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https://www.readbyqxmd.com/read/29351603/the-unexpected-function-of-a-flavin-dependent-oxidoreductase-fox-from-variovorax-paradoxus-tbea6
#1
Christina Meinert, Marc Schürmann, Jan-Eike Domeyer, Anja Poehlein, Rolf Daniel, Alexander Steinbüchel
3,3'-Thiodipropionic acid (TDP) is used as an additive in food and cosmetic industry and as precursor substrate for biotechnical polythioester production. Its catabolism was investigated in Variovorax paradoxus TBEA6 previous to this study. It was reported that the insertion of the transposon Tn5::mob into a gene showing high homology to flavin-dependent oxidoreductases (fox) resulted in impaired growth with TDP. Therefore, it was assumed that the initial cleavage of TDP is catalyzed by an FAD-dependent oxidoreductase (Fox, VPARA_05580)...
January 17, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29351588/sorghum-root-system-classification-in-contrasting-p-environments-reveals-three-main-rooting-types-and-root-architecture-related-marker-trait-associations
#2
Sebastian Parra-Londono, Mareike Kavka, Birgit Samans, Rod Snowdon, Silke Wieckhorst, Ralf Uptmoor
Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions...
January 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29351437/metabolic-reprogramming-in-the-pathogenesis-of-chronic-lung-diseases-including-bpd-copd-and-pulmonary-fibrosis
#3
Haifeng Zhao, Phyllis A Dennery, Hongwei Yao
The metabolism of nutrient substrates including glucose, glutamine and fatty acids provides acetyl-CoA for the tricarboxylic acid cycle to generate energy, and metabolites for the biosynthesis of biomolecules including nucleotides, proteins, and lipids. It has been shown that metabolism of glucose, fatty acid, and glutamine plays important roles in modulating cellular proliferation, differentiation, apoptosis, autophagy, senescence, and inflammatory responses. All these cellular processes contribute to the pathogenesis of chronic lung diseases, including bronchopulmonary dysplasia, chronic obstructive pulmonary disease, and pulmonary fibrosis...
January 4, 2018: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/29351348/interactions-of-2-o-methyl-oligoribonucleotides-with-the-rna-models-of-the-30s-subunit-a-site
#4
Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska
Synthetic oligonucleotides targeting functional regions of the prokaryotic rRNA could be promising antimicrobial agents. Indeed, such oligonucleotides were proven to inhibit bacterial growth. 2'-O-methylated (2'-O-Me) oligoribonucleotides with a sequence complementary to the decoding site in 16S rRNA were reported as inhibitors of bacterial translation. However, the binding mode and structures of the formed complexes, as well as the level of selectivity of the oligonucleotides between the prokaryotic and eukaryotic target, were not determined...
2018: PloS One
https://www.readbyqxmd.com/read/29351302/extension-of-the-viral-ecology-in-humans-using-viral-profile-hidden-markov-models
#5
Zurab Bzhalava, Emilie Hultin, Joakim Dillner
When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family)...
2018: PloS One
https://www.readbyqxmd.com/read/29351075/pathological-and-molecular-studies-of-the-renal-trematode-paratanaisia-bragai-in-indian-peafowls-pavo-cristatus
#6
M Asok Kumar, Deepak Kumar, Munuswamy Palanivelu, Latchumikanthan Annamalai, Karikalan Mathesh, Rajendra Singh, Anil Kumar Sharma, Kuldeep Dhama
Endoparasitic diseases are commonly encountered in free-ranging birds. Although not all endoparasites cause disease, persistent infection with large numbers of parasites almost always affects normal physiological functions, leading to deleterious effects on the host. This paper describes the anatomopathological alterations caused by the renal trematode Paratanaisia bragai in Indian peafowl (n = 3) and examines the phylogeny of these and related parasites. Peafowl from forests in and around the Bareilly region, Uttar Pradesh, India, were necropsied, and microscopic and molecular investigations were performed...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29351064/molecular-target-analysis-of-stearoyl-coa-desaturase-genes-of-protozoan-parasites
#7
He Lu, Xin Qin, Jing Zhang, Shuang Zhang, Yu Zhu, Wei Hua Wu
Protozoan parasites can synthesize polyunsaturated fatty acids. They possess stearoyl-CoA desaturase to convert stearate into oleate and linoleate. Stearoyl-CoA desaturase are the key enzymes required for the synthesis of unsaturated fatty acids. It seems attractive to evaluate the possibility of using unsaturated fatty acid biosynthesis pathways as drug targets. In this study, the authors investigate codon usage bias, base composition variations and protein sequence in ten available complete stearoyl-CoA desaturase gene sequences from Toxoplasma gondii, Neospora caninum etc...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29351063/morphological-and-molecular-characterization-of-seuratascaris-numidica-seurat-1917-ascaridida-ascarididae
#8
Hui-Xia Chen, Kuang Zhang, Lu-Ping Zhang, Liang Li
Seuratascaris numidica (Seurat, 1917) is a specialized nematode species parasitizing amphibians only. In the present study, the detailed morphology of this poorly known species was studied using light and scanning electron microscopy based on the newly material collected from Hoplobatrachus chinensis (Osbeck) (Amphibia: Anura) in China. We found that the relative length of intestinal caecum in our male specimens (representing 68.4-71.1% of oesophageal length) is slighter longer than the previously reported data (not over 60...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29350431/mifast-a-novel-and-rapid-microrna-target-capture-method
#9
Ashley M Poenitzsch Strong, Scott M Berry, David J Beebe, Jian-Liang Li, Vladimir S Spiegelman
MicroRNAs (miRNAs), small 22-25 nucleotide non-coding RNAs, play important roles in cellular and tumor biology. However, characterizing miRNA function remains challenging due to an abundance of predicted targets and an experimental bottleneck in identifying biologically relevant direct targets. Here we developed a novel technique (miFAST) to identify direct miRNA target genes. Using miFAST, we confirmed several previously reported miR-340 target genes and identified five additional novel direct miR-340 targets in melanoma cells...
