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Fine-Scale crossover Rate Variation on the caenorhabditis elegans X chromosome

G3-GENES GENOMES GENETIcS 2016年第6期6卷 1767-1776页

作者： Bernstein, Max R. Rockman, Matthew V. NYU Dept Biol New York NY 10003 USA NYU Ctr Genom & Syst Biol 12 Waverly Pl New York NY 10003 USA

Meiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa, and the distribution of crossovers can differ significantly among populations and between sexes. crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination hotspots. However, several species appear to lack hotspots despite significant crossover heterogeneity. The nematode caenorhabditis elegans was previously found to have the least fine-scale variation in crossover distribution among organisms studied to date. It is unclear whether this pattern extends to the X chromosome given its unique compaction through the pachytene stage of meiotic prophase in hermaphrodites. We generated 798 recombinant nested near-isogenic lines (NILs) with crossovers in a 1.41Mb region on the left arm of the X chromosome to determine if its recombination landscape is similar to that of the autosomes. We find that the fine-scale variation in crossover rate is lower than that of other model species, and is inconsistent with hotspots. The relationship of genomic features to crossover rate is dependent on scale, with Gc content, histone modifications, and nucleosome occupancy being negatively associated with crossovers. We also find that the abundances of 4- to 6-bp DNA motifs significantly explain crossover density. These results are consistent with recombination occurring at unevenly distributed sites of open chromatin.

关键词： crossovers recombination rate variation meiosis c elegans

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Polarity and cell division orientation in the cleavage embryo: from worm to human

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MOLEcULAR HUMAN REPRODUcTION 2016年第10期22卷 691-703页

作者： Ajduk, Anna Zernicka-Goetz, Magdalena Univ Warsaw Dept Embryol Fac Biol Miecznikowa 1 PL-02096 Warsaw Poland Univ Cambridge Dept Physiol Dev & Neurosci Downing St Cambridge CB2 3DY England

cleavage is a period after fertilization, when a 1-cell embryo starts developing into a multicellular organism. Due to a series of mitotic divisions, the large volume of a fertilized egg is divided into numerous smaller, nucleated cells-blastomeres. Embryos of different phyla divide according to different patterns, but molecular mechanism of these early divisions remains surprisingly conserved. In the present paper, we describe how polarity cues, cytoskeleton and cell-to-cell communication interact with each other to regulate orientation of the early embryonic division planes in model animals such as caenorhabditis elegans, Drosophila and mouse. We focus particularly on the Par pathway and the actin-driven cytoplasmic flows that accompany it. We also describe a unique interplay between Par proteins and the Hippo pathway in cleavage mammalian embryos. Moreover, we discuss the potential meaning of polarity, cytoplasmic dynamics and cell-to-cell communication as quality biomarkers of human embryos.

关键词： polarity par proteins Hippo signalling cytoplasmic flow embryo c elegans Drosophila mouse human preimplantation development

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Melittin induces human gastric cancer cell apoptosis via activation of mitochondrial pathway

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World Journal of Gastroenterology 2016年第11期22卷 3186-3195页

作者： Gui-Mei Kong Wen-Hua Tao Ya-Li Diao Peng-Hua Fang Ji-Jun Wang Ping Bo Feng Qian Department of Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesMedical School of Yangzhou University Department of Gastroenterology 1st Hospital of Yangzhou

AIM: To investigate the apoptotic effects of melittin on SGc-7901 cells via activation of the mitochondrial signaling pathway in ***: SGc-7901 cells were stimulated by melittin, and its effect on proliferation and apoptosis of was investigated by methyl thiazolyl tetrazolium assay, morphologic structure with transmission electron microscopy, annexin-V/propidium iodide double-staining assay, measuring mitochondrial membrane potential(MMP) levels, and analyzing reactive oxygen species(ROS) concentrations were analyzed by flow cytometry. cytochrome c(cyt c), apoptosis-inducing factor(AIF), endonuclease G(Endo G), second mitochondria-derived activator of caspases(Smac)/direct IAP binding protein with low isoelectric point(Diablo), and FAS were analyzed by western blot. The expression of caspase-3 and caspase-8 was measured using activity assay ***: Melittin was incubated at 1.0, 2.0, 4.0, or 6.0 μg/m L for 1, 2, 4, 6, or 8 h and showed a timeand concentration-dependent inhibition of SGc-7901 cell growth. Melittin induced SGc-7901 cell apoptosis, which was confirmed by typical morphological changes. Treatment with 4 μg/m L melittin induced early apoptosis of SGc-7901 cells, and the early apoptosis rates were 39.97% ± 3.19%, 59.27% ± 3.94%, and 71.50% ± 2.87% vs 32.63% ± 2.75% for 1, 2, and 4 h vs 0 h(n = 3, P < 0.05); the ROS levels were 616.53% ± 79.78%, 974.81% ± 102.40%, and 1330.94% ± 93.09% vs 603.74% ± 71.99%(n = 3, P < 0.05); the MMP values were 2.07 ± 0.05, 1.78 ± 0.29, and 1.16 ± 0.25 vs 2.55 ± 0.42(n = 3, P < 0.05); caspase-3 activity was significantly higher compared to the control(5492.3 ± 321.1, 6562.0 ± 381.3, and 8695.7 ± 449.1 vs 2330.0 ± 121.9), but the caspase activity of the non-tumor cell line L-O2 was not different from that of the control. With the addition of the caspase-3 inhibitor(Ac-DEVD-cHO), caspase-3 activity was significantly decreased compared to the control group(1067.0 ± 132.5 U/g vs 8695.7 ± 449.1 U/g). The expression

