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https://www.readbyqxmd.com/read/28100080/the-commercialization-of-genome-editing-technologies
#1
Katelyn Brinegar, Ali K Yetisen, Sun Choi, Emily Vallillo, Guillermo U Ruiz-Esparza, Anand M Prabhakar, Ali Khademhosseini, Seok-Hyun Yun
The emergence of new gene-editing technologies is profoundly transforming human therapeutics, agriculture, and industrial biotechnology. Advances in clustered regularly interspaced short palindromic repeats (CRISPR) have created a fertile environment for mass-scale manufacturing of cost-effective products ranging from basic research to translational medicine. In our analyses, we evaluated the patent landscape of gene-editing technologies and found that in comparison to earlier gene-editing techniques, CRISPR has gained significant traction and this has established dominance...
January 18, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28098961/angiogenic-and-osteogenic-regeneration-in-rats-via-calcium-phosphate-scaffold-and-endothelial-cell-coculture-with-hbmscs-hucmscs-hipsc-mscs-and-hesc-mscs
#2
Wenchuan Chen, Xian Liu, Qianmin Chen, Chongyun Bao, Liang Zhao, Zhimin Zhu, Hockin H K Xu
Angiogenesis is a limiting factor in regenerating large bone defects. The objective of this study was to investigate angiogenic and osteogenic effects of coculture on calcium phosphate cement (CPC) scaffold using human umbilical vein endothelial cells (hUVECs) and mesenchymal stem cells (MSCs) from different origins for the first time. hUVECs were cocultured with four types of cells: human umbilical cord MSCs (hUCMSCs), human bone marrow MSCs (hBMSCs), and MSCs from induced pluripotent stem cells (hiPSC-MSCs) and embryonic stem cells (hESC-MSCs)...
January 18, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28098174/novel-g9-rotavirus-strains-co-circulate-in-children-and-pigs-taiwan
#3
Fang-Tzy Wu, Krisztián Bányai, Baoming Jiang, Luke Tzu-Chi Liu, Szilvia Marton, Yhu-Chering Huang, Li-Min Huang, Ming-Hui Liao, Chao A Hsiung
Molecular epidemiologic studies collecting information of the spatiotemporal distribution of rotavirus VP7 (G) and VP4 (P) genotypes have shown evidence for the increasing global importance of genotype G9 rotaviruses in humans and pigs. Sequence comparison of the VP7 gene of G9 strains identified different lineages to prevail in the respective host species although some of these lineages appear to be shared among heterologous hosts providing evidence of interspecies transmission events. The majority of these events indicates the pig-to-human spillover, although a reverse route of transmission cannot be excluded either...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28095777/random-x-chromosome-inactivation-dynamics-in-vivo-by-single-cell-rna-sequencing
#4
Menghan Wang, Fangqin Lin, Ke Xing, Li Liu
BACKGROUND: Random X-chromosome inactivation (rXCI) is important for the maintenance of normal somatic cell functions in female eutherian mammals. The dynamics of X-chromosome inactivation initiation has been widely studied by assessing embryonic stem cell differentiation in vitro. To investigate the phenomenon in vivo, we applied RNA sequencing to single cells from female embryos obtained from a natural intercrossing of two genetically distant mouse strains. Instead of artificially assigning the parental origin of the inactive X chromosome, the inactive X chromosomes in this study were randomly selected from the natural developmental periods and thus included both paternal and maternal origins...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28095401/the-nuclear-receptor-hizr-1-uses-zinc-as-a-ligand-to-mediate-homeostasis-in-response-to-high-zinc
#5
Kurt Warnhoff, Hyun C Roh, Zuzana Kocsisova, Chieh-Hsiang Tan, Andrew Morrison, Damari Croswell, Daniel L Schneider, Kerry Kornfeld
Nuclear receptors were originally defined as endocrine sensors in humans, leading to the identification of the nuclear receptor superfamily. Despite intensive efforts, most nuclear receptors have no known ligand, suggesting new ligand classes remain to be discovered. Furthermore, nuclear receptors are encoded in the genomes of primitive organisms that lack endocrine signaling, suggesting the primordial function may have been environmental sensing. Here we describe a novel Caenorhabditis elegans nuclear receptor, HIZR-1, that is a high zinc sensor in an animal and the master regulator of high zinc homeostasis...
