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https://www.readbyqxmd.com/read/28454485/cheminformatics-based-anticoagulant-study-of-traditionally-used-medicinal-plants
#1
Mahdi Alikhani Pour, Soroush Sardari, Ali Eslamifar, Abid Azhar, Mohammad Rezvani, Milad Nazari
Backgroung: Medicinal plants, as a complementary medicine, have been used to treat various diseases since ancient times. These plants have numerous beneficial applications and are the source of certain conventional drugs. In diseases such as stroke and ischemia, which are caused by several factors, abnormal coagulation is an important causative factor. Accordingly, novel and effective therapies such as herbal remedies should be practiced to prevent such lethal diseases. Methods: Using the available databases such as Google Scholar and PubMed, the previously reported anticoagulant compounds and plants possessing anticoagulant activity were identified and collected in two separate lists...
April 29, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28453634/recent-sex-chromosome-divergence-despite-ancient-dioecy-in-the-willow-salix-viminalis
#2
Pascal Pucholt, Alison E Wright, Lei Liu Conze, Judith E Mank, Sofia Berlin
Sex chromosomes can evolve when recombination is halted between a pair of chromosomes, and this can lead to degeneration of the sex-limited chromosome. In the early stages of differentiation sex chromosomes are homomorphic, and even though homomorphic sex chromosomes are very common throughout animals and plants, we know little about the evolutionary forces shaping these types of sex chromosomes. We used DNA- and RNA-Seq data from females and males to explore the sex chromosomes in the female heterogametic willow, Salix viminalis, a species with ancient dioecy but with homomorphic sex chromosomes...
April 27, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28448771/geosmithia-associated-with-bark-beetles-and-woodborers-in-the-western-usa-taxonomic-diversity-and-vector-specificity
#3
Miroslav Kolařík, Jiri Hulcr, Ned Tisserat, Wilhelm De Beer, Martin Kostovčík, Zuzana Kolaříková, Steven J Seybold, David M Rizzo
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii) interpret the community composition of this region within the emerging global biogeography of Geosmithia...
April 24, 2017: Mycologia
https://www.readbyqxmd.com/read/28448743/circular-rnas-with-hammerhead-ribozymes-encoded-in-eukaryotic-genomes-the-enemy-at-home
#4
Marcos de la Peña, Amelia Cervera
A new family of non-autonomous retrotransposons with self-cleaving hammerhead ribozymes, the so called retrozymes, has recently been found encoded in a number of plant genomes. These retroelements can be actively transcribed, and their RNAs accumulate in the cells as abundant non-coding circular RNAs (circRNAs) of small size (600-1000 nt). Related circRNAs with self-cleaving ribozymes had already been described in plants, and belong to a group of infectious RNA agents with an uncertain origin: the viroids and viroid-like satellites of plant RNA viruses...
April 27, 2017: RNA Biology
https://www.readbyqxmd.com/read/28448578/evolutionary-history-of-tibetans-inferred-from-whole-genome-sequencing
#5
Hao Hu, Nayia Petousi, Gustavo Glusman, Yao Yu, Ryan Bohlender, Tsewang Tashi, Jonathan M Downie, Jared C Roach, Amy M Cole, Felipe R Lorenzo, Alan R Rogers, Mary E Brunkow, Gianpiero Cavalleri, Leroy Hood, Sama M Alpatty, Josef T Prchal, Lynn B Jorde, Peter A Robbins, Tatum S Simonson, Chad D Huff
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28447043/comparative-genomics-of-human-stem-cell-factor-scf
#6
Moein Dehbashi, Elahe Kamali, Sadeq Vallian
Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28446635/a-motif-and-amino-acid-bias-bioinformatics-pipeline-to-identify-hydroxyproline-rich-glycoproteins
#7
Kim L Johnson, Andrew M Cassin, Andrew Lonsdale, Antony Bacic, Monika Susanne Doblin, Carolyn J Schultz
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signalling and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive post-translational modifications (glycosylation) and have been implicated in many biological functions...
April 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28446240/molecular-mechanisms-by-which-herv-k-gag-interferes-with-hiv-1-gag-assembly-and-particle-infectivity
#8
Kazuaki Monde, Hiromi Terasawa, Yusuke Nakano, Ferri Soheilian, Kunio Nagashima, Yosuke Maeda, Akira Ono
BACKGROUND: Human endogenous retroviruses (HERVs), the remnants of ancient retroviral infections, constitute approximately 8% of human genomic DNA. Since HERV-K Gag expression is induced by HIV-1 Tat in T cells, induced HERV-K proteins could affect HIV-1 replication. Indeed, previously we showed that HERV-K Gag and HIV-1 Gag coassemble and that this appears to correlate with the effect of HERV-K Gag expression on HIV-1 particle release and its infectivity. We further showed that coassembly requires both MA and NC domains, which presumably serve as scaffolding for Gag via their abilities to bind membrane and RNA, respectively...
April 26, 2017: Retrovirology
https://www.readbyqxmd.com/read/28446157/natural-products-isolated-from-tetragonula-carbonaria-cerumen-modulate-free-radical-scavenging-and-5-lipoxygenase-activities-in-vitro
#9
Karina D Hamilton, Peter R Brooks, Steven M Ogbourne, Fraser D Russell
BACKGROUND: Propolis and cerumen are plant-derived products found in honeybees and stingless bees, respectively. Although propolis is an ancient folk medicine, the bioactivities of cerumen obtained from Australian native stingless bees (Tetragonula carbonaria) have not been widely studied. Therefore, we investigated selected anti-oxidant and anti-inflammatory properties of T. carbonaria cerumen. METHODS: A methanolic extract was prepared from the combined cerumen of 40 T...
