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https://www.readbyqxmd.com/read/28938749/the-testicular-transcriptome-associated-with-spermatogonia-differentiation-initiated-by-gonadotrophin-stimulation-in-the-juvenile-rhesus-monkey-macaca-mulatta
#1
Suresh Ramaswamy, William H Walker, Paula Aliberti, Rahil Sethi, Gary R Marshall, Alyxzandria Smith, Seyedmehdi Nourashrafeddin, Alicia Belgorosky, Uma R Chandran, Mark P Hedger, Tony M Plant
STUDY QUESTION: What is the genetic landscape within the testis of the juvenile rhesus monkey (Macaca mulatta) that underlies the decision of undifferentiated spermatogonia to commit to a pathway of differentiation when puberty is induced prematurely by exogenous LH and FSH stimulation? SUMMARY ANSWER: Forty-eight hours of gonadotrophin stimulation of the juvenile monkey testis resulted in the appearance of differentiating B spermatogonia and the emergence of 1362 up-regulated and 225 down-regulated testicular mRNAs encoding a complex network of proteins ranging from enzymes regulating Leydig cell steroidogenesis to membrane receptors, and from juxtacrine and paracrine factors to transcriptional factors governing spermatogonial stem cell fate...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938025/the-kaposi-s-sarcoma-associated-herpesvirus-kshv-non-structural-membrane-protein-k15-is-required-for-viral-lytic-replication-and-may-represent-a-therapeutic-target
#2
Bizunesh Abere, Tamrat M Mamo, Silke Hartmann, Naira Samarina, Elias Hage, Jessica Rückert, Sven-Kevin Hotop, Guntram Büsche, Thomas F Schulz
Kaposi's sarcoma-associated herpesvirus (KSHV) is the infectious cause of the highly vascularized tumor Kaposi's sarcoma (KS), which is characterized by proliferating spindle cells of endothelial origin, extensive neo-angiogenesis and inflammatory infiltrates. The KSHV K15 protein contributes to the angiogenic and invasive properties of KSHV-infected endothelial cells. Here, we asked whether K15 could also play a role in KSHV lytic replication. Deletion of the K15 gene from the viral genome or its depletion by siRNA lead to reduced virus reactivation, as evidenced by the decreased expression levels of KSHV lytic proteins RTA, K-bZIP, ORF 45 and K8...
September 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28934487/supernalign-a-new-tool-for-flexible-superposition-of-homologous-rna-structures-and-inference-of-accurate-structure-based-sequence-alignments
#3
Pawel Piatkowski, Jagoda Jablonska, Adriana Zyla, Dorota Niedzialek, Dorota Matelska, Elzbieta Jankowska, Tomasz Walen, Wayne K Dawson, Janusz M Bujnicki
RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933547/investigating-molecular-structures-of-brassica-carinata-and-canola-seeds-as-predictors-to-estimate-protein-bioavailability-for-ruminants-by-advanced-non-destructive-vibrational-molecular-spectroscopy
#4
Yajing Ban, Luciana Louzada Prates, Peiqiang Yu
This study was conducted to (1) determine protein and carbohydrate molecular structure profiles, (2) quantify the relationship between structural features and protein bioavailability of newly developed carinata and canola seeds for dairy cows by using Fourier transform infrared molecular spectroscopy. Results showed similarity in protein structural make-up within the entire protein structural region between carinata and canola seeds. The highest area ratios related to structural CHO, total CHO and cellulosic compounds were obtained for carinata seeds...
September 21, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28931680/molecular-evolution-of-herpes-simplex-virus-2-complete-genomes-comparison-between-primary-and-recurrent-infections
#5
Miguel A Minaya, Travis Jensen, Johannes Goll, Maria Korom, Sree H Datla, Robert B Belshe, Lynda A Morrison
Herpes simplex virus (HSV)-1 and -2 are large, double-stranded DNA viruses that cause lifelong persistent infections characterized by periods of quiescence and recurrent disease. How HSV evolves within an infected individual experiencing multiple episodes of reactivation over time is not known. We determined genome sequences of viruses isolated from two subjects in the Herpevac Trial for Women who experienced primary HSV-2 genital disease and compared them with sequences of viruses isolated from the subsequent fifth or sixth episode of recurrent disease in the same individuals...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28930521/multifactorial-role-of-long-non-coding-rnas-lncrnas-in-hematopoiesis
#6
Muhammad Babar Khawar, Rabia Mehmood, Muddasir Hassan Abbasi, Nadeem Sheikh
  Human genome project unveiled that only 1.5.-2.0.% of the genome is protein coding. ENCODE and related studies showed that most part of the genome transcribed into RNAs, and most of them do not code for a functional proteins, hence the name non-coding RNAs (ncRNAs). ncRNAs are small ncRNAs (less than 200 nucleotides) and long ncRNAs (longer than 200 nucleotides up to 10 kb). They act as a direct link between highly ordered chromosome structures, gene expression and serve as a bridge between genome and chromatin modification complexes as guides, scaffolds, and decoys...
