Academic literature on the topic 'UrtA phylogeny'
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Journal articles on the topic "UrtA phylogeny"
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Hume, ID. "Nitrogen-Metabolism in the Parma Wallaby, Macropus-Parma." Australian Journal of Zoology 34, no. 2 (1986): 147. http://dx.doi.org/10.1071/zo9860147.
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The maintenance nitrogen requirement of the parma wallaby, Macropus parma, was found to be 566 mg per kg W*0.75 per day on a dietary basis, and 477 mg per kg W*0.75 per day on a truly digestible basis. This is similar to that of the red-necked pademelon, Thylogale thetis, another small wallaby which occupies a similar moist forest habitat, but much higher than (at least double) those of four other macropodid marsupials, all of which are from less mesic environments, that have been studied. Urea recycling decreased in response to water restriction in M. parma; in other published reports urea recycling did not change in T. thetis when water intake was restricted, but in three arid-adapted eutherian herbivores it increased. Voluntary intakes of dry matter and water by M. parma wefe also similar to those published for T. thetis, but higher than those of other macropodid species. These results support the hypothesis that within the Macropodidae nutrient requirements are linked closely with preferred habitat, regardless of phylogeny.
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Zhou, Yan, Zhuoying Liang, Shaoquan Wang, Huahan Zhong, Ning Wang, and Bin Liang. "A mitogenomic phylogeny of satyrid butterflies and complete mitochondrial genome of Oeneis urda (Lepidoptera: Nymphalidae: Satyrinae)." Mitochondrial DNA Part B 5, no. 2 (March 4, 2020): 1344–45. http://dx.doi.org/10.1080/23802359.2020.1735272.
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Gusmanizar, Neni, Yunus Shukor, Johari Ramli, and Mohd Arif Syed. "ISOLATION AND CHARACTERIZATION OF AN ACRYLAMIDE-DEGRADING Burkholderia sp. STRAIN DR.Y27." Jurnal Riset Kimia 2, no. 1 (February 11, 2015): 34. http://dx.doi.org/10.25077/jrk.v2i1.83.
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ABSTRACT Several local bacteria have been isolated from glyphosate-contaminated soils at various locations throughout Malaysia. Quantitative monitoring of acrylamide degradation was performed using High Performance Liquid Chromatography (HPLC) whilst bacterial growth was carried out by plate counting. The isolate was tentatively identified as Burkholderia sp. strain DR.Y27 based on carbon utilization profiles using Biolog GN plates and partial 16s rDNA molecular phylogeny. Highest growth was obtained at acrylamide concentrations of between 100 to 2000 mg L-1. Complete degradation of 850 mg L-1 of acrylamide occurs after ten days of incubation with concomitant cell growth. The isolate grew optimally in between pH 6.0 and 8.0. The effect of incubation temperature on the growth of this isolate shows an optimum growth at 30°C. Glucose, lactose, maltose, fructose, mannitol, citric acid and sucrose at an initial concentration of 1.0% (w/v) supported growth with glucose being the best carbon source. Aliphatic amides such as 2-chloroacetamide, methacrylamide, nicotinamide, acrylamide, acetamide, propionamide and urea supported growth with increasing assimilative capability from 2-chloroacetamide to urea. The characteristics of this isolate suggest that it would be useful in the bioremediation of acrylamide. Keywords: isolation, characterization, acrylamide-degrading, Bacterium
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Brito, SV, WO Almeida, LA Anjos, and RJ Silva. "New host records of Brazilian pentastomid species." Brazilian Journal of Biology 72, no. 2 (May 2012): 393–96. http://dx.doi.org/10.1590/s1519-69842012000200022.
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Pentastomida is a taxon of parasitic organisms infecting generally the respiratory system of vertebrates, mainly reptiles. Although this taxon is very important for understanding the phylogeny of the Metazoa, it has received little attention. In Brazil, there are few collections that include species of pentastomids, that is, only the Helminthological Collection of the Oswaldo Cruz Institute (CHIOC), the Invertebrate Collection of the Zoology Laboratory of the Regional University of Cariri (LAZ-URCA) and the Helminthological Collection of the Botucatu Institute of Biosciences (CHIBB). The present study describes the species of pentastomids deposited in CHIBB. When found, the pentastomids were mounted on slides in Hoyer's medium and identified. Four species of pentastomids were recognised and three others were identified at the genus level, while four new hosts for the species of pentastomids were recorded.
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Muttineni, Radhakrishna, Nagamani Kammili, Thrilok Chander Bingi, Raja Rao M., Kalyani Putty, Pankaj Singh Dholaniya, Ravi Kumar Puli, et al. "Clinical and whole genome characterization of SARS-CoV-2 in India." PLOS ONE 16, no. 2 (February 2, 2021): e0246173. http://dx.doi.org/10.1371/journal.pone.0246173.
