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https://www.readbyqxmd.com/read/30111830/understanding-explosive-diversification-through-cichlid-fish-genomics
#1
REVIEW
Walter Salzburger
Owing to their taxonomic, phenotypic, ecological and behavioural diversity and propensity for explosive diversification, the assemblages of cichlid fish in the East African Great Lakes Victoria, Malawi and Tanganyika are important role models in evolutionary biology. With the release of five reference genomes and many additional genomic resources, as well as the establishment of functional genomic tools, the cichlid system has fully entered the genomic era. The in-depth genomic exploration of the East African cichlid fauna - in combination with the examination of their ecology, morphology and behaviour - permits novel insights into the way organisms diversify...
August 15, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30111076/epidemiological-characteristics-of-patients-with-syphilis-in-gda%C3%A5-sk-and-warsaw-in-2016-of-patients-with-syphilis-in-gda%C3%A5-sk-and-warsaw-in-2016
#2
Magda Orzechowska, Elżbieta Krajewska-Kułak, Mateusz Cybulski, Ewelina Mystkowska, Anna Milewska
INTRODUCTION: Syphilis is a systemic disease with a complex natural history and a diversified clinical symptomology, taking various forms. It is characterized by a long-term course, often asymptomatic. The Global Estimates indicate that Treponema pallidum caused 5.6 million infections per year. AIM: Epidemiological characteristics of patients with syphilis in selected Polish urban agglomerations (Warsaw and Gdańsk) in 2016. MATERIAL AND METHODS: Cases of syphilis reported by doctors to The Provincial Sanitary and Epidemiological Stations in Gdańsk (50 cases) and in Warsaw (520 cases) in 2016 were analysed...
2018: Przegla̧d Epidemiologiczny
https://www.readbyqxmd.com/read/30109906/chemically-induced-inflammation-and-nerve-damage-affect-the-distribution-of-vasoactive-intestinal-polypeptide-like-immunoreactive-vip-li-nervous-structures-in-the-descending-colon-of-the-domestic-pig
#3
Krystyna Makowska
BACKGROUND: The enteric nervous system (ENS), situated in the wall of the gastrointestinal tract, regulates the majority of intestinal activities in physiological conditions and during pathological processes. Enteric neurons are diversified in terms of active substance expression. One of the most important neuropeptides within the ENS is vasoactive intestinal polypeptide (VIP). It seems to be one among the important inhibitory peptides in addition to neuropeptide Y (NPY), nitric oxide (NO), and adenosine triphosphate (ATP) of the intestinal motility and secretion, however, many issues connected with distribution and roles of VIP in the large intestine, especially during pathological states, still remain unknown...
August 15, 2018: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/30109815/pam-identification-by-crispr-cas-effector-complexes-diversified-mechanisms-and-structures
#4
Daniel Gleditzsch, Patrick Pausch, Hanna Müller-Esparza, Ahsen Özcan, Xiaohan Guo, Gert Bange, Lennart Randau
Adaptive immunity of prokaryotes is mediated by CRISPR-Cas systems that employ a large variety of Cas protein effectors to identify and destroy foreign genetic material. The different targeting mechanisms of Cas proteins rely on the proper protection of the host genome sequence while allowing for efficient detection of target sequences, termed protospacers. A short DNA sequence, the protospacer-adjacent motif (PAM), is frequently used to mark proper target sites. Cas proteins have evolved a multitude of PAM-interacting domains, which enables them to cope with viral anti-CRISPR measures that alter the sequence or accessibility of PAM elements...
August 15, 2018: RNA Biology
https://www.readbyqxmd.com/read/30109393/meiotic-homoeologous-recombination-based-mapping-of-wheat-chromosome-2b-and-its-homoeologues-in-aegilops-speltoides-and-thinopyrum-elongatum
#5
Wei Zhang, Xianwen Zhu, Mingyi Zhang, Shiaoman Chao, Steven Xu, Xiwen Cai
We physically dissected and mapped wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum based on meiotic homoeologous recombination, providing a unique physical framework for genome studies. Common wheat has a large and complex genome with narrow genetic diversity and various degrees of recombination between the A, B, and D subgenomes. This has limited the homologous recombination-based genome studies in wheat. Here, we exploited meiotic homoeologous recombination for molecular mapping of wheat chromosome 2B and its homoeologue 2S from Aegilops speltoides and 2E from Thinopyrum elongatum...
