Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.
AuthorsBlane B, Raven KE, Leek D, Brown N, Parkhill J, Peacock SJ,
JournalJ Antimicrob Chemother
PubMed ID31039248
'Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay associated with this step could reduce the time to infection control interventions. To develop and evaluate rapid sequencing of MRSA using ... More
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
Dietary Adaptation of Microbiota in Drosophila Requires NF-?B-Dependent Control of the Translational Regulator 4E-BP.
AuthorsVandehoef C, Molaei M, Karpac J,
JournalCell Rep
PubMed ID32521261
'Dietary nutrients shape complex interactions between hosts and their commensal gut bacteria, further promoting flexibility in host-microbiota associations that can drive nutritional symbiosis. However, it remains less clear if diet-dependent host signaling mechanisms also influence these associations. Using Drosophila, we show here that nuclear factor ?B (NF-?B)/Relish, an innate immune ... More
Glucose-6-phosphate dehydrogenase correlates with tumor immune activity and programmed death ligand-1 expression in Merkel cell carcinoma.
AuthorsNakamura M, Nagase K, Yoshimitsu M, Magara T, Nojiri Y, Kato H, Kobayashi T, Teramoto Y, Yasuda M, Wada H, Ozawa T, Umemori Y, Ogata D, Morita A,
JournalJ Immunother Cancer
PubMed ID33361404
'Merkel cell carcinoma (MCC) is a rare and highly malignant skin cancer. Some cases have a good prognosis and spontaneous regression can occur. Reported prognostic markers, such as Merkel cell polyoma virus infection or programmed death ligand-1 (PD-L1) expression, remain insufficient for precisely estimating the vastly different patient outcomes. We ... More
Geographical reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase.
AuthorsMicheli V, Rimoldi SG, Romeri F, Comandatore F, Mancon A, Gigantiello A, Perini M, Mileto D, Pagani C, Lombardi A, Gismondo MR,
JournalJ Med Virol
PubMed ID32816316
'The first identification of autochthonous transmission of SARS-CoV-2 in Italy was documented by the Laboratory of Clinical Microbiology, Virology and Bioemergencies of L. Sacco Hospital (Milano, Italy) on 20th February 2020 in a 38 years old male patient, who was found positive for pneumonia at the Codogno Hospital. Thereafter Lombardy ... More
Questions around mutation T1010I in MET gene: results of next generation sequencing in Polish patient with suspected hereditary adenoid cystic carcinoma.
AuthorsGrenda A, Krawczyk P, Chmielewska I, Nicos M, Milanowski J,
JournalEur Rev Med Pharmacol Sci
PubMed ID32964978
'Adenoid cystic carcinoma (ACC) is a slowly growing cancer, which is the most common malignant tumor of the salivary glands. It is claimed that it is a non-inherited cancer. People with family history of ACC are reported extremely rarely. We present patients with suspected hereditary ACC. Next generation sequencing (NGS) ... More
An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus.
AuthorsBazghaleh N, Bell JK, Mamet SD, Moreira ZM, Taye ZM, Williams S, Norris C, Dowhy T, Arcand M, Lamb EG, Links M, Shirtliffe S, Vail S, Siciliano SD, Helgason B,
JournalData Brief
PubMed ID32953951
'The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of bacterial and ... More
Detailed genetic and functional analysis of the hDMDdel52/mdx mouse model.
AuthorsYavas A, Weij R, van Putten M, Kourkouta E, Beekman C, Puoliväli J, Bragge T, Ahtoniemi T, Knijnenburg J, Hoogenboom ME, Ariyurek Y, Aartsma-Rus A, van Deutekom J, Datson N,
JournalPLoS One
PubMed ID33362201
'Duchenne muscular dystrophy (DMD) is a severe, progressive neuromuscular disorder caused by reading frame disrupting mutations in the DMD gene leading to absence of functional dystrophin. Antisense oligonucleotide (AON)-mediated exon skipping is a therapeutic approach aimed at restoring the reading frame at the pre-mRNA level, allowing the production of internally ... More
Trehalose as an osmolyte in Candidatus Accumulibacter phosphatis.
