209,676 results match your criteria Genomics [Journal]


Effective communication in the era of precision medicine: A pilot intervention with low health literacy patients to improve genetic counseling communication.

Eur J Med Genet 2018 Dec 12. Epub 2018 Dec 12.

Department of Social & Behavioral Sciences, University of California, San Francisco, United States.

Effective communication, where all parties share a common understanding, is necessary to realize the promise of Genomic Medicine. It is especially salient given the imperative to increase the participation of diverse populations in genomics research and to expand the reach of clinical genomics. We have previously shown that cancer genetic counseling is suboptimal for patients with limited health literacy. Read More

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December 2018
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Characterization of HPV integration, viral gene expression and E6E7 alternative transcripts by RNA-Seq: A descriptive study in invasive cervical cancer.

Genomics 2018 Dec 12. Epub 2018 Dec 12.

Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil. Electronic address:

Scarce data are available on the expression of Papillomavirus genome and the frequency of alternatively spliced E6/E7 mRNAs in invasive cervical cancer. We carried out a comprehensive characterization of HPV expression by RNA-Seq analysis in 22 invasive cervical cancer with HPV16 or HPV18, characterizing the presence of integrated/episomal viral DNA, the integration sites in human genome and the proportion of alternative splicing products of E6 and E7 genes. The expression patterns suggested the presence of episomal and/or integrated viral DNA, with integration detected in most tumors, frequently occurring within human genes in HPV18+ and in intergenic regions in HPV16+ tumors. Read More

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December 2018

Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons.

Genomics 2018 Dec 12. Epub 2018 Dec 12.

CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, India. Electronic address:

Metagenome from refinery wastewater treatment plant running under nitrogen stress was analyzed for mining of novel aromatic hydrocarbon-degrading bacteria. The sequence data were assembled using metaspade followed by binning using the Metabat tool to assemble genome; where coverage and depth were calculated using bowtie and samtools. The analysis picked a novel genome belonging to family Bradyrhizobiaceae, identified based on 16S rDNA gene which was supported by CheckM and Kraken analysis. Read More

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December 2018

Tobacco smoking, alcohol drinking, betel quid chewing, and the risk of head and neck cancer in an East Asian population.

Head Neck 2018 Dec 15. Epub 2018 Dec 15.

Division of Public Health, Department of Family and Preventive Medicine, and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah.

Background: The smoking prevalence among men in China is high, but the head and neck cancer incidence rates are low. This study's purpose was to investigate the impact of tobacco, betel quid, and alcohol on head and neck cancer risk in East Asia.

Methods: A multicenter case-control study (921 patients with head and neck cancer and 806 controls) in East Asia was conducted. Read More

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December 2018

Characterization of two steroid hydroxylases from different Streptomyces spp. and their ligand-bound and -unbound crystal structures.

FEBS J 2018 Dec 15. Epub 2018 Dec 15.

Department of Life Science and Biochemical Engineering, Sunmoon University, Asansi, 31460, Republic of Korea.

Bacterial cytochrome P450 (CYP) enzymes are involved in the hydroxylation of various endogenous substrates while using a heme molecule as a cofactor. CYPs have gained biotechnological interest as useful biocatalysts capable of altering chemical structures by adding a hydroxyl group in a regiospecific manner. Here, we identified, purified, and characterized two CYP154C4 proteins from Streptomyces sp. Read More

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December 2018

BRD4 interacts with PML/RARα in acute promyelocytic leukemia.

Front Med 2018 Dec 14;12(6):726-734. Epub 2018 Dec 14.

State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.

Bromodomain-containing 4 (BRD4) has been considered as an important requirement for disease maintenance and an attractive therapeutic target for cancer therapy. This protein can be targeted by JQ1, a selective small-molecule inhibitor. However, few studies have investigated whether BRD4 influenced acute promyelocytic leukemia (APL), and whether BRD4 had interaction with promyelocytic leukemia-retinoic acid receptor α (PML/RARα) fusion protein to some extent. Read More

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December 2018

Moonshot to Cancer Cure: Recruiting Policy to Break Down Silos.

Cancer Treat Res 2019 ;171:119-128

Robert H. Lurie Comprehensive Cancer Center, Survivorship Institute, Northwestern University, Chicago, IL, 60611, USA.

