Characterization of an African swine fever virus outbreak in India and comparative analysis of immune genes in infected and surviving crossbreed vs. indigenous Doom pigs.

Since 2020, African swine fever (ASF) has affected all pig breeds in Northeast India except Doom pigs, a unique indigenous breed from Assam and the closest relatives of Indian wild pigs. ASF outbreaks result in significant economic losses for pig farmers in the region. Based on sequencing and phylogenetic analysis of the B646L (p72) gene, it has been determined that ASFV genotype II is responsible for outbreaks in this region. Recent studies have shown that MYD88, LDHB, and IFIT1, which are important genes of the immune system, are involved in the pathogenesis of ASFV. The differential expression patterns of these genes in surviving ASFV-infected and healthy Doom breed pigs were compared to healthy controls at different stages of infection. The ability of Doom pigs to withstand common pig diseases, along with their genetic resemblance to wild pigs, make them ideal candidates for studying tolerance to ASFV infection. In the present study, we investigated the natural resistance to ASF in Doom pigs from an endemic area in Northeast India. The results of this study provide important molecular insights into the regulation of ASFV tolerance genes.

Transcriptome signatures of host tissue infected with African swine fever virus reveal differential expression of associated oncogenes.

African swine fever (ASF) has emerged as a threat to swine production worldwide. Evasion of host immunity by ASF virus (ASFV) is well understood. However, the role of ASFV in triggering oncogenesis is still unclear. In the present study, ASFV-infected kidney tissue samples were subjected to Illumina-based transcriptome analysis. A total of 2463 upregulated and 825 downregulated genes were differentially expressed (p < 0.05). A literature review revealed that the majority of the differentially expressed host genes were key molecules in signaling pathways involved in oncogenesis. Bioinformatic analysis indicated the activation of certain oncogenic KEGG pathways, including basal cell carcinoma, breast cancer, transcriptional deregulation in cancer, and hepatocellular carcinoma. Analysis of host-virus interactions revealed that the upregulated oncogenic RELA (p65 transcription factor) protein of Sus scrofa can interact with the A238L (hypothetical protein of unknown function) of ASFV. Differential expression of oncogenes was confirmed by qRT-PCR, using the H3 histone family 3A gene (H3F3A) as an internal control to confirm the RNA-Seq data. The levels of gene expression indicated by qRT-PCR matched closely to those determined through RNA-Seq. These findings open up new possibilities for investigation of the mechanisms underlying ASFV infection and offer insights into the dynamic interaction between viral infection and oncogenic processes. However, as these investigations were conducted on pigs that died from natural ASFV infection, the role of ASFV in oncogenesis still needs to be investigated in controlled experimental studies.

Development of triplex assay for simultaneous detection of Escherichia coli, methicillin resistant and sensitive Staphylococcus aureus in raw pork samples of retail markets.

Escherichia coli and Staphylococcus aureus are the most important food borne pathogen transmitting from animal meat and meat products. Therefore, it is vital to design an accurate and specific diagnostic tool for identifying those food-borne pathogens in animal meat and meat products. In the current study, E. coli, methicillin-resistant and sensitive S. aureus (MRSA and MSSA) were simultaneously detected using a developed triplex PCR-based technique. To obtain an optimal reaction parameter, the multiplex assay was optimised by changing just one parameter while holding the others constant. Specificity of the assay was assessed using several porcine bacterial template DNA. The plasmid DNA was used to test the multiplex PCR assay's sensitivity and interference in spiked pork samples. E. coli, MRSA, and MSSA each have PCR amplified products with sizes of 335, 533, and 209 bp, respectively. The assay detects a minimum microbial load of 102 CFU/µl for all the three pathogens and can identify bacterial DNA as low as 10-2 ng/µl. The assay was validated employing 210 pork samples obtained from retail meat shops and slaughter houses, with MRSA, E. coli, and MSSA with the occurrence rate of 1.9%, 42.38%, and 18.1%, respectively. The rate of mixed bacterial contamination in pork meat samples examined with the developed method was 6.19%, 1.43%, 1.90%, and 1.43% for MSSA & E. coli, MRSA & E. coli, MSSA & MRSA, and E. coli, MSSA & MRSA, respectively. The developed multiplex PCR assay is quick and efficient, and it can distinguish between different bacterial pathogens in a single reaction tube.

Clinicopathological and ultrastructural study of African swine fever outbreak in North-East India.

