSM 15731T = LMG 22844T) is also proposed.
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Nazina, Tamara N., Elena V. Lebedeva, Andrei B. Poltaraus, Tatyana P. Tourova, Alexandre A. Grigoryan, Diyana Sh Sokolova, Anatoliy M. Lysenko, and George A. Osipov. "Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov." International Journal of Systematic and Evolutionary Microbiology 54, no. 6 (November 1, 2004): 2019–24. http://dx.doi.org/10.1099/ijs.0.02932-0.
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A novel thermophilic spore-forming strain, GaT, was isolated from the Garga hot spring located in the northern part of the Transbaikal region (Russia). Strain GaT was found to be an aerobic, Gram-positive, rod-shaped, thermophilic (optimum growth temperature is 60–65 °C), chemo-organotrophic bacterium that grows on various sugars, carboxylic acids and hydrocarbons. The G+C content of its DNA is 52·9 mol%. The 16S rRNA gene sequence similarity data show that strain GaT is closely related to members of the genus Geobacillus. Relevant chemotaxonomic data (in particular, the major fatty acid profile of strain GaT, which includes iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 acids) support the assignment of this strain to the genus Geobacillus. The physiological, biochemical and DNA–DNA hybridization studies of strain GaT showed that it differs both genotypically and phenotypically from the recognized Geobacillus species. Based on these data, strain GaT belongs to a novel species, Geobacillus gargensis sp. nov. (type strain, GaT=VKM B-2300T=DSM 15378T). The analysis of the phenotypic characteristics (additional to those given in the original description) of the type strain of Bacillus vulcani (DSM 13174T) showed that they are very similar to the major phenotypic characteristics of the genus Geobacillus. The low DNA–DNA reassociation values of strain DSM 13174T with various species of this genus (from 38 to 54 %) clearly demonstrate a sufficient genomic distinction of this strain and its taxonomic status as a species. The physiological characteristics, phylogenetic position and DNA–DNA reassociation values of B. vulcani allow this species to be reclassified as Geobacillus vulcani comb. nov. The main properties that differentiate G. vulcani from the other species of the genus are its ability to produce acids from glycerol, lactose and ribose.
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Pandey, Dheeraj, Michal Szczesniak, Julia Maclean, Howard Chi Ho Yim, Fan Zhang, Peter Graham, Emad M. El-Omar, and Peter Wu. "Dysbiosis in Head and Neck Cancer: Determining Optimal Sampling Site for Oral Microbiome Collection." Pathogens 11, no. 12 (December 16, 2022): 1550. http://dx.doi.org/10.3390/pathogens11121550.
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Recent research suggests that dysbiosis of the oral microbial community is associated with head and neck cancer (HNC). It remains unclear whether this dysbiosis causes chemo-radiotherapy (CRT)-related complications. However, to address this question, it is essential to determine the most representative oral site for microbiome sampling. In this study, our purpose was to determine the optimal site for oral sample collection and whether the presence of HNC is associated with altered oral microbiome from this site. In 21 newly diagnosed HNC patients and 27 healthy controls, microbiome samples were collected from saliva, swabs from buccal mucosa, tongue, hard palate, faucial pillars and all mucosal sites combined. Microbial DNA was extracted and underwent 16S rRNA amplicon gene sequencing. In healthy controls, analysis of observed taxonomic units detected differences in alpha- and beta-diversity between sampling sites. Saliva was found to have the highest intra-community microbial diversity and lowest within-subject (temporal) and between-subject variance. Feature intersection showed that most species were shared between all sites, with saliva demonstrating the most unique species as well as highest overlap with other sites. In HNC patients, saliva was found to have the highest diversity but differences between sites were not statistically significant. Across all sites, HNC patients had lower alpha diversity than healthy controls. Beta-diversity analysis showed HNC patients’ microbiome to be compositionally distinct from healthy controls. This pattern was confirmed when the salivary microbiome was considered alone. HNC patients exhibited reduced diversity of the oral microbiome. Salivary samples demonstrate temporal stability, have the richest diversity and are sufficient to detect perturbation due to presence of HNC. Hence, they can be used as representative oral samples for microbiome studies in HNC patients.
