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https://www.readbyqxmd.com/read/29792832/sperm-dna-fragmentation-in-the-total-and-vital-fractions-before-and-after-density-gradient-centrifugation-significance-in-male-fertility-diagnosis
#1
U Punjabi, H Van Mulders, I Goovaerts, K Peeters, K Clasen, P Janssens, O Zemtsova, D De Neubourg
BACKGROUND: Sperm DNA fragmentation measured by different techniques make comparisons impossible due to lack of standardization. Induction of DNA damage after sperm preparation in the entire fraction has been observed on independent occasions but findings are not consistent. METHODS: Men presenting at a University hospital setup for infertility treatment. DNA damage via TUNEL assay was validated on fresh semen samples, as conventional semen parameters, to reduce variability of results...
May 21, 2018: Clinical Biochemistry
https://www.readbyqxmd.com/read/29792566/clues-to-an-evolutionary-mystery-the-genes-for-t-toxin-enabler-of-the-devastating-1970-southern-corn-leaf-blight-epidemic-are-present-in-ancestral-species-suggesting-an-ancient-origin
#2
Bradford J Condon, Candace E Elliott, Jonathan Gonzalez, Sung-Hwan Yun, Yasunori Akagi, Tyr Wiesner-Hanks, Motoichiro Kodama, Gillian Turgeon
The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while P. zeae-maydis produces PM-toxin, both host selective polyketide toxins necessary for supervirulence. Present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species...
May 24, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29792428/structures-and-activities-of-tiahuramides-a-c-cyclic-depsipeptides-from-a-tahitian-collection-of-the-marine-cyanobacterium-lyngbya-majuscula
#3
Annabel Levert, Rebeca Alvariño, Louis Bornancin, Eliane Abou Mansour, Adam M Burja, Anne-Marie Genevière, Isabelle Bonnard, Eva Alonso, Luis Botana, Bernard Banaigs
The structures of three new cyclic depsipeptides, tiahuramides A (1), B (2), and C (3), from a French Polynesian collection of the marine cyanobacterium Lyngbya majuscula are described. The planar structures of these compounds were established by a combination of mass spectrometry and 1D and 2D NMR experiments. Absolute configurations of natural and nonproteinogenic amino acids were determined through a combination of acid hydrolysis, derivitization with Marfey's reagent, and HPLC. The absolute configuration of hydroxy acids was confirmed by Mosher's method...
May 24, 2018: Journal of Natural Products
https://www.readbyqxmd.com/read/29790754/epiprofile-2-0-a-computational-platform-for-processing-epi-proteomics-mass-spectrometry-data
#4
Zuo-Fei Yuan, Simone Sidoli, Dylan M Marchione, Johayra Simithy, Kevin A Janssen, Mary R Szurgot, Benjamin A Garcia
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here, we present EpiProfile 2.0, an extended version of our 2015 software (v1.0) for accurate quantification of histone peptides based on liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29790482/a-study-of-enterocyte-membranes-during-activation-of-apoptotic-processes-in-chronic-carrageenan-induced-gastroenterocolitis
#5
Anton Tkachenko, Dmytro Marakushyn, Iuliia Kalashnyk, Yevgen Korniyenko, Anatolii Onishchenko, Tatyana Gorbach, Oksana Nakonechna, Yevgen Posokhov, Alexander Tsygankov
Aim To investigate the lipid membranes of rat enterocytes in chronic carrageenan-induced gastroenterocolitis accompanied by the activation of apoptotic processes. Methods Steady-state fluorescence spectroscopy: a study by fluorescent probes - by ortho-hydroxy derivatives of 2,5-diaryl-1,3- oxazole. Activity of apoptosis signal-regulating kinase 1 and poly (ADP-ribose) polymerase in small intestinal homogenates, blood serum levels of matrix metalloproteinase-2 and caspase-3 and the level of DNA fragmentation in small intestinal homogenates were determined...
