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https://www.readbyqxmd.com/read/29777910/differentially-expressed-novel-alternatively-spliced-transcript-variant-of-tumor-suppressor-stk11-gene-in-mouse
#1
Hassan Mubarak Ishqi, Tarique Sarwar, Mohammed Amir Husain, Sayeed Ur Rehman, Mohammad Tabish
Serine/threonine kinase 11 (STK11) is a protein kinase that is encoded by Stk11 gene located on chromosome 19 and 10 in humans and mouse respectively. It acts as a master kinase of adenine monophosphate-activated protein kinase (AMPK) pathway that coordinates the regulation of cellular energy metabolism and cell division. STK11 exerts effect by activating more than 14 kinases including AMPK and AMPK-related kinases. It is also known to regulate cell polarity and acts as tumor suppressor. Alternative splicing of pre-mRNA is a mechanism which results in multiple transcript variants of a single gene...
May 16, 2018: Gene
https://www.readbyqxmd.com/read/29777339/characterization-of-a-cryptic-rolling-circle-replication-plasmid-pmk8-from-enterococcus-durans-1-8
#2
Penyu Zhou, Zhengyuan Zhai, Xiong Yao, Peihua Ma, Yanling Hao
A novel cryptic plasmid from Enterococcus durans 1-8, designated as pMK8, was sequenced and analyzed in this study. It consists of 3337 bp with a G + C content of 33.11%. Sequence analysis of pMK8 revealed three putative open reading frames (ORFs). Based on homology, two of them were identified as genes encoding replication initiation (RepC) and mobilization (Mob) protein, respectively. Sequence analysis revealed a pT181 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the repC gene...
May 17, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29776930/modifying-the-lantibiotic-mutacin-1140-for-increased-yield-activity-and-stability
#3
Mengxin Geng, Leif Smith
Mutacin 1140 belongs to the epidermin family of type AI lantibiotics. This family has a broad spectrum of activity against Gram-positive bacteria. The binding of mutacin 1140 to lipid II leads to the inhibition of cell wall synthesis. Pharmacokinetic experiments on type AI lantibiotics are generally discouraging for clinical applications due to their short half-life. The unprotected dehydrated and protease susceptible residues outside of the lanthionine rings may play a role in their short half-life in physiological settings...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29775563/anolis-carolinensis-as-a-model-to-understand-molecular-and-cellular-basis-of-foveal-development
#4
Naif S Sannan, Xianghong Shan, Kevin Gregory-Evans, Kenro Kusumi, Cheryl Y Gregory-Evans
The fovea is an anatomical specialization of the central retina containing closely packed cone-photoreceptors providing an area of high acuity vision in humans and primates. Despite its key role in the clarity of vision, little is known about the molecular and cellular basis of foveal development, due to the absence of a foveal structure in commonly used laboratory animal models. Of the amniotes the retina in birds of prey and some reptiles do exhibit a typical foveal structure, but they have not been studied in the context of foveal development due to lack of availability of embryonic tissue, lack of captive breeding programs, and limited genomic information...
May 15, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29775485/plasmodium-parasite-exploits-host-aquaporin-3-during-liver-stage-malaria-infection
#5
Dora Posfai, Kayla Sylvester, Anupama Reddy, Jack G Ganley, Johannes Wirth, Quinlan E Cullen, Tushar Dave, Nobutaka Kato, Sandeep S Dave, Emily R Derbyshire
Within the liver a single Plasmodium parasite transforms into thousands of blood-infective forms to cause malaria. Here, we use RNA-sequencing to identify host genes that are upregulated upon Plasmodium berghei infection of hepatocytes with the hypothesis that host pathways are hijacked to benefit parasite development. We found that expression of aquaporin-3 (AQP3), a water and glycerol channel, is significantly induced in Plasmodium-infected hepatocytes compared to uninfected cells. This aquaglyceroporin localizes to the parasitophorous vacuole membrane, the compartmental interface between the host and pathogen, with a temporal pattern that correlates with the parasite's expansion in the liver...
May 18, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29774518/huh-7-reference-genome-profile-complex-karyotype-composed-of-massive-loss-of-heterozygosity
#6
Fumio Kasai, Noriko Hirayama, Midori Ozawa, Motonobu Satoh, Arihiro Kohara
Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes...
