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https://www.readbyqxmd.com/read/28922357/analysis-of-nuclear-and-organellar-genomes-of-plasmodium-knowlesi-in-humans-reveals-ancient-population-structure-and-recent-recombination-among-host-specific-subpopulations
#1
Ernest Diez Benavente, Paola Florez de Sessions, Robert W Moon, Anthony A Holder, Michael J Blackman, Cally Roper, Christopher J Drakeley, Arnab Pain, Colin J Sutherland, Martin L Hibberd, Susana Campino, Taane G Clark
The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found...
September 18, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28911115/the-ires5-utr-of-the-dicistrovirus-cricket-paralysis-virus-is-a-type-iii-ires-containing-an-essential-pseudoknot-structure
#2
Lauriane Gross, Quentin Vicens, Evelyne Einhorn, Audrey Noireterre, Laure Schaeffer, Lauriane Kuhn, Jean-Luc Imler, Gilbert Eriani, Carine Meignin, Franck Martin
Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28905328/lessons-learned-from-protein-aggregation-toward-technological-and-biomedical-applications
#3
REVIEW
César L Avila, Silvina Chaves, Sergio B Socias, Esteban Vera-Pingitore, Florencia González-Lizárraga, Cecilia Vera, Diego Ploper, Rosana Chehín
The close relationship between protein aggregation and neurodegenerative diseases has been the driving force behind the renewed interest in a field where biophysics, neurobiology and nanotechnology converge in the study of the aggregate state. On one hand, knowledge of the molecular principles that govern the processes of protein aggregation has a direct impact on the design of new drugs for high-incidence pathologies that currently can only be treated palliatively. On the other hand, exploiting the benefits of protein aggregation in the design of new nanomaterials could have a strong impact on biotechnology...
September 13, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28904177/limited-proteolysis-as-a-tool-to-probe-the-tertiary-conformation-of-dysferlin-and-structural-consequences-of-patient-missense-variant-l344p
#4
Natalie Woolger, Adam Bournazos, Reece A Sophocleous, Frances J Evesson, Angela Lek, Birgit Driemer, R Bryan Sutton, Sandra T Cooper
Dysferlin is a large transmembrane protein that plays a key role in cell membrane repair, and underlies a recessive form of inherited muscular dystrophy. Dysferlinopathy is characterized by absence or marked reduction of dysferlin protein, with 43% of reported pathogenic variants being missense variants that span the length of the dysferlin protein. The unique structure of dysferlin, with seven tandem C2-domains separated by linkers, suggest dysferlin may dynamically associate with phospholipid membranes in response to Ca2+ signaling...
September 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28902411/functional-changes-in-the-neural-retina-occur-in-the-absence-of-mitochondrial-dysfunction-in-a-rodent-model-of-diabetic-retinopathy
#5
Dustin R Masser, Laura Otalora, Nicholas W Clark, Michael T Kinter, Michael H Elliott, Willard M Freeman
Diabetic retinopathy is a neurovascular diabetes complication resulting in vision loss. A wealth of literature reports retinal molecular changes indicative of neural deficits, inflammation, and vascular leakage with chronic diabetes, but the mechanistic causes of disease initiation and progression are unknown. Microvascular mitochondrial DNA (mtDNA) damage leading to mitochondrial dysfunction has been proposed to drive vascular dysfunction in retinopathy. However, growing evidence suggests that neural retina dysfunction precedes and may cause vascular damage...
September 13, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28901593/interactive-comparison-and-remediation-of-collections-of-macromolecular-structures
#6
Nigel W Moriarty, Dorothee Liebschner, Herbert E Klei, Nathaniel Echols, Pavel V Afonine, Jeff Headd, Billy K Poon, Paul D Adams
Often similar structures need to be compared to reveal local differences throughout the entire model or between related copies within the model. Therefore, a program to compare multiple structures and enable correction any differences not supported by the density map was written within the Phenix framework.(1) This program, called Structure Comparison, can also be used for structures with multiple copies of the same protein chain in the asymmetric unit, i.e. as a result of non-crystallographic symmetry (NCS)...
September 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28899628/a-novel-approach-to-a-rabies-vaccine-based-on-a-recombinant-single-cycle-flavivirus-vector
#7
Maryann Giel-Moloney, Alexander A Rumyantsev, Fred David, Monica Figueiredo, Brad Feilmeier, Teshome Mebatsion, Mark Parrington, Harry Kleanthous, Konstantin V Pugachev
The RepliVax® vaccine (RV) platform is based on flavivirus genomes that are rationally attenuated by deletion. These single-cycle RV vaccine candidates targeting flavivirus pathogens have been demonstrated to be safe, highly immunogenic, and efficacious in animal models, including non-human primates. Here we show utility of the technology for delivery of a non-flavivirus immunogen by engineering several West Nile-based RV vectors to express full-length rabies virus G protein. The rabies virus G protein gene was incorporated in place of different West Nile structural protein gene deletions...
