STREPTOMYCETE PLASMIDS CONTAINING BIOSYNTHESIS GENE CLUSTERS OF ANTITUMOR ANTIBIOTIC LIDAMICIN

Anticancer antibiotic lidamycin is produced by Streptomyces globisporus C-1027 strain. The lidamycin biosynthesis cluster (LDM-cluster) is localized on its plasmid SGLP1. Aim. To identify and characterize plasmid-localized gene clusters potentially involved in lidamycin biosynthesis in streptomycetes. Methods. Nucleotide sequences of streptomycetes from the Internet database Nucleotide Collection on the National Center for Biotechnology Information were objects of this study. Search for probable LDM clusters was performed using the Basic Local Alignment Search Tool. The LDM-cluster sequence of S. globisporus C-1027 was used as a query in BLASTN analysis. Results. The database contains information on the primary structures of thousands of chromosomes and dozens of plasmids of streptomycetes, which are fully defined (Compete genome). BLASTN-analysis of primary structures of DNAs revealed the presence of probable LDM clusters in 6 streptomycete plasmids. Nucleotide sequences of 7 plasmids were only partially identical – they all contained sequences that were similar to the fragment 7,747 bp – 112,237 bp of SGLP1. Conclusions. The findings have demonstrated that LDM clusters are predominantly localized on plasmids in Streptomyces species. Although the identified plasmids share substantial sequence similarity - spanning approximately 104.5 kb - with the reference SGLP1 plasmid, they are not genetically identical.

BioTechniquesVol. 53, No. 5 BioSpotlightOpen AccessBioSpotlightPatrick Lo & Kristie NyboPatrick LoSearch for more papers by this author & Kristie NyboSearch for more papers by this authorPublished Online:3 Apr 2018https://doi.org/10.2144/000113945AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit Titer countsPhage display enables researchers to identify interactions of protein sequences fused to a phage coat protein expressed on the viral surface. Displayed sequences can be selected based on their desired binding properties, following which the associated virus is propagated in a bacterial host for isolation and purification. It is common to repeat the selection steps three or more times for enrichment, with the phage concentration determined after each propagation step. Phage concentration is commonly calculated using the plating method, where Escherichia coli are infected with phage, mixed in soft agar, plated, and the resulting plaques or colonies counted. Although this is an effective means of quantification, the procedure is lengthy, requiring an overnight incubation period. UV photometry can be used as a quicker approach to assess phage concentrations, but this method requires complete removal of impurities that absorb UV light and adversely affect readings. In this issue of BioTechniques, Lehmusvuori et al. from the University of Turku, Finland describe a new approach for quantifying bacteriophage using lanthanide fluorescence probes, a technology previously developed by the authors for other applications, and demonstrate its effectiveness using the M13 phage display system. The method requires two non-fluorescent oligonucleotide probes, one carrying a lanthanide ion and the other an antenna probe. When the probes hybridize to adjacent positions on the chloramphenicol acetyl-transferase gene, a selectable marker on the M13 phagemid single stranded DNA, the lanthanide ion and antenna probe form a highly fluorescent lanthanide chelate complex that can be measured as an indication of the concentration of ssDNA in solution. After only four hours in culture, phage could be detected in supernatant, demonstrating a significant time savings for this important step in phage display technology compared to the plating method. Measurements were highly reliable, and even more accurate than phage counts obtained using absorbance measurements. Although demonstrated with the M13 phage display system, this methodology should be applicable to quantification of other ssDNA phage species.Diagram of the complementation probe-based bacteriophage quantification assay detailed in Lehmusvuori, et al.See “Homogenous M13 bacteriophage quantification assay using switchable lanthanide fluorescence probes”.Having a BLAST (on your own)The first step in identifying any novel DNA or protein sequence is to perform a sequence similarity search against databases of known sequences to establish identity or find sequence homologs. The principal algorithm used for such similarity searches is the Basic Local Alignment Search Tool (BLAST), which is conveniently done online using the National Center for Biotechnology Information (NCBI) server, in conjunction with various publicly available databases such as GenBank and UniProt. Under certain circumstances, however, researchers may prefer to carry out offline BLAST searches on a local computer against their own databases of proprietary or unpublished sequences. While NCBI provides stand-alone, command line versions of BLAST that can be freely downloaded and installed on a personal computer, these are not particularly user-friendly, especially for biological researchers lacking computer expertise. There are two graphical front ends with extensive features and options for the BLAST command line software currently available, but these are restricted to Unix-based systems. Windows users unfortunately are restricted to a pair of graphical user interfaces (GUIs) that suffer from several major limitations. In this issue, P. Santiago-Sotelo and J.H. Ramirez-Prado at the Centro de Investigación Científica de Yucatán (Mexico) describe prfectBLAST, an operating system-independent GUI for the NCBI stand-alone suite of the new BLAST+ command line executables. prfectBLAST is free, open-source, completely self-contained, and coded in Java version 6, allowing it to be executed on multiple platforms (including Windows, Mac OS X, and Linux). In addition, the software does not require installation or any dependencies, so it can be run from an external flash or hard drive if desired. Its graphical layout and choice of options was designed to mirror the NCBI web interface for BLAST+ searches, and all BLAST+ parameters can be easily changed through the GUI. Searches using any of the BLAST+ programs are carried out against locally stored, user-customized databases and can be run in the computer background; several searches can be carried out concurrently. prfectBLAST is ideally suited for novice and casual users, yet flexible enough to allow experts to fully utilize all the advanced options available for BLAST+.See “prfectBLAST: a platform independent portable front end for the command terminal BLAST+ stand-alone suite”.FiguresReferencesRelatedDetails Vol. 53, No. 5 Follow us on social media for the latest updates Metrics History Published online 3 April 2018 Published in print November 2012 Information© 2012 Author(s)PDF download