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Coccioni, Rodolfo, Nadia Sabatino, Fabrizio Frontalini, Silvia Gardin, Marianna Sideri, and Mario Sprovieri. "The neglected history of Oceanic Anoxic Event 1b: insights and new data from the Poggio le Guaine section (Umbria–Marche Basin)." Stratigraphy 11, no. 3-4 (2014): 245–82. http://dx.doi.org/10.29041/strat.11.3.03.
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The upper Aptian to lower Albian interval (~114–109 Ma) represents a crucial period during Earth’s history, with a major evolution in the nature of mid–Cretaceous tectonics, sea level, climate, and marine plankton communities. Interestingly, it also includes multiple prominent black shale horizons that are the sedimentary expression of oceanic anoxic event (OAE) 1b. However, due to a set of geological, stratigraphic, and taxonomic challenges, difficulties constraining this OAE may sometimes result in inaccurate correlation. At Poggio le Guaine (central Italy), a continuous and undisturbed section of central western Tethyan pelagic sediments deposited during the latest Aptian and earliest Albian, complete with black shale horizons that record the OAE1b carbon cycle perturbations, has provided a unique opportunity to address the shortcomings referred to above. High–resolution geochemical proxies (CaCO3, TOC, and δ13C), along with planktonic foraminifera and calcareous nannofossils, were used to establish an integrated and robust global stratigraphic framework in order to: (1) precisely correlate the prominent black shale horizons of OAE1b in different marine environments (the Vocontian Basin in southeast France, Deep Sea Drilling Project Site 545 and Ocean Drilling Program Hole 1049C in the eastern and western North Atlantic, respectively); and (2) provide an effective tool to reconstruct, in high resolution, the paleobiological, paleoceanographic and paleoclimatic changes across the upper Aptian to lower Albian interval. The Poggio le Guaine section stands out as a valuable reference section for OAE1b, its constituent subevents, and the δ13C record for the uppermost Aptian to lower Albian interval. The exceptional chemo- and biochronostratigraphic control allow direct comparison to the proposed candidate for the GSSP for the base of the Albian Stage at the Col de Pré-Guittard section in France.
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Cerda-Peña, Carol, and Sergio Contreras. "Characterization and chemo-taxonomic evaluation of plant leaf waxes (long chain n-alkanoic acids, n-alkanes and n-alkanols) as a vegetation biomarker from species of the South American temperate forest (STF)." Ecological Indicators 136 (March 2022): 108675. http://dx.doi.org/10.1016/j.ecolind.2022.108675.
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Dehodyuk, Eduard, Stanislav Dehodyuk, and Natalya Buslaeva. "Innovative approaches to risk management in nature and land use and their optimization." Problems of Innovation and Investment Development, no. 20 (November 2019): 119–30. http://dx.doi.org/10.33813/2224-1213.20.2019.12.
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Subject of research-theoretical and practical justification of risk managementfor climate change based on basin approach. The purpose of the article is to establish ecological equilibrium in the basins of small rivers of Ukraine through asystematic approach to the complex carrying out of nature-related works, agro-,chemo-, bio- and phyto-melioration in the small rivers basins. Methodology of work- system-structural and comparative analysis (for the definition of innovative approaches in environmental protection) as a landfill (in the determined cost of landfor optimizing land relations). Modeling and forecasting for risks reduction innature land use. The results of the work - degradation processes in the groundand water ecosystems of the basins of small rivers are considered. It is proposedto change the priorities in landscape studies by adopting the main taxonomic unitof any landscape of the small river basin instead of the abstract general principle“nature-territorial complex (PTC)”. A space-regulatory mechanism for the implementation of V.I. Vernadsky’s idea of Noosphere in the terrestrial ecosystems wasdeveloped. The sequence of ecologically-technogenic transformations of degradedsmall river basins in ecologically balanced ecosystems by means of restoration workswithout violating the basis of erosion and providing biocenosis of the self-healingmomentum has been determined. The system approach to the problem is to develop and adopt the laws of Ukraine on the restoration of small river basins, theircertification, land relations in the process of restorative works, and the increaseof natural biodiversity. Ways to overcome the risks of climate change are consistent implementation of the proposed programs. Conclusions-based on the resultsof the study, the lack of a scientifically grounded mechanism for overcomingdegradation processes in the basins of small rivers both in Ukraine and the international community and overcoming the risks to society for climate change in thepost-Holocene period was established. Proposed laws of Ukraine are proposed thatwill ensure the establishment of ecological balance in agro-and biogeocenosis forconducting relevant works in the basins of small rivers.