The present investigation focuses on examining the clinical, histopathological, and ultrastructural changes that occurred in pig, during an outbreak of African swine fever (ASF) in 2022 in Assam, India. The disease initially manifested as a per-acute case with high mortality but without any evident clinical signs. Subsequently, some animals exhibited an acute form of the disease characterized by high fever (104-106 °F), anorexia, vomiting, respiratory distress, and bleeding from the anal and nasal orifices. During acute African swine fever virus (ASFV) infections, elevated levels of pro-inflammatory IL-1α, IL-1ß, IL-6, TNF, CCL2, CCL5, and CXCL10 were detected in the palatine tonsil, lymph nodes, spleen, and kidney using qPCR assay. These molecular changes were associated with haemorrhages, edemas, and lymphoid depletion. Postmortem examinations revealed prominent features such as splenomegaly with haemorrhages, haemorrhagic lymphadenitis, severe petechial haemorrhage in the kidney, pneumonia in the lungs, and necrotic palatine tonsil. Histopathological analysis demonstrated lymphocyte depletion in lymphoid organs, multi-organ haemorrhages, and interstitial pneumonia in the lungs. Scanning electron microscopy (SEM) further confirmed lymphocyte depletion in lymphoid organs through lymphocyte apoptosis and kidney damage with distorted tubules due to red blood cell destruction. Transmission electron microscopy reaffirmed lymphocyte apoptosis by observing chromatin condensation and nucleus margination in lymphocytes of lymphoid organs. These findings provide comprehensive insights into the clinical, histopathological, and ultrastructural aspects of ASF outbreak in pigs. Understanding the pathological changes associated with ASF can contribute to improved diagnosis, prevention, and control measures for this highly contagious and economically devastating viral disease.

CRISPR/cas9 cassette targeting Escherichia coli blaCTX-M specific gene of mastitis cow milk origin can alter the antibiotic resistant phenotype for cefotaxime.

CTX-M beta-lactamases are one of the most important extended spectrum beta-lactamase (ESBL) resistance enzymes found in E. coli. In the present study, 59% of E. coli isolates from mastitis cow milk were reported to be positive for ESBL types. The prevalence of beta-lactam (ß-lactam) antibiotic resistance was reported to be 84%, 72.7%, 52.27%, 50%, and 45.4% for cefotaxime, cefepime, cefuroxime, oxacillin, and cephalexine, respectively. The blaCTX-M gene was found in 65% (n = 17) of the E. coli isolates when they were genotyped. Further, the use of a CRISPR/cas9 cassette to target the E. coli blaCTX-M gene revealed changes in antibiotic phenotypes for cefotaxime.

Rumen microbial diversity, enteric methane emission and nutrient utilization of crossbred Karan-Fries cattle (Bos taurus) and Murrah buffalo (Bubalus bubalis) consuming varied roughage concentrate ratio.

Dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance. The goal of this study was to see how the roughage concentrate ratio 70:30 (Low concentrate; LC) vs 40:60 (High concentrate; HC) and the host species crossbred cattle vs buffalo affected rumen microbial diversity, enteric methane emissions and nutrient utilization. Dry matter intake (kg/d) and dry matter percent digestibility were considerably (p < 0.05) higher in the HC ration and buffalo compared to LC ration and crossbred cattle, respectively. Both dietary mix and host species had a substantial (p < 0.05) impact on intake of various nutrients, including organic matter (OM), crude protein (CP), ether extract (EE), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Increased concentrate proportion in the ration improved nitrogen balance, resulting in increased average daily gain and considerably reduced methane (g/d) output (p < 0.05). Furthermore, 16S rRNA genes were sequenced using Oxford Nanopore Technology (ONT) and subsequently annotated using the Centrifuge workflow to uncover ruminal bacterial diversity. Firmicutes was considerably (p < 0.01) greater in the LC diet, whereas, Bacteroidetes was higher in the HC ration. Genus Prevotella dominated all rumen samples, and buffalo fed LC ration had significantly (p < 0.01) higher Oscillospira abundance. At the species level, simple sugar-utilizing bacteria such as Prevotella spp. and Selenomonas ruminantium predominated in the crossbred cattle, but fibrolytic bacteria such as Oscillospira guilliermondii were statistically (p < 0.01) more abundant in the buffalo. Overall, dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance, however, host species remained a major driving force to change ruminal community composition as compared to roughage concentrate ratio under similar environmental conditions.

