RNA N6-Methyladenosine Affects Copper-Induced Oxidative Stress Response in Arabidopsis thaliana.

Recently, post-transcriptional regulation of mRNA mediated by N6-methyladenosine (m6A) has been found to have profound effects on transcriptome regulation during plant responses to various abiotic stresses. However, whether this RNA modification can affect an oxidative stress response in plants has not been studied. To assess the role of m6A modifications during copper-induced oxidative stress responses, m6A-IP-seq was performed in Arabidopsis seedlings exposed to high levels of copper sulfate. This analysis revealed large-scale shifts in this modification on the transcripts most relevant for oxidative stress. This altered epitranscriptomic mark is known to influence transcript abundance and translation; therefore we scrutinized these possibilities. We found an increased abundance of copper-enriched m6A-containing transcripts. Similarly, we also found increased ribosome occupancy of copper-enriched m6A-containing transcripts, specifically those encoding proteins involved with stress responses relevant to oxidative stressors. Furthermore, the significance of the m6A epitranscriptome on plant oxidative stress tolerance was uncovered by assessing germination and seedling development of the mta (N6-methyladenosine RNA methyltransferase A mutant complemented with ABI3:MTA) mutant exposed to high copper treatment. These analyses suggested hypersensitivity of the mta mutant compared to the wild-type plants in response to copper-induced oxidative stress. Overall, our findings suggest an important role for m6A in the oxidative stress response of Arabidopsis.

The Diversity and Functions of Plant RNA Modifications: What We Know and Where We Go from Here.

Since the discovery of the first ribonucleic acid (RNA) modifications in transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), scientists have been on a quest to decipher the identities and functions of RNA modifications in biological systems. The last decade has seen monumental growth in the number of studies that have characterized and assessed the functionalities of RNA modifications in the field of plant biology. Owing to these studies, we now categorize RNA modifications based on their chemical nature and the RNA on which they are found, as well as the array of proteins that are involved in the processes that add, read, and remove them from an RNA molecule. Beyond their identity, another key piece of the puzzle is the functional significance of the various types of RNA modifications. Here, we shed light on recent studies that help establish our current understanding of the diversity of RNA modifications found in plant transcriptomes and the functions they play at both the molecular (e.g., RNA stability, translation, and transport) and organismal (e.g., stress response and development) levels. Finally, we consider the key research questions related to plant gene expression and biology in general and highlight developments in various technologies that are driving our insights forward in this research area.

Covalent RNA modifications and their budding crosstalk with plant epigenetic processes.

Our recent cognizance of diverse RNA classes undergoing dynamic covalent chemical modifications (or epitranscriptomic marks) in plants has provided fresh insight into the underlying molecular mechanisms of gene expression regulation. Comparatively, epigenetic marks comprising heritable modifications of DNA and histones have been extensively studied in plants and their impact on plant gene expression is quite established. Based on our growing knowledge of the plant epitranscriptome and epigenome, it is logical to explore how the two regulatory layers intermingle to intricately determine gene expression levels underlying key biological processes such as development and response to stress. Herein, we focus on the emerging evidence of crosstalk between the plant epitranscriptome with epigenetic regulation involving DNA modification, histone modification, and non-coding RNAs.

mRNA N6 -methyladenosine is critical for cold tolerance in Arabidopsis.

Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m6 A, m5 C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post-transcriptional regulation that plays an important role in modulating gene expression. The importance of m6 A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m6 A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m6 A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m6 A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m6 A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m6 A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m6 A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.

The impact of epitranscriptomic marks on post-transcriptional regulation in plants.

Ribonucleotides within the various RNA molecules in eukaryotes are marked with more than 160 distinct covalent chemical modifications. These modifications include those that occur internally in messenger RNA (mRNA) molecules such as N6-methyladenosine (m6A) and 5-methylcytosine (m5C), as well as those that occur at the ends of the modified RNAs like the non-canonical 5' end nicotinamide adenine dinucleotide (NAD+) cap modification of specific mRNAs. Recent findings have revealed that covalent RNA modifications can impact the secondary structure, translatability, functionality, stability and degradation of the RNA molecules in which they are included. Many of these covalent RNA additions have also been found to be dynamically added and removed through writer and eraser complexes, respectively, providing a new layer of epitranscriptome-mediated post-transcriptional regulation that regulates RNA quality and quantity in eukaryotic transcriptomes. Thus, it is not surprising that the regulation of RNA fate mediated by these epitranscriptomic marks has been demonstrated to have widespread effects on plant development and the responses of these organisms to abiotic and biotic stresses. In this review, we highlight recent progress focused on the study of the dynamic nature of these epitranscriptome marks and their roles in post-transcriptional regulation during plant development and response to environmental cues, with an emphasis on the mRNA modifications of non-canonical 5' end NAD+ capping, m6A and several other internal RNA modifications.

