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https://www.readbyqxmd.com/read/28645209/genome-wide-mapping-of-in-vivo-er%C3%AE-binding-sites-in-male-mouse-efferent-ductules
#1
Guangxin Yao, Shuanggang Hu, Lu Yu, Yanfei Ru, Charlie Degui Chen, Qiang Liu, Yonglian Zhang
As an important nuclear hormone receptor, estrogen receptor alpha (ERα), which is encoded by Esr1 gene, regulates the expression of hundreds of genes in a stimulus-specific, temporal and tissue-specific fashion, mainly by binding to specific DNA sequences-estrogen response elements (EREs). As an important estrogen target tissue in males, the function of the efferent ductules relies on the presence of the ERα protein, but the underlying regulatory mechanisms are poorly illustrated. In this study, genome-wide ERα-binding sites in mouse efferent ductules were mapped by ChIP-seq...
June 22, 2017: Endocrinology
https://www.readbyqxmd.com/read/28645099/harnessing-the-natural-diversity-and-in-vitro-evolution-of-cas9-to-expand-the-genome-editing-toolbox
#2
REVIEW
Tautvydas Karvelis, Giedrius Gasiunas, Virginijus Siksnys
In the past few years, the Cas9 endonuclease from the type II CRISPR-Cas bacterial antiviral defense system has revolutionized the genome editing field. Guided by an RNA molecule, Cas9 can be reprogrammed to target almost any DNA sequence: the only limitation being the short nucleotide sequence in the vicinity of the target, termed the PAM, which is characteristic for each Cas9 protein. Streptococcus pyogenes Cas9 which recognizes the NGG PAM is currently most widely used for genome manipulation. However, Cas9 orthologues and engineered Cas9 variants offer expanded genome targeting capabilities, improved specificity and biochemical properties...
June 20, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28645073/analysis-of-ldlr-variants-from-homozygous-fh-patients-carrying-multiple-mutations-in-the-ldlr-gene
#3
Long Jiang, Asier Benito-Vicente, Ling Tang, Aitor Etxebarria, Wei Cui, Kepa B Uribe, Xiao-Dong Pan, Helena Ostolaza, Shi-Wei Yang, Yu-Jie Zhou, Cesar Martin, Lu-Ya Wang
BACKGROUND AND AIMS: Familial hypercholesterolemia (FH) is an autosomal dominant disease with widespread global prevalence that partially accounts for the high prevalence of premature coronary heart disease. Although the majority of research on FH has focused on single heterozygous LDLR mutations, there have been limited reports of double LDLR mutations on the same chromosome. The aim of this study was to gain insight into the clinical consequences of the presence of multiple mutations in the LDLR gene...
June 8, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28645043/in-vitro-and-in-vivo-behavior-of-dna-tetrahedrons-as-tumor-targeting-nanocarriers-for-doxorubicin-delivery
#4
Ji Hee Kang, Kyoung-Ran Kim, Hyukjin Lee, Dae-Ro Ahn, Young Tag Ko
Deoxyribonucleic acid (DNA) is a versatile material with high applicability and inherent biocompatibility. L-DNA, the perfect mirror form of the naturally occurring D-DNA, has been used in DNA nanotechnology. It has thermodynamically identical properties to D-DNA, is capable of self-assembly and bio-orthogonal base-pairing, and is resistant to nuclease activity. We previously constructed an L-DNA tetrahedron (L-Td) and found that this nanostructure has remarkably higher capacity for cell penetration than its natural counterpart (D-Td)...
June 16, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28644986/designing-novel-inhibitors-against-histone-acetyltransferase-hat-%C3%A2-gcn5-of-plasmodium-falciparum
#5
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar
During active proliferation phase of intra-erythrocytic cycle, the genome of P. falciparum is regulated epigenetically and evolutionary conserved parasite-specific histone proteins are extensively acetylated. The reversible process of lysine acetylation, causing transcriptional activation and its deacetylation, causing transcriptional repression is regulated by balanced activities of HATs and HDACs. They are also known to regulate antigenic variations and gametocytic conversion in P. falciparum. These histone modifying enzymes have been identified as potential targets for development of anitmalarials in literature...
June 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28644921/targeted-memory-reactivation-during-sleep-but-not-wake-enhances-sensorimotor-skill-performance-a-pilot-study
#6
Brian P Johnson, Steven M Scharf, Kelly P Westlake
The benefits of sleep on memory consolidation have been enhanced for declarative and motor sequence learning through replaying classically conditioned auditory stimuli during sleep, known as targeted memory reactivation (TMR). However, it is unknown if TMR can influence performance of a sensorimotor skill, in the absence of the cognitive requirements of sequence learning. Here, young adults performed a nondominant arm throwing task separated by a full night of sleep or a full day of wake, with half of all participants receiving TMR between sessions...
