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https://www.readbyqxmd.com/read/28934437/group-b-streptococcus-and-the-vaginal-microbiota
#1
Geoffrey H Rosen, Tara M Randis, Purnahamsi V Desai, Katherine J Sapra, Bing Ma, Pawel Gajer, Michael S Humphrys, Jacques Ravel, Shari E Gelber, Adam J Ratner
Background: Streptococcus agalactiae (group B Streptococcus [GBS]) is an important neonatal pathogen and emerging cause of disease in adults. The major risk factor for neonatal disease is maternal vaginal colonization. However, little is known about the relationship between GBS and vaginal microbiota. Methods: Vaginal lavage samples from nonpregnant women were tested for GBS, and amplicon-based sequencing targeting the 16S ribosomal RNA V3-V4 region was performed...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934335/genetic-diversity-of-entamoeba-novel-ribosomal-lineages-from-cockroaches
#2
Tetsuro Kawano, Mihoko Imada, Pennapa Chamavit, Seiki Kobayashi, Tetsuo Hashimoto, Tomoyoshi Nozaki
Our current taxonomic perspective on Entamoeba is largely based on small-subunit ribosomal RNA genes (SSU rDNA) from Entamoeba species identified in vertebrate hosts with minor exceptions such as E. moshkovskii from sewage water and E. marina from marine sediment. Other Entamoeba species have also been morphologically identified and described from non-vertebrate species such as insects; however, their genetic diversity remains unknown. In order to further disclose the diversity of the genus, we investigated Entamoeba spp...
2017: PloS One
https://www.readbyqxmd.com/read/28932888/assessment-of-molecular-detection-of-anaerobic-ammonium-oxidizing-anammox-bacteria-in-different-environmental-samples-using-pcr-primers-based-on-16s-rrna-and-functional-genes
#3
Ping Han, Uli Klümper, Alex Wong, Meng Li, Jih-Gaw Lin, Zhexue Quan, Martin Denecke, Ji-Dong Gu
Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd 1-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples...
September 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28931158/new-mitogenomes-of-two-chinese-stag-beetles-coleoptera-lucanidae-and-their-implications-for-systematics
#4
Zi-Qi Lin, Fan Song, Teng Li, Yuan-Yuan Wu, Xia Wan
Although conspicuous and well-studied, stag beetles have been slow to join the genomic era. In this study, mitochondrial genomes of two stag beetles, Sinodendron yunnanense and Prosopocoilus confucius, are sequenced for the first time. Both of their genomes consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. The mitogenome of S. yunnanense was 16,921 bp in length, and P. confucius was 16,951 bp. The location of the gene trnL(UUR), between the A + T-rich and control region in S...
January 1, 2017: Journal of Insect Science
https://www.readbyqxmd.com/read/28930607/transcriptomics-in-amyotrophic-lateral-sclerosis
#5
Marios G Krokidis, Panagiotis Vlamos
Amyotrophic lateral sclerosis (ALS) is an adult-onset, incurable neurodegenerative disease characterized by the selective death of upper and lowers motor neurons in the spinal cord, brainstem and motor cortex, which ultimately leads to paralysis and death within 2-3 years of onset. ALS is poorly understood, although multiple studies have been proposed to explain the pathophysiological mechanisms of the disorder. The development of microarray technology, for simultaneous analysis of the transcriptional expression of thousands of genes, has provided new possibilities to get better insights into the pathogenesis of ALS, and most important, potential new candidate targets for novel treatments...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28930151/perk-signal-modulated-protein-translation-promotes-the-survivability-of-dengue-2-virus-infected-mosquito-cells-and-extends-viral-replication
#6
Jiun-Nan Hou, Tien-Huang Chen, Yi-Hsuan Chiang, Jing-Yun Peng, Tsong-Han Yang, Chih-Chieh Cheng, Eny Sofiyatun, Cheng-Hsun Chiu, Chuan Chiang-Ni, Wei-June Chen
Survival of mosquitoes from dengue virus (DENV) infection is a prerequisite of viral transmission to the host. This study aimed to see how mosquito cells can survive the infection during prosperous replication of the virus. In C6/36 cells, global protein translation was shut down after infection by DENV type 2 (DENV2). However, it returned to a normal level when infected cells were treated with an inhibitor of the protein kinase RNA (PKR)-like ER kinase (PERK) signaling pathway. Based on a 7-Methylguanosine 5'-triphosphate (m7GTP) pull-down assay, the eukaryotic translation initiation factor 4F (eIF4F) complex was also identified in DENV2-infected cells...
