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https://www.readbyqxmd.com/read/28945022/-progress-of-gene-editing-technologies-and-prospect-in-traditional-chinese-medicine
#1
REVIEW
Yan-Yan Ma, Jing-Zhe Li, Er-Ning Gao, Dan Qian, Ju-Ying Zhong, Chang-Zhen Liu
Gene editing is a kind of technologies that makes precise modification to the genome. It can be used to knock out/in and replace the specific DNA fragment, and make accurate gene editing on the genome level. The essence of the technique is the DNA sequence change with use of non homologous end link repair and homologous recombination repair, combined with specific DNA target recognition and endonuclease.This technology has wide range of development prospects and high application value in terms of scientific research, agriculture, medical treatment and other fields...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28944917/application-of-a-co%C3%A2-expression-network-for-the-analysis-of-aggressive-and-non%C3%A2-aggressive-breast-cancer-cell-lines-to-predict-the-clinical-outcome-of-patients
#2
Ling Guo, Kun Zhang, Zhitong Bing
Breast cancer metastasis is a demanding problem in clinical treatment of patients with breast cancer. It is necessary to examine the mechanisms of metastasis for developing therapies. Classification of the aggressiveness of breast cancer is an important issue in biological study and for clinical decisions. Although aggressive and non‑aggressive breast cancer cells can be easily distinguished among different cell lines, it is very difficult to distinguish in clinical practice. The aim of the current study was to use the gene expression analysis from breast cancer cell lines to predict clinical outcomes of patients with breast cancer...
September 25, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28944843/microarray-and-bioinformatics-analyses-of-gene-expression-profiles-in-balb-c-murine-macrophage-polarization
#3
Li Jiang, Xueqin Li, Yingying Zhang, Mengying Zhang, Zongsheng Tang, Kun Lv
Macrophages possess the hallmark feature of plasticity, allowing them to undergo a dynamic transition between M1 and M2 polarized phenotypes. The aim of the present study was to screen for differentially-expressed genes (DEGs) that were associated with BALB/c murine macrophage polarization. The transcription profiles of three M1 and three M2 samples were obtained using microarray analysis. Based on the threshold of fold‑change >2.0 and P‑value <0.05, a total of 1,253 DEGs were identified, of which 696 were upregulated and 557 downregulated in M1 macrophages compared with M2 macrophages...
September 19, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28944404/differential-expression-of-genes-and-differentially-perturbed-pathways-associated-with-very-high-evening-fatigue-in-oncology-patients-receiving-chemotherapy
#4
Elena Flowers, Christine Miaskowski, Yvette Conley, Marilyn J Hammer, Jon Levine, Judy Mastick, Steven Paul, Fay Wright, Kord Kober
PURPOSE: Fatigue is the most common symptom associated with cancer and its treatment. Investigation of molecular mechanisms associated with fatigue in oncology patients may identify new therapeutic targets. The objectives of this study were to evaluate the relationships between gene expression and perturbations in biological pathways and evening fatigue severity in oncology patients who received chemotherapy (CTX). METHODS: The Lee Fatigue Scale (LFS) and latent class analysis were used to identify evening fatigue phenotypes...
September 25, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/28944311/integrating-genomic-information-and-signaling-dynamics-for-efficient-cancer-therapy
#5
Jacob Stewart-Ornstein, Galit Lahav
The field of cancer systems biology has made great strides in understanding oncogenic pathway signaling and enumerating mutations involved in oncogenesis. However, application of these datasets to patient stratification, and to the design of personalized therapy, is in its infancy. We review BRAF and BRCA mutant targeted therapy, where patient stratification has had critical, albeit mixed success. We contrast the work on genomic targeted therapy with orthogonal studies on the dynamics of signaling pathways for designing optimal treatment schedules...
February 2017: Current opinion in systems biology
https://www.readbyqxmd.com/read/28944281/adenovirus-mediated-gene-delivery-potential-applications-for-gene-and-cell-based-therapies-in-the-new-era-of-personalized-medicine
#6
Cody S Lee, Elliot S Bishop, Ruyi Zhang, Xinyi Yu, Evan M Farina, Shujuan Yan, Chen Zhao, Zongyue Zheng, Yi Shu, Xingye Wu, Jiayan Lei, Yasha Li, Wenwen Zhang, Chao Yang, Ke Wu, Ying Wu, Sherwin Ho, Aravind Athiviraham, Michael J Lee, Jennifer Moriatis Wolf, Russell R Reid, Tong-Chuan He
With rapid advances in understanding molecular pathogenesis of human diseases in the era of genome sciences and systems biology, it is anticipated that increasing numbers of therapeutic genes or targets will become available for targeted therapies. Despite numerous setbacks, efficacious gene and/or cell-based therapies still hold the great promise to revolutionize the clinical management of human diseases. It is wildly recognized that poor gene delivery is the limiting factor for most in vivo gene therapies...