Funded by the 21 Century Cures Act, The Beau Biden Cancer Moonshot Initiative is broad, deep, integrative, and intended to expediently address cancer's most vexing problems. Launched in 2015, it is an effort to accelerate the pace of cancer research with a focus on breaking down silos through cross-pollination of research, recruitment of multidisciplinary clinical and basic science research teams, sharing of complex scientific databases, and the creation of public-private research partnerships. This audacious approach to cancer treatment is intended to alleviate the current burden of cancer within countries and across borders. Read More

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January 2019
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Recent Progress on Functional Genomics Research of Enterovirus 71.

Virol Sin 2018 Dec 14. Epub 2018 Dec 14.

Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.

Enterovirus 71 (EV71) is one of the main pathogens that causes hand-foot-and-mouth disease (HFMD). HFMD caused by EV71 infection is mostly self-limited; however, some infections can cause severe neurological diseases, such as aseptic meningitis, brain stem encephalitis, and even death. There are still no effective clinical drugs used for the prevention and treatment of HFMD. Read More

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December 2018
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Correction to: Structural modeling of a novel TERC variant in a patient with aplastic anemia and short telomeres.

Ann Hematol 2018 Dec 14. Epub 2018 Dec 14.

Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy.

The original version of this article contained a mistake in the affiliation of E. Bellacchio. Correct affiliation is presented here. Read More

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December 2018

Upregulation of MLK4 promotes migratory and invasive potential of breast cancer cells.

Oncogene 2018 Dec 14. Epub 2018 Dec 14.

Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, Warsaw, Poland.

Metastasis to distant organs is a major cause for solid cancer mortality, and the acquisition of migratory and invasive phenotype is a key factor in initiation of malignancy. In this study we investigated the contribution of Mixed-Lineage Kinase 4 (MLK4) to aggressive phenotype of breast cancer cells. Our TCGA cancer genomic data analysis revealed that amplification or mRNA upregulation of MLK4 occurred in 23% of invasive breast carcinoma cases. Read More

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December 2018

Transcriptome 3'end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma.

Nat Commun 2018 Dec 14;9(1):5331. Epub 2018 Dec 14.

Posttranscriptional Gene Regulation, Cancer Research and Experimental Haemostasis, University Medical Centre Mainz, Mainz, 55131, Germany.

Diversification at the transcriptome 3'end is an important and evolutionarily conserved layer of gene regulation associated with differentiation and dedifferentiation processes. Here, we identify extensive transcriptome 3'end-alterations in neuroblastoma, a tumour entity with a paucity of recurrent somatic mutations and an unusually high frequency of spontaneous regression. Utilising extensive RNAi-screening we reveal the landscape and drivers of transcriptome 3'end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including a differentiation RNA-operon. Read More

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December 2018

Exploratory genome-wide association analysis of response to ketamine and a polygenic analysis of response to scopolamine in depression.

Transl Psychiatry 2018 Dec 14;8(1):280. Epub 2018 Dec 14.

Statistical Genomics and Data Analysis Core, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.

Growing evidence suggests that the glutamatergic modulator ketamine has rapid antidepressant effects in treatment-resistant depressed subjects. The anticholinergic agent scopolamine has also shown promise as a rapid-acting antidepressant. This study applied genome-wide markers to investigate the role of genetic variants in predicting acute antidepressant response to both agents. Read More

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December 2018

Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas.

Nat Commun 2018 Dec 14;9(1):5330. Epub 2018 Dec 14.

Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, 14263, NY, USA.

Understanding metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Here, using transcriptomic data for 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we present a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. We confirm pathway dysregulation in separate patient populations, demonstrating the robustness of our approach. Read More

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December 2018

Population genetics and characterization of isolates in western jackdaws and game birds in Finland.

Appl Environ Microbiol 2018 Dec 14. Epub 2018 Dec 14.

Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, FI-00014, Finland

Poultry is considered a major reservoir and source of human campylobacteriosis but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized from western jackdaws (n=91, 43%), mallard ducks (n=82, 76%) and pheasants (n=9, 9%). Most of the western jackdaw and mallard duck isolates represented MLST sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Read More

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December 2018

Targeting early changes in the synovial microenvironment: a new class of immunomodulatory therapy?

Ann Rheum Dis 2018 Dec 14. Epub 2018 Dec 14.

Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK

Objectives: Controlled immune responses rely on integrated crosstalk between cells and their microenvironment. We investigated whether targeting proinflammatory signals from the extracellular matrix that persist during pathological inflammation provides a viable strategy to treat rheumatoid arthritis (RA).

Methods: Monoclonal antibodies recognising the fibrinogen-like globe (FBG) of tenascin-C were generated by phage display. Read More

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December 2018

Towards Greater Inclusion in Cancer Genomics Studies.

Authors:
Franklin W Huang

Cancer Res 2018 Dec;78(24):6726-6727

Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California.

The study by Jaratlerdsiri and colleagues represents the first whole-genome sequencing study of prostate cancer from men in sub-Saharan Africa. Preliminary findings include a higher tumor mutation burden in these tumors compared with data from other available prostate cancer cohorts. Although larger studies are needed and greater effort and investment to include patients of African ancestry in cancer genomic studies overall, the findings begin to catalog the diversity of prostate cancer genomics in the African population, which has a high burden of disease and mortality from prostate cancer. Read More

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December 2018

Development of an anti-hepatitis B virus (HBV) agent through the structure-activity relationship of the interferon-like small compound CDM-3008.

Bioorg Med Chem 2018 Dec 5. Epub 2018 Dec 5.

Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

Hepatitis B, a viral infectious disease caused by hepatitis B virus (HBV), is a life-threatening disease that leads liver cirrhosis and liver cancer. Because the current treatments for HBV, such as an interferon (IFN) formulation or nucleoside/nucleotide analogues, are not sufficient, the development of a more effective agent for HBV is urgent required. CDM-3008 (1, 2-(2,4-bis(trifluoromethyl)imidazo[1,2-a][1,8]naphthyridin-8-yl)-1,3,4-oxadiazole) (RO8191)) is a small molecule with an imidazo[1,2-a][1,8]naphthyridine scaffold that shows anti-HCV activity with an IFN-like effect. Read More

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December 2018

New views on the Malpighian tubule from post-genomic technologies.

Curr Opin Insect Sci 2018 Oct 25;29:7-11. Epub 2018 May 25.

Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom.

Successful insect diversification depends at least in part on the ability to osmoregulate successfully across a broad range of ecological niches. First described in the 17th Century, and Malpighian tubules have been studied physiologically for 70 years. However, our understanding has been revolutionized by the advent of genomics, transcriptomics, proteomics and metabolomics. Read More

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October 2018

Omics approaches to study juvenile hormone synthesis.

Curr Opin Insect Sci 2018 Oct 26;29:49-55. Epub 2018 May 26.

Department of Biological Sciences and Biomolecular Science Institute, Florida International University, Miami, FL, USA. Electronic address:

The juvenile hormones (JHs) are a family of insect acyclic sesquiterpenoids produced by the corpora allata (CA), a pair of endocrine glands connected to the brain. They are involved in the regulation of development, reproduction, behavior, caste determination, diapause, stress response, and numerous polyphenisms. In the post-genomics era, comprehensive analyses using functional 'omics' technologies such as transcriptomics, proteomics and metabolomics have increased our understanding of the activity of the minute CA. Read More

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October 2018

Gene editing technologies and applications for insects.

Curr Opin Insect Sci 2018 Aug 22;28:66-72. Epub 2018 May 22.

Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

Initially discovered in bacteria, CRISPR-based genome editing endonucleases have proven remarkably amenable for adaptation to insects. To date, these endonucleases have been utilized in a plethora of both model and non-model insects including diverse flies, bees, beetles, butterflies, moths, and grasshoppers, to name a few, thereby revolutionizing functional genomics of insects. In addition to basic genome editing, they have also been invaluable for advanced genome engineering and synthetic biology applications. Read More

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DPYD, TYMS and MTHFR Genes Polymorphism Frequencies in a Series of Turkish Colorectal Cancer Patients.

J Pers Med 2018 Dec 13;8(4). Epub 2018 Dec 13.

Personalized Medicine and Pharmacogenomics/Genomics Research Centre-BIFAGEM, Izmir 35350, Turkey..

Fluoropyrimidine-based chemotherapy is extensively used for the treatment of solid cancers, including colorectal cancer. However, fluoropyrimidine-driven toxicities are a major problem in the management of the disease. The grade and type of the toxicities depend on demographic factors, but substantial inter-individual variation in fluoropyrimidine-related toxicity is partly explained by genetic factors. Read More

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December 2018
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Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome.

