PBMCs transcriptome profiles identified breed-specific transcriptome signatures for PRRSV vaccination in German Landrace and Pietrain pigs

Porcine reproductive and respiratory syndrome (PRRS) is a devastating viral disease affecting the swine industry worldwide. Genetic variation in host immunity has been considered as one of the potential determinants to improve the immunocompetence, thereby resistance to PRRS. Therefore, the present study aimed to investigate the breed difference in innate immune response to PRRSV vaccination between German Landrace (DL) and Pietrain (Pi) pigs. We analyzed microarray-based transcriptome profiles of peripheral blood mononuclear cells (PBMCs) collected before (0 h) and 24 h after PRRSV vaccination from purebred DL and Pi pigs with three biological replicates. In total 4,269 transcripts were identified to be differentially expressed in PBMCs in at least any of four tested contrast pairs (i.e. DL-24h vs. DL-0h, Pi-24h vs. Pi-0h, DL-0h vs. Pi-0h and DL-24h vs. Pi-24h). The number of vaccine-induced differentially expressed genes (DEGs) was much higher (2,459) in DL pigs than that of Pi pigs (291). After 24 h of PRRSV vaccination, 1,046 genes were differentially expressed in PMBCs of DL pigs compared to that of Pi (DL-24h vs. Pi-24h), indicating the breed differences in vaccine responsiveness. The top biological pathways significantly affected by DEGs of both breeds were linked to immune response functions. The network enrichment analysis identified ADAM17, STAT1, MMS19, RPA2, BAD, UCHL5 and APC as potential regulatory genes for the functional network of PRRSV vaccine response specific for DL; while FOXO3, IRF2, ADRBK1, FHL3, PPP2CB and NCOA6 were found to be the most potential hubs of Pi specific transcriptome network. In conclusion, our data provided insights of breed-specific host transcriptome responses to PRRSV vaccination which might contribute in better understanding of PPRS resistance in pigs

Conservation agriculture for rice-based intensive cropping by smallholders in the Eastern Gangetic Plain

We review the recent development of Conservation Agriculture (CA) for rice-based smallholder farms in the Eastern Gangetic Plain (EGP) and the underpinning research on agronomy, weed control, soil properties and greenhouse gas emissions being tested to accelerate its adoption in Bangladesh. The studies are based mostly on minimum soil disturbance planting in strip planting (SP) mode, using the Versatile Multi-crop Planter (VMP), powered by a two-wheel tractor (2WT). One-pass SP with the VMP decreased fuel costs for crop establishment by up to 85% and labour requirements by up to 50%. We developed strip-based non-puddled rice (Oryza sativa) transplanting (NPT) in minimally-disturbed soil and found that rice grain yield increased (by up to 12%) in longer-term practice of CA. On farms, 75% of NPT crops increased gross margin. For non-rice crops, relative yield increases ranged from 28% for lentil (Lens culinaris) to 6% for wheat (Triticum aestivum) on farms that adopted CA planting. Equivalent profit increases were from 47% for lentil to 560% for mustard (Brassica juncea). Moreover, VMP and CA adopting farms saved 34% of labour costs and lowered total cost by up to 10% for production of lentil, mustard, maize (Zea mays) and wheat. Effective weed control was obtained from the use of a range of pre-emergent and post-emergence herbicides and retention of increased crop residue. In summary, a substantial body of research has demonstrated the benefits of CA and mechanized planting for cost savings, yield increases in many cases, increased profit in most cases and substantial labour saving. Improvement in soil quality has been demonstrated in long-term experiments together with reduced greenhouse gas emissions

Evaluation of TRMM rainfall products for hydrological uses at different scales

The principal objectives of the thesis are two: firstly to study the accuracy of the satellite rainfall products in climatologically distinctive places at different scales and secondly to find the possibility of using satellite-rain gauge blended rainfall products for hydrological purposes.Three case study areas Catalunya, Bangladesh, and South Africa have been chosen for the analysis using the satellite rainfall products (TMPA) and rain gauge records for the period from January 2005 to December 2009. The areal pattern of rainfall has been presented using satellite rainfall products over the case study areas. Both daily and monthly products are showing good agreement with rain gauge records although it is highly variable with space and seasonality. From the results, it can be shown that TRMM satellite identified the seasonal variability of rainfall. Moreover, the mean TRMM rainfall products show same pattern as like mean rain gauge observations in daily and monthly scale in all case study areas.Finally, a blending technique is applied (originally used for radar-rain gauge blending) to conform satellite rainfall products to rain gauge observations. This blended product is also tested against the rain gauge records to verify the improvement of the blended rainfall products over the original satellite products. Results of blended rainfall products enlightens few aspects or issues that should consider before applying blending technique including density of rain gauge network and resolution of TRMM pixel

Modification of nutrient requirements for a four Crop-Based cropping system to increase system productivity, maintain soil fertility, and achieve sustainable intensification

