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https://www.readbyqxmd.com/read/29667761/plant-glycosylphosphatidylinositol-gpi-anchored-proteins-at-the-plasma-membrane-cell-wall-nexus
#1
REVIEW
Trevor H Yeats, Antony Bacic, Kim L Johnson
Approximately 1% of plant proteins are predicted to be post-translationally modified with a glycosylphosphatidylinositol (GPI) anchor that tethers the polypeptide to the outer leaflet of the plasma membrane. While the synthesis and structure of GPI anchors is largely conserved across eukaryotes, the repertoire of functional domains present in the GPI-anchored proteome has diverged substantially. In plants, this includes a large fraction of the GPI-anchored proteome being further modified with plant-specific arabinogalactan (AG) O-glycans...
April 18, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29667432/identification-and-characterisation-of-micrornas-and-piwi-interacting-rnas-in-cockerels-spermatozoa-by-solexa-sequencing
#2
Shengru Wu, Jiacheng Guo, Liqin Zhu, Jiantao Yang, Si Chen, Xiaojun Yang
1. There has been substantial research focused on the roles of microRNAs (miRNA) and PIWI-interacting RNAs (piRNA) delivered from mammalian spermatozoa, however comparatively little is known about the role of spermatozoa-delivered miRNAs and piRNAs within breeding cockerels' spermatozoa. 2. A small RNA library of cockerels' spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to a piRNA database...
April 18, 2018: British Poultry Science
https://www.readbyqxmd.com/read/29667327/novel-west-syndrome-candidate-genes-in-a-chinese-cohort
#3
Jing Peng, Ying Wang, Fang He, Chen Chen, Li-Wen Wu, Li-Fen Yang, Yu-Ping Ma, Wen Zhang, Zi-Qing Shi, Chao Chen, Kun Xia, Hui Guo, Fei Yin, Nan Pang
AIMS: West syndrome (WS) is a classic form of early infantile epileptic encephalopathy (EIEE) characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on electroencephalography. Genetic defects play a critical role in the pathology of WS, and 54 EIEE genes have been identified till date. This study was designed to uncover new candidate genes for West syndrome. METHODS: In this study, we recruited 56 Chinese families with WS of unknown etiology...
April 17, 2018: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/29666780/identification-expression-analysis-and-molecular-modeling-of-iron-deficiency-specific-clone-3-ids3-like-gene-in-hexaploid-wheat
#4
Priyanka Mathpal, Upendra Kumar, Anuj Kumar, Sanjay Kumar, Sachin Malik, Naveen Kumar, H S Dhaliwal, Sundip Kumar
Graminaceous plants secrete hydroxylated phytosiderophores encoded by the genes iron-deficiency-specific clone 2 ( Ids2 ) and iron-deficiency-specific clone 3 ( Ids3 ). An effort was made to identify a putative ortholog of Hodeum vulgare Ids3 gene in hexaploid wheat. The protein structure of TaIDS3 was modeled using homology modeling and structural behavior of modeled structure was analyzed at 20 ns. The simulation trajectory using molecular dynamics simulation suggested the model to be stable with no large fluctuations in residues and local domain level RMSF values (< 2...
