Construction and Functional Analysis of the Recombinant Bacteriocins Weissellicin-MBF from Weissella confusa MBF8-1

2020 ◽  
Vol 22 (1) ◽  
pp. 115-122
Author(s):  
Amarila Malik ◽  
Elita Yuliantie ◽  
Nisa Yulianti Suprahman ◽  
Theresa Linardi ◽  
Angelina Wening Widiyanti ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Large Scale ◽  
Micrococcus Luteus ◽  
Affinity Column ◽  
Gene Expressions ◽  
His Tag ◽  
Recombinant Peptides ◽  
Weak Activity ◽  
Potential Alternative ◽  
Weissella Confusa

Background: Bacteriocins (Bac1, Bac2, and Bac3) from Weissella confusa MBF8-1, weissellicin- MBF, have been reported as potential alternative substances as well as complements to the existing antibiotics against many antimicrobial-resistant pathogens. Previously, the genes encoded in the large plasmid, pWcMBF8-1, and the spermicidal activity of their synthetic peptides, originally discovered Indonesia, have been studied. Three synthetic bacteriocins peptides of this weissellicin-MBF have been reported for their potential activities, i.e. antibacterial and spermicidal. Objective: The aim of this study was to construct the recombinant Bacteriocin (r-Bac) genes, as well as to investigate the gene expressions and their functional analysis. Method: Here, the recombinant Bacteriocin (r-Bac) genes were constructed and the recombinant peptides (r-Bac1, r-Bac2, and r-Bac3) in B. subtilis DB403 cells were produced on a large scale. After purification, using the His-tag affinity column, their potential bioactivities were measured as well as their antibacterial minimum inhibitory concentrations against Leuconostoc mesenteroides and Micrococcus luteus, were determined. Results: Pure His-tag-recombinant Bac1, Bac2, and Bac3 were obtained and they could inhibit the growth of L. mesenteroides and M. luteus. Conclusion: The recombinant bacteriocin could be obtained although with weak activity in inhibiting gram-positive bacterial growth.

scholarly journals Discovering Distinct Patterns in Gene Expression Profiles

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Li Teng ◽  
Laiwan Chan
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Clustering Methods ◽  
Gene Expressions ◽  
Real Gene ◽  
Large Scale Dataset ◽  
Coexpressed Genes

SummaryTraditional analysis of gene expression profiles use clustering to find groups of coexpressed genes which have similar expression patterns. However clustering is time consuming and could be diffcult for very large scale dataset. We proposed the idea of Discovering Distinct Patterns (DDP) in gene expression profiles. Since patterns showing by the gene expressions reveal their regulate mechanisms. It is significant to find all different patterns existing in the dataset when there is little prior knowledge. It is also a helpful start before taking on further analysis. We propose an algorithm for DDP by iteratively picking out pairs of gene expression patterns which have the largest dissimilarities. This method can also be used as preprocessing to initialize centers for clustering methods, like K-means. Experiments on both synthetic dataset and real gene expression datasets show our method is very effective in finding distinct patterns which have gene functional significance and is also effcient.

scholarly journals Ice sheet flow with thermally activated sliding. Part 2: the stability of subtemperate regions

2019 ◽  
Vol 475 (2231) ◽  
pp. 20190411
Author(s):  
E. Mantelli ◽  
C. Schoof
Keyword(s):  
Melting Point ◽  
Large Scale ◽  
Thermal Structure ◽  
Ice Sheet ◽  
Temperature Dependent ◽  
Length Scales ◽  
Thermally Activated ◽  
Potential Alternative ◽  
The Stability ◽  
Alternative Structure

The onset of sliding in ice sheets may not take the form of a sharp boundary between regions at the melting point, in which sliding is permitted, and regions below that temperature, in which there is no slip. Such a hard switch leads to the paradox of the bed naturally wanting to refreeze as soon as sliding has commenced. A potential alternative structure is a region of subtemperate sliding. Here temperatures are marginally below the melting point and sliding velocities slower than they would if the bed was fully temperate. Rather than being controlled by a standard sliding law, sliding velocities are then constrained by the need to maintain energy balance. This thermal structure arises in temperature-dependent sliding laws in the limit of strong sensitivity to temperature. Here, we analyse the stability of such subtemperate regions, showing that they are subject to a set of instabilities that occur at all length scales between ice thickness and ice sheet length. The fate of these instabilities is to cause the formation of patches of frozen bed, raising the possibility of highly complicated cold-to-temperate transitions with spatial structures at short length scales that cannot be resolved in large-scale ice sheet simulation codes.

