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Farm production and natural forest extraction remain principal livelihood strategies of local people in many rural areas of the developing world. In this paper, we apply stochastic frontier analysis to evaluate farm production efficiency and simultaneous equations modelling to estimate the interrelationship between farm production efficiency and natural forest extraction. We use a two-year panel dataset of 430 rural households in Stung Treng province of Cambodia. We find that natural forest extraction is decreasing in farm production efficiency. Our results suggest that improving farm production efficiency, via the promotion of rural education and privatization of farm land, should be considered an integral component of natural forest conservation policy.
2.
- Title: A novel strain of porcine deltacoronavirus in Vietnam
- Journal: Arch Virol
- Author from VNUA:1. Lê Văn Phan 2. Phạm Ngọc Thạch
- Authors: Van Phan Le, Sok Song, Byung‑Hyun An, Gyu‑Nam Park, Ngoc Thach Pham, Dinh Quyen Le, Van Tam Nguyen, Thi Thu Hang Vu, Ki‑Sun Kim, SeEun Choe, Dong‑Jun An
- Abstract:
Two porcine deltacoronavirus [PDCoV] strains [Binh21 and HaNoi6] were isolated from two pig farms in North Vietnam. Phylogenetic analysis of the complete
genomes and the Spike and Membrane genes revealed that the two Vietnam PDCoVs belong to the same lineage as PDCoVs from Thailand and Laos; however, the N genes belonged to the same lineage as PDCoVs from the USA, Korea, China, and Hong Kong. The recombination detection program subsequently identified the major parent [S5011 strain] and minor parent [HKU15-44 strain] of the two Vietnam PDCoV strains [p < 0.01].
3.
- Title: Spectral monodromy of small non-selfadjoint quantum perturbations of completely integrable Hamiltonians
- Journal: Journal of Mathematical Analysis and Applications
- Author from VNUA:Phan Quang Sáng
- Authors: Phan Quang Sáng
- Abstract:
We define a monodromy, directly from the spectrum of small non-selfadjoint perturbations of a selfadjoint semiclassical operator with two degrees of freedom, which is classically integrable. It is a combinatorial invariant that obstructs globally the existence of lattice structure of the spectrum, in the semiclassical limit. Moreover this spectral monodromy allows to recover a topological invariant [the classical monodromy] of the corresponding integrable system.
4.
- Title: Degradation of β-casomorphins and identification of degradation products during yoghurt processing using liquid chromatography coupled with high resolution mass spectrometry
- Journal: Food Research International
- Author from VNUA:Nguyễn Đức Doan
- Authors: Nguyễn Đức Doan, Francesco Busetti, Stuart Johnson, Vicky Solah
- Abstract:
Liquid chromatography-high resolution mass spectrometry [LC-HRMS] was used to investigate the degradation of β-casomorphin 5 [β-CM5] and β-casomorphin 7 [β-CM7] by Streptococcus thermophilus and/or Lactobacillus delbrueckii ssp. bulgaricus, and to identify the degradation products forming during yoghurt processing. Bovine UHT milk was fermented with: [i] a single strain of L. delbrueckii ssp. bulgaricus, [ii] a single strain of S. thermophilus and [iii] the mixture of S. thermophilus and L. delbrueckii ssp. bulgaricus to pH 4.5 and then stored at 4 °C for 1 and 7 days. Results showed that L. delbrueckii ssp. bulgaricus and/or S. thermophilus completely degraded β-CM5 and β-CM7 upon fermentation to pH 4.5 and degradation products were significantly influenced by bacteria strains and storage time. Four peptides, β-CNf60–61 [YP], β-CNf62–63 [FP], β-CNf64–66 [GPI] and β-CNf62–66 [FPGPI] were tentatively identified through high resolution MS/MS experiments; however, it was not possible to confirm if either milk protein or β-casomorphins was a source releasing these peptides. Nonetheless, in this study peptides YP and GPI were released by L. delbrueckii ssp. bulgaricus. This is the first time GPI has been identified and thus future investigation of its bioactivity is warranted.
5.
- Title: Acquiring qualified samples for RANSAC using geometrical constraints
- Journal: Pattern Recognition Letters, Elsevier
- Author from VNUA:Nguyễn Thị Thủy [CNTT]
- Authors: Van-Hung Le, Hai Vu, Thi-Thuy Nguyen, Thi-Lan Le, Thanh-Hai Tran
- Abstract:
Estimating parameters of a geometrical model from 3-D point cloud data is an important problem in computer vision. Random sample consensus [RANSAC] and its variations have been proposed for the estimation of the models parameters. However, RANSAC is computationally expensive and the problem is challenging when the measured 3-D data contain noise and outliers. This paper presents an efficient sampling technique for RANSAC, in which geometrical constraints are utilized for selecting good samples for a robust estimation. The constraints are based on two predefined criteria. First, the samples must ensure being consistent with the estimated model; second, the selected samples must satisfy explicit geometrical constraints of the interested objects. The proposed approach is wrapped as a robust estimator, named GCSAC [Geometrical Constraint SAmple Consensus], for estimating a cylindrical object from a 3-D point cloud. Extensive experiments on various data sets show that our method outperforms other robust estimators [e.g. MLESAC] tested in term of both precision of the estimated model and computational time. The implementations and evaluation datasets used in this paper are made publicly available.