September 9, 2017: Vaccine
https://www.readbyqxmd.com/read/28899424/clade-homogeneity-and-low-rate-of-delta-virus-despite-hyperendemicity-of-hepatitis-b-virus-in-ethiopia
#8
Yeshambel Belyhun, Uwe Gerd Liebert, Melanie Maier
BACKGROUND: Although hepatitis B virus (HBV) is hyperendemic and heterogeneous in its genetic diversity in Ethiopia, little is known about hepatitis D virus (HDV) circulating genotypes and molecular diversity. METHODS: A total of 321 hepatitis B surface antigen (HBsAg) positives (125 HIV co-infected, 102 liver disease patients and 94 blood donors) were screened for anti-HDV antibody. The anti-HDV positive sera were subjected to Real time PCR for HDV-RNA confirmation...
September 12, 2017: Virology Journal
https://www.readbyqxmd.com/read/28893508/regulation-of-protein-phosphatase-2a-during-embryonic-diapause-process-in-the-silkworm-bombyx-mori
#9
Shi-Hong Gu, Hsiao-Yen Hsieh, Pei-Ling Lin
Regulation of protein phosphorylation requires coordinated interactions between protein kinases and protein phosphatases. In the present study, we investigated regulation of protein phosphatase 2A (PP2A) during the embryonic diapause process of B. mori. An immunobloting analysis showed that Bombyx eggs contained a catalytic C subunit, a major 55-kDa regulatory B subunit (B55/PR55 subunit), and a structural A subunit, with the A and B subunits undergoing differential changes between diapause and non-diapause eggs during embryonic process...
September 8, 2017: Journal of Insect Physiology
https://www.readbyqxmd.com/read/28890721/development-and-application-of-transcriptome-derived-microsatellites-in-actinidia-eriantha-actinidiaceae
#10
Rui Guo, Jacob B Landis, Michael J Moore, Aiping Meng, Shuguang Jian, Xiaohong Yao, Hengchang Wang
Actinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28889242/zinc-oxide-nanoparticle-inhibits-the-biofilm-formation-of-streptococcus-pneumoniae
#11
Purnita Bhattacharyya, Bikash Agarwal, Madhurankhi Goswami, Debasish Maiti, Sunandan Baruah, Prosun Tribedi
Biofilms are structured consortia of microbial cells that grow on living and non living surfaces and surround themselves with secreted polymers. Infections with bacterial biofilms have emerged as a foremost public health concern because biofilm growing cells can be highly resistant to both antibiotics and host immune defenses. Zinc oxide nanoparticles have been reported as a potential antimicrobial agent, thus, in the current study, we have evaluated the antimicrobial as well as antibiofilm activity of zinc oxide nanoparticles against the bacterium Streptococcus pneumoniae which is a significant cause of disease...
September 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28887406/maize-npf6-proteins-are-homologs-of-arabidopsis-chl1-that-are-selective-for-both-nitrate-and-chloride
#12
Zhengyu Wen, Stephen Tyerman, Julie Dechorgnat, Evgenia Ovchinnikova, Kanwarpal Dhugga, Brent N Kaiser
Nitrate uptake by plant cells requires both high and low-affinity transport activities. Arabidopsis (Arabidopsis thaliana, At) nitrate transporter 1/peptide transporter family (NPF) 6.3 is a dual-affinity plasma membrane transport protein that has both high and low-affinity functions. At-NPF6.3 imports and senses nitrate and is regulated by phosphorylation at Thr-101 (T101). A detailed functional analysis of two maize (Zea mays, Zm) homologs of At-NPF6.3 (Zm-NPF6.6 and Zm-NPF6.4) showed that Zm-NPF6.6 was a pH dependent non-biphasic high-affinity nitrate-specific transport protein...
September 8, 2017: Plant Cell
https://www.readbyqxmd.com/read/28881968/snapdock-template-based-docking-by-geometric-hashing
#13
Michael Estrin, Haim J Wolfson
Motivation: A highly efficient template-based protein-protein docking algorithm, nicknamed SnapDock, is presented. It employs a Geometric Hashing-based structural alignment scheme to align the target proteins to the interfaces of non-redundant protein-protein interface libraries. Docking of a pair of proteins utilizing the 22 600 interface PIFACE library is performed in < 2 min on the average. A flexible version of the algorithm allowing hinge motion in one of the proteins is presented as well...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28876229/3-6-anhydro-l-galactonate-cycloisomerase-from-vibrio-sp-strain-ejy3-crystallization-and-x-ray-crystallographic-analysis
#14
Saeyoung Lee, Eun Ju Yun, Kyoung Heon Kim, Hye Yeon Kim, In Geol Choi
3,6-Anhydro-L-galactonate cycloisomerase (ACI), which is found in the marine bacterium Vibrio sp. strain EJY3, converts 3,6-anhydro-L-galactonate into 2-keto-3-deoxygalactonate. ACI is a key enzyme in the metabolic pathway of 3,6-anhydro-L-galactose (AHG). Study of AHG metabolism is important for the efficient fermentation of agar and biofuel production, because AHG is a sugar that is non-fermentable by commercial microorganisms. The aci gene from Vibrio sp. strain EJY3 was cloned, and the recombinant protein was overexpressed and crystallized in order to determine the structure and understand the function of the protein...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28875416/nmr-study-of-non-structural-proteins-part-iii-1-h-13-c-15-n-backbone-and-side-chain-resonance-assignment-of-macro-domain-from-chikungunya-virus-chikv
#15
Michail V Lykouras, Aikaterini C Tsika, Julie Lichière, Nicolas Papageorgiou, Bruno Coutard, Detlef Bentrop, Georgios A Spyroulias
Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130-190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids...
