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https://www.readbyqxmd.com/read/29036914/molecular-characterization-and-functional-analysis-of-a-ferritin-heavy-chain-subunit-from-the-eri-silkworm-samia-cynthia-ricini
#1
Hai-Zhong Yu, Shang-Zhi Zhang, Yan Ma, Dong-Qiong Fei, Bing Li, Li-Ang Yang, Jie Wang, Zhen Li, Azharuddin Muhammad, Jia-Ping Xu
Ferritins are conserved iron-binding proteins that are primarily involved in iron storage, detoxification and the immune response. Despite the importance of ferritin in organisms, little is known about their roles in the eri-silkworm (Samia cynthia ricini). We previously identified a ferritin heavy chain subunit named ScFerHCH in the S. c. ricini transcriptome database. The full-length S. c. ricini ferritin heavy chain subunit (ScFerHCH) was 1863 bp and encoded a protein of 231 amino acids with a deduced molecular weight of 25...
October 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29036646/de-novo-deleterious-sequence-variants-that-alter-the-transcriptional-activity-of-the-homeoprotein-pbx1-are-associated-with-intellectual-disability-and-pleiotropic-developmental-defects
#2
Anne Slavotinek, Maurizio Risolino, Marta Losa, Megan T Cho, Kristin G Monaghan, Dina Schneidman-Duhovny, Sarah Parisotto, Johanna C Herkert, Alexander P A Stegmann, Kathryn Miller, Natasha Shur, Jacqueline Chui, Eric Muller, Suzanne DeBrosse, Justin O Szot, Gavin Chapman, Nicholas S Pachter, David S Winlaw, Bryce A Mendelsohn, Joline Dalton, Kyriakie Sarafoglou, Peter I Karachunski, Jane M Lewis, Helio Pedro, Sally L Dunwoodie, Licia Selleri, Joseph Shieh
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads...
September 22, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036432/copb2-is-essential-for-embryogenesis-and-hypomorphic-mutations-cause-human-microcephaly
#3
Andrew DiStasio, Ashley Driver, Kristen Sund, Milene Donlin, Ranjith M Muraleedharan, Shabnam Pooya, Beth Kline-Fath, Kenneth M Kaufman, Cynthia A Prows, Elizabeth Schorry, Biplab DasGupta, Rolf W Stottmann
Primary microcephaly is a congenital brain malformation characterized by a head circumference less than three standard deviations below the mean for age and sex and results in moderate to severe mental deficiencies and decreased lifespan. We recently studied two children with primary microcephaly in an otherwise unaffected family. Exome sequencing identified an autosomal recessive mutation leading to an amino acid substitution in a WD40 domain of the highly conserved Coatomer Protein Complex, Subunit Beta 2 (COPB2)...
September 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036401/the-all-rounder-sodalis-a-new-bacteriome-associated-endosymbiont-of-the-lygaeoid-bug-henestaris-halophilus-heteroptera-henestarinae-and-a-critical-examination-of-its-evolution
#4
Diego Santos-Garcia, Francisco J Silva, Shai Morin, Konrad Dettner, Stefan Martin Kuechler
Hemipteran insects are well-known in their ability to establish symbiotic relationships with bacteria. Among them, heteropteran insects present an array of symbiotic systems, ranging from the most common gut crypt symbiosis to the more restricted bacteriome-associated endosymbiosis, which have only been detected in members of the superfamily Lygaeoidea and the family Cimicidae so far. Genomic data of heteropteran endosymbionts are scarce and have merely been analyzed from the Wolbachia endosymbiont in bed bug and a few gut crypt-associated symbionts in pentatomoid bugs...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036367/phenylalanine-as-a-nitrogen-source-induces-root-growth-and-nitrogen-use-efficiency-in-populus-%C3%A3-canescens
#5
Yu Jiao, Yinghao Chen, Chaofeng Ma, Jingjing Qin, Thi Hong Nhung Nguyen, Di Liu, Honghao Gan, Shen Ding, Zhi-Bin Luo
To investigate the physiological responses of poplars to amino acids as sole nitrogen (N) sources, Populus × canescens (Ait.) Smith plants were supplied with one of three nitrogen fertilizers (NH4NO3, phenylalanine (Phe) or the mixture of NH4NO3 and Phe) in sand culture. A larger root system, and decreased leaf size and CO2 assimilation rate was observed in Phe- versus NH4NO3-treated poplars. Consistently, a greater root biomass and a decreased shoot growth were detected in Phe-supplied poplars. Decreased enzymatic activities of nitrate reductase (NR), glutamate synthase (GOGAT) and glutamate dehydrogenase (GDH) and elevated activities of nitrite reductase (NiR), phenylalanine ammonia lyase (PAL), glutamine synthetase (GS) and asparagine synthase (AS) were found in Phe-treated roots...
