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Zhang, Kai, Hai-Tao Xiang, and Shan-Cen Zhao. "The complete mitochondrial genome of the drill (Mandrillus leucophaeus)." Mitochondrial DNA Part A 28, no. 1 (December 21, 2015): 69–70. http://dx.doi.org/10.3109/19401736.2015.1110802.
Повний текст джерела
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Hu, Jinjie, William M. Switzer, Brian T. Foley, David L. Robertson, Robert M. Goeken, Bette T. Korber, Vanessa M. Hirsch, and Brigitte E. Beer. "Characterization and Comparison of Recombinant Simian Immunodeficiency Virus from Drill (Mandrillus leucophaeus) and Mandrill (Mandrillus sphinx) Isolates." Journal of Virology 77, no. 8 (April 15, 2003): 4867–80. http://dx.doi.org/10.1128/jvi.77.8.4867-4880.2003.
Повний текст джерелаАнотація:
ABSTRACT Since simian immunodeficiency virus (SIV) was found to be the source of the human AIDS pandemic, a major goal has been to characterize the diversity of SIV strains in the wild and to assess their potential for crossover into humans. In the present study, SIV was isolated from a seropositive drill (Mandrillus leucophaeus) and three seropositive mandrills (Mandrillus sphinx) by using macaque peripheral blood mononuclear cells (PBMC). Full-length sequences were obtained from a drill and mandrill and designated SIVdrl1FAO and SIVmnd5440, respectively. A 182-bp fragment of the pol genes of the two remaining mandrill SIV isolates was also analyzed. Phylogenetic analyses demonstrated that SIVdrl1FAO formed a monophyletic clade with SIVmnd5440 and SIVmndM14, recently designated SIVmnd type 2. Both the SIVdrl and SIVmnd type 2 genomes carried a vpx gene and appeared to share a common ancestor with SIVrcm in the 5′ region of the genome and with SIVmndGB1 (type 1) in the 3′ region of the genome. A statistically significant recombination breakpoint was detected at the beginning of envelope, suggesting that the viruses were descendents of the same recombinant. Phylogenetic analysis of vpx and vpr genes demonstrated that the vpx genes formed a monophyletic cluster that grouped with vpr from SIVagm. In addition, both SIVdrl1FAO and SIVmnd5440 replicated in human PBMC and therefore could pose a risk of transmission to the human population.
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Clewley, J. P., J. C. M. Lewis, D. W. G. Brown, and E. L. Gadsby. "A Novel Simian Immunodeficiency Virus (SIVdrl)pol Sequence from the Drill Monkey, Mandrillus leucophaeus." Journal of Virology 72, no. 12 (December 1, 1998): 10305–9. http://dx.doi.org/10.1128/jvi.72.12.10305-10309.1998.
Повний текст джерелаАнотація:
ABSTRACT The drill monkey has been shown by serology and PCR to harbor a unique simian immunodeficiency virus (SIVdrl). A polsequence, amplified from uncultured peripheral blood cells, is most closely related to the equivalent SIV sequences from the red-capped mangabey (SIVrcm), the sabaeus African green monkey (SIVagmSAB), and the chimpanzee (SIVcpz) and to the human immunodeficiency virus type 1 (HIV-1) sequence of humans. It is as yet unclear whether SIVdrl has a mosaic genome like SIVrcm and SIVagmSAB, is a member of the SIVcpz/HIV-1 lineage, or represents a novel primate lentivirus lineage.
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Rossi, Federico, Alessandro Crnjar, Federico Comitani, Rodrigo Feliciano, Leonie Jahn, George Malim, Laura Southgate, et al. "Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling." PLOS ONE 16, no. 11 (November 18, 2021): e0254971. http://dx.doi.org/10.1371/journal.pone.0254971.
Повний текст джерелаАнотація:
Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.
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Vanderpool, Dan, Bui Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R. Alan Harris, Muthuswamy Raveendran, et al. "Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression." PLOS Biology 18, no. 12 (December 3, 2020): e3000954. http://dx.doi.org/10.1371/journal.pbio.3000954.
Повний текст джерелаАнотація:
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.
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Choi, Y. H., M. C. T. Penedo, P. Daftari, I. C. Velez, and K. Hinrichs. "Accuracy of preimplantation genetic diagnosis in equine in vivo-recovered and in vitro-produced blastocysts." Reproduction, Fertility and Development 28, no. 9 (2016): 1382. http://dx.doi.org/10.1071/rd14419.
