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https://www.readbyqxmd.com/read/28098913/diets-link-metabolic-syndrome-and-colorectal-cancer-development-review
#1
Jirakrit Saetang, Surasak Sangkhathat
Diets have been believed to be an important factor in the development of metabolic syndrome and colorectal cancer (CRC). In recent years, many studies have shown an intimate relationship between mucosal immunity, metabolism and diets, which has led to a greater understanding of the pathophysiology of metabolic syndrome and CRC development. Although the precise effects of diets on oncogenesis have not been compl-etely elucidated, microbiota changes and inflammation are believed to be important factors that influence the development of CRC...
January 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28098506/capsicum-annuum-var-grossum-bell-pepper-inhibits-%C3%AE-secretase-activity-and-%C3%AE-amyloid1-40-aggregation
#2
Omodesola Oluwafisayo Ogunruku, Ganiyu Oboh, Sabina Passamonti, Federica Trammer, Aline Augusti Boligon
The deposition of amyloid protein as senile plaques is the major signature of Alzheimer's disease (AD). It is produced by the sequential cleavage of the amyloid precursor protein by secretases. Moreover, peppers are noted for their antiaging and cognitive enhancing properties. Thus, in this study, the effects of polyphenol-rich extracts from bell pepper on amyloid production and aggregation in vitro were investigated. Bell pepper (ripe and unripe) was extracted with methanol-1 N HCl (1:1 v/v). Thereafter, the inhibitory potentials of the extracts on β-secretase and β-amyloid1-40 aggregation were determined...
January 18, 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28098303/topologically-inferring-pathway-activity-for-precise-survival-outcome-prediction-breast-cancer-as-a-case
#3
Wei Liu, Wei Wang, Guohua Tian, Wenming Xie, Li Lei, Jiujin Liu, Wanxun Huang, Liyan Xu, Enmin Li
Accurately predicting the survival outcome of patients is of great importance in clinical cancer research. In the past decade, building survival prediction models based on gene expression data has received increasing interest. However, the existing methods are mainly based on individual gene signatures, which are known to have limited prediction accuracy on independent datasets and unclear biological relevance. Here, we propose a novel pathway-based survival prediction method called DRWPSurv in order to accurately predict survival outcome...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28098175/correlated-electronic-decay-in-expanding-clusters-triggered-by-intense-xuv-pulses-from-a-free-electron-laser
#4
Tim Oelze, Bernd Schütte, Maria Müller, Jan P Müller, Marek Wieland, Ulrike Frühling, Markus Drescher, Alaa Al-Shemmary, Torsten Golz, Nikola Stojanovic, Maria Krikunova
Irradiation of nanoscale clusters and large molecules with intense laser pulses transforms them into highly-excited non- equilibrium states. The dynamics of intense laser-cluster interaction is encoded in electron kinetic energy spectra, which contain signatures of direct photoelectron emission as well as emission of thermalized nanoplasma electrons. In this work we report on a so far not observed spectrally narrow bound state signature in the electron kinetic energy spectra from mixed Xe core - Ar shell clusters ionized by intense extreme-ultraviolet (XUV) pulses from a free-electron-laser...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28098149/characterising-private-and-shared-signatures-of-positive-selection-in-37-asian-populations
#5
Xuanyao Liu, Dongsheng Lu, Woei-Yuh Saw, Philip J Shaw, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Suthat Fucharoen, Worachart Lert-Itthiporn, Kwanrutai Chin-Inmanu, Tran Nguyen Bich Chau, Katie Anders, Anuradhani Kasturiratne, H Janaka de Silva, Tomohiro Katsuya, Ryosuke Kimura, Toru Nabika, Takayoshi Ohkubo, Yasuharu Tabara, Fumihiko Takeuchi, Ken Yamamoto, Mitsuhiro Yokota, Dolikun Mamatyusupu, Wenjun Yang, Yeun-Jun Chung, Li Jin, Boon-Peng Hoh, Ananda R Wickremasinghe, RickTwee-Hee Ong, Chiea-Chuen Khor, Sarah J Dunstan, Cameron Simmons, Sissades Tongsima, Prapat Suriyaphol, Norihiro Kato, Shuhua Xu, Yik-Ying Teo
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28097886/reagent-free-lc-ms-ms-based-pharmacokinetic-quantification-of-polyhistidine-tagged-therapeutic-proteins
#6
Jianxia Shi, Jing Man Wong, Ji Ma, Tiffany Dickerson, Colin Hall, Dan A Rock, Timothy J Carlson
AIM: Immobilized metal ion affinity chromatography is widely employed for purifying polyhistidine-tagged recombinant proteins from cell lysates. The technique can be applied for quantification of therapeutic proteins in biological matrices by LC-MS/MS. RESULTS: A protein reagent-free workflow was developed for quantifying polyhistidine-tagged proteins by LC-MS/MS. The workflow includes target protein enrichment by immobilized metal ion affinity chromatography, on-bead trypsin digestion and quantification of signature peptides by LC-MS/MS...
