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https://www.readbyqxmd.com/read/27910017/fluorescence-in-situ-hybridization-probe-preparation
#1
Doron Tolomeo, Roscoe R Stanyon, Mariano Rocchi
The public human genome sequencing project utilized a hierarchical approach. A large number of BAC/PAC clones, with an insert size approximate from 50 kb to 300 kb, were identified and finely mapped with respect to the Sequence Tagged Site (STS) physical map and with respect to each other. A "golden path" of BACs, covering the entire human genome, was then selected and each clone was fully sequenced. The large number of remaining BACs was not fully sequenced, but the availability of the end sequence (~800-1000 bp) at each end allowed them to be very precisely mapped on the human genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27903645/upgrading-short-read-animal-genome-assemblies-to-chromosome-level-using-comparative-genomics-and-a-universal-probe-set
#2
Joana Damas, Rebecca O'Connor, Marta Farré, Vasileios Panagiotis E Lenis, Henry J Martell, Anjali Mandawala, Katie Fowler, Sunitha Joseph, Martin T Swain, Darren K Griffin, Denis M Larkin
Most recent initiatives to sequence and assemble new species' genomes de-novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification and physical mapping to chromosomes. Multi-genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27898804/fine-mapping-of-two-wheat-powdery-mildew-resistance-genes-located-at-the-cluster
#3
Junchao Liang, Bisheng Fu, Wenbin Tang, Nasr U Khan, Na Li, Zhengqiang Ma
Powdery mildew caused by (DC.) f. sp. () is a globally devastating foliar disease of wheat ( L.). More than a dozen genes against this disease, identified from wheat germplasms of different ploidy levels, have been mapped to the region surrounding the locus on the long arm of chromosome 7A, which forms a resistance ()-gene cluster. and from einkorn wheat ( L.) were two of the genes belonging to this cluster. This study was initiated to fine map these two genes toward map-based cloning. Comparative genomics study showed that macrocolinearity exists between L...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27896813/transcriptional-and-post-transcriptional-regulation-of-histone-variant-h2a-z-during-sea-urchin-development
#4
Mihai Hajdu, Jasmine Calle, Andrea Puno, Aminat Haruna, César Arenas-Mena
Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A...
November 29, 2016: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/27895582/introduction-of-an-n-glycosylation-site-into-udp-glucuronosyltransferase-2b3-alters-its-sensitivity-to-cytochrome-p450-3a1-dependent-modulation
#5
Tatsuro Nakamura, Naho Yamaguchi, Yuu Miyauchi, Tomoki Takeda, Yasushi Yamazoe, Kiyoshi Nagata, Peter I Mackenzie, Hideyuki Yamada, Yuji Ishii
Our previous studies have demonstrated functional protein-protein interactions between cytochrome P450 (CYP) 3A and UDP-glucuronosyltransferase (UGT). However, the role of carbohydrate chains of UGTs in the interaction with CYP is not well understood. To address this issue, we examined whether CYP3A1 modulates the function of UGT2B3 which lacks potential glycosylation sites. We also examined whether the introduction of N-glycosylation to UGT2B3 affects CYP3A-dependent modulation of UGT function. To introduce a potential glycosylation site into UGT2B3, Ser 316 of UGT2B3 was substituted with Asn by site-directed mutagenesis...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27890869/an-improved-red-et-recombineering-system-and-mouse-es-cells-culture-conditions-for-the-generation-of-targeted-mutant-mice
#6
Katsuyoshi Kumagai, Masakatsu Takanashi, Shin-Ichiro Ohno, Masahiko Kuroda, Katsuko Sudo
Targeted mutant mice generated on a C57BL/6 background are powerful tools for analysis of the biological functions of genes, and gene targeting technologies using mouse embryonic stem (ES) cells have been used to generate such mice. Recently, a bacterial artificial chromosome (BAC) recombineering system was established for the construction of targeting vectors. However, gene retrieval from BACs for the generation of gene targeting vectors using this system remains difficult. Even when construction of a gene targeting vector is successful, the efficiency of production of targeted mutant mice from ES cells derived from C57BL/6 mice are poor...
November 25, 2016: Experimental Animals
https://www.readbyqxmd.com/read/27889800/polymorphism-at-expressed-dq-and-dr-loci-in-five-common-equine-mhc-haplotypes
#7
Donald Miller, Rebecca L Tallmadge, Matthew Binns, Baoli Zhu, Yasmin Ali Mohamoud, Ayeda Ahmed, Samantha A Brooks, Douglas F Antczak
The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci...
November 26, 2016: Immunogenetics
https://www.readbyqxmd.com/read/27882771/functional-marine-metagenomic-screening-for-anti-quorum-sensing-and-anti-biofilm-activity
#8
Karin Yaniv, Karina Golberg, Esti Kramarsky-Winter, Robert Marks, Alina Pushkarev, Oded Béjà, Ariel Kushmaro
Quorum sensing (QS), a cell-to-cell communication process, entails the production of signaling molecules that enable synchronized gene expression in microbial communities to regulate myriad microbial functions, including biofilm formation. QS disruption may constitute an innovative approach to the design of novel antifouling and anti-biofilm agents. To identify novel quorum sensing inhibitors (QSI), 2,500 environmental bacterial artificial chromosomes (BAC) from uncultured marine planktonic bacteria were screened for QSI activity using soft agar overlaid with wild type Chromobacterium violaceum as an indicator...