January 19, 2018: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29350394/genetic-variants-in-the-polish-population-of-patients-with-pulmonary-arterial-hypertension-sequencing-of-bmpr2-alk1-and-eng-genes
#10
Barbara Uznańska-Loch, Kamil Wikło, Dominika Kulczycka-Wojdala, Bożena Szymańska, Łukasz Chrzanowski, Karina Wierzbowska-Drabik, Ewa Trzos, Jarosław Damian Kasprzak, Małgorzata Kurpesa
BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with a very serious prognosis. It seems that mutations in genes related to the transforming growth factor-beta signaling pathway are often related to the development of the disease. There was no study in Polish population that would cover this problem. AIM: To screen for genetic mutations in Polish cohort of patients with pulmonary hypertension, especially with idiopathic PAH, treated in a single hospital in Poland...
January 19, 2018: Kardiologia Polska
https://www.readbyqxmd.com/read/29350304/defective-mitochondrial-atpase-due-to-rare-mtdna-m-8969g-a-mutation-causing-lactic-acidosis-intellectual-disability-and-poor-growth
#11
Pirjo Isohanni, Christopher J Carroll, Christopher B Jackson, Max Pohjanpelto, Tuula Lönnqvist, Anu Suomalainen
Mutations in mitochondrial ATP synthase 6 (MT-ATP6) are a frequent cause of NARP (neurogenic muscle weakness, ataxia, and retinitis pigmentosa) or Leigh syndromes, especially a point mutation at nucleotide position 8993. M.8969G>A is a rare MT-ATP6 mutation, previously reported only in three individuals, causing multisystem disorders with mitochondrial myopathy, lactic acidosis, and sideroblastic anemia or IgA nephropathy. We present two siblings with the m.8969G>A mutation and a novel, substantially milder phenotype with lactic acidosis, poor growth, and intellectual disability...
January 19, 2018: Neurogenetics
https://www.readbyqxmd.com/read/29350289/small-rna-pathways-responsible-for-non-cell-autonomous-regulation-of-plant-reproduction
#12
REVIEW
Ken-Ichi Nonomura
In angiosperms, germline precursors and germ cells are always attached to or engulfed within somatic companion cells until just before fertilization. This is because sperm and egg cells develop as part of the multicellular gametophyte. Thus, the non-cell-autonomous regulation by somatic companions plays important roles in efficient reproduction, in addition to the cell-autonomous regulation. Epigenetic silencing of transposable elements is one of the central events by which the germline transmits the error-free genome to the next generation...
January 19, 2018: Plant Reproduction
https://www.readbyqxmd.com/read/29350180/genetic-characterization-of-three-mitochondrial-gene-sequences-of-goat-sheep-derived-coenurus-cerebralis-and-cysticercus-tenuicollis-isolates-in-inner-mongolia-china
#13
Yichi Zhang, Wei Zhao, Di Yang, Yuan Tian, Weizhe Zhang, Aiqin Liu
Taenia multiceps and Taenia hydatigena are widely distributed tapeworms of canids. Due to a lack of genetic information on these two parasites in China, in this study we analyzed six coenurus cerebralis and two cysticercus tenuicollis cysts from goats or sheep in Inner Mongolia, northern China by amplifying three mitochondrial genes (cox1, nad4, and cytb). Two haplotypes were obtained at each locus for either of the two Taenia cestode species, with ten nucleotide sequences being novel. The degrees of genetic variations were 1...
