Read by QxMD icon Read

genome research

Nigel W Beebe
Mosquitoes' importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification - a target whose utility for discriminating mosquitoes is now escalating...
March 22, 2018: Parasitology
Haoyang Cai
ChromothripsisDB ( ) is a manually curated database containing a unified description of published chromothripsis cases and relevant genomic aberrations. Available data includes copy number alterations, chromosome structural variations, and gene annotations. The criteria used for detecting chromothripsis in each study are also provided. At present, the molecular mechanisms involved in chromothripsis phenomenon are not fully understood. Thus, further studies with large number of identified chromothripsis samples are needed...
2018: Methods in Molecular Biology
Kazuko Koshiba-Takeuchi
In situ hybridization is defined as one of the most useful and powerful methods to know where genes (e.g., mRNA, ncRNA) of interest are expressed in tissues. Expression of mRNA can be detected as blue or dark purple signals though hybridization, immunoreaction and coloring steps. Genome-wide approaches in various model animals have been conducted thoroughly, and have led to new research areas aimed at uncovering novel gene functions in cell differentiation and development. To elucidate gene function, spatiotemporal gene expression analysis is very important...
2018: Methods in Molecular Biology
Ensaf M Al-Hujaily, Tanvir Khatlani, Zeyad Alehaideb, Rizwan Ali, Bader Almuzaini, Bahauddeen M Alrfaei, Jahangir Iqbal, Imadul Islam, Shuja Malik, Bader A Marwani, Salam Massadeh, Atef Nehdi, Barrak Alsomaie, Bader Debasi, Ibraheem Bushnak, Saeed Noibi, Syed Hussain, Wahid Abdul Wajid, Jean-Pierre Armand, Sheraz Gul, Julen Oyarzabal, Rana Rais, Chas Bountra, Ahmed Alaskar, Bander Al Knawy, Mohamed Boudjelal
The 'Therapeutics discovery: From bench to first in-human trials' conference, held at the King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGHA), Kingdom of Saudi Arabia (KSA) from October 10-12, 2017, provided a unique opportunity for experts worldwide to discuss advances in drug discovery and development, focusing on phase I clinical trials. It was the first event of its kind to be hosted at the new research center, which was constructed to boost drug discovery and development in the KSA in collaboration with institutions, such as the Academic Drug Discovery Consortium in the United States of America (USA), Structural Genomics Consortium of the University of Oxford in the United Kingdom (UK), and Institute of Materia Medica of the Chinese Academy of Medical Sciences in China...
March 2018: Biomedical Reports
Guoli Shi, Tetsuro Suzuki
Hepatitis C virus (HCV), a major etiologic agent of human liver diseases, is a positive-sense single-stranded RNA virus and is classified in the Flaviviridae family. Although research findings for the assembly of HCV particles are accumulating due to development of HCV cell culture system, the mechanism(s) by which the HCV genome becomes encapsidated remains largely unclear. In general, viral RNA represents only a small fraction of the RNA molecules in the cells infected with RNA viruses, but the viral genomic RNA is considered to selectively packaged into virions...
2018: Frontiers in Microbiology
Jian Weng, Peixun Zhang, Xiaofeng Yin, Baoguo Jiang
Peripheral nerve injury (PNI) usually leads to progressive muscle atrophy and poor functional recovery. Previous studies have demonstrated that non-coding ribonucleic acid (ncRNA) is a key regulator of muscle atrophy and beneficial for the treatment of PNI. We aimed to analyze the whole transcriptome involved in denervated muscle atrophy after PNI. Animal models of sciatic nerve injury were assessed at 0 (control group), 1, 2, 4, and 8 weeks after injury. The expression patterns in the whole transcriptome in the gastrocnemius muscle were profiled using RNA sequencing at each time point and compared to that obtained in the control group...
2018: Frontiers in Molecular Neuroscience
DaYang Chen, HeFu Zhen, Yong Qiu, Ping Liu, Peng Zeng, Jun Xia, QianYu Shi, Lin Xie, Zhu Zhu, Ya Gao, GuoDong Huang, Jian Wang, HuanMing Yang, Fang Chen
Research based on a strategy of single-cell low-coverage whole genome sequencing (SLWGS) has enabled better reproducibility and accuracy for detection of copy number variations (CNVs). The whole genome amplification (WGA) method and sequencing platform are critical factors for successful SLWGS (<0.1 × coverage). In this study, we compared single cell and multiple cells sequencing data produced by the HiSeq2000 and Ion Proton platforms using two WGA kits and then comprehensively evaluated the GC-bias, reproducibility, uniformity and CNV detection among different experimental combinations...
