Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2

Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes

Analog signal path circuit for a four transistor pixel in standard 0.13μm CMOS technology

This project is aimed to develop the layout for the analog signal path of a 4 transistor pixel CMOS image sensor using EDA tools in standard 0.13μm Silterra fabrication technology. The sub-circuit blocks that define the analog input-output path consists of the 320×240 pixel array, 320 column parallel correlated double sampling circuits, an output buffer amplifier and all associated bias circuitry. