ProtRepeatsDB: a database of amino acid repeats in genomes

BACKGROUND: Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. DESCRIPTION: ProtRepeatsDB (v1.2) consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO) annotation IDs and regular expressions (REGEXP) describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. CONCLUSION: ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific repeat markers, interspecies variations and polymorphism

Basic fibroblast growth factor modulates cell cycle of human umbilical cord-derived mesenchymal stem cells.

Background: Mesenchymal stem cells (MSC) have great potential in regenerative medicine, immunotherapy and gene therapy due to their unique properties of self-renewal, high plasticity, immune modulation and ease for genetic modification. However, production of MSC at sufficient clinical scale remains an issue as in vitro generation of MSC inadequately fulfils the demand with respect to patients. Objectives: This study has aimed to establish optimum conditions to generate and characterize MSC from human umbilical cord (UC-MSC). Materials and methods: To optimize MSC population growth, basic fibroblast growth factor (bFGF) was utilized in culture media. Effects of bFGF on expansion kinetics, cell cycle, survival of UC-MSC, cytokine secretion, expression of early stem-cell markers and immunomodulation were investigated. Results: bFGF supplementation profoundly enhanced UC-MSC proliferation by reducing population doubling time without altering immunophenotype and immunomodulatory function of UC-MSC. However, cell cycle studies revealed that bFGF drove the cells into the cell cycle, as a higher proportion of cells resided in S phase and progressed into M phase. Consistent with this, bFGF was shown to promote expression of cyclin D proteins and their relevant kinases to drive UC-MSC to transverse cell cycle check points, thus, committing the cells to DNA synthesis. Furthermore, supplementation with bFGF changed the cytokine profiles of the cells and reduced their apoptotic level. Conclusion: Our study showed that bFGF supplementation of UC-MSC culture enhanced the cells' growth kinetics without compromising their nature

A SURVEY OF IRRIGATION PRACTICES FOR SUGAR CANE IN MAURITIUS

Abstract Irrigation is vital in subhumid areas to sustain economic production of sugar cane. It is also important input data for a GIs database for sugar cane land management. A survey was conducted in Mauritius in 1999 to collect data on irrigation practices and irrigation systems in use. The objectives were, inter alia, to provide up to date information on irrigation status in the sugar industry and allow studies on yield relationship to land characteristics for re-assessment of land suitability. Valuable statistics on the distribution and practices of irrigation were derived and a map was also prepared. Twenty two per cent of the total cane area in Mauritius was irrigated, the three main irrigation systems being overhead, drip (trickle) and surface. Low-pressure overhead irrigation systems, such as the centre pivot and dragline, were gradually replacing high-pressure overhead systems

A novel 13 residue acyclic peptide from the marine snail, Conus monile, targets potassium channels

A novel 13-residue peptide Mo1659 has been isolated from the venom of a vermivorous cone snail, Conus monile. HPLC fractions of the venom extract yielded an intense UV absorbing fraction with a mass of 1659 Da. De novo sequencing using both matrix assisted laser desorption and ionization and electrospray MS/MS methods together with analysis of proteolytic fragments successfully yielded the amino acid sequence, FHGGSWYRFPWGY-NH2. This was further confirmed by comparison with the chemically synthesized peptide and by conventional Edman sequencing. Mo1659 has an unusual sequence with a preponderance of aromatic residues and the absence of apolar, aliphatic residues like Ala, Val, Leu, and Ile. Mo1659 has no disulfide bridges distinguishing it from the conotoxins and bears no sequence similarity with any of the acyclic peptides isolated thus far from the venom of cone snails. Electrophysiological studies on the effect of Mo1659 on measured currents in dorsal root ganglion neurons suggest that the peptide targets non-inactivating voltage-dependent potassium channels

Polymorphisms in pattern recognition receptor genes of indigenous and White Leghorn breeds of chicken

Functional polymorphisms in pattern recognition receptors (PRRs) modulate innate immunity and play a crucial role in resistance or susceptibility to diseases. The present study was carried out to explore polymorphic patterns in the coding sequences of PRR genes TLR3, TLR1LA (TLRs), MDA5, LGP2 (RLRs) and NOD1 (NLR) in chicken breeds of India, namely Ghagus (GH), Nicobari (NB) and the exotic White Leghorn (WLH) breed. Out of 209 SNPs observed in five genes among three breeds, 117 were synonymous (Syn) and 92 were non-synonymous (NS) SNPs. In TLR genes the highest polymorphism was observed in NB (16, 28) compared to GH (14, 16) and WLH (13, 19) breeds. In the MDA5 gene the highest polymorphism was observed in GH (12) compared to NB (eight) and WLH (four) breeds. However, an almost similar level of polymorphism was observed in the LGP2 gene among the three breeds. In the NOD1 gene, the highest polymorphism was observed in NB (27), followed by WLH (11) and GH (10) breeds. The overall highest number of SNPs was observed in NB (90), followed by GH (62) and the WLH (57) breed. With regard to variation in polymorphism among different classes of PRRs, the study revealed the highest polymorphism in TLRs compared to NOD1 and the RLR class of PRRs. Further, the domain locations of various Syn and NS SNPs in each PRR among the three breeds were identified. In silico analysis of NS SNPs revealed that most of them had a neutral effect on protein function. However, two each in TLR1LA and LGP2 and one in the MDA5 gene were predicted to be deleterious to protein function. The present study unravelled extensive polymorphism in the coding sequences of the TLR and NLR class of PRR genes, and the polymorphism was higher in indigenous chicken breeds.</p