6.
- Title: A lytic bacteriophage of the newly emerging rainbow trout pathogen Weissella ceti
- Journal: Virus Research
- Author from VNUA:Trương Đình Hoài
- Authors: Truong Dinh Hoai, Kyoka Mitomi, Issei Nishiki, Terutoyo Yoshida
- Abstract:
This study was conducted to isolate and characterize a bacteriophage of a newly emerging pathogen, Weissella ceti, which causes weissellosis outbreaks of intensively farmed rainbow trout worldwide. The phage appeared together with the cultured Weissella ceti during isolation of pathogen from kidney of diseased rainbow trout. The morphological, physiological, proteomic and lytic spectrum were characterized. This phage, named PWc, belonged to the family Siphoviridae and possessed an isometric head [approximately 65 nm in diameter] and a flexible, non-contractile tail of 170–180 nm in length. The latent time and burst size of PWc were approximately 25 min and 16 PFU/infected cells, respectively. The PWc was relatively stable over a wide range of temperatures and pH values and possessed a broad lytic spectrum, lysing all 36 tested W. ceti strains isolated from diseased rainbow trout in Japan. The protein profile of the phage was obtained using SDS-PAGE analysis, and the potential packaging strategy was determined based on terminase large subunit sequence analysis. This is the first study to investigate a lytic bacteriophage of a newly emerging pathogen W. ceti that causes infectious disease in rainbow trout.
7.
- Title: First isolation of Weissella ceti responsible for outbreaks of weissellosis in farmed rainbow trout in Japan
- Journal: Journal of Fish Diseases
- Author from VNUA:Trương Đình Hoài
- Authors: Truong Dinh Hoai, Kyoka Mitomi, Issei Nishiki, Terutoyo Yoshida
- Abstract:Disease of rainbow trout
8.
- Title: Characterization and Genetic Structure of a Tospovirus Causing Chlorotic Ring Spots and Chlorosis Disease on Peanut; Comparison with Iranian and Polish Populations of Tomato yellow fruit ring virus
- Journal: Plant Disease
- Author from VNUA:Nguyễn Đức Huy
- Authors: Ali Reza Golnaraghi, Nooh Shahraeen, H. D. Nguyen
- Abstract:
A Tospovirus was isolated from peanut plants showing chlorotic ring spots and chlorosis, and identified as Tomato yellow fruit ring virus [TYFRV] on the basis of its biological, serological and molecular properties. In host range studies, a broad range of indicator plants was infected by the five isolates studied; all the isolates systemically infected Nicotiana tabacum cultivars, and so, they were classified into the N host-infecting type isolates of the virus. These isolates strongly reacted with TYFRV antibodies, but not with the specific antibodies of other tospoviruses tested. Recombination analyses showed that the nucleoprotein gene of the peanut isolates and other isolates studied were non-recombinant. In phylogenetic trees, the virus isolates were clustered in three genogroups: IRN-1, IRN-2 and a new group, namely POL; the peanut isolates fell into IRN-2 group. Multiple sequence alignments showed some genogroup-specific amino acid substitutions among the virus isolates studied. The results revealed the presence of negative selection in TYFRV populations. Also, the Iranian populations had higher nucleotide diversity as compared with the Polish population. Genetic differentiation and gene flow analyses indicated that the populations from Iran and Poland, and those belonging to different genogroups were partial differentiated populations. Our findings seem to suggest that there has been frequent gene flow between some populations of the virus in the mid-Eurasia of Iran.
9.
- Title: STAT6, PBX2, and PBRM1 Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers
- Journal: Frontiers in Genetics
- Author from VNUA:Nguyễn Tố Loan
- Authors: Loan T. Nguyen, Antonio Reverter, Angela Cánovas, Bronwyn Venus, Stephen T. Anderson, Alma Islas-Trejo, Marina M. Dias, Natalie F. Crawford, Sigrid A. Lehnert, Juan F. Medrano, Milt G. Thomas, Stephen S. Moore and Marina R. S. Fortes
- Abstract:
The liver plays a central role in metabolism and produces important hormones. Hepatic estrogen receptors and the release of insulin-like growth factor 1 [IGF1] are critical links between liver function and the reproductive system. However, the role of liver in pubertal development is not fully understood. To explore this question, we applied transcriptomic analyses to liver samples of pre- and post-pubertal Brahman heifers and identified differentially expressed [DE] genes and genes encoding transcription factors [TFs]. Differential expression of genes suggests potential biological mechanisms and pathways linking liver function to puberty. The analyses identified 452 DE genes and 82 TF with significant contribution to differential gene expression by using a regulatory impact factor metric. Brain-derived neurotrophic factor was observed as the most down-regulated gene [P = 0.003] in post-pubertal heifers and we propose this gene influences pubertal development in Brahman heifers. Additionally, co-expression network analysis provided evidence for three TF as key regulators of liver function during pubertal development: the signal transducer and activator of transcription 6, PBX homeobox 2, and polybromo 1. Pathway enrichment analysis identified transforming growth factor-beta and Wnt signaling pathways as significant annotation terms for the list of DE genes and TF in the co-expression network. Molecular information regarding genes and pathways described in this work are important to further our understanding of puberty onset in Brahman heifers.