Authorsde Graaff DR, van Loosdrecht MCM, Pronk M,
JournalAppl Microbiol Biotechnol
PubMed ID33074418
'Candidatus Accumulibacter phosphatis is an important microorganism for enhanced biological phosphorus removal (EBPR). In a previous study, we found a remarkable flexibility regarding salinity, since this same microorganism could thrive in both freshwater- and seawater-based environments, but the mechanism for the tolerance to saline conditions remained unknown. Here, we identified ... More
De novo sequencing, assembly and functional annotation of Armillaria borealis genome.
AuthorsAkulova VS, Sharov VV, Aksyonova AI, Putintseva YA, Oreshkova NV, Feranchuk SI, Kuzmin DA, Pavlov IN, Litovka YA, Krutovsky KV,
JournalBMC Genomics
PubMed ID32912216
'Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a ... More
CCN6 mutation detection in Chinese patients with progressive pseudo-rheumatoid dysplasia and identification of four novel mutations.
AuthorsWang Y, Xiao K, Yang Y, Wu Z, Jin J, Qiu G, Weng X, Zhao X,
JournalMol Genet Genomic Med
PubMed ID32351055
'No formal diagnostic criteria for progressive pseudo-rheumatoid dysplasia (PPD) are available because of insufficient clinical data, which results in that PPD is often misdiagnosed with other diseases. Whole exome sequencing (WES) and Sanger sequencing were employed to reveal the novel mutations on CCN6 of five patients with PPD from China ... More
Altered PTPRD DNA methylation associates with restricted adipogenesis in healthy first-degree relatives of Type 2 diabetes subjects.
AuthorsParrillo L, Spinelli R, Longo M, Desiderio A, Mirra P, Nigro C, Fiory F, Hedjazifar S, Mutarelli M, Carissimo A, Formisano P, Miele C, Smith U, Raciti GA, Beguinot F,
JournalEpigenomics
PubMed ID32483983
'Aim: First-degree relatives (FDR) of individuals with Type 2 diabetes (T2D) feature restricted adipogenesis, which render them more vulnerable to T2D. Epigenetics may contribute to these abnormalities. Methods: FDR pre-adipocyte Methylome and Transcriptome were investigated by MeDIP- and RNA-Seq, respectively. Results:Methylome analysis revealed 2841 differentially methylated regions (DMR) in FDR. ... More
Draft genome assembly and annotation of the masked birch caterpillar, Drepana arcuata (Lepidoptera: Drepanoidea).
AuthorsYadav C, Smith M, Ogunremi D, Yack J,
JournalData Brief
PubMed ID33299908
'The masked birch caterpillar, Drepana arcuata Walker (Lepidoptera: Drepanidae), and other Drepanoidea (Lepidoptera) species are excellent organisms for investigating the function and evolution of vibratory communication and sociality in caterpillars. We present a de novo assembled draft genome and functional annotation for D. arcuata, using a combination of short and ... More
Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.
AuthorsHale H, Gardner EM, Viruel J, Pokorny L, Johnson MG,
JournalAppl Plant Sci
PubMed ID32351798
'The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which ... More
Beneficial Effect of Virgin Coconut Oil on Alloxan-Induced Diabetes and Microbiota Composition in Rats.
'The gut microbiota is composed of a diverse population of obligate and facultative anaerobic microorganisms which are shown to influence host metabolism and immune homeostasis. This study investigated the effects of virgin coconut oil on the weekly fasting glycaemia, daily food and water intake and weekly body mass gain over ... More
Anti-Inflammatory Effects of 5a,8a-Epidioxycholest-6-en-3ß-ol, a Steroidal Endoperoxide Isolated from Aplysia depilans, Based on Bioguided Fractionation and NMR Analysis.