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Lau, Stanley C. K., Mandy M. Y. Tsoi, Xiancui Li, Ioulia Plakhotnikova, Sergey Dobretsov, Madeline Wu, Po-Keung Wong, Joseph R. Pawlik, and Pei-Yuan Qian. "Description of Fabibacter halotolerans gen. nov., sp. nov. and Roseivirga spongicola sp. nov., and reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov." International Journal of Systematic and Evolutionary Microbiology 56, no. 5 (May 1, 2006): 1059–65. http://dx.doi.org/10.1099/ijs.0.64104-0.
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Bacterial strains UST030701-097T and UST030701-084T were isolated from a marine sponge in the Bahamas. Both strains were pink-pigmented, Gram-negative, strictly aerobic and chemo-organotrophic. Cells of strain UST030701-097T were short, curved rods with fast-gliding motility, whereas those of strain UST030701-084T were straight rods with a less rapid gliding motion. The two strains had MK-7 as the major respiratory quinone and did not produce flexirubin-type pigments. The DNA G+C contents of strains UST030701-097T and UST030701-084T were 42.5 and 43.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the family ‘Flexibacteraceae’ of the phylum Bacteroidetes. 16S rRNA gene sequence similarity between strains UST030701-097T and UST030701-084T was 95.0 %; their closest relative was [Marinicola] seohaensis, with 93.3 % and 96.0 % sequence similarity, respectively. Phylogenetic tree topology indicated that the two strains belonged to the same lineage, but were on separate branches. Whilst strain UST030701-084T and [Marinicola] seohaensis were found on one branch, strain UST030701-097T was in another branch that had no species with validly published names. Based on the polyphasic taxonomic data obtained in the present study, we propose that strain UST030701-097T represents a novel genus and that strain UST030701-084T represents a novel species in the phylum Bacteroidetes. The genus Fabibacter gen. nov. is proposed, with strain UST030701-097T (=NRRL B-41220T=JCM 13334T) as the type strain of the type species, Fabibacter halotolerans sp. nov. Strain UST030701-084T (=NRRL B-41219T=JCM 13337T) is proposed as the type strain of Roseivirga spongicola sp. nov. In an earlier study, it was suggested that the genus Marinicola is a later heterotypic synonym of the genus Roseivirga. However, a formal proposal to reclassify [Marinicola] seohaensis, the only member of the genus Marinicola, has not yet been made. The results of phylogenetic analyses in this study support the reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov.
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Thommen, Ludmila, Vitor Heidrich, Rosângela Vieira de Andrade, Luiza Nardin Weis, Maria Sueli Soares Felipe, Melissa Lole Da Cas Vita, Thiago David Alves Pinto, Anamaria Camargo, and Romualdo Barroso-Sousa. "Abstract PO4-03-04: Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy." Cancer Research 84, no. 9_Supplement (May 2, 2024): PO4–03–04—PO4–03–04. http://dx.doi.org/10.1158/1538-7445.sabcs23-po4-03-04.