关键词： Melittin Gastric cancer Mitochondrial Apoptosis cytochrome c

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Streamlining Whole Function Vectorization in c using Higher Order Vector Semantics 29

Streamlining Whole Function Vectorization in C using Higher ...

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29th IEEE International Parallel and Distributed Processing Symposium (IPDPS)

作者： Rapaport, Gil Zaks, Ayal Ben-Asher, Yosi Intel Corp Haifa Israel Univ Haifa Dept Comp Sci Haifa Israel

ISBN: (纸本)9781467376846

Taking full advantage of SIMD instructions in c programs still requires tedious and non-portable programming using intrinsics, despite considerable efforts spent developing auto-vectorization capabilities in recent decades. Whole Function Vectorization (WFV) is a recent technique for extending the use of SIMD across entire functions. WFV has so far only been used in data-parallel languages such as OpencL and ISPc. We propose a vector-oriented programming framework that facilitates WFV directly in c. We show that our framework achieves competitive performance to OpencL and ISPc while maintaining c's original syntax and semantics. This allows c programmers to gain better performance for their applications by improving SIMD utilization, without stepping out of c.

关键词： SIMD Whole Function Vectorization c

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Stability and Sensory Quality of Dried Papaya

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Food and Nutrition Sciences 2018年第5期9卷 489-501页

作者： Ronielli cardoso Reis Eliseth de Souza Viana Siomara costa Santana da Silva Maria Eug&ecirc nia de Oliveira Mamede &Iacute dila Maria da Silva Ara&uacute jo National Cassava &amp amp Fruits Research Center Brazilian Agricultural Research Corporation (EMBRAPA) Cruz das Almas Brazil Federal University of Bahia (UFBA) Salvador Brazil State University of Feira de Santana (UEFS) Feira de Santana Brazil Tropical Agroindustry Center Brazilian Agricultural Research Corporation (EMBRAPA) Fortaleza Brazil

Fruit dehydration is a way of supplying the population with healthy and nutritious foods. The shelf life of dried fruit can be defined by the evaluation of changes occurred in chemical characteristics during storage. This study aims to evaluate the sensory quality and the stability of papaya cv. Tainung n° 1 dehydrated by convective drying. Fresh and dried papaya were evaluated for color, moisture, pH, acidity, water activity, soluble solids, vitamin c, carotenoids, total extractable polyphenols (TEP) and antioxidant activity (ABTS). The sensorial acceptance of the dried papaya was evaluated using a structured nine-point hedonic scale. For the stability study, the analysis of moisture, pH, titratable acidity, water activity, total carotenoids and vitamin c were carried out every 30 days of storage until 120 days. During storage, the moisture content of dried papaya remained constant, but there were undesirable changes in color, increase of acidity and reduction of soluble solids. The degradation of total carotenoids and vitamin c followed the first order reaction, and the half-life time was 346 days for carotenoids, whereas for vitamin c it was only 29 days. In the sensory analysis, the dried papaya received grades between 5.0 and 6.0 for all evaluated attributes. Dried papaya is recommended to be consumed up to 30 days, since within this period a product with higher total carotenoids content, vitamin c and with satisfactory physicochemical and sensorial characteristics were obtained.