'Sea hares of Aplysia genus are recognized as a source of a diverse range of metabolites. 5a,8a-Endoperoxides belong to a group of oxidized sterols commonly found in marine organisms and display several bioactivities, including antimicrobial, anti-tumor, and immunomodulatory properties. Herein we report the isolation of 5a,8a-epidioxycholest-6-en-3ß-ol (EnP(5,8)) from Aplysia depilans ... 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 sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies.
AuthorsZhou Z, Liu B, Chen B, Shi Y, Pu F, Bai H, Li L, Xu P,
JournalSci Data
PubMed ID31570724
Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to ... More
Monitoring early S-phase origin firing and replication fork movement by sequencing nascent DNA from synchronized cells.
AuthorsMacheret M, Halazonetis TD,
JournalNat Protoc
PubMed ID30487655
A better understanding of DNA replication initiation in human cells and how this process is altered upon DNA replication stress requires the ability to study origin firing genome wide. Previously described methods of mapping DNA replication origins in higher eukaryotes rely principally on fractionation of DNA fragments based on their ... More
Full Chloroplast Genome Sequence of the Economically Important Dietary Supplement and Spice Curcuma longa.
AuthorsWindsor AM, Ott BM, Zhang N, Wen J, Hsu E, Handy SM,
JournalMicrobiol Resour Announc
PubMed ID31395636
Curcuma longa L. is a native species of Asia that is commonly known as turmeric. It is a spice also used in traditional medicine to treat a wide range of illnesses. Here, we present the fully annotated chloroplast genome of Curcuma longa. ... More
Identification of a native Bacillus thuringiensis strain from Sri Lanka active against Dipel-resistant Plutella xylostella.
Biopesticides based on strains of the bacterium Bacillus thuringiensis (Bt) are used globally for effective and environmentally friendly pest control. The most serious threat to the sustainable use of these microbial pesticides is the development of resistance on targeted pests. Populations of Plutella xylostella (diamondback moth) have evolved field resistance ... More
Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study.
AuthorsLeite GGS, Morales W, Weitsman S, Celly S, Parodi G, Mathur R, Sedighi R, Barlow GM, Rezaie A, Pimentel M,
JournalBMC Microbiol
PubMed ID31675917
The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associated methodologies are ill-suited for the viscosity and low microbial biomass of small intestine samples. As part of the REIMAGINE ... More
Interlaboratory study to validate a STR profiling method for intraspecies identification of mouse cell lines.
AuthorsAlmeida JL, Dakic A, Kindig K, Kone M, Letham DLD, Langdon S, Peat R, Holding-Pillai J, Hall EM, Ladd M, Shaffer MD, Berg H, Li J, Wigger G, Lund S, Steffen CR, Fransway BB, Geraghty B, Natoli M, Bauer B, Gollin SM, Lewis DW, Reid Y,
JournalPLoS One
PubMed ID31220119
The Consortium for Mouse Cell Line Authentication was formed to validate Short Tandem Repeat (STR) markers for intraspecies identification of mouse cell lines. The STR profiling method is a multiplex polymerase chain reaction (PCR) assay comprised of primers targeting 19 mouse STR markers and two human STR markers (for interspecies ... More
A genome resource for several North American Venturia inaequalis isolates with multiple fungicide resistance phenotypes.
The apple scab pathogen, Venturia inaequalis, is amongst the most economically important fungal pathogens that effects apples. Fungicide applications are an essential part of disease management. Implementation of cultural practices and genetic sources of resistance in the host are vital components of scab management. This is the first presentation of ... More
High density DNA data storage library via dehydration with digital microfluidic retrieval.
DNA promises to be a high density data storage medium, but physical storage poses a challenge. To store large amounts of data, pools must be physically isolated so they can share the same addressing scheme. We propose the storage of dehydrated DNA spots on glass as an approach for scalable ... More
Serum cell-free DNA levels are a useful marker for extramammary Paget disease.
