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https://www.readbyqxmd.com/read/29778329/the-kinetoplast-dna-of-the-australian-trypanosome-trypanosoma-copemani-shares-features-with-trypanosoma-cruzi-and-trypanosoma-lewisi
#1
Adriana Botero, Irit Kapeller, Crystal Cooper, Peta L Clode, Joseph Shlomai, R C Andrew Thompson
Kinetoplast DNA (kDNA) is the mitochondrial genome of trypanosomatids. It consists of a few dozen maxicircles and several thousand minicircles, all catenated topologically to form a two-dimensional DNA network. Minicircles are heterogeneous in size and sequence among species. They present one or several conserved regions that contain three highly conserved sequence blocks (CSBs). CSB-1 (10 bp sequence) and CSB-2 (8 bp sequence) present lower interspecies homology, while CSB-3 (12 bp sequence) or the Universal Minicircle Sequence (UMS) is conserved within most trypanosomatids...
May 17, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29777991/co-evolutionary-associations-between-root-associated-microbiomes-and-root-transcriptomes-in-wild-and-cultivated-rice-varieties
#2
Lei Tian, Shaohua Shi, Lina Ma, Fahad Nasir, Xiujun Li, Lam-Son Phan Tran, Chunjie Tian
The plants and root-associated microbiomes are closely related. Plant metabolic substances can serve as a nutrient source for the microbiome, and in return, the microbiome can regulate the production of plant metabolic substances. Wild rice (Oryza rufipogon), as the ancestor of cultivated rice (Oryza sativa), has changed several metabolic pathways and root-associated microbiome during evolution. Thus, the study of the different associations between metabolic pathways and root-associated microbiomes in wild and cultivated rice varieties is important for rice breeding...
April 13, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29777775/genome-analysis-of-the-ancient-tracheophyte-selaginella-tamariscina-reveals-evolutionary-features-relevant-to-the-acquisition-of-desiccation-tolerance
#3
Zhichao Xu, Tianyi Xin, Dorothea Bartels, Ying Li, Wei Gu, Hui Yao, Sai Liu, Haoying Yu, Xiangdong Pu, Jianguo Zhou, Jiang Xu, Caicai Xi, Hetian Lei, Jingyuan Song, Shilin Chen
Resurrection plants, which are the "gifts" of natural evolution, are ideal models for studying genetic basis of plant desiccation tolerance. Here, we report a high-quality genome assembly of 301 Mb for the diploid spike moss Selaginella tamariscina, a primitive vascular resurrection plant. We predicated 27,761 protein-coding genes from the assembled S. tamariscina genome, 11.38% (2363) of which showed significant expression changes in response to desiccation. Approximately 60.58% of the S. tamariscina genome was annotated as repetitive DNA, which is almost 2-fold increase of that in the genome of desiccation-sensitive S...
May 16, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29777767/biglycan-is-a-new-high-affinity-ligand-for-cd14-in-macrophages
#4
Heiko Roedig, Madalina V Nastase, Helena Frey, Kristin Moreth, Jinyang Zeng-Brouwers, Chiara Poluzzi, Louise Tzung-Harn Hsieh, Christian Brandts, Simone Fulda, Malgorzata Wygrecka, Liliana Schaefer
Sterile inflammation is a therapeutic target in many diseases where it represents an important initiator of disease progression. However, the detailed mechanisms underlying its evolution and biological relevance are not yet completely elucidated. Biglycan, a prototype extracellular matrix-derived damage-associated molecular pattern, mediates sterile inflammation in macrophages through Toll-like receptor (TLR) 2 and/or TLR4-dependent signaling pathways. Here we discovered that soluble biglycan is a novel high-affinity ligand for CD14, a well-known GPI-anchored co-receptor for TLRs...
May 16, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29777385/changes-in-selection-intensity-on-the-mitogenome-of-subterranean-and-fossorial-rodents-respective-to-aboveground-species
#5
William Corrêa Tavares, Hector N Seuánez
Several rodent lineages independently acquired the ability to dig complex networks of tunnels where fossorial and subterranean species spend part or their whole life, respectively. Their underground lifestyles imposed harsh physiological demands, presumably triggering strong selective pressures on genes involved in energy metabolism like those coding for mitochondrial proteins. Moreover, underground lifestyles must have increased inbreeding and susceptibility to population bottlenecks as well as restricted migration, leading to small effective population size (Ne ) that, in turn, must have reduced the effectiveness of selection...
May 18, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29777163/evolution-of-cll-treatment-from-chemoimmunotherapy-to-targeted-and-individualized-therapy
#6
REVIEW
Jan A Burger, Susan O'Brien
During the past 5 years, a number of highly active novel agents, including kinase inhibitors targeting BTK or PI3Kδ, an antagonist of the antiapoptotic protein BCL-2, and new anti-CD20 monoclonal antibodies, have been added to the therapeutic armamentarium for patients with chronic lymphocytic leukaemia (CLL). In these exciting times, care is needed to optimally integrate these novel agents into the traditional treatment algorithm without overlooking or compromising the benefits of established treatments, especially chemoimmunotherapy...