关键词： carica papaya carotenoids color Dehydrated Fruit Drying Vitamin c

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Anti-aging treatments slow propagation of synucleinopathy by restoring lysosomal function

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AUTOPHAGY 2016年第10期12卷 1849-1863页

作者： Kim, Dong-Kyu Lim, Hee-Sun Kawasaki, Ichiro Shim, Yhong-Hee Vaikath, Nishant N. El-Agnaf, Omar M. A. Lee, He-Jin Lee, Seung-Jae Seoul Natl Univ Coll Med Dept Biomed Sci 103 Daehak Ro Seoul 03080 South Korea Seoul Natl Univ Coll Med Neurosci Res Inst Seoul South Korea Konkuk Univ Dept Biomed Sci & Technol Seoul South Korea Konkuk Univ Dept Biosci & Biotechnoloy Seoul South Korea Konkuk Univ Inst KU Biotechnol Seoul South Korea United Arab Univ Coll Med & Hlth Sci Dept Biochem Al Ain U Arab Emirates QBRI Neurol Disorders Ctr Doha Qatar HBKU Qatar Fdn Coll Sci & Engn Doha Qatar Konkuk Univ Sch Med Dept Anat Seoul South Korea Celltrion Inc Inchon South Korea

Aging is the major risk factor for neurodegenerative diseases that are also associated with impaired proteostasis, resulting in abnormal accumulation of protein aggregates. However, the role of aging in development and progression of disease remains elusive. Here, we used caenorhabditis elegans models to show that aging-promoting genetic variations accelerated the rate of cell-to-cell transmission of SNcA/-synuclein aggregates, hallmarks of Parkinson disease, and the progression of disease phenotypes, such as nerve degeneration, behavioral deficits, and reduced life span. Genetic and pharmacological anti-aging manipulations slowed the spread of aggregates and the associated phenotypes. Lysosomal degradation was significantly impaired in aging models, while anti-aging treatments reduced the impairment. Transgenic expression of hlh-30p::hlh-30, the master controller of lysosomal biogenesis, alleviated intercellular transmission of aggregates in the aging model. Our results demonstrate that the rate of aging closely correlates with the rate of aggregate propagation and that general anti-aging treatments can slow aggregate propagation and associated disease progression by restoring lysosomal function.

关键词： aggregate propagation aging bimolecular fluorescence complementation c elegans lysosome Parkinson disease SNcA -synuclein

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Loss of the integral nuclear envelope protein SUN1 induces alteration of nucleoli

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NUcLEUS 2016年第1期7卷 68-83页

作者： Matsumoto, Ayaka Sakamoto, chiyomi Matsumori, Haruka Katahira, Jun Yasuda, Yoko Yoshidome, Katsuhide Tsujimoto, Masahiko Goldberg, Ilya G. Matsuura, Nariaki Nakao, Mitsuyoshi Saitoh, Noriko Hieda, Miki Osaka Univ Grad Sch Med & Hlth Sci Yamadaoka 1-7 Suita Osaka 5650871 Japan Kumamoto Univ Dept Med Cell Biol Inst Mol Embryol & Genet Kumamoto Japan Osaka Univ Grad Sch Frontier Biosci Suita Osaka Japan Osaka Police Hosp Dept Breast Surg Tennoji Ku Osaka Japan Osaka Police Hosp Dept Pathol Tennoji Ku Osaka Japan NIA Image Informat & Computat Biol Unit Genet Lab NIH Baltimore MD 21224 USA Japan Agcy Med Res & Dev CREST Tokyo Japan

A supervised machine learning algorithm, which is qualified for image classification and analyzing similarities, is based on multiple discriminative morphological features that are automatically assembled during the learning processes. The algorithm is suitable for population-based analysis of images of biological materials that are generally complex and heterogeneous. Here we used the algorithm wndchrm to quantify the effects on nucleolar morphology of the loss of the components of nuclear envelope in a human mammary epithelial cell line. The linker of nucleoskeleton and cytoskeleton (LINc) complex, an assembly of nuclear envelope proteins comprising mainly members of the SUN and nesprin families, connects the nuclear lamina and cytoskeletal filaments. The components of the LINc complex are markedly deficient in breast cancer tissues. We found that a reduction in the levels of SUN1, SUN2, and lamin A/c led to significant changes in morphologies that were computationally classified using wndchrm with approximately 100% accuracy. In particular, depletion of SUN1 caused nucleolar hypertrophy and reduced rRNA synthesis. Further, wndchrm revealed a consistent negative correlation between SUN1 expression and the size of nucleoli in human breast cancer tissues. Our unbiased morphological quantitation strategies using wndchrm revealed an unexpected link between the components of the LINc complex and the morphologies of nucleoli that serves as an indicator of the malignant phenotype of breast cancer cells.