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Abstract Objective: The gut microbiome (GM) has been identified as one of the major environmental factors that can regulate the development and maintenance of the immune system. In oncology, while the importance of GM has been evaluated in more immunogenic tumors such as melanoma, lung carcinoma and clear cell carcinoma, its importance in early-stage breast cancer (eBC) is underexplored. The aim of this study was to characterize the GM of patients with eBC who underwent neoadjuvant chemotherapy (NACT) and to evaluate its association with clinicopathologic prognostic factors and outcomes. Methods: This was a prospective study conducted at two Brazilian institutions. Fecal samples were collected at baseline (time 1) and prior to surgery (time 2) from 55 patients who received NACT with anthracycline/taxane. Gut microbiome was analyzed by 16S rRNA amplicon sequencing to characterize the α (InvSimpson index) and β (weighted UniFrac distance metric) diversity, as well as taxonomic composition. Clinicopathologic prognostic factors were retrieved from medical records. Pathological complete response (pCR) was defined as the absence of invasive carcinoma in breast and axillary nodes (ypT0/Tis ypN0). Stromal tumor-infiltrating lymphocytes (sTIL) were reported according to the TIL working group criteria. Information about prior use (< 60 days before stating on NACT) of antibiotic (ATB) was obtained directly from patients. Statistical significance was set at P ≤ 0.05 and analysis of composition of microbiomes (ANCOM-BC2) was used to identify enriched genera with p-values adjusted using FDR correction ≤ 0.25. Results: Median age was 49 years (range 31-73). Eleven patients (20%) reported prior antibiotic use at baseline. About 34.5% of patients had HR+/HER2- tumors, 45.4% had triple negative breast cancer (TNBC), and 20% had HER2-positive breast cancer. Fourteen (25%) patients achieved a pCR. Out of 55, 47 (85.4%) had sTIL information. There was no significant difference in alpha diversity (p = 0.6) or beta-diversity (p = 0.8) between the pCR and residual disease group nor within clinical pathologic factors (age, staging, histological tumor grade, subtype of breast cancer based on IHC, sTIL). The most abundant taxon in both time 1 and time 2 were the same (Blautia at genus level, Lachnospiraceae at family level, and Lachnospirales at order level), and longitudinal samples collected during NACT showed no significant changes in GM composition. At baseline, we found an enrichment for Clostridia sp. among patients who did not use ATB (p < 0.05, pFDR ≤ 0.25). Additionally, we found enrichment for Bifidobacterium (p < 0.05, pFDR ≤ 0.25) among patients with HER2 subtype who presented residual disease. Conclusions: Gut microbiome analysis in early breast cancer is feasible and to our knowledge, this is the first study to evaluate the intestinal microbiota of Brazilian patients with breast cancer. We did not observe any significant association between GM diversity and taxonomic composition with clinical pathologic factors and pCR in this study, nor did we observe changes in the ecological balance of the GM following NACT in breast cancer. Further studies are needed to explore the potential influence of the gut microbial ecosystem on tumor biology and response to neoadjuvant chemo-immunotherapy. Citation Format: Ludmila Thommen, Vitor Heidrich, Rosângela Vieira de Andrade, Luiza Nardin Weis, Maria Sueli Soares Felipe, Melissa Lole Da Cas Vita, Thiago David Alves Pinto, Anamaria Camargo, Romualdo Barroso-Sousa. Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-04.
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Wakamori, Chisato, Marco A. De Velasco, Yurie Kura, Naomi Ando, Noriko Sako, Kazutoshi Fujita, Kazuko Sakai, et al. "Abstract 3044: Integrative gut microbiome analysis of human and mouse prostate cancer." Cancer Research 83, no. 7_Supplement (April 4, 2023): 3044. http://dx.doi.org/10.1158/1538-7445.am2023-3044.
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Abstract Gut microbes are intricately involved in maintaining normal physiology and homeostasis and have become a major area of study to determine their relevance in human disease. In cancer, alterations to gut microbiota has been associated to resistance to chemo- and immuno-therapy, whereas supplementation with specific taxa improves antitumor treatment responses. Mouse models have been essential to study disease biology and drug discovery. However, mice are fundamentally quite different from humans, thus, questions have arisen regarding their utility as pertinent tools to study microbial influences and their impact on human disease. To address these questions, we have performed a cross-species comparative analysis of the fecal microbiota from a human cohort of prostate cancer patients and a preclinical mouse model of prostate cancer. Microbiota composition was determined by 16s RNA gene sequencing on stool samples from tumor-bearing prostate-specific conditional Pten-knockout and disease-free wildtype mice and 16s RNA gene sequencing data from a human cohort of patients with suspected prostate cancer was used. Human cases were assigned to no cancer and cancer groups based on diagnosis from prostate biopsy and as low-risk (negative biopsy of Gleason grade <3) or high-risk (Gleason grade ≥3). Community composition differed significantly between stool samples of cancer and disease-free individuals in mice but not humans. Operational taxonomic units (OTUs) corresponding to taxa associated with cancer in both mice and humans included Odoribacter spp. and Desulfovibrio spp. Comparing the profiles predicted with Tax4Fun revealed KEGG metabolic pathways associated prostate cancer. Pathways enriched in cancer bearing-mice and that are also associated in patients with prostate cancer included folate biosynthesis, biotin metabolism and ubiquinone & other terpenoid-quinone biosynthesis. Carbon metabolism was a pathway discordant between high-risk prostate cancer patients and cancer bearing mice. Although the basal composition of gut microbes differed between humans and mice, the functional microbiome showed greater similarities. Our cross-species comparative analysis shows that gut microbial dysbiosis is connected to prostate cancer provides additional insights into the biological processes involved. This study provides additional data that may help to bridge the gap between humans and mice. Citation Format: Chisato Wakamori, Marco A. De Velasco, Yurie Kura, Naomi Ando, Noriko Sako, Kazutoshi Fujita, Kazuko Sakai, Makoto Matsushita, Eri Banno, Yasunori Mori, Masahiro Nozawa, Mitsuhisa Nishimoto, Kazuhiro Yoshimura, Norio Nonomura, Kazuto Nishio, Hirotsugu Uemura. Integrative gut microbiome analysis of human and mouse prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3044.
