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landscape genetics

Kerry A Geiler-Samerotte, Yuan O Zhu, Benjamin E Goulet, David W Hall, Mark L Siegal
The protein-folding chaperone Hsp90 has been proposed to buffer the phenotypic effects of mutations. The potential for Hsp90 and other putative buffers to increase robustness to mutation has had major impact on disease models, quantitative genetics, and evolutionary theory. But Hsp90 sometimes contradicts expectations for a buffer by potentiating rapid phenotypic changes that would otherwise not occur. Here, we quantify Hsp90's ability to buffer or potentiate (i.e., diminish or enhance) the effects of genetic variation on single-cell morphological features in budding yeast...
October 2016: PLoS Biology
Ishfaq A Sheikh, Ejaz Ahmad, Mohammad S Jamal, Mohd Rehan, Mourad Assidi, Iftikhar A Tayubi, Samera F AlBasri, Osama S Bajouh, Rola F Turki, Adel M Abuzenadah, Ghazi A Damanhouri, Mohd A Beg, Mohammed Al-Qahtani
BACKGROUND: Preterm birth (PTB), birth at <37 weeks of gestation, is a significant global public health problem. World-wide, about 15 million babies are born preterm each year resulting in more than a million deaths of children. Preterm neonates are more prone to problems and need intensive care hospitalization. Health issues may persist through early adulthood and even be carried on to the next generation. Majority (70 %) of PTBs are spontaneous with about a half without any apparent cause and the other half associated with a number of risk factors...
October 17, 2016: BMC Genomics
Sung-Hwan Cho, Sang-Min Park, Ho-Sung Lee, Hwang-Yeol Lee, Kwang-Hyun Cho
BACKGROUND: Colorectal cancer arises from the accumulation of genetic mutations that induce dysfunction of intracellular signaling. However, the underlying mechanism of colorectal tumorigenesis driven by genetic mutations remains yet to be elucidated. RESULTS: To investigate colorectal tumorigenesis at a system-level, we have reconstructed a large-scale Boolean network model of the human signaling network by integrating previous experimental results on canonical signaling pathways related to proliferation, metastasis, and apoptosis...
October 20, 2016: BMC Systems Biology
Daniela Lopes Paim Pinto, Lucio Brancadoro, Silvia Dal Santo, Gabriella De Lorenzis, Mario Pezzotti, Blake C Meyers, Mario E Pè, Erica Mica
Understanding the molecular mechanisms involved in the interaction between the genetic composition and the environment is crucial for modern viticulture. We approached this issue by focusing on the small RNA transcriptome in grapevine berries of the two varieties Cabernet Sauvignon and Sangiovese, growing in adjacent vineyards in three different environments. Four different developmental stages were studied and a total of 48 libraries of small RNAs were produced and sequenced. Using a proximity-based pipeline, we determined the general landscape of small RNAs accumulation in grapevine berries...
2016: Frontiers in Plant Science
Kirby Rickel, Fang Fang, Jianning Tao
Osteosarcoma is the predominant form of bone cancer, affecting mostly adolescents. Recent progress made in molecular genetic studies of osteosarcoma has changed our view on the cause of the disease and ongoing therapeutic approaches for patients. As we draw closer to gaining more complete catalogs of candidate cancer driver genes in common forms of cancer, the landscape of somatic mutations in osteosarcoma is emerging from its first phase. In this review, we summarize recent whole genome and/or whole exome genomic studies, and then put these findings in the context of genetic hallmarks of somatic mutations and mutational processes in human osteosarcoma...
October 16, 2016: Bone
Magda Silva Carneiro, Caroline Cambraia Furtado Campos, Luiz Alberto Beijo, Flavio Nunes Ramos
Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition...
2016: PloS One
Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer, Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics...
October 19, 2016: Molecular Ecology
Antonino Neri, Katia Todoerti, Marta Lionetti, Vittorio Simeon, Marzia Barbieri, Filomena Nozza, Gabriella Vona, Alessandra Pompa, Luca Baldini, Pellegrino Musto
Primary plasma cell leukemia (PPCL) is a rare and aggressive variant of multiple myeloma. The introduction of novel agents and modern technologies has recently partially changed the clinical and biological scenario of this malignancy, allowing limited, but not negligible, progresses. Areas covered: We will discuss the complex landscape of genetic alterations in PPCL, derived from conventional and high-throughput technologies; the best available treatments for PPCL; the possible future therapeutic perspectives...
October 19, 2016: Expert Review of Hematology
Jessica A Castillo, Clinton W Epps, Mackenzie R Jeffress, Chris Ray, Thomas J Rodhouse, Donelle Schwalm
Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Sharon Downes, Darren Kriticos, Hazel Parry, Cate Paull, Nancy Schellhorn, Myron P Zalucki
Helicoverpa armigera is a major pest of agriculture, horticulture and floriculture throughout the old world and recently invaded parts of the new world. We overview of the evolution in thinking about the application of area-wide approaches to assist with its control by the Australian Cotton Industry to highlight important lessons and future challenges to achieving the same in the New World. An over-reliance of broad-spectrum insecticides led to Helicoverpa spp. in Australian cotton rapidly became resistant to DDT, synthetic pyrethroids, organophosphates, carbamates and endosulfan...