Повний текст джерелаАнотація:
Preimplantation genetic diagnosis has great potential in the horse, but information on evaluation of equine embryo biopsy samples is limited. Blastocysts were biopsied using a Piezo drill and methods for whole-genome amplification (WGA) investigated. Results for 33 genetic loci were then compared between biopsy samples from in vitro-produced (IVP) and in vivo-recovered (VIV) blastocysts. Under the experimental conditions described, WGA using the Qiagen Repli-g Midi kit was more accurate than that using the Illustra Genomiphi V2 kit (98.2% vs 25.8%, respectively). Using WGA with the Qiagen kit, three biopsy samples were evaluated from each of eight IVP and 19 VIV blastocysts, some produced using semen from stallions carrying the genetic mutations associated with the diseases hereditary equine regional dermal asthenia (HERDA), hyperkalemic periodic paralysis (HYPP) or polysaccharide storage myopathy 1 (PSSM1). Three of 81 biopsy samples (3.7%) returned <50% accuracy. In the remaining 78 samples, overall accuracy was 99.3% (2556/2574 loci interrogated). Accuracy did not differ significantly between samples from IVP and VIV blastocysts. Allele drop-out in heterozygous loci was 1.6% (17/1035). Accuracy for sex determination was 100%; accuracy for heterozygosity for disease-causing mutations was 97.7% (43/44). In conclusion, Piezo-driven embryo biopsy with WGA has >95% overall accuracy in IVP and VIV embryos, and this technique is suitable for use in a clinical setting.
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Chakrabarty, Sanjiban, Periyasamy Govindaraj, Bindu Parayil Sankaran, Madhu Nagappa, Shama Prasada Kabekkodu, Pradyumna Jayaram, Sandeep Mallya, et al. "Contribution of nuclear and mitochondrial gene mutations in mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome." Journal of Neurology 268, no. 6 (January 23, 2021): 2192–207. http://dx.doi.org/10.1007/s00415-020-10390-9.
Повний текст джерелаАнотація:
Abstract Background Mitochondrial disorders are clinically complex and have highly variable phenotypes among all inherited disorders. Mutations in mitochon drial DNA (mtDNA) and nuclear genome or both have been reported in mitochondrial diseases suggesting common pathophysiological pathways. Considering the clinical heterogeneity of mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) phenotype including focal neurological deficits, it is important to look beyond mitochondrial gene mutation. Methods The clinical, histopathological, biochemical analysis for OXPHOS enzyme activity, and electron microscopic, and neuroimaging analysis was performed to diagnose 11 patients with MELAS syndrome with a multisystem presentation. In addition, whole exome sequencing (WES) and whole mitochondrial genome sequencing were performed to identify nuclear and mitochondrial mutations. Results Analysis of whole mtDNA sequence identified classical pathogenic mutation m.3243A > G in seven out of 11 patients. Exome sequencing identified pathogenic mutation in several nuclear genes associated with mitochondrial encephalopathy, sensorineural hearing loss, diabetes, epilepsy, seizure and cardiomyopathy (POLG, DGUOK, SUCLG2, TRNT1, LOXHD1, KCNQ1, KCNQ2, NEUROD1, MYH7) that may contribute to classical mitochondrial disease phenotype alone or in combination with m.3243A > G mutation. Conclusion Individuals with MELAS exhibit clinical phenotypes with varying degree of severity affecting multiple systems including auditory, visual, cardiovascular, endocrine, and nervous system. This is the first report to show that nuclear genetic factors influence the clinical outcomes/manifestations of MELAS subjects alone or in combination with m.3243A > G mutation.
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Krieg, Rene C., Cloud P. Paweletz, Lance A. Liotta, and Emanuel F. Petricoin. "Clinical Proteomics for Cancer Biomarker Discovery and Therapeutic Targeting." Technology in Cancer Research & Treatment 1, no. 4 (August 2002): 263–72. http://dx.doi.org/10.1177/153303460200100407.