January 2017: PLoS Biology
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#6
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28092027/classification-and-lineage-tracing-of-sh2-domains-throughout-eukaryotes
#7
Bernard A Liu
Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091750/ectomycorrhizal-fungal-diversity-associated-with-endemic-tristaniopsis-spp-myrtaceae-in-ultramafic-and-volcano-sedimentary-soils-in-new-caledonia
#8
Muhammad Waseem, Marc Ducousso, Yves Prin, Odile Domergue, Laure Hannibal, Clarisse Majorel, Philippe Jourand, Antoine Galiana
New Caledonian serpentine (ultramafic) soils contain high levels of toxic heavy metals, in particular nickel, (up to 20 g kg(-1)) and are deficient in essential elements like carbon, nitrogen and phosphorus while having a high magnesium/calcium ratio. Although previous studies showed that ectomycorrhizal symbioses could play an important role in the adaptation of the endemic plants to ultramafic soils (FEMS Microbiol Ecol 72:238-49, 2010), none of them have compared the diversity of microbial communities from ultramafic vs non-ultramafic soils in New Caledonia...
January 13, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28088165/genomic-characterization-of-ensifer-aridi-a-proposed-new-species-of-nitrogen-fixing-rhizobium-recovered-from-asian-african-and-american-deserts
#9
Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf, Jose-Antonio Munive
BACKGROUND: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. RESULTS: Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087881/role-of-stim2-in-cell-function-and-physiopathology
#10
Alejandro Berna-Erro, Isaac Jardin, Gines M Salido, Juan A Rosado
An endoplasmic reticulum (ER)-resident protein that regulates cytosolic and ER free-Ca(2+) concentration by induction of store-operated calcium entry. That is the original definition of STIM2 and its function. While its activity strongly depends on the amount of calcium stored in the ER, its function goes further to intracellular signalling and gene expression. Initially undercovered by the prominent function of STIM1, STIM2 became to be vital in mice, gradually emerging as an important player in the nervous system, and cooperating with STIM1 in the immune system...
January 14, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28087778/no-evidence-for-phylostratigraphic-bias-impacting-inferences-on-patterns-of-gene-emergence-and-evolution
#11
Tomislav Domazet-Lošo, Anne-Ruxandra Carvunis, M Mar Albà, Martin Sebastijan Šestak, Robert Bakarić, Rafik Neme, Diethard Tautz
Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087696/genetic-and-biochemical-characterization-of-a-gene-operon-for-trans-aconitic-acid-a-novel-nematicide-from-bacillus-thuringiensis
#12
Cuiying Du, Shiyun Cao, Xiangyu Shi, Xiangtao Nie, Jinshui Zheng, Yun Deng, Lifang Ruan, Donghai Peng, Ming Sun
Trans-aconitic acid (TAA) is an isomer of cis-aconitic acid (CAA), an intermediate of the tricarboxylic acid (TCA) cycle that is synthesized by aconitase. Although TAA production has been detected in bacteria and plants for many years and is known to be a potent inhibitor of aconitase, its biosynthetic origins and the physiological relevance of its activity have remained unclear. We have serendipitously uncovered key information relevant to both of these questions. Specifically, in a search for novel nematicidal factors from Bacillus thuringiensis, a significant nematode pathogen harboring many protein virulence factors, we discovered a high-yielding component that showed activity against the plant-parasitic nematode Meloidogyne incognita and surprisingly identified it as TAA...
January 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28081303/the-novel-fusion-transcript-nr5a2-klhl29ft-is-generated-by-an-insertion-at-the-klhl29-locus
#13
Zhenguo Sun, Xiquan Ke, Steven L Salzberg, Daehwan Kim, Valentin Antonescu, Yulan Cheng, Binbin Huang, Jee Hoon Song, John M Abraham, Sariat Ibrahim, Hui Tian, Stephen J Meltzer
BACKGROUND: Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers. METHODS: RNA sequencing (RNA-Seq) and TopHat-Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement...
