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https://www.readbyqxmd.com/read/28645177/mobile-genetic-elements-in-neisseria-gonorrhoeae-movement-for-change
#1
Ana Cehovin, Steven B Lewis
Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoeae, possesses several mobile genetic elements (MGEs). The MGEs such as transposable elements mediate intra-chromosomal rearrangements, while plasmids and the gonococcal genetic island are involved in inter-chromosomal gene transfer. Additionally, gonococcal MGEs serve as hotspots for recombination and integration of other genetic elements such as bacteriophages, contribute to gene regulation or spread genes through gonococcal populations by horizontal gene transfer...
June 22, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28645168/genomic-reconstruction-of-the-history-of-native-sheep-reveals-the-peopling-patterns-of-nomads-and-the-expansion-of-early-pastoralism-in-east-asia
#2
Yong-Xin Zhao, Ji Yang, Feng-Hua Lv, Xiao-Ju Hu, Xing-Long Xie, Min Zhang, Wen-Rong Li, Ming-Jun Liu, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Yan-Ling Ren, Feng Wang, EEr Hehua, Juha Kantanen, Johannes Arjen Lenstra, Jian-Lin Han, Meng-Hua Li
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in more than 1,000 modern samples. Population genomic analyses combined with archaeological records and historical ethnic demographics data revealed genetic signatures of their origins, secondary expansions and admixtures, thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645141/does-the-seed-bank-contribute-to-the-build-up-of-a-genetic-extinction-debt-in-the-grassland-perennial-campanula-rotundifolia
#3
Jan Plue, Katrien Vandepitte, Olivier Honnay, Sara A O Cousins
Background and Aims: Habitat fragmentation threatens global biodiversity. Many plant species persist in habitat fragments via persistent life cycle stages such as seed banks, generating a species extinction debt. Here, seed banks are hypothesized to cause a temporal delay in the expected loss of genetic variation, which can be referred to as a genetic extinction debt, as a possible mechanism behind species extinction debts. Methods: Fragmented grassland populations of Campanula rotundifolia were examined for evidence of a genetic extinction debt, investigating if the seed bank contributed to the extinction debt build-up...
June 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28645082/local-populations-and-inaccuracies-determining-the-relevant-mitochondrial-haplotype-distributions-for-north-west-european-cats
#4
Monique Wesselink, Stijn Desmyter, Irene Kuiper
Typing of different portions of the feline mitochondrial control region has illustrated pronounced differences in haplotype distributions between cats from the Netherlands and other parts of the world. To gain a better understanding of the haplotype distribution of North West Continental Europe, 605bp of mitochondrial DNA was typed from randomly selected cats from the Netherlands (N=146), Belgium (N=64) and South West Germany (N=128). The genetic differences between these randomly sampled European populations correlate to the geographical distances, with the Dutch and the South West German populations furthest apart and the Belgian population as an intermediate (Fst values 0...
June 4, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28644894/northward-dispersal-of-sea-kraits-laticauda-semifasciata-beyond-their-typical-range
#5
Jaejin Park, Il-Hun Kim, Jonathan J Fong, Kyo-Soung Koo, Woo-Jin Choi, Tein-Shun Tsai, Daesik Park
Marine reptiles are declining globally, and recent climate change may be a contributing factor. The study of sea snakes collected beyond their typical distribution range provides valuable insight on how climate change affects marine reptile populations. Recently, we collected 12 Laticauda semifasciata (11 females, 1 male) from the waters around southern South Korea-an area located outside its typical distribution range (Japan, China including Taiwan, Philippines and Indonesia). We investigated the genetic origin of Korean specimens by analyzing mitochondrial cytochrome b gene (Cytb) sequences...
2017: PloS One
https://www.readbyqxmd.com/read/28644860/time-dependent-genetic-analysis-links-field-and-controlled-environment-phenotypes-in-the-model-c4-grass-setaria
#6
Max J Feldman, Rachel E Paul, Darshi Banan, Jennifer F Barrett, Jose Sebastian, Muh-Ching Yee, Hui Jiang, Alexander E Lipka, Thomas P Brutnell, José R Dinneny, Andrew D B Leakey, Ivan Baxter
Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments...
June 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28644839/genomic-introgression-mapping-of-field-derived-multiple-anthelmintic-resistance-in-teladorsagia-circumcincta
#7
Young-Jun Choi, Stewart A Bisset, Stephen R Doyle, Kymberlie Hallsworth-Pepin, John Martin, Warwick N Grant, Makedonka Mitreva
Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance...