10.
- Title: Transcription analysis of the ethylene receptor and CTR genes in tomato: The effects of on and off-vine ripening and 1-MCP
- Journal: Postharvest Biology and Technology
- Author from VNUA:Trần Thị Định
- Authors: Clara I.Mata, Bram Van de Poel, Maarten Hertog, Dinh T. Tran, Bart Nicolaï
- Abstract:Transcription analysis of the ethylene receptor and CTR genes in tomato: The effects of on and off-vine ripening and 1-MCP
11.
- Title: Enhancement of immune response and resistance against Vibrio parahaemolyticus in kuruma shrimp [Marsupenaeus japonicus] by dietary supplementation of β-1,4-mannobiose
- Journal: Fish & Shellfish Immunology Volume Issue Pages Advanced searchnew
- Author from VNUA:Vũ Đức Hạnh
- Authors: Gehad E.Elshopakey, Engy F.Risha, Osama A.Abdall, YoOkamura, Vu DucHanh, MasahisaIbukie, RajaSudhakaran, ToshiakiItami
- Abstract:
Abstract
Supplementation of prebiotic carbohydrates can act as a potent immunomodulator and have the efficacy to induce immune-related genes which are involved in host defense. Pure β-1,4-mannobiose [MNB] showed activation of prophenoloxidase system of shrimp hemocytes in vitro. The resistance of kuruma shrimp Marsupenaeus japonicus against Vibrio parahaemolyticus was examined after the shrimp were fed with 0 [control], 0.02, 0.2, and 2% MNB supplemented diets. The results showed significantly higher survival rates in MNB supplemented shrimp than those of the control one from 2 to 12 days post challenge. In another experiment, the hemocyte count, ROS production, phagocytic, phenoloxidase and bactericidal activities, and expression of immune-related genes were investigated in the control and MNB supplemented groups at day 1, 4, 6, 8 and 11 of the feeding. These immune parameters were significantly enhanced in MNB supplemented groups. Furthermore, the gene expression analysis showed that transcripts of lysozyme, crustin, penaeidin and TNF were significantly up-regulated in hemolymph, lymphoid organs and intestines of MNB treated shrimp. Overall, the results provided evidence that MNB supplementation could improve the immune response and increase shrimp resistance against V. parahaemolyticus infection.
12.
- Title: Host range and the influence of a cell capsule on the phage efficacy of three Lactococcus garvieae lytic phages
- Journal: Diseases of Aquatic Organisms
- Author from VNUA:Trương Đình Hoài
- Authors: Truong Dinh Hoai, Issei Nishiki, Terutoyo Yoshida, Toshihiro Nakai
- Abstract:
13.
- Title: Molecular Characterization of Novel Porcine Circovirus 3 [PCV3] in Pig Populations in the North of Vietnam
- Journal: Archives of Gene and Genome Research
- Author from VNUA:1. Nguyễn Văn Giáp 2. Huỳnh Thị Mỹ Lệ 3. Cao Thị Bích Phượng 4. Lê Văn Trường 5. Vũ Thị Ngọc
- Authors: Van Giap Nguyen, Hee Chun Chung, Thi My Le Huynh, Thi Bich Phuong Cao, Thi Ngoc Vu, Van Truong Le, Hong Quan Pham
- Abstract:
In 2015, a novel circovirus [Porcine circovirus 3, PCV3] was detected for the first time from pigs suffered from porcine dermatitis and nephropathy syndrome and reproductive failure. Since then, PCV3 has been reported in several pig producing countries. This study was carried out in order to investigate the presence and further genetic characterization of PCV3 in the pig populations in northern Vietnam. The screening PCR detected the presence of PCV3 in 6 out of 135 samples [4.44%] which were collected from seven northern provinces in 2011 and 2016-2017. The capsid-coding gene [ORF2, 645 nucleotides in length] was successfully sequenced from 5 out of 6 field strains. Compared to a highly diverse PCV3 strain [GD2016-1, KY421347] 5 Vietnamese PCV3 strains contained 39 point nucleotide mutations and 9 of those were non-synonymous. The Bayesian phylogenetic analysis on the basic of ORF2 revealed that PCV3 evolved at a comparable evolutionary rate of the pathogenic PCV2 [2.284 × 10-3 and 1.440 × 10-3, respectively]. Besides, this analysis suggested PCV3 could be separated into PCV3a and PCV3b groups, of which the majority of Vietnamese PCV3 strains belong to PCV3a [sub-cluster a1].