March 21, 2018: Scientific Reports
Brian S White, Irena Lanc, Julie O'Neal, Harshath Gupta, Robert S Fulton, Heather Schmidt, Catrina Fronick, Edward A Belter, Mark Fiala, Justin King, Greg J Ahmann, Mary DeRome, Elaine R Mardis, Ravi Vij, John F DiPersio, Joan Levy, Daniel Auclair, Michael H Tomasson
Multiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide variants (SNVs). To enable integrative studies across these diverse mutation types, we developed a capture-based sequencing platform to detect their occurrence in 465 genes altered in MM and used it to sequence 95 primary tumor-normal pairs to a mean depth of 104×. We detected cases of hyperdiploidy (23%), deletions of 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), and 17p (4%), and amplification of 1q (19%)...
March 21, 2018: Blood Cancer Journal
Marlena S Fejzo, Olga V Sazonova, J Fah Sathirapongsasuti, Ingileif B Hallgrímsdóttir, Vladimir Vacic, Kimber W MacGibbon, Frederic P Schoenberg, Nicholas Mancuso, Dennis J Slamon, Patrick M Mullin
Hyperemesis gravidarum (HG), severe nausea and vomiting of pregnancy, occurs in 0.3-2% of pregnancies and is associated with maternal and fetal morbidity. The cause of HG remains unknown, but familial aggregation and results of twin studies suggest that understanding the genetic contribution is essential for comprehending the disease etiology. Here, we conduct a genome-wide association study (GWAS) for binary (HG) and ordinal (severity of nausea and vomiting) phenotypes of pregnancy complications. Two loci, chr19p13...
March 21, 2018: Nature Communications
José A Del Campo, Rocío Gallego-Durán, Paloma Gallego, Lourdes Grande
Genetics and epigenetics play a key role in the development of several diseases, including nonalcoholic fatty liver disease (NAFLD). Family studies demonstrate that first degree relatives of patients with NAFLD are at a much higher risk of the disease than the general population. The development of the Genome Wide Association Study (GWAS) technology has allowed the identification of numerous genetic polymorphisms involved in the evolution of diseases (e.g., PNPLA3 , MBOAT7 ). On the other hand, epigenetic changes interact with inherited risk factors to determine an individual's susceptibility to NAFLD...
March 19, 2018: International Journal of Molecular Sciences
Paul D Blischak, Julia Chifman, Andrea D Wolfe, Laura S Kubatko
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees...
March 19, 2018: Systematic Biology
Ulrike Bechtold, John N Ferguson, Philip M Mullineaux
The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterisation of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding in how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) is a great asset to understand the mechanisms of multiple stress tolerances...
March 17, 2018: Journal of Experimental Botany
A E Webb, I A Youngworth, M Kaya, C L Gitter, E A O'Hare, B May, H H Cheng, M E Delany
Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element...
March 19, 2018: Poultry Science
Joshua S Talboom, Matthew J Huentelman
Advances in information technology (IT) hardware in the last decade has led to the advent of small connected devices broadly referred to as the Internet of Things (IoT). The IoT and its subcategory of wearable devices (wearables) both have the potential to greatly impact biomedical research. This focused review covers recent biomedical research using the IoT and wearables in the area of neurological traits and disease. In addition, a look into the future of biomedical research using the IoT/wearables as well as some areas requiring further consideration by the field will be discussed...
March 19, 2018: Human Molecular Genetics
Yanting Luo, Jianlin He, Xiguang Xu, Ming-An Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie
Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data...
March 2018: PLoS Computational Biology
Kathy H Y Shair, Akhil Reddy, Vaughn S Cooper
Latent membrane protein 1 (LMP1) is an Epstein-Barr virus (EBV) oncogenic protein that has no intrinsic enzymatic activity or sequence homology to cellular or viral proteins. The oncogenic potential of LMP1 has been ascribed to pleiotropic signaling properties initiated through protein-protein interactions in cytosolic membrane compartments, but the effects of LMP1 extend to nuclear and extracellular processes. Although LMP1 is one of the latent genes required for EBV-immortalization of B cells, the biology of LMP1 in the pathogenesis of the epithelial cancer nasopharyngeal carcinoma (NPC) is more complex...