January 18, 2017: Bioanalysis
https://www.readbyqxmd.com/read/28097693/distinguishing-between-biochemical-and-cellular-function-are-there-peptide-signatures-for-cellular-function-of-proteins
#7
Shruti Jain, Kausik Bhattacharyya, Rachit Bakshi, Ankita Narang, Vani Brahmachari
The genome annotation and identification of gene function depends on conserved biochemical activity. However, in the cell, proteins with the same biochemical function can participate in different cellular pathways and cannot complement one another. Similarly, two proteins of very different biochemical functions are put in the same class of cellular function; for example, the classification of a gene as an oncogene or a tumour suppressor gene is not related to its biochemical function, but is related to its cellular function...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28097652/mdm4-is-a-rational-target-for-treating-breast-cancers-with-mutant-p53
#8
Panimaya Jeffreena Miranda, Daniel Buckley, Dinesh Raghu, Jia-Min B Pang, Elena A Takano, Reshma Vijayakumaran, Amina F A S Teunisse, Atara Posner, Tahlia Procter, Marco J Herold, Cristina Gamell, Jean-Christophe Marine, Stephen B Fox, Aart Jochemsen, Sue Haupt, Ygal Haupt
Mutation of the key tumour suppressor p53 defines a transition in the progression toward aggressive and metastatic breast cancer (BC) with the poorest outcome. Specifically, p53 mutation frequency exceeds 50% in Triple Negative BC (TNBC). Key regulators of mutant p53 that facilitate its oncogenic functions are potential therapeutic targets. We report here that the MDM4 protein is frequently abundant in the context of mutant p53 in basal-like BC samples. Importantly, we show that MDM4 plays a critical role in the proliferation of these BC cells...
January 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28097600/network-forming-nanoclusters-in-binary-as-s-se-glasses-from-ab-initio-quantum-chemical-modeling-to-experimental-evidences
#9
M Hyla
Network-forming As2(S/Se)m nanoclusters are employed to recognize expected variations in a vicinity of some remarkable compositions in binary As-Se/S glassy systems accepted as signatures of optimally constrained intermediate topological phases in earlier temperature-modulated differential scanning calorimetry experiments. The ab initio quantum chemical calculations performed using the cation-interlinking network cluster approach show similar oscillating character in tendency to local chemical decomposition but obvious step-like behavior in preference to global phase separation on boundary chemical compounds (pure chalcogen and stoichiometric arsenic chalcogenides)...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28097058/determining-virus-host-interactions-and-glycerol-metabolism-profiles-in-geographically-diverse-solar-salterns-with-metagenomics
#10
Abraham G Moller, Chun Liang
Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics...
2017: PeerJ
https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#11
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28096648/identification-of-genetic-and-epigenetic-variants-associated-with-breast-cancer-prognosis-by-integrative-bioinformatics-analysis
#12
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K Patra, Ramana V Davuluri
INTRODUCTION: Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28096406/shifting-diets-and-the-rise-of-male-biased-inequality-on-the-central-plains-of-china-during-eastern-zhou
#13
Yu Dong, Chelsea Morgan, Yurii Chinenov, Ligang Zhou, Wenquan Fan, Xiaolin Ma, Kate Pechenkina
Farming domesticated millets, tending pigs, and hunting constituted the core of human subsistence strategies during Neolithic Yangshao (5000-2900 BC). Introduction of wheat and barley as well as the addition of domesticated herbivores during the Late Neolithic (∼2600-1900 BC) led to restructuring of ancient Chinese subsistence strategies. This study documents a dietary shift from indigenous millets to the newly introduced cereals in northcentral China during the Bronze Age Eastern Zhou Dynasty (771-221 BC) based on stable isotope analysis of human and animal bone samples...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096377/comparative-genomics-reveals-convergent-evolution-between-the-bamboo-eating-giant-and-red-pandas
#14
Yibo Hu, Qi Wu, Shuai Ma, Tianxiao Ma, Lei Shan, Xiao Wang, Yonggang Nie, Zemin Ning, Li Yan, Yunfang Xiu, Fuwen Wei
Phenotypic convergence between distantly related taxa often mirrors adaptation to similar selective pressures and may be driven by genetic convergence. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution. However, the genetic bases of these morphological and physiological convergences remain unknown. Through de novo sequencing the red panda genome and improving the giant panda genome assembly with added data, we identified genomic signatures of convergent evolution...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096374/phylogenetic-analysis-of-the-human-antibody-repertoire-reveals-quantitative-signatures-of-immune-senescence-and-aging