June 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28644772/risk-stratification-for-second-primary-lung-cancer
#8
Summer S Han, Gabriel A Rivera, Martin C Tammemägi, Sylvia K Plevritis, Scarlett L Gomez, Iona Cheng, Heather A Wakelee
Purpose This study estimated the 10-year risk of developing second primary lung cancer (SPLC) among survivors of initial primary lung cancer (IPLC) and evaluated the clinical utility of the risk prediction model for selecting eligibility criteria for screening. Methods SEER data were used to identify a population-based cohort of 20,032 participants diagnosed with IPLC between 1988 and 2003 and who survived ≥ 5 years after the initial diagnosis. We used a proportional subdistribution hazards model to estimate the 10-year risk of developing SPLC among survivors of lung cancer LC in the presence of competing risks...
June 23, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28644570/clinical-and-genetic-analysis-of-patients-with-cherubism
#9
R A Machado, H A R Pontes, F R Pires, H M Silveira, A Bufalino, R Carlos, F M Tuji, D B M Alves, A R Santos-Silva, M A Lopes, H M Capistrano, R D Coletta, F P Fonseca
OBJECTIVE: To describe the clinical and genetic features of patients with cherubism. MATERIAL AND METHODS: A descriptive analysis of 14 cases from 9 different families was carried out. Clinicopathological, imaging and follow-up data were retrieved from patients' medical files and correlated with the genetic profile of each patient. Genomic DNA isolated from buccal mucosa cells was subjected to direct sequencing analysis of the SH3BP2 gene. RESULTS: Females were more affected than males (8:6), and the mean age at diagnosis was 8...
June 23, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28644542/the-conservation-significance-of-natural-hybridisation-in-mediterranean-plants-from-a-case-study-on-cyclamen-primulaceae-to-a-general-perspective
#10
John D Thompson, Perrine Gauthier, Guillaume Papuga, Virginie Pons, Max Debussche, Emmanuele Farris
Hybridisation plays a prominent role in plant evolution due to its influence on genetic diversity, fitness and adaptive potential We identify a case of on-going hybrid evolution of floral phenotypes in disjunct populations of Cyclamen balearicum and C. repandum subsp. repandum on Corsica and Sardinia. Hybrid populations on the two islands contain similar patterns of variation in flower colour and size but are probably at different stages in the evolutionary process of hybridisation and differences in the frequency of floral types and flower size suggest hybrid vigour that may contribute to the dynamics and maintenance of hybrid forms...
June 23, 2017: Plant Biology
https://www.readbyqxmd.com/read/28644154/acute-promyelocytic-leukemia-and-chronic-lymphocytic-leukemia-concomitant-presentation-of-two-molecularly-distinct-entities
#11
Jingdong Su, Diana Veillon, Rodney Shackelford, James Cotelingam, Hazem El-Osta, Glenn Mills, Reinhold Munker, Srinivas Devarakonda
Acute myeloid leukemia (AML) developing in patients with chronic lymphocytic leukemia (CLL) is very uncommon and usually associated with prior treatment. Acute promyelocytic leukemia (APL) accounts for a very small proportion of treatment-associated AML. So far, there has been only one reported case of APL occurring post radiation for prostate cancer in a patient with CLL. We report herein the first case of APL and CLL presenting concomitantly in an untreated patient. Evaluation of peripheral blood and bone marrow aspirate with immunohistochemistry, flow cytometry, and FISH to confirm two morphologically, molecularly and genetically distinct leukemic populations characteristic of APL and CLL is required...
May 2017: Journal of the Louisiana State Medical Society: Official Organ of the Louisiana State Medical Society
https://www.readbyqxmd.com/read/28644142/acyp2-polymorphisms-are-associated-with-the-risk-of-liver-cancer-in-a-han-chinese-population
#12
Zhong Chen, Yu Sun, Zhenxiong Xu, Junnv Xu, Jingjie Li, Mengdan Yan, Jing Li, Tianbo Jin, Haifeng Lin
We explored the association between single nucleotide polymorphisms (SNPs) in ACYP2 and liver cancer risk. Thirteen SNPs were genotyped in 473 cases and 564 controls. Genetic model, linkage disequilibrium, and haplotype analyses were performed to evaluate the association between ACPY2 SNPs and liver cancer risk. We found that rs6713088 (G allele: odds ratio [OR] = 1.27, 95% confidence interval [CI]: 1.07-1.52, P = 0.007; GG vs. CC: OR = 1.49, 95% CI: 1.02-2.1, P = 0.038), rs843711 (T allele: OR = 1.29, 95% CI: 1...