April 2018: 3 Biotech
https://www.readbyqxmd.com/read/29666611/genome-sequence-assembly-and-characterization-of-two-metschnikowia-fructicola-strains-used-as-biocontrol-agents-of-postharvest-diseases
#5
Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, Maria L Gullino, Marc W Allard, Elena Levin, Davide Spadaro, Samir Droby
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29666397/insight-into-the-cold-adaptation-and-hemicellulose-utilization-of-cladosporium-neopsychrotolerans-from-genome-analysis-and-biochemical-characterization
#6
Rui Ma, Huoqing Huang, Yingguo Bai, Huiying Luo, Yunliu Fan, Bin Yao
The occurrence of Cladosporium in cold ecosystems has been evidenced long before, and most of the knowledge about nutrient utilization of this genus is sporadic. An alpine soil isolate C. neopsychrotolerans SL-16, showing great cold tolerance and significant lignocellulose-degrading capability, was sequenced to form a 35.9 Mb genome that contains 13,456 predicted genes. Functional annotation on predicted genes revealed a wide array of proteins involved in the transport and metabolism of carbohydrate, protein and lipid...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666162/two-abscisic-acid-responsive-plastid-lipase-genes-involved-in-jasmonic-acid-biosynthesis-in-arabidopsis-thaliana
#7
Kun Wang, Qiang Guo, John E Froehlich, Hope Lynn Hersh, Agnieszka Zienkiewicz, Gregg A Howe, Christoph Benning
Chloroplast membranes with their unique lipid composition are crucial for photosynthesis. Maintenance of the chloroplast membranes requires finely tuned lipid anabolic and catabolic reactions. Despite the presence of a large number of predicted lipid-degrading enzymes in the chloroplasts, their biological functions remain largely unknown. Recently, we described PLASTID LIPASE1 (PLIP1), a plastid phospholipase A1 that contributes to seed oil biosynthesis. The Arabidopsis thaliana genome encodes two putative PLIP1 paralogs, which we designated PLIP2 and PLIP3...
April 17, 2018: Plant Cell
https://www.readbyqxmd.com/read/29666032/the-rs1256031-of-estrogen-receptor-%C3%AE-gene-is-associated-with-type-2-diabetes
#8
Ema Herrera-Lopez, Osvaldo Castelan-Martinez, Fernando Suarez-Sanchez, Jaime H Gomez-Zamudio, Jose J Peralta-Romero, Miguel Cruz, Adan Valladares-Salgado
AIM: To determine the association between the rs1256031 polymorphism and risk of developing type 2 diabetes. MATERIALS AND METHODS: Cases and controls study. 597 individuals with type 2 diabetes and 605 without it participated. Genotyping of the rs1256031 polymorphism of the ERβ gene was performed by real-time PCR using TaqMan assay. For the multivariate analysis, a multiple logistic regression was performed that included the main confounding variables. RESULTS AND CONCLUSION: A multiple logistic regression analysis was performed, adjusting for age, WHR, BMI and gender...
April 12, 2018: Diabetes & Metabolic Syndrome
https://www.readbyqxmd.com/read/29666004/biallelic-tp53-gain-of-function-mutations-in-rapidly-progressing-solid-tumors
#9
Christopher M Sande, Brian Chang, Varun Monga, Aaron D Bossler, Deqin Ma
Recent studies are discovering TP53 mutations with gain of function (GOF) properties that promote tumorigenesis via a variety of mechanisms. To our knowledge, all reported compound mutations are allelic. We identified two patients with biallelic GOF TP53 mutations in their tumors and a third with allelic compound variants. The correlation with p53 expression was also examined. Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue and mutational analysis was performed using Ion AmpliSeq™Cancer HotSpot Panel V2...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29665924/-analysis-of-phenotype-and-l12r-mutation-in-signal-peptide-and-3-non-translation-region-c11814-insaa-mutation-of-f7-gene-in-a-family-with-hereditary-coagulation-factor-vii-deficiency
#10
Shan Liu, Jing-Yu Zhang, Zheng-Rong Li, Yan Wang, Zhi-Yun Niu, Feng-Ru Lin
OBJECTIVE: To examine one young female patient with hereditary FVII deficiency and her family members, to observe the gene mutation and clinical phenotype, and to investigate the molecular mechanism of the dysfunction. METHODS: Prothrombin time (PT), activated partial thromoploastin time (APTT), fibrinogen (Fg) and FVII activity (FVII:C) and FVII antigen (FVII:Ag) were tested. The gene mutations were sought by DNA sequencing for all of the exons and flanks, 5' and 3' non-translation region of F7 gene...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/29665451/tgf-%C3%AE-1-resulting-in-differential-microrna-expression-in-bovine-granulosa-cells
#11
Yefen Xu, Jiaqiang Niu, Guangying Xi, Xuezhi Niu, Yuheng Wang, Ming Guo, Qiangba Yangzong, Yilong Yao, Suolang Sizhu, Jianhui Tian
To explore the expression profile of the cellular miRNAs in bovine ovarian granulosa cells responding to transforming growth factor-β1 (TGF-β1), the effect of TGF-β1 on cell proliferation was firstly investigated by CCK-8 method and the results showed that there was a significant inhibitory effect on bovine granulosa cell proliferation treated with 5/10 ng/mL human recombinant TGF-β1 for 24 h compared to the control (P < 0.05). Then, we performed high-throughput sequencing of two small RNA libraries prepared from cultured bovine granulosa cells stimulated with or without 10 ng/mL human recombinant TGF-β1...