Life (Basel) 2018 Dec 13;8(4). Epub 2018 Dec 13.

Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.

Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with , , and , evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions. Read More

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December 2018

Pharmacogenomic assessment of herbal drugs in affective disorders.

Biomed Pharmacother 2019 Jan 6;109:1148-1162. Epub 2018 Nov 6.

Sunandan Divatia School of Science, NMIMS (Deemed-to-be University), Vile Parle (W), Mumbai, 400 056, Maharashtra, India. Electronic address:

Anxiety and depression, the most prevalent psychiatric disorders are co-morbid in nature affecting several people across the world. There is an increase in demand for complementary and alternative medicines, specifically herbal botanicals due to various side effects exhibited by conventional drugs. Herbal drugs mentioned in traditional medicines, face acceptance issues by the medical community due to lack of scientific data regarding their neurochemical pathways. Read More

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January 2019

Children's untreated decay is positively associated with past caries experience and with current salivary loads of mutans Streptococci; negatively with self-reported maternal iron supplements during pregnancy: a multifactorial analysis.

J Public Health Dent 2018 Dec 14. Epub 2018 Dec 14.

Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.

Objectives: This study explored the association of children's salivary characteristics, past caries experience, birth weight, and reported maternal prenatal vitamin and mineral supplementation with the dental untreated decay of the child.

Methods: This cross-sectional study, a sub-study of Griffith University Environments for Healthy Living birth cohort study, was conducted on 174 mother-child dyads. Mother's prenatal usage of vitamin and mineral supplements; child's birthweight; salivary pH, buffering capacity, and levels of salivary MS and LB were explored as risk indicators. Read More

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December 2018

Survival and outcome in MELAS not only depends on onset and disease duration.

J Neurol Sci 2018 Dec 6;397:9-10. Epub 2018 Dec 6.

University of Tunis El Manar and Genomics Platform, Pasteur Institute of Tunis, Tunisia.

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December 2018

Investigating the physiological mechanisms underlying Salicornia ramosissima response to atmospheric CO enrichment under coexistence of prolonged soil flooding and saline excess.

Plant Physiol Biochem 2018 Dec 6;135:149-159. Epub 2018 Dec 6.

Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 1095, 41080, Sevilla, Spain.

A 45-days long climatic chamber experiment was design to evaluate the effect of 400 and 700 ppm atmospheric CO treatments with and without soil water logging in combination with 171 and 510 mM NaCl in the halophyte Salicornia ramosissima. In order to ascertain the possible synergetic impact of these factors associate to climatic change in this plant species physiological and growth responses. Our results indicated that elevated atmospheric CO concentration improved plant physiological performance under suboptimal root-flooding and saline conditions plants. Read More

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December 2018

Identification of the full 26 cytochrome P450 (CYP) genes and analysis of their expression in response to benzo[α]pyrene in the marine rotifer Brachionus rotundiformis.

Comp Biochem Physiol Part D Genomics Proteomics 2018 Dec 4;29:185-192. Epub 2018 Dec 4.

Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea. Electronic address:

Cytochrome P450s (CYPs) are a large gene superfamily that are found in all living organisms. CYPs have a key role in detoxification of xenobiotics and endogenous chemicals. Although aquatic invertebrate CYPs and their detoxification mechanisms have been reported, little is known about interspecific comparison of CYPs and their detoxification mechanism in the rotifer Brachionus spp. Read More

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December 2018

Molecular systematics of the Triplophysa robusta (Cobitoidea) complex: extensive gene flow in a depauperate lineage.

Mol Phylogenet Evol 2018 Dec 11. Epub 2018 Dec 11.

Key Laboratory of Adaptation and Evolution of Plateau Biota, and Laboratory of Plateau Fish Evolutionary and Functional Genomics, and Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China. Electronic address:

Gene flow between populations assumed to be isolated frequently leads to incorrect inferences of evolutionary history. Understanding gene flow and its causes has long been a key topic in evolutionary biology. In this study, we explored the evolutionary history of the Triplophysa robusta complex, using a combination of multilocus analyses and coalescent simulation. Read More

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December 2018

Research Update and Opportunity of Non-hormonal Male Contraception: Histone Demethylase KDM5B-Based Targeting.