May 17, 2018: Human Cell
https://www.readbyqxmd.com/read/29773790/crispr-cas9-mediated-gene-targeting-in-arabidopsis-using-sequential-transformation
#7
Daisuke Miki, Wenxin Zhang, Wenjie Zeng, Zhengyan Feng, Jian-Kang Zhu
Homologous recombination-based gene targeting is a powerful tool for precise genome modification and has been widely used in organisms ranging from yeast to higher organisms such as Drosophila and mouse. However, gene targeting in higher plants, including the most widely used model plant Arabidopsis thaliana, remains challenging. Here we report a sequential transformation method for gene targeting in Arabidopsis. We find that parental lines expressing the bacterial endonuclease Cas9 from the egg cell- and early embryo-specific DD45 gene promoter can improve the frequency of single-guide RNA-targeted gene knock-ins and sequence replacements via homologous recombination at several endogenous sites in the Arabidopsis genome...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29772751/what-we-do-not-know-about-fungal-cell-adhesion-molecules
#8
REVIEW
Peter N Lipke
There has been extensive research on structure and function of fungal cell adhesion molecules, but the most of the work has been about adhesins in Candida albicans and Saccharomyces cerevisiae. These yeasts are members of a single ascomycete order, and adhesion molecules from the six other fungal phyla are only sparsely described in the literature. In these other phyla, most of the research is at the cellular level, rather than at the molecular level, so there has been little characterization of the adhesion molecules themselves...
May 17, 2018: Journal of Fungi (Basel, Switzerland)
https://www.readbyqxmd.com/read/29772011/induction-of-influenza-specific-local-cd8-t-cells-in-the-respiratory-tract-after-aerosol-delivery-of-vaccine-antigen-or-virus-in-the-babraham-inbred-pig
#9
Katie Tungatt, Garry Dolton, Sophie B Morgan, Meriem Attaf, Anna Fuller, Thomas Whalley, Johanneke D Hemmink, Emily Porter, Barbara Szomolay, Maria Montoya, John A Hammond, John J Miles, David K Cole, Alain Townsend, Mick Bailey, Pierre J Rizkallah, Bryan Charleston, Elma Tchilian, Andrew K Sewell
There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer vaccine antigens. Current animal models used to study respiratory pathogens suffer from anatomical disparity with humans. The pig is a natural and important host of influenza viruses and is physiologically more comparable to humans than other animal models in terms of size, respiratory tract biology and volume...
May 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29771291/long-noncoding-rnas-exchange-during-zygotic-genome-activation-in-goat
#10
Mingtian Deng, Yongjie Wan, Zifei Liu, Caifang Ren, Guomin Zhang, Jing Pang, Yanli Zhang, Feng Wang
In mammals, their proper development during the early cleavage stages strongly relies on the gene products newly transcribed by zygotic genome activation (ZGA). Long noncoding RNAs (lncRNAs) have been characterized as key regulators of the ZGA process in mice and human. However, the ZGA stage has not yet been identified and epigenetic regulations of the ZGA process remain largely unknown in goats. Here, we show that ZGA occurred at the 8-cell stage in goats. During ZGA, tri-methylation of H3K9 was dynamically changed but maintained strong staining in development arrested embryos...
May 15, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29771290/single-cell-clustering-based-on-cell-pair-differentiability-correlation-and-variance-analysis
#11
Hao Jiang, Lydia Sohn, Haiyan Huang, Luonan Chen
Motivation: The rapid advancement of single cell technologies has shed new light on the complex mechanisms of cellular heterogeneity. Identification of intercellular transcriptomic heterogeneity is one of the most critical tasks in single-cell RNA-sequencing studies. Results: We propose a new cell similarity measure based on cell-pair differentiability correlation, which is derived from gene differential pattern among all cell pairs. Through plugging into the framework of hierarchical clustering with this new measure, we further develop a variance analysis based clustering algorithm 'Corr' that can determine cluster number automatically and identify cell types accurately...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29770350/centromere-chromosome-orientation-fluorescent-in-situ-hybridization-cen-co-fish-detects-sister-chromatid-exchange-at-the-centromere-in-human-cells
#12
Simona Giunta
Human centromeres are composed of large tandem arrays of repetitive alpha satellite DNA, which are often sites of aberrant rearrangement in cancers (Mitelman et al ., 1997; Padilla-Nash et al ., 2001). To date, annotation of the human centromere repetitive sequences remains incomplete, greatly hindering in-depth functional studies of these regions essential for chromosome segregation. In order to monitor sister chromatid exchange happening at the centromere (C-SCE) due to recombination and mutagenic events, I have applied the Chromosome-Orientation Fluorescence in situ Hybridization (CO-FISH) technique to centromeres (Cen-CO-FISH) in human cells...
April 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29769698/mutation-screening-using-formalin-fixed-paraffin-embedded-tissues-a-stratified-approach-according-to-dna-quality
#13
Francesco Cucco, Alexandra Clipson, Hannah Kennedy, Joe Sneath Thompson, Ming Wang, Sharon Barrans, Moniek van Hoppe, Eguzkine Ochoa Ruiz, Josh Caddy, Debbie Hamid, Thomas Cummin, Cathy Burton, Andrew J Davies, Peter Johnson, Ming-Qing Du
DNA samples from formalin-fixed paraffin-embedded tissues are highly degraded with variable quality, and this imposes a big challenge for targeted sequencing due to false positives, largely caused by PCR errors and cytosine deamination. To eliminate false positives, a common practice is to validate the detected variants by Sanger sequencing or perform targeted sequencing in duplicate. Technically, PCR errors could be removed by molecular barcoding of template DNA prior to amplification as in the HaloPlexHS design...
