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https://www.readbyqxmd.com/read/29134741/contemporary-evolution-of-a-lepidopteran-species-heliothis-virescens-in-response-to-modern-agricultural-practices
#1
Megan L Fritz, Alexandra M DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook, Fred Gould
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other hosts, or 3) loss of resistance to previously used management practices including insecticides...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133448/origin-of-life-in-a-digital-microcosm
#2
Nitash C G, Thomas LaBar, Arend Hintze, Christoph Adami
While all organisms on Earth share a common descent, there is no consensus on whether the origin of the ancestral self-replicator was a one-off event or whether it only represented the final survivor of multiple origins. Here, we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry)...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29131160/human-primary-liver-cancer-derived-organoid-cultures-for-disease-modeling-and-drug-screening
#3
Laura Broutier, Gianmarco Mastrogiovanni, Monique Ma Verstegen, Hayley E Francies, Lena Morrill Gavarró, Charles R Bradshaw, George E Allen, Robert Arnes-Benito, Olga Sidorova, Marcia P Gaspersz, Nikitas Georgakopoulos, Bon-Kyoung Koo, Sabine Dietmann, Susan E Davies, Raaj K Praseedom, Ruby Lieshout, Jan N M IJzermans, Stephen J Wigmore, Kourosh Saeb-Parsy, Mathew J Garnett, Luc Jw van der Laan, Meritxell Huch
Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC/CC (CHC) tumors...
November 13, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29125854/raaaf-s-office-landscape-the-end-of-sitting-energy-expenditure-and-temporary-comfort-when-working-in-non-sitting-postures
#4
Simone R Caljouw, Rutger de Vries, Rob Withagen
An earlier study suggested that the activity-inviting office landscape called "The End of Sitting", designed by Rietveld Architecture Art Affordances (RAAAF), should be considered as an alternative working environment to prevent sedentary behavior. The End of Sitting lacks chairs and tables but consists instead of a myriad of sloped surfaces at different heights that afford workers to stand, lean or recline at different locations. In this study, we assessed the impact of four of its workspaces on physical intensity, temporary comfort and productivity of office work and compared the outcomes with sitting and standing behind a desk...
2017: PloS One
https://www.readbyqxmd.com/read/29118750/an-rna-virome-associated-to-the-golden-orb-weaver-spider-nephila-clavipes
#5
Humberto J Debat
The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29064024/measurement-of-residual-disease-in-acute-myeloid-leukemia
#6
REVIEW
Rahul S Vedula, R Coleman Lindsley
PURPOSE OF REVIEW: Assessment of measurable residual disease (MRD) after treatment can identify patients with acute myeloid leukemia (AML) that are at high risk of poor outcomes. However, there is no consensus yet regarding a standardized approach to measuring MRD that is most clinically meaningful. We review multiparameter flow cytometry (MFC) and reverse transcriptase polymerase chain reaction (RT-PCR), and discuss a framework for assessing remission MRD using next-generation sequencing (NGS)...
October 24, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/29045649/understanding-evolutionary-impacts-of-seasonality-an-introduction-to-the-symposium
#7
Caroline M Williams, Gregory J Ragland, Gustavo Betini, Lauren B Buckley, Zachary A Cheviron, Kathleen Donohue, Joe Hereford, Murray M Humphries, Simeon Lisovski, Katie E Marshall, Paul S Schmidt, Kimberly S Sheldon, Øystein Varpe, Marcel E Visser
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging...
November 1, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#8
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29031612/variants-at-hla-a-hla-c-and-hla-dqb1-confer-risk-of-psoriasis-vulgaris-in-japanese
#9
Jun Hirata, Tomomitsu Hirota, Takeshi Ozeki, Masahiro Kanai, Takeaki Sudo, Toshihiro Tanaka, Nobuyuki Hizawa, Hidemi Nakagawa, Shinichi Sato, Taisei Mushiroda, Hidehisa Saeki, Mayumi Tamari, Yukinori Okada
Psoriasis vulgaris (PsV) is an autoimmune disease of skin and joints with heterogeneity in epidemiological and genetic landscapes of global populations. We conducted an initial genome-wide association study (GWAS) and a replication study of PsV in the Japanese population (606 PsV cases and 2,052 controls). We identified significant associations of the SNPs with PsV risk at TNIP1 and the MHC region (P = 3.7×10(-10) and 6.6×10(-15), respectively). By updating the HLA imputation reference panel of Japanese (n = 908) to expand HLA gene coverage, we fine-mapped the HLA variants associated with PsV risk...
October 12, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29026114/the-driver-landscape-of-sporadic-chordoma
#10
Patrick S Tarpey, Sam Behjati, Matthew D Young, Inigo Martincorena, Ludmil B Alexandrov, Sarah J Farndon, Charlotte Guzzo, Claire Hardy, Calli Latimer, Adam P Butler, Jon W Teague, Adam Shlien, P Andrew Futreal, Sohrab Shah, Ali Bashashati, Farzad Jamshidi, Torsten O Nielsen, David Huntsman, Daniel Baumhoer, Sebastian Brandner, Jay Wunder, Brendan Dickson, Patricia Cogswell, Josh Sommer, Joanna J Phillips, M Fernanda Amary, Roberto Tirabosco, Nischalan Pillay, Stephen Yip, Michael R Stratton, Adrienne M Flanagan, Peter J Campbell
Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases...
