scholarly journals Life's (more than) a BLAST™: Proteomics software

2002 ◽  
Vol 24 (4) ◽  
pp. 21-23 ◽  
Author(s):  
Ronan O’Malley
Keyword(s):  
Proteomics Data ◽  
Software Suite ◽  
Efficient Manner ◽  
Exponential Increase ◽  
A Genome ◽  
Recent Developments ◽  
Automated Processing ◽  
Protein Complement ◽  
Identification And Characterization

Proteomics, the study of the expressed protein complement of a genome, centres on the identification and characterization of protein mixtures isolated from biological systems. Mass spectrometry (MS), in combination with one or more pre-separation steps, is currently the preferred method for analysing protein samples. Recent developments in these disciplines, particularly the emergence of high-throughput, automated techniques, have led to an exponential increase in data quantity -- gigabytes of data can be produced daily. A major challenge lies in processing these data to extract the maximum amount of information in a time- and labour-efficient manner. To meet this challenge, Micromass UK Ltd has developed a comprehensive proteomics software suite, ProteinLynxTM GlobalSERVER 2.0, which enables the automated processing, analysis, storage and reporting of proteomics data.

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

scholarly journals Genetic dissection of drug resistance in trypanosomes

Parasitology ◽  
2013 ◽  
Vol 140 (12) ◽  
pp. 1478-1491 ◽  
Author(s):  
SAM ALSFORD ◽  
JOHN M. KELLY ◽  
NICOLA BAKER ◽  
DAVID HORN
Keyword(s):  
Neglected Tropical Diseases ◽  
Sub Saharan Africa ◽  
Genetic Dissection ◽  
Molecular Tools ◽  
Sequencing Technology ◽  
Exponential Increase ◽  
Technological Developments ◽  
Sub Saharan ◽  
Identification And Characterization

SUMMARYThe trypanosomes cause two neglected tropical diseases, Chagas disease in the Americas and African trypanosomiasis in sub-Saharan Africa. Over recent years a raft of molecular tools have been developed enabling the genetic dissection of many aspects of trypanosome biology, including the mechanisms underlying resistance to some of the current clinical and veterinary drugs. This has led to the identification and characterization of key resistance determinants, including transporters for the anti-Trypanosoma bruceidrugs, melarsoprol, pentamidine and eflornithine, and the activator of nifurtimox-benznidazole, the anti-Trypanosoma cruzidrugs. More recently, advances in sequencing technology, combined with the development of RNA interference libraries in the clinically relevant bloodstream form ofT. bruceihave led to an exponential increase in the number of proteins known to interact either directly or indirectly with the anti-trypanosomal drugs. In this review, we discuss these findings and the technological developments that are set to further revolutionise our understanding of drug-trypanosome interactions. The new knowledge gained should inform the development of novel interventions against the devastating diseases caused by these parasites.

A genome-wide identification and characterization of mircoRNAs and their targets in ‘Suli’ pear (Pyrus pyrifolia white pear group)

Planta ◽  
2013 ◽  
Vol 238 (6) ◽  
pp. 1095-1112 ◽  
Author(s):  
Qingfeng Niu ◽  
Minjie Qian ◽  
Guoqin Liu ◽  
Fengxia Yang ◽  
Yuanwen Teng
Keyword(s):  
Pyrus Pyrifolia ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

scholarly journals Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible FungusPleurotus ostreatus

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Jibin Qu ◽  
Mengran Zhao ◽  
Tom Hsiang ◽  
Xiaoxing Feng ◽  
Jinxia Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Noncoding Rnas ◽  
Genome Sequences ◽  
Small Noncoding Rnas ◽  
Basidiomycetous Fungus ◽  
A Genome ◽  
Genome Assemblies ◽  
Genome Scale ◽  
Identification And Characterization

Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) ofPleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs inP. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved inP. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs ofP. ostreatuswere not conserved across Agaricomycotina fungi.

scholarly journals Identification and Characterization of the Glutathione Peroxidase (GPX) Gene Family in Watermelon and Its Expression under Various Abiotic Stresses

Agronomy ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 206 ◽  
Author(s):  
Yong Zhou ◽  
Jingwen Li ◽  
Junhong Wang ◽  
Wenting Yang ◽  
Youxin Yang
Keyword(s):  
Abiotic Stress ◽  
Glutathione Peroxidase ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization ◽  
Lower Expression

Plant glutathione peroxidase (GPX) is an important antioxidant enzyme to maintain H2O2 homeostasis and regulate plant response to abiotic stress. In this paper, we present the first report of a genome-wide identification of GPX genes in watermelon. A total of six genes (ClGPX1–ClGPX6) were identified, which were unevenly located on four chromosomes of the watermelon genome. Based on phylogenetic analysis, the GPX genes of Arabidopsis, rice, cucumber, and sorghum were classified into four groups. Through analyzing the promoter regions of ClGPX genes, many development-, stress-, and hormone-responsive cis-acting regulatory elements were also identified. Expression pattern analysis by qRT-PCR indicated that all ClGPX genes were actively expressed in flowers and fruits, and exhibited relatively lower expression in other tissues, particularly roots and stems. In addition, the expression of ClGPX genes was significantly induced by salt, drought, and cold stresses, as well as abscisic acid (ABA) treatment at different time points, suggesting that they may be involved in response to abiotic stress and ABA. Taken together, our findings demonstrated that ClGPX genes might function in watermelon development, especially in flower and fruit tissue, as well as in response to abiotic stress and hormones.

