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https://www.readbyqxmd.com/read/28635966/testing-models-of-refugial-isolation-colonization-and-population-connectivity-in-two-species-of-montane-salamanders
#1
S M Rovito, S D Schoville
Pleistocene glaciations have profoundly affected patterns of genetic diversity within many species. Temperate alpine organisms likely experienced dramatic range shifts, given that much of their habitat was glaciated during this time. While the effects of glaciations are relatively well understood, the spatial locations of refugia and processes that gave rise to current patterns of diversity are less well known. We use a microsatellite data set to test hypotheses of population connectivity and refugial isolation in the web-toed salamanders (Hydromantes) of the Sierra Nevada...
June 21, 2017: Heredity
https://www.readbyqxmd.com/read/28635682/relationship-between-human-mutl-homolog-1-hmlh1-hypermethylation-and-colorectal-cancer-a-meta-analysis
#2
Hui-Feng Zhang, You-Wang Lu, Zhen-Rong Xie, Kun-Hua Wang
BACKGROUND Hypermethylation of CpG islands in gene promoter regions is an important mechanism of gene inactivation in cancers. Promoter hypermethylation of human mutL homolog 1 (hMLH1) has been implicated in a subset of colorectal cancers that show microsatellite instability (MSI), while the connection of the epigenetic inactivation of hMLH1 in colorectal cancers remains unknown. The aim of this study was to evaluate the relationship between the promoter hypermethylation of hMLH1 and colorectal cancers by performing a meta-analysis...
June 21, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28635639/immune-checkpoints-as-a-target-for-colorectal-cancer-treatment
#3
REVIEW
Alessandro Passardi, Matteo Canale, Martina Valgiusti, Paola Ulivi
Anti-tumor immunity is a new line of research for the treatment of patients with solid tumors. In this field, negative regulators of the immune system called immune checkpoints play a key role in limiting antitumor immunologic responses. For this reason, immune checkpoint-inhibiting agents, such as those directed against cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed death-1 receptor (PD1) and its ligand PD-L1, have been developed as antitumor drugs, producing interesting results in preclinical and clinical studies...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28634825/a-rapid-and-cost-effective-approach-for-the-development-of-polymorphic-microsatellites-in-non-model-species-using-paired-end-rad-sequencing
#4
Dong-Xiu Xue, Yu-Long Li, Jin-Xian Liu
As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28633358/phylogeography-of-herbarium-specimens-of-asexually-propagated-paper-mulberry-broussonetia-papyrifera-l-l-h%C3%A3-r-ex-vent-moraceae-reveals-genetic-diversity-across-the-pacific
#5
Claudia Payacan, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, Andrea Seelenfreund
Background and Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28632152/isolation-and-characterization-of-microsatellite-loci-for-cotesia-plutellae-hymenoptera-braconidae
#6
Tiansheng Liu, Fushi Ke, Shijun You, Wenbin Chen, Weiyi He, Minsheng You
Fourteen polymorphic microsatellite loci were isolated in this transcriptome-based data analysis for Cotesia plutellae, which is an important larval parasitoid of the worldwide pest Plutella xylostella. A subsequent test was performed for a wild C. plutellae population (N = 32) from Fuzhou, Fujian, southeastern China, to verify the effectiveness of the 14 microsatellite loci in future studies on C. plutellae genetic diversity. The observed number of alleles ranged from two to six. The expected and observed heterozygosity ranged from 0...
June 20, 2017: Insects
https://www.readbyqxmd.com/read/28631344/evaluation-of-the-genetic-structure-of-sika-deer-cervus-nippon-in-japan-s-kanto-and-tanzawa-mountain-areas-based-on-microsatellite-markers
#7
Sayaka Konishi, Shoko Hata, Sayumi Matsuda, Kazushi Arai, Yasushi Mizoguchi
The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II)...
June 19, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28630801/characterization-of-the-transcriptome-and-est-ssr-development-in-boea-clarkeana-a-desiccation-tolerant-plant-endemic-to-china
#8
Ying Wang, Kun Liu, De Bi, Shoubiao Zhou, Jianwen Shao
BACKGROUND: Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown...
2017: PeerJ
https://www.readbyqxmd.com/read/28628639/small-molecule-inhibitors-uncover-synthetic-genetic-interactions-of-human-flap-endonuclease-1-fen1-with-dna-damage-response-genes
#9
Thomas A Ward, Peter J McHugh, Stephen T Durant
Flap endonuclease 1 (FEN1) is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI) as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response...
2017: PloS One
https://www.readbyqxmd.com/read/28627509/corrigendum-developing-informative-microsatellite-markers-for-non-model-species-using-reference-mapping-against-a-model-species-genome
#10
Chih-Ming Hung, Ai-Yun Yu, Yu-Ting Lai, Pei-Jen L Shaner
This corrects the article DOI: 10.1038/srep23087.
