Abstract:
It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a backsplicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into proteins that displayed proviral functions. Furthermore, two highly abundant, nontranslated vcircRNAs were shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus.

Keyword: circular RNAs; hepatitis C virus; translation

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85184535497&doi=10.1073%2fpnas.2313002121&partnerID=40&md5=7919d945536f4493606112017c924145

DOI: 10.1073/pnas.2313002121

Abstract:
The study explored using a hot-air oven at various temperatures (35, 45, and 55 °C) as a promising alternative to traditional sun-drying for salted shrimp paste production. Comparing drying profiles, fermentation rate, quality, and acceptability with conventional sun-drying (CON), it was found that the alternative hot-air oven led to lower enzymatic activities and degree of hydrolysis during a 30-day fermentation (p < 0.05). Consequently, the alternative samples exhibited lower development of distinctive characteristics (color, browning intensity, formal, ammonia, nitrogen contents, and antioxidant capabilities) resulting in lower sensory scores compared to CON (p < 0.05). Interestingly, microbial populations in hot-air-dried samples were also lower than CON (p < 0.05). Based on PCA biplots and drying duration, drying at 45 °C with a hot-air oven seemed optimal for shrimp paste production. However, adjustments, such as prolonging fermentation or using a starter culture, are needed to make the alternative process comparable to the traditional product. © 2023 Taylor & Francis Group, LLC.

Keyword: drying process; fermentation rate; fermented shrimp; hot-air oven; Shrimp paste

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85173787448&doi=10.1080%2f07373937.2023.2267665&partnerID=40&md5=b58503a85299a15b8cb7efae02ccb975

DOI: 10.1080/07373937.2023.2267665

Abstract:
The study explored using a hot-air oven at various temperatures (35, 45, and 55 °C) as a promising alternative to traditional sun-drying for salted shrimp paste production. Comparing drying profiles, fermentation rate, quality, and acceptability with conventional sun-drying (CON), it was found that the alternative hot-air oven led to lower enzymatic activities and degree of hydrolysis during a 30-day fermentation (p < 0.05). Consequently, the alternative samples exhibited lower development of distinctive characteristics (color, browning intensity, formal, ammonia, nitrogen contents, and antioxidant capabilities) resulting in lower sensory scores compared to CON (p < 0.05). Interestingly, microbial populations in hot-air-dried samples were also lower than CON (p < 0.05). Based on PCA biplots and drying duration, drying at 45 °C with a hot-air oven seemed optimal for shrimp paste production. However, adjustments, such as prolonging fermentation or using a starter culture, are needed to make the alternative process comparable to the traditional product. © 2023 Taylor & Francis Group, LLC.

Keyword: drying process; fermentation rate; fermented shrimp; hot-air oven; Shrimp paste

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85173787448&doi=10.1080%2f07373937.2023.2267665&partnerID=40&md5=b58503a85299a15b8cb7efae02ccb975

DOI: 10.1080/07373937.2023.2267665

Abstract:
This study aimed to evaluate Bacillus subtilis K-C3 as a potential starter to improve shrimp paste quality, particularly in terms of nutritional profiles. The quality/characteristic changes of shrimp paste with and without inoculation during storage for 18 months when stored at low (4 °C) and room (28 °C) temperature were also investigated. The results found that this B. strain increased essential amino acids (EAAs) and polyunsaturated fatty acids (PUFAs), as well as antioxidant properties including 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) radical scavenging activities, ferric reducing antioxidant power (FRAP) and metal chelating activity in the experimental shrimp paste compared to traditional shrimp paste (p < 0.05). The faster development of some characteristics of inoculated samples were also noted, as indicated by the higher total viable count (TVC), formal and amino nitrogen content, pH, and browning index, as well as biogenic amines, indicating different quality which may be further responsible for different product acceptability. The changes in quality/characteristics of shrimp paste were observed throughout the 18 months of storage. Shrimp paste stored at room temperature accelerated those changes faster than samples stored at low temperature (p < 0.05); however, the quality of them still meets the product’s standard even storage for 18 months. Meanwhile, shrimp paste stored at a low temperature had an amount of yeast and mold over the limitation (>3.00 log CFU/g), indicating food spoilage. Thus, storage at room temperature can extend this product’s shelf-life better than storage at low temperature. Overall, inoculation with B. subtilis K-C3, in conjunction with storage at room temperature, resulted in quality improvement and maintenance in shrimp paste, particularly in the aspects of nutritional profiles and safety concern, as the shrimp paste should have a shelf-life of at least 18 months. © 2023 by the authors.

