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https://www.readbyqxmd.com/read/29909272/insights-into-the-structural-features-and-stability-of-peptide-nucleic-acid-with-a-d-prolyl-2-aminocyclopentane-carboxylic-acid-backbone-that-binds-to-dna-and-rna
#1
Nattawee Poomsuk, Tirayut Vilaivan, Khatcharin Siriwong
Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences...
June 12, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29909066/characterization-of-a-plasmodium-falciparum-rrna-methyltransferase
#2
Kirti Gupta, Ankit Gupta, Saman Habib
The ribosomal RNA adenine dimethyltransferases (rAD) of KsgA/Dim1 family are universally conserved with eukaryotic rADs separated into distinct cytosolic Dim1 and organellar KsgA/TFB homologs. Among the two putative KsgA proteins encoded by the Plasmodium falciparum genome, we found that PfKsgA1 was dually localised in the cytoplasm and the mitochondrion. The protein interacted specifically with small ribosomal subunit as detected by ribosome pull-down using anti-PfKsgA1 antibodies. Recombinant PfKsgA1 exhibited methyltransferase activity which was further confirmed by complementation in an Escherichia coli KsgA knockout strain...
June 14, 2018: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29908759/cutibacterium-acnes-and-the-shoulder-microbiome
#3
Boyang Qiu, Kait Al, Ana M Pena-Diaz, George S Athwal, Darren Drosdowech, Kenneth J Faber, Jeremy P Burton, David B O'Gorman
BACKGROUND: Advances in DNA sequencing technologies have made it possible to detect microbial genome sequences (microbiomes) within tissues once thought to be sterile. We used this approach to gain insights into the likely sources of Cutibacterium acnes (formerly Propionibacterium acnes) infections within the shoulder. METHODS: Tissue samples were collected from the skin, subcutaneous fat, anterior supraspinatus tendon, middle glenohumeral ligament, and humeral head cartilage of 23 patients (14 male and 9 female patients) during primary arthroplasty surgery...
June 13, 2018: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/29908643/investigating-human-placentation-and-pregnancy-using-first-trimester-chorionic-villi
#4
Roberta L Hannibal, Margarida Cardoso-Moreira, Shilpa P Chetty, Joanne Lau, Zhongxia Qi, Eduardo Gonzalez-Maldonado, Athena M Cherry, Jingwei Yu, Mary E Norton, Julie C Baker
Chorionic villus sampling (CVS), routinely used for prenatal diagnosis of cytogenetic disorders, also possesses great potential for the study of placentation. To better understand villus biology, human placentation, and how these relate to pregnancy outcomes, we examined the morphology and transcriptomes of villi obtained via CVS from 10 to 14 weeks of pregnancy and correlated these with pregnancy attributes and clinical outcomes. First, we established a morphological scoring system based on three main villus features: branching, budding and vascularization...
May 2018: Placenta
https://www.readbyqxmd.com/read/29908642/defining-the-rhesus-macaque-placental-mirnaome-conservation-of-expression-of-placental-mirna-clusters-between-the-macaque-and-human
#5
Jenna Kropp Schmidt, Lindsey N Block, Thaddeus G Golos
OBJECTIVE: Expression of microRNAs (miRNAs) in the human placenta is dynamic across gestation, with expression of miRNAs belonging to the C14MC, C19MC and miR-371-3 clusters. Specifically, miRNAs within the C19MC cluster are exclusively expressed in primates with predominant expression in the placenta. Non-human primates can be utilized to study developmental processes of placentation in vivo that cannot be assessed in the human placenta, however, miRNA expression has not been defined in the macaque placenta...
May 2018: Placenta
https://www.readbyqxmd.com/read/29908593/viruses-in-polar-lake-and-soil-ecosystems
#6
Alberto Rastrojo, Antonio Alcamí
Viruses play an important role in the control of microbial communities, and it has been suggested that the influence of viruses in polar ecosystems, with low nutrients and under extreme environmental conditions, may be greater. Viral metagenomics allows the genetic characterization of complex viral communities without the need to isolate and grow viruses. Recent investigations in Antarctica and the Arctic are uncovering a great diversity of DNA viruses, including bacteriophages, circular single-stranded DNA viruses, algal-infecting phycodnaviruses, and virophages, adapted to these extreme environments...
2018: Advances in Virus Research
https://www.readbyqxmd.com/read/29908293/reversible-rna-modification-n-1-methyladenosine-m-1-a-in-mrna-and-trna
#7
REVIEW
Chi Zhang, Guifang Jia
More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6 -methyladenosine (m6 A), N1 -methyladenosine (m1 A) has been found as a reversible modification in tRNA and mRNA. m1 A occurs at positions 9, 14, and 58 of tRNA, with m1 A58 being critical for tRNA stability. Other than the hundreds of m1 A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1 A also identifies > 20 m1 A sites in mitochondrial genes...