Повний текст джерелаАнотація:
As we emerge into the post-genome era, proteomics finds itself as the driving force field as we translate the nucleic acid information archive into understanding how the cell actually works and how disease processes operate. Even so, the traditionally held view of proteomics as simply cataloging and developing lists of the cellular protein repertoire of a cell are now changing, especially in the sub-discipline of clinical proteomics. The most relevant information archive to clinical applications and drug development involves the elucidation of the information flow of the cell; the “software” of protein pathway networks and circuitry. The deranged circuitry of the cell as the drug target itself as well as the effect of the drug on not just the target, but also the entire network, is what we now are striving towards. Clinical proteomics, as a new and most exciting sub-discipline of proteomics, involves the bench-to-bedside clinical application of proteomic tools. Unlike the genome, there are potentially thousands of proteomes: each cell type has its own unique proteome. Moreover, each cell type can alter its proteome depending on the unique tissue microenvironment in which it resides, giving rise to multiple permutations of a single proteome. Since there is no polymerase chain reaction equivalent to proteomics- identifying and discovering the “wiring diagram” of a human diseased cell in a biopsy specimen remains a daunting challenge. New micro-proteomic technologies are being and still need to be developed to drill down into the proteomes of clinically relevant material. Cancer, as a model disease, provides a fertile environment to study the application of proteomics at the bedside. The promise of clinical proteomics and the new technologies that are developed is that we will detect cancer earlier through discovery of biomarkers, we will discover the next generation of targets and imaging biomarkers, and we can then apply this knowledge to patient-tailored therapy.
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Choi, Y. H., M. C. T. Penedo, P. Daftari, I. C. Velez, and K. Hinrichs. "102 ACCURACY OF PRE-IMPLANTATION GENETIC DIAGNOSIS USING CELLS BIOPSIED FROM EQUINE BLASTOCYSTS." Reproduction, Fertility and Development 24, no. 1 (2012): 163. http://dx.doi.org/10.1071/rdv24n1ab102.
Повний текст джерелаАнотація:
There is growing interest in pre-implantation genetic diagnosis (PGD) for management of inherited genetic disease in the horse. In a previous study (Choi et al. 2010 Reproduction 140, 893–902), we demonstrated normal viability of equine blastocysts after biopsy. However, genome amplification was only moderately successful and only 1 of 2 analyses of heterozygous loci accurately detected both alleles. In the current study, we investigated different methods for amplification of DNA to improve the efficiency of PGD. To evaluate allele drop-out, multiple commonly-heterozygous gene loci were evaluated. In Experiment 1, using a piezo drill, 3 to 5 biopsy samples of 20 to 30 cells each were obtained from each of 4 in vitro-produced blastocysts. The samples and embryos were stored at –20°C, then shipped to the Veterinary Genetics Laboratory at the University of California, Davis. Whole genome amplification was done with an Illustra Genomiphi V2 kit (GE Healthcare, Waukesha, WI) before PCR for specific markers. Two disease-related (SCN4A and PPIB), one gender (AME) and 17 microsatellite identification markers were genotyped, for a total of 20 loci. Results for biopsy samples were compared with those for the corresponding embryo. A DNA signal was obtained from 14/15 biopsy samples, but for only 59.6% of the 280 total genotypes. Of 40 heterozygous loci, the signal from the corresponding biopsy sample showed only one allele (underwent allele dropout) in 60/80 instances (75%). In Experiment 2, 4 biopsies were obtained from each of 4 additional in vitro-produced blastocysts, then all samples were stored at –20°C. The Repli-G Mid kit (Qiagen, Valencia, CA) was used for whole genome amplification. Two disease-related (SCN4A and PPIB), 2 gender (AME and eSRY), 10 coat colour and 17 identification markers (total of 31 loci) were examined in each biopsy sample and were compared with results for the embryos. One biopsy sample was lost. Signal was obtained from 14/15 of the remaining biopsy samples and gave a 100% match at the 2 gender loci, 2 disease-related loci and 10 coat colour loci. One identification locus, LEX33, amplified in only 8 of 22 analyses. At the remaining 16 identification loci, 223/224 biopsy results matched those for the embryos. Overall, of 51 heterozygous loci among the 4 embryos, biopsy samples exhibited allele dropout in 1/180 instances (0.6%). In conclusion, results obtained using piezo-driven embryo biopsy and whole genome amplification using the Qiagen Repli-G kit have high accuracy and this technique may be suitable for use in a clinical setting. Further studies are needed with in vivo-derived embryos and to optimize accuracy of PCR of some identification markers. This work was supported by the American Quarter Horse Foundation, the Link Equine Research Endowment Fund, Texas A&M University and by Ms Kit Knotts.