September 19, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29036229/cloning-and-characterization-of-the-cerasus-humilis-sucrose-phosphate-synthase-gene-chsps1
#6
Juan Wang, Junjie Du, Xiaopeng Mu, Pengfei Wang
Sucrose is crucial to the growth and development of plants, and sucrose phosphate synthase (SPS) plays a key role in sucrose synthesis. To understand the genetic and molecular mechanisms of sucrose synthesis in Cerasus humilis, ChSPS1, a homologue of SPS, was cloned using RT-PCR. Sequence analysis showed that the open reading frame (ORF) sequence of ChSPS1 is 3174 bp in length, encoding a predicted protein of 1057 amino acids. The predicted protein showed a high degree of sequence identity with SPS homologues from other species...
2017: PloS One
https://www.readbyqxmd.com/read/29036220/defective-replication-initiation-results-in-locus-specific-chromosome-breakage-and-a-ribosomal-rna-deficiency-in-yeast
#7
Joseph C Sanchez, Elizabeth X Kwan, Thomas J Pohl, Haley M Amemiya, M K Raghuraman, Bonita J Brewer
A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty...
October 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29035972/hyperammonemia-and-proteostasis-in-cirrhosis
#8
Srinivasan Dasarathy, Maria Hatzoglou
PURPOSE OF REVIEW: Skeletal muscle loss or sarcopenia is a frequent complication of cirrhosis that adversely affects clinical outcomes. As skeletal muscle is the largest store of proteins in the body, proteostasis or protein homeostasis is required for maintenance of muscle mass. This review will focus on disordered skeletal muscle proteostasis in liver disease. RECENT FINDINGS: Increased skeletal muscle uptake of ammonia initiates responses that result in disordered proteostasis including impaired protein synthesis and increased autophagy...
October 14, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/29035970/emerging-perspectives-on-branched-chain-amino-acid-metabolism-during-adipocyte-differentiation
#9
Daniela Salinas-Rubio, Armando R Tovar, Lilia G Noriega
PURPOSE OF REVIEW: Adipogenesis has been extensively studied in the context of carbohydrate and lipid metabolism. However, little information exists on the role of amino acid metabolism during adipocyte differentiation. Here, we review how branched-chain amino acid (BCAA) metabolism is modified during adipogenesis and, due to the limited information in the area, address questions that remain to be answered with further research. RECENT FINDINGS: BCAAs are rapidly consumed during adipocyte differentiation and are indispensable for this process...
October 14, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/29035969/effects-of-medical-food-leucine-content-in-the-management-of-methylmalonic-and-propionic-acidemias
#10
Jennifer G Myles, Irini Manoli, Charles P Venditti
PURPOSE OF REVIEW: The current review highlights the varied effects of medical foods high in leucine (Leu) and devoid of valine (Val) and isoleucine (Ile) in the management of methylmalonic acidemia (MMA) and propionic acidemia and cobalamin C (cblC) deficiency, aiming to advance dietary practices. RECENT FINDINGS: Leu is a key metabolic regulator with a multitude of effects on different organ systems. Recent observational studies have demonstrated that these effects can have unintended consequences in patients with MMA as a result of liberal use of medical foods...
October 14, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/29035868/comparative-analysis-of-codon-usage-pattern-and-its-influencing-factors-in-schistosoma-japonicum-and-ascaris-suum
#11
Gulshana A Mazumder, Arif Uddin, Supriyo Chakraborty
Schistosoma japonicum and Ascaris suum are considered as the major parasites of human which cause various life threatening diseases such as schistomiasis and ascariasis. The codon usage bias (CUB) is known as the phenomenon of more usage of a specific codon than the other synonymous codons for an amino acid. The factors that influence the codon usage bias are mutation pressure, natural selection, gene expression, gene length, GC content, RNA stability, recombination rates, codon position etc. Here we had used various bioinformatic tools and statistical analyses to understand the compositional features, expression level and codon usage bias in the genes of these two species...
December 20, 2017: Acta Parasitologica
https://www.readbyqxmd.com/read/29035834/synergistic-effect-of-mild-hypothermia-and-the-notch-inhibitor-dapt-against-post-stroke-seizures
#12
Guo-Shuai Yang, Xiao-Yan Zhou, Xue-Fang An, Xuan-Jun Liu, Yan-Jun Zhang, Dan Yu
Seizure is a serious complication of stroke, indicating poor prognosis. Notch signaling is associated with neuronal activity. Inhibition of Notch signaling suppresses seizure activity induced by kainic acid. The present study investigated the effect of the Notch inhibitor, DAPT, alone or in combination with mild hypothermia, on post-stroke seizures. A global cerebral ischemia (GCI) model was performed in Sprague Dawley (SD) male rats. Seizure activity was evaluated by the frequency of seizure attacks, seizure severity scores, and seizure discharges...
