Publications by authors named "Tanaporn Uengwetwanit"

20 Publications

  • Page 1 of 1

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of .

Life (Basel) 2021 Aug 23;11(8). Epub 2021 Aug 23.

Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.

With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. Selecting an appropriate sequencing platform is undoubtedly crucial for the success of the research outcome, thus there is a need to compare these long-read sequencing platforms and evaluate them for specific research questions. This study aims to compare the performance of PacBio and ONT platforms for transcriptomic analysis by utilizing transcriptome data from three different tissues (hepatopancreas, intestine, and gonads) of the juvenile black tiger shrimp, . We compared three important features: (i) main characteristics of the sequencing libraries and their alignment with the reference genome, (ii) transcript assembly features and isoform identification, and (iii) correlation of the quantification of gene expression levels for both platforms. Our analyses suggest that read-length bias and differences in sequencing throughput are highly influential factors when using long reads in transcriptome studies. These comparisons can provide a guideline when designing a transcriptome study utilizing these two long-read sequencing technologies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/life11080862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8399832PMC
August 2021

Insights Into Transcriptome Profiles Associated With Wooden Breast Myopathy in Broilers Slaughtered at the Age of 6 or 7 Weeks.

Front Physiol 2021 28;12:691194. Epub 2021 Jun 28.

National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, Thailand.

Transcriptomes associated with wooden breast (WB) were characterized in broilers at two different market ages. Breasts () were collected, 20-min postmortem, from male Ross 308 broilers slaughtered at 6 and 7 weeks of age. The breasts were classified as "non-WB" or "WB" based on palpation hardness scoring (non-WB = no abnormal hardness, WB = consistently hardened). Total RNA was isolated from 16 samples ( = 3 for 6 week non-WB, = 3 for 6 week WB; = 5 for 7 week non-WB, = 5 for 7 week WB). Transcriptome was profiled using a chicken gene expression microarray with one-color hybridization technique, and compared between non-WB and WB samples of the same age. Among 6 week broilers, 910 transcripts were differentially expressed (DE) (false discovery rate, FDR < 0.05). Pathway analysis underlined metabolisms of glucose and lipids along with gap junctions, tight junction, and focal adhesion (FA) signaling as the top enriched pathways. For the 7 week broilers, 1,195 transcripts were identified (FDR < 0.05) with regulation of actin cytoskeleton, mitogen-activated protein kinase (MAPK) signaling, protein processing in endoplasmic reticulum and FA signaling highlighted as the enriched affected pathways. Absolute transcript levels of eight genes (actinin-1 - , integrin-linked kinase - , integrin subunit alpha 8 - , integrin subunit beta 5 - , protein tyrosine kinase 2 - , paxillin - , talin 1 - , and vinculin - ) of FA signaling pathway were further elucidated using a droplet digital polymerase chain reaction. The results indicated that, in 6 week broilers, abundance in WB was greater than that of non-WB samples ( < 0.05). Concerning 7 week broilers, greater absolute levels of , , , and , accompanied with a reduced were found in WB compared with non-WB ( < 0.05). Transcriptional modification of FA signaling underlined the potential of disrupted cell-cell communication that may incite aberrant molecular events in association with development of WB myopathy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fphys.2021.691194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273767PMC
June 2021

Transcriptomic analysis of the black tiger shrimp (Penaeus monodon) reveals insights into immune development in their early life stages.

Sci Rep 2021 07 6;11(1):13881. Epub 2021 Jul 6.

National Center for Genetic Engineering and Biotechnology, National Science and Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120, Thailand.

With the rapid growth in the global demand, the shrimp industry needs integrated approaches for sustainable production. A high-quality shrimp larva is one of the crucial key requirements to maximize shrimp production. Survival and growth rates during larval development are often criteria to evaluate larval quality, however many aspects of gene regulation during shrimp larval development have not yet been identified. To further our understanding of biological processes in their early life, transcriptomic analysis of larval developmental stages (nauplius, zoea, mysis, and postlarva) were determined in the black tiger shrimp, Penaeus monodon using next-generation RNA sequencing. Gene clustering and gene enrichment analyses revealed that most of the transcripts were mainly related to metabolic processes, cell and growth development, and immune system. Interestingly, Spätzle and Toll receptors were found in nauplius stage, providing evidence that Toll pathway was a baseline immune system established in early larval stages. Genes encoding pathogen pattern-recognition proteins (LGBP, PL5-2 and c-type lectin), prophenoloxidase system (PPAE2, PPAF2 and serpin), antimicrobial peptides (crustin and antiviral protein), blood clotting system (hemolymph clottable protein) and heat shock protein (HSP70) were expressed as they developed further, suggesting that these immune defense mechanisms were established in later larval stages.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-93364-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8260638PMC
July 2021

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes.