August 1, 2018: Medicinski Glasnik
https://www.readbyqxmd.com/read/29790084/cloning-and-expression-of-nlpa-gene-as-dna-vaccine-candidate-against-acinetobacter-baumannii
#6
Rassoul Hashemzehi, Abbas Doosti, Mohammad Kargar, Mojtaba Jaafarinia
Acinetobacter baumannii is one of the highly antibiotic-resistant bacteria that cause infections with high rate of death. This bacterium is one the common causes of infection worldwide leading to endemic and epidemic nosocomial infections. Despite many efforts, there is no effective vaccine against A. baumannii. As NlpA is one of the important antigenic factors in biogenesis of outer membrane vesicles, and OMV-based reported vaccines in A. baumannii stimulated the immune responses, this study was aimed to clone and express nlpA gene in eukaryotic HDF cells and evaluate the induced immunization following the administration of resulting construct as DNA vaccine in BALB/c mice...
May 22, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29790063/in-vitro-and-in-vivo-evaluation-of-antitumor-activity-of-ligustrum-robustum-a-chinese-herbal-tea
#7
Hao-Jiang Zuo, Shan Liu, Chun Yan, Li-Man Li, Xiao-Fang Pei
OBJECTIVE: To examine the effect of the aqueous extract of Ligustrum robustum on tumor growth in vitro and in vivo and explore the possible molecular mechanisms. METHODS: In in vitro study, cell viabilities of human cervical carcinoma cells (HeLa), human breast cancer cells (MCF-7), human prostate cancer cells (PC-3), human hepatoma cells (7721) and human colon carcinoma cells (SW480) were evaluated with cell counting kit-8. For L. robustum-treated Hela cells, early or late apoptosis were evaluated by annexin V/PI staining...
May 22, 2018: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29789886/gcttca-as-a-novel-motif-for-regulating-mesocarp-specific-expression-of-the-oil-palm-elaeis-guineensis-jacq-stearoyl-acp-desaturase-gene
#8
Farah Hanan Abu Hanifiah, Siti Nor Akmar Abdullah, Ashida Othman, Noor Azmi Shaharuddin, Halimi Mohd Saud, Hasnul Abdul Hakim Hasnulhadi, Umaiyal Munusamy
TAAAAT and a novel motif, GCTTCA found in the oil palm stearoyl-ACP desaturase (SAD1) promoter are involved in regulating mesocarp-specific expression. Two key fatty acid biosynthetic genes, stearoyl-ACP desaturase (SAD1), and acyl-carrier protein (ACP3) in Elaeis guineensis (oil palm) showed high level of expression during the period of oil synthesis in the mesocarp [12-19 weeks after anthesis (w.a.a.)] and kernel (12-15 w.a.a.). Both genes are expressed in spear leaves at much lower levels and the expression increased by 1...
May 22, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29789800/-lra-i-from-lactococcus-raffinolactis-bgtrk10-1-an-isoschizomer-of-eco-ri-exhibits-ion-concentration-dependent-specific-star-activity
#9
Marija Miljkovic, Milka Malesevic, Brankica Filipic, Goran Vukotic, Milan Kojic
Restriction enzymes are the main defence system against foreign DNA, in charge of preserving genome integrity. Lactococcus raffinolactis BGTRK10-1 expresses Lra I Type II restriction-modification enzyme, whose activity is similar to that shown for Eco RI; Lra I methyltransferase protects DNA from Eco RI cleavage. The gene encoding Lra I endonuclease was cloned and overexpressed in E. coli . Purified enzyme showed the highest specific activity at lower temperatures (between 13°C and 37°C) and was stable after storage at -20°C in 50% glycerol...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29789185/variation-in-post-thaw-sperm-quality-of-white-tailed-deer-bucks-odocoileus-virginianus-during-rut
#10
Jamie L Stewart, Clifford F Shipley, Robyn E Ellerbrock, Fabio S Lima, Igor F Canisso
White-tailed deer farming is a growing industry in the United States, with breeding operations contributing significantly to the industry's economic impact. Artificial insemination with frozen semen allows for selection and dissemination of valuable genetics, yet surprisingly little is known regarding the best time throughout rut to perform semen cryopreservation. The objective of this study was to compare semen quality following cryopreservation of white-tailed deer bucks collected early in the breeding season (September, n = 6), at peak rut (December, n = 8), and late season (March, n = 7)...