November 24, 2016: Biofouling
https://www.readbyqxmd.com/read/27881156/klotho-sensitive-regulation-of-dendritic-cell-functions-by-vitamin-e
#9
Nguyen Thi Xuan, Phi Thi Thu Trang, Nguyen Van Phong, Nguyen Linh Toan, Do Minh Trung, Nguyen Duy Bac, Viet Linh Nguyen, Nguyen Huy Hoang, Nong Van Hai
BACKGROUND: Dendritic cells (DCs) are the most potent professional antigen-presenting cells for naive T cells to link innate and acquired immunity. Klotho, an anti-aging protein, participates in the regulation of Ca(2+) dependent migration in DCs. Vitamin E (VitE) is an essential antioxidant to protect cells from damage and elicits its inhibitory effects on NF-κB-mediated inflammatory response. However, the roles of VitE on mouse DC functions and the contribution of klotho to those effects both are unknown...
November 24, 2016: Biological Research
https://www.readbyqxmd.com/read/27880090/the-differential-impact-of-alcohol-and-interpersonal-violence-on-the-severity-of-violent-traumatic-brain-injuries-among-american-indians
#10
Kristen F Linton, Paul B Perrin
Research shows connections between substance use and traumatic brain injury (TBI), high rates of substance use and interpersonal violence (IPV) in American Indians with TBI, and connections between IPV and TBI. This study assessed the effects of substance use at the time of a violent TBI and possible mediators such as American Indian race on injury severity (injury severity score [ISS]). A secondary data analysis of 3,351 individuals who experienced a TBI due to violence was conducted. American Indians with TBI were more likely to experience IPV (χ(2) = 4...
November 23, 2016: Social Work in Public Health
https://www.readbyqxmd.com/read/27879269/basophils-promote-tumor-rejection-via-chemotaxis-and-infiltration-of-cd8-t-cells
#11
Ibrahim M Sektioglu, Rafael Carretero, Nadja Bulbuc, Tobias Bald, Thomas Tüting, Alexander Y Rudensky, Günter J Hämmerling
Elevated numbers of regulatory T-cells (Tregs) in patient tumors are known to inhibit efficient anti-tumor T-cell responses. To study the mechanisms controlling tumor rejection, we assessed different mouse models for Treg depletion. In Foxp3DTR knock-in mice, about 99% Treg depletion was achieved, resulting in complete rejection of transplanted HCmel12 melanomas in a CD8+ T cell-dependent way. In contrast, about 90% Treg depletion obtained in BAC transgenic Foxp3.LuciDTR4 mice failed to induce complete rejection of HCmel12 melanomas, demonstrating that residual Tregs were able to control CD8+ T cell responses against the tumor...
November 22, 2016: Cancer Research
https://www.readbyqxmd.com/read/27872490/use-of-zebrafish-larvae-as-a-multi-endpoint-platform-to-characterize-the-toxicity-profile-of-silica-nanoparticles
#12
Duc-Hung Pham, Bert De Roo, Xuan-Bac Nguyen, Mattias Vervaele, Angela Kecskés, Annelii Ny, Daniëlle Copmans, Hanne Vriens, Jean-Pierre Locquet, Peter Hoet, Peter A M de Witte
Nanomaterials are being extensively produced and applied in society. Human and environmental exposures are, therefore, inevitable and so increased attention is being given to nanotoxicity. While silica nanoparticles (NP) are one of the top five nanomaterials found in consumer and biomedical products, their toxicity profile is poorly characterized. In this study, we investigated the toxicity of silica nanoparticles with diameters 20, 50 and 80 nm using an in vivo zebrafish platform that analyzes multiple endpoints related to developmental, cardio-, hepato-, and neurotoxicity...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871234/a-genome-wide-bac-end-sequence-survey-provides-first-insights-into-sweetpotato-ipomoea-batatas-l-lam-genome-composition
#13
Zengzhi Si, Bing Du, Jinxi Huo, Shaozhen He, Qingchang Liu, Hong Zhai
BACKGROUND: Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27865864/construction-and-manipulation-of-a-full-length-infectious-bacterial-artificial-chromosome-clone-of-equine-herpesvirus-type-3-ehv-3
#14
Maksat Akhmedzhanov, Mariela Scrochi, Maria Barrandeguy, Aldana Vissani, Nikolaus Osterrieder, Armando Mario Damiani
Equine herpesvirus type 3 (EHV-3) is the causal agent of equine coital exanthema, a disease characterized by pox-like lesions on the penis of stallions and the vulva of mares. Although the complete genomic sequence of EHV-3 has been recently made available, its genomic content remains poorly characterized and the molecular mechanisms of disease development not yet elucidated. In an attempt to facilitate genetic manipulation of EHV-3, we describe here the construction of a full-length infectious bacterial artificial chromosome (BAC) clone of EHV-3...