April 26, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28445788/an-emerging-role-for-the-ribosome-as-a-nexus-for-post-translational-modifications
#10
REVIEW
Deniz Simsek, Maria Barna
The ribosome is one of life's most ancient molecular machines that has historically been viewed as a backstage participant in gene regulation, translating the genetic code across all kingdoms of life in a rote-like fashion. However, recent studies suggest that intrinsic components of the ribosome can be regulated and diversified as a means to intricately control the expression of the cellular proteome. In this review, we discuss advances in the characterization of ribosome post-translational modifications (PTMs) from past to present...
April 22, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#11
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28444560/y-chromosomal-sequences-of-diverse-indian-populations-and-the-ancestry-of-the-andamanese
#12
Mayukh Mondal, Anders Bergström, Yali Xue, Francesc Calafell, Hafid Laayouni, Ferran Casals, Partha P Majumder, Chris Tyler-Smith, Jaume Bertranpetit
We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations...
April 25, 2017: Human Genetics
https://www.readbyqxmd.com/read/28444234/inferring-allele-frequency-trajectories-from-ancient-dna-indicates-that-selection-on-a-chicken-gene-coincided-with-changes-in-medieval-husbandry-practices
#13
Liisa Loog, Mark G Thomas, Ross Barnett, Richard Allen, Naomi Sykes, Ptolemaios D Paxinos, Ophelie Lebrasseur, Keith Dobney, Joris Peters, Andrea Manica, Greger Larson, Anders Eriksson
Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both argued to have undergone strong and recent selection in domestic chickens...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28444138/the-evolution-of-neuropeptide-signalling-insights-from-echinoderms
#14
Dean C Semmens, Maurice R Elphick
Neuropeptides are evolutionarily ancient mediators of neuronal signalling that regulate a wide range of physiological processes and behaviours in animals. Neuropeptide signalling has been investigated extensively in vertebrates and protostomian invertebrates, which include the ecdysozoans Drosophila melanogaster (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda). However, until recently, an understanding of evolutionary relationships between neuropeptide signalling systems in vertebrates and protostomes has been impaired by a lack of genome/transcriptome sequence data from non-ecdysozoan invertebrates...
April 21, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28443617/the-therapeutic-potential-of-psychedelic-drugs-past-present-and-future
#15
Robin L Carhart-Harris, Guy M Goodwin
Plant-based psychedelics such as psilocybin have an ancient history of medicinal use. After the first English-language report on LSD in 1950, psychedelics enjoyed a short-lived relationship with psychology and psychiatry. Used most notably as aides to psychotherapy for the treatment of mood disorders and alcohol dependence, drugs such as LSD showed initial therapeutic promise before prohibitive legislature in the mid-1960s effectively ended all major psychedelic research programmes. Since the early 1990s, there has been a steady revival of human psychedelic research: last year saw reports on the first modern brain imaging study with LSD and 3 separate clinical trials of psilocybin for depressive symptoms...
April 26, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28443052/gih-qi-beyond-affordance
#16
Yang Lee, Robert E Shaw, Zheng Jin
Ancient Eastern thought posited the ontological integration of the "mind-body world". The body-mind syncretism was a foundational precept in Eastern philosophy in which "Gih" ("Qi") was considered the basic entity of the universe and the human being. This study attempts to build a meta-theory and to demonstrate empirical designs for Gih, discussing the problems of the mind and body, or the subject and object, compared with the concept of "affordance" proposed by ecological approaches. The notion of Gih extends beyond that of affordance in that Gih activates a psychosomatic process between the physical condition and the mental state that facilitates the bi-directional interactions between subject and object...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28442558/gene-flow-ancient-polymorphism-and-ecological-adaptation-shape-the-genomic-landscape-of-divergence-among-darwin-s-finches
#17
Fan Han, Sangeet Lamichhaney, B Rosemary Grant, Peter R Grant, Leif Andersson, Matthew T Webster
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances...
April 25, 2017: Genome Research
https://www.readbyqxmd.com/read/28441559/hydra-imaging-nerve-nets-in-action
#18
Ni Ji, Steven W Flavell
Mapping whole-brain activity during behavior represents one of the biggest and most exciting challenges of systems neuroscience. New research has taken advantage of the unique biology of an ancient organism to bring us a step closer to that goal.
April 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28441401/ancient-genes-establish-stress-induced-mutation-as-a-hallmark-of-cancer
#19
Luis Cisneros, Kimberly J Bussey, Adam J Orr, Milica Miočević, Charles H Lineweaver, Paul Davies
Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes...
2017: PloS One
https://www.readbyqxmd.com/read/28440191/cannabis-a-neurological-remedy-or-a-drug-of-abuse-in-india
#20
Pronit Biswas, Pooja Mishra, Devasish Bose, Abhilasha Durgbanshi
Since ancient times it is well documented the use of cannabis as a medicine due to its potential therapeutic activity while subsequently its use as drug of abuse spread increasingly. The present review sought to give an insight in the history of medical and recreational use of cannabis in India. Indian use of cannabis dates back to Vedic time, mostly for the ritualistic and religious purposed, as documented in the ancient literature. It was India that introduced the medical use of cannabis to neighboring countries...
April 23, 2017: CNS & Neurological Disorders Drug Targets
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