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https://www.readbyqxmd.com/read/28934591/combining-traditional-mutagenesis-with-new-high-throughput-sequencing-and-genome-editing-to-reveal-hidden-variation-in-polyploid-wheat
#1
Cristobal Uauy, Brande B H Wulff, Jorge Dubcovsky
Induced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28934498/widespread-intra-dependencies-in-the-removal-of-introns-from-human-transcripts
#2
Seong Won Kim, Allison J Taggart, Claire Heintzelman, Kamil J Cygan, Caitlin G Hull, Jing Wang, Barsha Shrestha, William G Fairbrother
Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934469/hnrnp-l-controls-hpv16-rna-polyadenylation-and-splicing-in-an-akt-kinase-dependent-manner
#3
Naoko Kajitani, Jacob Glahder, Chengjun Wu, Haoran Yu, Kersti Nilsson, Stefan Schwartz
Inhibition of the Akt kinase activates HPV16 late gene expression by reducing HPV16 early polyadenylation and by activating HPV16 late L1 mRNA splicing. We identified 'hot spots' for RNA binding proteins at the early polyA signal and at splice sites on HPV16 late mRNAs. We observed that hnRNP L was associated with sequences at all HPV16 late splice sites and at the early polyA signal. Akt kinase inhibition resulted in hnRNP L dephosphorylation and reduced association of hnRNP L with HPV16 mRNAs. This was accompanied by an increased binding of U2AF65 and Sam68 to HPV16 mRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934394/microrna-455-3p-as-a-potential-peripheral-biomarker-for-alzheimer-s-disease
#4
Subodh Kumar, Murali Vijayan, P Hemachandra Reddy
The purpose of our study was to identify microRNAs (miRNAs) as early detectable peripheral biomarkers in Alzheimer's disease (AD). To achieve our objective, we assessed miRNAs in serum samples from AD patients and Mild cognitive impairment (MCI) subjects relative to healthy controls. We used Affymetrix microarray analysis and validated differentially expressed miRNAs using qRT-PCR. We further validated miRNA data using AD postmortem brains, amyloid precursor protein transgenic mice and AD cell lines. We identified a gradual upregulation of four miRNAs: miR-455-3p, miR-4668-5p, miR-3613-3p and miR-4674...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934365/murine-glomerular-transcriptome-links-endothelial-cell-specific-molecule-1-deficiency-with-susceptibility-to-diabetic-nephropathy
#5
Xiaoyi Zheng, Fariborz Soroush, Jin Long, Evan T Hall, Puneeth K Adishesha, Sanchita Bhattacharya, Mohammad F Kiani, Vivek Bhalla
Diabetic nephropathy (DN) is the leading cause of kidney disease; however, there are no early biomarkers and no cure. Thus, there is a large unmet need to predict which individuals will develop nephropathy and to understand the molecular mechanisms that govern this susceptibility. We compared the glomerular transcriptome from mice with distinct susceptibilities to DN at four weeks after induction of diabetes, but before histologic injury, and identified differential regulation of genes that modulate inflammation...
2017: PloS One
https://www.readbyqxmd.com/read/28934227/hemorrhage-enhances-cytokine-complement-component-3-and-caspase-3-and-regulates-micrornas-associated-with-intestinal-damage-after-whole-body-gamma-irradiation-in-combined-injury
#6
Juliann G Kiang, Joan T Smith, Marsha N Anderson, Thomas B Elliott, Paridhi Gupta, Nagaraja S Balakathiresan, Radha K Maheshwari, Barbara Knollmann-Ritschel
Hemorrhage following whole-body γ-irradiation in a combined injury (CI) model increases mortality compared to whole-body γ-irradiation alone (RI). The decreased survival in CI is accompanied by increased bone marrow injury, decreased hematocrit, and alterations of miRNA in the kidney. In this study, our aim was to examine cytokine homeostasis, susceptibility to systemic bacterial infection, and intestinal injury. More specifically, we evaluated the interleukin-6 (IL-6)-induced stress proteins including C-reactive protein (CRP), complement 3 (C3), Flt-3 ligand, and corticosterone...