January 12, 2017: Cancer
https://www.readbyqxmd.com/read/28077090/gbs-based-single-dosage-markers-for-linkage-and-qtl-mapping-allow-gene-mining-for-yield-related-traits-in-sugarcane
#14
Thiago Willian Almeida Balsalobre, Guilherme da Silva Pereira, Gabriel Rodrigues Alves Margarido, Rodrigo Gazaffi, Fernanda Zatti Barreto, Carina Oliveira Anoni, Cláudio Benício Cardoso-Silva, Estela Araújo Costa, Melina Cristina Mancini, Hermann Paulo Hoffmann, Anete Pereira de Souza, Antonio Augusto Franco Garcia, Monalisa Sampaio Carneiro
BACKGROUND: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28072976/-establishment-and-validation-of-human-cancer-cell-lines-with-stable-cas9-expression
#15
X C Bian, Z L Yang, H L Feng, X M Zhao, B Gu, J Li, H Sun, Y Q Liu
Objective: To establish human cancer cell strains with stable Cas9 expression, and to validate the gene editing activity of Cas9 for simple gene editing in future study. Methods: Fifteen cancer cell lines of different tissue origins were infected with pLv-EF1α-Cas9-Flag-Neo or pLv-EF1α-Cas9-Flag-Puro by lentivirus and clone selection was employed to screen Cas9 stably expressed cancer cell lines. Afterward designed guide RNA vectors targeting TSC22 gene were transiently transfected into 3 of cell lines, and subsequently the gene editing activity of Cas9 was evaluated by genomic PCR, sequencing and Western blot...
January 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/28072419/an-acid-tolerant-ammonia-oxidizing-%C3%AE-proteobacterium-from-soil
#16
Masahito Hayatsu, Kanako Tago, Ikuo Uchiyama, Atsushi Toyoda, Yong Wang, Yumi Shimomura, Takashi Okubo, Futoshi Kurisu, Yuhei Hirono, Kunihiko Nonaka, Hiroko Akiyama, Takehiko Itoh, Hideto Takami
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28071684/genome-wide-identification-of-novel-ovarian-predominant-mirnas-new-insights-from-the-medaka-oryzias-latipes
#17
Amine Bouchareb, Aurélie Le Cam, Jérôme Montfort, Stéphanie Gay, Thaovi Nguyen, Julien Bobe, Violette Thermes
MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068523/rs12941170-at-sox9-gene-associated-with-orofacial-clefts-in-chinese
#18
Zhong-Lin Jia, Sha He, Shu-Yuan Jiang, Bi-He Zhang, Shi-Jun Duan, Jia-Yu Shi, Ning Huang, Wen-Chao Zhu, Bing Shi
OBJECTIVE: Non-syndromic orofacial cleftings (NSOCs) are considered as complex trait, which results from genetic and/or environmental modifiers. Current findings could only explain small portion of the NSOCs. SOX9 gene plays an important role during craniofacial development in animal models and the Pierre Robin sequence (PRS). However, its role in non-syndromic clefts remains unknown. DESIGN: In this study, we selected eight SNPs in and around SOX9 gene to make maximum coverage, and genotyped them by using RFLP-PCR and ligase detection reaction (LDR) methods to test its associations among 151 NSOCs (53 NSCLP, 52 NSCLO and 46 NSCPO) from Western Han Chinese population...
December 30, 2016: Archives of Oral Biology
https://www.readbyqxmd.com/read/28063933/dna-methylation-and-clinical-response-to-antidepressant-medication-in-major-depressive-disorder-a-review-and-recommendations
#19
REVIEW
A J Lisoway, C C Zai, A K Tiwari, J L Kennedy
Antidepressant medications are the most common treatment for major depression and related disorders. Pharmacogenetic studies have demonstrated that response to these medications is associated with genetic variation. While these studies have been invaluable they have yet to explain why a significant number of patients do not respond to their initial medication. The epigenetic modification known as DNA methylation has recently been studied in the context of antidepressant treatment response. As such, the purpose of this article is to review the advances made in the relatively new field of pharmaco-epigenetics of antidepressant response...
January 4, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28063346/integrating-genomic-resources-of-flatfish-pleuronectiformes-to-boost-aquaculture-production
#20
Diego Robledo, Miguel Hermida, Juan A Rubiolo, Carlos Fernández, Andrés Blanco, Carmen Bouza, Paulino Martínez
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes...
December 24, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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