The ORNATE India project: Building research capacity and capability to tackle the burden of diabetic retinopathy-related blindness in India

The ORNATE India project is an interdisciplinary, multifaceted United Kingdom (UK)–India collaborative study aimed to build research capacity and capability in India and the UK to tackle the burden of diabetes-related visual impairment. For 51 months (October 2017–December 2021), this project built collaboration between six institutions in the UK and seven in India, including the Government of Kerala. Diabetic retinopathy (DR) screening models were evaluated in the public system in Kerala. An epidemiological study of diabetes and its complications was conducted through 20 centers across India covering 10 states and one union territory. The statistical analysis is not yet complete. In the UK, risk models for diabetes and its complications and artificial intelligence-aided tools are being developed. These were complemented by joint studies on various aspects of diabetes between collaborators in the UK and India. This interdisciplinary team enabled increased capability in several workstreams, resulting in an increased number of publications, development of cost-effective risk models, algorithms for risk-based screening, and policy for state-wide implementation of sustainable DR screening and treatment programs in primary care in Kerala. The increase in research capacity included multiple disciplines from field workers, administrators, project managers, project leads, screeners, graders, optometrists, nurses, general practitioners, and research associates in various disciplines. Cross-fertilization of these disciplines enabled the development of several collaborations external to this project. This collaborative project has made a significant impact on research capacity development in both India and the UK

Cotton waste research follows the effect of pre-treatment and the observation of physical appearance

This paper aims to evaluate the waste cotton quality and its commercialization. The recycled cotton demand seems to be increased day by day: although the lower quality of the resulting items is the biggest barrier to cotton recycling. A thorough analysis of recycled cotton processes is therefore necessary from separation/shredding to completion. To that end, textile wastes made of pre-consumer cotton were systematically collected from the spinning mill. After pretreatment of cotton waste cellulose by caustic soda, alkali, and detergent in 100°C temperature for 30 minutes have produced white clean cotton. Following the next process by sodium hydroxide and isopropyl alcohol must produce Carboxymethyl Cellulose (CMC). CMC has big use in Textile printing, finishing, and warp sizing even in Ice-cream and food baking industry. Recent success stories will be addressed with the steady cotton processing to altering the properties of cell wall cotton and cotton fiber. The prospects of conducting experiments of waste cotton and checking the properties of treated cotton have a great value in the production of commercial products and the results relived that the value addition of waste cotton is a very easy method

Enhancement of the heat transfer in radiator with louvered fin by using graphene-based hybrid nanofluids

Newly developed hybrid nanofluids can enhance heat transfer performance of various automotive appliances. Improved thermophysical properties of this hybrid nanoparticles when used as coolants will enhance the effectiveness of the car radiators with improved engine cooling system. The present study involves the simulation-based analysis of thermal enhancement of Graphene based Hybrid Nanofluids in a Car radiator. System analysis is performed considering single tube component in the radiator for pattern development. CFD analysis is conducted using ANSYS FLUENT module. Graphene/Crystal Nanocellulose hybrid (Graphene + CNC) nanoparticles are suspended in water & ethylene glycol base fluids (40:60) at 0.01%,0.05%,0.1% &0.2 % volume concentration considering at 3-7 LPM inlet mass flow rate. The effect of various volume concentration, inlet temperature and flow rate on Pressure, Enthalpy, Entropy, Heat transfer coefficient, and Heat transfer rate has been examined by simulation. The results indicate that when using a Louvered fin in a radiator, Maximum enhancement of 60% in heat transfer rate, 53% increase of heat transfer coefficient, 65% increase in pressure are achieved for Graphene with CNC hybrid nanofluids when compared with Graphene based nanofluids. Using this type of hybrid coolants along with louvered fin in radiator can significantly improve the heat transfer performance of radiators

Applications of graphene nanomaterials in energy storage—A state-of-art short review

The study presents the usage behavior of graphene in the energy field. Graphene has been comprehensively studied in the energy-related application due to higher conductivity and mechanical flexibility. The architecture of graphene permits it to strengthen and facilitate its application in the energy arena. Herein, the application of graphene in various energy storages such as fuel cells, dye-sensitized solar cells, batteries, nuclear power plants, and thermoelectric has been studied neatly. Graphene reacts towards these substances chemically, mechanically, and electrically to a great extend and appears with the excellent output of these objects. In the future graphene could be applied to the others field of energy and science successfully

Amorphous carbon film deposition on inner surface of tubes using atmospheric pressure pulsed filamentary plasma source

Uniform amorphous carbon film is deposited on the inner surface of quartz tube having the inner diameter of 6 mm and the outer diameter of 8 mm. A pulsed filamentary plasma source is used for the deposition. Long plasma filaments (~ 140 mm) as a positive discharge are generated inside the tube in argon with methane admixture. FTIR-ATR, XRD, SEM, LSM and XPS analyses give the conclusion that deposited film is amorphous composed of non-hydrogenated sp2 carbon and hydrogenated sp3 carbon. Plasma is characterized using optical emission spectroscopy, voltage-current measurement, microphotography and numerical simulation. On the basis of observed plasma parameters, the kinetics of the film deposition process is discussed