2017: PloS One
https://www.readbyqxmd.com/read/28934121/current-status-of-early-blight-resistance-in-tomato-an-update
#7
REVIEW
Pragya Adhikari, Yeonyee Oh, Dilip R Panthee
Early blight (EB) is one of the dreadful diseases of tomato caused by several species of Alternaria including Alternaria linariae (which includes A. solani and A. tomatophila), as well as A. alternata. In some instances, annual economic yield losses due to EB have been estimated at 79%. Alternaria are known only to reproduce asexually, but a highly-virulent isolate has the potential to overcome existing resistance genes. Currently, cultural practices and fungicide applications are employed for the management of EB due to the lack of strong resistant cultivars...
September 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28933985/acn-1-a-c-elegans-homologue-of-ace-genetically-interacts-with-the-let-7-microrna-and-other-heterochronic-genes
#8
Chanatip Metheetrairut, Yuri Ahuja, Frank J Slack
The heterochronic pathway in C. elegans controls the relative timing of cell fate decisions during post-embryonic development. It includes a network of microRNAs (miRNAs), such as let-7, and protein-coding genes, such as the stemness factors, LIN-28 and LIN-41. Here we identified the acn-1 gene, a homologue of mammalian angiotensin-converting enzyme (ACE), as a new suppressor of the stem cell developmental defects of let-7 mutants. Since acn-1 null mutants die during early larval development, we used RNAi to characterize the role of acn-1 in C...
September 21, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28933666/regulation-of-proliferation-in-developing-human-tooth-germs-by-msx-muscle-segment-homeodomain-proteins-and-cyclin-dependent-kinase-inhibitor-p19-ink4d
#9
Darko Kero, Katarina Vukojevic, Petra Stazic, Danijela Sundov, Snjezana Mardesic Brakus, Mirna Saraga-Babic
Before the secretion of hard dental tissues, tooth germs undergo several distinctive stages of development (dental lamina, bud, cap and bell). Every stage is characterized by specific proliferation patterns, which is regulated by various morphogens, growth factors and homeodomain proteins. The role of MSX homeodomain proteins in odontogenesis is rather complex. Expression domains of genes encoding for murine Msx1/2 during development are observed in tissues containing highly proliferative progenitor cells. Arrest of tooth development in Msx knockout mice can be attributed to impaired proliferation of progenitor cells...
September 21, 2017: Organogenesis
https://www.readbyqxmd.com/read/28933279/zinc-transporter-protein-tzn-1-may-also-play-a-role-in-conidiation-pathway-of-neurospora-crassa-an-insight-using-proteogenomic-approachusing-proteogenomic-approach
#10
Divya Rupa Venkata Pandala, Jogeswar Gadi, Kiranmayi Patnala
Zinc transporter (tzn-1) of Neurospora crassa plays a crucial role in conidiation pathway, as its removal results in aconidiation which was reported in our earlier studies. Present study depicts the role of tzn-1 in conidiation process, by comparing knockout (KO) mutants zinc transporter KO (Δtzn-1) and aconidiating gene KO (Δacon-3) with wild oak ridge (OR) 74 'A' strain by 'Proteo-genomic' approach. Firstly, nine commonly overexpressed protein spots from the two sets (Δtzn-1 to wild and Δacon-3 to wild) were analyzed by combining 2-Dimensional gel electrophoresis (2DE) with Matrix Associated Laser Desorption/Ionization mass spectrometry -Peptide Mass Fingerprint (MALDI-PMF)...