Keyword: Bacillus subtilis; fermented food; inoculation; shrimp paste; starter culture

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85148733358&doi=10.3390%2ffermentation9020107&partnerID=40&md5=5420069eef3fe11ba884472c8a6de6f5

DOI: 10.3390/fermentation9020107

Abstract:
Cercospora leaf spot (CLS) is caused by Cercospora canescens and is one of the most important diseases of mungbean (Vigna radiata). Cercospora leaf spot may result in economic loss in production areas. The present study investigated the potential of Bacillus velezensis S141 as a biocontrol agent for C. canescens PAK1 growth on culture plates. Cell-free secretions from a dual culture of S141+PAK1 inhibited fungal growth more than those from a single culture of S141. The biocontrol efficiency of S141 against Cercospora leaf spot on mungbean was then evaluated by spraying. The disease severity of Cercospora leaf spot was significantly reduced in plants treated with S141, with a control efficiency of 83% after 2 days of infection. Comparative transcriptomics and qRT-PCR analyses of S141 during C. canescens inhibition were performed to elucidate the antifungal mechanisms underlying its antifungal activity against Cercospora leaf spot. According to the differentially expressed genes, most up-regulated genes involved in the biosynthetic genes encoding enzymatic hydrolases, including protease, β-glucanase, and N-acyl glucosaminase, were detected in strain S141 following its interaction. Moreover, genes related to secondary metabolites (surfactin, bacilysin, and bacillomycin D) were up-regulated. Collectively, these results suggest that S141 exhibited strong antifungal activity against C. canescens due to multiple enzymatic hydrolases and secondary metabolites. Therefore, the present study provides insights into the biological network responsible for the antifungal activity of B. velezensis S141 against C. canescens. © 2023, Japanese Society of Microbial Ecology. All rights reserved.

Keyword: antifungal activity; Bacillus velezensis; biocontrol agent; Cercospora leaf spot; transcriptome analysis

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85150531576&doi=10.1264%2fjsme2.ME22079&partnerID=40&md5=d87ad8b485e70e117cb3e2b10a96b04d

DOI: 10.1264/jsme2.ME22079

Abstract:
Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) originating from a post-transcriptional modification process called back-splicing. Despite circRNAs being traditionally considered by-products rather than independently functional, circRNAs play many vital roles, such as in host immunity during viral infection. However, in shrimp, these remain largely unexplored. Therefore, this study aims to identify circRNAs in Litopenaeus vannamei in the context of WSSV infection, one of the most eradicative pathogens threatening shrimp populations worldwide. We identified 290 differentially expressed circRNAs (DECs) in L. vannamei upon WSSV infection. Eight DECs were expressed from their parental genes, including alpha-1-inhibitor-3, calpain-B, integrin-V, hemicentin-2, hemocytin, mucin-17, proPO2, and rab11-FIP4. These were examined quantitatively by qRT-PCR, which revealed the relevant expression profiles to those obtained from circRNA-Seq. Furthermore, the structural and chemical validation of the DECs conformed to the characteristics of circRNAs. One of the functional properties of circRNAs as a miRNA sponge was examined via the interaction network between DECs and WSSV-responsive miRNAs, which highlighted the targets of miRNA sponges. Our discovery could provide insight into the participation of these ncRNAs in shrimp antiviral responses. © 2022 Elsevier Ltd

Keyword: circRNA-Seq; circRNAs; miRNA-circRNA network; RNase R; White spot syndrome virus