August 14, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/30108968/the-semi-synthesis-biological-evaluation-and-docking-analysis-of-the-oxime-hydrazine-and-hydrazide-derivatives-of-platensimycin
#6
Youchao Deng, Dingding Kang, Jie Shi, Wenqing Zhou, Aijun Sun, Jianhua Ju, Xiangcheng Zhu, Ben Shen, Yanwen Duan, Yong Huang
A dozen oxime, hydrazine and hydrazide derivatives of platensimycin (PTM) analogues were synthesized, some of which showed strong antibacterial activities and were shown to be stable under the bioassay conditions. Docking analysis revealed that they have certain new interactions with β-ketoacyl-[acyl carrier protein] synthase II (FabF), suggesting that Schiff base formation on its terpene scaffold is an effective strategy to diversify PTM structure.
May 1, 2018: MedChemComm
https://www.readbyqxmd.com/read/30107246/artepillin-c-drupanin-aromadendrin-4-o-methyl-ether-and-kaempferide-from-brazilian-green-propolis-promote-gastroprotective-action-by-diversified-mode-of-action
#7
Philipe Costa, Marilia O Almeida, Marivane Lemos, Caroline Arruda, Rosana Casoti, Lincon Bordignon Somensi, Thaise Boeing, Marihá Mariott, Rita de Cássia Melo Vilhena de Andrade Fonseca da Silva, Bruna De Paoli Stein, Priscila de Souza, Ana Caroline Dos Santos, Jairo K Bastos, Luísa Mota da Silva, Sérgio Faloni de Andrade
ETHOPHARMACOLOGICAL RELEVANCE: The propolis is extensively used in folk medicine in natura or to prepare pharmaceutical formulations since ancient time to improve health or prevent diseases, among them gastrointestinal disorders. Aiming to contribute in the scientific validation about the popular use of Brazilian Green propolis (BGP) against gastritis and gastric ulcer, this work evaluated the antiulcer potential of isolated compounds from BGP, three prenylated p-coumaric acid derivatives and two flavonoids, respectively named: 3,5 diprenyl-4-hydroxycinnamic acid (artepillin C) (1), 3-prenyl-4-dihydroxycinnamoiloxy cinnamic acid (baccharin) (2), 3-prenyl-4-hydroxycinnamic acid (drupanin) (3), aromadendrin-4'-O-methyl-ether (4) and kaempferide (5)...
August 11, 2018: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/30104667/the-landscape-of-the-a-to-i-rna-editome-from-462-human-genomes
#8
Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological processes in metazoans. However, how and to what extent A-to-I editing diversifies and shapes population diversity at the RNA level are largely unknown. Here, we used 462 mRNA-sequencing samples from five populations of the Geuvadis Project and identified 16,518 A-to-I editing sites, with false detection rate of 1.03%. These sites form the landscape of the RNA editome of the human genome...
August 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30104386/jum-is-a-computational-method-for-comprehensive-annotation-free-analysis-of-alternative-pre-mrna-splicing-patterns
#9
Qingqing Wang, Donald C Rio
Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the junction usage model (JUM) that uses a bottom-up approach to identify, analyze, and quantitate global AS profiles without any prior transcriptome annotations...
August 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30103656/concerning-trends-in-allopathic-medical-school-faculty-rank-for-indigenous-people-2014-2016
#10
Erik Brodt, Amanda Bruegl, Erin K Thayer, M Patrice Eiff, Kelly Gonzales, Carlos Crespo, Dove Spector, Martina Kamaka, Dee-Ann Carpenter, Patricia A Carney
BACKGROUND: Trends in faculty rank according to racial and ethnic composition have not been reviewed in over a decade. OBJECTIVE:  To study trends in faculty rank according to racial and ethnicity with a specific focus on Indigenous faculty, which has been understudied. METHODS: Data from the Association of American Medical Colleges' Faculty Administrative Management Online User System was used to study trends in race/ethnicity faculty composition and rank between 2014 and 2016, which included information on 481,753 faculty members from 141 US allopathic medical schools...