September 19, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28932990/treatment-opportunities-in-patients-with-metabolic-myopathies
#11
REVIEW
Mette Cathrine Ørngreen, John Vissing
Metabolic myopathies are disorders affecting utilization of carbohydrates or fat in the skeletal muscle. Adult patients with metabolic myopathies typically present with exercise-induced pain, contractures or stiffness, fatigue, and myoglobinuria. Symptoms are related to energy failure. Purpose of review In this review, the current treatment options, including exercise therapy, dietary treatment, pharmacological supplementation, gene transcription, and enzyme replacement therapy, are described. Recent findings Recognition of the metabolic block in the metabolic myopathies has started the development of new therapeutic options...
September 21, 2017: Current Treatment Options in Neurology
https://www.readbyqxmd.com/read/28932774/transcriptomic-and-bioinformatics-analysis-of-the-early-time-course-of-the-response-to-prostaglandin-f2-alpha-in-the-bovine-corpus-luteum
#12
Heather Talbott, Xiaoying Hou, Fang Qiu, Pan Zhang, Chittibabu Guda, Fang Yu, Robert A Cushman, Jennifer R Wood, Cheng Wang, Andrea S Cupp, John S Davis
RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069). Subsequent statistical analysis determined differentially expressed transcripts ± 1.5-fold change from saline control with P ≤ 0.05. Gene ontology of differentially expressed transcripts was annotated by DAVID and Panther. Physiological characteristics of the study animals are presented in a figure...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28932485/incontinentia-pigmenti-in-a-child-with-suspected-retinoblastoma
#13
Stephanie J Weiss, Archana Srinivasan, Michael A Klufas, Carol L Shields
BACKGROUND: Incontinentia pigmenti is a rare X-linked dominant syndrome caused by mutation in the NEMO/IKKgamma gene, and characterized by a spectrum of cutaneous, ocular, neurologic and dental abnormalities. In the eye, findings include retinal vascular non-perfusion, occasionally with traction retinal detachment, retinal fibrosis, and retinal pigment epithelium defects. These findings can resemble retinoblastoma, especially when vitreoretinal fibrosis produces leukocoria. CASE REPORT: A 2-month-old girl born full-term presented with leukocoria, suspicious for retinoblastoma...
2017: International Journal of Retina and Vitreous
https://www.readbyqxmd.com/read/28932414/hox-gene-cluster-of-the-ascidian-halocynthia-roretzi-reveals-multiple-ancient-steps-of-cluster-disintegration-during-ascidian-evolution
#14
Yuka Sekigami, Takuya Kobayashi, Ai Omi, Koki Nishitsuji, Tetsuro Ikuta, Asao Fujiyama, Noriyuki Satoh, Hidetoshi Saiga
BACKGROUND: Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28932075/role-of-tissue-microenvironment-resident-adipocytes-in-colon-cancer
#15
EDITORIAL
Maria Tabuso, Shervanthi Homer-Vanniasinkam, Raghu Adya, Ramesh P Arasaradnam
Colorectal cancer (CRC) is a multifactorial disease characterized by several genetic and epigenetic alterations occurring in epithelial cells. It is increasingly recognized that tumour progression is also regulated by tumour microenvironment (TME). The bidirectional cross-talk between tumour resident adipocytes and cancer cells within TME has been proposed as active contributor to carcinogenesis. Tumour resident adipocytes exhibit an activated phenotype characterized by increased secretion of pro-tumorigenic factors (angiogenic/inflammatory/immune) which contribute to cancer cell proliferation, invasion, neoangiogenesis, evasion of immune surveillance and therapy resistance...