June 13, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29908270/complete-mitochondrial-genome-of-parasesarma-affine-brachyura-sesarmidae-gene-rearrangements-in-sesarmidae-and-phylogenetic-analysis-of-the-brachyura
#8
Zhengfei Wang, Ziqian Wang, Xuejia Shi, Qiong Wu, Yitao Tao, Huayun Guo, Chenyao Ji, Yuze Bai
In this study, the complete mitochondrial DNA (mtDNA) sequence of the crab Parasesarma affine is determined, characterized and compared with other decapod crustaceans. The P. affine mitochondrial genome (mitogenome) is 15,638 bp in size, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a control region (CR). Then, 23 of the 37 genes are encoded by the heavy (+) strand while 14 are encoded by the light (-) strand. All PCGs are initiated by ATN codons and 4 of the 13 PCGs harbored the incomplete termination codon by T or TA...
June 13, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29908248/detection-of-single-alpha-helices-in-large-protein-sequence-sets-using-hardware-acceleration
#9
Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán Gáspári
Single alpha-helices (SAHs) are increasingly recognized as important structural and functional elements of proteins. Comprehensive identification of SAH segments in large protein datasets was largely hindered by the slow speed of the most restrictive prediction tool for their identification, FT_CHARGE on common hardware. We have previously implemented an FPGA-based version of this tool allowing fast analysis of a large number of sequences. Using this implementation, we have set up of a semi-automated pipeline capable of analyzing full UniProt releases in reasonable time and compiling monthly updates of a comprehensive database of SAH segments...
June 13, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29908171/screening-of-natural-wolbachia-infection-in-aedes-aegypti-aedes-taeniorhynchus-and-culex-quinquefasciatus-from-guadeloupe-french-west-indies
#10
D Goindin, A Cannet, C Delannay, C Ramdini, J Gustave, C Atyame, A Vega-Rúa
Guadeloupe islands are threatened by several mosquito-borne viruses such as Dengue, Chikungunya, Zika and West Nile virus. It appears essential to look for alternative mosquito control methods such as the incompatible insect technique (ITT) aiming at sterilizing wild females by inundative releases of incompatible males. Before considering the implementation of such a strategy, the characterization of genetic diversity of the endocellular bacterium Wolbachia regarding the local mosquito populations is a critical issue...
June 13, 2018: Acta Tropica
https://www.readbyqxmd.com/read/29907786/a-gene-co-expression-network-model-identifies-yield-related-vicinity-networks-in-jatropha-curcas-shoot-system
#11
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Ratnam Wickneswari
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes...
June 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29907784/accurate-and-precise-real-time-rt-pcr-assays-for-the-identification-of-astrovirus-associated-encephalitis-in-cattle
#12
Ramona Lüthi, Céline L Boujon, Ronja Kauer, Michel C Koch, Ilias G Bouzalas, Torsten Seuberlich
A novel bovine astrovirus genotype species (BoAstV-CH13/NeuroS1) was recently identified in brain tissues of cattle as a plausible cause of encephalitis. The purpose of the present study was to develop and validate real time RT-PCR assays for the detection of BoAstV-CH13/NeuroS1 in brain tissues of cattle. Three different primer-probe combinations were designed based on BoAstV-CH13/NeuroS1 full-genome sequences of 11 different strains identified in cattle, and established in three distinct one-step real time RT-PCR protocols...
June 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29907695/cancer-cells-copy-migratory-behavior-and-exchange-signaling-networks-via-extracellular-vesicles
#13
Sander C Steenbeek, Thang V Pham, Joep de Ligt, Anoek Zomer, Jaco C Knol, Sander R Piersma, Tim Schelfhorst, Rick Huisjes, Raymond M Schiffelers, Edwin Cuppen, Connie R Jimenez, Jacco van Rheenen
Recent data showed that cancer cells from different tumor subtypes with distinct metastatic potential influence each other's metastatic behavior by exchanging biomolecules through extracellular vesicles (EVs). However, it is debated how small amounts of cargo can mediate this effect, especially in tumors where all cells are from one subtype, and only subtle molecular differences drive metastatic heterogeneity. To study this, we have characterized the content of EVs shed in vivo by two clones of melanoma (B16) tumors with distinct metastatic potential...
June 14, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29907651/lncrna-papas-tethered-to-the-rdna-enhancer-recruits-hypophosphorylated-chd4-nurd-to-repress-rrna-synthesis-at-elevated-temperatures
#14
Zhongliang Zhao, Nevcin Sentürk, Chenlin Song, Ingrid Grummt
Attenuation of pre-rRNA synthesis in response to elevated temperature is accompanied by increased levels of PAPAS ("promoter and pre-rRNA antisense") , a long noncoding RNA (lncRNA) that is transcribed in an orientation antisense to pre-rRNA. Here we show that PAPAS interacts directly with DNA, forming a DNA-RNA triplex structure that tethers PAPAS to a stretch of purines within the enhancer region, thereby guiding associated CHD4/NuRD (nucleosome remodeling and deacetylation) to the rDNA promoter...