Development of multiplex PCR assay for simultaneous detection of African swine fever, porcine circo and porcine parvo viral infection from clinical samples.

A diagnostic method for simultaneously detecting and distinguishing African Swine Fever (ASF), porcine circovirus type 2 (PCV2), and porcine parvovirus (PPV) in clinical specimens is critical for differential diagnosis, monitoring, and control in the field. Three primer pairs were designed and used to create a multiplex PCR assay. In addition, 356 porcine post mortem tissue samples from various parts of India's North Eastern region were tested by the developed multiplex PCR assay to demonstrate its accuracy. Using the designed primers, each of the ASF, PCV2 and PPV target genes was amplified, but no other porcine virus genes were detected. The assay's limit of detection was 102 copies/µl of PCV2, PPV, or ASFV. The detection of PCV2, PPV, and ASF in postmortem tissue samples revealed that they are co-circulating in India's North-Eastern region. The percentage positivity (PP) for PCV2, PPV and ASF single infection were 7.02% (25/356), 3.93% (14/356), and 3.37% (12/356), respectively, while the PP for PCV2& PPV co-infection was 2.80% (10/356), ASF & PCV2 co infection was 1.4% (5/356) and the ASF, PPV& PCV2 co-infection was1.40% (5/356). The results also indicate that the ASF can infect pigs alongside PCV and PPV.

Differentially expressed microRNAs in biochemically characterized FrieswalTM crossbred bull semen.

In addition to the transmission of paternal genome, spermatozoa also carry coding as well as noncoding microRNAs (miRNAs) into the female oocyte during the process of biological fertilization. Based on RNA deep sequencing, a total 28 number of differentially expressed miRNAs were cataloged in categorized FrieswalTM crossbred (Holstein Friesian X Sahiwal) bull semen on the basis of conception rate (CR) in field progeny testing program. Validation of selected miRNAs viz. bta-mir-182, bta-let-7b, bta-mir-34c and bta-mir-20a revealed that, superior bull semen having comparatively (p < .05) lower level of all the miRNAs in contrast to inferior bull semen. Additionally, it was illustrated that, bta-mir-20a and bta-mir-34c miRNAs are negatively (p < .01) correlated with seminal plasma catalase (CAT) activity and glutathione peroxidase (GPx) level. Interactome studies identified that bta-mir-140, bta-mir-342, bta-mir-1306 and bta-mir-217 can target few of the important solute carrier (SLC) proteins viz. SLC30A3, SLC39A9, SLC31A1 and SLC38A2, respectively. Interestingly, it was noticed that all the SLCs were significantly (p < .05) expressed at higher level in superior quality bull semen and they are negatively correlated (p < .01) with their corresponding miRNAs as mentioned. This study may reflect the role of miRNAs in regulating few of the candidate genes and thus may influence the bull semen quality traits.

Genetic variants in 5'UTR and exonic region of NPY gene alter the reproduction performance in Indian cattle breeds.

Neuropeptide Y (NPY) is one of the most potent orexigenic factors which can produce diverse effects on behaviour and other physiological functions and is highly conserved in evolution. The present study was aimed to identify and associate SNPs in the 5' UTR and exon2 region of the NPY gene with reproduction and production traits in Kankrej cattle of Indian origin. Three mutations in the 5'-UTR region and one mutation in the exon2 region of the NPY gene were identified by PCR-SSCP and PCR-RFLP, respectively, followed by sequencing. Further, association studies were conducted with reproduction and production traits in Kankrej cattle. The GACCGA genotyped animals based on the 5'UTR variants indicated better dry period and calving interval, whereas with GGCCGG genotypes showed higher total lactation milk yield and 305-day milk yield in comparison to other genotypes. Also, service period and inter calving period varied significantly among the genotypes of exon2, as the GG genotyped animals had significantly longer calving interval. Other traits like age at first heat, age at first service and age at first calving were not affected by the mutations. So, the present study outlined that the bovine NPY gene may be considered to be one of the candidate gene for improvement of reproductive performance of cattle, after validation on large sample size.

Development of an on-site lateral flow immune assay based on mango leaf derived colloidal silver nanoparticles for rapid detection of Staphylococcus aureus in milk.

