Epidemiology of rumen fluke infection in selected buffalo farms in perak, malaysia: prevalence, molecular species identification, and associated risk factors

Rumen flukes cause heavy economic losses in the ruminant industry worldwide, especially in tropical and subtropical countries. This study estimated the prevalence of rumen flukes in buffaloes, identified the species diversity, and determined risk factors associated with rumen fluke prevalence in Perak, Peninsular Malaysia. A cross-sectional study was conducted, and 321 faecal samples were collected from six buffalo farms. A structured questionnaire was developed, and farmers were interviewed to obtain information regarding risk factors associated with rumen fluke infection. The faecal samples were examined using sedimentation and Flukefinder® techniques. Genomic DNA was extracted from the fluke eggs recovered using the Flukefinder® method, and the internal transcribed spacer 2 (ITS2) fragment was amplified and sequenced to facilitate species identification. The results showed that the overall prevalence of rumen fluke across the sampled farms was 40.2% (129/321). Three rumen fluke species were identified, namely, Fischoederius elongatus, F. cobboldi, and Orthocoelium streptocoelium. Several management factors had a significant association (P < 0.05) with rumen fluke prevalence, including production type, cleaning of the stable, drinking water system, flooding around the farm, grazing system, pasture sharing with other livestock, and deworming program. This work constitutes the first attempt to understand the epidemiology of rumen fluke infection in the region and suggests that good farm management, pasture management, choosing appropriate drugs, and proper husbandry practices may improve buffalo health and production in areas where rumen flukes are prevalent.

Assessment of Evaporative Demand Drought Index for drought analysis in Peninsular Malaysia

An effective drought monitoring tool is essential for the development of timely drought early warning system. This study evaluates Evaporative Demand Drought Index (EDDI) as a drought indicator in measuring spatiotemporal evolution of droughts over Peninsular Malaysia during 1989-2018. The modified Mann-Kendall and Sen's slope tests were performed to detect the presence of monotonic trends in EDDI, Standardized Precipitation Index (SPI), Standardized Precipitation Evapotranspiration Index (SPEI) and their related climate variables. The performance of EDDI in capturing the drought onset, evolutions and demise of historical severe droughts was also compared with SPI and SPEI at multiple timescales. EDDI demonstrates strong spatiotemporal correlations with SPI and SPEI and comparable performance in historical drought events identification. At sub-monthly timescale, 2-week EDDI displays equivalent drought severities and durations for all historical severe droughts corresponding to the monthly EDDI. In the case when rainfall deficits are normalized in an otherwise warm and dry month, EDDI may serve as a great alternative to SPI and SPEI due to it being sensitive to the changes in prevalent atmospheric conditions. Collectively, the results fill in the knowledge gaps on drought evolutions from the evaporative perspective and highlight the efficacy of EDDI as a valuable drought early warning tool for Peninsular Malaysia. Future study should explore the physical mechanisms behind the development of flash drought and the role of evaporation in the drought propagation processes.

Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling

The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.

Heatwaves in Peninsular Malaysia: a spatiotemporal analysis

One of the direct and unavoidable consequences of global warming-induced rising temperatures is the more recurrent and severe heatwaves. In recent years, even countries like Malaysia seldom had some mild to severe heatwaves. As the Earth's average temperature continues to rise, heatwaves in Malaysia will undoubtedly worsen in the future. It is crucial to characterize and monitor heat events across time to effectively prepare for and implement preventative actions to lessen heatwave's social and economic effects. This study proposes heatwave-related indices that take into account both daily maximum (Tmax) and daily lowest (Tmin) temperatures to evaluate shifts in heatwave features in Peninsular Malaysia (PM). Daily ERA5 temperature dataset with a geographical resolution of 0.25° for the period 1950-2022 was used to analyze the changes in the frequency and severity of heat waves across PM, while the LandScan gridded population data from 2000 to 2020 was used to calculate the affected population to the heatwaves. This study also utilized Sen's slope for trend analysis of heatwave characteristics, which separates multi-decadal oscillatory fluctuations from secular trends. The findings demonstrated that the geographical pattern of heatwaves in PM could be reconstructed if daily Tmax is more than the 95th percentile for 3 or more days. The data indicated that the southwest was more prone to severe heatwaves. The PM experienced more heatwaves after 2000 than before. Overall, the heatwave-affected area in PM has increased by 8.98 km2/decade and its duration by 1.54 days/decade. The highest population affected was located in the central south region of PM. These findings provide valuable insights into the heatwaves pattern and impact.

Genetic polymorphism and clustering of the Plasmodium cynomolgi Duffy binding protein 1 region II of recent macaque isolates from Peninsular Malaysia

Plasmodium cynomolgi is a simian malaria parasite that has been increasingly infecting humans. It is naturally present in the long-tailed and pig-tailed macaques in Southeast Asia. The P. cynomolgi Duffy binding protein 1 region II [PcDBP1(II)] plays an essential role in the invasion of the parasite into host erythrocytes. This study investigated the genetic polymorphism, natural selection and haplotype clustering of PcDBP1(II) from wild macaque isolates in Peninsular Malaysia. The genomic DNA of 50 P. cynomolgi isolates was extracted from the macaque blood samples. Their PcDBP1(II) gene was amplified using a semi-nested PCR, cloned into a plasmid vector and subsequently sequenced. The polymorphism, natural selection and haplotypes of PcDBP1(II) were analysed using MEGA X and DnaSP ver.6.12.03 programmes. The analyses revealed high genetic polymorphism of PcDBP1(II) (π = 0.026 ± 0.004; Hd = 0.996 ± 0.001), and it was under purifying (negative) selection. A total of 106 haplotypes of PcDBP1(II) were identified. Phylogenetic and haplotype analyses revealed two groups of PcDBP1(II). Amino acid length polymorphism was observed between the groups, which may lead to possible phenotypic difference between them.

species

The Amomum genus comprises of perennial, tropical, herbaceous plants that are distributed globally and possess both medicinal and ornamental properties. These plants contain a variety of secondary metabolites, including compounds with antioxidant and antimicrobial properties. This is the first transcriptomic analysis of seven Amomum species from Peninsular Malaysia, utilizing leaves, stems, and roots as sample material. Paired-end Illumina HiSeq technology was used for data generation which includes raw data, cleaned reads, de novo assembly, and functional annotation. The data is accessible via NCBI BioProject (PRJNA936673).

Global Terrapin Character-Based DNA Barcodes: Assessment of the Mitochondrial COI Gene and Conservation Status Revealed a Putative Cryptic Species

Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia's Southern River Terrapin population to better understand the species' genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world's terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population.

Hydrogeophysical modeling of the groundwater aquifer units under climate variability in parts of Peninsular Malaysia: A case study of the climate-water nexus approach to sustainability

Understanding of the climate-water nexus for sustainability, required good knowledge of the climate effects on groundwater aquifer units, particularly in rural communities. The studies were achieved using RES2-D modelling of the subsurface structures at the study site. Geophysical exploration with the application of 2-D Electrical Resistivity Imaging (ERI), combined with Induced Polarization (IP) method, were carried out to identify groundwater aquifers during extreme weather at Kampung Kuala Pajam, Beranang, Selangor, Peninsular Malaysia. The signatures obtained from geophysical explorations were used to better understand the phenomena that are responsible for groundwater depletion in the area. In recent times, there had been seasonal fluctuations in the water supply from boreholes serving the community. During the drought season, subsurface underlain this area experienced perennial acute shortages of groundwater supplies due to annual climatic variations that call for immediate solution by meeting the agricultural, domestic, and industrial water usage of the State of Selangor. A Pole-dipole techniques, using seven parallel lines of 400 m each at 5 m inter electrode spacing deployed to study the groundwater accumulation/aquifers within the area. Saturated groundwater occurrences zones were delineated as areas with average resistivity values of about 125 Ω-m, with corresponding chargeability of 30 ms. The methods used identified major faults along the northeast-southwest (NE-SW) directions, suitable for groundwater occurrences with approximate volume of about 2.86 Mega cubic metre (CBM), to proffer lasting solutions to the challenges being experienced by the community using a climate-water nexus sustainability.