Pharmacol Res 2018 Dec 11. Epub 2018 Dec 11.

Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea. Electronic address:

With the continued increase in global human population, diverse contraception approaches have become increasingly essential, including non-hormonal male contraception. Non-hormonal approaches to contraception are very convenient; however, such options are limited because data regarding the identification and characterization of tissue/cell-specific targets and appropriate small molecule candidate contraceptives are lacking. Based on in-silico studies of genomics, transcriptomics, and proteomics, performed by mining datasets in PubMed, we first reviewed testis-, epididymis-, and germline cell-specific genes/proteins, with the aim of presenting evidence that many of these could become 'druggable' targets for the development of non-hormonal male contraceptives in the future. Read More

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December 2018

Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree.

Genomics Proteomics Bioinformatics 2018 Dec 11. Epub 2018 Dec 11.

T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes by using the CVTree method, which is based on whole-genome information. Read More

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December 2018

COPI localizes to the early Golgi in Aspergillus nidulans.

Fungal Genet Biol 2018 Dec 11. Epub 2018 Dec 11.

Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, Madrid 28040, Spain. Electronic address:

Coatomer-I (COPI) is a heteromeric protein coat that facilitates the budding of membranous carriers mediating Golgi-to-ER and intra-Golgi transport. While the structural features of COPI have been thoroughly investigated, its physiological role is insufficiently understood. Here we exploit the amenability of A. Read More

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December 2018
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Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis.

Microb Pathog 2018 Dec 11. Epub 2018 Dec 11.

Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan.

Acinetobacter baumannii, the gram-negative bacteria emerged as an extremely critical pathogen causing nosocomial and different kinds of infections. A. baumannii exhibit resistivity towards various classes of antibiotics that shows that there is a dire need to search more drug targets by exploiting the full genome of the bacteria. Read More

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December 2018

Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida.

Microb Pathog 2018 Dec 11. Epub 2018 Dec 11.

Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok, 10900, Thailand. Electronic address:

Pasteurella multocida causes respiratory infectious diseases in a multitude of birds and mammals. A number of virulence-associated genes were reported across different strains of P. multocida, including those involved in the iron transport and metabolism. Read More

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December 2018

Detection of Pediatric Bacterial Meningitis Pathogens from Cerebrospinal Fluid by Next-Generation Sequencing Technology.

J Infect 2018 Dec 11. Epub 2018 Dec 11.

Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China. Electronic address:

Objectives: Bacterial meningitis remains one of the major challenges in infectious diseases, leading to sequel in many cases. A prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bacterial meningitis. Although various targeted tests for cerebrospinal fluid (CSF) samples are available, it is a big problem for the identification of etiology of bacterial meningitis. Read More

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December 2018

Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure.

Genomics 2018 Dec 11. Epub 2018 Dec 11.

College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao 266061, China; Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao 266061, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China. Electronic address:

The identification of drug-target interactions has great significance for pharmaceutical scientific research. Since traditional experimental methods identifying drug-target interactions is costly and time-consuming, the use of machine learning methods to predict potential drug-target interactions has attracted widespread attention. This paper presents a novel drug-target interactions prediction method called LRF-DTIs. Read More

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December 2018

Organoid Modeling of the Tumor Immune Microenvironment.

Cell 2018 Dec;175(7):1972-1988.e16

Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA. Electronic address:

In vitro cancer cultures, including three-dimensional organoids, typically contain exclusively neoplastic epithelium but require artificial reconstitution to recapitulate the tumor microenvironment (TME). The co-culture of primary tumor epithelia with endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has been particularly elusive. Here, an air-liquid interface (ALI) method propagated patient-derived organoids (PDOs) from >100 human biopsies or mouse tumors in syngeneic immunocompetent hosts as tumor epithelia with native embedded immune cells (T, B, NK, macrophages). Read More

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December 2018
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A review of lifestyle, metabolic risk factors and blood-based biomarkers for early diagnosis of pancreatic ductal adenocarcinoma.

J Gastroenterol Hepatol 2018 Dec 14. Epub 2018 Dec 14.

Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health|, University of Oxford, Oxford, UK.