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Garassino, Marina Chiara, Claudia Proto, James M. Dolezal, Arsela Prelaj, Luca Agnelli, Tiziana Triulzi, Alessandra Fabbri, et al. "PEOPLE (NTC03447678), a phase II trial to test pembrolizumab as first-line treatment in patients with advanced NSCLC with PD-L1 < 50%: A multiomics approach." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 9051. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.9051.
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9051 Background: Chemo-immunotherapy is the standard of care for patients with advanced NSCLC and PD-L1 < 50%. Efficacy has been reported in this setting with single agent pembrolizumab, but no reliable biomarkers yet exist for selecting patients likely to respond to single agent immunotherapy. The aim of this trial was to identify potential new immune biomarkers associated with PFS in NSCLC patients with PD-L1 < 50% treated with first line pembrolizumab. Methods: Advanced EGFR and ALK wild type treatment-naïve NSCLC patients with PD-L1 < 50% were enrolled. Gene expression profile was performed using nCounter PanCancer IO 360 Panel (Nanostring) on baseline tissue. Circulating immune profiling was performed by determination of absolute cell counts with multiparametric flow cytometry on freshly isolated whole blood samples at baseline and at first radiological evaluation. Gut bacterial taxonomic abundance was obtained by shotgun metagenomic sequencing of stool sample at baseline. Pembrolizumab was administered at 200 mg flat dose every 3 weeks until 35 cycles, disease progression or unacceptable toxicity. Omics data was analyzed with sequential univariate Cox Proportional Hazards regression predicting PFS, with Benjamini-Hochberg multiple comparisons correction. Biological features significant with univariate analysis were analyzed with multivariate Least Absolute Shrinkage and Selection Operator (LASSO). Results: From May 2018 to October 2020 65 patients were enrolled. Main characteristics were: male 67.6%, smokers 87.7%, PD-L1 positive 70.8%. Median follow up and PFS were 26.4 and 2.9 months, respectively. Gene expression profile was performed in 48 patients, microbiome in 54 patients and circulating immune profiling in 56 patients at baseline and in 46 patients at first radiologic evaluation. LASSO multivariate analysis with optimal lambda of 0.28 showed high expression levels of IRF9 and COMP genes was associated with an unfavorable PFS (HR 3.03, 1.52 – 6.02, p = 0.08 and HR 1.22, 1.08 – 1.37, corrected p = 0.06, respectively). High expression levels of CD244 (HR 0.74, 0.62- 0.67, p = 0.05), PTPRC (HR 0.55, 0.38 – 0.81, p = 0.098), KLRB1 (HR 0.76, 0.66 – 0.89, p = 0.05) in tissue samples and NK cells/CD56dimCD16+ (HR 0.56, 0.41 – 0.76, p = 0.006) in peripheral blood at baseline and non classical CD14dim CD16+ monocytes (HR 0.52, 0.36 – 0.75, p = 0.004), eosinophils (CD 15+CD16-) (HR 0.62, 0.44 – 0.89, p = 0.003) lymphocytes (HR 0.28, 0.15 – 0.5, p < 0.001) in peripheral blood after first radiologic evaluation were associated to a favorable PFS. No microbiome features were selected by LASSO. Conclusions: To the best of our knowledge, this is the first prospective trial in NSCLC with PD-L1 < 50% performed with a multi-omic approach able to identify immune cell subsets and expression levels of genes associated to PFS under first line treatment with pembrolizumab. Clinical trial information: NTC03447678.