Erratum to "Sero-prevalence of Toxoplasma gondii in sheep in different geographical regions of Nepal" [5C (June 2018) 7-9].

[This corrects the article DOI: 10.1016/j.vas.2018.01.001.].

A Novel Live Attenuated Vaccine Candidate Protects Against Heterologous Senecavirus A Challenge.

Senecavirus A (SVA) is an emerging picornavirus causing vesicular disease (VD) clinically indistinguishable from foot-and-mouth disease (FMD) in pigs. Currently there are no vaccines currently available for SVA. Here we developed a recombinant SVA strain (rSVAm SacII) using reverse genetics and assessed its immunogenicity and protective efficacy in pigs. In vivo characterization of the rSVAm SacII strain demonstrated that the virus is attenuated, as evidenced by absence of lesions, decreased viremia and virus shedding in inoculated animals. Notably, while attenuated, rSVA mSacII virus retained its immunogenicity as high neutralizing antibody (NA) responses were detected in inoculated animals. To assess the immunogenicity and protective efficacy of rSVA mSacII, 4-week-old piglets were sham-immunized or immunized with inactivated or live rSVA mSacII virus-based formulations. A single immunization with live rSVA mSacII virus via the intramuscular (IM) and intranasal (IN) routes resulted in robust NA responses with antibodies being detected between days 3-7 pi. Neutralizing antibody responses in animals immunized with the inactivated virus via the IM route were delayed and only detected after a booster on day 21 pi. Immunization with live virus resulted in recall T cell proliferation (CD4+, CD8+, and CD4+/CD8+ T cells), demonstrating efficient stimulation of cellular immunity. Notably, a single dose of the live attenuated vaccine candidate resulted in protection against heterologous SVA challenge, as demonstrated by absence of overt disease and reduced viremia, virus shedding and viral load in tissues. The live attenuated vaccine candidate developed here represents a promising alternative to prevent and control SVA in swine.

Deletion of the thymidine kinase gene attenuates Caprine alphaherpesvirus 1 in goats.

Caprine alphaherpesvirus 1 (CpHV-1) is a pathogen associated with systemic infection and respiratory disease in kids and subclinical infection or reproductive failure and abortions in adult goats. The enzyme thymidine kinase (TK) is an important viral product involved in nucleotide synthesis. This property makes the tk gene a common target for herpesvirus attenuation. Here we deleted the tk gene of a CpHV-1 isolate and characterized the recombinant CpHV-1ΔTKin vitro and in vivo. In vitro characterization revealed that the recombinant CpHV-1ΔTK replicated to similar titers and produced plaques of similar size to the parental CpHV-1 strain in BT and CRIB cell lines. Upon intranasal inoculation of young goats, the parental virus replicated more efficiently and for a longer period than the recombinant virus. In addition, infection with the parental virus resulted in mild systemic and respiratory signs whereas the kids inoculated with the recombinant CpHV-1ΔTK virus remained healthy. Goats inoculated with the parental virus also developed higher neutralizing antibody titers when compared to CpHV-1ΔTK inoculated animals. Dexamethasone (Dx) administration on days 35-39 post-inoculation did not result in virus shedding in nasal secretions, indicating lack of reactivation from latency. However, viral DNA was detected in the trigeminal ganglia of animals euthanized at 14 days post-Dx, indicating that both viruses successfully established latent infection. Our results show that the recombinant CpHV-1ΔTK presents an attenuated phenotype when compared to the parental virus, and hence may represent a promising vaccine candidate to prevent CpHV-1 disease in goats.

Persistent Infection and Transmission of Senecavirus A from Carrier Sows to Contact Piglets.

