NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture

2015 ◽  
Author(s):  
Arun Seetharam ◽  
Antonio Gomez ◽  
Catherine M. Purcell ◽  
John R. Hyde ◽  
Philip D. Blood ◽  
...  
Keyword(s):  
Sustainable Aquaculture ◽  
Ncbi Blast

Efficiency of β-glucan utilisation in fish culture

2019 ◽  
Vol 19 (4A) ◽  
pp. 167-174
Author(s):  
Do Huu Hoang
Keyword(s):  
Human Health ◽  
Stress Resistance ◽  
Antibiotic Use ◽  
Fish Culture ◽  
Growth Promoter ◽  
Sustainable Aquaculture ◽  
Major Benefit

In the last three decades aquaculture is a rapidly developing sector worldwide and antibiotics are used popularly as growth promoter. Antibiotic use was banned because research proved that antibiotic has caused many effects on environment and human health. Therefore, finding antibiotic alternatives is the first priority. The most prospect products today are probiotic and prebiotic. β-glucan is one of the immunostimulants which showed a variety of benefits to the health of many aquaculture species. In this paper only the results of β-glucan, a kind of prebiotic supplied in aquaculture, were summarized. The major benefit of β-glucan are to boost growth, to reduce mortality, to enhance tolerance or stress resistance to environmental or pathogen challenges. Although the applications of β-glucan are popular worldwide, its use in aquaculture in Vietnam is still limited. This paper provides an important reference for β-glucan utilisation which may help to develop a sustainable aquaculture in Vietnam.

Sustainable Aquaculture

2004 ◽  
Vol 33 (2) ◽  
pp. 796
Author(s):  
Junda Lin
Keyword(s):  
Sustainable Aquaculture

IMPLEMENTATION OF SUSTAINABLE AQUACULTURE AS A MODEL OF SATO UMI TO IMPROVE PRODUCTIVITY WITHIN COASTAL AREA OF INDONESIA

2017 ◽  
Author(s):  
Suhendar I Sachoemar ◽  
Suhendar I Sachoemar ◽  
Tetsuo Yanagi ◽  
Tetsuo Yanagi ◽  
Mitsutaku Makino ◽  
...  
Keyword(s):  
Coastal Area ◽  
Sustainable Aquaculture ◽  
The South ◽  
West Java ◽  
The Public ◽  
Central Java ◽  
South Sulawesi ◽  
Similar Program ◽  
Technology Dissemination

The development of sustainable model of aquaculture by applying Sato Umi concept within coastal area of Indonesia has expanded from the center of first experiment in the northern coastal area of west Java to central Java (western Indonesia) and Bantaeng in the South Sulawesi of central Indonesia. The similar program has also been proposed for Maluku Province in the eastern part of Indonesia. In the next 5 years, Indonesia is developing the Techno Parks Program in some areas, in which aquaculture and fisheries activities development on the base of Sato Umi concept in the coastal area are involves in this program. The development of Techno Parks are directed as a center application of technology to stimulate the economy in the regency, and a place of training, apprenticeship, technology dissemination center, and center business advocacy for the public. Hopely, Sato Umi concept that has a similar spirit with Techno Park can be applied to support the implementation of Techno Park program in Indonesia

scholarly journals The Gene Regulatory Roles of Herbal Extracts on the Growth, Immune System, and Reproduction of Fish

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2167
Author(s):  
Ehsan Ahmadifar ◽  
Hamideh Pourmohammadi Fallah ◽  
Morteza Yousefi ◽  
Mahmoud A. O. Dawood ◽  
Seyed Hossein Hoseinifar ◽  
...  
Keyword(s):  
Immune System ◽  
Mode Of Action ◽  
Medicinal Herbs ◽  
Environmental Stressors ◽  
Fish Diet ◽  
Sustainable Aquaculture ◽  
Herbal Supplements ◽  
Aquatic Animals ◽  
Gene Regulatory

The crucial need for safe and healthy aquatic animals obligates researchers in aquaculture to investigate alternative and beneficial additives. Medicinal herbals and their extracts are compromised with diverse effects on the performances of aquatic animals. These compounds can affect growth performance and stimulate the immune system when used in fish diet. In addition, the use of medicinal herbs and their extracts can reduce oxidative stress induced by several stressors during fish culture. Correspondingly, aquatic animals could gain increased resistance against infectious pathogens and environmental stressors. Nevertheless, the exact mode of action where these additives can affect aquatic animals’ performances is still not well documented. Understanding the mechanistic role of herbal supplements and their derivatives is a vital tool to develop further the strategies and application of these additives for feasible and sustainable aquaculture. Gene-related studies have clarified the detailed information on the herbal supplements’ mode of action when administered orally in aquafeed. Several review articles have presented the potential roles of medicinal herbs on the performances of aquatic animals. However, this review article discusses the outputs of studies conducted on aquatic animals fed dietary, medicinal herbs, focusing on the gene expression related to growth and immune performances. Furthermore, a particular focus is directed to the expected influence of herbal supplements on the reproduction of aquatic animals.

scholarly journals The Secreted Protein C10orf118 Is a New Regulator of Hyaluronan Synthesis Involved in Tumour-Stroma Cross-Talk