14.
- Title: Towards global applicability? Erosion source discrimination across catchments using compound-specific δ13 C isotopes
- Journal: Agriculture, Ecosystems and Environment
- Author from VNUA:Nguyễn Thanh Lâm
- Authors: Christian Brandt, Gerd Derconb, Georg Cadisch, Làm T. Nguyễn, Paulina Schuller, Claudio Bravo Linares, Alejandra Castillo Santana, Valentin Golosove, Moncef Benmansour, Nourredine Amenzoug, Zhang Xinbaoh, Frank Rasche
- Abstract:
Accurate identification of soil erosion hot spots across catchments of different sizes and agro-ecologies through the use of conventional tracing techniques has proven challenging. Since this problem hinders implementation of precise soil conservation measures by land managers and decision-making bodies, novel evidence-based techniques are needed. To meet this need, the International Atomic Energy Agency [IAEA, Vienna, Austria] initiated the Coordinated Research Project entitled “Integrated Isotopic Approaches for an Area-wide Precision Conservation to Control the Impacts of Agricultural Practices on Land Degradation and Soil Erosion – D1.20.11” in 2008. This project emphasized the application of isotopic approaches to identify hot spots of land degradation
in agricultural catchments to develop effective soil conservation measures. As one key outcome of this project, we present here an aligned protocol to explore the potential of compound-specific stable isotope [CSSI] analysis of individual fatty acids [FA] combined with Bayesian statistics to discriminate sediment sources across six catchments of different sizes and agro-ecologies. The global applicability of the CSSI approach was first tested on the basis of major land use categories [i.e., forest, cultivated and non-cultivated land] as potential sediment sources in the studied catchments. These land use categories were then further resolved into specific land use types [e.g., cassava and maize fields, orchards] to assess the potential resolution threshold of the CSSI technique.
In a final step, the influence of miscellaneous sources [e.g., roads, channel banks] that had the potential to distort proportional contributions to sediment deposition was assessed. The introduced aligned protocol of the CSSI technique was applied to discriminate individual erosion sources based on land use types of tested catchments. Merging catchment-specific land use types with broader land use categories made it possible to determine intercatchment comparisons of isotopic signatures due to significant differences in δ13C values of fatty acids when cultivated land was present. Notably, no correlations were found between different catchment sizes, agro-ecologies, number and type of land use types, or soil organic carbon concentrations and the number of significant δ13C fatty acid values of the various land use types. Thus, we propose that the presented CSSI technique has the potential to identify soil erosion hot spots in contrasting catchments of different sizes and agro-ecologies.
15.
- Title: Integrating compound-specific δ13 C isotopes and fallout radionuclides to retrace land use type-specific net erosion rates in a small tropical catchment exposed to intense land use change
- Journal: Geoderma
- Author from VNUA:Nguyễn Thanh Lâm
- Authors: Christian Brandt, Moncef Benmansour, Leander Walza, Lam T. Nguyen, Georg Cadischa, Frank Raschea
- Abstract:
Retracing net erosion rates linked to land use change in tropical agricultural catchments dominated by smallholder farmers is challenging, due largely to catchment heterogeneity and uncontrolled farming practices. To tackle this problem and to complement a preceding study [Brandt et al., 2016], we introduce here an advanced approach that integrates compound-specific δ13C isotopes [CSSI] and fallout radionuclides [FRN], Excess lead-210 [210Pbex] and Cesium-137 [137Cs] to estimate past net erosion rates of dominant land use types in themountainous catchment Chieng Khoi [207 ha, Northwest Vietnam]. Spatially-integrated topsoil [0 to 2 cm]samples of dominant land use types [e.g., protected and secondary forests, teak, fruit orchards, maize, cassava]were collected from at least three discrete plots of each land use type within the upland area [i.e., erosion sites]of the studied catchment. In the corresponding lowland area, a representative sediment profile was localized and divided into sections of 2 to 4 cm for CSSI and FRN analysis. Samples for FRN reference data were taken from undisturbed areas in close proximity. At a soil deposition site near a lakeshore,
210 Pb ex data determined the age and sediment accumulation rates of 19 sediment layers to a depth of 38 cm. Based on 210 Pbex activity, maximum
sediment accumulation rates of 127 t ha−1 y−1 were calculated, corresponding to erosion rates of about 16 t ha−1 y−1
for the total catchment area. CSSI data confirmed that maize and cassava were the most important erosion sources during a period of dramatic land use change [1987 to 2004], when forests were cleared and high-yielding maize hybrids were introduced. Based on integrated FRN and CSSI data, net erosion rates of maize and cassava reached maximum rates of 4.8 t ha−1, y−1, [maize], 6.2 t ha−1, y−1 [cassava]. This major finding verified the potential of integrating FRN and CSSI to accurately estimate land use type-specific net erosion rates. In conclusion, determining past sediment budgets for specific land use types provides insight into the accelerating impact of specific land use change on soil retrogression and degradation. Such knowledge is of prime importance for effective soil conservation through evidence-based land management and decision making.
