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Fulltext -Chemical profiling and biological activity of Peperomia blanda (Jacq.) Kunth

Al-Madhagi WM, Mohd Hashim N, Awad Ali NA, Alhadi AA, Abdul Halim SN, Othman R

PeerJ, 2018;6:e4839.
PMID: 29892499 DOI: 10.7717/peerj.4839

Background: Peperomia belongs to the family of Piperaceae. It has different uses in folk medicine and contains rare compounds that have led to increased interest in this genus. Peperomia blanda (Jacq.) Kunth is used as an injury disinfectant by Yemeni people. In addition, the majority of Yemen's population still depend on the traditional remedy for serious diseases such as cancer, inflammation and infection. Currently, there is a deficiency of scientific evidence with regards to the medicinal plants from Yemen. Therefore, this study was performed to assess the chemical profile and in vitro antioxidant and cytotoxic activities of P. blanda.
Methods: Chemical profiling of P. blanda was carried out using gas chromatography mass spectrometry (GCMS) followed by isolation of bioactive compounds by column chromatography. DPPH• and FRAP assays were used to evaluate antioxidant activity and the MTT assay was performed to estimate the cytotoxicity activity against three cancer cell lines, namely MCF-7, HL-60 and WEHI-3, and three normal cell lines, MCF10A, WRL-68 and HDFa.
Results: X-ray crystallographic data for peperomin A is reported for the first time here and N,N'-diphenethyloxamide was isolated for the first time from Peperomia blanda. Methanol and dichloromethane extracts showed high radical scavenging activity with an IC50 of 36.81 ± 0.09 µg/mL, followed by the dichloromethane extract at 61.78 ± 0.02 µg/mL, whereas the weak ferric reducing activity of P. blanda extracts ranging from 162.2 ± 0.80 to 381.5 ± 1.31 µg/mL were recorded. In addition, petroleum ether crude extract exhibited the highest cytotoxic activity against all the tested cancer cell lines with IC50 values of 9.54 ± 0.30, 4.30 ± 0.90 and 5.39 ± 0.34 µg/mL, respectively. Peperomin A and the isolated mixture of phytosterol (stigmasterol and β-sitosterol) exhibited cytotoxic activity against MCF-7 and WE-HI cell lines with an IC50 of (5.58 ± 0.47, 4.62 ± 0.03 µg/mL) and (8.94 ± 0.05, 9.84 ± 0.61 µg/mL), respectively, compared to a standard drug, taxol, that has IC50 values of 3.56 ± 0.34 and 1.90 ± 0.9 µg/mL, respectively.
Conclusion: The activities of P. blanda extracts and isolated compounds recorded in this study underlines the potential that makes this plant a valuable source for further study on anticancer and antioxidant activities.
Fulltext 13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses

Azizan KA, Ressom HW, Mendoza ER, Baharum SN

PeerJ, 2017;5:e3451.
PMID: 28695065 DOI: 10.7717/peerj.3451

Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C) and agitation (with and without agitation at 150 rpm). Collectively, the concentrations of proteinogenic amino acids (PAAs) and free fatty acids (FAAs) were compared, and Pearson correlation analysis (r) was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP) pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA). Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis' central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA) from pyruvate (PYR) reaction in all conditions suggested the activation of pyruvate carboxylate (pycA) in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP) pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall, the integration of systematic analysis of amino acids and flux ratio analysis provides a systems-level understanding of how L. lactis regulates central metabolism under various conditions.
A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions

Azaman SNA, Nagao N, Yusoff FM, Tan SW, Yeap SK

PeerJ, 2017;5:e3473.
PMID: 28929006 DOI: 10.7717/peerj.3473

The responses of two species of microalgae, Chlorella sorokiniana and Chlorella zofingiensis, were compared regarding their morphological and biochemical properties under photoautotrophic and mixotrophic conditions. These microalgae were cultured under both conditions, and their crude ethanolic extracts were examined for their pigment and total phenolic contents. In addition, the microalgae's antioxidant activities were determined using a DPPH radical scavenging assay and a ferric reducing antioxidant power (FRAP) assay. Both strains showed increases in cell size due to the accumulation of lipid bodies and other cell contents, especially carotenoids, under the mixotrophic condition. Notably, reductions in phenolic and chlorophyll contents were observed to be associated with lower antioxidant activity. C. zofingiensis compared with C. sorokiniana, demonstrated higher antioxidant activity and carotenoid content. This study showed that different species of microalgae responded differently to varying conditions by producing different types of metabolites, as evidenced by the production of higher levels of phenolic compounds under the photoautotrophic condition and the production of the same levels of carotenoids under both photoautotrophic and mixotrophic conditions.
Fulltext A genetic programming approach to oral cancer prognosis

Tan MS, Tan JW, Chang SW, Yap HJ, Abdul Kareem S, Zain RB

PeerJ, 2016;4:e2482.
PMID: 27688975 DOI: 10.7717/peerj.2482

The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis.
Fulltext A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Moyle RG, Manthey JD, Hosner PA, Rahman M, Lakim M, Sheldon FH

PeerJ, 2017;5:e3335.
PMID: 28533979 DOI: 10.7717/peerj.3335

Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric "species-pump" model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by "ecological speciation" along an elevational gradient.
Fulltext A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae)

Gorin VA, Solovyeva EN, Hasan M, Okamiya H, Karunarathna DMSS, Pawangkhanant P, et al.

PeerJ, 2020;8:e9411.
PMID: 32685285 DOI: 10.7717/peerj.9411

Frogs of the genus Microhyla include some of the world's smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla-Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene-early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla-Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15-33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.
Fulltext A metagenomic comparison of clearwater, probiotic, and Rapid BFTTM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures

Waiho K, Abd Razak MS, Abdul Rahman MZ, Zaid Z, Ikhwanuddin M, Fazhan H, et al.

PeerJ, 2023;11:e15758.
PMID: 37790619 DOI: 10.7717/peerj.15758

Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture.
Fulltext A molecular phylogeny of Geotrochus and Trochomorpha species (Gastropoda: Trochomorphidae) in Sabah, Malaysia reveals convergent evolution of shell morphology driven by environmental influences

Chang ZY, Liew TS

PeerJ, 2021;9:e10526.
PMID: 33604162 DOI: 10.7717/peerj.10526

There are currently eleven Geotrochus and four Trochomorpha species in Sabah. The primary diagnostic character that separates the two genera is the intensity of sculpture on the shell upper surface. All Trochomorpha species have a coarse nodular sculpture while Geotrochus species has a non-nodular sculpture or smooth shell. However, it is known that shell characters are often evolutionary labile with high plasticity in response to environmental factors. Hence, identifying the phylogenetic and ecological determinants for the shell characters will shed light on the shell-based taxonomy. This study aims to estimate the phylogenetic relationship between Geotrochus and Trochomorpha species in Sabah based in two mitochondrial genes (COI, 16S) and one nuclear gene (ITS) and also to examine the influence of temperature, elevation and annual precipitation on the coarseness of shell upper surface sculpture and shell sizes of the species of both genera. Additionally, we also investigated the phylogenetic signal of the shell characters. The phylogenetic analysis showed that Geotrochus and Trochomorpha species are not reciprocally monophyletic. The phylogenetic signal test suggested that shell size and upper surface sculpture are homoplastic, and these shell traits are strongly influenced by elevation and annual precipitation, particularly at the cloud zone of Mount Kinabalu. The highland species of both genera have a coarser shell surface than lowland species. The shell and aperture width decrease with increasing elevation and annual precipitation. In the view of finding above, the current taxonomy of Geotrochus and Trochmorpha in this region and elsewhere that based on shell characters need to be revised with sufficient specimens throughout the distribution range of the two genera.
Fulltext A multicentre study to determine the in vitro efficacy of flomoxef against extended-spectrum beta-lactamase producing Escherichia coli in Malaysia

Yap PSX, Chong CW, Ponnampalavanar S, Ramli R, Harun A, Tengku Jamaluddin TZM, et al.