Background & Objective: Acute appendicitis is the predominant etiology of emergency cases on a global scale, and it may have serious consequences. If there is no precise diagnosis. Toll-like receptors (TLRs) are a crucial group of receptors that form the initial barrier against infections. The study aimed to investigate the molecular structure of Toll-like receptor (TLRs) genes by conventional Polymerase Chain Reaction) PCR) and deoxyribonucleic acid (DNA) sequencing in acute appendicitis patients and investigate whether any alteration in this gene may act as a risk factor for appendicitis. Methodology: A case-control investigation was conducted at Al-Sadr Teaching Hospital and Al-Shifaa Teaching Hospital in Basrah, Iraq, from July to November 2023. The study involved 20 blood samples from 15 patients previously diagnosed with appendicitis; and 5 healthy individuals included as a control group. We randomly selected six samples from patients with appendicitis, with two samples for each primer, for DNA sequencing. Results: The results of conventional PCR and electrophoresis showed different molecular weights at different temperatures for TLR1, TLR4, and TLR5. DNA sequencing results showed several different mutations for each TLRs gene primer for both reverse and forward when compared by the Basic Local Alignment Search Tool (BLAST) to sequences from the National Centre for Biotechnology Information (NCBI). Six new mutations were recorded in the gene bank (NCBI), two mutations per TLR. The study found that TLR1’s forward primer had two mutations, while the reverse primer had four. Four alterations were found in TLR4, while one in TLR5 was found in the reverse primer. Conclusion: Through altering the immune system’s reaction to pathogenic stimuli, excessive immunological activation, and inflammation, genetic differences in TLRs may influence the pathophysiology or outcome of disease. These factors can also contribute to the development of appendicitis. Abbreviations: AA, Acute Appendicitis; AHC, apparently healthy controls, “BLAST, Basic Local Alignment Search Tool”; CD, cluster of differentiation; EDTA, ethylene diamine tetra acetic acid; GBD, Global Burden of Disease Study; GC, gastric cancer; GIT, gastrointestinal tract; IBD, inflammatory bowel disease; LPS, lipopolysaccharide; “MyD88, myeloid differentiation primary response 88”; NCBI, National Center for Biotechnology Information; PRRs, “Pathogen Recognition Receptors; PAMPs Pathogen Associated Molecular patterns”; SNPs, single-nucleotide polymorphisms; TE, Tris-EDTA; TIR, Toll-interleukin (IL)-1 receptor. Keywords: Appendicitis, TLR1, TLR4, TLR5, PCR, DNA sequencing, Molecular Detection Citation: Shaker ZN, Mahdi DS, AlSaimary IE. Molecular detection of Toll-like receptors 1, 4, and 5 genes among patients with appendicitis. Anaesth. pain intensive care 2024;28(6):1050-1060; DOI: 10.35975/apic.v28i6.2622 Received: August 22, 2024; Reviewed: October 06, 2024; Accepted: October 18, 2024

Basic local alignment search tool (BLAST) is a sequence similarity search program. The National Center for Biotechnology Information (NCBI) maintains a BLAST server with a home page at . We report here on recent enhancements to the results produced by the BLAST server at the NCBI. These include features to highlight mismatches between similar sequences, show where the query was masked for low-complexity sequence, and integrate information about the database sequences from the NCBI Entrez system into the BLAST display. Changes to how the database sequences are fetched have also improved the speed of the report generator.

Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA’s graphics processing units (GPUs) and multicore processors. Depending on the sensitivity settings, this makes it possible to quickly reduce the sequence database by factors between 50% and 95%, while rejecting no significant sequences. Furthermore, this prefiltering application can be used together with multiple homology detection algorithms as a part of a next-generation sequencing system. Extensive performance and accuracy tests have been carried out in the Spanish National Centre for Biotechnology (NCB). The results show that GPU hardware can accelerate the execution times of former homology detection applications, such as National Centre for Biotechnology Information (NCBI), Basic Local Alignment Search Tool for Proteins (BLASTP), up to a factor of 4.KEY POINTS:Owing to the increasing size of the current sequence datasets, filtering approach and high-performance computing (HPC) techniques are the best solution to process all these information in acceptable processing times.Graphics processing unit cards and their corresponding programming models are good options to carry out these processing methods.Combination of filtration models with HPC techniques is able to offer new levels of performance and accuracy in homology detection algorithms such as National Centre for Biotechnology Information Basic Local Alignment Search Tool.

The National Center for Biotechnology Information (NCBI) provides a data-rich environment in support of genomic research by collecting the biological data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains and integrating the data with analytical, search, and retrieval resources through the NCBI Web site. Entrez, an integrated search and retrieval system, enables text searches across various diverse biological databases maintained at NCBI. Map Viewer, the genome browser developed at NCBI, displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allows maps from all plant genomes available in the Map Viewer to be searched to produce a display of aligned maps from several species. Customized Plant Basic Local Alignment Search Tool (PlantBLAST) allows the user to perform sequence similarity searches in a special collection of mapped plant sequence data and to view the resulting alignments within a genomic context using Map Viewer. In addition, pre-computed sequence similarities, such as those for proteins offered by BLAST Link (BLink), enable fluid navigation from un-annotated to annotated sequences, quickening the pace of discovery. Plant Genome Central (PGC) is a Web portal that provides centralized access to all NCBI plant genome resources. Also, there are links to plant-specific Web resources external to NCBI such as organism-specific databases, genome-sequencing project Web pages, and homepages of genomic bioinformatics organizations.

In this paper, a design of a Field Programmable Gate Array (FPGA)-based parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm with multi-hits Detection is proposed. Basic Local Alignment Search Tool algorithm is a heuristic biological sequence alignment algorithm and has been widely used in the computational biology domain. The architecture contains several different blocks. Each block will perform a different step of National Center for Biotechnology Information (NCBI) BLAST family algorithms in parallel. The most appealing and distinguishing features of this architecture are the Multiple Hits Finder Array and Hits Combination Block. In the hits detection stage, we apply a Multiple Hits Finder Array approach to realize the multi-hits in one clock cycle. Then the multiple overlapping hits are merged together in the Hits Finder Block to reduce memory consumption and save implementation time. The parallel design makes this FPGA-based BLAST algorithm implementation much faster than an equivalent software program would in a PC. Multiple Hits Finder Array architecture prototype is implemented and the storage expense and synthesis performance of the prototype are discussed.

IntroductionThe most commonly noted reactions in leprosy patients are type 1 reactions and erythema nodosum leprosum, with some rare phenomenon of host response known as Lucio phenomenon or leprosy of Lucio and Latapi which is caused by Mycobacterium lepromatosis. So far, no case of M. lepromatosis has been reported from India.Materials and methodsThe main objective of this study was to detect any positive cases of M. lepromatosis in India with such a complication. We screened slit skin smear/biopsy samples from lepromatous leprosy (LL) patients reporting to The Leprosy Mission Community Hospitals across the country. Eighty-eight slit skin smears were collected from leprosy patients in 70% ethanol. DNA was extracted from all these samples. Polymerase chain reaction (PCR) was done for 2 genes; one set was for 16S rRNA and the other set was for coproporphyrinogen III oxidase (hemN) gene. Then, sequencing was done for all positive amplicons. Homology of the sequences was analyzed using the Basic Local Alignment Search Tool at the National Center of Biotechnology Information database.ResultsAmong 88 isolates, we found 4 positive cases for M. lepromatosis. All 4 were LL cases with a bacteriological index ranging from 2+ to 4+. On the basis of the National Center of Biotechnology Information Basic Local Alignment Search Tool analysis, the sequenced amplicons of both genes matched with the M. lepromatosis 16S rRNA and phosphofructokinase genes but not with hemN gene of lepromatosis. This is the first report for the presence of M. lepromatosis in LL cases from India.ConclusionThis new species M. lepromatosis exists beyond Mexico, Singapore and it is the cause of DLL in India also. It may cause dual infections along with M. leprae in endemic areas like India.