Preparation of a fluorescent (anthracene labeled) cardiolipin on a large scale using the metabolic machinery of the bacterium Micrococcus luteus

1990 ◽  
Vol 68 (1) ◽  
pp. 373-376 ◽  
Author(s):  
E. Pérochon ◽  
J. de Bony ◽  
J. F. Tocanne
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
Micrococcus Luteus ◽  
High Rate ◽  
Nonanoic Acid

Micrococcus luteus bacterium has been used as a tool for the preparation of a fluorescent (anthracene labeled) cardiolipin by a method involving two steps. First, 9-(2-anthryl)nonanoic acid is incorporated into the lipids of the bacterium by usual metabolic pathways; then phosphatidylglycerol, a major lipid in this bacterium, is converted into cardiolipin by endogeneous cardiolipin synthetase. It is shown that cardiolipin synthetase transforms anthracene–phosphatidylglycerol into anthracene–cardiolipin at a high rate. The method can be extended to the synthesis of cardiolipin molecules bearing other hydrophobic marker groups.Key words: cardiolipin, fluorescence, biosynthesis, Micrococcus luteus.

scholarly journals Recent Advancements in Crystalline Pb-Free Halide Double Perovskites

Crystals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 62 ◽  
Author(s):  
Muhammad Usman ◽  
Qingfeng Yan
Keyword(s):  
Large Scale ◽  
Optoelectronic Properties ◽  
Double Perovskites ◽  
Ambient Conditions ◽  
Photoelectric Properties ◽  
Potential Alternative ◽  
High Carrier Mobility ◽  
Halide Perovskites ◽  
Synthesis Composition ◽  
Lead Halide

Lead halide perovskites have gained more and more attention because of their ease of synthesis and excellent photoelectric properties including a large absorption coefficient, long carrier lifetime, long carrier diffusion length, and high carrier mobility. However, their toxicity, instability, and phase degradation in ambient environments impede their large-scale applications. To address these concerns, it is desirable to find stable alternative halide perovskites without toxicity and with comparable optoelectronic properties to lead-based perovskites. Over the years, a considerable number of lead-free halide perovskites have been added to this family of materials, including A2B’B’’X6, A2BX6, and A3B2X9 type perovskites. Among these, double perovskites with the general formula A2B’B’’X6 are deemed to be a potential alternative to lead halide perovskites as they possess good stability under ambient conditions and excellent optoelectronic properties. In this review, recent progress in exploring Pb-free halide double perovskites is highlighted. The synthesis, composition-tuning, physical properties, and applications of representative 3D, 2D, and nanocrystal A2B’B’’X6 double perovskites are introduced. In addition, perspectives about current challenges and solutions in this field are also provided.

scholarly journals FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0126967 ◽  
Author(s):  
Takeru Uchiyama ◽  
Mitsuru Irie ◽  
Hiroshi Mori ◽  
Ken Kurokawa ◽  
Takuji Yamada
Keyword(s):  
Functional Analysis ◽  
Large Scale ◽  
Omics Data

scholarly journals A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome

2003 ◽  
Vol 100 (17) ◽  
pp. 9918-9922 ◽  
Author(s):  
J. Hansen ◽  
T. Floss ◽  
P. Van Sloun ◽  
E.-M. Fuchtbauer ◽  
F. Vauti ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Large Scale ◽  
Mouse Genome

Visualization of large-scale correlations in gene expressions

2004 ◽  
Vol 4 (4) ◽  
Author(s):  
KasperAstrup Eriksen ◽  
Michael H�rnquist ◽  
Kim Sneppen
Keyword(s):  
Large Scale ◽  
Gene Expressions

scholarly journals Proteomic Characterization of Primary and Metastatic Prostate Cancer Reveals Reduced Proteinase Activity in Aggressive Tumors