December 2018: Medical Education Online
https://www.readbyqxmd.com/read/30102881/different-roles-of-insulin-receptor-a-and-b-in-maintaining-blood-glucose-homeostasis-in-zebrafish
#11
Yulong Gong, Gang Zhai, Jingzhi Su, Binyuan Yang, Junyan Jin, Haokun Liu, Zhan Yin, Shouqi Xie, Dong Han
An inability of insulin to signal glycolysis and gluconeogenesis would largely result in type 2 diabetes. In this study, the physiological roles of zebrafish insulin receptor a and b in maintaining blood glucose homeostasis were characterized. We observed that, though blood glucose in insra-/- fish and insrb-/- fish were comparable with the control siblings at 0 hours postprandium (hpp), the most evident hyperglycemia have been observed in insra-/- fish from 1 hpp to 3 hpp. A mild increase of blood glucose in insrb-/- fish has been seen only at 1...
August 10, 2018: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/30099551/piercing-fishes-porin-expansion-and-adaptation-to-hematophagy-in-the-vampire-snail-cumia-reticulata
#12
M Gerdol, M Cervelli, M Oliverio, M V Modica
Cytolytic pore-forming proteins are widespread in living organisms, being mostly involved in both sides of the host-pathogen interaction, either contributing to the innate defence or promoting infection. In venomous organisms, such as spiders, insects, scorpions and sea anemones, pore-forming proteins are often secreted as key components of the venom. Coluporins are pore-forming proteins recently discovered in the Mediterranean hematophagous snail Cumia reticulata (Colubrariidae), highly expressed in the salivary glands that discharge their secretion at close contact with the host...
August 7, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30097779/evolving-view-of-membrane-trafficking-and-signaling-systems-for-g-protein-coupled-receptors
#13
Silvia Sposini, Aylin C Hanyaloglu
The G protein-coupled receptor (GPCR) superfamily activates complex signal pathways, yet untangling these signaling systems to understand how specificity in receptor signaling pathways is achieved, has been a challenging question. The roles of membrane trafficking in GPCR signal regulation has undergone a recent paradigm shift, from a mechanism that programs the plasma membrane G protein signaling profile to providing distinct signaling platforms critical for specifying receptor function in vivo. In this chapter, we discuss this evolution of our understanding in the endocytic trafficking systems employed by GPCRs, and how such systems play a deeply integrated role with signaling...
2018: Progress in Molecular and Subcellular Biology
https://www.readbyqxmd.com/read/30097031/the-portfolio-effect-cushions-mosquito-populations-and-malaria-transmission-against-vector-control-interventions
#14
Gerry F Killeen, Thomas E Reed
BACKGROUND: Portfolio effects were first described as a basis for mitigating against financial risk by diversifying investments. Distributing investment across several different assets can stabilize returns and reduce risks by statistical averaging of individual asset dynamics that often correlate weakly or negatively with each other. The same simple probability theory is equally applicable to complex ecosystems, in which biological and environmental diversity stabilizes ecosystems against natural and human-mediated perturbations...
August 10, 2018: Malaria Journal
https://www.readbyqxmd.com/read/30093903/optimized-threshold-inference-for-partitioning-of-clones-from-high-throughput-b-cell-repertoire-sequencing-data
#15
Nima Nouri, Steven H Kleinstein
During adaptive immune responses, activated B cells expand and undergo somatic hypermutation of their B cell receptor (BCR), forming a clone of diversified cells that can be related back to a common ancestor. Identification of B cell clones from high-throughput Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) data relies on computational analysis. Recently, we proposed an automated method to partition sequences into clonal groups based on single-linkage hierarchical clustering of the BCR junction region with length-normalized Hamming distance metric...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30093826/gaps-in-the-capacity-of-modern-forage-crops-to-adapt-to-the-changing-climate-in-northern-europe
#16
Mäkinen Hanna, Kaseva Janne, Virkajärvi Perttu, Kahiluoto Helena
The within-species diversity in response to weather and the gaps in the response diversity in the modern set of forage crop cultivars were determined using an approach that assessed the adaptive capacity under global climate change. The annual dry matter (DM) yields were recorded in multi-location MTT (Maa- ja elintarviketalouden tutkimuskeskus) Agrifood Research Official Variety Trials in Finland for modern forage crop cultivars from 2000 to 2012, as a response to agroclimatic variables critical to yield based on the year-round weather data...