16.
- Title: Identification of drought-induced genes in giant leucaena [Leucaena leucocephala subsp. glabrata]
- Journal: Trees- Springer
- Author from VNUA:Phạm Thị Dung
- Authors: Michael D. H. Honda · Kazue L. Ishihara · Dung T. Pham· Dulal Borthakur
- Abstract:
Abstract Leucaena leucocephala subspecies glabrata [leucaena], which is also known as ‘giant leucaena’, is a multipurpose tree legume that can be grown and maintained as a woody tree for wood and paper pulp production, or as a shrubby legume through repeated harvest of foliage for use as a fodder. Leucaena is naturally resistant to most biotic and abiotic stresses including drought. The objective of this research was to identify drought-responsive genes in leucaena seedlings through microarray and qRT-PCR analyses. Ten thousand cDNA sequences selected from a leucaena transcriptome were screened for higher expression in a 4 × 180 k microarray using RNA isolated from drought-treated and untreated leucaena seedlings. Microarray analysis identi ed 73 and 39 drought-responsive genes sequences that were upregulated in the root and shoot, respectively. qRT-PCR analyses con rmed the root- and shoot-speci c upregulation of some of the most highly expressed gene sequences identi ed in the microarray analysis. The proteins encoded by these genes could be grouped into four classes: [1] receptors that sense osmotic and oxidative stresses, [2] transcription factors, [3] degradation pathway enzymes, and [4] biosynthetic enzymes and structural proteins. The functions of these four classes of proteins can be used to explain the drought response in leucaena. The NB-LRR class of disease-resistance proteins may serve as receptors for detecting osmotic and oxi- dative stresses induced by drought, leading to induction of transcription factors such as zinc nger CCCH domain-containing protein and TCP14. As result, the genes for some degradative pathway enzymes, such as GDSL esterase/lipase, lipid acyl hydrolase patatin, and serine carboxypeptidase, were induced. Similarly, the expression of certain biosynthetic enzymes and structural proteins such as avonoid 3-O-galactosyl transferase, ca eoyl-CoA O-methyltransferase, 9-cis-epoxy carotenoid dioxygenase, β-amyrin synthase, pentatricopeptide-containing protein, GPI-anchored protein COBRA, and peroxin, were also induced. High expression of some of these drought-inducible genes in leucaena seedlings may be used as a selection criterion in future breeding programs for drought resistance in leucaena and other legumes.
17.
- Title: Host-associated probiotics boosted mucosal and serum immunity, disease resistance and growth performance of Nile tilapia [Oreochromis niloticus]
- Journal: Aquaculture
- Author from VNUA:Kim Văn Vạn
- Authors: Hien Van Doan,, Seyed Hossein Hoseinifar, Chartchai Khanongnuch, Apinun Kanpiengjai, Kridsada Unban, Van Van Kim, Satawat Srichaiyo
- Abstract:
The investigation was conducted to evaluate the possible effects of singular or combined administration of hostassociated probiotics [Lactobacillus plantarum N11 and Bacillus velezensis H3.1] on several innate-immune parameters, disease resistance, and growth performance of Nile tilapia, [O. niloticus]. Tilapia fingerlings were assigned for te following diets: Diet 1 [0 - control], Diet 2 [107 CFU g−1 B. velezensis H3.1], Diet 3 [108 CFU g−1 L.
plantarum N11], and Diet 4 [107 CFU g−1 B. velezensis H3.1 + 108 CFU g−1 L. plantarum N11]. At days 15 and 30 post feeding, skin mucus and innate immune parameters as well as growth performance were collected. The challenge test was conducted at the end of feeding trial [i.e 30 days post feeding]. The results showed that dietary administration of Lactobacillus plantarum N11 and Bacillus velezensis H3.1 resulted in significant increase skin mucus lysozyme and peroxidase activities of the fish [P < 0.05]. However, no significant difference was detected among supplemented groups [P > 0.05]. For serum immunity, serum lysozyme activity of fish fed probiotics diets was significantly higher than the control group, except for fish fed B. velezensis H3.1, where no significant was observed when compared with the control [P > 0.05]. Likewise, serum peroxidase, alternative complement, phagocytosis, and respiratory burst activities were significantly higher in treated groups compared to the control [P < 0.05]. Also, the relative percent of survival [RPS] in L. plantarum N11 and B. velezensis H3.1, L. plantarum N11, and B. velezensis H3.1 treatments were 58.33%, 54.17%, 41.67%, respectively. Nonetheless, no significant differences were observed among supplemented groups regarding RPS [P > 0.05]. However, dietary administration of host-associated probiotics remarkably improved the growth performance, specific growth rate, weight gain, final weight, and feed conversion ratio [P < 0.05]. The present results indicated that singular or combined administration Lactobacillus plantarum N11 and Bacillus velezensis H3.1 can be considered as beneficial feed additives for Nile tilapia.