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1105
Author(s):  
Ilaria Caon ◽  
Maria Luisa D’Angelo ◽  
Barbara Bartolini ◽  
Elena Caravà ◽  
Arianna Parnigoni ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Patient Survival ◽  
Breast Tumour ◽  
Surrounding Area ◽  
Uncharacterized Protein ◽  
Stromal Fibroblasts ◽  
Tumour Cell Lines ◽  
Cell Niche ◽  
Hyaluronan Synthase 2 ◽  
Ncbi Blast

Interaction between cancer cells and their microenvironment is central in defining the fate of cancer development. Tumour cells secrete signals (cytokines, chemokines, growth factors) that modify the surrounding area, while the niche supplies structures and activities necessary for tumour maintenance and growth. Hyaluronan (HA) is a glycosaminoglycan that constitute cancer cell niche and is known to influence tumour functions such as proliferation, migration and neoangiogenesis. The knowledge of the factors regulating HA synthesis and size is crucial in understanding the mechanisms sustaining tumour development. Here we show that a yet uncharacterized protein secreted by breast tumour cell lines, named c10orf118 (accession number NM_018017 in NCBI/BLAST, and Q7z3E2 according to the Uniprot identifier), with a predicted length of 898 amino acids, can induce the secretion of HA by stromal fibroblasts through the up-regulation of the hyaluronan synthase 2 gene (HAS2). Intracellularly, this protein is localized in the Golgi apparatus with a possible role in vesicle maturation and transport. The expression of c10orf118 was verified in breast cancer patient specimens and was found to be associated with the presence of estrogen receptor that characterizes a good patient survival. We suggest c10orf118 as a new player that influences the HA amount in breast cancer microenvironment and is associated with low aggressiveness of cancer.

scholarly journals PSV-37 Reemergence of cyathostomins species demonstrates anthelmintic resistance following drug administration in horses

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 335-335
Author(s):  
Alexa C Johnson ◽  
Amy S Biddle
Keyword(s):  
Anthelmintic Resistance ◽  
Macrocyclic Lactones ◽  
Number Of Species ◽  
Molecular Approaches ◽  
Pyrantel Pamoate ◽  
Drug Classes ◽  
Blast Database ◽  
Resistance Patterns ◽  
Near Future ◽  
Ncbi Blast

Abstract Arbitrary administration of anthelmintics to control equine gastrointestinal worms has led to increased resistance to the three broad-spectrum drug classes; benzimidazoles, tetrahydropyrimidines, and macrocyclic lactones. With little promise of new drug classes to target cyathostomins being introduced to the market in the near future, anthelmintic drugs must be administered judiciously to prevent complete anthelmintic parasite resistance. The objective of this study is to determine the reemergence rate of cyathostomins following three commercial horse dewormers during summer. Nine horses housed at two locations were enrolled to the study and was repeated June–September through 2017–2019. Horses were removed from the study if sequencing failed due to low egg recovery for more than 50% of the timepoints. Ivermectin (macrocyclic lactones; n = 6), Moxidectin (macrocyclic lactones; n = 8) and Strongid (pyrantel pamoate; n = 8) were administered to horses and fecal samples were collected every 14d for 98d. Samples were tested using fecal egg counts with a modified McMaster technique and 18S rRNA profiling of the V5.8 and ITS1 regions. Sequences were clustered and taxonomy was assigned against a custom NCBI Blast+ database with the aligned sequences of 19 cyathostomins. Data were analyzed using presence/absence methods in R studio. Treatment and Day significantly impacted the average number of species present (P < 0.001). Moxidectin had the lowest number of species present followed by Strongid then Ivermectin (7.14, 10.17, 11.09, respectively). Equine shedder status had no effect on the average number of species present (P > 0.05). Six species, CO. labiatus, CS. catinatum, CY. auriculatus, CY. elongatus, CT. goldi and CT. longibursatus, showed resistance to the three treatments (P > 0.05). Moxidectin was the most effective at eradicating cyathostomins infestations (P < 0.05). Identifying resistance patterns at the species level will enable mechanistic molecular approaches to determine anthelmintic resistance in cyathostomins.

scholarly journals Efficient alternatives to PSI-BLAST

2012 ◽  
Vol 60 (3) ◽  
pp. 495-505
Author(s):  
M. Startek ◽  
S. Lasota ◽  
M. Sykulski ◽  
A. Bułak ◽  
L. Noé ◽  
...  
Keyword(s):  
Amino Acid ◽  
Finite Automata ◽  
Protein Family ◽  
Homology Search ◽  
Amino Acid Residues ◽  
Protein Alignment ◽  
Substitution Model ◽  
Hierarchical Tree ◽  
Context Specific ◽  
Ncbi Blast

Abstract In this paper we present two algorithms that may serve as efficient alternatives to the well-known PSI BLAST tool: SeedBLAST and CTX-PSI Blast. Both may benefit from the knowledge about amino acid composition specific to a given protein family: SeedBLAST uses the advisedly designed seed, while CTX-PSI BLAST extends PSI BLAST with the context-specific substitution model. The seeding technique became central in the theory of sequence alignment. There are several efficient tools applying seeds to DNA homology search, but not to protein homology search. In this paper we fill this gap. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The seeds are represented by deterministic finite automata (DFAs) and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. The contextual substitution model has been proven to increase sensitivity of protein alignment. In this paper we perform a next step in the contextual alignment program. We announce a contextual version of the PSI-BLAST algorithm, an iterative version of the NCBI-BLAST tool. The experimental evaluation has been performed demonstrating a significantly higher sensitivity compared to the ordinary PSI-BLAST algorithm.

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