October 17, 2016: Pest Management Science
Michael Medinger, Claudia Lengerke, Jakob Passweg
Acute myeloid leukemia (AML) is a biologically complex and molecularly and clinically heterogeneous disease, and its incidence is increasing as the population ages. Cytogenetic anomalies and mutation testing remain important prognostic tools for tailoring treatment after induction therapy. Despite major advances in understanding the genetic landscape of AML and its impact on the pathophysiology and biology of the disease, as well as the rapid development of new drugs, standard treatment options have not experienced major changes during the past three decades...
2016: Leukemia Research Reports
Cecilia C S Yeung, H Joachim Deeg, Colin Pritchard, David Wu, Min Fang
Jumping translocations (JT) have been identified in numerous malignancies, including leukemia, but infrequently in patients with myelodysplastic syndromes (MDS). The responsible genetic region has been mapped to the JTB gene at 1q21, but breakpoints involving other chromosomal loci, such as 3q and 11q, have been described as well. We have characterized the pathological and mutational landscape, and the clinical course of 6 new MDS patients with jumping mutations using chromosome genomic array testing (CGAT) and target gene panel next generation sequencing...
September 2016: Cancer Genetics
Keping Sun, Rebecca T Kimball, Tong Liu, Xuewen Wei, Longru Jin, Tinglei Jiang, Aiqing Lin, Jiang Feng
Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry...
October 17, 2016: Scientific Reports
Beryl Royer-Bertrand, Matteo Torsello, Donata Rimoldi, Ikram El Zaoui, Katarina Cisarova, Rosanna Pescini-Gobert, Franck Raynaud, Leonidas Zografos, Ann Schalenbourg, Daniel Speiser, Michael Nicolas, Laureen Vallat, Robert Klein, Serge Leyvraz, Giovanni Ciriello, Nicolò Riggi, Alexandre P Moulin, Carlo Rivolta
Uveal melanoma (UM) is a rare intraocular tumor that, similar to cutaneous melanoma, originates from melanocytes. To gain insights into its genetics, we performed whole-genome sequencing at very deep coverage of tumor-control pairs in 33 samples (24 primary and 9 metastases). Genome-wide, the number of coding mutations was rather low (only 17 variants per tumor on average; range 7-28), thus radically different from cutaneous melanoma, where hundreds of exonic DNA insults are usually detected. Furthermore, no UV light-induced mutational signature was identified...
October 6, 2016: American Journal of Human Genetics
Vanessa Tripp, Roman Martin, Alvaro Orell, Omer S Alkhnbashi, Rolf Backofen, Lennart Randau
Archaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2'-O-methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes...
October 14, 2016: Molecular Microbiology
Priyakshi Kalita-de Croft, Fares Al-Ejeh, Amy E McCart Reed, Jodi M Saunus, Sunil R Lakhani
Our understanding of the natural history of breast cancer has evolved alongside technologies to study its genomic, transcriptomic, proteomic, and metabolomics landscapes. These technologies have helped decipher multiple molecular pathways dysregulated in breast cancer. First-generation 'omics analyses considered each of these dimensions individually, but it is becoming increasingly clear that more holistic, integrative approaches are required to fully understand complex biological systems. The 'omics represent an exciting era of discovery in breast cancer research, although important issues need to be addressed to realize the clinical utility of these data through precision cancer care...
November 2016: Advances in Anatomic Pathology
Bryce A Richardson, Lindsay Chaney, Nancy L Shaw, Shannon M Still
Rising temperatures have begun to shift flowering time, but it is unclear whether phenotypic plasticity can accommodate projected temperature change for this century. Evaluating clines in phenological traits and the extent and variation in plasticity can provide key information on assessing risk of maladaptation and developing strategies to mitigate climate change. In this study, flower phenology was examined in 52 populations of big sagebrush (Artemisia tridentata) growing in three common gardens. Flowering date (anthesis) varied 91 days from late July to late November among gardens...
October 14, 2016: Global Change Biology
Humberto Ossa, Juliana Aquino, Rui Pereira, Adriana Ibarra, Rafael H Ossa, Luz Adriana Pérez, Juan David Granda, Maria Claudia Lattig, Helena Groot, Elizeu Fagundes de Carvalho, Leonor Gusmão
The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population...
2016: PloS One
C Brandon Ogbunugafor, Daniel L Hartl
Much of the public lacks a proper understanding of Darwinian evolution, a problem that can be addressed with new learning and teaching approaches to be implemented both inside the classroom and in less formal settings. Few analogies have been as successful in communicating the basics of molecular evolution as John Maynard Smith's protein space analogy (1970), in which he compared protein evolution to the transition between the terms WORD and GENE, changing one letter at a time to yield a different, meaningful word (in his example, the preferred path was WORD → WORE → GORE → GONE → GENE)...
October 2016: PLoS Computational Biology
Tamara K Moyo, Michael R Savona
Myelodysplastic syndromes (MDS) comprise a heterogeneous group of clonal hematologic malignancies characterized by a hypercellular bone marrow and morphologic dysplasia in one or more lineage (i.e., myeloid, erythroid, or megakaryocytic), presenting clinically with leukopenia, anemia, and/or thrombocytopenia and with a propensity to transform to acute myelogenous leukemia. Newer technologies such as next-generation sequencing have allowed better understanding of the genetic landscape in MDS. Nearly 80 % of MDS patients have at least one mutation, and approximately 40 recurrent somatic mutations have been identified to occur in >1 % of cases...
October 12, 2016: Current Hematologic Malignancy Reports
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