May 18, 2018: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/29776931/shuffling-the-neutral-drift-of-unspecific-peroxygenase-in-saccharomyces-cerevisiae
#7
Javier Martin-Diaz, Carmen Paret, Eva García-Ruiz, Patricia Molina-Espeja, Miguel Alcalde
Unspecific peroxygenase (UPO) is a highly promiscuous biocatalyst and its selective mono(per)oxygenase activity makes it useful for many synthetic chemistry applications. Among the broad repertory of library creation methods for directed enzyme evolution, genetic drift allows neutral mutations to be accumulated gradually within a polymorphic network of variants. In this study, we conducted a campaign of genetic drift with UPO in Saccharomyces cerevisiae so that neutral mutations were simply added and recombined in vivo With low mutational loading and an activity threshold of 45% of the parent's native function, mutant libraries enriched in folded and active UPO variants were generated...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29776407/comparative-genomics-of-the-miniature-wasp-and-pest-control-agent-trichogramma-pretiosum
#8
Amelia R I Lindsey, Yogeshwar D Kelkar, Xin Wu, Dan Sun, Ellen O Martinson, Zhichao Yan, Paul F Rugman-Jones, Daniel S T Hughes, Shwetha C Murali, Jiaxin Qu, Shannon Dugan, Sandra L Lee, Hsu Chao, Huyen Dinh, Yi Han, Harsha Vardhan Doddapaneni, Kim C Worley, Donna M Muzny, Gongyin Ye, Richard A Gibbs, Stephen Richards, Soojin V Yi, Richard Stouthamer, John H Werren
BACKGROUND: Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Trichogramma are frequently used in agriculture, released as biological control agents against major moth and butterfly pests...
May 18, 2018: BMC Biology
https://www.readbyqxmd.com/read/29776336/phylogenomic-analysis-of-apoidea-sheds-new-light-on-the-sister-group-of-bees
#9
Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, Michael Ohl
BACKGROUND: Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families...
May 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29776055/optimal-methylation-noise-for-best-chemotactic-performance-of-e-coli
#10
Subrata Dev, Sakuntala Chatterjee
In response to a concentration gradient of chemoattractant, E. coli bacterium modulates the rotational bias of flagellar motors which control its run-and-tumble motion, to migrate towards regions of high chemoattractant concentration. Presence of stochastic noise in the biochemical pathway of the cell has important consequences on the switching mechanism of motor bias, which in turn affects the runs and tumbles of the cell in a significant way. We model the intracellular reaction network in terms of coupled time evolution of three stochastic variables-kinase activity, methylation level, and CheY-P protein level-and study the effect of methylation noise on the chemotactic performance of the cell...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775751/expression-pattern-and-functional-analysis-of-the-two-ring-box-protein-rbx-in-spermatogenesis-of-chinese-mitten-crab-eriocheir-sinensis
#11
Jia-Shun Zhang, Xue-Jie Li, Lei Yang, Wei-Wei Li, Qun Wang
Studies in E. sinensis have shown that ubiquitination mediated by Cullin-RING E3 ligases (CRLs) plays important roles in spermatogenesis. In other species, CRLs are also essential in cell cycle progression, DNA replication, signal transduction, gene transcription, and development. The catalytic RING component, the RING box protein, is an important part of CRLs. However, there have been few studies on CRLs in crustaceans. In this study, we cloned two RING box protein genes from the Chinese mitten crab, Eriocheir sinensis, termed Es-RBX1 and Es-RBX2 The full length Es-RBX1 cDNA comprises 741 nucleotides, and encodes a protein of 124 amino acid residues, whereas the Es-RBX2 cDNA comprises 1325 nucleotides, and encodes a protein of 110 amino acid residues...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775634/the-direction-of-protein-evolution-is-destined-by-the-stability
#12
Natsuko Ota, Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
Protein evolution is potentially governed by protein stability. Here, we investigated the relationship between protein evolution and stability through the random mutational drift of a thermophilic bacterial protein, an esterase of Alicyclobacillus acidocaldarius (Aac-Est), at high and low temperatures. In the first random mutation of Aac-Est, few proteins exhibit increased activity at 65°C, indicating that the wild-type (WT) Aac-Est is located on the peak of a mountain in a fitness landscape for activity at high temperature...