18.
- Title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus [PEDV] that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks
- Journal: BMC Veterinary Research
- Author from VNUA:Nguyễn Văn Điệp
- Authors: Nguyen Van Diep, Masuo Sueyoshi, Junzo Norimine, Takuya Hirai, Ohnmar Myint, Angeline Ping Ping Teh, Uda Zahli Izzati, Naoyuki Fuke, and Ryoji Yamaguchi
- Abstract:
Since late 2013, porcine epidemic diarrhea virus [PEDV] has reemerged in Japan and caused severe economic losses to the swine industry. Although PEDV vaccines have been used widely, the disease has swept rapidly across the county, and is commonly observed in PED-vaccinated farms, and has recurred in domestic herds. To better understand PEDVs responsible for the reemerging outbreaks in Japan, full-length spike [S], membrane [M], and nucleocapsid [N] genes of 45 PEDVs collected in Japan during 2013–2016, were sequenced and analyzed.
Results
Phylogenetic analysis based on S gene sequences revealed that all the recent field PEDVs were genetically distinct from the classical Japanese strains, and were classified into three genotypes: North American [NA], S INDEL, and Asian non-S INDEL. Our data suggested a possibility that multiple parental PEDV strains were introduced into Japan from abroad at the same time or similar times. The newly identified Japanese strains showed the closest relationship to the US strains. Two sublineages of Japanese strains circulating in Japan were similar to two sublineages identified in the US, suggesting common ancestors for these strains. In comparison with two vaccine strains used in Japan, the field strains had various changes in epitope regions, glycosylation sites, and phosphorylation sites. These substitutions, particularly observed in epitope regions of the S [521, 553, 568, and 570], M [5], and N [123, 252, and 255] proteins, may have affected antigenicity and vaccine efficacy, resulting in an unsuccessful PEDV control. Sequence comparisons between PEDVs collected from primary and secondary outbreaks in three herds revealed that the disease has developed to an endemic stage in which PEDV could persist for nearly two years in the herds or local regions, causing subsequent epidemics.
Conclusions
These results elucidate the genetic characteristics, origin, and molecular epidemiology of PEDVs circulating in Japan, as well as the PEDV strains causing recurrent outbreaks. This study provides a better insight into the PEDVs responsible for recent outbreaks in Japan, and could potentially help to develop measures for controlling and preventing the disease.
19.
- Title: Merkel cell carcinoma in a Steer
- Journal: Journal of Comparative Pathology
- Author from VNUA:Nguyễn Văn Điệp
- Authors: Angeline Ping Ping Teh, Uda Zahli Izzati, Nguyen Van Diep, Takuya Hirai,
Naoyuki Fuke, and Ryoji Yamaguchi
- Abstract:
Merkel cell carcinoma is a rare and aggressive cutaneous neuroendocrine tumour reported only in man, dogs and cats. A 20-month-old Japanese black fattening steer was presented with necrotic protruding skin masses over the left thoracic area and a 20 25 cm subcutaneous mass in the left abdominal area. Microscopical evaluation of the masses revealed cords of small to medium-sized round tumour cells with marked anisocytosis and anisokaryosis and clear and vacuolated cytoplasm, which were separated by a delicate fibrovascular stroma and arranged in a trabecular and nested pattern. Necropsy examination revealed multiple solid white nodular masses in the lungs. Immunohistochemistry [IHC] for cytokeratin [CK] 20 and CKAE1/3 revealed focal perinuclear labelling of tumour cells. IHC for the neuroendocrine markers chromogranin A and neuron specific enolase, the neuroepithelial stem cell marker nestin and the hormonal markers adrenocorticotropic hormone and calcitonin revealed diffuse cytoplasmic labelling of all tumour cells. Ultrastructurally, the tumour cells contained few neurosecretory granules and abundant glycogen pools. The tumours were diagnosed as Merkel cell carcinoma with pulmonary metastases and this case represents the first such diagnosis in cattle.
20.
- Title: Land Surface Temperature Variation Due to Changes in Elevation in Northwest Vietnam
- Journal: Climate, volume 6, issue 2
- Author from VNUA:1. Trần Trọng Phương 2. Phan Thành Nội
- Authors: Thanh Noi Phan[1], Martin Kappas and Trong Phuong Tran[1]
- Abstract:
Land surface temperature [LST] is one of the most important variables for applications relating to the physics of land surface processes. LST rapidly changes in both space and time, and knowledge of LST and its spatiotemporal variation is essential to understand the interactions between human activity and the environment
21.