Mol Ecol Resour 2021 Jul 16;21(5):1620-1640. Epub 2021 Mar 16.

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1755-0998.13357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8197738PMC
July 2021

Nutritional Properties and Oxidative Indices of Broiler Breast Meat Affected by Wooden Breast Abnormality.

Animals (Basel) 2020 Dec 2;10(12). Epub 2020 Dec 2.

National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand.

Wooden breast (WB) abnormality adversely impacts the quality of chicken meat and has been linked with oxidative stress. In this study, breast samples were taken from carcasses of 7-week-old Ross 308 broilers 20-min and 24-h postmortem. Five WB and seven non-WB control samples were assigned based on palpatory hardness (non-WB = no unusual characteristics and WB = focal or diffused hardness). WB exhibited lower contents of protein and the amino acids, i.e., isoleucine, leucine and valine, lighter surface color, lower shear force, greater drip loss and altered mineral profiles ( ≤ 0.05). Despite no difference in lipid oxidation, a greater degree of protein oxidation was found in the WB meat ( ≤ 0.05). Absolute transcript abundances of superoxide dismutase, hypoxia inducible factor 1 alpha and pyruvate dehydrogenase kinase 1 were greater in WB ( ≤ 0.05), whereas lactate dehydrogenase A expression was lower in WB ( ≤ 0.05). The findings support an association between oxidative stress and the altered nutritional and technological properties of chicken meat in WB.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ani10122272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759853PMC
December 2020

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform.

PeerJ 2020 13;8:e10340. Epub 2020 Nov 13.

Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.10340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668203PMC
November 2020

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp () with different growth performance.

PeerJ 2020 14;8:e9646. Epub 2020 Aug 14.

Microarray Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand.

Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal's growth performance. Here, we compared the bacterial profiles along with the shrimp's gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp () were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes ( and ) and Bacteroidetes (), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might contribute to different degrees of shrimp growth performance. A non-targeted metabolome analysis from shrimp intestines revealed different metabolic responsive patterns, in which the Top-weight shrimp contained significantly higher levels of short chain fatty acids, lipids and organic compounds than the Bottom-weight shrimp. The identified metabolites included those that were known to be produced by intestinal bacteria such as butyric acid, 4-indolecarbaldehyde and L-3-phenyllactic acid as well as those produced by shrimp such as acyl-carnitines and lysophosphatidylcholine. The functions of these metabolites were related to nutrient absorption and metabolisms. Our findings provide the first report utilizing multi-omics integration approach to investigate microbiota, metabolic and transcriptomics profiles of the host shrimp and their potential roles and relationship to shrimp growth performance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.9646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430268PMC
August 2020

Engineering of β-mannanase from Aspergillus niger to increase product selectivity towards medium chain length mannooligosaccharides.

J Biosci Bioeng 2020 Nov 26;130(5):443-449. Epub 2020 Jul 26.

Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand.

Mannooligosaccharides (MOSs) are one of the most commonly used biomass-derived feed additives. The effectiveness of MOS varies with the length of oligosaccharides, medium length MOSs such as mannotetraose and mannopentaose being the most efficient. This study aims at improving specificity of β-mannanase from Aspergillus niger toward the desirable product size through rational-based enzyme engineering. Tyr 42 and Tyr 132 were mutated to Gly to extend the substrate binding site, allowing higher molecular weight MOS to non-catalytically bind to the enzyme. Hydrolysis product content was analyzed by high-performance anion-exchange chromatography with pulsed amperometric detection. Instead of mannobiose, the enzyme variants yielded mannotriose and mannotetraose as the major products, followed by mannobiose and mannopentaose. Overall, 42% improvement in production yield of highly active mannotetraose and mannopentaose was achieved. This validates the use of engineered β-mannanase to selectively produce larger MOS, making them promising candidates for large-scale MOS enzymatic production process.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jbiosc.2020.07.001DOI Listing
November 2020

Transcriptional Profiles of Skeletal Muscle Associated With Increasing Severity of White Striping in Commercial Broilers.

