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Journal of Biological Research

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https://www.readbyqxmd.com/read/27508170/dna-methylation-changes-and-te-activity-induced-in-tissue-cultures-of-barley-hordeum-vulgare-l
#1
Renata Orłowska, Joanna Machczyńska, Sylwia Oleszczuk, Janusz Zimny, Piotr Tomasz Bednarek
BACKGROUND: In vitro plant regeneration via androgenesis or somatic embryogenesis is capable of inducing (epi)mutations that may affect sexual progenies. While epimutations are associated with DNA methylation, mutations could be due to the movement of transposons. The common notion is that both processes are linked. It is being assumed that demethylation activates transposable elements (TEs). Analysis of methylation changes and their relation with TEs activation in tissue cultures requires uniquely derived donor plants (Ds), their regenerants (Rs) and respective progeny (Ps) that would allow discrimination of processes not related to changes introduced via in vitro cultures...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27437194/identification-and-validation-of-aeluropus-littoralis-reference-genes-for-quantitative-real-time-pcr-normalization
#2
Seyyed Hamidreza Hashemi, Ghorbanali Nematzadeh, Gholamreza Ahmadian, Ahad Yamchi, Markus Kuhlmann
BACKGROUND: The use of stably expressed genes as normalizers has crucial role in accurate and reliable expression analysis estimated by quantitative real-time polymerase chain reaction (qPCR). Recent studies have shown that, the expression levels of common housekeeping genes are varying in different tissues and experimental conditions. The genomic DNA contamination in RNA samples is another important factor that also influence the interpretation of the data obtained from qPCR. It is estimated that the gDNA contamination in gene expression analysis lead to an overestimation of the RNA transcript level...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27429943/hominin-interbreeding-and-the-evolution-of-human-variation
#3
REVIEW
Kwang Hyun Ko
Mitochondrial Eve confirms the "out of Africa" theory, but the evidence also supports interbreeding between Homo sapiens and other hominins: Neanderthals, Denisovans, and Homo heidelbergensis. This article explains how interbreeding between early H. sapiens and archaic hominins occurred. The availability of edible insects in East Asia aided the spread of the unaggressive, highly cooperative Neanderthals, who interbred with H. sapiens in Asia, resulting in a higher admixture of Neanderthal DNA in East Asian populations...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27429942/ganges-special-at-its-origin
#4
Krishna Khairnar
No abstract text is available yet for this article.
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27376033/targeted-cyp2e1-quantification-and-its-correlation-to-currently-acceptable-clinical-biochemical-indices
#5
Christina Gertrude Yap, Anuar Zaini, Iekhsan Othman
BACKGROUND: The Cytochrome P450 enzymes are commonly known for their major role in metabolism. Besides its metabolic role, CYP2E1 gene expression has been associated with the onset of diabetic nephropathy. CYP2E1 protein elevation has also been reported to be responsible for the production of reactive oxygen species. The aims of this study were (i) to optimize and validate a targeted proteomic approach for quantitating CYP2E1 and validating it as a suitable clinical test, (ii) to investigate the concurrency between ESI-LCMS-MS quantitated circulating CYP2E1 and gold standard indices in the context of outpatient point-of-care clinical settings involving various groups of diabetic patients and (iii) to investigate the concurrency profile of circulating CYP2E1 protein, CYP2E1 gene expression and reactive oxygen species (ROS)...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27347488/mir-10b-decreases-sensitivity-of-glioblastoma-cells-to-radiation-by-targeting-akt
#6
Limin Zhen, Jian Li, Mingran Zhang, Kun Yang
BACKGROUND: Glioblastomas are the most aggressive brain tumors with extremely poor prognosis despite advances in treatment techniques. MiR-10b is highly expressed in glioblastoma and regulates cell proliferation, migration and invasion. Here, we examined the role of MiR-10b on radiotherapy of glioblastomas. METHODS: MiR-10b mimic or anti-MiR-10b inhibitor was transfected in glioblastoma cells. WST-1 assay was used to examine the effect of MiR-10b on proliferation of transfected glioblastoma cells after radiation treatment...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27134846/polymorphism-of-the-melatonin-receptor-1a-mntr1a-gene-and-association-with-seasonality-of-reproductive-activity-in-a-local-greek-sheep-breed
#7
Ioannis A Giantsis, George P Laliotis, Olympia Stoupa, Melpomeni Avdi
BACKGROUND: Sheep's reproductive physiology in temperate latitudes (such as Greece), is characterized by seasonality and is also regulated by photoperiodic exposure. Melatonin is the key hormone involved in this regulation. However, the melatonin secretion and therefore the ewes reproductive activity underlies variation, proposed to be linked with the melatonin receptor subtype 1A (MNTR1A) gene structure. This study was designed to investigate the polymorphism of the MNTR1A gene in a local Greek sheep breed and to determine its potential association with reproductive seasonality...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27119075/co-culturing-bacteria-and-microalgae-in-organic-carbon-containing-medium
#8
Jichang Han, Lin Zhang, Song Wang, Guanpin Yang, Lu Zhao, Kehou Pan
BACKGROUND: Microalgae frequently grow in natural environment and long-term laboratory cultures in association with bacteria. Bacteria benefit the oxygen and extracellular substances generated by microalgae, and reimburse microalgae with carbon dioxide, vitamins and so on. Such synergistic relationship has aided in establishing an efficient microalga-bacterium co-culturing mode. Obviously, the mutually beneficial relationship can be strengthened with the increase of the densities of microalgae and bacteria...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27119074/effects-of-laminaria-japonica-polysaccharides-on-exercise-endurance-and-oxidative-stress-in-forced-swimming-mouse-model