关键词： breast cancer LINc complex lamin A c nuclear morphology nuclear envelope SUN1 SUN2 wndchrm

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Genomic change in hepatitis B virus associated with development of hepatocellular carcinoma

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World Journal of Gastroenterology 2016年第23期22卷 5393-5399页

作者： Danbi Lee Heather Lyu Young-Hwa chung Jeong A Kim Priya Mathews Elizabeth Jaffee Lei Zheng Eunsil Yu Young Joo Lee Soo Hyung Ryu Department of Internal Medicine University of Ulsan College of MedicineAsan Medical Center Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University School of MedicineBaltimore Department of Pathology University of Ulsan College of MedicineAsan Medical Center Department of Hepatobiliary Surgery University of Ulsan College of MedicineAsan Medical Center Department of Internal Medicine Inje Uni-versity College of MedicineSeoul Paik Hospital

AIM: To determine the genomic changes in hepatitis B virus(HBV) and evaluate their role in the development of hepatocellular carcinoma(Hcc) in patients chronically infected with genotype c ***: Two hundred and forty chronic hepatitis B(cHB) patients were subjected and followed for a median of 105 mo. Hcc was diagnosed in accordance with AASLD guidelines. The whole X, S, basal core promoter(BcP), and precore regions of HBV were sequenced using the direct sequencing ***: All of the subjects were infected with genotype c HBV. Out of 240 cHB patients, 25(10%) had c1653 T and 33(14%) had T1753 V mutation in X region; 157(65%) had A1762T/G1764 A mutations in BcP region, 50(21%) had G1896 A mutation in precore region and 67(28%) had pre-S deletions. Hcc occurred in 6 patients(3%). The prevalence of T1753 V mutation was significantly higher in patients who developed Hcc than in those without Hcc. The cumulative occurrence rates of Hcc were 5% and 19% at 10 and 15 years, respectively, in patients with T1753 V mutant, which were significantly higher than 1% and 1% in those with wild type HBV(P < 0.001).cONcLUSION: The presence of T1753 V mutation in HBV X-gene significantly increases the risk of Hcc development in patients chronically infected with genotype c HBV.

关键词： Hepatocellular carcinoma chronic hepatitis B Genomic change Hepatitis B virus Genotype c

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The caenorhabditis elegans p38 MAPK Gene plays a key role in protection from mycobacteria

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MIcROBIOLOGYOPEN 2016年第3期5卷 436-452页

作者： Galbadage, Thushara Shepherd, Tonya F. cirillo, Suat L. G. Gumienny, Tina L. cirillo, Jeffrey D. Texas A&M Hlth Sci Ctr Dept Microbial Pathogenesis Bryan TX 77807 USA Texas A&M Hlth Sci Ctr Dept Immunol Bryan TX 77807 USA Texas Womans Univ Dept Biol Denton TX 76204 USA

Mitogen-activated protein kinases (MAPK) are critical mediators of cellular responses to pathogens and are activated in response to infection, but investigation is difficult in multi-cell hosts due to developmental lethality of mutations. Mycobacterium marinum (Mm) is an established model for tuberculosis, a disease afflicting nearly one-third of the world's population. We found that Mm-infected caenorhabditis elegans display >80% mortality, but nonpathogenic M. smegmatis cause <15% mortality. c. elegans display pathological changes when infected with Mm, whereas Mm mutants produce lower mortality, suggesting that *** is a promising virulence model for detailed genetic analysis. c. elegans MAPK mutants are hypersusceptible to mycobacterial infection;however, the c. elegans TOL-like, TGF- and insulin-like pathway genes do not play important roles in susceptibility. We show that pathogenic mycobacteria inhibit MAPK-mediated protection through the MAPK phosphatase gene and demonstrate that *** provide a genetically tractable pathogenicity model of both the host and pathogen.

关键词： c elegans innate immunity Mycobacterium

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cPViolation Sensitivity at the Belle II Experiment

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International Journal of Modern Physics: conference Series 2018年第46期ijmpcs卷

作者： Tao Luo Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) and Institute of Modern Physics Fudan University Shanghai China 200443 Supported by Fudan University Grant No. JIH5913023 No. IDH5913011/003.

The sensitivity on the measurements of the angles of the cKM unitarity triangle, i.e. ϕ 1 , ϕ 2 and ϕ 3 , for Belle II experiment is presented in this letter, the cKM mechanism is expected to be tested at 1% level on ... 详细信息

关键词： c P Violation the angles of the cKM unitarity triangle the Belle II experiment

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