We aimed to review the epidemiologic literature examining lifestyle, metabolic risk factors, and blood-based biomarkers including multi-omics (genomics, proteomics, and metabolomics) and to discuss how these predictive markers can inform early diagnosis of pancreatic ductal adenocarcinoma (PDAC). A search of the PubMed database was conducted in June 2018 to review epidemiologic studies of (1) lifestyle and metabolic risk factors for PDAC, genome-wide association studies (GWAS), and risk prediction models incorporating these factors and (2) blood-based biomarkers for PDAC (conventional diagnostic markers, metabolomics, and proteomics). Prospective cohort studies have reported at least twenty possible risk factors for PDAC, including smoking, heavy alcohol drinking, adiposity, diabetes, and pancreatitis, but the relative risks (RR) and population attributable fractions of individual risk factors are small (mostly <10%). Read More

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December 2018
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The human visual system estimates angle features in an internal reference frame: A computational and psychophysical study.

J Vis 2018 Dec;18(13):10

Shanghai Key Laboratory of Brain Functional Genomics, Key Laboratory of Brain Functional Genomics, Ministry of Education, School of Psychology and Cognitive Science, East China Normal University, Shanghai, China.

Angle perception is an important middle-level visual process, combining line features to generate an integrated shape percept. Previous studies have proposed two theories of angle perception-a combination of lines and a holistic feature following Weber's law. However, both theories failed to explain the dual-peak fluctuations of the just-noticeable difference (JND) across angle sizes. Read More

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December 2018

Sugarcane apoplast fluid modulates the global transcriptional profile of the diazotrophic bacteria Paraburkholderia tropica strain Ppe8.

PLoS One 2018 14;13(12):e0207863. Epub 2018 Dec 14.

Embrapa Agrobiologia, Seropédica-RJ-CEP, Brazil.

The stalk apoplast fluid of sugarcane contains different sugars, organic acids and amino acids that may supply the demand for carbohydrates by endophytic bacteria including diazotrophs P. tropica (syn. B. Read More

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December 2018

CD71+VISTA+ erythroid cells promote the development and function of regulatory T cells through TGF-β.

PLoS Biol 2018 Dec 14;16(12):e2006649. Epub 2018 Dec 14.

Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.

Cell-surface transferrin receptor (CD71+) erythroid cells are abundant in newborns with immunomodulatory properties. Here, we show that neonatal CD71+ erythroid cells express significant levels of V-domain Immunoglobulin (Ig) Suppressor of T Cell Activation (VISTA) and, via constitutive production of transforming growth factor (TGF)- β, play a pivotal role in promotion of naïve CD4+ T cells into regulatory T cells (Tregs). Interestingly, we discovered that CD71+VISTA+ erythroid cells produce significantly higher levels of TGF-β compared to CD71+VISTA- erythroid cells and CD71+ erythroid cells from the VISTA knock-out (KO) mice. Read More

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December 2018

Enteropathogenic E. coli relies on collaboration between the formin mDia1 and the Arp2/3 complex for actin pedestal biogenesis and maintenance.

PLoS Pathog 2018 Dec 14;14(12):e1007485. Epub 2018 Dec 14.

Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America.

Enteropathogenic and enterohemorrhagic E. coli (EPEC and EHEC) are closely related extracellular pathogens that reorganize host cell actin into "pedestals" beneath the tightly adherent bacteria. This pedestal-forming activity is both a critical step in pathogenesis, and it makes EPEC and EHEC useful models for studying the actin rearrangements that underlie membrane protrusions. Read More

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December 2018

Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus).

PLoS One 2018 14;13(12):e0208986. Epub 2018 Dec 14.

Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain.

Molecular techniques allow non-invasive dietary studies from faeces, providing an invaluable tool to unveil ecological requirements of endangered or elusive species. They contribute to progress on important issues such as genomics, population genetics, dietary studies or reproductive analyses, essential knowledge for conservation biology. Nevertheless, these techniques require general methods to be tailored to the specific research objectives, as well as to substrate- and species-specific constraints. Read More

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December 2018
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What Should a Psychiatrist Know About Genetics? Review and Recommendations From the Residency Education Committee of the International Society of Psychiatric Genetics.

J Clin Psychiatry 2018 Nov 27;80(1). Epub 2018 Nov 27.

Centre for Addiction and Mental Health and University of Toronto, Toronto, Ontario, Canada.

