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https://www.readbyqxmd.com/read/28644379/physical-forces-may-cause-the-hoxd-gene-cluster-elongation
#1
Spyros Papageorgiou
Hox gene collinearity was discovered be Edward B. Lewis in 1978. It consists of the Hox1, Hox2, Hox3 ordering of the Hox genes in the chromosome from the telomeric to the centromeric side of the chromosome. Surprisingly, the spatial activation of the Hox genes in the ontogenetic units of the embryo follows the same ordering along the anterior-posterior embryonic axis. The chromosome microscale differs from the embryo macroscale by 3 to 4 orders of magnitude. The traditional biomolecular mechanisms are not adequate to comprise phenomena at so divergent spatial domains...
June 23, 2017: Biology
https://www.readbyqxmd.com/read/28538658/seed-coating-increases-seed-moisture-uptake-and-restricts-embryonic-oxygen-availability-in-germinating-cereal-seeds
#2
Linda Gorim, Folkard Asch
Seed coating is a technology to improve germination and homogenize stand establishment. Although coating often results in lower germination rates, seeds that do germinate grow more vigorously and show strongly reduced respiratory losses during reserve mobilization. We hypothesize that the higher mobilization efficiency is due to a shift in the enzymatic cleavage of sucrose from invertase to sucrose synthase in the embryonic tissue caused by a reduced oxygen availability induced by oversaturation with water caused by the coating during early germination...
May 24, 2017: Biology
https://www.readbyqxmd.com/read/28486403/treatment-of-real-world-hcv-genotype-2-infected-japanese-patients-with-sofosbuvir-plus-ribavirin
#3
Tatsuo Kanda, Masato Nakamura, Shin Yasui, Yuki Haga, Akinobu Tawada, Eiichiro Suzuki, Yoshihiko Ooka, Koji Takahashi, Reina Sasaki, Shuang Wu, Shingo Nakamoto, Makoto Arai, Fumio Imazeki, Osamu Yokosuka
The aim of this study was to characterize the treatment response and tolerability of sofosbuvir plus ribavirin therapies in Japanese patients infected with hepatitis C virus (HCV) genotype (GT)-2. This retrospective study analyzed 114 Japanese HCV GT-2 patients treated for 12 weeks with 400 mg of sofosbuvir plus weight-based ribavirin daily. This treatment led to higher sustained virologic response at 12-weeks post-treatment (SVR12) rates in both treatment-naïve and treatment-experienced patients. The efficacy of this treatment in compensated cirrhotics was the same as that in patients with chronic hepatitis...
May 9, 2017: Biology
https://www.readbyqxmd.com/read/28481257/characterisation-of-arctic-bacterial-communities-in-the-air-above-svalbard
#4
Lewis Cuthbertson, Herminia Amores-Arrocha, Lucie A Malard, Nora Els, Birgit Sattler, David A Pearce
Atmospheric dispersal of bacteria is increasingly acknowledged as an important factor influencing bacterial community biodiversity, biogeography and bacteria-human interactions, including those linked to human health. However, knowledge about patterns in microbial aerobiology is still relatively scarce, and this can be attributed, in part, to a lack of consensus on appropriate sampling and analytical methodology. In this study, three different methods were used to investigate aerial biodiversity over Svalbard: impaction, membrane filtration and drop plates...
May 6, 2017: Biology
https://www.readbyqxmd.com/read/28467369/developmental-control-of-nramp1-slc11a1-expression-in-professional-phagocytes
#5
Mathieu F M Cellier
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs)...
May 3, 2017: Biology
https://www.readbyqxmd.com/read/28448442/rai1-haploinsufficiency-is-associated-with-social-abnormalities-in-mice
#6
Nalini R Rao, Clemer Abad, Irene C Perez, Anand K Srivastava, Juan I Young, Katherina Walz
Background: Autism is characterized by difficulties in social interaction, communication, and repetitive behaviors; with different degrees of severity in each of the core areas. Haploinsufficiency and point mutations of RAI1 are associated with Smith-Magenis syndrome (SMS), a genetic condition that scores within the autism spectrum range for social responsiveness and communication, and is characterized by neurobehavioral abnormalities, intellectual disability, developmental delay, sleep disturbance, and self-injurious behaviors...