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Gaile, D. P., L. Shepherd, S. Liu, K. Darcy, M. Brady, and C. Morrison. "iGenomicViewer, a Gynecologic Oncology Group software library for the creation of highly customizable, portable, interactive, and linked visualizations of high throughput genomic data." Journal of Clinical Oncology 27, no. 15_suppl (May 20, 2009): e16544-e16544. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.e16544.
Повний текст джерелаАнотація:
e16544 Background: An R software library was created with the goal of creating customizable, platform independent, and portable visualization tools for the annotation, dissemination and interrogation of high dimensioned genomic data. Methods: A set of R functions were created to extend the functionality of the sendplot R library. The functions were applied to BAC aCGH data generated for several GOG studies. Results: The iGenomicViewer function calls created and populated a directory structure which was then ported to a password protected server for interrogation by research team members. The linked html and image output allows users to examine genome wide plots of aberration frequencies and p-values and then drill down to visualizations of regions of interest. Users can interrogate a panel of plots which includes: 1) a heat map of the aCGH data for with tool-tip display of sample and assay specific data (e.g., assay values, sample IDs, and hyperlinks to UCSC browser and sample specific images); 2) a set of interactive annotation tracks which display location of cancer, disease and DNA repair genes; and 3) a plot which displays -log10 p-values and/or aberration frequencies for the BAC assays depicted in the heatmap. For the smallest regions of interest, the panel of plots contains a tiled heatmap which depicts the overlap and gaps in BAC coverage and their alignment with the gene locations represented in the adjacent annotation track. Conclusions: The iGenomicViewer library provides open source software for creation of customizable visualization tools for collaborative research projects involving high dimensioned genomic data. No significant financial relationships to disclose.
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Beer, Brigitte E., Brian T. Foley, Carla L. Kuiken, Zena Tooze, Robert M. Goeken, Charles R. Brown, Jinjie Hu, Marisa St. Claire, Bette T. Korber, and Vanessa M. Hirsch. "Characterization of Novel Simian Immunodeficiency Viruses from Red-Capped Mangabeys from Nigeria (SIVrcmNG409 and -NG411)." Journal of Virology 75, no. 24 (December 15, 2001): 12014–27. http://dx.doi.org/10.1128/jvi.75.24.12014-12027.2001.
Повний текст джерелаАнотація:
ABSTRACT Two novel simian immunodeficiency virus (SIV) strains from wild-caught red-capped mangabeys (Cercocebus torquatus torquatus) from Nigeria were characterized. Sequence analysis of the fully sequenced SIV strain rcmNG411 (SIVrcmNG411) andgag and pol sequence of SIVrcmNG409 revealed that they were genetically most closely related to the recently characterized SIVrcm from Gabon (SIVrcmGB1). Thus, red-capped mangabeys from distant geographic locations harbor a common lineage of SIV. SIVrcmNG411 carried a vpx gene in addition tovpr, suggesting a common evolutionary ancestor with SIVsm (from sooty mangabeys). However, SIVrcm was only marginally closer to SIVsm in that region than to any of the other lentiviruses. SIVrcm showed the highest similarity inpol with SIVdrl, isolated from a drill, a primate that is phylogenetically distinct from mangabey monkeys, and clustered with other primate lentiviruses (primarily SIVcpz [from chimpanzees] and SIVagmSab [from African green monkeys]) discordantly in different regions of the genome, suggesting a history of recombination. Despite the genetic relationship to SIVcpz in the pol gene, SIVrcmNG411 did not replicate in chimpanzee peripheral blood mononuclear cells (PBMC), although two other viruses unrelated to SIVcpz, SIVmndGB1 (from mandrills) and SIVlhoest (from L'Hoest monkeys), were able to grow in chimpanzee PBMC. The CCR5 24-bp deletion previously described in red-capped mangabeys from Gabon was also observed in Nigerian red-capped mangabeys, and SIVrcmNG411, like SIVrcmGB1, used CCR2B and STRL33 as coreceptors for virus entry. SIVrcm, SIVsm, SIVmndGB1, and all four SIVlhoest isolates but not SIVsun (from sun-tailed monkeys) replicated efficiently in human PBMC, suggesting that the ability to infect the human host can vary within one lineage.