May 19, 2018: Animal Reproduction Science
https://www.readbyqxmd.com/read/29788485/enzymatic-synthesis-of-random-sequences-of-rna-and-rna-analogues-by-dna-polymerase-theta-mutants-for-the-generation-of-aptamer-libraries
#11
Irina Randrianjatovo-Gbalou, Sandrine Rosario, Odile Sismeiro, Hugo Varet, Rachel Legendre, Jean-Yves Coppée, Valérie Huteau, Sylvie Pochet, Marc Delarue
Nucleic acid aptamers, especially RNA, exhibit valuable advantages compared to protein therapeutics in terms of size, affinity and specificity. However, the synthesis of libraries of large random RNAs is still difficult and expensive. The engineering of polymerases able to directly generate these libraries has the potential to replace the chemical synthesis approach. Here, we start with a DNA polymerase that already displays a significant template-free nucleotidyltransferase activity, human DNA polymerase theta, and we mutate it based on the knowledge of its three-dimensional structure as well as previous mutational studies on members of the same polA family...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788141/a-single-nucleotide-polymorphism-in-the-vitamin-d-receptor-gene-is-associated-with-decreased-levels-of-the-protein-and-a-penetrating-pattern-in-crohn-s-disease
#12
Laura Gisbert-Ferrándiz, Pedro Salvador, Dolores Ortiz-Masiá, Dulce Carolina Macías-Ceja, Samuel Orden, Juan Vicente Esplugues, Sara Calatayud, Joaquín Hinojosa, Maria Dolores Barrachina, Carlos Hernández
Background: Vitamin D signaling modulates inflammation through the vitamin D receptor (VDR). The synonymous single nucleotide polymorphism (SNP) rs731236, located in the VDR gene, has been associated with a higher risk of Crohn's disease (CD). We analyzed differences in VDR expression levels among CD patients who were homozygous for allelic variants in this SNP and their relevance for disease course. Methods: DNA was extracted from blood samples of CD patients, and SNP genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism...
May 18, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29787745/modeling-transposable-element-dynamics-with-fragmentation-equations
#13
Mario Banuelos, Suzanne Sindi
Transposable elements (TEs), segments of DNA capable of self-replication, are abundant in the genomes of most organisms and thus serve as a record of past mutational events. While some work suggests TEs may serve a regulatory function for the host, most empirical and theoretical studies have shown that TEs often have deleterious effects on a host. Because they are not essential, the host genome consists of both full-length (actively replicating) and partial length (inactive remnant) copies of TEs. We developed a novel mathematical formulation of TE dynamics by modeling the density of full and partial length copies resulting from mutations (insertions and deletions) and TE replication within the host genome...
May 19, 2018: Mathematical Biosciences
https://www.readbyqxmd.com/read/29787607/differential-sequences-of-exosomal-nanog-dna-as-a-potential-diagnostic-cancer-marker
#14
Manjusha Vaidya, Michael Bacchus, Kiminobu Sugaya
NANOG has been demonstrated to play an essential role in the maintenance of embryonic stem cells, and its pseudogene, NANOGP8, is suggested to promote the cancer stem cell phenotype. As the roles of these genes are intimately involved with glioblastoma multiforme progression and exosomes are critical in intercellular communication, we conducted a detailed analysis of the association of the NANOG gene family with exosomes to identify diagnostic markers for cancer. Exosomes were precipitated from conditioned culture media from various cell lines, and NANOG gene fragments were directly amplified without DNA isolation using multiple primer sets...
2018: PloS One
https://www.readbyqxmd.com/read/29787328/megakaryocyte-apoptosis-in-immune-thrombocytopenia
#15
John R Vrbensky, Ishac Nazy, Lisa J Toltl, Catherine Ross, Nikola Ivetic, James W Smith, John G Kelton, Donald M Arnold
The mechanisms of platelet underproduction in immune thrombocytopenia (ITP) remain unknown. While the number of megakaryocytes is normal or increased in ITP bone marrow, further studies of megakaryocyte integrity are needed. Megakaryocytes are responsible for the production of platelets in the bone marrow, and they are possible targets of immune-mediated injury in ITP. Since the biological process of megakaryocyte apoptosis impacts platelet production, we investigated megakaryocyte DNA fragmentation as a marker of apoptosis from ITP bone marrow biopsies...
