scholarly journals INDI - Integrated Nanobody Database for Immunoinformatics

2021 ◽  
Author(s):  
Piotr Deszynski ◽  
Jakub Mlokosiewicz ◽  
Adam Volanakis ◽  
Igor Jaszczyszyn ◽  
Natalie Castellana ◽  
...  
Keyword(s):  
Sequence Information ◽  
Text Search ◽  
Scientific Publications ◽  
Specific Sequence ◽  
Molecular Binding ◽  
The Public ◽  
Tumor Penetration ◽  
Single Polypeptide Chain ◽  
Single Polypeptide ◽  
Generation Sequencing

Nanobodies, a subclass of antibodies found in camelids, are a versatile molecular binding scaffold composed of a single polypeptide chain. The small size of nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first therapeutic approval in 2018 cementing the clinical viability of this format. Structured data and sequence information of nanobodies will enable the accelerated clinical development of nanobody-based therapeutics. Though the nanobody sequence and structure data are deposited in the public domain at an accelerating pace, the heterogeneity of sources and lack of standardization hampers reliable harvesting of nanobody information. We address this issue by creating the Integrated Database of Nanobodies for Immunoinformatics (INDI, http://research.naturalantibody.com/nanobodies). INDI collates nanobodies from all the major public outlets of biological sequences: patents, GenBank, next-generation sequencing repositories, structures and scientific publications. We equip INDI with powerful nanobody-specific sequence and text search facilitating access to more than 11 million nanobody sequences. INDI should facilitate development of novel nanobody-specific computational protocols helping to deliver on the therapeutic promise of this drug format.

Professional and Communicative Proficiency of a Mentor as a Tool of Image Building in Public Service

Communicology ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 74-88
Author(s):  
D.A. Kemenev
Keyword(s):  
Public Service ◽  
Role Models ◽  
Communicative Competence ◽  
Public Servants ◽  
Scientific Publications ◽  
Communicative Skills ◽  
The Public ◽  
Public Servant ◽  
Professional Business ◽  
Image Building

The article investigates the imageological aspect of mentor’s communicative competence in public service and reveals the communicative functions of mentor’s image in relation to the mentees. The author determines the communicative skills necessary for the mentor in all processes and stages of this personnel technology. Based on the analysis of scientific publications, the author discloses and justifies the role models of mentor’s behavior in relation to the mentees from the perspective of the mentor’s image, authority, and communicative competence. The author has conducted an expert survey among public servants, which allowed identify the main professional, business, moral, psychological, and integral qualities that are the most effectively developed by the public servant in the process of performing mentor’s functions. As a result, the author suggests a structural-logical model of the communicative competence of a mentor in the public service in the process of perceiving its communicative knowledge, skills, and competencies for achieving the effectiveness of mentoring.

IsoDetect: Detection of splice isoforms from third generation long reads based on short feature sequences

2020 ◽  
Vol 15 ◽  
Author(s):  
Hongdong Li ◽  
Wenjing Zhang ◽  
Yuwen Luo ◽  
Jianxin Wang
Keyword(s):  
Sequence Similarity ◽  
Detection Methods ◽  
Sequence Information ◽  
Third Generation ◽  
Sequencing Data ◽  
Splice Isoforms ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Feature Sequence ◽  
Generation Sequencing

Aims: Accurately detect isoforms from third generation sequencing data. Background: Transcriptome annotation is the basis for the analysis of gene expression and regulation. The transcriptome annotation of many organisms such as humans is far from incomplete, due partly to the challenge in the identification of isoforms that are produced from the same gene through alternative splicing. Third generation sequencing (TGS) reads provide unprecedented opportunity for detecting isoforms due to their long length that exceeds the length of most isoforms. One limitation of current TGS reads-based isoform detection methods is that they are exclusively based on sequence reads, without incorporating the sequence information of known isoforms. Objective: Develop an efficient method for isoform detection. Method: Based on annotated isoforms, we propose a splice isoform detection method called IsoDetect. First, the sequence at exon-exon junction is extracted from annotated isoforms as the “short feature sequence”, which is used to distinguish different splice isoforms. Second, we aligned these feature sequences to long reads and divided long reads into groups that contain the same set of feature sequences, thereby avoiding the pair-wise comparison among the large number of long reads. Third, clustering and consensus generation are carried out based on sequence similarity. For the long reads that do not contain any short feature sequence, clustering analysis based on sequence similarity is performed to identify isoforms. Result: Tested on two datasets from Calypte Anna and Zebra Finch, IsoDetect showed higher speed and compelling accuracy compared with four existing methods. Conclusion: IsoDetect is a promising method for isoform detection. Other: This paper was accepted by the CBC2019 conference.