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28626615/getting-off-to-a-good-start-genetic-evaluation-of-the-ex-situ-conservation-project-of-the-critically-endangered-montseny-brook-newt-calotriton-arnoldi
#11
Emilio Valbuena-Ureña, Anna Soler-Membrives, Sebastian Steinfartz, Mònica Alonso, Francesc Carbonell, Raquel Larios-Martín, Elena Obon, Salvador Carranza
Ex situ management strategies play an important role in the conservation of threatened species when the wild survival of the species cannot be ensured. Molecular markers have become an outstanding tool for the evaluation and management of captive breeding programs. Two main genetic objectives should be prioritized when planning breeding programs: the maintenance of maximum neutral genetic diversity, and to obtain "self-sustaining" captive populations. In this study, we use 24 microsatellite loci to analyze and evaluate the genetic representativity of the initial phases of the captive breeding program of the Montseny brook newt, Calotriton arnoldi, an Iberian endemic listed as Critically Endangered...
2017: PeerJ
https://www.readbyqxmd.com/read/28626278/natural-stranding-of-atlantic-sturgeon-acipenser-oxyrinchus-mitchill-1815-in-scot-s-bay-bay-of-fundy-nova-scotia-from-populations-of-concern-in-the-united-states-and-canada
#12
N D Stewart, Y Cormier, L M Logan-Chesney, G Gibson, I Wirgin, M J Dadswell, M J W Stokesbury
Natural mortality of Atlantic sturgeon (Acipenser oxyrinchus) has been determined to be low (M = 0.07). Reported herein is the mortality by beach stranding of 11 Atlantic sturgeon in Scot's Bay, part of the inner Bay of Fundy in Nova Scotia, Canada on 22 June 2014. Genetic analyses, histological analysis and age determination were performed to determine origin, maturity stage and age of the stranded Atlantic sturgeon. Microsatellite and mitochondrial DNA analyses indicated that four of the Atlantic sturgeon (2 males and 2 females) were from the Saint John River, NB population, which was designated as threatened by the Committee on the Status of Endangered Wildlife in Canada...
June 2017: Zeitschrift Für Angewandte Ichthyologie, Journal of Applied Ichthyology
https://www.readbyqxmd.com/read/28624625/a-formalin-fixed-paraffin-embedded-ffpe-based-prognostic-signature-to-predict-metastasis-in-clinically-low-risk-stage-i-ii-microsatellite-stable-colorectal-cancer
#13
Yee Syuen Low, Christopher Blöcker, John R McPherson, See Aik Tang, Ying Ying Cheng, Joyner Y S Wong, Clarinda Chua, Tony K H Lim, Choong Leong Tang, Min Hoe Chew, Patrick Tan, Iain B Tan, Steven G Rozen, Peh Yean Cheah
Approximately 20% early-stage (I/II) colorectal cancer (CRC) patients develop metastases despite curative surgery. We aim to develop a formalin-fixed and paraffin-embedded (FFPE)-based predictor of metastases in early-stage, clinically-defined low risk, microsatellite-stable (MSS) CRC patients. We considered genome-wide mRNA and miRNA expression and mutation status of 20 genes assayed in 150 fresh-frozen tumours with known metastasis status. We selected 193 genes for further analysis using NanoString nCounter arrays on corresponding FFPE tumours...
June 15, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28623901/biomarker-correlation-network-in-colorectal-carcinoma-by-tumor-anatomic-location
#14
Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A Nowak, Zhi Rong Qian, Peter Kraft, Edward L Giovannucci, Charles S Fuchs, Andrew T Chan, John Quackenbush, Shuji Ogino, Jukka-Pekka Onnela
BACKGROUND: Colorectal carcinoma evolves through a multitude of molecular events including somatic mutations, epigenetic alterations, and aberrant protein expression, influenced by host immune reactions. One way to interrogate the complex carcinogenic process and interactions between aberrant events is to model a biomarker correlation network. Such a network analysis integrates multidimensional tumor biomarker data to identify key molecular events and pathways that are central to an underlying biological process...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28623239/-ccug-n-rna-toxicity-in-a-drosophila-model-for-myotonic-dystrophy-type-2-dm2-activates-apoptosis
#15
Vildan Betul Yenigun, Mario Sirito, Alla Amcheslavky, Tomek Czernuszewicz, Jordi Colonques-Bellmunt, Irma García-Alcover, Marzena Wojciechowska, Clare Bolduc, Zhihong Chen, Arturo López Castel, Ralf Krahe, Andreas Bergmann
The myotonic dystrophies are prototypic toxic RNA gain-of-function diseases. Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are caused by different unstable, noncoding microsatellite repeat expansions -- (CTG)DM1 in DMPK and (CCTG)DM2 in CNBP Although transcription of mutant repeats into (CUG)DM1 or (CCUG)DM2 appears to be necessary and sufficient to cause disease, their pathomechanisms remain incompletely understood. To study the mechanisms of (CCUG)DM2 toxicity and develop a convenient model for drug screening, we generated a transgenic DM2 model in the fruit fly Drosophila melanogaster with (CCUG)n repeats of variable length (n=16 and 106)...