Sustainable and resilient cropping intensity is now a global focus to address the food demand and nutrition security of the growing population. For sustainable intensification, maintaining soil fertility is a key concern. The nutrient management for the recently developed four crop-based cropping system in Bangladesh has not yet been studied. Hence, field experiments were conducted on the nutrient management of the four crop-based cropping system [Aus (pre-monsoon rice), Aman (monsoon rice), lentil, and mungbean] in calcareous soil in Bangladesh during the years of 2016/17 and 2017/18 to determine the appropriate fertilizer management package to improve crop productivity and sustain soil fertility. The experiment had six treatments assigned in a randomized complete block design with three replications. The treatments included T1 = control (without synthetic fertilizer), T2 = 50% recommended dose of fertilizer (RDF), T3 = 75% RDF, T4 = 100% RDF, T5 = 125% RDF, and T6 = farmers’ practice (FP). The results revealed that the 125% RDF significantly contributed to higher yields of all four crops. The rice equivalent yield (REY) was the highest for the fertilizer management of 125% RDF, which was 45.5%, 9.4%, and 12.2% higher than the control (T1), 100% RDF (T4), and FP, respectively. Considering the uptake of nutrients (N, P, K, S, Zn, and B) by the crops in the cropping system, the 125% RDF was superior to the other treatments. The nutrient management practices had a positive influence on the apparent nutrient recovery (ANR) efficiency of the cropping system. The fertilizer management of 125% RDF was also economically more profitable due to the increment in the cost–benefit ratio of 26.8%, 4.4%, and 4.9% over the control, 100% RDF, and FP, respectively. The results indicate that the current fertilizer recommendations and FP for aus, aman, lentil, and mungbean are not adequate for the change from the three crop to the four crop-based pattern, and an increased dose of fertilizer is required to increase the yield of each individual crop as well as the total system’s productivity. The fertilizer use efficiency is also higher for 125% RDF than the 100% RDF and FP indicating that to sustain the soil fertility in the four crop-based system, the current RDF and FP are not sufficient. This finding will help intensive cropping areas in preventing nutrient deficiencies that would lead to a reduction in the crop yield

Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology

Disease occurrence adversely affects livestock production and animal welfare, and have an impact on both human health and public perception of food–animals production. Combined efforts from farmers, animal scientists, and veterinarians have been continuing to explore the effective disease control approaches for the production of safe animal-originated food. Implementing the immunogenomics, along with genome editing technology, has been considering as the key approach for safe food–animal production through the improvement of the host genetic resistance. Next-generation sequencing, as a cutting-edge technique, enables the production of high throughput transcriptomic and genomic profiles resulted from host-pathogen interactions. Immunogenomics combine the transcriptomic and genomic data that links to host resistance to disease, and predict the potential candidate genes and their genomic locations. Genome editing, which involves insertion, deletion, or modification of one or more genes in the DNA sequence, is advancing rapidly and may be poised to become a commercial reality faster than it has thought. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) [CRISPR/Cas9] system has recently emerged as a powerful tool for genome editing in agricultural food production including livestock disease management. CRISPR/Cas9 mediated insertion of NRAMP1 gene for producing tuberculosis resistant cattle, and deletion of CD163 gene for producing porcine reproductive and respiratory syndrome (PRRS) resistant pigs are two groundbreaking applications of genome editing in livestock. In this review, we have highlighted the technological advances of livestock immunogenomics and the principles and scopes of application of CRISPR/Cas9-mediated targeted genome editing in animal breeding for disease resistance

Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigs

Background Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important viral diseases affecting swine industry worldwide. Despite routine farm vaccination, effective control strategies for PRRS remained elusive which underscores the need for in-depth studies to gain insight into the host immune response to vaccines. The current study aimed to investigate transcriptional responses to PRRS Virus (PRRSV) vaccine in the peripheral blood mononuclear cells (PBMCs) within 3 days following vaccination in German Landrace pigs. Results Transcriptome profiling of PBMCs from PRRSV vaccinated and age-matched unvaccinated pigs at right before (0 h), and at 6, 24 and 72 h after PRRSV vaccination was performed using the Affymetrix gene chip porcine gene 1.0 st array. Comparison of PBMCs transcriptome profiles between vaccinated and unvaccinated pigs revealed a distinct host innate immune transcriptional response to PRRSV vaccine. There was a significant temporal variation in transcriptional responses of PRRSV vaccine in PBMCs accounting 542, 2,263 and 357 differentially expressed genes (DEGs) at 6, 24 and 72 h post vaccination, respectively compared to the time point before vaccination (controls). Gene ontology analysis revealed the involvement of these DEGs in various biological process including innate immune response, signal transduction, positive regulation of MAP kinase activity, TRIF-dependent toll-like receptor signaling pathway, T cell differentiation and apoptosis. Immune response specific pathways such as cytokine-cytokine receptor interaction, chemokine signaling pathway, signal transduction, JAK-STAT pathway and regulation, TRAF6 mediated induction of NF-kB and MAPK, the NLRP3 inflammasome, endocytosis and interferon signaling were under regulation during the early stage of PRRSV vaccination. Network enrichment analysis revealed APP, TRAF6, PIN1, FOS, CTNNB1, TNFAIP3, TIP1, CDKN1, SIRT1, ESR1 and HDAC5 as the highly interconnected hubs of the functional network of PRRSV vaccine induced transcriptome changes in PBMCs. Conclusions This study showed that a massive gene expression change occurred in PBMCs following PRRSV vaccination in German Landrace pigs. Within first 3 days of vaccine exposure, the highest transcript abundance was observed at 24 h after vaccination compared to that of control. Results of this study suggest that APP, TRAF6, PIN1, FOS, CDKN1A and TNFAIP3 could be considered as potential candidate genes for PRRSV vaccine responsiveness