PeerJ, 2023;11:e16393.
PMID: 38047021 DOI: 10.7717/peerj.16393

BACKGROUND: The high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.
METHODS: Therefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.
RESULTS: A total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1, blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes.
Fulltext A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon

Mohd Ghani F, Bhassu S

PeerJ, 2019;7:e8107.
PMID: 31875142 DOI: 10.7717/peerj.8107

The emergence of diseases such as white spot disease has become a threat to Penaeus monodon cultivation. Although there have been a few studies utilizing RNA-Seq, the cellular processes of host-virus interaction in this species remain mostly anonymous. In the present study, P. monodon was challenged with WSSV by intramuscular injection and survived for 12 days. The effect of the host gene expression by WSSV infection in the haemocytes, hepatopancreas and muscle of P. monodon was studied using Illumina HiSeq 2000. The RNA-Seq of cDNA libraries was developed from surviving WSSV-challenged shrimp as well as from normal healthy shrimp as control. A comparison of the transcriptome data of the two groups showed 2,644 host genes to be significantly up-regulated and 2,194 genes significantly down-regulated as a result of the infection with WSSV. Among the differentially expressed genes, our study discovered HMGB, TNFSF and c-Jun in P. monodon as new potential candidate genes for further investigation for the development of potential disease resistance markers. Our study also provided significant data on the differential expression of genes in the survived WSSV infected P. monodon that will help to improve understanding of host-virus interactions in this species.
Fulltext A novel histozoic myxosporean, Enteromyxum caesio n. sp., infecting the redbelly yellowtail fusilier, Caesio cuning, with the creation of the Enteromyxidae n. fam., to formally accommodate this commercially important genus

Freeman MA, Yanagida T, Kristmundsson À

PeerJ, 2020;8:e9529.
PMID: 32742799 DOI: 10.7717/peerj.9529

Gastrointestinal myxosporean parasites from the genus Enteromyxum are known to cause severe disease, resulting in high mortalities in numerous species of cultured marine fishes globally. Originally described as Myxidium spp., they were transferred to a new genus, Enteromyxum, to emphasize their novel characteristics. Their retention in the family Myxidiidae at the time was warranted, but more comprehensive phylogenetic analyses have since demonstrated the need for a new family for these parasites. We discovered a novel Enteromyxum in wild fish from Malaysia and herein describe the fourth species in the genus and erect a new family, the Enteromyxidae n. fam., to accommodate them. Enteromyxum caesio n. sp. is described infecting the tissues of the stomach in the redbelly yellowtail fusilier, Caesio cuning, from Malaysia. The new species is distinct from all others in the genus, as the myxospores although morphologically similar, are significantly smaller in size. Furthermore, small subunit ribosomal DNA sequence data reveal that E. caesio is <84% similar to others in the genus, but collectively they form a robust and discrete clade, the Enteromyxidae n. fam., which is placed as a sister taxon to other histozoic marine myxosporeans. In addition, we describe, using transmission electron microscopy, the epicellular stages of Enteromyxum fugu and show a scanning electron micrograph of a mature myxospore of E. caesio detailing the otherwise indistinct sutural line, features of the polar capsules and spore valve ridges. The Enteromyxidae n. fam. is a commercially important group of parasites infecting the gastrointestinal tract of marine fishes and the histozoic species can cause the disease enteromyxosis in intensive finfish aquaculture facilities. Epicellular and sloughed histozoic stages are responsible for fish-to-fish transmission in net pen aquaculture systems but actinospores from an annelid host are thought to be necessary for transmission to fish in the wild.
Fulltext A phylogenetic taxonomy of the Cyrtodactylus peguensis group (Reptilia: Squamata: Gekkonidae) with descriptions of two new species from Myanmar

Grismer LL, Wood PL, Quah ESH, Murdoch ML, Grismer MS, Herr MW, et al.