November 16, 2016: Virus Research
https://www.readbyqxmd.com/read/27857056/inter-isoform-hetero-dimerization-of-human-udp-glucuronosyltransferases-ugts-1a1-1a9-and-2b7-and-impacts-on-glucuronidation-activity
#15
Ling-Min Yuan, Zhang-Zhao Gao, Hong-Ying Sun, Sai-Nan Qian, Yong-Sheng Xiao, Lian-Li Sun, Su Zeng
Human UDP-glucuronosyltransferases (UGTs) play a pivotal role in phase II metabolism by catalyzing the glucuronidation of endobiotics and xenobiotics. The catalytic activities of UGTs are highly impacted by both genetic polymorphisms and oligomerization. The present study aimed to assess the inter-isoform hetero-dimerization of UGT1A1, 1A9, and 2B7, including the wild type (1A1*1, 1A9*1, and 2B7*1) and the naturally occurring (1A1*1b, 1A9*2/*3/*5, and 2B7*71S/*2/*5) variants. The related enzymes were double expressed in Bac-to-Bac systems...
November 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852112/emotional-intelligence-and-cognitive-abilities-associations-and-sex-differences
#16
Silvia Pardeller, Beatrice Frajo-Apor, Georg Kemmler, Alex Hofer
In order to expand on previous research, this cross-sectional study investigated the relationship between Emotional Intelligence (EI) and cognitive abilities in healthy adults with a special focus on potential sex differences. EI was assessed by means of the Mayer-Salovey-Caruso-Emotional-Intelligence Test (MSCEIT), whereas cognitive abilities were investigated using the Brief Assessment of Cognition in Schizophrenia (BACS), which measures key aspects of cognitive functioning, i.e. verbal memory, working memory, motor speed, verbal fluency, attention and processing speed, and reasoning and problem solving...
November 17, 2016: Psychology, Health & Medicine
https://www.readbyqxmd.com/read/27852011/a-new-chicken-genome-assembly-provides-insight-into-avian-genome-structure
#17
Wesley C Warren, LaDeana W Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D Pruitt, Francoise Thibaud-Nissen, Valerie Schneider, Tamer A Mansour, C Titus Brown, Aleksey Zimin, Rachel Hawken, Mitch Abrahamsen, Alexis B Pyrkosz, Mireille Morisson, Valerie Fillon, Alain Vignal, William Chow, Kerstin Howe, Janet E Fulton, Marcia M Miller, Peter Lovell, Claudio V Mello, Morgan Wirthlin, Andrew S Mason, Richard Kuo, David W Burt, Jerry B Dodgson, Hans H Cheng
The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3) built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized...
November 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27835824/alcohol-related-blackouts-across-55-weeks-of-college-effects-of-european-american-ethnicity-female-sex-and-low-level-of-response-to-alcohol
#18
Marc A Schuckit, Tom L Smith, Priscila Dib Goncalves, Robert Anthenelli
BACKGROUND: While high blood alcohol concentrations (BACs) are required for alcohol-related blackouts (ARBs), additional characteristics also contribute to the risk, including a person's ethnicity, sex, and phenotypes relating to heavier drinking. Few prospective studies of ARBs have evaluated how these additional characteristics interact. METHOD: Data regarding 398 European American (EA), Asian and Hispanic students were extracted from a 55-week prospective study of different approaches to decrease heavy drinking among college freshmen...
October 26, 2016: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/27834006/centromere-repositioning-explains-fundamental-number-variability-in-the-new-world-monkey-genus-saimiri
#19
Giorgia Chiatante, Oronzo Capozzi, Marta Svartman, Polina Perelman, Lucy Centrone, Svetlana S Romanenko, Takafumi Ishida, Mirela Valeri, Melody E Roelke-Parker, Roscoe Stanyon
Cytogenetics has historically played a key role in research on squirrel monkey (genus Saimiri) evolutionary biology. Squirrel monkeys have a diploid number of 2n = 44, but vary in fundamental number (FN). Apparently, differences in FN have phylogenetic implications and are correlated with geographic regions. A number of hypothetical mechanisms were proposed to explain difference in FN: translocations, heterochromatin, or, most commonly, pericentric inversions. Recently, an additional mechanism, centromere repositioning, was discovered, which can alter chromosome morphology and FN...
November 10, 2016: Chromosoma
https://www.readbyqxmd.com/read/27829352/short-tandem-repeats-segmental-duplications-gene-deletion-and-genomic-instability-in-a-rapidly-diversified-immune-gene-family
#20
Matan Oren, Megan A Barela Hudgell, Brian D'Allura, Jacob Agronin, Alexandra Gross, Daniele Podini, L Courtney Smith
BACKGROUND: Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence...
November 9, 2016: BMC Genomics
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