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Revanaiah Yogisharadhya, Veerakyathappa Bhanuprakash, Amit Kumar, Mianak Mondal, Sathish Bhadravati Shivachandra
Orf virus (ORFV), a member of the genus Parapoxvirus in the family Poxviridae, is the cause of orf, a highly contagious zoonotic viral disease that affects mainly sheep and goats. In the present study, the sequence and phylogenetic analysis of Indian ORFV isolates (n = 15) from natural outbreaks in sheep and goats belonging to different geographical regions were analysed on the basis of F1L gene along with homology modelling of F1L protein. Multiple sequence alignments revealed highly conserved C-terminus and heterogeneity of N-terminus region of F1L among all orf viruses studied...
April 12, 2018: Gene
Tuanwei Li, Le Liu, Titao Jing, Zheng Ruan, Pan Yuan, Lifeng Yan
Photobleaching and bio-toxicity are the main bottlenecks for organic fluorescent dyes applied in real-time dynamic monitoring of living cells. Here, an unnatural amino acid (UAA), 4-nitro-3-phenyl-L-alanine (NPA), was used as a scaffold to covalently link a near infrared (NIR) fluorophore Cy5.5, and an amphiphilic polypeptide Poly[oligo(ethylene glycol) methyl ether methacrylate]-block-poly[2-Amino-N4-(2-diisopropylamino-ethyl)-L-Aspartic acid] (P(OEGMA)21-P(Asp)16-iPr) was then conjugated for increasing the photostability and improving the biocompatibility simultaneously...
April 13, 2018: ACS Applied Materials & Interfaces
Takashi Temma, Naoya Kondo, Keiko Yoda, Kantaro Nishigori, Satoru Onoe, Masashi Shiomi, Masahiro Ono, Hideo Saji
OBJECTIVE: Oxidized low-density lipoprotein (OxLDL) plays a pivotal role in atherosclerotic plaque destabilization, which suggests its potential as a nuclear medical imaging target. We previously developed radioiodinated 125 I-AHP7, a peptide probe carrying a 7-residue sequence from the OxLDL-binding protein Asp-hemolysin, for specific OxLDL imaging. Although 125 I-AHP7 recognized OxLDL, it had low stability. Thus, to improve stability, we designed radiolabeled 22-residue peptide probes, 125 I-AHP22 and 111 In-AHP22, which include the entire AHP7 sequence, and evaluated the stability, activity, and applications of these probes in vitro and in vivo...
April 12, 2018: Annals of Nuclear Medicine
Hajar Eftekhari, Maryam Pilehchian Langroudi, Ali Banihashemi, Mandana Azizi, Reza Youssefi Kamangar, Haleh Akhavan-Niaki
α-Thalassemia (α-thal) is considered as the most common inherited hemoglobin disorder worldwide. The present study describes the first observation of a combination of rare α-chain variants, and β-globin gene cluster deletion. A 21-year-old woman with thalassemia trait, marked microcytosis, mild anemia, and normal range of Hb F was referred to Amirkola genetic center in the North of Iran for routine molecular test of thalassemia in the context of carrier detection and prevention of thalassemia major birth...
April 2018: Indian Journal of Clinical Biochemistry: IJCB
Haiyang Zhang, Chunhua Yin, Yang Jiang, David van der Spoel
Thermodynamic and kinetic properties are of critical importance for the applicability of computational models to biomolecules such as proteins. Here we present an extensive evaluation of the Amber ff99SB-ILDN force field for modeling hydration and diffusion of amino acids with three-site (SPC, SPC/E, SPC/Eb, and TIP3P), four-site (TIP4P, TIP4P-Ew, and TIP4P/2005), and five-site (TIP5P and TIP5P-Ew) water models. Hydration free energies (HFEs) of neutral amino acid side chain analogues have little dependence on the water models with a root-mean-square error (RMSE) of ~1 kcal/mol from experimental observations...
April 12, 2018: Journal of Chemical Information and Modeling
Naoki Kamo, Gosuke Hayashi, Akimitsu Okamoto
An efficient method for peptide ligation between C-terminal Asp(OAllyl) and N-terminal Cys has been developed. Peptide ligation and removal of the allyl group at the Asp carboxylate side chain proceeded in one pot by adding a small amount of Pd/TPPTS complex. Based on this efficient synthetic method, PEP-19 (61 amino acids), which is highly expressed in Purkinje cells, was synthesized.