Senecavirus A (SVA) is a picornavirus that causes acute vesicular disease (VD), that is clinically indistinguishable from foot-and-mouth disease (FMD), in pigs. Notably, SVA RNA has been detected in lymphoid tissues of infected animals several weeks following resolution of the clinical disease, suggesting that the virus may persist in select host tissues. Here, we investigated the occurrence of persistent SVA infection and the contribution of stressors (transportation, immunosuppression, or parturition) to acute disease and recrudescence from persistent SVA infection. Our results show that transportation stress leads to a slight increase in disease severity following infection. During persistence, transportation, immunosuppression, and parturition stressors did not lead to overt/recrudescent clinical disease, but intermittent viremia and virus shedding were detected up to day 60 postinfection (p.i.) in all treatment groups following stress stimulation. Notably, real-time PCR and in situ hybridization (ISH) assays confirmed that the tonsil harbors SVA RNA during the persistent phase of infection. Immunofluorescence assays (IFA) specific for double-stranded RNA (dsRNA) demonstrated the presence of double-stranded viral RNA in tonsillar cells. Most importantly, infectious SVA was isolated from the tonsil of two animals on day 60 p.i., confirming the occurrence of carrier animals following SVA infection. These findings were supported by the fact that contact piglets (11/44) born to persistently infected sows were infected by SVA, demonstrating successful transmission of the virus from carrier sows to contact piglets. Results here confirm the establishment of persistent infection by SVA and demonstrate successful transmission of the virus from persistently infected animals.IMPORTANCE Persistent viral infections have significant implications for disease control strategies. Previous studies demonstrated the persistence of SVA RNA in the tonsil of experimentally or naturally infected animals long after resolution of the clinical disease. Here, we showed that SVA establishes persistent infection in SVA-infected animals, with the tonsil serving as one of the sites of virus persistence. Importantly, persistently infected carrier animals shedding SVA in oral and nasal secretions or feces can serve as sources of infection to other susceptible animals, as evidenced by successful transmission of SVA from persistently infected sows to contact piglets. These findings unveil an important aspect of SVA infection biology, suggesting that persistently infected pigs may function as reservoirs for SVA.

Transcription Is Just the Beginning of Gene Expression Regulation: The Functional Significance of RNA-Binding Proteins to Post-transcriptional Processes in Plants.

Plants have developed sophisticated mechanisms to compensate and respond to ever-changing environmental conditions. Research focus in this area has recently shifted towards understanding the post-transcriptional mechanisms that contribute to RNA transcript maturation, abundance and function as key regulatory steps in allowing plants to properly react and adapt to these never-ending shifts in their environments. At the center of these regulatory mechanisms are RNA-binding proteins (RBPs), the functional mediators of all post-transcriptional processes. In plants, RBPs are becoming increasingly appreciated as the critical modulators of core cellular processes during development and in response to environmental stimuli. With the majority of research on RBPs and their functions historically in prokaryotic and mammalian systems, it has more recently been unveiled that plants have expanded families of conserved and novel RBPs compared with their eukaryotic counterparts. To better understand the scope of RBPs in plants, we present past and current literature detailing specific roles of RBPs during stress response, development and other fundamental transition periods. In this review, we highlight examples of complex regulation coordinated by RBPs with a focus on the diverse mechanisms of plant RBPs and the unique processes they regulate. Additionally, we discuss the importance for additional research into understanding global interactions of RBPs on a systems and network-scale, with genome mining and annotation providing valuable insight for potential uses in improving crop plants in order to maintain high-level production in this era of global climate change.

Sero-prevalence of Toxoplasma gondii in sheep in different geographical regions of Nepal.

The present study was conducted to investigate the prevalence of Toxoplasma gondii in sheep in Nepal. Blood samples were collected from 235 sheep from three districts of three different eco-zones namely, mountainous Jumla (88), hilly Pokhara (62) and plain/terai Chitwan (85). The samples were tested by using commercial ELISA kit. The overall prevalence of T. gondii infection in sheep was 36.17% (CI: 30.29-42.49%). The region wise prevalence showed highest in Chitwan (57.65%; CI: 47.04-67.60%), followed by Pokhara (32.94%; CI: 23.88-43.48%) and Jumla (9.41%; CI: 4.85-17.49%). Prevalence of T. gondii in Jumla was significantly lower than Pokhara and Chitwan (p < 0.05) but no significant difference in seroprevalence was encountered between Pokhara and Chitwan (p > 0.05). Similarly, no significant difference (p > 0.05) in prevalence of T. gondii was found in sex and age groups (p > 0.05). The result showed that T. gondii parasite is widely spread in the studied geographical regions of Nepal.