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer’s health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value 1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program

PBMC transcriptome profiles identifies potential candidate genes and functional networks controlling the innate and the adaptive immune response to PRRSV vaccine in Pietrain pig

The porcine reproductive and respiratory syndrome (PRRS) is a devastating viral disease affecting swine production, health and welfare throughout the world. A synergistic action of the innate and the adaptive immune system of the host is essential for mounting a durable protective immunity through vaccination. Therefore, the current study aimed to investigate the transcriptome profiles of peripheral blood mononuclear cells (PBMCs) to characterize the innate and the adaptive immune response to PRRS Virus (PRRSV) vaccination in Pietrain pigs. The Affymetrix gene chip porcine gene 1.0 ST array was used for the transcriptome profiling of PBMCs collected at immediately before (D0), at one (D1) and 28 days (D28) post PRRSV vaccination with three biological replications. With FDR <0.05 and log2 fold change ±1.5 as cutoff criteria, 295 and 115 transcripts were found to be differentially expressed in PBMCs during the stage of innate and adaptive response, respectively. The microarray expression results were technically validated by qRT-PCR. The gene ontology terms such as viral life cycle, regulation of lymphocyte activation, cytokine activity and inflammatory response were enriched during the innate immunity; cytolysis, T cell mediated cytotoxicity, immunoglobulin production were enriched during adaptive immunity to PRRSV vaccination. Significant enrichment of cytokine-cytokine receptor interaction, signaling by interleukins, signaling by the B cell receptor (BCR), viral mRNA translation, IFN-gamma pathway and AP-1 transcription factor network pathways were indicating the involvement of altered genes in the antiviral defense. Network analysis revealed that four network modules were functionally involved with the transcriptional network of innate immunity, and five modules were linked to adaptive immunity in PBMCs. The innate immune transcriptional network was found to be regulated by LCK, STAT3, ATP5B, UBB and RSP17. While TGFß1, IL7R, RAD21, SP1 and GZMB are likely to be predictive for the adaptive immune transcriptional response to PRRSV vaccine in PBMCs. Results of the current immunogenomics study advances our understanding of PRRS in term of host-vaccine interaction, and thereby contribute to design a rationale for disease control strategy

Tilapia from most of the sources in Bangladesh are safe for human consumption: A Hazard Index (HI) based study on heavy metals

The present study was conducted to determine the variations of heavy metal (Cu, Pb, Ni, Cr, Cd, and Zn) bioaccumulation in edible muscles among the wild, pond-, gher- and cage-cultured tilapia, followed by risk assessment in humans caused by consumption of the contaminated fish. A total of 120 fishes from four different aquatic environments were collected, and the heavy metal levels were analyzed using an atomic absorption spectrophotometer (AAS). The result found the highest Zn concentration in all tilapia samples; however, the Ni was below the detection limit. The average concentrations of metals were found as Zn > Pb > Cr > Cu in wild tilapia, Zn > Pb > Cr > Cu > Cd in pond-cultured tilapia, Zn > Pb > Cr > Cd in gher-cultured tilapia, and Zn > Cd > Cr > Pb > Cu in cage-cultured tilapia. The estimated daily intake (EDI) value was lower than the maximum tolerable daily intake value, and target hazard quotient (THQ) and hazard index (HI) for adults, adolescent, and children was < 1 for wild and cultured tilapia, indicating that tilapia is safe for human consumption. However, high HI of Pb and Cd might be alarming and need further investigation in the near future

Autonomous Driving Vehicle System using LiDAR sensor

An overview of light detection and ranging (LiDAR) sensor technology for autonomous vehicles is presented in this paper. The sensor called LiDAR sensors is a key component of autonomous driving’s for the upcoming generation as an assistance function. LiDAR technology is discussed, including its characteristics, a technical overview, prospects as well as limitations in relation to other sensors available in the industry. Comparison and comment on sensor quality are based on factory parameters. The basic components of a LiDAR system from the laser transmitter to the beam scanning mechanism are explained