April 12, 2018: Chemical Communications: Chem Comm
Fang Chen, Shihai Zhang, Zixiao Deng, Qiqi Zhou, Lin Cheng, Sung Woo Kim, Jun Chen, Wutai Guan
Background: Milk protein is crucial for milk quality in sows and health of newborn piglets. Plasma amino acids (AA) in sows are important precursors for milk protein synthesis in the mammary gland. In order to study the regulation of AA transported in sow mammary glands and possible underlying mechanisms, we measured the expression of genes coding for milk proteins, AA transporter expressions, and plasma AA concentrations in sows at three different physiological stages (D-17, D1 and D17 of lactation), and then further investigated the regulation of AA transport across the cell membrane by adaptive mechanisms using pig mammary epithelial cells (PMEC) as an in vitro model...
2018: Journal of Animal Science and Biotechnology
Dimard E Foudraine, Martijn P Bauer, Anne Russcher, Elske Kusters, Christa M Cobbaert, Martha T van der Beek, Janneke E Stalenhoef
Background: Automated standardized quantitative urine analysis such as iQ200 analysis is on the rise because of its high accuracy and efficiency compared to traditional urine analysis. Previous research on automated urinalysis focused mainly on predicting culture results but not on the clinical diagnosis of urinary tract infection (UTI). Methods: A retrospective analysis was conducted of consecutive urine samples sent in for culture because of suspected UTI. UTI was defined by expert opinion based on reported symptoms, conventional urine sediment analysis and urine cultures...
April 11, 2018: Journal of Clinical Microbiology
Wenyu Cheng, Guohua Chen, Huaijie Jia, Xiaobing He, Zhizhong Jing
Asp-Glu-Ala-Asp (DEAD)-box polypeptide 5 (DDX5), also called p68, is a prototypical member of the large ATP-dependent RNA helicases family and is known to participate in all aspects of RNA metabolism ranging from transcription to translation, RNA decay, and miRNA processing. The roles of DDX5 in cell cycle regulation, tumorigenesis, apoptosis, cancer development, adipogenesis, Wnt-β-catenin signaling, and viral infection have been established. Several RNA viruses have been reported to hijack DDX5 to facilitate various steps of their replication cycles...
April 9, 2018: International Journal of Molecular Sciences
Hideyuki Takahashi, Hironari Fujiki, Shun Yokoyama, Takayuki Kai, Kazuyuki Tohji
To apply CuInSe₂ (CIS)-based printable solar batteries; an aqueous phase synthesis method of Cu-In (CI) alloy nanoparticles is studied. Metal complexes in the original solution are restricted to homogenized species by utilizing calculations. For example; [(Cu2+ )(ASP2- )₂] [ASP: the "body (C₄H₅O₄N)" of aspartic acid (C₄H₇O₄N)] is predominant in the pH 6-13 region (CASP /CCu > 6); while In complexes can be restricted to [(In3+ )(OH- )(EDTA4- )] (pH 10-12; CEDTA /CIn = 2) and/or [(In3+ )(ASP2- )₂] (pH 7-9; CASP /CIn = 5)...
April 6, 2018: Nanomaterials
Kaizhu Zeng, Qian Li, Jing Wang, Guowei Yin, Yajun Zhang, Chaoni Xiao, Taiping Fan, Xinfeng Zhao, Xiaohui Zheng
Protein immobilization techniques play an important role in the development of assays for disease diagnosis and drug discovery. However, many of these approaches are not applicable to transmembrane proteins. G protein-coupled receptors (GPCRs) are the largest protein superfamily encoded by the human genome and are targeted by a quarter of all prescription drugs. GPCRs are highly dynamic and sensitive to changes in the ambient environment, and current immobilization methodologies are not suitable for GPCRs. We used haloalkane dehalogenase (Halo) as an immobilization tag fused to the β2 -adrenoceptor (β2 -AR), angiotensin II type 1 (AT1 ) and angiotensin II type 2 (AT2 ) receptors...
January 14, 2018: Chemical Science
Yu-Kuan Lin, Po-Kuei Wu, Cheng-Fong Chen, Chao-Ming Chen, Shang-Wen Tsia, Paul Chih-Hsueh Chen, Wei-Ming Chen
BACKGROUND: Alveolar soft part sarcoma (ASPS) is a rare soft tissue tumor that typically affects young patients. Similar to other soft tissue sarcomas, it has high pulmonary metastasis ability, whereas compared with other soft tissue sarcomas, it has high brain metastasis ability. Because of the rarity of the disease, most studies on ASPS have been case reports and small series studies. METHOD: We performed a retrospective study to evaluate the clinical and pathological features and oncological results in a consecutive series of patients with localized or metastatic ASPS treated at our institute between 1994 and 2014...