April 27, 2017: Biology
https://www.readbyqxmd.com/read/28448440/is-polysialylated-ncam-not-only-a-regulator-during-brain-development-but-also-during-the-formation-of-other-organs
#7
REVIEW
Christina E Galuska, Thomas Lütteke, Sebastian P Galuska
In mammals several cell adhesion molecules are involved during the pre- and postnatal development of all organ systems. A very prominent member of this family is the neural cell adhesion molecule (NCAM). Interestingly, NCAM can be a target for a special form of posttranslational modification: polysialylation. Whereas nearly all extracellular proteins bear mono-sialic acid residues, only a very small group can be polysialylated. Polysialic acid is a highly negatively-charged sugar polymer and can comprise more than 90 sialic acid residues in postnatal mouse brains increasing dramatically the hydrodynamic radius of their carriers...
April 27, 2017: Biology
https://www.readbyqxmd.com/read/28445413/identification-of-highly-specific-scfvs-against-total-adiponectin-for-diagnostic-purposes
#8
Peter Wilton, Michael Steidel, Gabriele Krczal, Iris Hermanns, Andreas Pfützner, Alisa Konnerth, Kajohn Boonrod
Adiponectin is one of the most abundant adipokines secreted from adipose tissue. It acts as an endogenous insulin sensitizer and plasma concentrations are inversely correlated with obesity and metabolic syndrome. A decrease in plasma adiponectin levels normally indicates increased hormonal activity of the visceral lipid tissue, which is associated with decreased insulin sensitivity. It may therefore be considered a valuable biomarker for elucidating the underlying deteriorations resulting in type 2 diabetes and macrovascular disease...
April 26, 2017: Biology
https://www.readbyqxmd.com/read/28358347/the-enzymology-of-2-hydroxyglutarate-2-hydroxyglutaramate-and-2-hydroxysuccinamate-and-their-relationship-to-oncometabolites
#9
Vivek A Hariharan, Travis T Denton, Sarah Paraszcszak, Kyle McEvoy, Thomas M Jeitner, Boris F Krasnikov, Arthur J L Cooper
Many enzymes make "mistakes". Consequently, repair enzymes have evolved to correct these mistakes. For example, lactate dehydrogenase (LDH) and mitochondrial malate dehydrogenase (mMDH) slowly catalyze the reduction of 2-oxoglutarate (2-OG) to the oncometabolite l-2-hydroxyglutarate (l-2-HG). l-2-HG dehydrogenase corrects this error by converting l-2-HG to 2-OG. LDH also catalyzes the reduction of the oxo group of 2-oxoglutaramate (2-OGM; transamination product of l-glutamine). We show here that human glutamine synthetase (GS) catalyzes the amidation of the terminal carboxyl of both the l- and d- isomers of 2-HG...
March 30, 2017: Biology
https://www.readbyqxmd.com/read/28358327/coenzyme-a-independent-transacylation-system-possible-involvement-of-phospholipase-a2-in-transacylation
#10
REVIEW
Atsushi Yamashita, Yasuhiro Hayashi, Naoki Matsumoto, Yoko Nemoto-Sasaki, Takanori Koizumi, Yusuke Inagaki, Saori Oka, Takashi Tanikawa, Takayuki Sugiura
The coenzyme A (CoA)-independent transacylation system catalyzes fatty acid transfer from phospholipids to lysophospholipids in the absence of cofactors such as CoA. It prefers to use C20 and C22 polyunsaturated fatty acids such as arachidonic acid, which are esterified in the glycerophospholipid at the sn-2 position. This system can also acylate alkyl ether-linked lysophospholipids, is involved in the enrichment of arachidonic acid in alkyl ether-linked glycerophospholipids, and is critical for the metabolism of eicosanoids and platelet-activating factor...