March 21, 2018: Cancers
Christiana Leimena, Hongyu Qiu
Hypertension is a complex, multifactorial disease that involves the coexistence of multiple risk factors, environmental factors and physiological systems. The complexities extend to the treatment and management of hypertension, which are still the pursuit of many researchers. In the last two decades, various genes have emerged as possible biomarkers and have become the target for investigations of specialized drug design based on its risk factors and the primary cause. Owing to the growing technology of microarrays and next-generation sequencing, the non-protein-coding RNAs (ncRNAs) have increasingly gained attention, and their status of redundancy has flipped to importance in normal cellular processes, as well as in disease progression...
March 21, 2018: International Journal of Molecular Sciences
Seyma Katrinli, G Nilay Karatas Erkut, Kamil Ozdil, Feruze Yilmaz Enc, Oguzhan Ozturk, Resul Kahraman, Ilyas Tuncer, Gizem Dinler Doganay, Levent Doganay
AIM: Chronic hepatitis B (CHB) is a global health problem. Recent genome-wide association studies (GWAS) exposed signifi-cant association between the human leukocyte antigen (HLA) class II region, including both DP and DQ loci, and chronic hepatitis B. Previous research also indicated the involvement of adaptive immune system in Hepatitis B seroconversion. The aim of this study is to investigate possible polymorphisms in the HLA-DP locus that can contribute to immune response to Hepatitis B virus (HBV)...
July 2017: Acta Gastro-enterologica Belgica
Maria José Carregosa Pinheiro Dos Santos, André Uchimura Bastos, Vitor Rodrigues da Costa, Rosana Delcelo, Susan Chow Lindsey, Gabriel Avelar Colozza-Gama, Hongzhuang Peng, Frank J Rauscher, Gisele Oler, Janete Maria Cerutti
We previously described that LIM domain containing 2 (LIMD2) overexpression was closely correlated with metastatic process in papillary thyroid carcinoma (PTC). We here evaluated the expression of LIMD2 in a series of non-metastatic and metastatic PTC and their matched lymph node metastases via immunohistochemistry. LIMD2 was expressed in 74 (81%) of primary PTC and 35 (95%) of lymph node metastases. Sub-analysis performed in 37 matched samples demonstrated that in four cases, LIMD2 is expressed in lymph node metastases, while it is not expressed in primary tumors...
March 20, 2018: Endocrine Pathology
Azmeraw T Amare, Klaus Oliver Schubert, Fasil Tekola-Ayele, Yi-Hsiang Hsu, Katrin Sangkuhl, Gregory Jenkins, Ryan M Whaley, Poulami Barman, Anthony Batzler, Russ B Altman, Volker Arolt, Jürgen Brockmöller, Chia-Hui Chen, Katharina Domschke, Daniel K Hall-Flavin, Chen-Jee Hong, Ari Illi, Yuan Ji, Olli Kampman, Toshihiko Kinoshita, Esa Leinonen, Ying-Jay Liou, Taisei Mushiroda, Shinpei Nonen, Michelle K Skime, Liewei Wang, Masaki Kato, Yu-Li Liu, Verayuth Praphanphoj, Julia C Stingl, William V Bobo, Shih-Jen Tsai, Michiaki Kubo, Teri E Klein, Richard M Weinshilboum, Joanna M Biernacka, Bernhard T Baune
Studies reported a strong genetic correlation between the Big Five personality traits and major depressive disorder (MDD). Moreover, personality traits are thought to be associated with response to antidepressants treatment that might partly be mediated by genetic factors. In this study, we examined whether polygenic scores (PGSs) derived from the Big Five personality traits predict treatment response and remission in patients with MDD who were prescribed selective serotonin reuptake inhibitors (SSRIs). In addition, we performed meta-analyses of genome-wide association studies (GWASs) on these traits to identify genetic variants underpinning the cross-trait polygenic association...
2018: Frontiers in Psychiatry
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"