Assessing the changes in river water quality across a land-use change (forest to oil palm plantation) in peninsular Malaysia using the stable isotopes of water and nitrate

Land conversion from natural forests to plantations (e.g., oil palm) in Southeast Asia is one of the most intensive land-use changes occurring worldwide. To clarify the effects of oil palm plantations on water quality, we conducted multipoint river and stream water sampling in peninsular Malaysia at the end of the rainy season over a 3-year period (2013-2015). We measured the major dissolved ions and stable isotope ratios of water (δ²H-H₂O and δ¹⁸O-H₂O) and nitrate (δ¹⁵N-NO₃^- and δ¹⁸O-NO₃^-) in water from the upper streams in mountainous forests to the midstream areas of two major rivers in peninsular Malaysia. The electrical conductivity increased, and the d-excess value (as an index of the degree of evaporation) decreased with increasing distance from the headwaters, suggesting the effect of evaporative enrichment and the addition of pollutants. We separated the sampling points into four groups (G1-G4) through cluster analysis of the water quality data. From the land use/land cover (LULC) classification maps developed from satellite images and local information, we found that G1 and G2 mainly consisted of sampling points in forested areas, while G3 and G4 were located in oil-palm-affected areas. The concentrations of major ions were higher in the oil palm areas, indicating the effects of fertilizer and limestone (i.e., pH adjustment) applications. The dissolved inorganic nitrogen concentration did not differ among the groups, but the dissolved organic carbon, total dissolved nitrogen, and δ¹⁵N-NO₃^- were higher in the oil palm area than in the forested area. Although the nitrogen concentration was low, even in the oil palm area, the significantly higher δ¹⁵N-NO₃^- in the oil palm area indicated substantial denitrification. This implies that denitrification contributed to the lowering of the NO₃^- concentration in rivers in the oil palm area, in addition to nutrient uptake by oil palm trees.

The Impact of Geographical Variation in Plasmodium knowlesi Apical Membrane Protein 1 (PkAMA-1) on Invasion Dynamics of P. knowlesi

Plasmodium knowlesi has emerged as an important zoonotic parasite that causes persistent symptomatic malaria in humans. The signs and symptoms of malaria are attributed to the blood stages of the parasites, which start from the invasion of erythrocytes by the blood stage merozoites. The apical membrane protein 1 (AMA-1) plays an important role in the invasion. In this study, we constructed and expressed recombinant PkAMA-1 domain II (PkAMA-1-DII) representing the predominant haplotypes from Peninsular Malaysia and Malaysian Borneo and raised specific antibodies against the recombinant proteins in rabbits. Despite the minor amino acid sequence variation, antibodies raised against haplotypes from Peninsular Malaysia and Malaysian Borneo demonstrated different invasion inhibition (46.81% and 39.45%, respectively) to P. knowlesi A1-H.1, a reference strain derived from Peninsular Malaysia. Here, we demonstrated how a minor variation in a conserved parasite protein could cast a significant impact on parasite invasion biology, suggesting a complex host-switching of P. knowlesi from different locations. This may challenge the implementation of a standardized One Health approach against the transmission of knowlesi malaria.

Predicting Plasmodium knowlesi transmission risk across Peninsular Malaysia using machine learning-based ecological niche modeling approaches

The emergence of potentially life-threatening zoonotic malaria caused by Plasmodium knowlesi nearly two decades ago has continued to challenge Malaysia healthcare. With a total of 376 P. knowlesi infections notified in 2008, the number increased to 2,609 cases in 2020 nationwide. Numerous studies have been conducted in Malaysian Borneo to determine the association between environmental factors and knowlesi malaria transmission. However, there is still a lack of understanding of the environmental influence on knowlesi malaria transmission in Peninsular Malaysia. Therefore, our study aimed to investigate the ecological distribution of human P. knowlesi malaria in relation to environmental factors in Peninsular Malaysia. A total of 2,873 records of human P. knowlesi infections in Peninsular Malaysia from 1st January 2011 to 31st December 2019 were collated from the Ministry of Health Malaysia and geolocated. Three machine learning-based models, maximum entropy (MaxEnt), extreme gradient boosting (XGBoost), and ensemble modeling approach, were applied to predict the spatial variation of P. knowlesi disease risk. Multiple environmental parameters including climate factors, landscape characteristics, and anthropogenic factors were included as predictors in both predictive models. Subsequently, an ensemble model was developed based on the output of both MaxEnt and XGBoost. Comparison between models indicated that the XGBoost has higher performance as compared to MaxEnt and ensemble model, with AUC_ROC values of 0.933 ± 0.002 and 0.854 ± 0.007 for train and test datasets, respectively. Key environmental covariates affecting human P. knowlesi occurrence were distance to the coastline, elevation, tree cover, annual precipitation, tree loss, and distance to the forest. Our models indicated that the disease risk areas were mainly distributed in low elevation (75-345 m above mean sea level) areas along the Titiwangsa mountain range and inland central-northern region of Peninsular Malaysia. The high-resolution risk map of human knowlesi malaria constructed in this study can be further utilized for multi-pronged interventions targeting community at-risk, macaque populations, and mosquito vectors.

Molecular Detection, Risk Factors and Public Awareness of Avian Bornavirus among Captive and Non-captive Birds in Peninsular Malaysia

Introduction

Proventricular dilatation disease (PDD) is caused by avian bornavirus (ABV) has been identified in psittacine, non-psittacine birds and waterfowl. Birds may show signs of gastrointestinal tract deficit or neurological dysfunction or even both. The objectives of this study were to determine the molecular prevalence, risk factors and public awareness of ABV and PDD among captive and non-captive birds in Peninsular Malaysia.

Material and Methods

A total of 344 cloacal swabs or faeces were collected and subjected to detection using the RT-PCR assay. Meanwhile, KAP questionnaires were distributed by using the Google forms platform.

Results

Molecular prevalence studies revealed that 4.5% (9/201) of the pet birds were ABV-positive, whereas 0% (0/143) in waterfowl. Nine positive pet birds were identified to be PaBV-2, which is closest to ABV isolates EU781967 (USA). Among the risk factors analysed, category, age and, location, were found to show an association with the ABV positivity. The KAP survey result showed: the respondents have low knowledge (32.9%), however, they showed positive attitude (60.8%) and good practice (94.9%). The association between knowledge, attitude and practice showed that there was a significant association between knowledge-attitude and also attitude-practice (P<0.05).

Conclusion

This study proved that avian bornavirus (ABV) causes proventricular dilatation disease (PDD) among a group of pet birds of Psittaciformes, but it is present in Peninsular Malaysia with a low prevalence rate. Furthermore, in addition to the useful databases obtained from this study, the level of public awareness on the importance of avian bornavirus that causes fatal disorders among a wide range of bird species is satisfactorily raised.