June 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644125/exploiting-crispr-cas-to-manipulate-enterococcus-faecalis-populations
#13
Karthik Hullahalli, Marinelle Rodrigues, Kelli L Palmer
CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. It was of interest to investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes E. faecalis populations. Here, we demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28643794/enrichment-of-low-frequency-functional-variants-revealed-by-whole-genome-sequencing-of-multiple-isolated-european-populations
#14
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643793/genomic-rearrangements-in-sporadic-lymphangioleiomyomatosis-an-evolving-genetic-story
#15
Stephen J Murphy, Simone B Terra, Faye R Harris, Aqsa Nasir, Jesse S Voss, James B Smadbeck, Sarah H Johnson, Vishnu Serla, Jay H Ryu, Eunhee S Yi, Benjamin R Kipp, George Vasmatzis, Eva M Carmona
Sporadic lymphangioleiomyomatosis is a progressive pulmonary cystic disease resulting from the infiltration of smooth muscle-like lymphangioleiomyomatosis cells into the lung. The migratory/metastasizing properties of the lymphangioleiomyomatosis cell together with the presence of somatic mutations, primarily in the tuberous sclerosis complex gene (TSC2), lead many to consider this a low-grade malignancy. As malignant tumors characteristically accumulate somatic structural variations, which have not been well studied in sporadic lymphangioleiomyomatosis, we utilized mate pair sequencing to define structural variations within laser capture microdissected enriched lymphangioleiomyomatosis cell populations from five sporadic lymphangioleiomyomatosis patients...
June 23, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28643631/the-anopheles-gambiae-2la-chromosome-inversion-is-associated-with-susceptibility-to-plasmodium-falciparum-in-africa
#16
Michelle M Riehle, Tullu Bukhari, Awa Gneme, Wamdaogo M Guelbeogo, Boubacar Coulibaly, Abdrahamane Fofana, Adrien Pain, Emmanuel Bischoff, Francois Renaud, Abdoul H Beavogui, Sekou F Traore, N'Fale Sagnon, Kenneth D Vernick
Chromosome inversions suppress genetic recombination and establish co-adapted gene complexes, or supergenes. The 2La inversion is a widespread polymorphism in the Anopheles gambiae species complex, the major African mosquito vectors of human malaria. Here we show that alleles of the 2La inversion are associated with natural malaria infection levels in wild-captured vectors from West and East Africa. Mosquitoes carrying the more-susceptible allele (2L+(a)) are also behaviorally less likely to be found inside houses...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28643617/preselection-statistics-and-random-forest-classification-identify-population-informative-single-nucleotide-polymorphisms-in-cosmopolitan-and-autochthonous-cattle-breeds
#17
F Bertolini, G Galimberti, G Schiavo, S Mastrangelo, R Di Gerlando, M G Strillacci, A Bagnato, B Portolano, L Fontanesi
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna)...
June 23, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28643196/genetic-variants-in-cell-death-pathway-genes-and-hbv-related-hepatocellular-carcinoma-among-a-chinese-han-population
#18
Fei Liu, Fuqiang Li, Limei Luo, Hanteng Yang, Yonggang Wei, Wentao Wang, Lvnan Yan, Tianfu Wen, Jiayin Yang, Bo Li
Cell death pathway plays an important role in apoptosis, and corruption of this signaling pathway has been shown to participate in carcinogenesis. We aimed at determining whether genetic variants in CASP8, CASP10 and CFLAR influence the development and clinical outcomes of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). A hospital-based case-control study, including 600 HCC cases and 600 HBsAg positive controls without HCC, was conducted to assess the relationship between 11 tagging SNPs in CASP8, CASP10 and CFLAR and HBV-related HCC risk and prognosis in a Chinese Han population...
June 22, 2017: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/28642997/pd-1-and-cancer-molecular-mechanisms-and-polymorphisms
#19
REVIEW
Arash Salmaninejad, Vahid Khoramshahi, Alireza Azani, Ehsan Soltaninejad, Saeed Aslani, Mohammad Reza Zamani, Masoud Zal, Abolfazl Nesaei, Sayed Mostafa Hosseini
The programmed cell death protein 1 (PD-1) is expressed by activated T cells that act as an immunoregulatory molecule, and are responsible for the negative regulation of T cell activation and peripheral tolerance. The PD-1 gene also encodes an inhibitory cell surface receptor involved in the regulation of T cell functions during immune responses/tolerance. Beyond potent inhibitory effects on T cells, PD-1 also has a role in regulating B cell and monocyte responses. An overexpression of PD-1 has been reported to contribute to immune system avoidance in different cancers...
June 22, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28642824/identification-of-quantitative-trait-loci-that-determine-plasma-total-cholesterol-and-triglyceride-concentrations-in-ddd-sgn-and-c57bl-6j-inbred-mice
#20
Jun-Ichi Suto, Misaki Kojima
DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG...
2017: Cholesterol
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