Front Physiol 2020 16;11:580. Epub 2020 Jun 16.

National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, Thailand.

Development of the white striping (WS) abnormality adversely impacts overall quality of broiler breast meat. Its etiology remains unclear. This study aimed at exploring transcriptional profiles of broiler skeletal muscles exhibiting different WS severity to elucidate molecular mechanisms underlying the development and progression of WS. Total RNA was isolated from pectoralis major of male 7-week-old Ross 308 broilers. The samples were classified as mild ( = 6), moderate ( = 6), or severe ( = 4), based on number and thickness of the white striations on the meat surface. The transcriptome was profiled using a chicken gene expression microarray with one-color hybridization technique. Gene expression patterns of each WS severity level were compared against each other; hence, there were three comparisons: moderate vs. mild (C1), severe vs. moderate (C2), and severe vs. mild (C3). Differentially expressed genes (DEGs) were identified using the combined criteria of false discovery rate ≤ 0.05 and absolute fold change ≥1.2. Differential expression of 91, 136, and 294 transcripts were identified in C1, C2, and C3, respectively. There were no DEGs in common among the three comparisons. Based on pathway analysis, the enriched pathways of C1 were related with impaired homeostasis of macronutrients and small biochemical molecules with disrupted Ca-related pathways. Decreased abundance of the period circadian regulator suggested the shifted circadian phase when moderate WS developed. The enriched pathways uniquely obtained in C2 were RNA degradation, Ras signaling, cellular senescence, axon guidance, and salivary secretion. The DEGs identified in those pathways might play crucial roles in regulating cellular ion balances and cell-cycle arrest. In C3, the pathways responsible for phosphatidylinositol 3-kinase-Akt signaling, p53 activation, apoptosis, and hypoxia-induced processes were modified. Additionally, pathways associated with a variety of diseases with the DEGs involved in regulation of [Ca], collagen formation, microtubule-based motor, and immune response were identified. Eight pathways were common to all three comparisons (i.e., calcium signaling, Ras-associated protein 1 signaling, ubiquitin-mediated proteolysis, vascular smooth muscle contraction, oxytocin signaling, and pathway in cancer). The current findings support the role of intracellular ion imbalance, particularly Ca, oxidative stress, and impaired programmed cell death on WS progression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fphys.2020.00580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7308426PMC
June 2020

Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon).

Sci Rep 2020 03 17;10(1):4896. Epub 2020 Mar 17.

Microarray Research Team, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120, Thailand.

Microbial colonization is an essential process in the early life of animal hosts-a crucial phase that could help influence and determine their health status at the later stages. The establishment of bacterial community in a host has been comprehensively studied in many animal models; however, knowledge on bacterial community associated with the early life stages of Penaeus monodon (the black tiger shrimp) is still limited. Here, we examined the bacterial community structures in four life stages (nauplius, zoea, mysis and postlarva) of two black tiger shrimp families using 16S rRNA amplicon sequencing by a next-generation sequencing. Although the bacterial profiles exhibited different patterns in each developmental stage, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes were identified as common bacterial phyla associated with shrimp. Interestingly, the bacterial diversity became relatively stable once shrimp developed to postlarvae (5-day-old and 15-day-old postlarval stages), suggesting an establishment of the bacterial community in matured shrimp. To our knowledge, this is the first report on bacteria establishment and assembly in early developmental stages of P. monodon. Our findings showed that the bacterial compositions could be shaped by different host developmental stages where the interplay of various host-associated factors, such as physiology, immune status and required diets, could have a strong influence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-61559-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078212PMC
March 2020

Absolute expressions of hypoxia-inducible factor-1 alpha (HIF1A) transcript and the associated genes in chicken skeletal muscle with white striping and wooden breast myopathies.

PLoS One 2019 8;14(8):e0220904. Epub 2019 Aug 8.

National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Nueng, Khlong Luang, Pathum Thani, Thailand.