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85144835962&doi=10.1016%2fj.fsi.2022.108499&partnerID=40&md5=aa55fc541487ef84edcee82fe12c28f7

DOI: 10.1016/j.fsi.2022.108499

Abstract:
The Vago interferon-like protein participates in the interplay between interferon regulatory factors and the expression of immune-responsive genes. Vago was initially perceived to participate only in the antiviral activation through JAK/STAT pathway. However, certain isoforms of Vago can stimulate antimicrobial responses. Here we identify Vago isoforms in Fenneropenaeus merguiensis (FmVagos) and how they function in antiviral and antibacterial responses against highly invasive pathogens, including white spot syndrome virus (WSSV) and Vibrio parahaemolyticus (VPAHPND). Three isoforms of FmVagos were identified: FmVago4, FmVago5a, and FmVago5b, and expressed throughout tissues of the shrimp. During infection, FmVago4, FmVago5a, and FmVago5b, were up-regulated after WSSV and VPAHPND challenges at certain time points. Pre-injection of purified recombinant FmVago4 (rVago4), FmVago5a (rVago5a), and FmVago5b (rVago5b) proteins could significantly reduce the mortality of shrimp upon WSSV infection, while the increase of survival rate of VPAHPND-infected shrimp was observed only in rVago4 treatment. The immunity routes that FmVagos might instigate in response to the pathogens were examined by qRT-PCR, revealing that the JAK/STAT pathway was activated after introducing rVago4, rVago5a, and rVago5b, while the Toll/IMD pathway and proPO system, combined with PO activity, were provoked only in the rVago4-treated shrimp. Our finding suggests cross-talk between Vago's antiviral and antimicrobial responses in shrimp immunity. These findings complement previous studies in which Vago and its specific isoform could promote viral and bacterial clearance in shrimp. © 2022 Elsevier Ltd

Keyword:

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140977073&doi=10.1016%2fj.fsi.2022.10.037&partnerID=40&md5=9ddc71cd262474cd4ef383055d463e65

DOI: 10.1016/j.fsi.2022.10.037

Abstract:
Quality changes of salted shrimp paste, one of the most popular traditional Thai fermented food ingredients, stored in different packaging containers including polypropylene containers (PP), polyethylene terephthalate containers (PET), glass jar containers (GJ) as well as LLDPE/Nylon vacuum bags (VB) at room temperature (28 ± 1 °C) for 15 months were studied. The relationship between quality attributes (i.e., volatiles, browning index (A420), biogenic amines, TBARS) and consumer acceptability as indicated by sensory scores were also investigated using principal component analysis (PCA). During storage, some desirable quality characteristics of shrimp paste were improved as indicated by the higher sensory scores of all samples when stored for 6 months, compared with the sample at day 0 (p ≤ 0.05). However, further changes in all compositions when extended storage time can conversely diminish those desirable characteristics and led to lowering consumers’ acceptability. In this study, GJ seem to be the most potential packaging for preserving original products’ quality during storage for this product since it exhibited the lower rate of quality changing than others throughout the storage. Conversely, VB exhibited unique volatiles and microbial profiles, compared with others, which led to the lowest sensory scores at all period test (p ≤ 0.05), implying that vacuum conditions may not be suitable for the storage of this product. Moreover, based on PCA results, the intensity of nitrogen-containing compounds correlated well with sensory acceptability, particularly flavor-likeness. Our study provides useful knowledge for understanding the different quality characteristics, particularly flavors, associated with different packaging containers during prolonged storage of salted shrimp paste. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

Keyword: Biogenic amines; Fermented shrimp paste; Packaging; Salted shrimp paste; Storage; Volatiles

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124620868&doi=10.3390%2ffermentation8020069&partnerID=40&md5=5da0aa68c8262e80e179c71afaf24caa