AuthorsMijiddorj T, Kajihara I, Tasaki Y, Otsuka-Maeda S, Sakamoto R, Sawamura S, Kanazawa-Yamada S, Egashira S, Inoue K, Makino K, Miyashita A, Aoi J, Igata T, Makino T, Masuguchi S, Fukushima S, Jinnin M, Morinaga J, Ikeda T, Ihn H,
JournalBr J Dermatol
PubMed ID30706452
Although carcinoembryonic antigen (CEA) and cytokeratin 19 fragment (CYFRA) are useful markers for extramammary Paget disease (EMPD), serum CEA and CYFRA levels are not elevated in most patients with EMPD without metastasis. Cell-free (cf)DNA has attracted attention as an indicator of clinical conditions in several cancers. To identify further useful ... More
Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition.
AuthorsGowers GF, Vince O, Charles JH, Klarenberg I, Ellis T, Edwards A,
JournalGenes (Basel)
PubMed ID31703372
Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth's surface. The principal reason for this is the inaccessibility of most of these areas due to their extreme isolation and challenging environmental conditions. While remote research stations have ... More
Porcine Circovirus Type 2 Induces Single Immunoglobulin Interleukin-1 Related Receptor (SIGIRR) Downregulation to Promote Interleukin-1ß Upregulation in Porcine Alveolar Macrophage.
AuthorsYang S, Liu B, Yin S, Shang Y, Zhang X, Khan MUZ, Liu X, Cai J
JournalViruses
PubMed ID31684202
Multisystemic inflammation in pigs affected by porcine circovirus type 2 (PCV2) indicates the disordered expression of inflammatory cytokines. However, the PCV2-induced expression profile of inflammation cytokines and its regulating mechanism remain poorly understood. In this study, inflammatory cytokines and receptors in porcine alveolar macrophages (PAMs) after PCV2 infection were profiled ... More
Complete Genome Sequences of Two Distinct Strains of Serratia marcescens Isolated from Contaminated Platelet Concentrates from Canadian Donors.
AuthorsDiamandas A, Razon RM, Sykes E, Kumar A, Ramirez-Arcos S, Brassinga AKC,
JournalMicrobiol Resour Announc
PubMed ID33033127
In this report, we present the genome sequences of two Serratia marcescens strains isolated as contaminants from platelet concentrates by Canadian Blood Services and designated CBS2010/11 (CBS11) and CBS2010/12 (CBS12). Genomic sequence analyses showed that CBS11 has one chromosome and one plasmid (pAM01), whereas CBS12 has no plasmids. ... More
Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions.
Authorsde Jonge PA, Smit Sibinga DJC, Boright OA, Costa AR, Nobrega FL, Brouns SJJ, Dutilh BE,
JournalJ Virol
PubMed ID32938760
The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on ... More
Laboratory Optimization Tweaks for Sanger Sequencing in a Resource-Limited Setting.
AuthorsOnwuamah CK, Okwuraiwe AP, Ahmed RA, Sokei JO, Ponmak J, Okoli LC, Kagurusi BA, Anejo-Okopi J,
JournalJ Biomol Tech
PubMed ID33100921
Despite various challenges that hinder the implementation of high-tech molecular methods in resource-limited settings, we have been able to implement and achieve International Organization for Standardization 15189:2012 accreditation for genotypic HIV drug resistance testing in our facility. At the Center for Human Virology and Genomics, Nigerian Institute of Medical Research, ... More
MiR-455-3p downregulation facilitates cell proliferation and invasion and predicts poor prognosis of osteosarcoma.
AuthorsYi X, Wang Y, Xu S,
JournalJ Orthop Surg Res
PubMed ID33008443
Osteosarcoma (OS) is one of the most primary malignant bone tumors, mainly attracting children and young adults. The microRNAs are mentioned to play vital roles in many cancers, including OS. The purpose of this study was to explore the expression and function of miR-455-3p in OS and predict the potential ... More
Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana.
The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within ... More
CRISPR off-target detection with DISCOVER-seq.