2018: Parasite: Journal de la Société Française de Parasitologie
https://www.readbyqxmd.com/read/29349811/genetic-analysis-of-interleukin-18-gene-polymorphisms-in-alopecia-areata
#14
Sumeyya Deniz Celik, Omer Ates
BACKGROUND: Alopecia areata (AA), which appears as nonscarring hair shedding on any hair-bearing area, is a common organ-specific autoimmune condition. Cytokines have important roles in the development of AA. Interleukin (IL) 18 is a significant proinflammatory cytokine that was found higher in the patients with AA. We aimed to investigate whether the IL-18 (rs187238 and rs1946518) single nucleotide polymorphisms (SNPs) may be associated with AA and/or clinical outcome of patients with AA in Turkish population...
January 18, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29349714/dbda-as-a-novel-matrix-for-the-analyses-of-small-molecules-and-quantification-of-fatty-acids-by-negative-ion-maldi-tof-ms
#15
Ling Ling, Ying Li, Sheng Wang, Liming Guo, Chunsheng Xiao, Xuesi Chen, Xinhua Guo
Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H]-) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0...
January 18, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29349673/pharmacological-dissection-of-the-cellular-mechanisms-associated-to-the-spontaneous-and-the-mechanically-stimulated-atp-release-by-mesentery-endothelial-cells-roles-of-thrombin-and-trpv
#16
M Verónica Donoso, Felipe Hernández, Tania Villalón, Claudio Acuña-Castillo, J Pablo Huidobro-Toro
Endothelial cells participate in extracellular ATP release elicited by mechanosensors. To characterize the dynamic interactions between mechanical and chemical factors that modulate ATP secretion by the endothelium, we assessed and compared the mechanisms participating in the spontaneous (basal) and mechanically stimulated secretion using primary cultures of rat mesentery endothelial cells. ATP/metabolites were determined in the cell media prior to (basal) and after cell media displacement or a picospritzer buffer puff used as mechanical stimuli...
January 19, 2018: Purinergic Signalling
https://www.readbyqxmd.com/read/29349565/description-of-alteromonas-abrolhosensis-sp-nov-isolated-from-sea-water-of-abrolhos-bank-brazil
#17
Maria S Nóbrega, Bruno S Silva, Luciana Leomil, Diogo Antonio Tschoeke, Mariana E Campeão, Gizele D Garcia, Graciela A Dias, Verônica V Vieira, Cristiane C Thompson, Fabiano L Thompson
Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67ET and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47T and Alteromonas macleodii ATCC 27126T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67ET and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A...
January 18, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29349559/a-mutant-hcn4-channel-in-a-family-with-bradycardia-left-bundle-branch-block-and-left-ventricular-noncompaction
#18
Ryosuke Yokoyama, Koshi Kinoshita, Yukiko Hata, Masayoshi Abe, Kenta Matsuoka, Keiichi Hirono, Masanobu Kano, Makoto Nakazawa, Fukiko Ichida, Naoki Nishida, Toshihide Tabata
We found that a female infant presenting with left bundle branch block and left ventricular noncompaction carries uninvestigated gene mutations HCN4(G811E), SCN5A(L1988R), DMD(S2384Y), and EMD(R203H). Here, we explored the possible pathogenicity of HCN4(G811E), which results in a G811E substitution in hyperpolarization-activated cyclic nucleotide-gated channel 4, the main subunit of the cardiac pacemaker channel. Voltage-clamp measurements in a heterologous expression system of HEK293T cells showed that HCN4(G811E) slightly reduced whole-cell HCN4 channel conductance, whereas it did not affect the gating kinetics, unitary conductance, or cAMP-dependent modulation of voltage-dependence...
January 18, 2018: Heart and Vessels
https://www.readbyqxmd.com/read/29349538/capturing-pair-wise-epistatic-effects-associated-with-three-agronomic-traits-in-barley
#19
Yi Xu, Yajun Wu, Jixiang Wu
Genetic association mapping has been widely applied to determine genetic markers favorably associated with a trait of interest and provide information for marker-assisted selection. Many association mapping studies commonly focus on main effects due to intolerable computing intensity. This study aims to select several sets of DNA markers with potential epistasis to maximize genetic variations of some key agronomic traits in barley. By doing so, we integrated a MDR (multifactor dimensionality reduction) method with a forward variable selection approach...
January 18, 2018: Genetica
https://www.readbyqxmd.com/read/29349042/an-optimized-targeted-next-generation-sequencing-approach-for-sensitive-detection-of-single-nucleotide-variants
#20
S Stasik, C Schuster, C Ortlepp, U Platzbecker, M Bornhäuser, J Schetelig, G Ehninger, G Folprecht, C Thiede
Monitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torrent PGM system. As a model case we used the c.1849G > T (p.Val617Phe) mutation of the JAK2-gene. Several reaction parameters (e...
May 2018: Biomolecular Detection and Quantification
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