January 1, 2018: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28927677/std-nmr-experiments-identify-a-structural-motif-with-novel-second-site-activity-against-west-nile-virus-ns2b-ns3-protease
#7
Tobias Schöne, Lena Lisbeth Grimm, Naoki Sakai, Linlin Zhang, Rolf Hilgenfeld, Thomas Peters
West Nile virus (WNV) belongs to the genus Flavivirus of the family Flaviviridae. This mosquito-borne virus that is highly pathogenic to humans has been evolving into a global threat during the past two decades. Despite many efforts, neither antiviral drugs nor vaccines are available. The viral protease NS2B-NS3(pro) is essential for viral replication, and therefore it is considered a prime drug target. However, success in the development of specific NS2B-NS3(pro) inhibitors had been moderate so far. In the search for new structural motifs with binding affinity for NS2B-NS3(pro), we have screened a fragment library, the Maybridge Ro5 library, employing saturation transfer difference (STD) NMR experiments as readout...
September 16, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28927344/structural-elucidation-of-transmembrane-domain-zero-tmd0-of-ecdl-a-multidrug-resistance-associated-protein-mrp-family-of-atp-binding-cassette-transporter-protein-revealed-by-atomistic-simulation
#8
Krishnendu Bera, Priyanka Rani, Gaurav Kishor, Shikha Agarwal, Antresh Kumar, Durg Vijay Singh
ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known...
September 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28926086/common-variants-in-dlg1-locus-are-associated-with-non-syndromic-cleft-lip-with-or-without-cleft-palate
#9
Adrianna Mostowska, Agnieszka Gaczkowska, Kacper Żukowski, Kerstin U Ludwig, Kamil K Hozyasz, Piotr Wójcicki, Elizabeth Mangold, Anne C Böhmer, Stefanie Heilmann-Heimbach, Michael Knapp, Małgorzata Zadurska, Barbara Biedziak, Margareta Budner, Agnieszka Lasota, Agata Daktera-Micker, Paweł P Jagodziński
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common craniofacial anomaly with a complex and heterogeneous etiology. Knowledge regarding specific genetic factors underlying this birth defect is still not well understood. Therefore, we conducted an independent replication analysis for the top-associated variants located within the DLG1 locus at chromosome 3q29, which was identified as a novel cleft-susceptibility locus in our genome-wide association study (GWAS). Mega-analysis of the pooled individual data from the GWAS and replication study confirmed that common DLG1 variants are associated with the risk of nsCL/P...
September 19, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28924833/rho-inhibiting-c2in-c3-fusion-toxin-inhibits-chemotactic-recruitment-of-human-monocytes-ex-vivo-and-in-mice-in-vivo
#10
Tobias Martin, Amelie Möglich, Ina Felix, Christina Förtsch, Anne Rittlinger, Annette Palmer, Stephanie Denk, Julian Schneider, Lena Notbohm, Mona Vogel, Hartmut Geiger, Stephan Paschke, Markus Huber-Lang, Holger Barth
Bacterial protein toxins became valuable molecular tools for the targeted modulation of cell functions in experimental pharmacology and attractive therapeutics because of their potent and specific mode of action in human cells. C2IN-C3lim, a recombinant fusion toxin (~50 kDa) of the Rho-inhibiting C3lim from Clostridium (C.) limosum and a non-toxic portion of the C. botulinum C2 toxin (C2IN), is selectively internalized into the cytosol of monocytic cells where C3lim specifically ADP-ribosylates Rho A and -B, thereby inhibiting Rho-mediated signaling...