June 2017: Genes & Diseases
https://www.readbyqxmd.com/read/28944239/analysis-of-sequence-data-to-identify-potential-risk-variants-for-oral-clefts-in-multiplex-families
#7
Emily R Holzinger, Qing Li, Margaret M Parker, Jacqueline B Hetmanski, Mary L Marazita, Elisabeth Mangold, Kerstin U Ludwig, Margaret A Taub, Ferdouse Begum, Jeffrey C Murray, Hasan Albacha-Hejazi, Khalid Alqosayer, Giath Al-Souki, Abdullatiff Albasha Hejazi, Alan F Scott, Terri H Beaty, Joan E Bailey-Wilson
BACKGROUND: Nonsyndromic oral clefts are craniofacial malformations, which include cleft lip with or without cleft palate. The etiology for oral clefts is complex with both genetic and environmental factors contributing to risk. Previous genome-wide association (GWAS) studies have identified multiple loci with small effects; however, many causal variants remain elusive. METHODS: In this study, we address this by specifically looking for rare, potentially damaging variants in family-based data...
September 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28943871/global-screening-of-salmonella-enterica-serovar-typhimurium-genes-for-desiccation-survival
#8
Rabindra K Mandal, Young M Kwon
Salmonella spp., one of the most common foodborne bacterial pathogens, has the ability to survive under desiccation conditions in foods and food processing facilities for years. This raises the concerns of Salmonella infection in humans associated with low water activity foods. Salmonella responds to desiccation stress via complex pathways involving immediate physiological actions as well as coordinated genetic responses. However, the exact mechanisms of Salmonella to resist desiccation stress remain to be fully elucidated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28943297/transcriptome-analysis-of-kuruma-shrimp-marsupenaeus-japonicus-hepatopancreas-in-response-to-white-spot-syndrome-virus-wssv-under-experimental-infection
#9
Shengping Zhong, Yong Mao, Jun Wang, Min Liu, Man Zhang, Yongquan Su
Kuruma shrimp (Marsupenaeus japonicus) is one of the most valuable crustacean species in capture fisheries and mariculture in the Indo-West Pacific. White spot syndrome virus (WSSV) is a highly virulent pathogen which has seriously threatened Kuruma shrimp aquaculture sector. However, little information is available in relation to underlying mechanisms of host-virus interaction in Kuruma shrimp. In this study, we performed a transcriptome analysis from the hepatopancreas of Kuruma shrimp challenged by WSSV, using Illumina-based RNA-Seq...
September 21, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28943090/genome-architecture-and-evolution-of-a-unichromosomal-asexual-nematode
#10
Hélène Fradin, Karin Kiontke, Charles Zegar, Michelle Gutwein, Jessica Lucas, Mikhail Kovtun, David L Corcoran, L Ryan Baugh, David H A Fitch, Fabio Piano, Kristin C Gunsalus
Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair...
September 14, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28943084/horizontal-transfer-of-a-synthetic-metabolic-pathway-between-plant-species
#11
Yinghong Lu, Sandra Stegemann, Shreya Agrawal, Daniel Karcher, Stephanie Ruf, Ralph Bock
Transgene expression from the plastid (chloroplast) genome provides unique advantages, including high levels of foreign protein accumulation, convenient transgene stacking in operons, and increased biosafety due to exclusion of plastids from pollen transmission [1, 2]. However, applications in biotechnology and synthetic biology are severely restricted by the very small number of plant species whose plastid genomes currently can be transformed [3, 4]. Here we report a simple method for the introduction of useful plastid transgenes into non-transformable species...
September 16, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28942923/transcriptional-architecture-of-synaptic-communication-delineates-gabaergic-neuron-identity
#12
Anirban Paul, Megan Crow, Ricardo Raudales, Miao He, Jesse Gillis, Z Josh Huang
Understanding the organizational logic of neural circuits requires deciphering the biological basis of neuronal diversity and identity, but there is no consensus on how neuron types should be defined. We analyzed single-cell transcriptomes of a set of anatomically and physiologically characterized cortical GABAergic neurons and conducted a computational genomic screen for transcriptional profiles that distinguish them from one another. We discovered that cardinal GABAergic neuron types are delineated by a transcriptional architecture that encodes their synaptic communication patterns...
September 20, 2017: Cell
https://www.readbyqxmd.com/read/28942849/analysis-of-the-pho-regulon-in-streptomyces-tsukubaensis
#13
María Ordóñez-Robles, Fernando Santos-Beneit, Antonio Rodríguez-García, Juan F Martín
Phosphate regulation of antibiotic biosynthesis in Streptomyces has been studied due to the importance of this genus as a source of secondary metabolites with biological activity. Streptomyces tsukubaensis is the main producer of tacrolimus (or FK506), an immunosuppressant macrolide that generates important benefits for the pharmaceutical market. However, the production of tacrolimus is under a negative control by phosphate and, therefore, is important to know the molecular mechanism of this regulation. Despite its important role, there are no reports about the Pho regulon in S...