- Title: Isolation and application of bacteriophages to reduce Salmonella contamination in raw chicken meat
- Journal: LWT-Food Science and Technology
- Author from VNUA:1. Hoàng Minh Đức 2. Hoàng Minh Sơn
- Authors: Hoang Minh Duc, Hoang Minh Son, Ken-ichi Honjoh, Takahisa Miyamoto
- Abstract:
Chicken meats are considered as main sources associated with Salmonella infections in humans. In this study, lytic phages against Salmonella were isolated and examined for their efficacy to control Salmonella. Eighteen lytic phages were isolated from raw chicken skin and gizzard. Five phages belonging to Myoviridae and Siphoviridae families were characterized and selected for bacterial challenge tests. The treatment of raw chicken breast samples contaminated with S. Enteritidis and S. Typhimurium at 8 °C by the cocktail of five phages significantly reduced [P < 0.05] viable counts by 1.41 and 1.86 log CFU/piece, respectively. When incubated at 25 °C, the highest reductions of viable counts of S. Enteritidis and S. Typhimurium in the phage-treated samples were 3.06 and 2.21 log CFU/piece, respectively [P < 0.05]. These data suggested that the phages isolated from raw chicken meats are potential agents for controlling Salmonella in raw meats.
22.
- Title: Genotypic variations in the plasticity of nodal root penetration through the hardpan during soil moisture fluctuations among four rice varieties.
- Journal: Plant Production Science
- Author from VNUA:Nguyễn Thị Ngọc Dinh
- Authors: Dinh Thi Ngoc Nguyena, Roel Rodriguez Suraltab, Mana Kano-Nakataa,c, Shiro Mitsuyaa, Stella Owusu-Nketiaa and Akira Yamauchia
aGraduate School of Bioagricultural Sciences, nagoya university, nagoya, Japan; bagronomy, Soils and Plant Physiology division,
- Abstract:
Rainfed lowland rice fields are characterized by soil moisture fluctuations [SMF] and the presence of hardpan that impedes deep rooting and thus limits water extraction from deep soil layer during the periods of drought. In this study, we used rootboxes with three layers; shallow layer, artificial hardpan, and deep and wet layer below the hardpan, to evaluate differences in the plasticity of nodal roots elongation through the hardpan and promote root branching below the hardpan in response to SMF among four rice varieties; Sasanishiki, Habataki, Nipponbare and Kasalath. Experiments were conducted during the summer and autumn seasons. Plasticity was computed as the difference in root traits within each variety between the SMF and continuously well-watered treatments. In both experiments, Habataki consistently tended to exhibit higher root plasticity than the other three varieties by increasing number of nodal roots that penetrated the hardpan during rewatering period in SMF, when the soil moisture increased and penetration resistance decreased. This root plasticity then contributed to greater water use at the deeper soil during the subsequent drought period and overall shoot dry matter production. Habataki had significantly higher δ13C value in roots at deep layer than roots at the shallow and hardpan layers under SMF, which may indicate that these were relatively newly grown roots as a consequence of root plasticity. This study also indicates that CSSLs derived from Sasanishiki and Habataki varieties may be suitable for the analysis of QTLs associated with root plasticity expression in rainfed lowland with hardpan and experiencing SMF.
23.
- Title: Root plasticity under fluctuating soil moisture stress exhibited by backcross inbred line of a rice variety, Nipponbare carrying introgressed segments from KDML105 and detection of the associated QTLs
- Journal: Plant Production Science Vol 21 Issue 2
- Author from VNUA:Nguyễn Thị Ngọc Dinh
- Authors: Stella Owusu-Nketiaa, Yoshiaki Inukaib, Satomi Ohashia, Roel Rodriguez Suraltac, Kazuyuki Doia, Shiro Mitsuyaa, Mana Kano-Nakataa,d, Jonathan Manito Nionese, Dinh Thi Ngoc Nguyena,f, Kabuki Takuyaa, Daigo Makiharab and Akira Yamauchia a Graduate School of
- Abstract:
In rainfed lowland rice ecosystem, rice plants are often exposed to alternating recurrences of waterlogging and drought due to erratic rainfall. Such soil moisture fluctuation [SMF] which is completely different from simple or progressive drought could be stressful for plant growth, thereby causing reduction in yield. Root plasticity is one of the key traits that play important roles for plant adaptation under such conditions. This study aimed to evaluate root plasticity expression and its functional roles in dry matter production and yield under SMF using Nipponbare, KDML 105 and three backcross inbred lines [BILs] and to identify QTL[s] associated with root traits in response to SMF at two growth stages using Nipponbare/KDML105 F2 plants. A BIL, G3-3 showed higher shoot dry matter production and yield than Nipponbare due to its greater ability to maintain stomatal conductance concomitant with greater root system development caused by promoted production of nodal and lateral roots under SMF. QTLs were identified for total nodal root length, total lateral root length, total root length, number of nodal roots, and branching index under SMF at vegetative and reproductive stages. The QTLs detected at vegetative and reproductive stages were different. We discuss here that relationship between root system of G3-3 and the detected QTLs. Therefore, G3-3 and the identified QTLs could be useful genetic materials in breeding program for improving the adaptation of rice plants in target rainfed lowland areas.