April 3, 2018: Journal of the Chinese Medical Association: JCMA
Natasha C Pflanz, Anna W Daszkowski, Garrett L Cornelison, James R Trudell, S John Mihic
Benzodiazepines are positive allosteric modulators of the GABAA receptor (GABAA R), acting at the α-γ subunit interface to enhance GABAA R function. GABA or benzodiazepine binding induces distinct conformational changes in the GABAA R. The molecular rearrangements in the GABAA R following benzodiazepine binding remain to be fully elucidated. Using two molecular models of the GABAA R, we identified electrostatic interactions between specific amino acids at the α-γ subunit interface which were broken by, or formed after, benzodiazepine binding...
April 5, 2018: Journal of Biological Chemistry
Jay Prakash A Yadav, Arvind K Bansal, Sanyog Jain
In eutectic, a lamellar microstructure offers better tableting as compared to non-reacted physical mixture. However, bulk deformation remains elusive in two binary eutectics. We hypothesized that binary eutectic of a drug with different component having different H-bonding dimensionalities and crystal structure shall allow the understanding of structural integrity in bulk deformation behavior. Shearing molecular solid (FXT Q) shared common composition with viscoelastic crystal (ASP I) and brittle (PCM I) forming EM-1 (1 = 41...
April 5, 2018: Molecular Pharmaceutics
Wanli You, Chia-En A Chang
Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif...
April 5, 2018: Journal of Chemical Information and Modeling
Gaurav Jain, Martin Pendola, Yu-Chieh Huang, Denis Gebauer, Eleni Koutsoumpeli, Steven D Johnson, John Spencer Evans
In the nacre layer of the Pinctada fucata oyster shell there exists a multi-member proteome, known as the framework family, which regulates the formation of the aragonite mesoscale tablets and participates in the creation of an organic coating around each tablet. Several approaches have been developed to understand protein-associated mechanisms of nacre formation, yet we still lack insight into how protein ensembles or proteomes manage nucleation and crystal growth. To provide additional insights we have created a proportionally-defined combinatorial model consisting of two recombinant framework proteins, r-Pif97 (containing a von Willebrand Factor Type A domain) and r-n16...
April 5, 2018: Biochemistry
Wei Li, Yi Bing Ma, Ying Qiu Mao, Tong Lin
Dehydrocostus lactone is considered to be the major cholagogic ingredient of the Costus genus of plants. It exhibits strong cholagogic effects, and also exerts antimicrobial and antineoplastic activity. The present study aimed to investigate the effects of dehydrocostus lactone on the cell growth and apoptosis of recombinant human papilloma virus (HPV)‑18 HaCaT cells. The HPV‑18 genome was transfected into HaCaT cells, which were subsequently used for analysis. The results demonstrated that dehydrocostus lactone reduced the cell proliferation and induced apoptosis of HPV‑18 HaCaT cells, as determined by MTT and N‑acetyl‑Asp‑Glu‑Val‑Asp p‑nitroanilide assays, respectively...
March 28, 2018: Molecular Medicine Reports
Ronaldo Correia da Silva, Andrei Santos Siqueira, Alex Ranieri Jerônimo Lima, Adonis de Melo Lima, Alberdan Silva Santos, Délia Cristina Figueira Aguiar, Evonnildo Costa Gonçalves
Asparaginases are found in a range of organisms, although those found in cyanobacteria have been little studied, in spite of their great potential for biotechnological application. This study therefore sought to characterize the molecular structure of an L-asparaginase from the cyanobacterium Limnothrix sp. CACIAM 69d, which was isolated from a freshwater Amazonian environment. After homology modeling, model validation was performed using a Ramachandran plot, VERIFY3D, and the RMSD. We also performed molecular docking and dynamics simulations based on binding free-energy analysis...
April 4, 2018: Journal of Molecular Modeling
Fabio Cericola, Ingo Lenk, Dario Fè, Stephen Byrne, Christian S Jensen, Morten G Pedersen, Torben Asp, Just Jensen, Luc Janss
Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS) assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction in accuracy when identifying the allele-frequency at each locus. As a consequence of the latter, genomic relationship matrices (GRMs) will be biased. This bias in GRMs affects variance estimates and the accuracy of GBLUP for genomic prediction (GBLUP-GP)...
2018: Frontiers in Plant Science
B Asokan, P Ramanan, M Sundararaj, E Kovarthini
Alveolar soft part sarcoma (ASPS) is a rare form of soft-tissue sarcoma arising from connective tissue. It is most often seen in adolescents and young adults and has high propensity for recurrence and metastasis. Clinically, it mimics haemangioma or arteriovenous malformations. In our case report, an 18-year-old female presented with markedly vascular tumour in the left forearm, for which excision biopsy was done. Histopathological report revealed ASPS. The patient was screened for metastasis. Ultrasound abdomen, computed tomography (CT) chest, CT brain and whole-body skeletal survey was done...
September 2017: Indian Journal of Plastic Surgery: Official Publication of the Association of Plastic Surgeons of India
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