September 20, 2017: Viruses
https://www.readbyqxmd.com/read/28929238/nuclease-integrated-kinase-super-assemblies-niks-and-their-role-in-rna-processing
#7
REVIEW
Monica C Pillon, Robin E Stanley
Here we highlight the Grc3/Las1 complex, an essential RNA processing machine that is well conserved across eukaryotes and required for processing the pre-ribosomal RNA (pre-rRNA). Las1 is an endoribonuclease that cleaves the pre-rRNA while Grc3 is a polynucleotide kinase that phosphorylates the Las1-cleaved RNA product. Recently we showed that Grc3 and Las1 assemble into a higher-order complex composed of a dimer of Grc3/Las1 heterodimers that is required for nuclease and kinase activity. Unexpectedly, we found that the Grc3/Las1 complex draws numerous parallels with two other eukaryotic nucleases, Ire1 and RNase L...
September 19, 2017: Current Genetics
https://www.readbyqxmd.com/read/28928861/down-regulation-of-rps9-inhibits-osteosarcoma-cell-growth-through-inactivation-of-mapk-signaling-pathway
#8
Dong-Dong Cheng, Bin Zhu, Shi-Jie Li, Ting Yuan, Qing-Cheng Yang, Cun-Yi Fan
Objectives: Osteosarcoma is the most common malignant bone tumor in adolescents; however, the mechanisms involved in the pathogenesis and progression of osteosarcoma remain to be elucidated. Researchers have provided valuable insights into the tumorigenesis of Ribosomal protein S9 (RPS9) in some cancers. The purpose of this study was to elucidate the expression, functions, and mechanisms of RPS9 in human osteosarcoma. Methods: The expression of RPS9 in osteosarcoma tissues and cell lines was evaluated by qRT-PCR and western blotting...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28926641/impact-of-monotherapy-on-hiv-1-reservoir-immune-activation-and-co-infection-with-epstein-barr-virus
#9
Maria Raffaella Petrara, Anna Maria Cattelan, Lolita Sasset, Riccardo Freguja, Francesco Carmona, Silvia Sanavia, Marisa Zanchetta, Paola Del Bianco, Anita De Rossi
OBJECTIVES: Although monotherapy (mART) effectiveness in maintaining viral suppression and CD4 cell count has been extensively examined in HIV-1-infected patients, its impact on HIV-1 reservoir, immune activation, microbial translocation and co-infection with Epstein-Barr Virus (EBV) is unclear. METHODS: This retrospective study involved 32 patients who switched to mART; patients were studied at baseline, 48 and 96 weeks after mART initiation. Thirty-two patients who continued combined antiretroviral therapy (cART) over the same period of time were included in the study...
2017: PloS One
https://www.readbyqxmd.com/read/28926633/effects-of-salinity-on-the-cellular-physiological-responses-of-natrinema-sp-j7-2
#10
Yunjun Mei, Huan Liu, Shunxi Zhang, Ming Yang, Chun Hu, Jian Zhang, Ping Shen, Xiangdong Chen
The halophilic archaea (haloarchaea) live in hyersaline environments such as salt lakes, salt ponds and marine salterns. To cope with the salt stress conditions, haloarchaea have developed two fundamentally different strategies: the "salt-in" strategy and the "compatible-solute" strategy. Although investigation of the molecular mechanisms underlying the tolerance to high salt concentrations has made outstanding achievements, experimental study from the aspect of transcription is rare. In the present study, we monitored cellular physiology of Natrinema sp...
2017: PloS One
https://www.readbyqxmd.com/read/28925931/gut-microbiota-dependent-trimethylamine-n-oxide-and-serum-biomarkers-in-patients-with-t2dm-and-advanced-ckd
#11
Mohammed A I Al-Obaide, Ruchi Singh, Palika Datta, Kathy A Rewers-Felkins, Maria V Salguero, Ibtisam Al-Obaidi, Kameswara Rao Kottapalli, Tetyana L Vasylyeva
Trimethylamine-N-oxide (TMAO) is a product of dietary, gut microbiome, and tissues metabolism. Elevated blood TMAO levels are associated with heart attack, stroke and chronic kidney disease (CKD). The purpose of our study was to investigate the gut microbiota associated with trimethylamine (TMA) production, the precursor of TMAO, and the serum levels of TMAO and inflammatory biomarkers associated with type 2 diabetes mellitus (T2DM) and CKD. Twenty adults with T2DM and advanced CKD and 20 healthy adults participated in the study...
September 19, 2017: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/28924511/barcoded-ns31-aml2-primers-for-sequencing-of-arbuscular-mycorrhizal-communities-in-environmental-samples
#12
Benjamin S T Morgan, Louise M Egerton-Warburton
PREMISE OF THE STUDY: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28924186/interactome-analysis-reveals-znf804a-a-schizophrenia-risk-gene-as-a-novel-component-of-protein-translational-machinery-critical-for-embryonic-neurodevelopment
#13
Y Zhou, F Dong, T A Lanz, V Reinhart, M Li, L Liu, J Zou, H S Xi, Y Mao
Recent genome-wide association studies identified over 100 genetic loci that significantly associate with schizophrenia (SZ). A top candidate gene, ZNF804A, was robustly replicated in different populations. However, its neural functions are largely unknown. Here we show in mouse that ZFP804A, the homolog of ZNF804A, is required for normal progenitor proliferation and neuronal migration. Using a yeast two-hybrid genome-wide screen, we identified novel interacting proteins of ZNF804A. Rather than transcriptional factors, genes involved in mRNA translation are highly represented in our interactome result...