March 30, 2017: Biology
https://www.readbyqxmd.com/read/28353646/intraguild-predation-dynamics-in-a-lake-ecosystem-based-on-a-coupled-hydrodynamic-ecological-model-the-example-of-lake-kinneret-israel
#11
Vardit Makler-Pick, Matthew R Hipsey, Tamar Zohary, Yohay Carmel, Gideon Gal
The food web of Lake Kinneret contains intraguild predation (IGP). Predatory invertebrates and planktivorous fish both feed on herbivorous zooplankton, while the planktivorous fish also feed on the predatory invertebrates. In this study, a complex mechanistic hydrodynamic-ecological model, coupled to a bioenergetics-based fish population model (DYCD-FISH), was employed with the aim of revealing IGP dynamics. The results indicate that the predation pressure of predatory zooplankton on herbivorous zooplankton varies widely, depending on the season...
March 29, 2017: Biology
https://www.readbyqxmd.com/read/28287479/stat5-interacting-proteins-a-synopsis-of-proteins-that-regulate-stat5-activity
#12
REVIEW
Ashley A Able, Jasmine A Burrell, Jacqueline M Stephens
Signal Transducers and Activators of Transcription (STATs) are key components of the JAK/STAT pathway. Of the seven STATs, STAT5A and STAT5B are of particular interest for their critical roles in cellular differentiation, adipogenesis, oncogenesis, and immune function. The interactions of STAT5A and STAT5B with cytokine/hormone receptors, nuclear receptors, transcriptional regulators, proto-oncogenes, kinases, and phosphatases all contribute to modulating STAT5 activity. Among these STAT5 interacting proteins, some serve as coactivators or corepressors to regulate STAT5 transcriptional activity and some proteins can interact with STAT5 to enhance or repress STAT5 signaling...
March 11, 2017: Biology
https://www.readbyqxmd.com/read/28287462/snp-discovery-using-a-pangenome-has-the-single-reference-approach-become-obsolete
#13
REVIEW
Bhavna Hurgobin, David Edwards
Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation...
March 11, 2017: Biology
https://www.readbyqxmd.com/read/28272331/ornithine-aminotransferase-an-important-glutamate-metabolizing-enzyme-at-the-crossroads-of-multiple-metabolic-pathways
#14
REVIEW
Antonin Ginguay, Luc Cynober, Emmanuel Curis, Ioannis Nicolis
Ornithine δ-aminotransferase (OAT, E.C. 2.6.1.13) catalyzes the transfer of the δ-amino group from ornithine (Orn) to α-ketoglutarate (aKG), yielding glutamate-5-semialdehyde and glutamate (Glu), and vice versa. In mammals, OAT is a mitochondrial enzyme, mainly located in the liver, intestine, brain, and kidney. In general, OAT serves to form glutamate from ornithine, with the notable exception of the intestine, where citrulline (Cit) or arginine (Arg) are end products. Its main function is to control the production of signaling molecules and mediators, such as Glu itself, Cit, GABA, and aliphatic polyamines...
March 7, 2017: Biology
https://www.readbyqxmd.com/read/28272328/epiphytic-terrestrial-algae-trebouxia-sp-as-a-biomarker-using-the-free-air-carbon-dioxide-enrichment-face-system
#15
Asmida Ismail, Sarah Diyana Marzuki, Nordiana Bakti Mohd Yusof, Faeiza Buyong, Mohd Nizam Mohd Said, Harinder Rai Sigh, Amyrul Rafiq Zulkifli
The increasing concentration of CO₂ in the atmosphere has caused significant environmental changes, particularly to the lower plants such as terrestrial algae and lichens that alter species composition, and therefore can contribute to changes in community landscape. A study to understand how increased CO₂ in the atmosphere will affect algal density with minimal adjustment on its natural ecosystem, and the suitability of the algae to be considered as a biomarker, has been conducted. The current work was conducted in the Free-Air-Carbon Dioxide-Enrichment (FACE) system located in Universiti Kebangsaan Malaysia, Bangi, Malaysia...