Volatile Organic Compounds of Bryophytes from Peninsular Malaysia and Their Roles in Bryophytes

Volatile emissions from 22 bryophyte species from Peninsular Malaysia were collected using a dynamic headspace technique and analyzed by gas chromatography-mass spectrometry (GC-MS). Thirty organic compounds (VOCs) from eight different groups were detected in bryophytes from the montane forest in Cameron Highlands and the lowland dipterocarp forest in Lata Belatan. The headspace of bryophytes in Cameron Highlands was dominated by tetradecane, 2-ethyl-1-hexanol, decanal, pentanoic acid, 2,2,4-trimethyl-3-carboxyisopropyl, isobutyl ester, D-limonene and naphthalene. On the contrary, in the bryophyte headspace of Lata Belatan, naphthalene and tetradecane were dominant compounds. The elevational pattern detected in VOC composition of bryophytes appears to be an evolutionary feature at the family level that needs verification at other sites. The results also confirmed that the VOC composition of bryophytes is species-specific. The roles of VOCs in bryophytes are presented, including plant-plant communication and plant-insect interaction and as an additional taxonomic character in chemotaxonomy.

Isolated from Cultured Shrimp in Peninsular Malaysia

Vibrio is the most common bacterium associated with diseases in crustaceans. Outbreaks of vibriosis pose a serious threat to shrimp production. Therefore, antibiotics are commonly used as preventative and therapeutic measures. Unfortunately, improper use of antibiotics leads to antibiotic resistance. Nevertheless, information on the occurrence of Vibrio spp. and antibiotic use in shrimp, particularly in Malaysia, is minimal. This study aimed to provide information on the occurrence of Vibrio spp., its status of antibiotic resistance and the plasmid profiles of Vibrio spp. isolated from cultured shrimp in Peninsular Malaysia. Shrimp were sampled from seven farms that were located in different geographical regions of Peninsular Malaysia. According to the observations, 85% of the shrimp were healthy, whereas 15% were unhealthy. Subsequently, 225 presumptive Vibrio isolates were subjected to biochemical tests and molecular detection using the pyrH gene. The isolates were also tested for antibiotic susceptibility against 16 antibiotics and were subjected to plasmid profiling. Eventually, 13 different Vibrio spp. were successfully isolated and characterized using the pyrH gene. They were the following: V. parahaemolyticus (55%), V. communis (9%), V. campbellii (8%), V. owensii (7%), V. rotiferianus (5%), Vibrio spp. (4%), V. alginolyticus (3%), V. brasiliensis (2%), V. natriegens (2%), V. xuii (1%), V. harveyi (1%), V. hepatarius (0.4%) and P. damselae (3%). Antibiotic susceptibility profiles revealed that all isolates were resistant to penicillin G (100%), but susceptible to norfloxacin (96%). Furthermore, 16% of the isolates revealed MAR of less than 0.2, while 84% were greater than 0.2. A total of 125 isolates harbored plasmids with molecular weights between 1.0 and above 10 kb, detected among the resistant isolates. The resistant isolates were mediated by both chromosomal and plasmid factors. These findings support the use of surveillance data on the emerging patterns of antimicrobial-resistance and plasmid profiles of Vibrio spp. in shrimp farms. The findings from this study can be used to develop a better disease management strategy for shrimp farming.

Finding the Link between Cyberbullying and Suicidal Behaviour among Adolescents in Peninsular Malaysia

Social media engagement has contributed to the rise of cyberbullying, which has recently triggered tragic suicides among adolescents. The objective of this cross-sectional study is to determine the prevalence of cyberbullying, suicidal behaviour, and their association among adolescents in Peninsular Malaysia. The study was conducted among 1290 secondary school adolescents aged between 13 and 17 years old in Peninsular Malaysia using a self-administered and anonymous online questionnaire. Our findings reveal that the prevalence of cyberbullying victimization and perpetrator is 13.7% and 3.8%, respectively. The prevalence of suicidal behaviour among adolescents is 17.1%, in which 11.9% had suicidal thoughts, 10.2% had a suicide plan, and 8.4% had made a suicide attempt. Multiple logistic regression shows that adolescents experiencing cyberbullying victimization is a significant risk factor (p < 0.001) for suicidal behaviour after adjusting for other confounders. An alarming number of adolescents in Peninsular Malaysia found to be involved in cyberbullying and its significant association with suicidal behaviour warrant the need to strengthen current interventions. Since the study was conducted during the COVID-19 pandemic, our findings make an important contribution in reporting current trends in cyberbullying and suicide among adolescents, especially when they are becoming ever-more present in cyberspaces.

Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis

Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis.

Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak

The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.

Capparis (Capparaceae) in Peninsular Malaysia, including a new species and two new varieties

As part of the Flora of Peninsular Malaysia Project, a species checklist of the genus Capparis in Peninsular Malaysia is presented here with a total of 11 species, two subspecies and four varieties. A new species and two varieties, endemic to Peninsular Malaysia, are described and illustrated: Cappariskenaboiensis, C.scortechiniivar.ruthiae and C.trinerviavar.chungiana. Cappariskenaboiensis is known from a single site in Negeri Sembilan and is assessed as Vulnerable (VU); C.scortechiniivar.ruthiae from Pahang is Vulnerable (VU); and Capparistrinerviavar.chungiana is known from Negeri Sembilan, Pahang and Selangor and its conservation status is assessed as Near Threatened (NT). A checklist and updated key to the genus in Peninsular Malaysia are provided.

Determining the Dietary Preferences of Wild Asian Elephants (Elephas maximus) in Taman Negara National Park, Malaysia Based on Sex and Age using trnL DNA Metabarcoding Analysis

The world's largest terrestrial mammal, Asian elephants, are known to have enormous feeding needs. Several factors such as season, sex, age, and daily activities influence the amount of food required by an individual. Generally, captive elephants have a limited choice of food on a daily basis compared with that of elephants in the wild. Elephants in captivity are fed according to a prepared feeding schedule, whereas wild elephants are free to choose the type of plants that they consume in their natural habitat. In the past, ecological observations have been widely used to determine the diet of wild elephants. However, the molecular approach has never been carried out. In the present study, we aimed to; 1) identify the plant diet of wild Asian elephants in Taman Negara National Park (TNNP) according to their sex and age using high-throughput DNA metabarcoding; and 2) determine the dietary formulation of captive elephants based on the generated plant metabarcoding database. DNA was extracted from 24 individual fecal samples collected using noninvasive sampling techniques from TNNP and the National Elephant Conservation Centre (NECC) Kuala Gandah. Seven pooled samples from male adult, female adult, male subadult, female subadult, male juvenile, female juvenile, and captive elephants were amplified and sequenced targeting the trnL region (50-150 base pairs). The CLC Genomic Workbench and PAST 4.02 software were used for data analysis. In total, 24 orders, 41 families, 233 genera, and 306 species of plants were successfully detected in the diet of the Asian elephants. The most abundant plant genera consumed were Sporobolus (21.88%), Musa (21.48%), and Ficus (10.80%). Plant variation was lower in samples from male elephants than in those from female elephants. The plant species identified were correlated with the nutrient benefits required by elephants. Adults and subadults consumed more plant species than were consumed by juvenile elephants. However, there was no significant difference between ages and sexes. The findings of this study can be used as guidance by the Department of Wildlife and National Parks for the management of captive elephants, especially in NECC Kuala Gandah.

Spatial and Temporal Variations in Nutrients During Upwelling Season Off the East Coast of Peninsular Malaysia

This study determines the bulk surface water (BSW) dissolved inorganic nutrients of nitrogen (DINi) and phosphate (DIP) during the upwelling season off the east coast of Peninsular Malaysia, South China Sea. BSW samples were analysed for DINi and DIP by using a standard automated colorimetric method. BSW DINi and DIP concentrations varied between 0.11 and 2.55 μM (mean 1.12 ± 0.63 μM), and below detection limit, and 0.29 μM (mean 0.11 ± 0.08 μM), respectively. The spatial distribution of higher concentrations between DINi and DIP was distinct. However, the highest concentrations of DINi and DIP were mostly recorded in the month of peak upwelling (July and August), where colder BSW temperatures were also encountered during field sampling. This study provides new evidence on the presence of BSW nutrients of DINi and DIP during upwelling season peak in July and August before their decline in September.