September 5, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28873987/understanding-the-role-of-residues-around-the-active-site-tunnel-towards-generating-a-glucose-tolerant-%C3%AE-glucosidase-from-agrobacterium-tumefaciens-5a
#16
Shubhasish Goswami, Shibashis Das, Supratim Datta
Most β-glucosidases are subjected to inhibition by the final hydrolysis product glucose resulting in the accumulation of cellobiose and oligosaccharides. This accumulated cellobiose and oligosaccharides further inhibit the activities of endoglucanase and cellobiohydrolases, resulting in the inhibition of cellulose degradation and a more expensive biofuel. To elucidate the mechanism(s) of glucose tolerance, we designed and characterised six mutations of a moderately glucose-tolerant β-glucosidase (H0HC94) from the mesophilic bacterium Agrobacterium tumefaciens 5A...
July 1, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28873466/rational-design-of-drug-like-compounds-targeting-mycobacterium-marinum-melf-protein
#17
Renu Dharra, Sakshi Talwar, Yogesh Singh, Rani Gupta, Jeffrey D Cirillo, Amit K Pandey, Mahesh Kulharia, Promod K Mehta
The mycobacterial mel2 locus (mycobacterial enhanced infection locus, Rv1936-1941) is Mycobacterium marinum and M. tuberculosis specific, which can withstand reactive oxygen species (ROS) and reactive nitrogen species (RNS) induced stress. A library of over a million compounds was screened using in silico virtual ligand screening (VLS) to identify inhibitors against the modeled structure of MelF protein expressed by melF of mel2 locus so that M. marinum's ability to withstand ROS/RNS stress could be reduced...
2017: PloS One
https://www.readbyqxmd.com/read/28873208/a-xanthomonas-citri-subsp-citri-hypothetical-protein-related-to-virulence-contains-a-non-functional-hd-domain-and-is-implicated-in-flagellar-motility
#18
F C F Vieira, A M Gonçalves, E F R Mendoza, R M Ferreira, M L M Costa, T S Balbuena, H G Sebinelli, P Ciancaglini, J M Pizauro Junior, J A Ferro
Citrus canker, caused by the Gram-negative bacterium Xanthomonas citri subsp citri (Xac), severely affects most economically important citrus varieties worldwide. A previous study showed that disruption of the ORF XAC1201 from the Xac 306 strain by transposon Tn5 decreased bacterium virulence in the Rangpur lime host (Citrus limonia L. Osbeck). However, little is known regarding the possible function of the hypothetical protein XAC1201 and how it affects the virulence of Xac 306. Here, we confirmed that disruption of ORF XAC1201 reduces Xac 306 virulence in two different hosts, delaying the onset of typical symptoms...
August 31, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28871236/non-visual-photopigments-effects-of-constant-light-emitting-diode-light-exposure-on-the-inner-retina-of-wistar-rats
#19
María M Benedetto, Mario E Guido, María A Contin
The retina is part of the central nervous system specially adapted to capture light photons and transmit this information to the brain through photosensitive retinal cells involved in visual and non-visual activities. However, excessive light exposure may accelerate genetic retinal diseases or induce photoreceptor cell (PRC) death, finally leading to retinal degeneration (RD). Light pollution (LP) caused by the characteristic use of artificial light in modern day life may accelerate degenerative diseases or promote RD and circadian desynchrony...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28869862/bmp-2-and-bmp-9-binding-specificities-with-alk-3-in-aqueous-solution-with-dynamics
#20
Orkid Coskuner, Vladimir N Uversky
Signal ligands of the transforming growth factor-β (TGF-β) superfamily include the bone morphogenetic proteins (BMPs). BMPs bind to type I and type II serine-threonine kinase receptors and trigger the transphosphorylation cascade, wherein the active type II receptor phosphorylates the inactive type I receptor. This process further activates the cytoplasmic effectors of the pathway, such as SMAD proteins, which are homologs of both the Drosophila protein MAD (mothers against decapentaplegic) and the Caenorhabditis elegans protein SMA (small body size)...
August 9, 2017: Journal of Molecular Graphics & Modelling
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