December 2017: Microbiological Research
https://www.readbyqxmd.com/read/28942792/evolutionary-trajectories-of-entomopathogenic-fungi-abc-transporters
#14
Bikash Baral
The ABC protein superfamily-also called traffic ATPases-are energy-dependent ubiquitous proteins, representing one of the crucial and the largest family in the fungal genomes. The ATP-binding cassette endows a characteristic 200-250 amino acids and is omnipresent in all organisms ranging from prokaryotes to eukaryotes. Unlike in bacteria with nutrient import functions, ABC transporters in fungal entomopathogens serve as effective efflux pumps that are largely involved in the shuttle of metabolites across the biological membranes...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/28942772/hook-line-and-infection-a-guide-to-culturing-parasites-establishing-infections-and-assessing-immune-responses-in-the-three-spined-stickleback
#15
Alexander Stewart, Joseph Jackson, Iain Barber, Christophe Eizaguirre, Rachel Paterson, Pieter van West, Chris Williams, Joanne Cable
The three-spined stickleback (Gasterosteus aculeatus) is a model organism with an extremely well-characterized ecology, evolutionary history, behavioural repertoire and parasitology that is coupled with published genomic data. These small temperate zone fish therefore provide an ideal experimental system to study common diseases of coldwater fish, including those of aquacultural importance. However, detailed information on the culture of stickleback parasites, the establishment and maintenance of infections and the quantification of host responses is scattered between primary and grey literature resources, some of which is not readily accessible...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28942770/the-battle-against-flystrike-past-research-and-new-prospects-through-genomics
#16
Clare A Anstead, Trent Perry, Stephen Richards, Pasi K Korhonen, Neil D Young, Vernon M Bowles, Philip Batterham, Robin B Gasser
Flystrike, or cutaneous myiasis, is caused by blow fly larvae of the genus Lucilia. This disease is a major problem in countries with large sheep populations. In Australia, Lucilia cuprina (Wiedemann, 1830) is the principal fly involved in flystrike. While much research has been conducted on L. cuprina, including physical, chemical, immunological, genetic and biological investigations, the molecular biology of this fly is still poorly understood. The recent sequencing, assembly and annotation of the draft genome and analyses of selected transcriptomes of L...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28942538/photoperiodism-dynamics-during-the-domestication-and-improvement-of-soybean
#17
REVIEW
Sheng-Rui Zhang, Huan Wang, Zhongyu Wang, Yao Ren, Lifang Niu, Jun Liu, Bin Liu
Soybean (Glycine max) is a facultative short-day plant with a sensitive photoperiod perception and reaction system, which allows it to adjust its physiological state and gene regulatory networks to seasonal and diurnal changes in environmental conditions. In the past few decades, soybean cultivation has spread from East Asia to areas throughout the world. Biologists and breeders must now confront the challenge of understanding the molecular mechanism of soybean photoperiodism and improving agronomic traits to enable this important crop to adapt to geographical and environmental changes...
September 21, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28942199/metabolomic-findings-in-sepsis-as-a-damage-of-host-microbial-metabolism-integration
#18
REVIEW
Natalia V Beloborodova, Andrei Yu Olenin, Alisa K Pautova
Metabolomics globally evaluates the totality of the endogenous metabolites in patient's body, at the same time reflecting gene function, enzyme activity and degree of organ dysfunction in sepsis. The authors performed the analysis of the main chemical classes of low molecular weight compounds (amino acids, polyols, fatty acids, hydroxy acids, amines, nucleotides and their derivatives) that quantitatively distinguish patients with sepsis from healthy ones. The following keywords were used to find papers published in the Scopus and Web of Science databases from 2008 to 2015: (marker OR biomarker) AND (sepsis OR critical ill OR pneumonia OR hypoxia)...
September 15, 2017: Journal of Critical Care
https://www.readbyqxmd.com/read/28941920/genomic-scores-are-independent-of-disease-volume-in-men-with-favorable-risk-prostate-cancer-implications-for-choosing-men-for-active-surveillance
#19
Yaw A Nyame, Dominic C Grimberg, Daniel J Greene, Karishma Gupta, Ganesh K Kartha, Ryan Berglund, Michael Gong, Andrew J Stephenson, Cristina Magi-Galluzzi, Eric A Klein
OBJECTIVE: To determine if disease volume at prostate biopsy correlates with genomic scores among men with favorable risk prostate cancer. METHODS: All men with NCCN very low (VLR) and low risk (LR) disease and OncotypeDx Prostate testing at our institution from 2013 to 2016 were identified. Volume of disease was characterized as percent of positive cores, number of cores with >50% involvement, largest involvement of any single core, and PSA density. Nonparametric testing was performed to compare the median genomic prostate score (GPS) and likelihood of favorable pathology (LFP) between quartiles of disease volume...
September 20, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28941788/network-module-identification-a-widespread-theoretical-bias-and-best-practices
#20
Iryna Nikolayeva, Oriol Guitart-Pla, Benno Schwikowski
Biological processes often manifest themselves as coordinated changes across modules, i.e., sets of interacting genes. Commonly, the high dimensionality of genome-scale data prevents the visual identification of such modules, and straightforward computational search through a set of known pathways is a limited approach. Therefore, tools for the data-driven, computational, identification of modules in gene interaction networks have become popular components of visualization and visual analytics workflows. However, many such tools are known to result in modules that are large, and therefore hard to interpret biologically...
September 20, 2017: Methods: a Companion to Methods in Enzymology
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