May 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29769334/reovirus-nonstructural-protein-%C3%AF-ns-acts-as-an-rna-stability-factor-promoting-viral-genome-replication
#14
Paula F Zamora, Liya Hu, Jonathan J Knowlton, Roni M Lahr, Rodolfo A Moreno, Andrea J Berman, B V Venkataram Prasad, Terence S Dermody
Viral nonstructural proteins, which are not packaged into virions, are essential for replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. Reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, activities of σNS during individual steps of the reovirus replication cycle are poorly understood...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29769267/functional-characterization-of-21-allelic-variants-of-dihydropyrimidine-dehydrogenase-identified-in-1-070-japanese-individuals
#15
Eiji Hishinuma, Yoko Narita, Sakae Saito, Masamitsu Maekawa, Fumika Akai, Yuya Nakanishi, Jun Yasuda, Masao Nagasaki, Masayuki Yamamoto, Hiroaki Yamaguchi, Nariyasu Mano, Noriyasu Hirasawa, Masahiro Hiratsuka
Dihydropyrimidine dehydrogenase (DPD, EC 1.3.1.2), encoded by the DPYD gene, is the rate-limiting enzyme in the degradation pathway of endogenous pyrimidine and fluoropyrimidine drugs such as 5-fluorouracil (5-FU). DPD catalyzes the reduction of uracil, thymine, and 5-FU. In Caucasians, DPYD mutations, including DPYD*2A, DPYD*13, c.2846A>T, and 1129-5923C>G/hapB3, are known to contribute to interindividual variations in the toxicity of 5-FU. However, none of these DPYD polymorphisms have been identified in the Asian population...
May 16, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29767366/expression-profiling-of-differentially-regulated-genes-in-fanconi-anemia
#16
Binita Zipporah E, Kavitha Govarthanan, Pavithra Shyamsunder, Rama S Verma
Gene expression analysis mainly helps to study gene quantification methods by using various downstream detection approaches like imaging, amplification, probe hybridization, or sequencing. With respect to DNA, which is less static, mRNA levels vary over time, between cell types under divergent conditions. Gene expression analysis is principally focused on determination of mRNA levels transcribed from DNA. DNA microarrays are one of the robust and powerful tools to detect changes in multiple transcripts in larger cohorts in parallel...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767365/current-and-future-methods-for-mrna-analysis-a-drive-toward-single-molecule-sequencing
#17
Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis
The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767364/single-cell-mrna-seq-using-the-fluidigm-c1-system-and-integrated-fluidics-circuits
#18
Haibiao Gong, Devin Do, Ramesh Ramakrishnan
Single-cell mRNA-seq is a valuable tool to dissect expression profiles and to understand the regulatory network of genes. Microfluidics is well suited for single-cell analysis owing both to the small volume of the reaction chambers and easiness of automation. Here we describe the workflow of single-cell mRNA-seq using C1 IFC, which can isolate and process up to 96 cells. Both on-chip procedure (lysis, reverse transcription, and preamplification PCR) and off-chip sequencing library preparation protocols are described...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29766818/cell-free-fetal-dna-a-novel-biomarker-for-early-prediction-of-pre-eclampsia-and-other-obstetric-complications
#19
Naina Kumar, Amit Kant Singh
Hypertensive disorder of pregnancy, especially Pre-eclampsia is one of the major causes of increased maternal and perinatal morbidity and mortality all over the world. Early prediction of pre-eclampsia is the need of modern obstetrics, as this can timely prevent the progress of disease as well as related fetal and maternal morbidity and mortality. In addition to the screening of fetal aneuploidies, Rhesus-D status, fetal sex, single gene disorders, the cell-free fetal Deoxyribonucleic acid (DNA) quantification has emerged out as a promising biomarker for prediction of pre-eclampsia...
May 16, 2018: Current Hypertension Reviews
https://www.readbyqxmd.com/read/29766023/adeno-associated-virus-genome-population-sequencing-achieves-full-vector-genome-resolution-and-reveals-human-vector-chimeras
#20
Phillip W L Tai, Jun Xie, Kaiyuen Fong, Matthew Seetin, Cheryl Heiner, Qin Su, Michael Weiand, Daniella Wilmot, Maria L Zapp, Guangping Gao
Recombinant adeno-associated virus (rAAV)-based gene therapy has entered a phase of clinical translation and commercialization. Despite this progress, vector integrity following production is often overlooked. Compromised vectors may negatively impact therapeutic efficacy and safety. Using single molecule, real-time (SMRT) sequencing, we can comprehensively profile packaged genomes as a single intact molecule and directly assess vector integrity without extensive preparation. We have exploited this methodology to profile all heterogeneic populations of self-complementary AAV genomes via bioinformatics pipelines and have coined this approach AAV-genome population sequencing (AAV-GPseq)...
June 15, 2018: Molecular Therapy. Methods & Clinical Development
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