June 16, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28621832/break-induced-replication-links-microsatellite-expansion-to-complex-genome-rearrangements
#16
REVIEW
Michael Leffak
The instability of microsatellite DNA repeats is responsible for at least 40 neurodegenerative diseases. Recently, Mirkin and co-workers presented a novel mechanism for microsatellite expansions based on break-induced replication (BIR) at sites of microsatellite-induced replication stalling and fork collapse. The BIR model aims to explain single-step, large expansions of CAG/CTG trinucleotide repeats in dividing cells. BIR has been characterized extensively in Saccharomyces cerevisiae as a mechanism to repair broken DNA replication forks (single-ended DSBs) and degraded telomeric DNA...
June 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28621686/pseudoprogression-in-microsatellite-instability-high-colorectal-cancer-during-treatment-with-combination-t-cell-mediated-immunotherapy-a-case-report-and-literature-review
#17
Young Kwang Chae, Si Wang, Halla Nimeiri, Aparna Kalyan, Francis J Giles
Evading tumor-mediated immunosuppression through antibodies to immune checkpoints has shown clinical benefit in patients with select solid tumors. There is a heterogeneity of responses in patients receiving immunotherapy, including pseudoprogression in which the tumor burden increases initially before decreasing to reach disease control. The characteristics and basis of pseudoprogression, however, remains poorly understood. We hereby report a case of microsatellite instability (MSI)-high metastatic colorectal cancer treated with combination of OX40 agonist and programmed death ligand-1 (PD-L1) antagonist that demonstrated pseudoprogression reaching 163% increase from baseline tumor burden...
June 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28620746/uniparental-disomy-as-an-unexpected-cause-of-meckel-gruber-syndrome-report-of-a-case
#18
Nadia Ortiz Bruechle, Peter Steuernagel, Klaus Zerres, Ingo Kurth, Thomas Eggermann, Cordula Knopp
BACKGROUND: Meckel-Gruber syndrome (MKS, OMIM #607361) is a rare pre- or perinatal lethal autosomal recessive ciliopathy caused by mutations in at least 12 known genes. It has a clinical and genetic overlap with other viable ciliopathies, especially Joubert syndrome and Joubert syndrome-related disorders. MKS is characterized by multicystic kidney dysplasia, central nervous system malformations (usually occipital encephalocele), ductal plate malformation of the liver, and postaxial polydactyly...
June 15, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28620721/a-novel-gain-of-function-mutation-in-the-itpr1-suppressor-domain-causes-spinocerebellar-ataxia-with-altered-ca-2-signal-patterns
#19
Jillian P Casey, Taisei Hirouchi, Chihiro Hisatsune, Bryan Lynch, Raymond Murphy, Aimee M Dunne, Akitoshi Miyamoto, Sean Ennis, Nick van der Spek, Bronagh O'Hici, Katsuhiko Mikoshiba, Sally Ann Lynch
We report three affected members, a mother and her two children, of a non-consanguineous Irish family who presented with a suspected autosomal dominant spinocerebellar ataxia characterized by early motor delay, poor coordination, gait ataxia, and dysarthria. Whole exome sequencing identified a novel missense variant (c.106C>T; p.[Arg36Cys]) in the suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor gene (ITPR1) as the cause of the disorder, resulting in a molecular diagnosis of spinocerebellar ataxia type 29...
June 15, 2017: Journal of Neurology
https://www.readbyqxmd.com/read/28619747/successful-immune-checkpoint-blockade-in-a-patient-with-advanced-stage-microsatellite-unstable-biliary-tract-cancer
#20
Elena Czink, Matthias Kloor, Benjamin Goeppert, Stefan Froehling, Sebastian Uhrig, Tim F Weber, Joern Meinel, Christian Sutter, Karl Heinz Weiss, Peter Schirmacher, Magnus von Knebel Doeberitz, Dirk Jaeger, Christoph Springfeld
Cancers acquire multiple somatic mutations that can lead to the generation of immunogenic mutation-induced neoantigens. These neoantigens can be recognized by the host's immune system. However, continuous stimulation of immune cells against tumor antigens can lead to immune cell exhaustion, which allows uncontrolled outgrowth of tumor cells. Recently, immune checkpoint inhibitors have emerged as a novel approach to overcome immune cell exhaustion and re-activate anti-tumor immune responses. In particular, antibodies blocking the exhaustion-mediating programmed death receptor (PD-1)/PD-L1 pathway have shown clinical efficacy...
June 15, 2017: Cold Spring Harbor Molecular Case Studies
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