Debranching enzyme from rabbit skeletal muscle; Evidence for the location of two active centres on a single polypeptide chain

FEBS Letters ◽  
1975 ◽  
Vol 58 (1-2) ◽  
pp. 181-185 ◽  
Author(s):  
Edna J. Bates ◽  
Gillian M. Heaton ◽  
Carol Taylor ◽  
John C. Kernohan ◽  
Philip Cohen
Keyword(s):  
Skeletal Muscle ◽  
Polypeptide Chain ◽  
Rabbit Skeletal Muscle ◽  
Debranching Enzyme ◽  
Single Polypeptide Chain ◽  
Single Polypeptide ◽  
Active Centres

N-Terminal amino acid sequence of rat tonin: homology with serine proteases

1978 ◽  
Vol 56 (9) ◽  
pp. 920-925 ◽  
Author(s):  
N. G. Seidah ◽  
R. Routhier ◽  
M. Caron ◽  
M. Chrétien ◽  
S. Demassieux ◽  
...  
Keyword(s):  
Serine Proteases ◽  
Terminal Sequence ◽  
Renin Substrate ◽  
Amino Terminal ◽  
Single Polypeptide Chain ◽  
Serine Protease Family ◽  
Terminal Amino ◽  
Single Polypeptide ◽  
Carboxy Terminal ◽  
Amino Terminal Sequence

In this paper, we present the amino-terminal sequence of rat tonin, an endopeptidase responsible for the conversion of angiotensinogen, the tetradecapeptide renin substrate, or angiotensin I to angiotensin II. It is shown that isoleucine and proline occupy the amino- and carboxy-terminal residues respectively. The N-terminal sequence analysis permitted the identification of 34 out of the first 40 residue s of the single polypeptide chain composed of 272 amino acids. The se results showed an extensive homology with the sequence of many serine proteases of the trypsin–chymotrypsin family. This information, coupled with the slow inhibition of tonin by diisopropylfluorophosphate, classified this enzyme as a selective endopeptidase of the active serine protease family.

scholarly journals Genetic Interactions WithCLF1Identify Additional Pre-mRNA Splicing Factors and a Link Between Activators of Yeast Vesicular Transport and Splicing

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 895-907 ◽  
Author(s):  
Kevin Vincent ◽  
Qiang Wang ◽  
Steven Jay ◽  
Kathryn Hobbs ◽  
Brian C Rymond
Keyword(s):  
Mrna Splicing ◽  
Splicing Factors ◽  
Sequence Information ◽  
Specific Sequence ◽  
Synthetic Lethal ◽  
Growth Defects ◽  
Mrna Maturation ◽  
Assembly Factor ◽  
Gtpase Activation ◽  
Synthetic Growth

AbstractClf1 is a conserved spliceosome assembly factor composed predominately of TPR repeats. Here we show that the TPR elements are not functionally equivalent, with the amino terminus of Clf1 being especially sensitive to change. Deletion and add-back experiments reveal that the splicing defect associated with TPR removal results from the loss of TPR-specific sequence information. Twelve mutants were found that show synthetic growth defects when combined with an allele that lacks TPR2 (i.e., clf1Δ2). The identified genes encode the Mud2, Ntc20, Prp16, Prp17, Prp19, Prp22, and Syf2 splicing factors and four proteins without established contribution to splicing (Bud13, Cet1, Cwc2, and Rds3). Each synthetic lethal with clf1Δ2 (slc) mutant is splicing defective in a wild-type CLF1 background. In addition to the splicing factors, SSD1, BTS1, and BET4 were identified as dosage suppressors of clf1Δ2 or selected slc mutants. These results support Clf1 function through multiple stages of the spliceosome cycle, identify additional genes that promote cellular mRNA maturation, and reveal a link between Rab/Ras GTPase activation and the process of pre-mRNA splicing.

scholarly journals Hepatic microsomal epoxide hydrase. Chemical evidence for a single polypeptide chain.

1979 ◽  
Vol 254 (14) ◽  
pp. 6240-6243 ◽  
Author(s):  
G C DuBois ◽  
E Appella ◽  
R Armstrong ◽  
W Levin ◽  
A Y Lu ◽  
...  
Keyword(s):  
Polypeptide Chain ◽  
Single Polypeptide Chain ◽  
Single Polypeptide ◽  
Chemical Evidence

scholarly journals Accelerating Scientific Publication in Biology

2015 ◽  
Author(s):  
Ronald D Vale
Keyword(s):  
Scientific Community ◽  
Scientific Publication ◽  
Scientific Publications ◽  
Postdoctoral Training ◽  
The Public ◽  
New Information ◽  
Funding Agencies ◽  
New Findings ◽  
Time Required ◽  
Catalytic Effects

Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. More experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training. Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and the scientific community.

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