DOI: 10.3390/fermentation8020069

Abstract:
The symbiotic properties of rhizobial bacteria are driven by the horizontal gene transfer of symbiotic genes, which are located in symbiosis islands or on plasmids. The symbiotic megaplasmid pDOA9 of Bradyrhizobium sp. DOA9, carrying the nod, nif, fix, and type three secretion system (T3SS) genes, has been conjugatively transferred to different Bradyrhizobium strains. In the present study, non-nodulating B. cosmicum S23321, which shows a close phylogenetic relationship with Bradyrhizobium sp. DOA9, but lacks symbiotic properties, was used to carry pDOA9 (annotated as chimeric S2:pDOA9). The results obtained showed that pDOA9 conferred symbiotic properties on S23321; however, nodulation phenotypes varied among the DOA9, chimeric ORS278:pDOA9, and S2:pDOA9 strains even though they all carried symbiotic pDOA9 plasmid. S23321 appeared to gain symbiotic nodulation from pDOA9 by processing nodulation genes and broadening the host range. The present results also showed the successful formation of active nodules in Arachis hypogaea (Dalbergoid) and Vigna radiata (Millitoid) by chimeric S2:pDOA9, while Crotalaria juncea (Genistoid) and Macroptilium atropurpureum (Millitoid) formed nodule-like structures. The formation of nodules and nodule-like structures occurred in a nod factor-dependent manner because the nod factor-lacking strain (S2:pDOA9ΩnodB) completely abolished nodulation in all legumes tested. Moreover, T3SS carried by S2:pDOA9 exerted negative effects on symbiosis with Crotalaria juncea, which was consistent with the results obtained on DOA9. T3SS exhibited symbiotic compatibility with V. radiata when nodulated by S23321. These outcomes implied that pDOA9 underwent changes during legume evolution that broadened host specificity and the compatibility of nodulation in a manner that was dependent on the chromosomal background of the recipient as well as legume host restrictions. © 2022, Japanese Society of Microbial Ecology. All rights reserved.

Keyword: chimeric; DOA9; horizontal gene transfer; nodulation; transconjugant

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131639621&doi=10.1264%2fjsme2.ME22008&partnerID=40&md5=77b488c8d3bd06cfe0e3e9703bed52a8

DOI: 10.1264/jsme2.ME22008

Abstract:
Acute hepatopancreatic necrosis disease, AHPND, caused by a specific Vibrio parahaemolyticus (VPAHPND) strain, results in a great loss of global shrimp production. This study performed suppression subtractive hybridization (SSH) to identify differentially expressed genes from white shrimp Penaeus vannamei hemocyte upon VPAHPND infection. Among the immune-related genes identified, Vago5, kunitz, secretory leukocyte proteinase inhibitor, and profilin are the most abundant genes classified as the up-regulated genes in the SSH library. The qRT-PCR results show that only Vago5 was highly up-regulated at 3 and 6 h post-VPAHPND challenge, whereas kunitz, secretory leukocyte proteinase inhibitor, and profilin were highly up-regulated at 48 h post-VPAHPND challenge. As an early VPAHPND infection-responsive gene, Vago5 was further functional characterized by RNA interference. Knockdown of Vago5 gene resulted in the significantly rapid increase of shrimp mortality and the number of bacteria in the stomach and hepatopancreas upon VPAHPND infection. Moreover, downstream genes of Toll, IMD, and JAK/STAT pathways and phenoloxidase system were analyzed for the expression in the VPAHPND-infected shrimp hemocyte after dsVago5 treatment. Vago5 gene knockdown resulted in a significant decrease in transcript levels of PEN4, TNF, and PO2 genes as well as PO activity in the hemolymph, suggesting that Vago5 might modulate antibacterial infection through activation of the genes in the NF-κB mediated pathways, JAK/STAT pathway, and phenoloxidase system. © 2021 Elsevier Ltd

Keyword: Penaeus vannamei; Shrimp immunity; Vago5; Vibrio parahaemolyticus AHPND

Scopus Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85119274500&doi=10.1016%2fj.fsi.2021.10.044&partnerID=40&md5=46b37fde0b21b8fec498a517dd1cabe3

DOI: 10.1016/j.fsi.2021.10.044