Acyl-coenzyme A synthetases (ACSs) catalyze the fundamental, initial reaction in fatty acid metabolism. "Activation" of fatty acids by thioesterification to CoA allows their participation in both anabolic and catabolic pathways. The availability of the sequenced human genome has facilitated the investigation of the number of ACS genes present. Using two conserved amino acid sequence motifs to probe human DNA databases, 26 ACS family genes/proteins were identified. ACS activity in either humans or rodents was demonstrated previously for 20 proteins, but 6 remain candidate ACSs. For two candidates, cDNA was cloned, protein was expressed in COS-1 cells, and ACS activity was detected. Amino acid sequence similarities were used to assign enzymes into subfamilies, and subfamily assignments were consistent with acyl chain length preference. Four of the 26 proteins did not fit into a subfamily, and bootstrap analysis of phylograms was consistent with evolutionary divergence. Three additional conserved amino acid sequence motifs were identified that likely have functional or structural roles. The existence of many ACSs suggests that each plays a unique role, directing the acyl-CoA product to a specific metabolic fate. Knowing the full complement of ACS genes in the human genome will facilitate future studies to characterize their specific biological functions.

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank, and sequence analysis tool BLAST (basic local alignment search tool). However, NCBI integrates many types of biomolecular data from a variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez System. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap, and UniGene DDD (found via UniGene Homepage). Genome Project and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid, and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

A One-Step, Real-Time PCR Assay for Rapid Detection of Rhinovirus

The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but indicate hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez and PubMed, as well as structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge. © 2017 by John Wiley & Sons, Inc.

The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user-friendliness. Beginner and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNA, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez, PUBMED, structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge.

Hookworms are blood-feeding intestinal parasites of mammalian hosts and are one of the major human ailments affecting approximately 600 million people worldwide. These parasites form an intimate association with the host and are able to avoid vigorous immune responses in many ways including skewing of the response phenotype to promote parasite survival and longevity. The primary interface between the parasite and the host is the excretory/secretory component, a complex mixture of proteins, carbohydrates, and lipids secreted from the surface or oral openings of the parasite. The composition of this complex mixture is for the most part unknown but is likely to contain proteins important for the parasitic lifestyle and hence suitable as drug or vaccine targets. Using a strategy combining the traditional technology of one-dimensional SDS-PAGE and the newer fractionation technology of OFFGEL electrophoresis we identified 105 proteins from the excretory/secretory products of the blood-feeding stage of the dog hookworm, Ancylostoma caninum. Highly represented among the identified proteins were lectins, including three C-type lectins and three beta-galactoside-specific S-type galectins, as well as a number of proteases belonging to the three major classes found in nematodes, aspartic, cysteine, and metalloproteases. Interestingly 28% of the identified proteins were homologous to activation-associated secreted proteins, a family of cysteine-rich secreted proteins belonging to the sterol carrier protein/Tpx-1/Ag5/PR-1/Sc-7 (TAPS) superfamily. Thirty-four of these proteins were identified suggesting an important role in host-parasite interactions. Other protein families identified included hyaluronidases, lysozyme-like proteins, and transthyretin-like proteins. This work identified a suite of proteins important for the parasitic lifestyle and provides new insight into the biology of hookworm infection.

Basic Local Alignment Search Tool (BLAST) is an essential algorithm that researchers use for sequence alignment analysis. The National Center for Biotechnology Information (NCBI)-BLAST application is the most popular implementation of the BLAST algorithm. It can run on a single multithreading node. However, the volume of nucleotide and protein data is fast growing, making single node insufficient. It is more and more important to develop high-performance computing solutions, which could help researchers to analyze genetic data in a fast and scalable way. This article presents execution of the BLAST algorithm on high performance computing (HPC) clusters and supercomputers in a massively parallel manner using thousands of processors. The Parallel Computing in Java (PCJ) library has been used to implement the optimal splitting up of the input queries, the work distribution, and search management. It is used with the nonmodified NCBI-BLAST package, which is an additional advantage for the users. The result application-PCJ-BLAST-is responsible for reading sequence for comparison, splitting it up and starting multiple NCBI-BLAST executables. Since I/O performance could limit sequence analysis performance, the article contains an investigation of this problem. The obtained results show that using Java and PCJ library it is possible to perform sequence analysis using hundreds of nodes in parallel. We have achieved excellent performance and efficiency and we have significantly reduced the time required for sequence analysis. Our work also proved that PCJ library could be used as an effective tool for fast development of the scalable applications.