scholarly journals Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhong-Qing Li ◽  
Yao Zhang ◽  
He Li ◽  
Ting-Ting Su ◽  
Cheng-Gong Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Function Analysis ◽  
Pcr Analysis ◽  
Functional Domain ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

scholarly journals Conical Intersections at the Nanoscale: Molecular Ideas for Materials

2019 ◽  
Vol 70 (1) ◽  
pp. 21-43 ◽  
Author(s):  
Benjamin G. Levine ◽  
Michael P. Esch ◽  
B. Scott Fales ◽  
Dylan T. Hardwick ◽  
Wei-Tao Peng ◽  
...  
Keyword(s):  
Materials Science ◽  
Theoretical Study ◽  
Nonradiative Recombination ◽  
Conical Intersections ◽  
Computational Tools ◽  
Recent Developments ◽  
Semiconductor Nanomaterials ◽  
Identification And Characterization ◽  
Nonradiative Processes

The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. After briefly introducing conical intersections, we argue that specific defects in materials can induce conical intersections between the ground and first excited electronic states, thus introducing pathways for nonradiative recombination. We present recent developments in theoretical methods, computational tools, and chemical intuition for the prediction of such defect-induced conical intersections. Through examples in various nanomaterials, we illustrate the significance of conical intersections for nanoscience. We also discuss challenges facing research in this area and opportunities for progress.

Giardia lamblia: identification and characterization of Rab and GDI proteins in a genome survey of the ER to Golgi endomembrane system

2002 ◽  
Vol 101 (1) ◽  
pp. 13-24 ◽  
Author(s):  
T Dianne Langford ◽  
Jeffrey D Silberman ◽  
Malin E-L Weiland ◽  
Staffan G Svärd ◽  
J Michael McCaffery ◽  
...  
Keyword(s):  
Giardia Lamblia ◽  
Endomembrane System ◽  
Genome Survey ◽  
A Genome ◽  
Identification And Characterization

Molecular dissection of meiotic silencing by unpaired DNA

2015 ◽  
Author(s):  
◽  
Logan M. Decker
Keyword(s):  
Messenger Rnas ◽  
Meiotic Silencing ◽  
University Of Missouri ◽  
A Genome ◽  
Unpaired Region ◽  
The University ◽  
Surveillance Mechanism ◽  
Interfering Rna ◽  
Identification And Characterization

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Meiotic silencing by unpaired DNA (MSUD) is a genome surveillance mechanism that uses RNAi to protect against genetic parasites such as retrotransposons and viruses. This is accomplished by scanning the genome for DNA segments not paired with a homologous partner during meiosis and targeting the corresponding messenger RNAs for destruction. MSUD begins when a single-stranded RNA is made from the unpaired region and subsequently converted into small interfering RNA (siRNA), which are used as sequence specific guides for mRNA destruction. To date, nine meiotic silencing genes have been characterized and here we report the identification and characterization of two new candidates that are orthologous to the conserved proteins CBP80 and EPS15.

scholarly journals An overview on the green synthesis of nanoparticles and other nano-materials using enzymes and their potential applications

2019 ◽  
Vol 9 (5) ◽  
pp. 4255-4271 ◽  
Keyword(s):  
Nano Materials ◽  
Reaction Conditions ◽  
Synthesis Of Nanoparticles ◽  
Toxic Materials ◽  
Recent Developments ◽  
Potential Applications ◽  
Biological Methods ◽  
Diverse Groups ◽  
Identification And Characterization

The applications of nanoparticles (NPs) and another nanomaterial (NM) are widely increasing in various fields including biomedical and clinical sciences. Conventional methods used for the synthesis of NM have several demerits like chemical procedures producing toxic materials and physical methods being costly and forming particles of non-uniform sizes. The use of such NM has prevented their applications in biomedical fields especially in clinical applications. In order to use NPs in clinical fields, there is a need to use reliable, nontoxic and eco-friendly methods for their synthesis. The use of eco-friendly and biological methods for the synthesis of NPs and other NM has attracted the attention of nanobiotechnologists due to synthesis of such particles by using nontoxic method. The enzymatic synthesis of NPs is highly specific as this procedure results in the formation of nontoxic materials of controlled shape, size and high stability. In this chapter an effort has been made to critically review recent developments in the area of biosynthesis of several types of NM by using enzymes of diverse groups such as oxidoreductases, transferases, hydrolases, lyases and ligases. The mechanisms of enzyme catalyzedsynthesis of NPs and the reaction conditions to control their shape, size, and stability of NPs have also been described. Numerous kinds of techniques employed for the identification and characterization of NM have been discussed. The biomedical and other applications of as-synthesized NM have also been mentioned in this article.

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