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We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.
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Gunawardana, Dilantha, and Venura Herath. "A Hypothesis on How the Azolla Symbiosis Mitigates Nitrous Oxide Based on In Silico Analyses." J 5, no. 1 (March 4, 2022): 166–85. http://dx.doi.org/10.3390/j5010013.
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Nitrous oxide is a long-lived greenhouse gas that exists for 114 years in the atmosphere and is 298-fold more potent than carbon dioxide in its global warming potential. Two recent studies showcased the utility of Azolla plants for a lesser footprint in nitrous oxide production from urea and other supplements to the irrigated ecosystem, which mandates exploration since there is still no clear solution to nitrous oxide in paddy fields or in other ecosystems. Here, we propose a solution based on the evolution of a single cytochrome oxidase subunit II protein (WP_013192178.1) from the cyanobiont Trichormus azollae that we hypothesize to be able to quench nitrous oxide. First, we draw attention to a domain in the candidate protein that is emerging as a sensory periplasmic Y_Y_Y domain that is inferred to bind nitrous oxide. Secondly, we draw the phylogeny of the candidate protein showcasing the poor bootstrap support of its position in the wider clade showcasing its deviation from the core function. Thirdly, we show that the NtcA protein, the apical N-effecting transcription factor, can putatively bind to a promoter sequence of the gene coding for the candidate protein (WP_013192178.1), suggesting a function associated with heterocysts and N-metabolism. Our fourth point involves a string of histidines at the C-terminal extremity of the WP_013192178.1 protein that is missing on all other T. azollae cytochrome oxidase subunit II counterparts, suggesting that such histidines are perhaps involved in forming a Cu center. As the fifth point, we showcase a unique glycine-183 in a lengthy linker region containing multiple glycines that is absent in all proximal Nostocales cyanobacteria, which we predict to be a DNA binding residue. We propose a mechanism of action for the WP_013192178.1 protein based on our in silico analyses. In total, we hypothesize the incomplete and rapid conversion of a likely heterocystous cytochrome oxidase subunit II protein to an emerging nitrous oxide sensing/quenching subunit based on bioinformatics analyses and past literature, which can have repercussions to climate change and consequently, future human life.
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Elshahawy, I. S., M. A. El-Seify, Z. K. Ahamed, and M. M. Fawaz. "Occurrence and phylogenetic description of cystic echinococcosis isolate from Egyptian camel (Camelus dromedarius)." Helminthologia 59, no. 3 (September 1, 2022): 253–64. http://dx.doi.org/10.2478/helm-2022-0026.
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Summary Cystic echinococcosis is one of the most significant cyclo-zoonotic diseases of major economic and public health significance worldwide. The current study was carried out to determine the epidemiological profile of cystic echinococcosis as well as to investigate its molecular and phylogenic status from one-humped camel (Camelus dromedarius) in the southern region of Egypt. In the present work, 110 camels freshly slaughtered at Daraw abattoirs, Aswan governorate were inspected for the presence of Hydatid cysts (HCs) visually and manually by palpation and incision, over a period of one year (June, 2018 – May, 2019). Furthermore, fourteen fertile hydatid cyst samples were collected from lungs of slaughtered camels. DNA extraction from two fertile samples was successfully achieved followed by phylogenetic analysis on two mitochondrial genes (cox1and nad1). Out of 110 camels slaughtered 11 (10 %) were found harboring hydatid cysts. The infection was found to prevail throughout the year, with the highest peak encountered in winter (45.5 %). The lungs were the most frequently infected organs (72.7 %) with liver cysts occurring at a significantly lower rate (27.3 %). The mean value of total protein, glucose, urea, cholesterol, magnesium, potassium, copper and creatinine was higher in cystic fluid from camels as compared to cattle. Blast and phylogenetic analysis on sequenced genes showed the presence of Echinococcus intermedius, originally the pig genotype (G7) in camels for the first time in Egypt. To the best of our knowledge, the current research provides a description of the current epidemiological and molecular situation of camel hydatidosis in the southern region of Egypt. Furthermore, the current results may have significant implications for hydatid disease control in the studied region.
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McMullen, John G., Eduardo Bueno, Frances Blow, and Angela E. Douglas. "Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome." Genome Biology and Evolution 13, no. 8 (June 3, 2021). http://dx.doi.org/10.1093/gbe/evab127.
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Abstract Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2–3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e., genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.
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Cheng, Yen-I., Yu-Chen Lin, Jyh-Yih Leu, Chih-Horng Kuo, and Hsiu-An Chu. "Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1." Frontiers in Microbiology 13 (August 11, 2022). http://dx.doi.org/10.3389/fmicb.2022.932840.