September 18, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28924046/in-silico-modeling-of-the-cryptic-e2-ubiquitin-binding-site-of-e6-associated-protein-e6ap-ube3a-reveals-the-mechanism-of-polyubiquitin-chain-assembly
#11
Virginia P Ronchi, Elizabeth D Kim, Christopher M Summa, Jennifer M Klein, Arthur L Haas
To understand the mechanism for assembly of Lys(48)-linked polyubiquitin degradation signals, we previously demonstrated the E6AP/UBE3A ligase harbors two functionally-distinct E2~ubiquitin binding sites: a high-affinity Site 1 required for E6AP Cys(820)~ubiquitin thioester formation and a canonical Site 2 responsible for subsequent chain elongation. Ordered binding to Sites 1 and 2 is here revealed by observation of UbcH7~ubiquitin-dependent substrate inhibition of chain formation at micromolar concentrations...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28923854/caveolae-mediated-endocytosis-is-critical-for-albumin-cellular-uptake-and-response-to-albumin-bound-chemotherapy
#12
Moumita Chatterjee, Edgar Ben-Josef, Ryan Robb, Marall Vedaie, Star Seum, Krishnan Thirumoorthy, Kamalakannan Palanichamy, Matthew Harbrecht, Arnab Chakravarti, Terence M Williams
Nab-paclitaxel, a nanoparticle conjugate of paclitaxel to human albumin, exhibits efficacy in pancreatic cancer, non-small cell lung cancer and breast cancer. However, there is a lack of predictive biomarkers to identify patients who might benefit most from its administration. This study addresses this gap in knowledge by identifying that caveolin-1 (Cav-1) is a candidate mechanism-based biomarker. Caveolae are small membrane invaginations important for trans-endothelial albumin uptake. Cav-1, the principal structural component of caveolae, is overexpressed in the cancers noted above which respond to nab-paclitaxel...
September 18, 2017: Cancer Research
https://www.readbyqxmd.com/read/28923567/a-water-soluble-polysaccharide-from-the-roots-of-polygala-tenuifolia-suppresses-ovarian-tumor-growth-and-angiogenesis-in-vivo
#13
Hua Yao, Ping Cui, Dan Xu, Yunduo Liu, Qinghua Tian, Fubin Zhang
PTP, one polysaccharide extracted from the roots of Polygala tenuifolia, has displayed anti-cancer activity in several types of ovarian cancer cells. This study aims to elucidate the structure of PTP and investigate its anticancer effects against SKOV3 xenograft tumor growth in BALB/c mice, as well as the underlying mechanisms involved. GC-MS and NMR data indicate that PTP has a backbone composed of 1,4,6-linked-β-Galp, 1,4-linked-β-Galp and 1,4-linked-β-Glcp, with non-reducing terminal 1-linked-α-Glcp attached to O-6 of 1,4,6-linked-β-Galp...
September 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28923281/genetic-diversity-and-intergenogroup-recombination-events-of-sapoviruses-detected-from-feces-of-pigs-in-japan
#14
Moegi Kuroda, Tsuneyuki Masuda, Mika Ito, Yuki Naoi, Yen Hai Doan, Kei Haga, Shinobu Tsuchiaka, Mai Kishimoto, Kaori Sano, Tsutomu Omatsu, Yukie Katayama, Mami Oba, Hiroshi Aoki, Toru Ichimaru, Fujikko Sunaga, Itsuro Mukono, Hiroshi Yamasato, Junsuke Shirai, Kazuhiko Katayama, Tetsuya Mizutani, Tomoichiro Oka, Makoto Nagai
Sapoviruses (SaV) are enteric viruses infecting humans and animals. SaVs are highly diverse and are divided into multiple genogroups based on structural protein (VP1) sequences. SaVs detected from pigs belong to eight genogroups (GIII, GV, GVI, GVII, GVIII, GIX, GX, and GXI), but little is known about the SaV genogroup distribution in the Japanese pig population. In the present study, 26 nearly complete genome (>6000 nucleotide: nt) and three partial sequences (2429nt, 4364nt, and 4419nt in length, including the entire VP1 coding region) of SaV were obtained from one diarrheic and 15 non-diarrheic porcine feces in Japan via a metagenomics approach...