#15
Charles F A de Bourcy, Cesar J Lopez Angel, Christopher Vollmers, Cornelia L Dekker, Mark M Davis, Stephen R Quake
The elderly have reduced humoral immunity, as manifested by increased susceptibility to infections and impaired vaccine responses. To investigate the effects of aging on B-cell receptor (BCR) repertoire evolution during an immunological challenge, we used a phylogenetic distance metric to analyze Ig heavy-chain transcript sequences in both young and elderly individuals before and after influenza vaccination. We determined that BCR repertoires become increasingly specialized over a span of decades, but less plastic...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096363/an-rna-based-signature-enables-high-specificity-detection-of-circulating-tumor-cells-in-hepatocellular-carcinoma
#16
Mark Kalinich, Irun Bhan, Tanya T Kwan, David T Miyamoto, Sarah Javaid, Joseph A LiCausi, John D Milner, Xin Hong, Lipika Goyal, Srinjoy Sil, Melissa Choz, Uyen Ho, Ravi Kapur, Alona Muzikansky, Huidan Zhang, David A Weitz, Lecia V Sequist, David P Ryan, Raymond T Chung, Andrew X Zhu, Kurt J Isselbacher, David T Ting, Mehmet Toner, Shyamala Maheswaran, Daniel A Haber
Circulating tumor cells (CTCs) are shed into the bloodstream by invasive cancers, but the difficulty inherent in identifying these rare cells by microscopy has precluded their routine use in monitoring or screening for cancer. We recently described a high-throughput microfluidic CTC-iChip, which efficiently depletes hematopoietic cells from blood specimens and enriches for CTCs with well-preserved RNA. Application of RNA-based digital PCR to detect CTC-derived signatures may thus enable highly accurate tissue lineage-based cancer detection in blood specimens...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095895/genome-wide-snp-analysis-using-2b-rad-sequencing-identifies-the-candidate-genes-putatively-associated-with-resistance-to-ivermectin-in-haemonchus-contortus
#17
Xiaoping Luo, Xiaona Shi, Chunxiu Yuan, Min Ai, Cheng Ge, Min Hu, Xingang Feng, Xiaoye Yang
BACKGROUND: The excessive and uncontrolled use of anthelmintics, e.g. ivermectin (IVM) for the treatment of livestock parasites has led to widespread resistance in gastrointestinal nematodes, such as Haemonchus contortus. There is an urgent need for better management of drug-use in nematode control and development of novel anthelmintics. Discovery and identification of anthelmintic resistance-associate molecules/markers can provide a basis for rational anthelmintics-use and development of novel drugs...
January 17, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28095546/comparison-of-the-cutaneous-thermal-signatures-over-twenty-four-hours-with-a-picosecond-alexandrite-laser-using-a-flat-or-fractional-optic
#18
Emil A Tanghetti, Danielle M Tartar
INTRODUCTION: This study explored immediate heat signatures with different passing techniques and the delayed thermal data points with the picosecond Alexandrite laser with the 6mm at and fractional optic during and after treatment. We sought to clarify the im- mediate effects of heating and understand the thermal and short term clinical difference when using these optics. RESULTS: There were no immediate differences or a signi cant temperature rise with different passing techniques using the at or the fractional optic...
November 1, 2016: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/28095488/metabolism-of-seriola-lalandi-during-starvation-as-revealed-by-fatty-acid-analysis-and-compound-specific-analysis-of-stable-isotopes-within-amino-acids
#19
Fernando Barreto-Curiel, Ulfert Focken, Louis R D'Abramo, María Teresa Viana
Fish starvation is defined as food deprivation for a long period of time, such that physiological processes become confined to basal metabolism. Starvation provides insights in physiological processes without interference from unknown factors in digestion and nutrient absorption occurring in fed state. Juveniles of amberjack Seriola lalandi were isotopically equilibrated to a formulated diet for 60 days. One treatment consisted of fish that continued to be fed and fish in the other treatment were not fed for 35 days...
2017: PloS One
https://www.readbyqxmd.com/read/28095480/inference-of-candidate-germline-mutator-loci-in-humans-from-genome-wide-haplotype-data
#20
Cathal Seoighe, Aylwyn Scally
The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles...
January 17, 2017: PLoS Genetics
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