In order to ensure food safety, screening food samples for the presence of pathogens has been categorised as a legal testing item throughout the globe. One of the most prevalent zoonotic bacteria transmitted through dairy milk is Staphylococcus aureus. Given the limitations of the conventional detection methods, in the current study we desigined a competitive lateral flow immune assay (LFIA) using colloidal silver nanoparticles derived from mango leaves for the detection of Staphylococcus aureus in cow milk. SpA, a recombinant protein of Staphylococcus aureus, was used to raised hyperimmune sera used for developing the assay followed by conjugation with the synthesized nanoparticles. To increase the specificity of the assay, the milk samples were prenriched with selective agar exclusively require for Staphyloccocus aureus. The assay was found to be completed within 7-8 h by observing test and control lines in LFIA strips. The developed assay was found to specifically detect the bacteria as low as 1000 cfu/ml of milk samples. With a total 230 number of raw and clinical mastitis milk samples, the assay was validated and achieved relative accuracy, specificity, and sensitivity values of 97.39, 98.03, and 96.1%, respectively. The developed LFIA, which uses economically feasible and stable silver nanoparticles derived from mango leaves, has the potential for routine screening of milk samples for the presence of Staphylococcus aureus, especially in low-resource settings, allowing for early diagnosis, which facilitates effective treatment for the dairy animals and prevents the transmission of the disease in consumers.

Profiling of key heat shock proteins and their relationship with male sexual behavior and seminal characteristics in Kankrej (Bos indicus) breeding bulls during different seasons.

The goal of this study is to use indirect ELISA to determine the concentration of major heat shock proteins (Hsps) in Kankrej (Bos indicus) breeding bulls and their relationship with certain male phenotypic traits including sexual behavior, sperm quality, and bull fertility in different seasons. The seasonal fluctuation in the concentration of three major Hsps (60, 70, and 90) was determined using an indirect enzyme-linked immunosorbent assay (ELISA). According to the findings, Hsps levels are significantly higher during the summer season and are associated with both fresh and post-thawed semen quality traits in Kankrej breeding bulls. The better sexual behavior of bulls and seminal parameters of fresh or thawed semen was observed in the winter season together with the lower concentrations of HSPs. These could suggest negative association between HSPs with bull sexual behavior and seminal parameters. As a result, the concentration of Hsps in breeding bulls may be a useful indicator for determining fertility traits.

Characterization of a putative ribosome binding site at the 5' untranslated region of bovine heat shock protein 90.

Untranslated regions (UTRs) of the transcripts play significant roles in translation regulation and continue to raise many intriguing questions in our understanding of cellular stress physiology. Internal ribosome entry site (IRES) mediated alternative translation initiations are emerging as unique mechanisms. Present study is aimed to indentify a functional short 92 base pair length putative sequence located at the 5' untranslated region of bovine heat shock protein 90 AA1 (Hsp90AA1) may interact with ribosomal as well as eukaryotic initiation factor binding site. Here we have predicted both the two and three dimensional structures of bovine Hsp90AA1 IRES (MF400854) element with their respective free energy. Molecular interactions between bovine RPS5 and IRES have been determined after the preparation of docking complex of IRES bound RPS5. Structure of bovine ribosomal translational initiation factor (TIF) has also been determined and docked with IRES. Molecular interaction between bovine TIF and IRES was analyzed from the complex structure. We further detected the relative expression efficiency of the viral (original) in relation with Hsp90AA1 IRES-driven GFP expression, which revealed that efficiency under the control of identified bovine Hsp90AA1 IRES was slightly lower than viral origin. It was also noted that identified bovine HSP90 IRES may increase the expression level of GFP under in vitro heat stressed condition.

Association of bovine KISS1 single nucleotide polymorphisms with reproductive traits in Indian Cattle.

Kisspeptins, a family of neuropeptide encoded by the Kiss1 gene, have emerged as crucial regulator of fertility and reproduction by regulating the hypothalamic-pituitary-gonadal axis. The present study was aimed to identify and associate SNPs in the KISS1 gene with reproductive traits in cattle of Indian origin. DNA samples collected from 300 individual cows of three Indian dairy breeds (Gir, Kankrej and Frieswal) of cattle were used in the study. The SNPs of KISS1 gene were identified with PCR-RFLP and sequence analysis using two sets of primer pairs. A total of 5 SNPs were identified in the targeted region of which, two were selected for screening the population and association studies. The analysis revealed that genotypes of rs442633552G>A and rs42022871C>T had a significant association with dry period. The SNP rs42022871C>T also established significant role in milk production traits, and selection of TT-genotyped animals will improve the reproduction and production potential of the animals.