March 7, 2017: Biology
https://www.readbyqxmd.com/read/28245547/glutamine-glutamate-cycle-flux-is-similar-in-cultured-astrocytes-and-brain-and-both-glutamate-production-and-oxidation-are-mainly-catalyzed-by-aspartate-aminotransferase
#16
REVIEW
Leif Hertz, Douglas L Rothman
The glutamine-glutamate cycle provides neurons with astrocyte-generated glutamate/γ-aminobutyric acid (GABA) and oxidizes glutamate in astrocytes, and it returns released transmitter glutamate/GABA to neurons after astrocytic uptake. This review deals primarily with the glutamate/GABA generation/oxidation, although it also shows similarity between metabolic rates in cultured astrocytes and intact brain. A key point is identification of the enzyme(s) converting astrocytic α-ketoglutarate to glutamate and vice versa...
February 24, 2017: Biology
https://www.readbyqxmd.com/read/28241499/selectin-ligands-sialyl-lewis-a-and-sialyl-lewis-x-in-gastrointestinal-cancers
#17
REVIEW
Marco Trinchera, Adele Aronica, Fabio Dall'Olio
The tetrasaccharide structures Siaα2,3Galβ1,3(Fucα1,4)GlcNAc and Siaα2,3Galβ1,4(Fucα1,3)GlcNAc constitute the epitopes of the carbohydrate antigens sialyl-Lewis a (sLe(a)) and sialyl-Lewis x (sLe(x)), respectively, and are the minimal requirement for selectin binding to their counter-receptors. Interaction of sLe(x) expressed on the cell surface of leucocytes with E-selectin on endothelial cells allows their arrest and promotes their extravasation. Similarly, the rolling of cancer cells ectopically expressing the selectin ligands on endothelial cells is potentially a crucial step favoring the metastatic process...
February 23, 2017: Biology
https://www.readbyqxmd.com/read/28218660/anaphase-a-disassembling-microtubules-move-chromosomes-toward-spindle-poles
#18
REVIEW
Charles L Asbury
The separation of sister chromatids during anaphase is the culmination of mitosis and one of the most strikingly beautiful examples of cellular movement. It consists of two distinct processes: Anaphase A, the movement of chromosomes toward spindle poles via shortening of the connecting fibers, and anaphase B, separation of the two poles from one another via spindle elongation. I focus here on anaphase A chromosome-to-pole movement. The chapter begins by summarizing classical observations of chromosome movements, which support the current understanding of anaphase mechanisms...
February 17, 2017: Biology
https://www.readbyqxmd.com/read/28218638/metagaap-a-novel-pipeline-to-estimate-community-composition-and-abundance-from-non-model-sequence-data
#19
Christopher Noune, Caroline Hauxwell
Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of 'meta-barcode' data. This approach relies on comparison of amplicon sequences of 'barcode' regions from a population with public-domain databases of reference sequences. However, for many organisms relevant 'barcode' regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, 'MetaGaAP,' was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom 'barcode' regions of less than 30 polymorphisms within the span of a single 'read', amplification and sequencing of the 'barcode', generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes...
February 17, 2017: Biology
https://www.readbyqxmd.com/read/28218637/mechanisms-of-chromosome-congression-during-mitosis
#20
REVIEW
Helder Maiato, Ana Margarida Gomes, Filipe Sousa, Marin Barisic
Chromosome congression during prometaphase culminates with the establishment of a metaphase plate, a hallmark of mitosis in metazoans. Classical views resulting from more than 100 years of research on this topic have attempted to explain chromosome congression based on the balance between opposing pulling and/or pushing forces that reach an equilibrium near the spindle equator. However, in mammalian cells, chromosome bi-orientation and force balance at kinetochores are not required for chromosome congression, whereas the mechanisms of chromosome congression are not necessarily involved in the maintenance of chromosome alignment after congression...
February 17, 2017: Biology
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