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Frontiers in Genetics

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https://www.readbyqxmd.com/read/29459883/transcriptomic-and-proteomic-profiling-revealed-high-proportions-of-odorant-binding-and-antimicrobial-defense-proteins-in-olfactory-tissues-of-the-house-mouse
#1
Barbora Kuntová, Romana Stopková, Pavel Stopka
Mammalian olfaction depends on chemosensory neurons of the main olfactory epithelia (MOE), and/or of the accessory olfactory epithelia in the vomeronasal organ (VNO). Thus, we have generated the VNO and MOE transcriptomes and the nasal cavity proteome of the house mouse, Mus musculus musculus . Both transcriptomes had low levels of sexual dimorphisms, while the soluble proteome of the nasal cavity revealed high levels of sexual dimorphism similar to that previously reported in tears and saliva. Due to low levels of sexual dimorphism in the olfactory receptors in MOE and VNO, the sex-specific sensing seems less likely to be dependent on receptor repertoires...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29459882/identification-of-a-new-mullet-species-complex-based-on-an-integrative-molecular-and-cytogenetic-investigation-of-mugil-hospes-mugilidae-mugiliformes
#2
Mauro Nirchio, Fabilene G Paim, Valentina Milana, Anna R Rossi, Claudio Oliveira
Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil , a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes , commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456555/a-bootstrap-based-measure-robust-to-the-choice-of-normalization-methods-for-detecting-rhythmic-features-in-high-dimensional-data
#3
Yolanda Larriba, Cristina Rueda, Miguel A Fernández, Shyamal D Peddada
Motivation: Gene-expression data obtained from high throughput technologies are subject to various sources of noise and accordingly the raw data are pre-processed before formally analyzed. Normalization of the data is a key pre-processing step, since it removes systematic variations across arrays. There are numerous normalization methods available in the literature. Based on our experience, in the context of oscillatory systems, such as cell-cycle, circadian clock, etc., the choice of the normalization method may substantially impact the determination of a gene to be rhythmic...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456554/compound-heterozygous-variants-in-the-coiled-coil-domain-containing-40-gene-in-a-chinese-family-with-primary-ciliary-dyskinesia-cause-extreme-phenotypic-diversity-in-cilia-ultrastructure
#4
Lin Yang, Santasree Banerjee, Jie Cao, Xiaohong Bai, Zhijun Peng, Haixia Chen, Hui Huang, Peng Han, Shunyu Feng, Na Yi, Xueru Song, Jing Wu
Purpose: Primary ciliary dyskinesia (PCD) is a rare genetic disorder manifested with recurrent infections of respiratory tract and infertility. Mutations in more than 20 genes including the Coiled-Coil Domain Containing 40 ( CCDC40 ) gene are associated with PCD. A Chinese proband with a clinical diagnosis of PCD was analyzed for mutations in these genes to identify the genetic basis of the disease in the family. The proband showed altered mucociliary clearance of the airways, various degree of hyperemia and edema of the mucous membrane, left/right body asymmetry, infertility and ultrastructural abnormality of cilia in both sperm and bronchioles...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456553/silencing-of-iron-and-heme-related-genes-revealed-a-paramount-role-of-iron-in-the-physiology-of-the-hematophagous-vector-rhodnius-prolixus
#5
Ana B Walter-Nuno, Mabel L Taracena, Rafael D Mesquita, Pedro L Oliveira, Gabriela O Paiva-Silva
Iron is an essential element for most organisms However, free iron and heme, its complex with protoporphyrin IX, can be extremely cytotoxic, due to the production of reactive oxygen species, eventually leading to oxidative stress. Thus, eukaryotic cells control iron availability by regulating its transport, storage and excretion as well as the biosynthesis and degradation of heme. In the genome of Rhodnius prolixus , the vector of Chagas disease, we identified 36 genes related to iron and heme metabolism We performed a comprehensive analysis of these genes, including identification of homologous genes described in other insect genomes...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456552/identification-of-single-nucleotide-non-coding-driver-mutations-in-cancer
#6
REVIEW
Kok A Gan, Sebastian Carrasco Pro, Jared A Sewell, Juan I Fuxman Bass
Recent whole-genome sequencing studies have identified millions of somatic variants present in tumor samples. Most of these variants reside in non-coding regions of the genome potentially affecting transcriptional and post-transcriptional gene regulation. Although a few hallmark examples of driver mutations in non-coding regions have been reported, the functional role of the vast majority of somatic non-coding variants remains to be determined. This is because the few driver variants in each sample must be distinguished from the thousands of passenger variants and because the logic of regulatory element function has not yet been fully elucidated...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456551/genetic-diversity-of-the-endangered-neotropical-cichlid-fish-gymnogeophagus-setequedas-in-brazil
#7