May 22, 2018: Platelets
https://www.readbyqxmd.com/read/29786746/luteolin-induces-myelodysplastic-syndrome%C3%A2-derived-cell-apoptosis-via-the-p53%C3%A2-dependent-mitochondrial-signaling-pathway-mediated-by-reactive-oxygen-species
#16
Weimin Dong, Yan Lin, Yang Cao, Yue Liu, Xiaobao Xie, Weiying Gu
Luteolin, a common dietary flavonoid, induces the apoptosis of cells in several types of cancer. However, its role in myelodysplastic syndrome (MDS) and the potential underlying mechanisms remain to be elucidated. To evaluate the potential benefit and underlying mechanisms of luteolin in MDS cells, the viability of SKM‑1 cells and primary bone marrow (PBM) mononuclear cells from patients with intermediate‑ or high‑risk MDS were assessed using a Cell Counting Kit‑8 assay. The apoptotic features of cell morphology were assessed using Wright‑Giemsa staining, DNA fragmentation was analyzed by agarose gel electrophoresis, and the extent of apoptosis was quantified by flow cytometry (FCM)...
May 18, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29785500/boosting-the-efficiency-of-site-saturation-mutagenesis-for-a-difficult-to-randomize-gene-by-a-two-step-pcr-strategy
#17
Aitao Li, Carlos G Acevedo-Rocha, Manfred T Reetz
Site-saturation mutagenesis (SSM) has been used in directed evolution of proteins for a long time. As a special form of saturation mutagenesis, it involves individual randomization at a given residue with formation of all 19 amino acids. To date, the most efficient embodiment of SSM is a one-step PCR-based approach using NNK codon degeneracy. However, in the case of difficult-to-randomize genes, SSM may not deliver all of the expected 19 mutants, which compels the user to invest further efforts by applying site-directed mutagenesis for the construction of the missing mutants...
May 21, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29784602/molecular-methods-for-diversity-assessment-among-xanthomonads-of-bulgarian-and-macedonian-pepper
#18
Taca Vancheva, Mariya Stoyanova, Elena Tasheva-Terzieva, Nevena Bogatzevska, Penka Moncheva
Bacterial spot is an important disease of pepper in Bulgaria and Macedonia. For characterization of Xanthomonas species associated with bacterial spot, 161 strains were collected from various field pepper-growing regions. Among them, 131 strains were identified as Xanthomonas euvesicatoria and 30 as Xanthomonas vesicatoria using species-specific primers and polymerase chain reaction followed by restriction fragment length polymorphism analysis. To assess the genetic diversity of the strains, two methods (Random Amplified Polymorphic DNA and Repetitive Element Palindromic-Polymerase Chain Reaction) were applied...
May 3, 2018: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29784069/first-molecular-phylogeny-of-agrilus-coleoptera-buprestidae-the-largest-genus-on-earth-with-dna-barcode-database-for-forestry-pest-diagnostics
#19
I Kelnarova, E Jendek, V V Grebennikov, L Bocak
All more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1-5' (DNA barcode fragment), cox1-3', and rrnL...
May 22, 2018: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/29783987/an-updated-review-of-the-genotoxicity-of-respirable-crystalline-silica
#20
REVIEW
Paul J A Borm, Paul Fowler, David Kirkland
Human exposure to (certain forms of) crystalline silica (CS) potentially results in adverse effects on human health. Since 1997 IARC has classified CS as a Group 1 carcinogen [1], which was confirmed in a later review in 2012 [2]. The genotoxic potential and mode of genotoxic action of CS was not conclusive in either of the IARC reviews, although a proposal for mode of actions was made in an extensive review of the genotoxicity of CS by Borm, Tran and Donaldson in 2011 [3]. The present study identified 141 new papers from search strings related to genotoxicity of respirable CS (RCS) since 2011 and, of these, 17 relevant publications with genotoxicity data were included in this detailed review...
May 21, 2018: Particle and Fibre Toxicology
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