PeerJ, 2018;6:e5575.
PMID: 30258710 DOI: 10.7717/peerj.5575

A phylogenetic taxonomy of species in the Cyrtodactylus peguensis group from the Ayeyarwady Basin of Myanmar is constructed based on color pattern, morphology, and molecular systematic analyses using the mitochondrial gene NADH dehydrogenase subunit 2. Newly collected samples from the type locality of C. peguensis and other localities indicate that this clade is endemic to central Myanmar and contains at least seven species, four of which are undescribed. Three species, including C. peguensis occur in the low hills of the Bago Yoma Range within the central portion of the Ayeyarwady Basin. Two of these, C. myintkyawthurai sp. nov. from the northern and central Bago Yoma and C. meersi sp. nov. which is syntopic with C. peguensis in the southern Bago Yoma are described herein. As more lowland hilly areas bordering, and within the Ayeyarwady Basin are surveyed, more new species of this group are likely to be discovered. These discoveries continue the recent surge of descriptions of new species of Cyrtodactylus that are being discovered in Myanmar.
Fulltext A preliminary study of the effect of a high-salt diet on transcriptome dynamics in rat hypothalamic forebrain and brainstem cardiovascular control centers

Ramachandran CD, Gholami K, Lam SK, Hoe SZ

PeerJ, 2020;8:e8528.
PMID: 32175184 DOI: 10.7717/peerj.8528

BACKGROUND: High dietary salt intake is strongly correlated with cardiovascular (CV) diseases and it is regarded as a major risk factor associated with the pathogenesis of hypertension. The CV control centres in the brainstem (the nucleus tractus solitarii (NTS) and the rostral ventrolateral medulla (RVLM)) and hypothalamic forebrain (the subfornical organ, SFO; the supraoptic nucleus, SON and the paraventricular nucleus, PVN) have critical roles in regulating CV autonomic motor outflows, and thus maintaining blood pressure (BP). Growing evidence has implicated autonomic regulatory networks in salt-sensitive HPN (SSH), but the genetic basis remains to be delineated. We hypothesized that the development and/ or maintenance of SSH is reliant on the change in the expression of genes in brain regions controlling the CV system.
METHODOLOGY: We used RNA-Sequencing (RNA-Seq) to describe the differential expression of genes in SFO, SON, PVN, NTS and RVLM of rats being chronically fed with high-salt (HS) diet. Subsequently, a selection of putatively regulated genes was validated with quantitative reverse transcription polymerase chain reaction (qRT-PCR) in both Spontaneously Hypertensive rats (SHRs) and Wistar Kyoto (WKY) rats.
RESULTS: The findings enabled us to identify number of differentially expressed genes in SFO, SON, PVN, NTS and RVLM; that are either up-regulated in both strains of rats (SON- Caprin2, Sctr), down-regulated in both strains of rats (PVN- Orc, Gkap1), up-regulated only in SHRs (SFO- Apopt1, Lin52, AVP, OXT; SON- AVP, OXT; PVN- Caprin2, Sclt; RVLM- A4galt, Slc29a4, Cmc1) or down-regulated only in SHRs (SON- Ndufaf2, Kcnv1; PVN- Pi4k2a; NTS- Snrpd2l, Ankrd29, St6galnac6, Rnf157, Iglon5, Csrnp3, Rprd1a; RVLM- Ttr, Faim).
CONCLUSIONS: These findings demonstrated the adverse effects of HS diet on BP, which may be mediated via modulating the signaling systems in CV centers in the hypothalamic forebrain and brainstem.
Fulltext A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia

Kong ZX, N Karunakaran R, Abdul Jabar K, Ponnampalavanar S, Chong CW, Teh CSJ

PeerJ, 2022;10:e12830.
PMID: 35223201 DOI: 10.7717/peerj.12830

BACKGROUND: Carbapenem resistant Enterobacteriaceae (CRE) has rapidly disseminated worldwide and has become a global threat to the healthcare system due to its resistance towards "last line" antibiotics. This study aimed to investigate the prevalence of CRE and the resistance mechanism as well as the risk factors associated with in-hospital mortality.
METHODS: A total of 168 CRE strains isolated from a tertiary teaching hospital from 2014-2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains were characterised by PFGE. The risk factors of patients infected by CRE associated with in-hospital mortality were determined statistically.
RESULTS: The predominant CRE species isolated was K. pneumoniae. The carbapenemases detected were blaOXA-48, blaOXA-232, blaVIM and blaNDM of which blaOXA-48 was the predominant carbapenemase detected among 168 CRE strains. A total of 40 CRE strains harboured two different carbapenemase genes. A total of seven clusters and 48 pulsotypes were identified among 140 CRKp strains. A predominant pulsotype responsible for the transmission from 2014 to 2015 was identified. Univariate statistical analysis identified that the period between CRE isolation and start of appropriate therapy of more than 3 days was statistically associated with in-hospital mortality.
Fulltext A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia

Tan SP, Ng LC, Lyndon N, Aman Z, Kannan P, Hashim K, et al.

PeerJ, 2023;11:e15228.
PMID: 37151297 DOI: 10.7717/peerj.15228

BACKGROUND: Malaysia is strongly supported by the agriculture sector as the backbone to drive the economy. However, COVID-19 has significantly affected agriculture across the production, supply, and marketing chains. It also disturbs the balance of food supply and demand in Malaysia. COVID-19 was an unexpected pandemic that resulted in shock and panic and caused a huge global impact. However, the impacts of this pandemic on the agriculture sector in Malaysia, particularly in the production and supply chains, are still unclear and scarce. This review offers insights into the challenges, particularly in sustaining agri-food production and supply chains. It also highlights the opportunity and relevant measures towards sustainability in agriculture to avoid agri-food disasters in the future.
METHODS: This study was carried out through a desk review of the secondary source of information covering the impact of COVID-19 in Malaysia particularly in the agri-food aspect, and a wide range of strategies and initiatives as the effective measures to overcome the crisis of this pandemic. Online desk research of the government published data and customer desk research were utilized to complete this study. Search engines such as Google Scholar and the statistical data from the official websites including the Department of Statistics Malaysia (DOSM) and the Food and Fertilizer Technology Center for the Asian and Pacific Region (FFTC-AP), were utilized. Keywords such as impact of COVID-19, pandemic, and agri-food supply chain were used to conduct the searches. The articles identified to be related to the study's objective were then downloaded and included in the study. Descriptive methods were used as the primary analysis technique following the descriptive analysis and visual data analysis in performing the sources obtained.
RESULTS: This devastating impact damages the lives by causing 4.3 million confirmed infections and more than 290,000 deaths. This disease presents an unprecedented challenge to the public health. The lockdown restriction under the movement control order (MCO), for more than of the world's population in the year 2020 to control the virus from spreading, has disrupted most of the economic sectors. The agriculture industry was seen as one of the essential industries and allowed to operate under strict standard operating procedures (SOP). Working under strict regulations came with a huge price paid for almost all industries.
CONCLUSION: This pandemic has affected the national agri-food availability and accessibility in Malaysia. This outbreak created a reflection of opportunity for sharing a more flexible approaches in handling emergencies on agricultural food production and supply chains. Therefore, the government should be ready with the roadmap and enforce the measures to control the pandemic without disrupting the agri-food supply chain in the near future.
Fulltext A systematic review on physical mutagens in rice breeding in Southeast Asia