June 15, 2018: Genes & Development
https://www.readbyqxmd.com/read/29907154/temporal-changes-in-macrophage-phenotype-after-peripheral-nerve-injury
#15
Joy E Tomlinson, Emilija Žygelytė, Jennifer K Grenier, Michael G Edwards, Jonathan Cheetham
BACKGROUND: Macrophages play a key role in peripheral nerve repair and demonstrate complex phenotypes that are highly dependent on microenvironmental cues. METHODS: We determined temporal changes in macrophage gene expression over time using RNA sequencing after fluorescence-activated cell sorting (FACS) macrophage populations from injured peripheral nerve. We identified key upstream regulators and dominant pathways using ingenuity pathway analysis and confirmed these changes with NanoString technology...
June 15, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29906497/translational-regulation-is-a-key-determinant-of-the-cellular-response-to-benzo-a-pyrene
#16
Evelyn Smit, Florian Caiment, Jolanda Piepers, Jos C S Kleinjans, Twan van den Beucken
Translational control is a cellular response mechanism which initiates adaptation during various stress situations. Here, we investigated the role of translational control after benzo[a]pyrene (BaP) exposure in primary mouse hepatocytes. Translated mRNAs were separated and captured based on the number of associated ribosomes using sucrose gradients and subjected to RNA sequencing (RNAseq) to investigate translational changes. Furthermore, unseparated RNA (total RNA) was used for RNAseq to determine the transcriptional alterations...
June 12, 2018: Toxicology Letters
https://www.readbyqxmd.com/read/29906491/recombinant-newcastle-disease-viruses-with-targets-for-pcr-diagnostics-for-rinderpest-and-peste-des-petits-ruminants
#17
P A van Rijn, J Boonstra, H G P van Gennip
Since February 1st 2011, rinderpest (RP) has been officially declared eradicated worldwide. National authorities have been requested to destroy all their RP related materials. Nonetheless, their national reference laboratories performing real time reverse transcription polymerase chain reaction assays (PCR diagnostics) need RP positive control samples, since some countries still prefer to maintain diagnostic capability for RP for several reasons. In the future, a similar situation will arise for peste des petits ruminants (PPR) as the ambition has been expressed to eradicate PPR...
June 12, 2018: Journal of Virological Methods
https://www.readbyqxmd.com/read/29906446/prospectively-isolated-tetraspanin-neoblasts-are-adult-pluripotent-stem-cells-underlying-planaria-regeneration
#18
An Zeng, Hua Li, Longhua Guo, Xin Gao, Sean McKinney, Yongfu Wang, Zulin Yu, Jungeun Park, Craig Semerad, Eric Ross, Li-Chun Cheng, Erin Davies, Kai Lei, Wei Wang, Anoja Perera, Kate Hall, Allison Peak, Andrew Box, Alejandro Sánchez Alvarado
Proliferating cells known as neoblasts include pluripotent stem cells (PSCs) that sustain tissue homeostasis and regeneration of lost body parts in planarians. However, the lack of markers to prospectively identify and isolate these adult PSCs has significantly hampered their characterization. We used single-cell RNA sequencing (scRNA-seq) and single-cell transplantation to address this long-standing issue. Large-scale scRNA-seq of sorted neoblasts unveiled a novel subtype of neoblast (Nb2) characterized by high levels of PIWI-1 mRNA and protein and marked by a conserved cell-surface protein-coding gene, tetraspanin 1 (tspan-1)...
June 14, 2018: Cell
https://www.readbyqxmd.com/read/29906414/guide-rna-selection-for-crispr-cas9-transfections-in-plasmodium-falciparum
#19
Jose M Ribeiro, Meera Garriga, Nicole Potchen, Anna K Crater, Ankit Gupta, Daisuke Ito, Sanjay A Desai
CRISPR-Cas9 mediated genome editing is addressing key limitations in the transfection of malaria parasites. While this method has already simplified the needed molecular cloning and reduced the time required to generate mutants in the human pathogen Plasmodium falciparum, optimal selection of required guide RNAs and guidelines for successful transfections have not been well characterized, leading workers to use time-consuming trial and error approaches. We used a genome-wide computational approach to create a comprehensive and publicly accessible database of possible guide RNA sequences in the P...
June 12, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29906029/gene%C3%A2-s-expression-profile-for-breast-cancer-clinical-and-therapeutic-approach
#20
Víctor Manuel Vargas-Aguilar, Karina Arroyo-Alvarez
The genes assay provides a clearer picture of individual tumor biology, hormonal- receptor and proliferation. Triple negative breast cancer have high proliferation index and no prognostic with this test. The first generation of gene assay (OncotypeDX, MammaPrint) predice recurrence at 5 years. The next generation (Prosigna, Endopredict) have better prognosis value for recurrence and predictive of early relapse. There are no useful genetic tests for tumors hormonal- negative with pronostic and predictive value...
March 2018: Revista Médica del Instituto Mexicano del Seguro Social
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