October 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29025848/ectopic-pregnancy-exploration-of-its-global-research-architecture-using-density-equalising-mapping-and-socioeconomic-benchmarks
#11
Dörthe Brüggmann, Jana Kollascheck, David Quarcoo, Michael H Bendels, Doris Klingelhöfer, Frank Louwen, Jenny M Jaque, David A Groneberg
OBJECTIVE: About 2% of all pregnancies are complicated by the implantation of the zygote outside the uterine cavity and termed ectopic pregnancy. Whereas a multitude of guidelines exists and related research is constantly growing, no thorough assessment of the global research architecture has been performed yet. Hence, we aim to assess the associated scientific activities in relation to geographical and chronological developments, existing research networks and socioeconomic parameters...
October 11, 2017: BMJ Open
https://www.readbyqxmd.com/read/28977439/the-genomic-landscape-of-african-populations-in-health-and-disease
#12
Charles N Rotimi, Amy R Bentley, Ayo P Doumatey, Guanjie Chen, Daniel Shriner, Adebowale Adeyemo
A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28977418/developmentally-regulated-higher-order-chromatin-interactions-orchestrate-b-cell-fate-commitment
#13
Ravi Boya, Anurupa Devi Yadavalli, Sameena Nikhat, Sreenivasulu Kurukuti, Dasaradhi Palakodeti, Jagan M R Pongubala
Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination...
August 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28972992/a-landscape-genetic-analysis-of-important-agricultural-pest-species-in-tunisia-the-whitefly-bemisia-tabaci
#14
Ahmed Ben Abdelkrim, Tarek Hattab, Hatem Fakhfakh, Mohamed Sadok Belkadhi, Faten Gorsane
Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status...
2017: PloS One
https://www.readbyqxmd.com/read/28969680/non-communicable-diseases-mapping-research-funding-organisations-funding-mechanisms-and-research-practices-in-italy-and-germany
#15
Victor Stephani, Silvia Sommariva, Anne Spranger, Oriana Ciani
BACKGROUND: Evidence shows that territorial borders continue to have an impact on research collaboration in Europe. Knowledge of national research structural contexts is therefore crucial to the promotion of Europe-wide policies for research funding. Nevertheless, studies assessing and comparing research systems remain scarce. This paper aims to further the knowledge on national research landscapes in Europe, focusing on non-communicable disease (NCD) research in Italy and Germany. METHODS: To capture the architecture of country-specific research funding systems, a three-fold strategy was adopted...
October 2, 2017: Health Research Policy and Systems
https://www.readbyqxmd.com/read/28967881/nuclear-topology-modulates-the-mutational-landscapes-of-cancer-genomes
#16
Kyle S Smith, Lin L Liu, Shridar Ganesan, Franziska Michor, Subhajyoti De
Nuclear organization of genomic DNA affects processes of DNA damage and repair, yet its effects on mutational landscapes in cancer genomes remain unclear. Here we analyzed genome-wide somatic mutations from 366 samples of six cancer types. We found that lamina-associated regions, which are typically localized at the nuclear periphery, displayed higher somatic mutation frequencies than did the interlamina regions at the nuclear core. This effect was observed even after adjustment for features such as GC percentage, chromatin, and replication timing...
November 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28964938/impact-of-dna-methylation-programming-on-normal-and-pre-leukemic-hematopoiesis
#17
REVIEW
Jens Langstein, Michael D Milsom, Daniel B Lipka
Epigenome regulation is a critical mechanism that governs cell identity, lineage specification and developmental cell fates. With the advent of low-input and single-cell technologies as well as sophisticated cell labeling techniques, our understanding of transcriptional and epigenetic regulation of hematopoiesis is currently undergoing dramatic changes. Increasingly, evidence suggests that the epigenome conformation acts as a critical decision-making mechanism that instructs self-renewal, differentiation and developmental fates of hematopoietic progenitor cells...
September 27, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28961967/diverse-cis-regulatory-mechanisms-contribute-to-expression-evolution-of-tandem-gene-duplicates
#18
Luís Baudouin-Gonzalez, Marília A Santos, Camille Tempesta, Élio Sucena, Fernando Roch, Kohtaro Tanaka
Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 million years ago. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog...
September 9, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28936767/smc-complexes-orchestrate-the-mitotic-chromatin-interaction-landscape
#19
REVIEW
Yasutaka Kakui, Frank Uhlmann
Chromatin is a very long DNA-protein complex that controls the expression and inheritance of the genetic information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes during mitosis. This process, known as chromosome condensation, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of the structural maintenance of chromosomes (SMC) family, are fundamental for chromosome architecture, both for establishment of chromatin structure in the interphase nucleus and for the formation of condensed chromosomes in mitosis...
September 21, 2017: Current Genetics
https://www.readbyqxmd.com/read/28931935/alpha-tc1-and-beta-tc-6-genomic-profiling-uncovers-both-shared-and-distinct-transcriptional-regulatory-features-with-their-primary-islet-counterparts
#20
Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L Stitzel
Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines are cellular models of islet (dys)function and type 2 diabetes (T2D). However, genomic characteristics of these cells, and their similarities to primary islet alpha and beta cells, are undefined. Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) landscapes of αTC1 and βTC6 cells. Each cell type exhibits hallmarks of its primary islet cell counterpart including cell-specific expression of beta (e.g., Pdx1) and alpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in αTC1/βTC6 cis-regulatory elements...
September 20, 2017: Scientific Reports
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