24.
- Title: Laws, Regulations, Guidelines, and Principles Pertaining to Laboratory Animals in Southeast Asia
- Journal: Laboratory Animals [Second Edition] Regulations and Recommendations for the Care and Use of Animals in Research 2018
- Author from VNUA:Nguyễn Bá Tiếp
- Authors: Montip Gettayacamin,1, Richard Grant2, Holl Davun3, John E. Heidrich4, Sorn San5, Yasmina Arditi Paramastri6, Imelda Liunanita Winoto7, Dondin Sajuthi7, Goh Yong Meng8, Abdul Rahim Mutalib8, Ranillo Rodrigo G. Resuello9, Maria Amelita C. Estacio10, Joel V
- Abstract:
This article describes current laws, regulations, guidelines, and principles pertaining to animals used for research, teaching, and testing in some countries of Southeast Asia region including Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam. There is no specific overarching legislation applied for animal welfare relevant directly to animals used for research, testing, and teaching in the region. All countries in the Southeast Asia subregion are members of the World Organisation for Animal Health [OIE]. The OIE Terrestrial Animal Health Code [the Terrestrial Code] sets out standards for the improvement of animal health and welfare and veterinary public health worldwide, including standards for safe international trade in terrestrial animals [mammals, birds, and bees] and their products. This is achieved through the detailing of animal health measures to be used by the veterinary authorities of importing and exporting countries to avoid the transfer of agents pathogenic for animals or humans, while avoiding unjustified trade barriers. In 2015, there was the publication of the Animal Welfare Act by the parliament of Malaysia and the Animals for Scientific Purposes Act by the Royal Thai Government. Recently, the Veterinary Law has come into effect in July 2016 marking a progress in animal welfare in Vietnam. There has been no recent development of any law pertaining to laboratory animals in Cambodia.
25.
- Title: Plasticity in nodal root elongation through the hardpan triggered by rewatering during soil moisture fluctuation stress in rice
- Journal: scientific reports
- Author from VNUA:Trần Thị Thiêm
- Authors: Roel Rodriguez Suralta, Jonathan Manito Niones, Mana Kano-Nakata, Thiem Thi Tran, Shiro Mitsuya & Akira Yamauchi
- Abstract:
Rainfed lowland [RFL] rice fields have hardpans and experience soil moisture fluctuations [SMF] stress, which influence root system development. Here, we clarify the expression and timing of the plasticity in nodal root elongation through the hardpan under SMF and its contribution to shoot growth using a shallow-rooting IR64 and its deep-rooting introgression line, YTH304. Under SMF, soil moisture content had negative relationship with soil penetration resistance, regardless of hardpan bulk densities. YTH304 had greater root system below the hardpan than IR64 in hardpan with 1.50 but not in 1.70 g cm−3 bulk density [BD]. YTH304 had greater plasticity in nodal root elongation through the hardpan than IR64 under SMF, which was clearly expressed during rewatering. YTH304 also had greater soil water uptake below the hardpan during drought and greater shoot growth than IR64. The results imply that deep root system development during SMF was due to the plasticity in nodal root elongation through the hardpan expressed during rewatering rather than during drought periods. This is against the long standing belief that active root elongation through the hardpan happens during drought. This also implies a need to revisit current root screening methods to identify rice lines with good hardpan penetration ability.
26.
- Title: By-product Originating from Artisan Distillers of Rice Alcohol in Northern Vietnam: Production, Use and Nutrient Value for Smallholder Pig Raising
- Journal: World Journal of Agricultural Research
- Author from VNUA:1. Nguyễn Công Oánh 2. Phạm Kim Đăng 3. Đỗ Đức Lực 4. Vũ Đình Tôn
- Authors: Nguyen Cong Oanh, Pham Kim Dang, Do Duc Luc, Jérôme Bindelle, Nassim Moula, Vu Dinh Ton, Jean-Luc Hornick
- Abstract:
The objective of this study was to investigate by-product production originating from artisan distillers of rice alcohol and its use as pig feed in three provinces [Hai Duong, Hung Yen and Bac Giang] of Northern Vietnam. A total of 120 rice alcohol producers classified by production scales [30 producers for Large-L, 45 producers for Medium-M and 45 producers for Small-S] were interviewed from January to August 2015. Additionally, sixty-three rice distiller’s by-product samples were collected from the study areas to determine their daily nutrient content according to one week storage time. The annual dry matter feedstuff production was estimated to 4.8, 3.0 and 2.1 tons per household for L, M and S scales, respectively [p