June 23, 2017: Journal of Motor Behavior
https://www.readbyqxmd.com/read/28644440/lncrna-sarcc-suppresses-renal-cell-carcinoma-rcc-progression-via-altering-the-androgen-receptor-ar-mirna-143-3p-signals
#7
Wei Zhai, Yin Sun, Changcheng Guo, Guanghui Hu, Mingchao Wang, Jiayi Zheng, WanYing Lin, Qingbo Huang, Gonghui Li, Junhua Zheng, Chawnshang Chang
While the androgen receptor (AR) might promote renal cell carcinoma (RCC) initiation and progression, the molecular mechanisms involved remain largely unclear. Here, we discovered the novel LncRNA-SARCC, which was suppressed and associated with better prognosis in RCC. Preclinical studies using multiple RCC cells and in vivo mouse model indicated that LncRNA-SARCC could attenuate RCC cell invasion, migration and proliferation in vitro and in vivo. Mechanistically, LncRNA-SARCC bound and destabilized AR protein with an inhibition of AR function, which led to transcriptionally de-repress miR-143-3p expression, thus inhibition of its downstream signals including AKT, MMP-13, K-RAS and P-ERK...
June 23, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#8
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644007/cyclotides-as-tools-in-chemical-biology
#9
Simon J de Veer, Joachim Weidmann, David J Craik
Among the various molecules that plants produce for defense against pests and pathogens, cyclotides stand out as exceptionally stable and structurally unique. These ribosomally synthesized peptides are around 30 amino acids in size, and are stabilized by a head-to-tail cyclic peptide backbone and three disulfide bonds that form a cystine knot. They occur in certain plants of the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, with an individual plant producing up to hundreds of different cyclotides...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28643897/a-novel-amino-acid-substitution-trp574arg-in-als-confers-broad-resistance-to-als-inhibiting-herbicides-in-crabgrass-digitaria-sanguinalis
#10
Jian Li, Mei Li, Xingxiang Gao, Feng Fang
BACKGROUND: Crabgrass (Digitaria sanguinalis) is an annual monocotyledonous weed. In recent years, field applications of nicosulfuron have been ineffective in controlling crabgrass populations in Shandong Province, China. To investigate the resistance mechanisms to nicosulfuron in crabgrass populations, the acetolactate synthase (ALS) gene fragment covering known resistance-confering mutation sites was amplified and sequenced. RESULTS: Dose-response experiments suggested that the resistant population SD13 (R) was highly resistant to nicosulfuron (resistance index R/S = 43...
June 23, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28643865/characterization-and-biological-function-of-milk-derived-mirnas
#11
Regina Golan-Gerstl, Yaffa Elbaum Shiff, Vardit Lavi-Moshayoff, Daniel Schecter Dena Leshkowitz, Shimon Reif
SCOPE: Breastfeeding is associated with reduced risk of infection, immune mediated disorders, obesity and even cancer. Recently it was found that breast milk contains a variety of microRNAs (miRNAs) in the skim and fat layer that can be transferred to infants, and appear to play important roles in those biological functions. METHODS AND RESULTS: This study applied Next Generation Sequencing and quantitative real time PCR analysis to determine the miRNA expression profile of the skim and fat fraction of human, goat, and bovine milk as well as infant formulas...
June 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28643680/-towards-precision-medicine-in-myeloma-new-evidence-and-challenges
#12
Verónica González-Calle, Rafael Fonseca
In the last few years, next-generation sequencing studies have provided insights into the mutational landscape of multiple myeloma. The identification of actionable mutations might give a precious opportunity for exploring new targeted therapies. Thus, the implementation of promising precision medicine strategies seems to be closer than ever. Throughout this review we describe the main challenges that should to be dealt with in this new era, in order to achieve the main goal of precision medicine, namely matching patients with their right drug...