Baadu R, Chong KP, Gansau JA, Mohamed Zin MR, Dayou J

PeerJ, 2023;11:e15682.
PMID: 37868055 DOI: 10.7717/peerj.15682

In the 1920s, Lewis Stadler initiated the introduction of permanent improvements to the genetic makeup of irradiated plants. Since then, studies related to breeding mutations have grown, as efforts have been made to expand and improve crop productivity and quality. Stadler's discovery began with x-rays on corn and barley and later extended to the use of gamma-rays, thermal, and fast neutrons in crops. Radiation has since been shown to be an effective and unique method for increasing the genetic variability of species, including rice. Numerous systematic reviews have been conducted on the impact of physical mutagens on the production and grain quality of rice in Southeast Asia. However, the existing literature still lacks information on the type of radiation used, the rice planting materials used, the dosage of physical mutagens, and the differences in mutated characteristics. Therefore, this article aims to review existing literature on the use of physical mutagens in rice crops in Southeast Asian countries. Guided by the PRISMA Statement review method, 28 primary studies were identified through a systematic review of the Scopus, Science Direct, Emerald Insight, Multidisciplinary Digital Publishing, and MDPI journal databases published between 2016 and 2020. The results show that 96% of the articles used seeds as planting materials, and 80% of the articles focused on gamma-rays as a source of physical mutagens. The optimal dosage of gamma-rays applied was around 100 to 250 Gy to improve plant development, abiotic stress, biochemical properties, and nutritional and industrial quality of rice.
Fulltext A versatile isothermal amplification assay for the detection of leptospires from various sample types

Othman S, Lee PY, Lam JY, Philip N, Azhari NN, Affendy NB, et al.

PeerJ, 2022;10:e12850.
PMID: 35291487 DOI: 10.7717/peerj.12850

BACKGROUND: Leptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene.
RESULTS: Several reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease.
CONCLUSIONS: In short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study.
Fulltext Absence of Helicobacter pylori is not protective against peptic ulcer bleeding in elderly on offending agents: lessons from an exceptionally low prevalence population

Lee YY, Noridah N, Syed Hassan SA, Menon J

PeerJ, 2014;2:e257.
PMID: 24688841 DOI: 10.7717/peerj.257

Aim. Helicobacter pylori (H. pylori) infection is exceptionally rare in population from the north-eastern region of Peninsular Malaysia. This provides us an opportunity to contemplate the future without H. pylori in acute non-variceal upper gastrointestinal (GI) bleeding. Methods. All cases in the GI registry with GI bleeding between 2003 and 2006 were reviewed. Cases with confirmed non-variceal aetiology were analysed. Rockall score > 5 was considered high risk for bleeding and primary outcomes studied were in-hospital mortality, recurrent bleeding and need for surgery. Results. The incidence of non-variceal upper GI bleeding was 2.2/100,000 person-years. Peptic ulcer bleeding was the most common aetiology (1.8/100,000 person-years). In-hospital mortality (3.6%), recurrent bleeding (9.6%) and need for surgery (4.0%) were uncommon in this population with a largely low risk score (85.2% with score ≤5). Elderly were at greater risk for bleeding (mean 68.5 years, P = 0.01) especially in the presence of duodenal ulcers (P = 0.04) despite gastric ulcers being more common. NSAIDs, aspirin and co-morbidities were the main risk factors. Conclusions. The absence of H. pylori infection may not reduce the risk of peptic ulcer bleeding in the presence of risk factors especially offending drugs in the elderly.
Fulltext Adaptation and potential culture of wild Amphipods and Mysids as potential live feed in aquaculture: a review