Population data for 15 autosomal STR loci in Orang Asli subgroups of Peninsular Malaysia

Short tandem repeats (STRs) data for the Orang Asli population in Peninsular Malaysia is still scanty, especially for specific Orang Asli subgroups. The Orang Asli is believed as the earliest population arrived in Peninsular Malaysia about 50,000 years ago and currently makes up only 0.6% of the total population of Malaysia. This study reports the allele frequencies and several forensic statistical parameters for 15 autosomal STR loci for six Orang Asli subgroups. A total of 164 Orang Asli individuals representing the Semai, Che Wong, Orang Kanaq, Lanoh, Bateq, and Kensui subgroups were recruited for this study. This STR data will enrich the existing Malaysian autosomal STR database and will be useful for kinship testing and forensic applications.

Population Genomic Structure and Recent Evolution of Plasmodium knowlesi, Peninsular Malaysia

Most malaria in Malaysia is caused by Plasmodium knowlesi parasites through zoonotic infection from macaque reservoir hosts. We obtained genome sequences from 28 clinical infections in Peninsular Malaysia to clarify the emerging parasite population structure and test for evidence of recent adaptation. The parasites all belonged to a major genetic population of P. knowlesi (cluster 3) with high genomewide divergence from populations occurring in Borneo (clusters 1 and 2). We also observed unexpected local genetic subdivision; most parasites belonged to 2 subpopulations sharing a high level of diversity except at particular genomic regions, the largest being a region of chromosome 12, which showed evidence of recent directional selection. Surprisingly, we observed a third subpopulation comprising P. knowlesi infections that were almost identical to each other throughout much of the genome, indicating separately maintained transmission and recent genetic isolation. Each subpopulation could evolve and present a broader health challenge in Asia.

Further Insights Into Caprine Arthritis Encephalitis (CAE): The Current Status of Seroprevalence Among Small Ruminants in Two Selected States of Peninsular Malaysia

Caprine arthritis-encephalitis virus (CAEV) is a member of the genus lentivirus causing caprine arthritis-encephalitis (CAE), a chronic inflammatory condition affecting the lungs, joints, udder and central nervous system of small ruminants such as sheep and goats. CAE is distributed worldwide and is recognised as a significant cause of morbidity and decreased milk production in dairy goats. Earlier studies highlighted the clinicopathological features and supplied preliminary serological evidence for the existence of CAE among selected goat herds in Malaysia. Therefore, this study aims to provide further insights into the seroprevalence and contributing factors of CAE among sheep and goat herds in two states of Peninsular Malaysia. The blood samples and biodata were randomly collected from a total of 262 individual sheep (40) and goat (222) in seven smallholder farms. Blood sera were tested for specific anti-CAEV antibodies using Qayee-Bio CAEV sandwich-ELISA test kits according to standard procedures. Our results of the study revealed 21.4% (95% CI: 15.8-28.6) apparent and 20.6% (95% CI: 14.5-27.8) true seroprevalence with significant differences (p < 0.05) in seroconversion rates between the states, farms, production systems and breeds of small ruminants. The prevalence of CAE in the Malaysian Peninsular is a potential threat to the small ruminant industry and developing agricultural economy. Further studies are required to determine the genetic characteristics, distribution and risk factors of CAEV for effective prevention and control in Malaysia.

Land snails and slugs of Bau limestone hills, Sarawak (Malaysia, Borneo), with the descriptions of 13 new species

This study presents a list of land snails and slugs found on limestone hills in the District of Bau, the state of Sarawak in Malaysian Borneo. Systematic and random sampling for land snails was conducted at eight limestone outcrops, namely, Gunung Stulang, Padang Pan, Gunung Kapor, Gunung Lobang Angin, Gunung Doya, Gunung Batu, Bukit Sekunyit and Gunung Sebayat. A total of 122 land snail species was documented with photographs of each species. Of the 122 species collected, 13 are new to science, namely, Acmellabauensissp. nov., Japoniabauensissp. nov., Plectostomamargaretchanaesp. nov., Microcystinaarabiisp. nov., Microcystinaatonisp. nov., Microcystinapariparisp. nov., Microcystinaliratasp. nov., Microcystinaoswaldbrakenisp. nov., Microcystinakilatsp. nov., Philalankajambusanensissp. nov., Everettiamicrorhytidasp. nov., Everettiaminutasp. nov., and Paralaomasarawakensissp. nov.

Thismia belumensis (Thismiaceae), a remarkable new species from The Royal Belum State Park, Gerik, Perak, Peninsular Malaysia

This report describes Thismia belumensis Siti-Munirah & Suhaimi-Miloko, a novel species of achlorophyllous herb discovered in the Royal Belum State Park, Peninsular Malaysia. This new species is unlike any previously described species of Thismia. In particular, T. belumensis possesses a unique annulus, which has been expanded and modified into a cucullate (hood-like) structure. This structure covers the apical floral tube and has an opening on one side facing a thickened part of the annulus, and the off-centre floral aperture confers a zygomorphic symmetry to the flower, indicating T. belumensis is more similar to Thismia labiata J.J.Sm. This morphological detail makes this new species distinct from all other described species of Thismia. In this report, we provide descriptions, illustrations, colour plates, and the provisional conservation status of Thismia belumensis.

The molecular prevalence, distribution and risk factors associated with Babesia bigemina infection in Peninsular Malaysia

Babesia bigemina is a tick-borne protozoan that affects cattle in almost all regions of the world. Despite its importance, there is no report of its prevalence in cattle using molecular detection methods in Peninsular Malaysia. This study describes the prevalence, distribution, and risk factors associated with B. bigemina infection using molecular diagnostic methods. Also, the species of ticks infesting cattle and the attitude of cattle farmers towards tick control in Peninsular Malaysia were studied. Blood samples were collected from 1045 cattle from 43 herds throughout the country, and were subjected to molecular studies to detect B. bigemina. Tick samples for entomological studies were also collected and identified. Epidemiological information of each cattle and farm were obtained using a well-structured questionnaire containing open-ended and closed-ended questions. Data were statistically analyzed using Univariate and Multivariate models. The 211-base pair of AMA-1 gene of B. bigemina was amplified and confirmed in 30.5 % (319/1045; 95 % CI = 27.8-33.4) of the sampled population, with the haemoprotozoan detected in all the sampled herds. Breed, age, physiological status, management type, rate of de-ticking, and closeness to human settlement were the risk factors significantly (p < 0.05) associated with the prevalence of B. bigemina in cattle. Rhipicephalus (Boophilus) microplus and Haemaphysalis bispinosa were the species of ticks collected from cattle, with the former been more prevalent. A large number of cattle farmers (12/43; 28 %) do not control ticks in their herds. The findings of this study will create baseline data on the epidemiology of the haemoprotozoan and control patterns of its tick vectors that will guide the government in enacting policies that will improve food security and the economy of the nation.

Isolation of Mycobacterium avium and other nontuberculous mycobacteria in chickens and captive birds in peninsular Malaysia

Background

Mycobacterium avium complex (MAC) causes a chronic infectious in the birds known as avian mycobacteriosis. Almost all species of the birds are susceptible to MAC which consists of two closely related species of mycobacteria, that is, M. avium and M. intracellulare. This study aimed to determine the occurrence of Mycobacterium avium subsp. avium (MAA) in chickens and captive birds in selected states of Peninsular Malaysia.