#9
Feiwei Yan, Haitao Hao
BACKGROUND: Polysaccharides are the major active ingredients responsible for the bioactivities of Laminaria japonica. However, the effects of L. japonica polysaccharides (LJP) on exercise endurance and oxidative stress have never been investigated. Therefore, this study was conducted to investigate the effects of LJP on exercise endurance and oxidative stress in a forced swimming mouse model. The animals were divided into four groups, namely the control (C), LJP-75, LJP-150, and LJP-300 groups, which received physiological saline and 75, 150, and 300 mg kg(-1) LJP, respectively, by gavage once a day for 28 days...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27096138/sequencing-and-characterization-of-leaf-transcriptomes-of-six-diploid-nicotiana-species
#10
Ni Long, Xueliang Ren, Zhidan Xiang, Wenting Wan, Yang Dong
BACKGROUND: Nicotiana belongs to the Solanaceae family that includes important crops such as tomato, potato, eggplant, and pepper. Nicotiana species are of worldwide economic importance and are important model plants for scientific research. Here we present the comparative analysis of the transcriptomes of six wild diploid Nicotiana species. Wild relatives provide an excellent study system for the analysis of the genetic basis for various traits, especially disease resistance. RESULTS: Whole transcriptome sequencing (RNA-seq) was performed for leaves of six diploid Nicotiana species, i...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27073787/effect-of-methyl-beta-cyclodextrin-on-the-viability-and-acrosome-damage-of-sex-sorted-sperm-in-frozen-thawed-bovine-semen
#11
Seunghyung Lee, Yong-Seung Lee, Sang-Hee Lee, Boo-Keun Yang, Choon-Keun Park
BACKGROUND: The regulation of methyl-beta-cyclodextrin (MBCD) on cryodamage on X- and Y-sperm during cryopreservation of semen was investigated. The semen was collected from ten healthy bulls of proven fertility by an artificial vagina. The bovine sperm treated with MBCD fresh solution (0, 1, 5, 10, and 20 mM). The sperms were evaluated for viability and acrosome damage using flow cytometry. Moreover, X- and Y-sperm in frozen-thawed bovine semen were sorted by flow cytometry after Hoechst 33342-dyed, and the viability and acrosome damage of sperms were analyzed...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27030819/the-zmrcp-1-promoter-of-maize-provides-root-tip-specific-expression-of-transgenes-in-plantain
#12
Stephen O Onyango, Hugh Roderick, Jaindra N Tripathi, Richard Collins, Howard J Atkinson, Richard O Oduor, Leena Tripathi
BACKGROUND: Bananas and plantains (Musa spp.) provide 25 % of the food energy requirements for more than 100 million people in Africa. Plant parasitic nematodes cause severe losses to the crop due to lack of control options. The sterile nature of Musa spp. hampers conventional breeding but makes the crop suitable for genetic engineering. A constitutively expressed synthetic peptide in transgenic plantain has provided resistance against nematodes. Previous work with the peptide in potato plants indicates that targeting expression to the root tip improves the efficacy of the defence mechanism...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/26973820/gram-negative-and-positive-bacteria-differentiation-in-blood-culture-samples-by-headspace-volatile-compound-analysis
#13
Michael E Dolch, Silke Janitza, Anne-Laure Boulesteix, Carola Graßmann-Lichtenauer, Siegfried Praun, Wolfgang Denzer, Gustav Schelling, Sören Schubert
BACKGROUND: Identification of microorganisms in positive blood cultures still relies on standard techniques such as Gram staining followed by culturing with definite microorganism identification. Alternatively, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or the analysis of headspace volatile compound (VC) composition produced by cultures can help to differentiate between microorganisms under experimental conditions. This study assessed the efficacy of volatile compound based microorganism differentiation into Gram-negatives and -positives in unselected positive blood culture samples from patients...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/26933651/addressing-huge-spatial-heterogeneity-induced-by-virus-infections-in-lentil-breeding-trials
#14
Anastasia Kargiotidou, Dimitrios N Vlachostergios, Constantinos Tzantarmas, Ioannis Mylonas, Chrysanthi Foti, George Menexes, Alexios Polidoros, Ioannis S Tokatlidis
BACKGROUND: Spatial heterogeneity can have serious effects on the precision of field experimentation in plant breeding. In the present study the capacity of the honeycomb design (HD) to sample huge spatial heterogeneity was appraised. For this purpose, four trials were conducted each comprising a lentil landrace being screened for response to viruses. RESULTS: Huge spatial heterogeneity was reflected by the abnormally high values for coefficient of variation (CV) of single-plant yields, ranging 123-162 %...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/26933650/nacl-stress-induced-transcriptomics-analysis-of-salix-linearistipularis-syn-salix-mongolica
#15
Guixian Nan, Yan Zhang, Song Li, Imshik Lee, Tetsuo Takano, Shenkui Liu
BACKGROUND: Salix linearistipularis (syn. S. mongolica) is a woody halophyte, which is distributed naturally in saline-alkali soil of Songnen plain, Heilongjiang, China. It plays an important role in maintaining ecological balance and in improving saline soil. Furthermore, S. linearistipularis is also a genetic resource; however, there is no available information of genomic background for salt tolerance mechanism. We conducted the transcriptome analysis of S. linearistipularis to understand the mechanisms of salt tolerance by using RNA-seq technology...