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Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that dominates microbial mats in Asian non-acidic hot springs. These cyanobacteria are the major primary producers in their ecological niches and are promising sources of thermostable enzymes for biotechnology applications. To improve our understanding of these organisms, we conducted whole-genome sequencing of a novel strain for comparative analysis with other representatives in the same genus. This newly characterized strain, Thermosynechococcus sp. TA-1, was isolated from the Taian hot springs in Taiwan. Analyses based on average nucleotide identity (ANI) and genome-scale phylogeny suggested that TA-1 and another Taiwanese strain CL-1 belong to a novel species-level taxon. Two metagenome-assembled genomes (MAGs) originated from India represent the sister group, and Thermosynechococcus elongatus PKUAC-SCTE542 from China is the next closest lineage. All cultivated strains and MAGs from Japan form a separate monophyletic clade and could be classified into two species-level taxa. Intriguingly, although TA-1 and CL-1 share 97.0% ANI, the genome alignment identified at least 16 synteny breakpoints that are mostly associated with transposase genes, which illustrates the dynamic nature of their chromosomal evolution. Gene content comparisons identified multiple features distinct at species- or strain-level among these Thermosynechococcus representatives. Examples include genes involved in bicarbonate transportation, nitric oxide protection, urea utilization, kanamycin resistance, restriction-modification system, and chemotaxis. Moreover, we observed the insertion of type II inteins in multiple genes of the two Taiwanese strains and inferred putative horizontal transfer of an asparagine synthase gene (asnB) associated with exopolysaccharides gene cluster. Taken together, while previous work suggested that strains in this genus share a highly conserved genomic core and no clear genetic differentiation could be linked to environmental factors, we found that the overall pattern of gene content divergence is largely congruent with core genome phylogeny. However, it is difficult to distinguish between the roles of phylogenetic relatedness and geographic proximity in shaping the genetic differentiation. In conclusion, knowledge of the genomic differentiation among these strains provides valuable resources for future functional characterization.
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ZULAIKA, ENNY, M. A. PRIO UTOMO, N. HIDAYATUL ALAMI, N. DWIANITA KUSWYTASARI, MAYA SHOVITRI, RIDHO BAYUAJI, and ENDRY N. PRASETYO. "Short communication: The diversity of ureolytic bacteria isolated from limestone in East Java, Indonesia based on amino acid sequences encoded by ureC." Biodiversitas Journal of Biological Diversity 20, no. 8 (July 30, 2019). http://dx.doi.org/10.13057/biodiv/d200829.
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Abstract. Zulaika E, Utomo MAP, Alami NH, Kuswytasari ND, Shovitri M, Bayuaji R, Prasetyo EN. 2019. Short communication: The diversity of ureolytic bacteria isolated from limestone in East Java, Indonesia based on amino acid sequences encoded by ureC. Biodiversitas 20: 2316-2320. Ureolytic bacteria isolated from limestone are capable to produce urease enzyme which can breaks down urea into carbonate (CO32), has been utilized for various building material bioremediation and restoration. In this present study, we figured out the diversity and genetic relationship of α sub-unit ureC gene among six ureolytic bacteria (JA1, JB2, JB3, JA4, AK4, and SU1) which were isolated from limestone area in East Java province. PCR was conducted to detect the gene which encoded active site of urease, ureC. Followed by sequences translation using BLAST-X (Basic Local Alignment Search Tool) based on the name and function of formed proteins and then aligned to the conserved domain database. Furthermore, the functions and characters of formed proteins were described. Based on PCR results, all isolates showed 340 bp DNA band which indicate the presence of ureC gene. The results of BLAST-X, JB2 isolates showed 100% similarity with the α sub-unit ureC gene from Lysinibacillus sphaericus B1-CDA (WP_054549252.1). Whereas, JA1 isolates showed 88% similarity (lowest) with the α sub-unit ureC gene from Bacillus cihuensis FJAT-14515 (WP_028391929.1). The present study reveals that ureC phylogeny can be used in order to investigate ureolytic bacteria species which isolated from calcareous area in East Java province.
Dissertations / Theses on the topic "UrtA phylogeny"
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ŘÍHOVÁ, Jana. "Evoluce genomu bakteriálních symbiontů vši \kur{Polyplax serrata} (Phthiraptera, Anoplura)." Master's thesis, 2017. http://www.nusl.cz/ntk/nusl-371718.
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Blood-sucking louse Polyplax serrata harbor two phylogenetically distinct symbiotic bacteria from the orders Legionellales (Gammaproteobacteria) and Neisseriales (Betaproteobacteria). Based on rigorous phylogenetic analyses, the first bacteria was confirmed as member of genus Legionella, and the name Candidatus Legionella polyplacis, sp. n. was proposed. Vertical transgeneration transmission was proved by visualisation of the symbiont in host tissues. Improved genome of latter symbiont is considerably larger and possesses more metabolic functions. In the genome, I found horizontally transferred operon, which encode synthesis of enzymes involved in urea cleavage.