Results

A 300 fecal samples were collected from village chickens (n = 100), layer chickens (n = 100) and captive birds (n = 100). Fecal samples were split into two aliquots for microbiological and molecular detection of MAA. Microbiology detection consisted of microscopy (Ziehl-Neelsen staining) and culture of samples decontaminated with 1% Cetylperidinium chloride and vancomycin, nalidixic acid and amphotericin B (VNA) antibiotic cocktail [vancomycin (VAN) 100 μg/ml, nalidixic acid (NAL) 100 μg/ml and amphotericin B (AMB) 50 μg/ml] onto Löwenstein-Jensen (L-J). Molecular detection (PCR-IS901) was performed to detect MAA DNA from the feces and PCR-16S rRNA and IS901 for identification of genus Mycobacterium and Mycobacterium avium sub species avium isolated onto L-J. All samples (296) were AFB negative smear. M. avium was isolated in 0.3% (1/296) samples by culture and detected in 2.5% (6/242) samples by PCR (IS901). Other mycobacteria were found in 1.7% (5/296) chickens. Of five isolates, two were identified as Mycobacterium terrae and M. engbaekii and remaining isolates were not sequenced. Birds positive for M. avium included White Pelican (n = 1) Black Hornbill (n = 1), Macaw (n = 2), Cockatoo (n = 2) and village chicken (n = 1).

Conclusion

It is concluded that chickens and birds were infected with M. avium in selected areas of Peninsular Malaysia. Although, PCR is rapid, reliable and cost effective method for detection of M. avium in a subclinical stage, the culture of the avian feces should still be used as a reference test for the diagnosis of avian tuberculosis.

Spatial distribution of fine and coarse particulate matter during a southwest monsoon in Peninsular Malaysia

This study aimed to determine the spatial distribution of PM_2.5 and PM₁₀ collected in four regions (North, Central, South and East Coast) of Peninsular Malaysia during the southwest monsoon. Concurrent measurements of PM_2.5 and PM₁₀ were performed using a high volume sampler (HVS) for 24 h (August to September 2018) collecting a total of 104 samples. All samples were then analysed for water soluble inorganic ions (WSII) using ion chromatography, trace metals using inductively coupled plasma-mass spectroscopy (ICP-MS) and polycyclic aromatic hydrocarbon (PAHs) using gas chromatography-mass spectroscopy (GC-MS). The results showed that the highest average PM_2.5 concentration during the sampling campaign was in the North region (33.2 ± 5.3 μg m^-3) while for PM₁₀ the highest was in the Central region (38.6 ± 7.70 μg m^-3). WSII recorded contributions of 22% for PM_2.5 and 20% for PM₁₀ mass, with SO₄^2- the most abundant species with average concentrations of 1.83 ± 0.42 μg m^-3 (PM_2.5) and 2.19 ± 0.27 μg m^-3 (PM₁₀). Using a Positive Matrix Factorization (PMF) model, soil fertilizer (23%) was identified as the major source of PM_2.5 while industrial activity (25%) was identified as the major source of PM₁₀. Overall, the studied metals had hazard quotients (HQ) value of <1 indicating a very low risk of non-carcinogenic elements while the highest excess lifetime cancer risk (ELCR) was recorded for Cr VI in the South region with values of 8.4E-06 (PM_2.5) and 6.6E-05 (PM₁₀). The incremental lifetime cancer risk (ILCR) calculated from the PAH concentrations was within the acceptable range for all regions.

Spatial and Temporal Analysis of Plasmodium knowlesi Infection in Peninsular Malaysia, 2011 to 2018

The life-threatening zoonotic malaria cases caused by Plasmodium knowlesi in Malaysia has recently been reported to be the highest among all malaria cases; however, previous studies have mainly focused on the transmission of P. knowlesi in Malaysian Borneo (East Malaysia). This study aimed to describe the transmission patterns of P. knowlesi infection in Peninsular Malaysia (West Malaysia). The spatial distribution of P. knowlesi was mapped across Peninsular Malaysia using Geographic Information System techniques. Local indicators of spatial associations were used to evaluate spatial patterns of P. knowlesi incidence. Seasonal autoregressive integrated moving average models were utilized to analyze the monthly incidence of knowlesi malaria in the hotspot region from 2012 to 2017 and to forecast subsequent incidence in 2018. Spatial analysis revealed that hotspots were clustered in the central-northern region of Peninsular Malaysia. Time series analysis revealed the strong seasonality of transmission from January to March. This study provides fundamental information on the spatial distribution and temporal dynamic of P. knowlesi in Peninsular Malaysia from 2011 to 2018. Current control policy should consider different strategies to prevent the transmission of both human and zoonotic malaria, particularly in the hotspot region, to ensure a successful elimination of malaria in the future.

Checklist of herpetofauna in the severely degraded ecosystem of Bidong Island, Peninsular Malaysia, South China Sea

A herpetofaunal inventory was conducted on Bidong Island, Terengganu, Peninsular Malaysia. It incorporates data from a recent herpetological survey conducted from 1 to 3 April 2019 with reptile records from previous publications. Specimens were collected with drift-fenced pitfall traps and taxa were recorded with visual encounter surveys (VES). In total, 18 species of reptiles and amphibians were recorded, including three species of frogs, 12 species of lizards, and three species of snakes. Six species from the present survey are new records for the island.

Modeling the spatio-temporal dynamics of air pollution index based on spatial Markov chain model

An environmental problem which is of concern across the globe nowadays is air pollution. The extent of air pollution is often studied based on data on the observed level of air pollution. Although the analysis of air pollution data that is available in the literature is numerous, studies on the dynamics of air pollution with the allowance for spatial interaction effects through the use of the Markov chain model are very limited. Accordingly, this study aims to explore the potential impact of spatial dependence over time and space on the distribution of air pollution based on the spatial Markov chain (SMC) model using the longitudinal air pollution index (API) data. This SMC model is pertinent to be applied since the daily data of API from 2012 to 2014 that have been gathered from 37 different air quality stations in Peninsular Malaysia is found to exhibit the property of spatial autocorrelation. Based on the spatial transition probability matrices found from the SMC model, specific characteristics of air pollution are studied in the regional context. These characteristics are the long-run proportion and the mean first passage time for each state of air pollution. It is found that the probability for a particular station's state to remain good is 0.814 if its neighbors are in a good state of air pollution and 0.7082 if its neighbors are in a moderate state. For a particular station having neighbors in a good state of air pollution, the proportion of time for it to continue being in a good state is 0.6. This proportion reduces to 0.4, 0.01, and 0 for the cell of moderate, unhealthy, and very unhealthy states, respectively. In addition, there exists a significant spatial dependence of API, indicating that air pollution for a particular station is dependent on the states of the neighboring stations.