Expression pattern of bta-mir-2898 miRNA and their correlation with heat shock proteins during summer heat stress among native vs crossbred cattle.

Earlier studies identified the role of bta-mir-2898 in bovine. Our earlier study identified that, bta-mir-2898 can be over expressed in crossbred cattle during heat stress. Nevertheless the differential expression of bta-mir-2898 among native vs crossbred cattle during summer stress along with it's correlation with different heat shock proteins (HSPs) is not yet studied. In the present context, we studied the differential expression of bta-mir-2898 among Frieswal (Bos indicus x Bos taurus) and Sahiwal (Bos indicus) breeds of cattle during a range of environmental air temperatures and further investigated the correlation of bta-mir-2898 with different HSPs (HSP70, HSP90, HSP60. HSF, HSPB8 and HSP27). It was observed that, at peak air temperature the relative miRNA expression level (p < 0.05) of bta-mir-2898 was 3.4 ± 0.41 and 0.79 ± 0.22 among Frieswal and Sahiwal, respectively. We also observed significant levels (p < 0.05) of mRNA abundance of HSP70, HSP90, HSPB8 and HSP27 among the breeds. In all the cases Sahiwal found to exhibited higher level of HSPs in comparison to Frieswal. Studies revealed that the expression profile of bta-mir-2898 was negatively correlated with the expression of all the HSPs during thermal stress in post anti-mir2898 treated PBMC invitro cultured model originated from both Frieswal and Sahiwal cattle breeds. However, significantly (p < 0.05) higher negative correlations were observed between bta-mir-2898 and HSP70, HSP60 and HSPB8. Present findings highlighted the preliminary role of overexpressed bta-mir-2898 in cattle during thermal stress and its impact on different heat shock proteins.

Effect of heat stress on superoxide anion production in native and crossbred cattle under in vitro whole blood culture model.

Impact of global warming on the dairy industry has gained attention due to huge economic losses through low production and fertility caused by heat stress. Exposure to hyperthermia provokes a series of complex responses in mammals which are been related to morphological and physiological alterations including the production of reactive oxygen species (ROS). A quantitative spectrophotometric based nitroblue tetrazolium (NBT) reduction assay was used to estimate the superoxide anion (•O2-) level in heat stressed (at 42 °C) whole blood cultures of native and crossbred bulls (Sahiwal and Frieswal), in vitro. The breed effect in the kinetics of •O2- production at different time periods of continual heat stress was analyzed by repeated measures ANOVA. Comparison between different time periods in reference to 37 °C was analyzed by paired t-test. The •O2- level was significantly different (p < 0.05) between cells at 37 °C and 42 °C at different periods of incubation. Kinetics study showed increment of •O2- production on the acute phase of stress followed by a reduction in both Sahiwal and Frieswal breeds. In Sahiwal breed, the inflated superoxide level continued abated till 4 h and raised again at 6 h, while in Frieswal •O2- level reverted to raise sooner with in 2 h of incubation itself. Contrarily, kinetic of •O2- level in plasma showed a significant reduction (p < 0.001) at 30 min of 42 °C incubation followed by increment of •O2- level. Further, the breed variation was significant (p < 0.05) and a significant high reduction of •O2- level was observed in Sahiwal breed. Our finding indicates that, a better and longer •O2- production homeostasis and higher plasma scavenging ability of native breed may be one of the reasons for the higher thermal tolerance of these breeds in tropical climate.

A Synonymous Mutation at Bovine Alpha Vitronectin Domain of Integrin Host Receptor (ITGAV) Gene Effect the Susceptibility of Foot-and-Mouth Disease in Crossbred Cattle.

Integrins are one of the major biologically active proteins responsible for Foot-and-mouth disease virus (FMDV)- host interaction. Out of various heterodimeric integrins discovered, αVß6 heterodimer serves as the chief receptor for FMDV host tropism. Earlier studies reported that, SNPs at beta 6 subunit (ITGB6) were associated with the occurrence of the diseases in cattle. In this study we report the association between a synonymous SNP (rs719257875) at bovine alpha vitronectin domain of integrin receptor (ITGAV) gene and FMD susceptibility in cattle. A strong significant association (P < 0.0001) of the genotypes with FMD susceptibility were obtained, where the CC genotypes play a major role in occurrence of FMD in crossbred cattle.