Lenice Souza-Shibatta, Thais Kotelok-Diniz, Dhiego G Ferreira, Oscar A Shibatta, Silvia H Sofia, Lucileine de Assumpção, Suelen F R Pini, Sergio Makrakis, Maristela C Makrakis
Gymnogeophagus setequedas is a rare and rheophilic species of tribe Geophagini, considered endangered in Brazilian red lists. Its previously known geographical distribution range was the Paraná River basin, in Paraguay, and a tributary of the Itaipu Reservoir in Brazil. Since its description no specimens have been collected in the original known distribution area. However, recent records of G. setequedas in the lower Iguaçu River, in a region considered highly endemic for the ichthyofauna, extended the known geographical distribution and may represent one of the last remnants of the species...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456550/genomic-analysis-revealed-new-oncogenic-signatures-in-tp53-mutant-hepatocellular-carcinoma
#8
Venkatesh Kancherla, Samir Abdullazade, Matthias S Matter, Manuela Lanzafame, Luca Quagliata, Guglielmo Roma, Yujin Hoshida, Luigi M Terracciano, Charlotte K Y Ng, Salvatore Piscuoglio
The TP53 gene is the most commonly mutated gene in human cancers and mutations in TP53 have been shown to have either gain-of-function or loss-of-function effects. Using the data generated by The Cancer Genome Atlas, we sought to define the spectrum of TP53 mutations in hepatocellular carcinomas (HCCs) and their association with clinicopathologic features, and to determine the oncogenic and mutational signatures in TP53 -mutant HCCs. Compared to other cancer types, HCCs harbored distinctive mutation hotspots at V157 and R249, whereas common mutation hotspots in other cancer types, R175 and R273, were extremely rare in HCCs...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29441089/identification-and-expression-analysis-of-wheat-tagf14-genes
#9
Jun Guo, Shuang Dai, Haosheng Li, Aifeng Liu, Cheng Liu, Dungong Cheng, Xinyou Cao, Xiusheng Chu, Shengnan Zhai, Jianjun Liu, Zhendong Zhao, Jianmin Song
The 14-3-3 gene family members play key roles in various cellular processes. However, little is known about the numbers and roles of 14-3-3 genes in wheat. The aims of this study were to identify TaGF14 numbers in wheat by searching its whole genome through blast, to study the phylogenetic relationships with other plant species and to discuss the functions of TaGF14s . The results showed that common wheat harbored 20 TaGF14 genes, located on wheat chromosome groups 2, 3, 4, and 7. Out of them, eighteen TaGF14s are non-ε proteins, and two wheat TaGF14 genes, TaGF14i and TaGF14f , are ε proteins...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29434621/extensive-karyotype-reorganization-in-the-fish-gymnotus-arapaima-gymnotiformes-gymnotidae-highlighted-by-zoo-fish-analysis
#10
Milla de Andrade Machado, Julio C Pieczarka, Fernando H R Silva, Patricia C M O'Brien, Malcolm A Ferguson-Smith, Cleusa Y Nagamachi
The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29434620/functional-analyses-of-a-novel-splice-variant-in-the-chd7-gene-found-by-next-generation-sequencing-confirm-its-pathogenicity-in-a-spanish-patient-and-diagnose-him-with-charge-syndrome
#11
Olatz Villate, Nekane Ibarluzea, Eugenia Fraile-Bethencourt, Alberto Valenzuela, Eladio A Velasco, Detelina Grozeva, F L Raymond, María P Botella, María-Isabel Tejada
Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosis. A splice donor variant in CHD7 (c.5665 + 1G > T) was identified. To study its potential pathogenicity, exons and flanking intronic sequences were amplified from patient DNA and cloned into the pSAD® splicing vector...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29434619/from-bioengineering-to-crispr-cas9-a-personal-retrospective-of-20-years-of-research-in-programmable-genome-targeting
#12
Albert Jeltsch
Genome targeting of restriction enzymes and DNA methyltransferases has many important applications including genome and epigenome editing. 15-20 years ago, my group was involved in the development of approaches for programmable genome targeting, aiming to connect enzymes with an oligodeoxynucleotide (ODN), which could form a sequence-specific triple helix at the genomic target site. Importantly, the target site of such enzyme-ODN conjugate could be varied simply by altering the ODN sequence promising great applicative values...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29422913/identifying-potential-plasmodium-vivax-sporozoite-stage-vaccine-candidates-an-analysis-of-genetic-diversity-and-natural-selection
#13
Diego Garzón-Ospina, Sindy P Buitrago, Andrea E Ramos, Manuel A Patarroyo
Parasite antigen genetic diversity represents a great obstacle when designing a vaccine against malaria caused by Plasmodium vivax. Selecting vaccine candidate antigens has been focused on those fulfilling a role in invasion and which are conserved, thus avoiding specific-allele immune responses. Most antigens described to date belong to the blood stage, thereby blocking parasite development within red blood cells, whilst studying antigens from other stages has been quite restricted. Antigens from different parasite stages are required for developing a completely effective vaccine; thus, pre-erythrocyte stage antigens able to block the first line of infection becoming established should also be taken into account...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29416549/actn3-morbidity-and-healthy-aging