Contrasting growth responses to aluminium addition among populations of the aluminium accumulator Melastoma malabathricum

Aluminium (Al) hyper-accumulation is a common trait expressed by tropical woody plants growing on acidic soils. Studies on Al accumulators have suggested that Al addition may enhance plant growth rates, but the functional significance of this trait and the mechanistic basis of the growth response are uncertain. This study aimed to test the hypothesis that differential growth responses to Al among populations of an Al accumulator species are associated with variation in biomass allocation and nutrient uptake. We conducted two experiments to test differential responses to the presence of Al in the growth medium for seedlings of the Al accumulator shrub Melastoma malabathricum collected from 18 populations across Peninsular Malaysia. Total dry mass and relative growth rate of dry mass were significantly greater for seedlings that had received Al in the growth medium than for control plants that did not receive Al, but growth declined in response to 5.0 mM Al addition. The increase in growth rate in response to Al addition was greater for a fast-growing than a slow-growing population. The increase in growth rate in response to Al addition occurred despite a reduction in dry mass allocation to leaves, at the expense of higher allocation to roots and stems, for plants grown with Al. Foliar concentrations of P, K, Mg and Ca increased in response to Al addition and the first axis of a PCA summarizing foliar nutrient concentrations among populations was correlated positively with seedling relative growth rates. Some populations of the Al hyper-accumulator M. malabathricum express a physiological response to Al addition which leads to a stimulation of growth up to an optimum value of Al in the growth medium, beyond which growth declines. This was associated with enhanced nutrient concentrations in leaves, which suggests that Al accumulation functions to optimize elemental stoichiometry and growth rate.

Influence of elevated river flow on hypoxia occurrence, nutrient concentration and microbial dynamics in a tropical estuary

We sampled the Klang estuary during the inter-monsoon and northeast monsoon period (July-Nov 2011, Oct-Nov 2012), which coincided with higher rainfall and elevated Klang River flow. The increased freshwater inflow into the estuary resulted in water column stratification that was observed during both sampling periods. Dissolved oxygen (DO) dropped below 63 μM, and hypoxia was observed. Elevated river flow also transported dissolved inorganic nutrients, chlorophyll a and bacteria to the estuary. However, bacterial production did not correlate with DO concentration in this study. As hypoxia was probably not due to in situ heterotrophic processes, deoxygenated waters were probably from upstream. We surmised this as DO correlated with salinity (R² = 0.664, df = 86, p < 0.001). DO also decreased with increasing flushing time (R² = 0.556, df = 11, p < 0.01), suggesting that when flushing time (> 6.7 h), hypoxia could occur at the Klang estuary. Here, we presented a model that related riverine flow rate to the post-heavy rainfall hypoxia that explicated the episodic hypoxia at Klang estuary. As Klang estuary supports aquaculture and cockle culture, our results could help protect the aquaculture and cockle culture industry here.

Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia

Alpinia belongs to a large genus with many species found in Peninsular Malaysia. Several species of Alpinia exhibit important medicinal potential. However, progressive studies on the genus Alpinia were hampered by difficulties encountered in species identification. With the advancement achieved in genomic technology, more sensitive tools such as DNA barcoding were developed, which can be used for species identification. Internal Transcribe Spacer 2 (ITS2) is a DNA barcode which has proven to be a promising tool for species identification. The criterions of ITS2 efficacy namely universality and efficacy for species identification were tested on Alpinia species collected from Peninsular Malaysia. The results showed that a success rate of 96.97% was achieved using ITS2 for screening 11 species of Alpinia and an outgroup sample (Zingiber specatabile). Combined with 15 additional sequences from the Genbank for five Alpinia species, ITS2 demonstrated high species identification efficacy with 88.2% of species identified using phylogenetic and distance analysis. The analysis was further improved with the use of ITS2 secondary structure. The results of both criterions demonstrated the ability of ITS2 to successfully discriminate Alpinia species, which will help to improve species identification of Alpinia species in Peninsular Malaysia.

Molecular detection, prevalence and risk factors of Theileria orientalis infection among cattle in Peninsular Malaysia

There is need to confirm the presence of Theileria orientalis among the cattle population in Peninsular Malaysia and to evaluate the risk factors associated with the infection. To this effect, blood samples were collected from 1045 cattle from 43 farms throughout the entire States of Peninsular Malaysia. The collected blood samples were subjected to DNA extraction and subsequent PCR amplification of the major piroplasm surface protein (MPSP) gene of the haemoprotozoan. Representative positive amplicons were purified, sequenced and compared with other sequences of the MPSP gene of T. orientalis curated from the GenBank. A well-structured questionnaire was used to get information about each cattle, it's demography, the bio-security, environmental and management factors. Univariate and multivariate analysis were used for the statistical evaluation, with significance set at p < 0.05. A total prevalence of 49.76% (520/1045; 95% CI: 46.73 - 52.79) was obtained. Types of breeds, age, production type, herd size, level of farm biosecurity, farm size, presence of other animal species in the farm, management systems and prophylaxis were significantly (p < 0.05) associated with the prevalence of T. orientalis. This study confirmed the presence of T. orientalis and establish that the haemoprotozoan is endemic among cattle in Peninsular Malaysia.

HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in 271 Southeast Asia Indians from Peninsular Malaysia

A total of 271 Southeast Asia Indians from Peninsular Malaysia were genotyped for HLA-A, -B, -C, -DRB1, and -DQB1 loci using polymerase chain reaction sequence-specific oligonucleotide probe hybridization methods. In this report, HLA-B and HLA-DQB1 was in Hardy-Weinberg proportions (HWEP) (p > 0.05). We observed significant deviation from the HWEP for HLA-A (p < 0.05), HLA-C (p < 0.01) and HLA-DRB1 (p < 0.01) loci. This genotype data is available in Allele Frequencies Network Database (AFND) Dos Santos et al. (2016).

Molecular Prevalence and Epidemiology of Trypanosoma evansi Among Cattle in Peninsular Malaysia

BACKGROUND

Animal trypanosomiasis (Surra) caused by Trypanosoma evansi (T. evansi) is known to be one of the important haemoprotozoan parasites that causes great economical loss on animal production due to mortality and loss of condition.

METHODS

A cross-sectional study was designed to evaluate the prevalence and risk factors associated with T. evansi infection among cattle in Peninsular Malaysia. Polymerase chain reaction (PCR) was employed on 1045 blood samples collected from 43 farms. A well-structured questionnaire was used to collect data on risk factors associated with T. evansi prevalence. The RoTat 1.2 set of primers was used to amplify products of 205 base pair.

RESULTS

The overall prevalence was found to be 17.9% (187/1045; 95% CI = 15.66-20.31). Trypanosoma evansi was detected among cattle in all the States of Peninsular Malaysia. Breeds of cattle and closeness to waste area, where the risk factors significantly (p < 0.05) associated with the PCR positivity of T. evansi among cattle in Peninsular Malaysia.

CONCLUSION

This appears to be the first time a comprehensive survey on the prevalence and risk factors of T. evansi infection in cattle using molecular tools is been carried out in the entire states of Peninsular Malaysia. The findings from this study will provide baseline information on the molecular prevalence of the haemoflagellate and its associated risk factors among cattle for an improved beef and dairy production in Peninsular Malaysia.

Are social media reports useful for assessing small ape occurrence? A pilot study from Peninsular Malaysia

Citizen science-based research has been used effectively to estimate animal abundance and breeding patterns, to monitor animal movement, and for biodiversity conservation and education. Here, we evaluate the feasibility of using social media observations to assess the distribution of small apes in Peninsular Malaysia. We searched for reports of small ape observations in Peninsular Malaysia on social media (e.g., blogs, Facebook, Instagram, Twitter, YouTube, iNaturalist, etc.), and also used online, radio, print messaging, and word of mouth to invite citizen scientists such as birders, amateur naturalists, hikers, and other members of the public to provide information about small ape observations made during their activities. These reports provided new information about the occurrence of all three species of small apes (Hylobates agilis, Hylobates lar, and Symphalangus syndactylus) in Peninsular Malaysia. Social media users reported observations of small apes in almost every state. Despite the fact that small apes are believed to occur primarily in the interior of large forested areas, most observations were from fairly small (<100 km² ) forests near areas of high traffic and high human population (roads and urban areas). This suggests that most outdoor enthusiasts primarily visit well-traveled and easily accessible areas, which results in biased sampling if only incidental observations reported on social media are used. A more targeted approach specifically soliciting reports from citizen scientists visiting large, less-accessible forests may result in better sampling in these habitats. Social media reports indicated the presence of small apes in at least six habitats where they had not been previously reported. We verified the reported data based on whether reports included a date, location, and uploaded photographs, videos and/or audio recordings. Well-publicized citizen science programs may also build awareness and enthusiasm about the conservation of vulnerable wildlife species.