2021 ◽  
Author(s):  
Qing Kay Li ◽  
Jing Chen ◽  
Yingwei Hu ◽  
Naseruddin Hoti ◽  
Stefani N Thomas ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Large Scale ◽  
Validation Cohort ◽  
Protein Profile ◽  
Specific Antigen ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Dipeptidyl Peptidase 4 ◽  
Molecular Abnormalities ◽  
Substrate Peptide

Abstract BackgroundProstate cancer (PCa) is a heterogeneous group of tumors with variable clinical courses. Clinically, it is critical to separate and treat aggressive PCa (AG) from non-aggressive PCa (NAG). Although recent genomic studies have identified a spectrum of molecular abnormalities associated with PCa, it is still challenge to separate AG from NAG. To better understand the functional consequence of PCa progression and the unique features of AG from NAG, we studied proteomic signatures of primary AG, NAG and metastatic PCa.Methodes39 PCa and 10 benign prostate controls in discovery cohort and 57 PCa in independent-collected validation cohort were analyzed using data-independent acquisition (DIA) SWATH–MS platform. Proteins with the highest variances (top 500 proteins) were annotated for the pathway enrichment analysis. Functional analysis of differentially expressed proteins in NAG and AG was performed. Data was further validated using validation cohort, as well as by comparison with TCGA mRNA expression and immnunochemistry on PCa tissue microarray (TMA).Results4,415 proteins were identified in the tumor and benign control tissues, including 158 up-regulated and 116 down-regulated proteins in AG tumors. A functional analysis of tumor-associated proteins revealed the reduced expression of several proteinases, including dipeptidyl peptidase 4 (DPP4), carboxypeptidase E (CPE) and prostate specific antigen (KLK3) in AG and metastatic PCa. A targeted analysis using SWATH data further identified that the reduced expression of DPP4 was associated with the accumulation of DPP4 substrates in AG tumors, including the reduced ratio of DPP4 cleaved peptide to intact substrate peptide. Findings were further validated using independent-collected cohort, by comparison with TCGA mRNA data, and the immunochemical stains of our tumor microarray (TMA).ConclusionsOur study is the first large-scale proteomics analysis of PCa tissue using DIA SWATH-MS platform. It not only provides an interrogative proteomic signature of PCa subtypes, but also indicates critical roles of certain proteinases, especially DPP4, in PCa progression. The spectrum map and protein profile generated in the study can be used to investigate potential biological mechanisms involved in the PCa progression as well as for the development of a clinical assay to distinguish aggressive from indolent PCa.

scholarly journals A closer look at an eroded dune landscape: first functional insights into the Federmessergruppen site of Lommel-Maatheide

2021 ◽  
Author(s):  
Sonja Tomasso ◽  
Dries Cnuts ◽  
Justin Coppe ◽  
Marijn Van Gils ◽  
Ferdi Geerts ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Microscopic Examination ◽  
Large Scale ◽  
Late Glacial ◽  
Sand Ridge ◽  
Functional Studies ◽  
Depositional Processes ◽  
Unique Possibility ◽  
Northern Edge ◽  
The Impact

The vast Federmessergruppen site of Lommel-Maatheide, which is located in the Campine region (Northern Belgium), revealed the presence of numerous Final Palaeolithic concentrations situated on a large Late Glacial sand ridge on the northern edge of a contemporary lake. This situation offers a unique possibility for a large-scale functional analysis in order to understand the occupation of such a Late Glacial dune landscape. The variable preservation state of the lithic artefacts permitted to evaluate in detail the impact of post-depositional processes on the potential of functional studies. Also, the impact of excavation protocols on the preservation of wear traces and residues was evaluated, in particular the impact of mechanical sieving. The integrated functional research that included the microscopic examination of wear traces, fractures and residues, next to experimentation, permitted the identification of a range of crafting and hunting activities, thereby demonstrating the potential of such assemblages for obtaining innovative insights into Late Glacial site dynamics in spite of a varying preservation state.

Sign in / Sign up

Export Citation Format

Share Document