Cross-sectional serosurvey and associated factors of bluetongue virus antibodies presence in small ruminants of Nepal.

BACKGROUND: Bluetongue (BT) is an infectious, insect-borne viral disease primarily affecting sheep and occasionally cattle and goats. In Nepal, BT is an emerging disease of economic importance. The objective of this study was to estimate the seroprevalence of BT virus (BTV) in small ruminants of two eco-zones of Nepal, Hills and Terai, and to identify the factors associated with virus exposure. We conducted a cross-sectional serosurvey from March 2012 through February 2013 by sampling 318 small ruminants (184 sheep and 134 goats) from seven clusters (villages) of selected vulnerable communities of Chitwan (Terai) and Lamjung (Hills) Districts of Nepal. RESULTS: Of the 318 serum sample tested, 27.9% [95% confidence interval (CI): 23.1- 33.2] were positive for BTV antibodies (25.0% sheep and 31.3% goats). Bivariate analysis indicated a positive association between seroconversion to BTV and flock size, eco-zone, breed, and contact history with cattle. Additionally, in female sheep and goats, a history of abortion was positively associated with seropositivity to BTV. However, the final multivariable model, after controlling for clustering of animals within the villages, identified only history of abortion and breed as the factors significantly associated with BT seropositivity in female sheep and goats. Based on this model, female small ruminants having a history of abortion were more likely to be seropositive compared to those without such history [Odds Ratio (OR) = 46.14 (95% CI: 11.66- 182.5)]. Exotic breeds were more likely to be seropositive compared to indigenous breeds [OR = 9.04 (95% CI: 3.08- 24.46)] while the risk for BTV seropositivity was not significantly different between indigenous and cross breeds. CONCLUSIONS: Our results showed that nearly a quarter of small ruminants in two regions of Nepal were seropositive for BTV, indicating wide exposure of small ruminants to this pathogen. We identified history of abortion and breed as factors significantly associated with the seropositivity of BTV. We recommend that surveillance for BTV infection in Nepal be strengthened and that it would be valuable to enhance the education of farmers about the possible impacts of this disease.

Prevalence, antibiogram and risk factors of thermophilic Campylobacter spp. in dressed porcine carcass of Chitwan, Nepal.

BACKGROUND: Campylobacter is the primary cause of food borne gastroenteritis. Moreover, the emergence of multiple drug resistant campylobacters from poultry and pork has produced a potential threat to public health. Research addressing these issues is sparse in Nepal. So, this cross-sectional study aims at determining the prevalence, antibiogram and risk factors of campylobacters from dressed porcine carcass of Chitwan, Nepal. RESULTS: We collected 139 samples of dressed porcine carcass from 10 different pork shops located in Chitwan district and processed according to OIE Terrestrial Manual, 2008, chapter 2.8.10. Antibiogram of identified Campylobacter spp. was evaluated against nine commonly used antibiotics by using disc diffusion method following CLSI guidelines. The prevalence of Campylobacter spp. was 38.84% (C. coli 76% and C. jejuni 24%). There was no significant difference (p > 0.05) between the prevalence rate of male (32.4%) and female (41%) carcass. Ampicillin and erythromycin showed the highest resistance (92.59% each) followed by colistin (72.2%), tetracycline (61.1%), nalidixic acid and cotrimoxazole (44.4% each), ciprofloxacin (31.5%) and gentamicin (5.56%). Moreover, 77.8% of the isolates were resistant to more than two antimicrobials. Nalidixic acid and tetracycline showed significant difference (p < 0.05) in the resistivity pattern among different species of Campylobacters. The association between prevalence rate and regular sanitization of slaughter slab equipments was significant (p < 0.05). Similarly, prevalence rate was significantly associated (p < 0.01) with chilling and contamination of intestinal content with carcass. CONCLUSIONS: The pork meat of Chitwan is highly contaminated with antibiotic-resistant Campylobacters and slaughtering practices play significant role in contamination. It is necessary to train the butchers about hygienic slaughtering practice. The consumers as well as butchers should adopt safety measures to prevent themselves from antibiotic resistant campylobacters. The veterinary practitioners should adopt prudent use of antibiotics in pigs.