Dataset on the diversity and distribution of biting flies collected from cattle farms in Peninsular Malaysia

This dataset investigated the diversity, the geographic and spatial distribution of haematophagous flies collected from cattle farms in Peninsular Malaysia. Biting flies were trapped from 25 cattle farms over a one-year period. One-way Analysis of Variance (ANOVA) was used to establish the presence/absence of statistical differences in the number of flies caught in relation to the different geographic distributions (zones). Three thousand eight hundred and eighty-nine haematophagous flies comprising of 36 different species, including Musca species (3189; 82.0%), Stomoxys species (588; 15.1%), Tabanus species (58; 1.5%), Chrysops species (19; 0.5%), Haematopota javana (3; 0.1%), Haematobosca species (29; 0.7%) and Haematobia exigua (3; 0.1%) were collected using three different types of fly traps. More biting flies were trapped in the southwest (1070; 27.5%) and south (1045; 26.9%) zones compared to other arbitrary zones of Peninsular Malaysia. Haematophagous flies were spatially distributed both in the inland and coastal parts of the country. The difference in the catch of Stomoxys species within zones was not significant (F = 1.299; df = 5; p = 0.306), although it was highest in the southwest zone. The number of Musca species caught was highest in the south zone compared to other zones, the differences was not significant (F = 0.770; df = 5; p = 0.583). Tabanidae fly species were most abundant in the southwest zone, the differences among zones was not significant (F = 1.179; df = 5; p = 0.356).

Updates on malaria incidence and profile in Malaysia from 2013 to 2017

Background

To date, most of the recent publications on malaria in Malaysia were conducted in Sabah, East Malaysia focusing on the emergence of Plasmodium knowlesi. This analysis aims to describe the incidence, mortality and case fatality rate of malaria caused by all Plasmodium species between Peninsular Malaysia and East Malaysia (Sabah and Sarawak) over a 5-year period (2013–2017).

Methods

This is a secondary data review of all diagnosed and reported malaria confirmed cases notified to the Ministry of Health, Malaysia between January 2013 and December 2017.

Results

From 2013 to 2017, a total of 16,500 malaria cases were notified in Malaysia. The cases were mainly contributed from Sabah (7150; 43.3%) and Sarawak (5684; 34.4%). Majority of the patients were male (13,552; 82.1%). The most common age group in Peninsular Malaysia was 20 to 29 years (1286; 35.1%), while Sabah and Sarawak reported highest number of malaria cases in age group of 30 to 39 years (2776; 21.6%). The top two races with malaria in Sabah and Sarawak were Bumiputera Sabah (5613; 43.7%) and Bumiputera Sarawak (4512; 35.1%), whereas other ethnic group (1232; 33.6%) and Malays (1025; 28.0%) were the two most common races in Peninsular Malaysia. Plasmodium knowlesi was the commonest species in Sabah and Sarawak (9902; 77.1%), while there were more Plasmodium vivax cases (1548; 42.2%) in Peninsular Malaysia. The overall average incidence rate, mortality rate and case fatality rates for malaria from 2013 to 2017 in Malaysia were 0.106/1000, 0.030/100,000 and 0.27%, respectively. Sarawak reported the highest average incidence rate of 0.420/1000 population followed by Sabah (0.383/1000). Other states in Peninsular Malaysia reported below the national average incidence rate with less than 0.100/1000.

Conclusions

There were different trends and characteristics of notified malaria cases in Peninsular Malaysia and Sabah and Sarawak. They provide useful information to modify current prevention and control measures so that they are customised to the peculiarities of disease patterns in the two regions in order to successfully achieve the pre-elimination of human-only species in the near future.

Salmonella in native "village" chickens (Gallus domesticus): prevalence and risk factors from farms in South-Central Peninsular Malaysia

Village chicken or Ayam Kampung, common to Southeast Asian countries, has always been regarded as superior in comparison to commercial broiler chicken in terms of wholesomeness and health benefits. The current study investigates the prevalence and risk factors of Salmonella among village chicken flocks from the central and southern states of Peninsular Malaysia. A total of 35 village flocks were sampled from Selangor (n = 19), Melaka (n = 10), Johor (n = 4), and Negeri Sembilan (n = 2). In total, 1,042 samples were collected; these included cloacal swabs (n = 675), eggs (n = 62), pooled drinking water (n = 175), pooled feeds (n = 70), and pooled flies (n = 60). Isolation of Salmonella from cloacal swabs, poultry drinking water, and feeds was carried out according to the protocols and recommendations of the World Organization for Animal Health (OIE) terrestrial manual. The prevalence of Salmonella at an individual bird-level was 2.5% (17/675, 95% CI: 1.6 to 4.0). All eggs screened were negative; in the case of environmental samples, however, Salmonella was detected in 5.14% (9/175), 7.14% (5/70), and 5.0% (3/60) for water, feed, and flies, respectively. A total of 34 isolates and 8 Salmonella serotypes were identified. Weltevreden (20.6%) was the most common, followed by Typhimurium and Agona (17.6%), Albany and Enteritidis (8.8%), Molade (5.9%), Corvallis and Schleissheim (2.9%), and others grouped as Salmonella spp. (11.8%). Multivariable logistic regression models revealed that Salmonella positivity among flocks could be strongly predicted by storage of feeds (uncovered feeds; OR = 10.38; 95% CI: 1.25 to 86.39; p = 0.030) and uncovered water tanks (uncovered tank; OR = 6.43; 95% CI: 1.02 to 40.60; p = 0.048). The presence of Salmonella in village chickens in the study area was lower than that of commercial chickens in Malaysia.

Data on sea surface biophysical parameters during different monsoon seasons

The biophysical data presented in this article were collected in the east coast of Peninsular Malaysia from May to November 2009. These monthly surface data were obtained from 32 stations along the coastal-offshore transect and were analyzed to understand the spatial and temporal distributions of biophysical parameters during different monsoon seasons. The data presented here include sea surface temperature (SST), sea surface salinity (SSS), Secchi disk depth (SDD), Chlorophyll-a (Chl-a), suspended particulate matter (SPM), mineral suspended solid (MSS) and chromophoric dissolved organic matter (CDOM).

Little Evidence of Zika Virus Infection in Wild Long-Tailed Macaques, Peninsular Malaysia

We tested a sample of 234 wild long-tailed macaques (Macaca fascicularis) trapped in Peninsular Malaysia in 2009, 2010, and 2016 for Zika virus RNA and antibodies. None were positive for RNA, and only 1.3% were seropositive for neutralizing antibodies. Long-tailed macaques are unlikely to be reservoirs for Zika virus in Malaysia.