September 19, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28923911/how-ribosomes-translate-cancer
#14
REVIEW
Sergey O Sulima, Isabel J F Hofman, Kim De Keersmaecker, Jonathan D Dinman
A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somatic ribosomal mutations in various cancers, have significantly increased our understanding of the relevance of ribosomes in oncogenesis. Here, we explore the growing list of mechanisms by which the ribosome is involved in carcinogenesis-from the hijacking of ribosomes by oncogenic factors and dysregulated translational control, to the effects of mutations in ribosomal components on cellular metabolism. Of clinical importance, the recent success of RNA polymerase inhibitors highlights the dependence on "onco-ribosomes" as an Achilles' heel of cancer cells and a promising target for further therapeutic intervention...
September 18, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28923054/a-novel-method-for-extracting-nucleic-acids-from-dried-blood-spots-for-ultrasensitive-detection-of-low-density%C3%A2-plasmodium-falciparum-and-plasmodium-vivax%C3%A2-infections
#15
Kayvan Zainabadi, Matthew Adams, Zay Yar Han, Hnin Wai Lwin, Kay Thwe Han, Amed Ouattara, Si Thura, Christopher V Plowe, Myaing M Nyunt
BACKGROUND: Greater Mekong Subregion countries are committed to eliminating Plasmodium falciparum malaria by 2025. Current elimination interventions target infections at parasite densities that can be detected by standard microscopy or rapid diagnostic tests (RDTs). More sensitive detection methods have been developed to detect lower density "asymptomatic" infections that may represent an important transmission reservoir. These ultrasensitive polymerase chain reaction (usPCR) tests have been used to identify target populations for mass drug administration (MDA)...
September 18, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28922802/succession-of-arbuscular-mycorrhizal-fungi-along-a-52-year-agricultural-recultivation-chronosequence
#16
Julien Roy, Rüdiger Reichel, Nicolas Brüggemann, Stefan Hempel, Matthias C Rillig
Arbuscular mycorrhizal (AM) fungi provide a range of functions in natural and managed ecosystems. However, the trajectory of AM fungal diversity after land degradation is poorly known. We studied the succession of AM fungi along an agricultural recultivation chronosequence after open-cast mining near Cologne, Germany. We used high-throughput sequencing of the large-subunit ribosomal RNA genes to characterize the soil AM fungal communities of 10 agricultural fields spanning 52 years of recultivation. During three years, soils are recultivated with a legume, and then converted to agriculture to be later returned to local farmers implementing conventional agriculture...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28922394/sequence-features-of-viral-and-human-internal-ribosome-entry-sites-predictive-of-their-activity
#17
Alexey A Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28920631/pneumocystis-jirovecii-genotyping-experience-in-a-tertiary-care-hospital-in-northern-italy
#18
Pietro Pini, Carlotta F Orsi, Annunziata La Regina, Samuele Peppoloni, Federica Berrilli, Elisabetta Blasi, David Di Cave
Respiratory samples from Pneumocystis jirovecii pneumonia (PJP) cases collected at a tertiary-care university hospital in Modena were analyzed for the presence of specific polymorphisms in the mitochondrial large subunit ribosomal RNA (mtLSU-rRNA). Retrospectively, 57 cases were selected in a six-year period and 34 out of the 57 processed BAL samples returned PCR positive results, thus allowing further molecular analysis. The following P.jirovecii genotype distribution was observed: genotype 3 (50%), genotype 2 (23%), genotype 1 (18%), genotypes 1 or 4 (9%)...
July 2017: New Microbiologica
https://www.readbyqxmd.com/read/28919899/emerging-roles-and-landscape-of-translating-mrnas-in-plants
#19
REVIEW
Gaurav Sablok, Jonathan J Powell, Kemal Kazan
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28919697/16s-ribosomal-rna-sequencing-and-molecular-serotyping-of-avibacterium-paragallinarum-isolated-from-indian-field-conditions
#20
Vihang Vithalrao Patil, Debendranath Mishra, Dilip Vithalrao Mane
AIM: This study was aimed at identifying Indian field isolates of Avibacterium paragallinarum on both molecular as well as serological levels that cause infectious coryza in chickens. MATERIALS AND METHODS: Species-specific polymerase chain reaction (HPG-2 PCR), and 16S ribosomal RNA (rRNA) sequencing were employed for molecular identification. Whereas, multiplex PCR technique was used for serological identification of Indian field isolates of A. paragallinarum...
August 2017: Veterinary World
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