Small interfering RNA based knock down of acute heat shock and or GGA inducible bovine heat shock protein 70 may interfere invitro expression pattern of TLR2/4 and NOD1/2.

Heat shock protein 70 (Hsp70) is a widely known mammalian stress-inducible protein critical for cytoprotection against different stressors. Despite the chaperone based cytoprotective functions, intracellular Hsp70 also participates in diverse immune modulatory activities. To investigate the immune modulatory effect of inducible bovine Hsp70, we examined the expression profile of four major pattern recognition receptors (PRRs) viz. TLR2/4 and NOD1/2 using two different invitro cell cultured models. We observed that, invitro acute heat stress and Geranylgeranylacetone (GGA) induction increased the level of Hsp70 which upregulated the expression of all the four PRRs in both the cell cultured models. However, the expression level of TLR4 was found to be highest followed by NOD2, TLR2 and NOD1. Conversely, specific siRNA based knockdown of Hsp70 showed a decreased expression level of all the four PRRs. This study may add some references pertaining to the innate immune modulatory effects of bovine heat shock protein 70.

RT-LAMP assay: an alternative approach for profiling of bovine heat shock protein 70 gene in PBMC cultured model.

The purpose of this study is to develop a novel Reverse Transcriptase Loop-mediated isothermal amplification (RT-LAMP) based assay for in vitro profiling of heat shock protein 70 (Hsp70) in bovine peripheral blood mononuclear cell (PBMC) culture model utilizing the absorbance level of magnesium pyrophosphate-a by-product of LAMP reaction. A set of bovine Hsp70 specific RT-LAMP primers were designed to detect the differential absorbance level of magnesium pyrophosphate by-product which signifies the degree of Hsp70 amplification from cDNA of thermally induced cultured cells at different recovery periods. The study revealed significant (P < 0.05) correlation between absorbance level and the fold change of Hsp70 transcripts at different kinetic intervals of heat stress recovery in bovine PBMC cell culture models. RT-LAMP based absorbance assay can be used as an indicator to measure the degree of bovine Hsp70 transcripts produced during thermal stress and can be used as an alternative to the traditional Real time PCR assay. Developed RT-LAMP assay can be used as a cost-effective method for profiling of bovine HSP70 gene.

Comparative expression profile of NOD1/2 and certain acute inflammatory cytokines in thermal-stressed cell culture model of native and crossbred cattle.

Thermotolerance depends mainly on the health and immune status of the animals. The variation in the immune status of the animals may alter the level of tolerance of animals exposed to heat or cold stress. The present study was conducted to investigate the expression profile of two important nucleotide binding and oligomerization domain receptors (NLRs) (NOD1 and NOD2) and their central signalling molecule RIP2 gene during in vitro thermal-stressed bovine peripheral blood mononuclear cells (PBMCs) of native (Sahiwal) and crossbred (Sahiwal X HF) cattle. We also examined the differential expression profile of certain acute inflammatory cytokines in in vitro thermal-stressed PBMC culture among native and its crossbred counterparts. Results revealed that the expression profile of NOD1/2 positively correlates with the thermal stress, signalling molecule and cytokines. Present findings also highlighted that the expression patterns during thermal stress were comparatively superior among indigenous compared to crossbred cattle which may add references regarding the better immune adaptability of Zebu cattle.

Untranslated regions (UTRs) orchestrate translation reprogramming in cellular stress responses.

Stress is the result of an organism's interaction with environmental challenges. Regulations of gene expression including translation modulations are critical for adaptation and survival under stress. Untranslated regions (UTRs) of the transcripts play significant roles in translation regulation and continue to raise many intriguing questions in our understanding of cellular stress physiology. IRES (Internal ribosome entry site) and uORF (upstream open reading frame) mediated alternative translation initiations are emerging as unique mechanisms. Recent studies have revealed novel means of mRNAs stabilization in stress granules and their reversible modifications. Differential regulation of select transcripts is possible by the interplay between the adenine/uridine-rich elements (AREs) in 3'UTR with their binding proteins (AUBP) and by microRNA-mediated effects. Coordination of these various mechanisms control translation and thereby enables appropriate responses to environmental stress. In this review, we focus on the role of sequence signatures both at 5' and 3'UTRs in translation reprogramming during cellular stress responses.