December 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27437198/iterative-ensemble-feature-selection-for-multiclass-classification-of-imbalanced-microarray-data
#16
Junshan Yang, Jiarui Zhou, Zexuan Zhu, Xiaoliang Ma, Zhen Ji
BACKGROUND: Microarray technology allows biologists to monitor expression levels of thousands of genes among various tumor tissues. Identifying relevant genes for sample classification of various tumor types is beneficial to clinical studies. One of the most widely used classification strategies for multiclass classification data is the One-Versus-All (OVA) schema that divides the original problem into multiple binary classification of one class against the rest. Nevertheless, multiclass microarray data tend to suffer from imbalanced class distribution between majority and minority classes, which inevitably deteriorates the performance of the OVA classification...
May 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27437197/predphos-an-ensemble-framework-for-structure-based-prediction-of-phosphorylation-sites
#17
Yong Gao, Weilin Hao, Jing Gu, Diwei Liu, Chao Fan, Zhigang Chen, Lei Deng
BACKGROUND: Post-translational modifications (PTMs) occur on almost all proteins and often strongly affect the functions of modified proteins. Phosphorylation is a crucial PTM mechanism with important regulatory functions in biological systems. Identifying the potential phosphorylation sites of a target protein may increase our understanding of the molecular processes in which it takes part. RESULTS: In this paper, we propose PredPhos, a computational method that can accurately predict both kinase-specific and non-kinase-specific phosphorylation sites by using optimally selected properties...
May 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27437196/an-approach-to-semantic-query-expansion-system-based-on-hepatitis-ontology
#18
Chen Yunzhi, Lu Huijuan, Linda Shapiro, Ravensara S Travillian, Li Lanjuan
BACKGROUND: Ontology development, as an increasingly practical vehicle applied in various fields, plays a significant role in knowledge management. This paper, focusing on constructing and querying a hepatitis ontology, aims to provide a framework for ontology-based medical services. The paper is devoted to the algorithm of query expansion for the hepatitis ontology, including synonym expansion, hypernym/hyponym expansion and expansion of similar words. It applies semantic similarity calculation to judge the similarity of retrieval terms...
May 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/27437195/prediction-of-protein-protein-interaction-sites-by-means-of-ensemble-learning-and-weighted-feature-descriptor
#19
Xiuquan Du, Shiwei Sun, Changlin Hu, Xinrui Li, Junfeng Xia
BACKGROUND: Reliable prediction of protein-protein interaction sites is an important goal in the field of bioinformatics. Many computational methods have been explored for the large-scale prediction of protein-protein interaction sites based on various data types, including protein sequence, structural and genomic data. Although much progress has been achieved in recent years, the problem has not yet been satisfactorily solved. RESULTS: In this work, we presented an efficient approach that uses ensemble learning algorithm with weighted feature descriptor (EL-WFD) to predict protein-protein interaction sites...
May 2016: Journal of Biological Research
https://www.readbyqxmd.com/read/26702402/identification-and-functional-analysis-of-the-bim-interactome-new-clues-on-its-possible-involvement-in-epstein-barr-virus-associated-diseases
#20
Erasmia Rouka, Despoina Kyriakou
Epigenetic deregulation is a common feature in the pathogenesis of Epstein-Barr Virus (EBV)-related lymphomas and carcinomas. Previous studies have demonstrated a strong association between EBV latency in B-cells and epigenetic silencing of the tumor suppressor gene BIM. This study aimed to the construction and functional analysis of the BIM interactome in order to identify novel host genes that may be targeted by EBV. Fifty-nine unique interactors were found to compose the BIM gene network. Ontological analysis at the pathway level highlighted infectious diseases along with neuropathologies...
December 2015: Journal of Biological Research
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