#14
REVIEW
Craig Pickering, John Kiely
As human longevity increases, recent research has focused on the maintenance of optimal health during old age. One such area of focus is that of muscle function in the elderly, with a loss of muscle mass increasing the risk of negative outcomes such as sarcopenia and a decrease in bone mineral density. In this mini-review, we focus on the impact of a single nucleotide polymorphism in ACTN3, shown to impact muscle phenotype in elite athletes, on loss of muscle function, maintenance of bone mineral density, and metabolic disorder risk in an elderly population...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29416548/modified-polyadenylation-based-rt-qpcr-increases-selectivity-of-amplification-of-3-microrna-isoforms
#15
Charlotte Nejad, Geneviève Pépin, Mark A Behlke, Michael P Gantier
MicroRNA (miRNA) detection by reverse transcription (RT) quantitative real-time PCR (RT-qPCR) is the most popular method currently used to measure miRNA expression. Although the majority of miRNA families are constituted of several 3'-end length variants ("isomiRs"), little attention has been paid to their differential detection by RT-qPCR. However, recent evidence indicates that 3'-end miRNA isoforms can exhibit 3'-length specific regulatory functions, underlining the need to develop strategies to differentiate 3'-isomiRs by RT-qPCR approaches...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29410677/development-of-a-method-to-implement-whole-genome-bisulfite-sequencing-of-cfdna-from-cancer-patients-and-a-mouse-tumor-model
#16
Elaine C Maggi, Silvia Gravina, Haiying Cheng, Bilal Piperdi, Ziqiang Yuan, Xiao Dong, Steven K Libutti, Jan Vijg, Cristina Montagna
The goal of this study was to develop a method for whole genome cell-free DNA (cfDNA) methylation analysis in humans and mice with the ultimate goal to facilitate the identification of tumor derived DNA methylation changes in the blood. Plasma or serum from patients with pancreatic neuroendocrine tumors or lung cancer, and plasma from a murine model of pancreatic adenocarcinoma was used to develop a protocol for cfDNA isolation, library preparation and whole-genome bisulfite sequencing of ultra low quantities of cfDNA, including tumor-specific DNA...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29410676/the-geographic-origins-of-ethnic-groups-in-the-indian-subcontinent-exploring-ancient-footprints-with-y-dna-haplogroups
#17
David G Mahal, Ianis G Matsoukas
Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29403527/microsatellites-associated-with-growth-performance-and-analysis-of-resistance-to-aeromonas-hydrophila-in-tambaqui-colossoma-macropomum
#18
Raquel B Ariede, Milena V Freitas, Milene E Hata, Vito A Mastrochirico-Filho, Fabiana Pilarski, Sergio R Batlouni, Fábio Porto-Foresti, Diogo T Hashimoto
Tambaqui, Colossoma macropomum, is the main native fish species produced in Brazil, and is an important species for genetic improvement in aquaculture. In addition, breeding studies on this species can be optimized with the use of molecular markers associated with productive phenotypes. The objective of the present study was to test the performance of growth traits and resistance to the bacteria, Aeromonas hydrophila, in association with microsatellite markers in C. macropomum. In this study, three full-sib families were subjected to bacterial challenge and morphometric growth assessments...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29387083/genetic-pattern-and-demographic-history-of-salminus-brasiliensis-population-expansion-in-the-pantanal-region-during-the-pleistocene
#19
Lívia A de Carvalho Mondin, Carolina B Machado, Emiko K de Resende, Debora K S Marques, Pedro M Galetti
Pleistocene climate changes were major historical events that impacted South American biodiversity. Although the effects of such changes are well-documented for several biomes, it is poorly known how these climate shifts affected the biodiversity of the Pantanal floodplain. Fish are one of the most diverse groups in the Pantanal floodplains and can be taken as a suitable biological model for reconstructing paleoenvironmental scenarios. To identify the effects of Pleistocene climate changes on Pantanal's ichthyofauna, we used genetic data from multiple populations of a top-predator long-distance migratory fish, Salminus brasiliensis...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29445391/zip13-a-study-of-drosophila-offers-an-alternative-explanation-for-the-corresponding-human-disease
#20
REVIEW
Guiran Xiao, Bing Zhou
The fruit fly Drosophila melanogaster has become an important model organism to investigate metal homeostasis and human diseases. Previously we identified dZIP13 (CG7816), a member of the ZIP transporter family (SLC39A) and presumably a zinc importer, is in fact physiologically primarily responsible to move iron from the cytosol into the secretory compartments in the fly. This review will discuss the implication of this finding for the etiology of Spondylocheirodysplasia-Ehlers-Danlos Syndrome (SCD-EDS), a human disease defective in ZIP13...
2017: Frontiers in Genetics
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