Suhaimi H, Abdul Rahman MI, Ashaari A, Ikhwanuddin M, Wan Rasdi N

PeerJ, 2024;12:e17092.
PMID: 38563012 DOI: 10.7717/peerj.17092

Live foods such as phytoplankton and zooplankton are essential food sources in aquaculture. Due to their small size, they are suitable for newly hatched larvae. Artemia and rotifer are commonly used live feeds in aquaculture; each feed has a limited dietary value, which is unsuitable for all cultured species. Whereas, copepod and cladocerans species exhibit favorable characteristics that make them viable candidates as sources of essential nutrients for hatchery operations. Due to their jerking movements, it stimulates the feeding response of fish larvae, and their various sizes make them suitable for any fish and crustacean. Even though Artemia is the best live feed due to its proficient nutritional quality, the cost is very expensive, which is about half of the production cost. A recent study suggests the use of amphipods and mysids as alternative live feeds in aquaculture. High nutritional value is present in amphipods and mysids, especially proteins, lipids, and essential fatty acids that are required by fish larvae during early development. Amphipods and mysids are considered abundant in the aquatic ecosystem and have been used by researchers in water toxicity studies. However, the culture of amphipods and mysids has been poorly studied. There is only a small-scale culture under laboratory conditions for scientific research that has been performed. Thus, further research is required to find a way to improve the mass culture of amphipods and mysids that can benefit the aquaculture industry. This review article is intended to provide the available information on amphipods and mysids, including reproductive biology, culture method, nutritional value, feed enhancement, and the importance of them as potential live feed in aquaculture. This article is useful as a guideline for researchers, hatchery operators, and farmers.
Fulltext Advances in the study of nodavirus

Yong CY, Yeap SK, Omar AR, Tan WS

PeerJ, 2017;5:e3841.
PMID: 28970971 DOI: 10.7717/peerj.3841

Nodaviruses are small bipartite RNA viruses which belong to the family of Nodaviridae. They are categorized into alpha-nodavirus, which infects insects, and beta-nodavirus, which infects fishes. Another distinct group of nodavirus infects shrimps and prawns, which has been proposed to be categorized as gamma-nodavirus. Our current review focuses mainly on recent studies performed on nodaviruses. Nodavirus can be transmitted vertically and horizontally. Recent outbreaks have been reported in China, Indonesia, Singapore and India, affecting the aquaculture industry. It also decreased mullet stock in the Caspian Sea. Histopathology and transmission electron microscopy (TEM) are used to examine the presence of nodaviruses in infected fishes and prawns. For classification, virus isolation followed by nucleotide sequencing are required. In contrast to partial sequence identification, profiling the whole transcriptome using next generation sequencing (NGS) offers a more comprehensive comparison and characterization of the virus. For rapid diagnosis of nodavirus, assays targeting the viral RNA based on reverse-transcription PCR (RT-PCR) such as microfluidic chips, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and RT-LAMP coupled with lateral flow dipstick (RT-LAMP-LFD) have been developed. Besides viral RNA detections, diagnosis based on immunological assays such as enzyme-linked immunosorbent assay (ELISA), immunodot and Western blotting have also been reported. In addition, immune responses of fish and prawn are also discussed. Overall, in fish, innate immunity, cellular type I interferon immunity and humoral immunity cooperatively prevent nodavirus infections, whereas prawns and shrimps adopt different immune mechanisms against nodavirus infections, through upregulation of superoxide anion, prophenoloxidase, superoxide dismutase (SOD), crustin, peroxinectin, anti-lipopolysaccharides and heat shock proteins (HSP). Potential vaccines for fishes and prawns based on inactivated viruses, recombinant proteins or DNA, either delivered through injection, oral feeding or immersion, are also discussed in detail. Lastly, a comprehensive review on nodavirus virus-like particles (VLPs) is presented. In recent years, studies on prawn nodavirus are mainly focused on Macrobrachium rosenbergii nodavirus (MrNV). Recombinant MrNV VLPs have been produced in prokaryotic and eukaryotic expression systems. Their roles as a nucleic acid delivery vehicle, a platform for vaccine development, a molecular tool for mechanism study and in solving the structures of MrNV are intensively discussed.

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