April 14, 2018: Gene
https://www.readbyqxmd.com/read/29665143/identification-of-potential-tumor-educated-platelets-rna-biomarkers-in-non-small-cell-lung-cancer-by-integrated-bioinformatical-analysis
#12
Linlin Xue, Li Xie, Xingguo Song, Xianrang Song
BACKGROUND: Platelets have emerged as key players in tumorigenesis and tumor progression. Tumor-educated platelet (TEP) RNA profile has the potential to diagnose non-small-cell lung cancer (NSCLC). The objective of this study was to identify potential TEP RNA biomarkers for the diagnosis of NSCLC and to explore the mechanisms in alternations of TEP RNA profile. METHODS: The RNA-seq datasets GSE68086 and GSE89843 were downloaded from Gene Expression Omnibus DataSets (GEO DataSets)...
April 17, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29664143/pathway-aggregation-for-survival-prediction-via-multiple-kernel-learning
#13
Jennifer A Sinnott, Tianxi Cai
Attempts to predict prognosis in cancer patients using high-dimensional genomic data such as gene expression in tumor tissue can be made difficult by the large number of features and the potential complexity of the relationship between features and the outcome. Integrating prior biological knowledge into risk prediction with such data by grouping genomic features into pathways and networks reduces the dimensionality of the problem and could improve prediction accuracy. Additionally, such knowledge-based models may be more biologically grounded and interpretable...
April 17, 2018: Statistics in Medicine
https://www.readbyqxmd.com/read/29663588/from-transects-to-transcripts-teasing-apart-the-architecture-of-reproductive-isolation
#14
Jill A Hamilton, Joshua M Miller
Understanding the processes underlying speciation has long been a challenge to evolutionary biologists. This spurs from difficulties teasing apart the various mechanisms that contribute to the evolution of barriers to reproduction. The study by Rafati et al. () in this issue of Molecular Ecology combines spatially explicit whole-genome resequencing with evaluation of differential gene expression across individuals with mixed ancestry to associate the genomic architecture of reproductive barriers with expression of reproductive incompatibilities...
March 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29662498/small-rna-and-degradome-deep-sequencing-reveals-the-roles-of-micrornas-in-seed-expansion-in-peanut-arachis-hypogaea-l
#15
Xingli Ma, Xingguo Zhang, Kunkun Zhao, Fapeng Li, Ke Li, Longlong Ning, Jialin He, Zeyu Xin, Dongmei Yin
Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut eighth-generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29662210/genome-wide-mutant-profiling-predicts-the-mechanism-of-a-lipid-ii-binding-antibiotic
#16
Marina Santiago, Wonsik Lee, Antoine Abou Fayad, Kathryn A Coe, Mithila Rajagopal, Truc Do, Fabienne Hennessen, Veerasak Srisuknimit, Rolf Müller, Timothy C Meredith, Suzanne Walker
Identifying targets of antibacterial compounds remains a challenging step in the development of antibiotics. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures identified from directional biases in insertions revealed known molecular targets and resistance mechanisms for the majority of these...
