A comparative analysis of drinking water employing metagenomics.
AuthorsBrumfield KD, Hasan NA, Leddy MB, Cotruvo JA, Rashed SM, Colwell RR, Huq A
JournalPLoS One
PubMed ID32271799
'The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can ... More
Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity.
AuthorsHilton HG, Rubinstein ND, Janki P, Ireland AT, Bernstein N, Fong NL, Wright KM, Smith M, Finkle D, Martin-McNulty B, Roy M, Imai DM, Jojic V, Buffenstein R
JournalPLoS Biol
PubMed ID31751331
'The immune system comprises a complex network of specialized cells that protects against infection, eliminates cancerous cells, and regulates tissue repair, thus serving a critical role in homeostasis, health span, and life span. The subterranean-dwelling naked mole-rat (NM-R; Heterocephalus glaber) exhibits prolonged life span relative to its body size, is ... More
Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast.
AuthorsTopal S, Vasseur P, Radman-Livaja M, Peterson CL
JournalNat Commun
PubMed ID31558720
'Dynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin. Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. We find ... More
Characterization of exosomes in peritoneal fluid of endometriosis patients.
AuthorsNazri HM, Imran M, Fischer R, Heilig R, Manek S, Dragovic RA, Kessler BM, Zondervan KT, Tapmeier TT, Becker CM
JournalFertil Steril
PubMed ID32106990
'To demonstrate the feasibility of studying exosomes directly from peritoneal fluid, we isolated exosomes from endometriosis patient samples and from controls, and characterized their cargo.'
Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula.
AuthorsLuria CM, Amaral-Zettler LA, Ducklow HW, Rich JJ
JournalFront Microbiol
PubMed ID27857708
The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and ... More
Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.
AuthorsPornsukarom S, van Vliet AHM, Thakur S,
JournalBMC Genomics
PubMed ID30400810
Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology ... More
Autoimmune-Mediated Retinopathy in CXCR5-Deficient Mice as the Result of Age-Related Macular Degeneration Associated Proteins Accumulation.
AuthorsLennikov A, Saddala MS, Mukwaya A, Tang S, Huang H
JournalFront Immunol
PubMed ID31474986
Previous research has shown that CXCR5
Repeated species radiations in the recent evolution of the key marine phytoplankton lineage Gephyrocapsa.
AuthorsBendif EM, Nevado B, Wong ELY, Hagino K, Probert I, Young JR, Rickaby REM, Filatov DA
JournalNat Commun
PubMed ID31530807
Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolithophore genus Gephyrocapsa with genomic analyses ... More
Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility.
AuthorsDoremus MR, Kelly SE, Hunter MS
JournalPLoS Pathog
PubMed ID31425566
Terrestrial arthropods, including insects, commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny. These symbionts may be especially vulnerable to thermal stress, potentially leading to destabilization of the symbiosis and imposing costs to the host. For example, increased ... More
Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children.
AuthorsLi Y, Fu X, Ma J, Zhang J, Hu Y, Dong W, Wan Z, Li Q, Kuang YQ, Lan K, Jin X, Wang JH, Zhang C
JournalNat Commun
PubMed ID31123265
Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance ... More
Nested PCR and the TaqMan SNP Genotyping Assay enhanced the sensitivity of drug resistance testing of Mycobacterium leprae using clinical specimens of leprosy patients.
AuthorsChen X, He J, Liu J, You Y, Yuan L, Wen Y
JournalPLoS Negl Trop Dis
PubMed ID31881061
Although leprosy is efficiently treated by multidrug therapy, resistance to first-line (dapsone, rifampin) and second-line (fluoroquinolones) drugs has been described worldwide. However, the characteristics of drug resistance in Southwest China remain unknown. Furthermore, the sensitivity of polymerase chain reaction (PCR)/sequencing for resistance detection is limited, especially for paucibacillary (PB) leprosy ... More
The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica.
AuthorsChen J, Yu R, Dai J, Liu Y, Zhou R
JournalBMC Plant Biol
PubMed ID32384868
With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with ... More
Isolation of Angola-like Marburg virus from Egyptian rousette bats from West Africa.
AuthorsAmman BR, Bird BH, Bakarr IA, Bangura J, Schuh AJ, Johnny J, Sealy TK, Conteh I, Koroma AH, Foday I, Amara E, Bangura AA, Gbakima AA, Tremeau-Bravard A, Belaganahalli M, Dhanota J, Chow A, Ontiveros V, Gibson A, Turay J, Patel K, Graziano J, Bangura C, Kamanda ES, Osborne A, Saidu E, Musa J, Bangura D, Williams SMT, Wadsworth R, Turay M, Edwin L, Mereweather-Thompson V, Kargbo D, Bairoh FV, Kanu M, Robert W, Lungai V, Guetiya Wadoum RE, Coomber M, Kanu O, Jambai A, Kamara SM, Taboy CH, Singh T,
JournalNat Commun
PubMed ID31980636
Marburg virus (MARV) causes sporadic outbreaks of severe Marburg virus disease (MVD). Most MVD outbreaks originated in East Africa and field studies in East Africa, South Africa, Zambia, and Gabon identified the Egyptian rousette bat (ERB; Rousettus aegyptiacus) as a natural reservoir. However, the largest recorded MVD outbreak with the highest ... More
ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response.
AuthorsNagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada JG, Couturier DL, Kumar S, Kishore K, Chilamakuri CSR, Glont SE, Archer Goode E, Brodie C, Guppy N, Natrajan R, Bruna A, Caldas C, Russell A, Siersbæk R, Yusa K, Chernukhin I, Carroll JS
JournalNat Genet
PubMed ID31913353
Using genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screens to understand endocrine drug resistance, we discovered ARID1A and other SWI/SNF complex components as the factors most critically required for response to two classes of estrogen receptor-alpha (ER) antagonists. In this context, SWI/SNF-specific gene deletion resulted in drug resistance. Unexpectedly, ... More
A Systems Chemoproteomic Analysis of Acyl-CoA/Protein Interaction Networks.
AuthorsLevy MJ, Montgomery DC, Sardiu ME, Montano JL, Bergholtz SE, Nance KD, Thorpe AL, Fox SD, Lin Q, Andresson T, Florens L, Washburn MP, Meier JL
JournalCell Chem Biol
PubMed ID31836350
Acyl-coenzyme A (CoA)/protein interactions are essential for life. Despite this importance, their global scope and selectivity remains undefined. Here, we describe CATNIP (CoA/AcetylTraNsferase Interaction Profiling), a chemoproteomic platform for the high-throughput analysis of acyl-CoA/protein interactions in endogenous proteomes. First, we apply CATNIP to identify acetyl-CoA-binding proteins through unbiased clustering of ... More
Transmission of antimicrobial resistant non-O157 Escherichia coli at the interface of animal-fresh produce in sustainable farming environments.
AuthorsGlaize A, Gutierrez-Rodriguez E, Hanning I, Díaz-Sánchez S, Gunter C, van Vliet AHM, Watson W, Thakur S
JournalInt J Food Microbiol
PubMed ID31901751
The interaction of typical host adapted enteric bacterial pathogens with fresh produce grown in fields is complex. These interactions can be more pronounced in co-managed or sustainable farms where animal operations are, by design, close to fresh produce, and growers frequently move between the two production environments. The primary objectives ... More