AuthorsWienert B, Wyman SK, Yeh CD, Conklin BR, Corn JE,
JournalNat Protoc
PubMed ID32313254
DISCOVER-seq (discovery of in situ Cas off-targets and verification by sequencing) is a broadly applicable approach for unbiased CRISPR-Cas off-target identification in cells and tissues. It leverages the recruitment of DNA repair factors to double-strand breaks (DSBs) after genome editing with CRISPR nucleases. Here, we describe a detailed experimental protocol ... More
The duodenal microbiome is altered in small intestinal bacterial overgrowth.
Small intestinal bacterial overgrowth (SIBO) is highly prevalent and is associated with numerous gastrointestinal disorders, but the microbes involved remain poorly defined. Moreover, existing studies of microbiome alterations in SIBO have utilized stool samples, which are not representative of the entire gastrointestinal tract. Therefore, we aimed to determine and compare ... More
An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus.
AuthorsBazghaleh N, Mamet SD, Bell JK, Moreira ZM, Taye ZM, Williams S, Arcand M, Lamb EG, Shirtliffe S, Vail S, Siciliano SD, Helgason B,
JournalData Brief
PubMed ID32346558
The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities ... More
Targeted next-generation sequencing identified a novel variant of SOX10 in a Chinese family with Waardenburg syndrome type 2.
AuthorsLiu XW, Wang SY, Xing ZK, Zhu YM, Ding WJ, Duan L, Cui X, Xu BC, Li SJ, Guo YF,
JournalJ Int Med Res
PubMed ID33251892
Waardenburg syndrome type 2 (WS2) is an autosomal dominant syndrome, characterized by bright blue eyes, hearing loss, and depigmented patches of hair and skin. It exhibits high phenotypic and genetic heterogeneity. We explored the molecular etiology in a Chinese family with WS2. We recruited a three-generation family with three affected ... More
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.
AuthorsCosta OYA, de Hollander M, Pijl A, Liu B, Kuramae EE,
JournalMicrobiome
PubMed ID32482164
Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are ... More
High-throughput Preparation of DNA, RNA, and Protein from Cryopreserved Human iPSCs for Multi-omics Analysis.
AuthorsZhang JX, Lau E, Paik DT, Zhuge Y, Wu JC,
JournalCurr Protoc Stem Cell Biol
PubMed ID32584494
We describe the procedure to isolate genomic DNA, RNA, and protein directly from cryopreserved induced pluripotent stem cell (iPSC) vials using commercially available solid-phase extraction kits, and we report the relationship between macromolecule yields and experimental and storage factors. Sufficient quantities of DNA, RNA, and protein are recoverable from as ... More
Draft Genome Sequence of a Multicountry Outbreak-Related Listeria monocytogenes Sequence Type 1247 Strain, VLTRLM2013.
AuthorsMäesaar M, Roasto M,
JournalMicrobiol Resour Announc
PubMed ID32763938
We sequenced the genome of a multicountry outbreak-related Listeria monocytogenes sequence type 1247 strain (VLTRLM2013) that was isolated from a vacuum-packaged sliced salted salmon product of an Estonian fish-processing company that was obtained from an Estonian retail outlet in 2013. ... More
Early life disruption of the microbiota affects organ development and cytokine gene expression in threespine stickleback.
AuthorsKirschman LJ, Khadjinova A, Ireland K, Milligan-Myhre KC,
JournalIntegr Comp Biol
PubMed ID32970813
The microbiota that inhabits vertebrates exerts strong effects on host physiology and can be crucial to the development of a normal phenotype. This includes development of the immune system, somatic growth and maintenance, and morphogenesis. However, the genetic background of the host can also affect these life history traits. To ... 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
Methods to Map Meiotic Recombination Proteins in Saccharomyces cerevisiae.
AuthorsSanchez A, Borde V,
JournalMethods Mol Biol
PubMed ID32840788
Meiotic recombination is triggered by programmed DNA double-strand breaks (DSBs), catalyzed by the type II topoisomerase-like Spo11 protein. Meiotic DSBs are repaired by homologous recombination, which produces either crossovers or noncrossovers, this decision being linked to the binding of proteins specific of each pathway. Mapping the binding of these proteins ... More