August 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28931951/screening-of-mirna-profiles-and-construction-of-regulation-networks-in-early-and-late-lactation-of-dairy-goat-mammary-glands
#16
Zhibin Ji, Zhaohua Liu, Tianle Chao, Lei Hou, Rui Fan, Rongyan He, Guizhi Wang, Jianmin Wang
In recent years, studies related to the expression profiles of miRNAs in the dairy goat mammary gland were performed, but regulatory mechanisms in the physiological environment and the dynamic homeostasis of mammary gland development and lactation are not clear. In the present study, sequencing data analysis of early and late lactation uncovered a total of 1,487 unique miRNAs, including 45 novel miRNA candidates and 1,442 known and conserved miRNAs, of which 758 miRNAs were co-expressed and 378 differentially expressed with P < 0...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931827/altered-methylations-of-h19-snrpn-mest-and-peg3-are-reversible-by-developmental-reprogramming-in-kidney-tissue-of-icsi-derived-mice
#17
Qitao Zhan, Xuchen Qi, Ning Wang, Fang Le, Luna Mao, Xinyun Yang, Mu Yuan, Hangying Lou, Xiangrong Xu, Xijing Chen, Fan Jin
Although the prevalence of Intracytoplasmic sperm injection (ICSI) has increased year by year, there remains concern about the safety of these procedures because of reports of the increased risk for imprinting disorders. Previous research has demonstrated that gonadotropin stimulation contributes to an increased incidence of epimutations in ICSI-derived mice. However, the epimutations in ICSI offspring after removing the effect of gonadotropin stimulation and the possibility that epimutations are reversible by developmental reprogramming has not been investigated...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931763/reversible-retinal-vessel-closure-from-vegf-induced-leukocyte-plugging
#18
Yuanyuan Liu, Jikui Shen, Seth D Fortmann, Jiangxia Wang, Dietmar Vestweber, Peter A Campochiaro
Clinical trials in patients with macular edema due to diabetic retinopathy or retinal vein occlusion (RVO) have shown that suppression of VEGF not only improves macular edema, but also reopens closed retinal vessels, prevents progression of vessel closure, and improves retinopathy. In this study, we show the molecular basis for those clinical observations. Increased retinal levels of VEGF in mice cause plugging of retinal vessels with leukocytes, vessel closure, and hypoxia. Suppression of VEGF reduces leukocyte plugging, causing reperfusion of closed vessels...
September 21, 2017: JCI Insight
https://www.readbyqxmd.com/read/28931746/voltage-gated-sodium-channel-gene-repertoire-of-lampreys-gene-duplications-tissue-specific-expression-and-discovery-of-a-long-lost-gene
#19
Harold H Zakon, Weiming Li, Nisha E Pillai, Sumanty Tohari, Prashant Shingate, Jianfeng Ren, Byrappa Venkatesh
Studies of the voltage-gated sodium (Nav) channels of extant gnathostomes have made it possible to deduce that ancestral gnathostomes possessed four voltage-gated sodium channel genes derived from a single ancestral chordate gene following two rounds of genome duplication early in vertebrates. We investigated the Nav gene family in two species of lampreys (the Japanese lamprey Lethenteron japonicum and sea lamprey Petromyzon marinus) (jawless vertebrates-agnatha) and compared them with those of basal vertebrates to better understand the origin of Nav genes in vertebrates...
September 27, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28931691/vertical-transmission-of-hepatitis-c-virus-variable-transmission-bottleneck-and-evidence-of-mid-gestation-in-utero-infection
#20
Sébastien Fauteux-Daniel, Ariane Larouche, Virginie Calderon, Jonathan Boulais, Chanel Béland, Doris G Ransy, Marc Boucher, Valérie Lamarre, Normand Lapointe, Isabelle Boucoiran, Armelle Le Campion, Hugo Soudeyns
Hepatitis C virus (HCV) can be transmitted from mother to child during pregnancy and childbirth. However, the timing and precise biologic mechanisms that are involved in this process are incompletely understood, as are the determinants that influence transmission of particular HCV variants. Here we report results of a longitudinal assessment of HCV quasispecies diversity and composition in 5 cases of vertical HCV transmission, including 3 women coinfected with HIV-1. The population structure of HCV variant spectra based on E2 envelope gene sequences (nucleotide positions 1491-1787), including hypervariable regions 1 and 2, was characterized using next-generation sequencing and median joining network analysis...
September 20, 2017: Journal of Virology
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