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Choi, Y. H., A. Gustafson-Seabury, I. C. Velez, D. L. Hartman, S. Bliss, F. L. Riera, J. E. Roldán, B. Chowdhary, and K. Hinrichs. "Viability of equine embryos after puncture of the capsule and biopsy for preimplantation genetic diagnosis." REPRODUCTION 140, no. 6 (December 2010): 893–902. http://dx.doi.org/10.1530/rep-10-0141.
Повний текст джерелаАнотація:
The equine embryo possesses a capsule that is considered essential for its survival. We assessed viability after breaching the capsule of early (Day 6) and expanded (Day 7 and 8) equine blastocysts by micromanipulation. The capsule was penetrated using a Piezo drill, and trophoblast biopsy samples were obtained for genetic analysis. Pregnancy rates for Day-6 embryos, which had intact zonae pellucidae at the time of recovery, were 3/3 for those biopsied immediately after recovery and 2/3 for those biopsied after being shipped overnight under warm (∼28 °C) conditions. The pregnancy rates for encapsulated Day-7 expanded blastocysts were 5/6 for those biopsied immediately and 5/6 for those biopsied after being shipped overnight warm. Two of four encapsulated Day-8 blastocysts, 790 and 1350 μm in diameter, established normal pregnancies after biopsy. Nine mares were allowed to maintain pregnancy, and they gave birth to nine normal foals. Biopsied cells from eight embryos that produced foals were subjected to whole-genome amplification. Sex was successfully determined from amplified DNA in 8/8 embryos. Identification of disease-causing mutations matched in the analyses of 6/6 samples for the sodium channel, voltage-gated, type IV, alpha subunit (SCN4A) gene and in 6/7 samples for the peptidylprolyl isomerase B (PPIB) gene, in embryo-foal pairs. Thus, the capsule of the equine embryo can be breached without impairing viability. Further work is needed to determine whether this breach is transient or permanent. These findings are relevant to the understanding of equine embryo development and to the establishment of methods for micromanipulation and embryo cryopreservation in this species.
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Abdalla Milad Faraj, Hisham Fathi Ali, Abdussalam Ali Ahmed, and Mohammed Khaled Akel. "CNC machine for image and PCB layout drawing." Global Journal of Engineering and Technology Advances 11, no. 2 (May 30, 2022): 013–24. http://dx.doi.org/10.30574/gjeta.2022.11.2.0078.
Повний текст джерелаАнотація:
Increment in the number of accidents in the workshops and due to the problems caused by the production of the complex part by traditional machining such as lack of quality and the need of plenty time for the production process and with the advancement of technology, all these demands for Computer Numerical Control machines in industries is rapidly rising. Computer Numerical Control machining is a process used in the manufacturing sector that involves the use of computers to control machine tools without direct human assistance. Computer Numerical Control is a very broad term that encompasses a variety of types of machines all with different sizes, shapes, and functions. Computer Numerical Control has found its applications mainly in lathes, drills, milling machines etc. In this paper, a two-dimensional Computer Numerical Control machine designed and implemented in efficient and low-cost hardware architecture, it is able to draw images/texts. In addition, the idea behind our project is to design and draw Printed Circuit Board layouts based on a low-cost Computer Numerical Control system. The control mechanism of the designed machine is based on using Arduino UNO, Inkscape and the Geode-sender software. The outcome of the paper is to help researchers and designers in the area of Computer Numerical Control machines.
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George, U., C. Simsek, T. O. C. Faleye, O. Arowolo, A. Oragwa, O. M. Adewumi, J. Matthijnssens, and J. A. Adeniji. "Genome Sequences of Novel Members of Previously Described DNA and RNA Virus Families, Isolated from Feces of a Drill Monkey in Nigeria." Microbiology Resource Announcements 9, no. 17 (April 23, 2020). http://dx.doi.org/10.1128/mra.00092-20.
Повний текст джерелаАнотація:
The genomes of seven novel members of previously described DNA and RNA virus families are described here. These viruses were recovered using a viral metagenomic approach from the stool of a drill monkey (Mandrillus leucophaeus) housed in a sanctuary in Cross River State, Nigeria.
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Amundson, Kaela K., Mikayla A. Borton, Rebecca A. Daly, David W. Hoyt, Allison Wong, Elizabeth Eder, Joseph Moore, Kenneth Wunch, Kelly C. Wrighton, and Michael J. Wilkins. "Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation." Microbiome 10, no. 1 (January 16, 2022). http://dx.doi.org/10.1186/s40168-021-01194-8.
Повний текст джерелаАнотація:
Abstract Background Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.