October 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29035735/transcriptome-profiling-identifies-genes-pathways-associated-with-experimental-resistance-to-paromomycin-in-leishmania-donovani
#13
Aditya Verma, Vasundhra Bhandari, Deepak Kumar Deep, Shyam Sundar, Jean Claude Dujardin, Ruchi Singh, Poonam Salotra
Widespread resistance towards antimony and reports of relapses following miltefosine treatment has severely affected the management of visceral leishmaniasis (VL) in the Indian subcontinent. Paromomycin (PMM), an aminoglycoside antibiotic, has been licensed for VL treatment in India in 2007. Although its use is still restricted in the field, unraveling the molecular mechanism of resistance towards PMM is the key to preserve the drug. In this study, PMM resistant lines were selected up to 100 μM of PMM in three distinct field isolates of Leishmania donovani at promastigote stage...
October 10, 2017: International Journal for Parasitology, Drugs and Drug Resistance
https://www.readbyqxmd.com/read/29035636/quantification-of-nitrogen-in-the-liquid-fraction-and-in-vitro-assessment-of-lysine-bioavailability-in-the-solid-fraction-of-soybean-meal-hydrolysates
#14
D Luján-Rhenals, R Morawicki, Z Shi, S C Ricke
Soybean meal (SBM) is a product generated from the manufacture of soybean oil and has the potential for use as a source of fermentable sugars for ethanol production or as a protein source for animal feeds. Knowing the levels of nitrogen available from ammonium is a necessary element of the ethanolic fermentation process while identifying the levels of essential amino acids such as lysine is important in determining usage as a feed source. As such the purpose of this study was to quantify total nitrogen and ammonium in the liquid fraction of hydrolyzed SBM and to evaluate total and bioavailable lysine in the solid fraction of the hydrolyzed SBM...
October 16, 2017: Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes
https://www.readbyqxmd.com/read/29035580/mutation-sensitivity-maps-identifying-residue-substitutions-that-impact-protein-structure-via-a-rigidity-analysis-in-silico-mutation-approach
#15
Michael Siderius, Filip Jagodzinski
Understanding how an amino acid substitution affects a protein's structure can aid in the design of pharmaceutical drugs that aim at countering diseases caused by protein mutants. Unfortunately, performing even a few amino acid substitutions in vitro is both time and cost prohibitive, whereas an exhaustive analysis that involves systematically mutating all amino acids in the physical protein is infeasible. Computational methods have been developed to predict the effects of mutations, but even many of them are computationally intensive or are else dependent on homology or experimental data that may not be available for the protein being studied...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29035536/hdac8-substrates-identified-by-genetically-encoded-active-site-photocrosslinking
#16
Jeffrey E Lopez, Sarah E Haynes, Jaimeen D Majmudar, Brent R Martin, Carol A Fierke
The histone deacetylase family comprises 18 enzymes that catalyze deacetylation of acetylated lysine residues, however, the specificity and substrate profile of each enzyme remains largely unknown. Due to transient enzyme-substrate interactions, conventional co-immunoprecipitation methods frequently fail to identify enzyme-specific substrates. Additionally, compensatory mechanisms often limit the ability of knockdown or chemical inhibition studies to achieve significant fold-changes observed by acetylation proteomics methods...
October 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29035420/modeling-the-secondary-structures-of-the-peptaibols-antiamoebin-i-and-zervamicin-ii-modified-with-d-amino-acids-and-proline-analogues
#17
Tarsila G Castro, Nuno M Micaêlo, Manuel Melle-Franco
Antiamoebin I (AAM-I) and zervamicin II (Zrv-IIB) are peptaibols that exert antibiotic activity through the insertion/disruption of cell membranes. In this study, we investigated how the folding of these peptaibols are affected when some of their native residues are replaced with proline analogues and asymmetrical D-α,α-dialkyl glycines (two classes of noncanonical amino acids). Systematic substitutions of native Aib, Pro, Hyp, and Iva residues were performed to elucidate the folding properties of the modified peptaibols incorporating noncanonical residues...
October 16, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29035374/design-of-coiled-coil-protein-origami-cages-that-self-assemble-in-vitro-and-in-vivo
#18
Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner-Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski, Tanja Ćirković Veličković, Adam Round, José María Carazo, Roberto Melero, Roman Jerala
Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter...
October 16, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29035363/crystal-structures-reveal-an-elusive-functional-domain-of-pyrrolysyl-trna-synthetase
#19
Tateki Suzuki, Corwin Miller, Li-Tao Guo, Joanne M L Ho, David I Bryson, Yane-Shih Wang, David R Liu, Dieter Söll
Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNA(Pyl). This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNA(Pyl) recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme...
October 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29035361/continuous-directed-evolution-of-aminoacyl-trna-synthetases
#20
David I Bryson, Chenguang Fan, Li-Tao Guo, Corwin Miller, Dieter Söll, David R Liu
Directed evolution of orthogonal aminoacyl-tRNA synthetases (AARSs) enables site-specific installation of noncanonical amino acids (ncAAs) into proteins. Traditional evolution techniques typically produce AARSs with greatly reduced activity and selectivity compared to their wild-type counterparts. We designed phage-assisted continuous evolution (PACE) selections to rapidly produce highly active and selective orthogonal AARSs through hundreds of generations of evolution. PACE of a chimeric Methanosarcina spp...
October 16, 2017: Nature Chemical Biology
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