May 15, 2018: Biochimie
https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#13
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29774431/complete-genome-sequences-of-three-novel-cycloviruses-identified-in-a-dragonfly-odonata-anisoptera-from-china
#14
Saif Ul Islam, Wenzhong Lin, Ran Wu, Chen Lin, Waqar Islam, Muhammad Arif, Zhenguo Du, Zujian Wu
Three cycloviruses (genus Cyclovirus, family Circoviridae) were recovered from a dragonfly (Odonata: Anisoptera) captured in Fuzhou, China. The three cycloviruses, named dragonfly associated cyclovirus 9, 10 and 11 (DfCyV-9, -10, -11), respectively, show 56.1-79.6% genome-wide identity to known cycloviruses and 61.6-65.1% among themselves. Thus, according to the current species demarcation criteria, they represent three novel cycloviruses. Notably, DfCyV-10 has a predicted replication-associated protein (Rep) that is most similar to that of bat associated cyclovirus 2 (BatACyV-2), a cyclovirus discovered in China, with 79...
May 17, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29773011/antibacterial-activity-of-novel-strains-of-bacteriophages-an-experimental-approach
#15
Muhammad Imran Qadir, Zunera Chauhdary
The evolution of antibiotic resistance in bacteria has increased research in the development of alternative therapies to conventional drugs. In this study, isolated phages were characterized and antibacterial activity was determined by standard agar disc diffusion method. The phages showed maximum propagation at 37°C to 40°C and highest viability at pH 7. Sugars influenced the bacteriophage viability. Sodium chloride decreased the phage propagation. Calcium chloride and magnesium chloride increased the phage propagation up to a certain limit...
2018: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/29772825/identification-and-characterization-of-the-wox-family-genes-in-five-solanaceae-species-reveal-their-conserved-roles-in-peptide-signaling
#16
Xiaoxu Li, Madiha Hamyat, Cheng Liu, Ahmad Salman, Xiaoming Gao, Cun Guo, Yuanying Wang, Yongfeng Guo
Members of the plant-specific WOX (WUSCHEL-related homeobox) transcription factor family have been reported to play important roles in peptide signaling that regulates stem cell maintenance and cell fate specification in various developmental processes. Even though remarkable advances have been made in studying WOX genes in Arabidopsis , little is known about this family in Solanaceae species. A total of 45 WOX members from five Solanaceae species were identified, including eight members from Solanum tuberosum , eight from Nicotiana tomentosiformis , 10 from Solanum lycopersicum , 10 from Nicotiana sylvestris and nine from Nicotiana tabacum ...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772002/lessons-from-bacteriophages-part-1-deriving-utility-from-protein-structure-function-and-evolution
#17
Kunica Asija, Carolyn M Teschke
No abstract text is available yet for this article.
May 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29771985/another-cat-and-mouse-game-deciphering-the-evolution-of-the-scgb-superfamily-and-exploring-the-molecular-similarity-of-major-cat-allergen-fel-d-1-and-mouse-abp-using-computational-approaches
#18
Rajesh Durairaj, Patrick Pageat, Cécile Bienboire-Frosini
The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches...
2018: PloS One
https://www.readbyqxmd.com/read/29771963/predictive-value-of-long-term-changes-of-growth-differentiation-factor-15-over-a-27-year-period-for-heart-failure-and-death-due-to-coronary-heart-disease
#19
Nina Fluschnik, Francisco Ojeda, Tanja Zeller, Torben Jørgensen, Kari Kuulasmaa, Peter Moritz Becher, Christoph Sinning, Stefan Blankenberg, Dirk Westermann
BACKGROUND: Growth differentiation factor-15 (GDF-15), Cystatin C and C-reactive protein (CRP) have been discussed as biomarkers for prediction of cardiac diseases. The aim of this study was to investigate the predictive value of single and repeated measurements of GDF-15 compared to Cystatin C and CRP for incidence of heart failure (HF) and death due to coronary heart disease (CHD) in the general population. METHODS AND RESULTS: Levels of GDF-15, CRP and Cystatin C were determined in three repeated measurements collected 5 years apart in the DAN-MONICA (Danish-Multinational MONitoring of trends and determinants in Cardiovascular disease) cohort (participants at baseline n = 3785)...
2018: PloS One
https://www.readbyqxmd.com/read/29770800/current-and-future-circulating-biomarkers-for-cardiac-amyloidosis
#20
REVIEW
Marco Luciani, Luca Troncone, Federica Del Monte
Cardiac amyloidosis (CA) comprises a heterogeneous group of medical conditions affecting the myocardium. It presents with proteinaceous infiltration with variable degrees of severity, prevalence and evolution. Despite this heterogeneity, erroneous protein folding is the common pathophysiologic process, yielding the formation of a single misfolded protein (monomer) that progressively evolves and ultimately forms amyloid fibers. Additionally, by seeding out from the organs of origin, intermediates called oligomers metastasize and restart the process...
May 17, 2018: Acta Pharmacologica Sinica
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