Development of white striping (WS) and wooden breast (WB) in broiler breast meat have been linked to hypoxia, but their etiologies are not fully understood. This study aimed at investigating absolute expression of hypoxia-inducible factor-1 alpha subunit (HIF1A) and genes involved in stress responses and muscle repair using a droplet digital polymerase chain reaction. Total RNA was isolated from pectoralis major collected from male 6-week-old medium (carcass weight ≤ 2.5 kg) and heavy (carcass weight > 2.5 kg) broilers. Samples were classified as "non-defective" (n = 4), "medium-WS" (n = 6), "heavy-WS" (n = 7) and "heavy-WS+WB" (n = 3) based on abnormality scores. The HIF1A transcript was up-regulated in all of the abnormal groups. Transcript abundances of genes encoding 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (PFKFB4), lactate dehydrogenase-A (LDHA), and phosphorylase kinase beta subunit (PHKB) were increased in heavy-WS but decreased in heavy-WS+WB. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was up-regulated in non-defective samples. The muscle-specific mu-2 isoform of glutathione S-transferases (GSTM2) was up-regulated in the abnormal samples, particularly in the heavy groups. The genes encoding myogenic differentiation (MYOD1) and myosin light chain kinase (MYLK) exhibited similar expression pattern, of which medium-WS and heavy-WS significantly increased compared to non-defective whereas expression in heavy-WS+WB was not different from either non-defective or WS-affected group. The greatest and the lowest levels of calpain-3 (CAPN3) and delta-sarcoglycan (SCGD) were observed in heavy-WS and heavy-WS+WB, respectively. Based on micrographs, the abnormal muscles primarily comprised fibers with cross-sectional areas ranging from 2,000 to 3,000 μm2. Despite induced glycolysis at the transcriptional level, lower stored glycogen in the abnormal muscles corresponded with the reduced lactate and higher pH within their meats. The findings support hypoxia within the abnormal breasts, potentially associated with oversized muscle fibers. Between WS and WB, divergent glucose metabolism, cellular detoxification and myoregeneration at the transcriptional level could be anticipated.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220904PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687142PMC
March 2020

Monitoring of white striping and wooden breast cases and impacts on quality of breast meat collected from commercial broilers (Gallus gallus).

Asian-Australas J Anim Sci 2018 Nov 27;31(11):1807-1817. Epub 2018 Aug 27.

Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.

Objective: This study aimed at investigating white striping (WS) and wooden breast (WB) cases in breast meat collected from commercial broilers.

Methods: A total of 183 breast samples were collected from male Ross 308 broilers slaughtered at the age of 6 weeks (n = 100) and 7 weeks (n = 83). The breasts were subjected to meat defect inspection, meat quality determination and histology evaluation.

Results: Of 183, 4 breasts from 6-week-old broilers were classified as non-defective while the others exhibited the WS lesion. Among the 6-week-old birds, the defective samples from the medium size birds (carcass weight ≤2.5 kg) showed mild to moderate WS degree with no altered meat quality. Some of the breasts from the 6-week-old birds with carcass weight above 2.5 kg exhibited WB in accompanied with the WS condition. Besides of a reduction of protein content, increases in collagen matter and pH values in the defective samples (p<0.05), no other impaired quality indices were detected within this group. All 7-week-old broilers yielded carcasses weighing above 2.5 kg and showed abnormal characteristics with progressive severity. The breasts affected with severe WS and WB showed the greatest cook loss, hardness, springiness and chewiness (p<0.05). Development of WB induced significantly increased drip loss in the samples (p<0.05). Histology indicated necrotic events in the defective myofibers. Based on logistic regression, increasing percent breast weight by one unit enhanced the chance of WS and WB development with advanced severity by 50.9% and 61.0%, respectively. Delayed slaughter age from 6 to 7 weeks increased the likelihood of obtaining increased WS severity by 56.3%.

Conclusion: Cases of WS and WB defects in Southeast Asia have been revealed. Despite few cases of the severe WS and WB, such abnormal conditions significantly impaired technological properties and nutritional quality of broiler breasts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5713/ajas.18.0355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212750PMC
November 2018

Transcriptome-based discovery of pathways and genes related to reproduction of the black tiger shrimp (Penaeus monodon).

Mar Genomics 2018 Feb 9;37:69-73. Epub 2017 Sep 9.