2018: Mitigation and adaptation strategies for global change
https://www.readbyqxmd.com/read/30093596/ancient-convergent-losses-of-paraoxonase-1-yield-potential-risks-for-modern-marine-mammals
#17
Wynn K Meyer, Jerrica Jamison, Rebecca Richter, Stacy E Woods, Raghavendran Partha, Amanda Kowalczyk, Charles Kronk, Maria Chikina, Robert K Bonde, Daniel E Crocker, Joseph Gaspard, Janet M Lanyon, Judit Marsillach, Clement E Furlong, Nathan L Clark
Mammals diversified by colonizing drastically different environments, with each transition yielding numerous molecular changes, including losses of protein function. Though not initially deleterious, these losses could subsequently carry deleterious pleiotropic consequences. We have used phylogenetic methods to identify convergent functional losses across independent marine mammal lineages. In one extreme case, Paraoxonase 1 ( PON1 ) accrued lesions in all marine lineages, while remaining intact in all terrestrial mammals...
August 10, 2018: Science
https://www.readbyqxmd.com/read/30091832/snapshot-of-an-early-paleoproterozoic-ecosystem-two-diverse-microfossil-communities-from-the-turee-creek-group-western-australia
#18
Erica Victoria Barlow, Martin Julian Van Kranendonk
Eighteen microfossil morphotypes from two distinct facies of black chert from a deep-water setting of the c. 2.4 Ga Turee Creek Group, Western Australia, are reported here. A primarily in situ, deep-water benthic community preserved in nodular black chert occurs as a tangled network of a variety of long filamentous microfossils, unicells of one size distribution and fine filamentous rosettes, together with relatively large spherical aggregates of cells interpreted as in-fallen, likely planktonic, forms. Bedded black cherts, in contrast, preserve microfossils primarily within, but also between, rounded clasts of organic material that are coated by thin, convoluted carbonaceous films interpreted as preserved extracellular polymeric substance (EPS)...
August 9, 2018: Geobiology
https://www.readbyqxmd.com/read/30091782/one-pot-synthesis-of-%C3%AE-lactams-by-the-ugi-and-michael-addition-cascade-reaction
#19
Xing Gao, Chunhui Shan, Zhihao Chen, Yan Liu, Xia Zhao, Ao Zhang, Peng Yu, Hervé Galons, Yu Lan, Kui Lu
Diversity-oriented synthesis of β-lactams was achieved via Ugi/Michael reaction cascades under mild conditions. The intramolecular hydrogen bonding between the heteroatom from an aldehyde component and the amide NH group controls the chemoselectivity of the Michael reaction versus the aza-Michael reaction. DFT calculation was performed to clarify the mechanism, chemo-selectivity and diastereoselectivity of this work. This one-pot protocol offers a straightforward method to build a diversified β-lactam library for drug discovery...
August 9, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/30091101/synthetic-gene-regulation-in-cyanobacteria
#20
Cheryl M Immethun, Tae Seok Moon
Cyanobacteria are appealing hosts for green chemical synthesis due to their use of light and carbon dioxide. To optimize product yields and titers, specific and tunable regulation of the metabolic pathways is needed. Synthetic biology has increased and diversified the genetic tools available for biological process control. While early tool development focused on commonly used heterotrophs, there has been a recent expansion of tools for cyanobacteria. CRISPR-Cas9 has been used to edit the genome of cyanobacterial strains, while transcriptional regulation has been accomplished with CRISPR interference and RNA riboswitches...
2018: Advances in Experimental Medicine and Biology
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