2017: Medicina
https://www.readbyqxmd.com/read/28643364/development-of-clinical-paroxysmal-nocturnal-haemoglobinuria-in-children-with-aplastic-anaemia
#13
Atsushi Narita, Hideki Muramatsu, Yusuke Okuno, Yuko Sekiya, Kyogo Suzuki, Motoharu Hamada, Shinsuke Kataoka, Daisuke Ichikawa, Rieko Taniguchi, Norihiro Murakami, Daiei Kojima, Eri Nishikawa, Nozomu Kawashima, Nobuhiro Nishio, Asahito Hama, Yoshiyuki Takahashi, Seiji Kojima
The clinical significance of paroxysmal nocturnal haemoglobinuria (PNH) in children with aplastic anaemia (AA) remains unclear. We retrospectively studied 57 children with AA between 1992 and 2010. During the follow-up, five patients developed clinical PNH, in whom somatic PIGA mutations were detected by targeted sequencing. The 10-year probability of clinical PNH development was 10·2% (95% confidence interval, 3·6-20·7%). Furthermore, the detection of minor PNH clones by flow cytometry at AA diagnosis was a risk factor for the subsequent development of clinical PNH...
June 23, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28643259/genome-editing-of-medaka
#14
Satoshi Ansai, Masato Kinoshita
Medaka (Oryzias latipes), along with zebrafish (Danio rerio), is a useful experimental model fish. Here, we describe a simple method for generating medaka gene knock-out strains using an automated microchip electrophoresis system. We also describe a method for targeted gene knock-in using a plasmid carrying a sequence that does not cause off-target effects in medaka.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643254/gene-targeting-in-rabbits-single-step-generation-of-knock-out-rabbits-by-microinjection-of-crispr-cas9-plasmids
#15
Yoshihiro Kawano, Arata Honda
The development of genome editing technology has allowed gene disruptions to be achieved in various animal species and has been beneficial to many mammals. Gene disruption using pluripotent stem cells is difficult to achieve in rabbits, but thanks to advances in genome editing technology, a number of gene disruptions have been conducted. This paper describes a simple and easy method for carrying out gene disruptions in rabbits using CRISPR/Cas9 in which the gene to be disrupted is marked, the presence or absence of off-target candidates is checked, and a plasmid allowing simultaneous expression of Cas9 and sgRNA is constructed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643252/generation-of-knock-in-mouse-by-genome-editing
#16
Wataru Fujii
Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-stranded oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643248/computational-prediction-of-crispr-cas9-target-sites-reveals-potential-off-target-risks-in-human-and-mouse
#17
Qingbo Wang, Kumiko Ui-Tei
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system is a prominent genome engineering technology. In the CRISPR/Cas system, the RNA-guided endonuclease Cas protein introduces a DNA double-stranded break at the genome position recognized by a guide RNA (gRNA) based on complementary base-pairing of about 20-nucleotides in length. The 8- or 12-mer gRNA sequence in the proximal region is especially important for target recognition, and the genes with sequence complementarity to such regions are often disrupted...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643245/construction-and-evaluation-of-zinc-finger-nucleases
#18
Hiroshi Ochiai, Takashi Yamamoto
Zinc-finger nucleases (ZFNs) are programmable nucleases that have opened the door to the genome editing era. The construction of ZFNs recognizing a target sequence of interest is laborious, and has not been widely used recently. However, key ZFN patents are expiring over the next 2-4 years, enabling a wide range of deployments for clinical and industrial applications. This article introduces a ZFN construction protocol that uses bacterial one-hybrid (B1H) selection and single-stranded annealing (SSA) assay.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28642971/high-diversity-of-bacterial-communities-in-developmental-stages-of-bactrocera-carambolae-insecta-tephritidae-revealed-by-illumina-miseq-sequencing-of-16s-rrna-gene
#19
Hoi-Sen Yong, Sze-Looi Song, Kah-Ooi Chua, Phaik-Eem Lim
Bactrocera carambolae is a highly polyphagous fruit pest of agricultural importance. This study reports the bacterial communities associated with the developmental stages of B. carambolae. The microbiota of the developmental stages were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. At 97% similarity, there were 19 bacterial phyla and unassigned bacteria, comprising 39 classes, 86 orders, 159 families and 311 genera. The bacterial composition varied among the specimens of developmental stage and across developmental stages as well as exuviae...
June 23, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28642764/xylella-fastidiosa-host-range-and-advance-in-molecular-identification-techniques
#20
REVIEW
Paolo Baldi, Nicola La Porta
In the never ending struggle against plant pathogenic bacteria, a major goal is the early identification and classification of infecting microorganisms. Xylella fastidiosa, a Gram-negative bacterium belonging to the family Xanthmonadaceae, is no exception as this pathogen showed a broad range of vectors and host plants, many of which may carry the pathogen for a long time without showing any symptom. Till the last years, most of the diseases caused by X. fastidiosa have been reported from North and South America, but recently a widespread infection of olive quick decline syndrome caused by this fastidious pathogen appeared in Apulia (south-eastern Italy), and several cases of X...
2017: Frontiers in Plant Science
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