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Nueung, Khlong Luang, Pathum Thani 12120, Thailand. Electronic address:

The black tiger shrimp (Penaeus monodon) is an aquatic animal with considerable economic importance. Poor reproductive maturation in captivity impedes sustainable aquaculture production of this species. This study aims to provide transcriptomic information on reproductive organs using 454 pyrosequencing technology. The transcriptome analysis of ovaries and testes revealed 41,136 transcripts with 20,192 contigs. We found novel sets of transcripts completing several important reproductive pathways such as gonadotropin-releasing hormone (GnRH) signaling and progesterone-mediated oocyte maturation. In addition, we found transcripts encoding for receptors crucial for initiation of the maturation process, such as GnRH receptor (GnRHR), voltage-dependent calcium channel L type alpha-1C (CACNA1C) and epidermal growth factor receptor (EGFR). Moreover, we found a putative novel vigillin encoding for an estrogen-induced polysome-associated protein, which has not been reported in penaeid shrimp. These results suggest that the regulatory mechanism of the pathways important to reproductive maturation might be similar to those in the vertebrate. The obtained data will consequently accelerate the study of reproductive biology of this important species to ensure a sustainable shrimp farming industry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.margen.2017.08.007DOI Listing
February 2018

Enantiomerically Pure 2-Methyltetrahydro-3-benzazepin-1-ols Selectively Blocking GluN2B Subunit Containing N-Methyl-D-aspartate Receptors.

J Med Chem 2015 Aug 30;58(15):6293-305. Epub 2015 Jul 30.

†Institut für Pharmazeutische und Medizinische Chemie der Universität Münster, Corrensstraße 48, D-48149 Münster, Germany.

A chiral pool synthesis was developed to obtain all four stereoisomeric 2-methyl-3-(4-phenylbutyl)tetrahydro-3-benzazepin-1-ols 21, 31, and 32 in a seven- to eight-step sequence. The phenols 32 reveal slightly higher GluN2B affinity than the methyl ethers 21. The GluN2B affinity increases in the order (1R,2S) < (1S,2S) < (1S,2R) < (1R,2R). The stereoisomeric phenols (R,R)-32 and (S,R)-32 show the highest GluN2B affinity and the highest cytoprotective activity. Both compounds represent GluN2B selective allosteric NMDA receptor antagonists. Docking of the 3-benzazepin-1-ols into the ifenprodil binding site of the crystallized GluN1b/GluN2B N-terminal domains led to free binding energies, which correlate nicely with the experimentally determined GluN2B affinities. The similar GluN2B affinity of the stereoisomeric phenols (S,S)-32, (R,R)-32, and (S,R)-32 is explained by different binding modes of the 3-benzazepine scaffold. The benzyl ethers 31 reveal unexpectedly high GluN2B affinity but do not show cytoprotective effects. The additional benzyl moiety of 31 binds into a previously unrecognized lipophilic subpocket.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jmedchem.5b00897DOI Listing
August 2015

Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.

Microb Ecol 2015 May 7;69(4):905-13. Epub 2015 Mar 7.

Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle (Saale), Germany,

Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00248-015-0585-8DOI Listing
May 2015

Analysis of the Resistance of Hepatitis C Virus NS5B Polymerase Inhibitors via Docking and Molecular Dynamics Simulation.

Mol Inform 2015 02 30;34(2-3):78-83. Epub 2015 Jan 30.

Department of Pharmaceutical Chemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany phone: +49-345-55-25040; fax: +49-345-55-27355.

In this work, we examined how known single point mutations (P495S, P495L, P495A, P496A, P496S and V499A) in Hepatitis C virus NS5B polymerase influence the binding of benzimidazole-5-carboxamide derivatives which are potent NS5B inhibitors. Docking and molecular dynamics simulations were performed to analyze the binding of the inhibitors to the wild-type and mutant enzymes. Binding free energy calculations (MM-GB/SA method) and analyzing the decomposed binding free energy of individual residues were able to explain the differences in the inhibitory potency of the compounds at wild-type and mutant enzymes and hence account for the appearance of resistance of mutant enzymes to the studied inhibitors. The obtained results were found to be in agreement with the known experimental data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/minf.201400048DOI Listing
February 2015

Identification and characterization of a cellulase-encoding gene from the buffalo rumen metagenomic library.

Biosci Biotechnol Biochem 2012 7;76(6):1075-84. Epub 2012 Jun 7.

Food Engineering and Bioprocess Technology, Asian Institute of Technology, Pathumthani, Thailand.