The International Society of Psychiatric Genetics (ISPG) created a Residency Education Committee with the purpose of identifying key genetic knowledge that should be taught in psychiatric training programs. Thirteen committee members were appointed by the ISPG Board of Directors, based on varied training, expertise, gender, and national origin. The Committee has met quarterly for the past 2 years, with periodic reports to the Board and to the members of the Society. Read More

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November 2018

A case of YY1-associated syndromic learning disability or Gabriele-de Vries syndrome with myasthenia gravis.

Am J Med Genet A 2018 Dec 14. Epub 2018 Dec 14.

Department of Neurology, Mayo Clinic, Mayo Clinic, Scottsdale, Arizona.

Exome sequencing is being used increasingly to evaluate patients with intellectual disability. YY1 is a ubiquitously distributed transcription factor belonging to the GLIKruppel class of zinc finger proteins recently recognized as the causative gene in 23 patients for the Gabriele-de Vries syndrome. We report a new case with similar features and a novel variant in YY1, in a region of the gene, which has not previously been reported. Read More

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December 2018

The Importance of Drug Safety and Tolerability in the Development of New Immunosuppressive Therapy for Transplant Recipients.

Am J Transplant 2018 Dec 14. Epub 2018 Dec 14.

Critical Path Institute, Tucson, AZ, USA.

The Transplant Therapeutics Consortium (TTC) is a public-private partnership between the Food and Drug Administration and the transplantation community including the transplantation societies and members of the biopharmaceutical industry. The TTC was formed to accelerate the process of developing new medical products for transplant patients. The initial goals of this collaboration are: 1) To define which aspects of the kidney transplant drug-development process have clear needs for improvement from an industry and regulatory perspective; 2) To define which of the unmet needs in the process could be positively impacted through the development of specific drug development tools based on available data; and 3) To determine the most appropriate pathway to achieve regulatory acceptance of the proposed process-accelerating tools. Read More

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December 2018

Compatibility of CO laser surgery and fluorescence detection in head and neck cancer cells.

Head Neck 2018 Dec 14. Epub 2018 Dec 14.

Department of Otorhinolaryngology and Head and Neck Surgery, Radboud University Medical Center, Nijmegen, The Netherlands.

Background: Surgical treatment of cancer requires tumor excision with emphasis on function preservation which is achieved in (early stage) laryngeal cancer by transoral carbon dioxide (CO ) laser surgery. Whereas conventional laser surgery is restricted by the surgeon's visual recognition of tumor tissue, new approaches based on fluorescence-guided surgery (FGS) improve the detection of the tumor and its margin. However, it is unclear whether fluorophores are compatible with high-power laser application or whether precision is compromised by laser-induced bleaching of the dye. Read More

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December 2018
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The -44 C/G (rs1800972) polymorphism of the β-defensin 1 is associated with increased risk of developing type 2 diabetes mellitus.

Mol Genet Genomic Med 2018 Dec 13. Epub 2018 Dec 13.

Department of Molecular Biology, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico.

Background: The aim of this study was to establish the association of two polymorphisms of the β-defensin 1 gene (DEFB1, OMIM#602056) with the risk of developing type 2 diabetes mellitus (T2DM) in a group of Mexican patients.

Methods: The 5'UTR -20 G/A, and -44 C/G polymorphisms of DEFB1 gene were genotyped by 5' exonuclease TaqMan assays in a group of 252 patients with T2DM and 522 healthy control.

Results: Under dominant and additive models adjusted for the risk factors, the C allele of the -44 C/G polymorphism was associated with increased risk of T2DM (OR = 1. Read More

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December 2018

xCas9 expands the scope of genome editing with reduced efficiency in rice.

Plant Biotechnol J 2018 Dec 13. Epub 2018 Dec 13.

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

CRISPR-Cas9 systems have been widely used in animals and plants for genome editing, epigenetic modification, etc. (Cong et al., 2013, Hilton et al. Read More

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December 2018
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Biallelic CCM3 mutations cause a clonogenic survival advantage and endothelial cell stiffening.

J Cell Mol Med 2018 Dec 13. Epub 2018 Dec 13.

Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany.

CCM3, originally described as PDCD10, regulates blood-brain barrier integrity and vascular maturation in vivo. CCM3 loss-of-function variants predispose to cerebral cavernous malformations (CCM). Using CRISPR/Cas9 genome editing, we here present a model which mimics complete CCM3 inactivation in cavernous endothelial cells (ECs) of heterozygous mutation carriers. Read More

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December 2018