April 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29661879/accelerating-early-anti-tuberculosis-drug-discovery-by-creating-mycobacterial-indicator-strains-that-predict-mode-of-action
#17
Maikel Boot, Susanna Commandeur, Amit K Subudhi, Meriem Bahira, Trever C Smith, Abdallah M Abdallah, Mae van Gemert, Joël Lelièvre, Lluís Ballell, Bree B Aldridge, Arnab Pain, Alexander Speer, Wilbert Bitter
Due to the rise of drug resistant forms of tuberculosis there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole cell analyses have been shown to be successful. However, current high-throughput screens focus mostly on stricto sensu life-death screening that give little qualitative information. In doing so, promising compound scaffolds or non-optimized compounds that fail to reach inhibitory concentrations are missed. To accelerate early TB drug discovery, we performed RNA sequencing on Mycobacterium tuberculosis and Mycobacterium marinum to map the stress responses that follow upon exposure to sub-inhibitory concentrations of antibiotics with known targets: ciprofloxacin, ethambutol, isoniazid, streptomycin and rifampicin...
April 16, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29661807/genetically-engineered-mouse-models-of-prostate-cancer-in-the-postgenomic-era
#18
Juan M Arriaga, Cory Abate-Shen
Recent genomic sequencing analyses have unveiled the spectrum of genomic alterations that occur in primary and advanced prostate cancer, raising the question of whether the corresponding genes are functionally relevant for prostate tumorigenesis, and whether such functions are associated with particular disease stages. In this review, we describe genetically engineered mouse models (GEMMs) of prostate cancer, focusing on those that model genomic alterations known to occur in human prostate cancer. We consider whether the phenotypes of GEMMs based on gain or loss of function of the relevant genes provide reliable counterparts to study the predicted consequences of the corresponding genomic alterations as occur in human prostate cancer, and we discuss exceptions in which the GEMMs do not fully emulate the expected phenotypes...
April 16, 2018: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/29661277/rt-pcr-of-peritoneal-washings-predicts-peritoneal-pancreatic-cancer-recurrence
#19
Kei Sato, Ryutaro Mori, Yukihiko Hiroshima, Mari S Oba, Ryusei Matsuyama, Michael Bouvet, Robert M Hoffman, Itaru Endo
BACKGROUND: Peritoneal recurrence of pancreatic cancer is a frequent and lethal outcome after R0 resection. A method to predict peritoneal recurrence could be helpful in its prevention. MATERIALS AND METHODS: Peritoneal washings were prospectively obtained from 29 patients in whom R0 resection was performed. Cytological examination (CY) and real-time reverse transcription polymerase chain reaction (RT-PCR) of the peritoneal washing for the detection of cancer-related genes, CEACAM5, KRT7, KRAS, and MUC1, were performed...
June 2018: Journal of Surgical Research
https://www.readbyqxmd.com/read/29661169/rna-seq-reveals-the-existence-of-a-cdkn1c-e2f1-tp53-axis-that-is-altered-in-human-t-cell-lymphoblastic-lymphomas
#20
Pilar López-Nieva, Pablo Fernández-Navarro, Concepción Vaquero-Lorenzo, María Villa-Morales, Osvaldo Graña-Castro, María Ángeles Cobos-Fernández, José Luis López-Lorenzo, Pilar Llamas, Laura González-Sanchez, Isabel Sastre, Marina Pollan, Marcos Malumbres, Javier Santos, José Fernández-Piqueras
BACKGROUND: Precursor T-cell lymphoblastic lymphomas (T-LBL) are rare aggressive hematological malignancies that mainly develop in children. As in other cancers, the loss of cell cycle control plays a prominent role in the pathogenesis in these malignancies that is primarily attributed to loss of CDKN2A (encoding protein p16INK4A). However, the impact of the deregulation of other genes such as CDKN1C, E2F1, and TP53 remains to be clarified. Interestingly, experiments in mouse models have proven that conditional T-cell specific deletion of Cdkn1c gene may induce a differentiation block at the DN3 to DN4 transition, and that the loss of this gene in the absence of Tp53 led to aggressive thymic lymphomas...
April 16, 2018: BMC Cancer
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