Microorganisms residing in the rumens of cattle represent a rich source of lignocellulose-degrading enzymes, since their diet consists of plant-based materials that are high in cellulose and hemicellulose. In this study, a metagenomic library was constructed from buffalo rumen contents using pCC1FOS fosmid vector. Ninety-three clones from the pooled library of approximately 10,000 clones showed degrading activity against AZCL-HE-Cellulose, whereas four other clones showed activity against AZCL-Xylan. Contig analysis of pyrosequencing data derived from the selected strongly positive clones revealed 15 ORFs that were closely related to lignocellulose-degrading enzymes belonging to several glycosyl hydrolase families. Glycosyl hydrolase family 5 (GHF5) was the most abundant glycosyl hydrolase found, and a majority of the GHF5s in our metagenomes were closely related to several ruminal bacteria, especially ones from other buffalo rumen metagenomes. Characterization of BT-01, a selected clone with highest cellulase activity from the primary plate screening assay, revealed a cellulase encoding gene with optimal working conditions at pH 5.5 at 50 °C. Along with its stability over acidic pH, the capability efficiently to hydrolyze cellulose in feed for broiler chickens, as exhibited in an in vitro digestibility test, suggests that BT-01 has potential application as a feed supplement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1271/bbb.110786DOI Listing
November 2012

Metagenomic analysis of novel lignocellulose-degrading enzymes from higher termite guts inhabiting microbes.

J Microbiol Biotechnol 2012 Apr;22(4):462-9

Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology-BIOTEC, Thailand Science Park, Pathumthani 12120, Thailand.

A metagenomic fosmid library was constructed from genomic DNA isolated from the microbial community residing in hindguts of a wood-feeding higher termite (Microcerotermes sp.) collected in Thailand. The library was screened for clones expressing lignocellulolytic activities. Fourteen independent active clones (2 cellulases and 12 xylanases) were obtained by functional screening at pH 10.0. Analysis of shotgun-cloning and pyrosequencing data revealed six ORFs, which shared less than 59% identity and 73% similarity of their amino acid sequences with known cellulases and xylanases. Conserved domain analysis of these ORFs revealed a cellulase belonging to the glycoside hydrolase family 5, whereas the other five xylanases showed significant identity to diverse families including families 8, 10, and 11. Interestingly, one fosmid clone was isolated carrying three contiguous xylanase genes that may comprise a xylanosome operon. The enzymes with the highest activities at alkaline pH from the initial activity screening were characterized biochemically. These enzymes showed a broad range of enzyme activities from pH 5.0 to 10.0, with pH optimal of 8.0 retaining more than 70% of their respective activities at pH 9.0. The optimal temperatures of these enzymes ranged from 50 degrees C to 55 degrees C. This study provides evidence for the diversity and function of lignocellulose-degrading enzymes in the termite gut microbial community, which could be of potential use for industrial processes such as pulp biobleaching and denim biostoning.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4014/jmb.1108.08037DOI Listing
April 2012

Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis.

Microb Ecol 2011 Apr 6;61(3):518-28. Epub 2010 Nov 6.

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Klong Luang, Pathumthani, Thailand.

A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00248-010-9766-7DOI Listing
April 2011

Identification and characterization of lipolytic enzymes from a peat-swamp forest soil metagenome.

Biosci Biotechnol Biochem 2010 7;74(9):1848-54. Epub 2010 Sep 7.

Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.

In this work, a metagenomic library was generated from peat-swamp forest soil obtained from Narathiwat Province, Thailand. From a fosmid library of approximately 15,000 clones, six independent clones were found to possess lipolytic activity at acidic pH. Analysis of pyrosequencing data revealed six ORFs, which exhibited 34-71% protein similarity to known lipases/esterases. A fosmid clone, designated LP8, which demonstrated the highest level of lipolytic activity under acidic conditions and demonstrated extracellular activity, was subsequently subcloned and sequenced. The full-length lipase/esterase gene, estPS2, was identified. Its deduced amino acid was closely related to a lipolytic enzyme of an uncultured bacterium, and contained the highly conserved motif of a hormone-sensitive family IV lipase. The EstPS2 enzyme exhibited highest activity toward p-nitrophenyl butyrate (C⁴) at 37 °C at pH 5, indicating that it was an esterase with activity and secretion characteristics suitable for commercial development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1271/bbb.100249DOI Listing
February 2011
-->