Thismiadomei and T.terengganuensis (Thismiaceae), two new species, and T.javanica, a new record from Terengganu, Peninsular Malaysia

Two new species of the mycoheterotrophic genus Thismia Griff. (Thismiaceae), Thismiadomei Siti-Munirah and T.terengganuensis Siti-Munirah from Peninsular Malaysia, are described and illustrated. Thismiadomei, characterized by its perianth lobes that are upright and curve inward, but are imperfectly connate, falls within sectionOdoardoa. Thismiaterengganuensis is characterized by its mitre with three appendages on its apex, so falls within sectionGeomitra. Both new species are unique and totally different from other described species, T.domei by the trichomes on its outer perianth tube surface and T.terengganuensis by its mitre with slender appendages. Thismiajavanica J.J.Sm, also from Terengganu, is a new record for Peninsular Malaysia.

Cheleionwatanabei sp. n., a new species of Stereomerini (Coleoptera, Scarabaeidae, Aphodiinae), and description of the male of C.jendeki

Cheleionwatanabeisp. n. is described from Pahang, Peninsular Malaysia and represents the third species of the genus Cheleion Vårdal & Forshage, 2010 (Coleoptera, Scarabaeidae, Aphodiinae, Stereomerini). A description of the previously unknown male of C.jendeki Král & Hájek, 2015, and a key to the species of the genus Cheleion are also provided.

Molecular detection and epidemiological risk factors associated with Cryptosporidium infection among cattle in Peninsular Malaysia

Enteric protozoa infection among cattle may pose a threat to productivity and survival leading to negative impacts on the livestock industry. A number of these pathogens are also known to be zoonotic and are of public health concern. Despite the importance of these enteric protozoa to both animal and human health, there remains a paucity of published information on the epidemiological risk factors that may be associated with bovine cryptosporidiosis in Southeast Asia. The present study was undertaken to determine the molecular prevalence and associated risk factors for Cryptosporidium infection among beef and dairy cattle in Peninsular Malaysia. Faecal samples were collected from 824 cattle in 39 farms (526 beef and 298 dairy) situated in 33 locations throughout the country, and subjected to PCR detection for Cryptosporidium using primers targeting the 18S SSUrRNA gene. Epidemiological variables including host, environment and management factors were subjected to univariate and multivariate logistic regression analyses to determine the potential risk factors for infection. The prevalence of Cryptosporidium among the cattle was 12.5%, with significant difference in the infection rate among the various breeds. There was no significant effect of gender, and both the beef and dairy cattle were at similar odds for infection. The younger cattle had a significantly higher infection rate compared to the older animals. Multivariate analysis revealed that deworming practice, distance to human settlement, geographical location (zone) and farm management system were significant risk factors associated with Cryptosporidium infection. The cattle that were reared on farms located in the northeast of the country, closest (≤200 m) to human settlements, reared extensively, and dewormed every four months were at highest risk of infection. The present study constitutes the first attempt to analyze the multivariable epidemiological risk factors involved in bovine cryptosporidiosis in Malaysia and in Southeast Asia. It is envisaged that the data obtained will facilitate better control and prevention measures for Cryptosporidium infection among cattle in the region. Due to the potential zoonotic nature of the infection, serious steps should be instituted for animal treatment and biohazard waste management on local cattle farms.

Assessing the comparative advantage of broiler production in Peninsular Malaysia using policy analysis matrix

Broiler meat is the largest and cheapest protein source in Malaysia. Using the policy analysis matrix (PAM), this study examines the comparative advantage of broiler production in Peninsular Malaysia. Three hundred and ten farms in Peninsular Malaysia were involved in a field survey. The results of the domestic resource cost (DRC) show that Malaysia has a comparative advantage in all scales of broiler production. Sensitivity analysis indicates that the changes in input prices have a significant effect on comparative advantage. Nonetheless, the industry should reduce its dependence on corn-based feed, which is expensive and has an unstable price, to increase competitiveness in further securing its comparative advantage.

Estimation of carbon pool in soil, above and below ground vegetation at different types of mangrove forests in Peninsular Malaysia

This paper evaluated the total carbon stock of mangrove ecosystems in two contrasting sites: a fishing village in Delta Kelantan (DK) and Ramsar sites in Johor Park (JP). In both sites, aboveground carbon was significantly higher than belowground carbon, and stems contained more carbon than leaf and root partitions. The average carbon concentration of individual mangrove species (44.9-48.1%) was not significantly different but the larger biomass of the DK samples resulted in vegetation carbon stock that was higher than that in JP. Season played an important role in soil carbon stock-a pronounced wet season in DK coincided with the dry season in JP. The total carbon pool was estimated to be 427.88 t ha^-1 in JP and 512.51 t ha^-1 in DK, where at least 80% was contributed by soil carbon. The carbon dioxide equivalent was 1570.32 t ha^-1 CO₂e (JP) and 1880.91 t ha^-1 CO₂e (DK).

Land snail fauna in Gunung Kuang Limestone Hill, Perak, Malaysia and its conservation implications (Mollusca, Gastropoda)

This paper presents the first land snail species checklist for Gunung Kuang (Kuang Hill), a limestone hill located next to Gunung Kanthan that is recognised as one of the most important limestone hills for its diverse land snail fauna in Kinta Valley. Samplings were carried out at five plots in Gunung Kuang. This survey documented 47 land snail species, in which six species were identified as unique to Gunung Kuang. Approximately half of the land snails from Gunung Kanthan were found in Gunung Kuang. In addition, one of six unique species from Gunung Kanthan was also found in Gunung Kuang. These rich land snail species in Gunung Kuang are similar to other hills in Kinta Valley, but it is relatively lesser than the adjacent Gunung Kanthan. In view of Gunung Kuang’s unique land snail species, and its location closest to disturbed Gunung Kanthan, Gunung Kuang should be considered in the conservation management plan for Gunung Kanthan.

in domestic and wildlife animals in Peninsular Malaysia

Anaplasma spp. are Gram-negative obligate intracellular, tick-borne bacteria which are of medical and veterinary importance. Little information is available on Anaplasma infection affecting domestic and wildlife animals in Malaysia. This study investigated the presence of Anaplasma spp. in the blood samples of domestic and wildlife animals in Peninsular Malaysia, using polymerase chain reaction (EHR-PCR) assays targeting the 16S rRNA gene of Anaplasmataceae. High detection rates (60.7% and 59.0%, respectively) of Anaplasma DNA were noted in 224 cattle (Bos taurus) and 78 deer (77 Rusa timorensis and one Rusa unicolor) investigated in this study. Of the 60 amplified fragments obtained for sequence analysis, Anaplasma marginale was exclusively detected in cattle while Anaplasma platys/Anaplasma phagocytophilum was predominantly detected in the deer. Based on sequence analyses of the longer fragment of the 16S rRNA gene (approximately 1000 bp), the occurrence of A. marginale, Anaplasma capra and Candidatus Anaplasma camelii in cattle, Candidatus A. camelii in deer and Anaplasma bovis in a goat was identified in this study. To assess whether animals were infected with more than one species of Anaplasma, nested amplification of A. phagocytophilum, A. bovis and Ehrlichia chaffeensis DNA was performed for 33 animal samples initially screened positive for Anaplasmataceae. No amplification of E. chaffeensis DNA was obtained from animals investigated. BLAST analyses of the 16S rDNA sequences from three deer (R. timorensis), a buffalo (Bubalus bubalis) and a cow (B. taurus) reveal similarity with that of Candidatus Anaplasma boleense strain (GenBank accession no.: KX987335). Sequence analyses of the partial gene fragments of major surface protein (msp4) gene from two deer (R. timorensis) and a monitor lizard (Varanus salvator) show the detection of a strain highly similar (99%) to that of A. phagocytophilum strain ZJ-China (EU008082). The findings in this study show the occurrence of various Anaplasma species including those newly reported species in Malaysian domestic and wildlife animals. The role of these animals as reservoirs/maintenance hosts for Anaplasma infection are yet to be determined.