September 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28921430/production-of-recombinant-rabies-virus-glycoprotein-by-insect-cells-in-a-single-use-fixed-bed-bioreactor
#15
Daniella C Ventini-Monteiro, Renato M Astray, Carlos A Pereira
A single-use fixed-bed bioreactor (iCELLis nano) can be used for cultivating non adherent insect cells, which can be then recovered for scaling up or for harvesting a membrane-associated viral glycoprotein with high quality in terms of preserved protein structure and biological function. Here, we describe the procedures for establishing genetically modified Drosophila melanogaster Schneider 2 (S2) cell cultures in the iCELLis nano bioreactor and for quantifying by ELISA the recombinant rabies virus glycoprotein (rRVGP) synthesized...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28919226/validation-of-hav-biomarker-2a-for-differential-diagnostic-of-hepatitis-a-infected-and-vaccinated-individuals-using-multiplex-serology
#16
Katrin Bohm, Angela Filomena, Nicole Schneiderhan-Marra, Gérard Krause, Claudia Sievers
BACKGROUND: Worldwide about 1.5 million clinical cases of hepatitis A virus (HAV) infections occur every year and increasingly countries are introducing HAV vaccination into the childhood immunization schedule with a single dose instead of the originally licenced two dose regimen. Diagnosis of acute HAV infection is determined serologically by anti-HAV-IgM detection using ELISA. Additionally anti-HAV-IgG can become positive during the early phase of symptoms, but remains detectable after infection and also after vaccination against HAV...
September 14, 2017: Vaccine
https://www.readbyqxmd.com/read/28916419/development-of-an-indirect-enzyme-linked-immunosorbent-assay-elisa-to-differentiate-antibodies-against-wild-type-porcine-reproductive-and-respiratory-syndrome-from-the-vaccine-strain-tjm-f92-based-on-a-recombinant-nsp2-protein
#17
X X Wang, F X Wang, Z G Li, Y J Wen, X Wang, N Song, H Wu
An accurate ELISA method to differentiate pigs infected with wild-type porcine reproductive and respiratory syndrome (PRRSV) strains from vaccinated ones would help to monitor PRRSV vaccination compliance. The recombinant protein GST-d120aa derived from the continuous deletion of 120 amino acids in the non-structural protein 2 region of the modified-live vaccine strain TJM-F92 was used to develop an indirect enzyme-linked immunosorbent assay (d120-ELISA) for differentiating serum antibodies against TJM-F92 from other PRRSV strains...
September 12, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28915040/elucidating-the-interdependence-of-drug-resistance-from-combinations-of-mutations
#18
Debra A Ragland, Troy W Whitfield, Sook-Kyung Lee, Ronald Swanstrom, Konstantin B Zeldovich, Nese Kurt Yilmaz, Celia A Schiffer
HIV-1 protease is responsible for the cleavage of 12 non-homologous sites within the Gag and Gag-Pro-Pol polyproteins in the viral genome. Under the selective pressure of protease inhibition, the virus evolves mutations within (primary) and outside of (secondary) the active site allowing the protease to process substrates while simultaneously countering inhibition. The primary protease mutations impede inhibitor binding directly, while the secondary mutations are considered accessory mutations that compensate for a loss in fitness...
September 15, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28913175/regulation-of-endoplasmic-reticulum-mitochondria-ca-2-transfer-and-its-importance-for-anti-cancer-therapies
#19
REVIEW
Gaia Pedriali, Alessandro Rimessi, Luigi Sbano, Carlotta Giorgi, Mariusz R Wieckowski, Maurizio Previati, Paolo Pinton
Inter-organelle membrane contact sites are emerging as major sites for the regulation of intracellular Ca(2+) concentration and distribution. Here, extracellular stimuli operate on a wide array of channels, pumps, and ion exchangers to redistribute intracellular Ca(2+) among several compartments. The resulting highly defined spatial and temporal patterns of Ca(2+) movement can be used to elicit specific cellular responses, including cell proliferation, migration, or death. Plasma membrane (PM) also can directly contact mitochondria and endoplasmic reticulum (ER) through caveolae, small invaginations of the PM that ensure inter-organelle contacts, and can contribute to the regulation of numerous cellular functions through scaffolding proteins such as caveolins...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28911812/relationships-between-residue-voronoi-volume-and-sequence-conservation-in-proteins
#20
Jen-Wei Liu, Chih-Wen Cheng, Yu-Feng Lin, Shao-Yu Chen, Jenn-Kang Hwang, Shih-Chung Yen
BACKGROUND: Functional and biophysical constraints can cause different levels of sequence conservation in proteins. Previously, structural properties, e.g., relative solvent accessibility (RSA) and packing density of the weighted contact number (WCN), have been found to be related to protein sequence conservation (CS). The Voronoi volume has recently been recognized as a new structural property of the local protein structural environment reflecting CS. However, for surface residues, it is sensitive to water molecules surrounding the protein structure...
September 11, 2017: Biochimica et Biophysica Acta
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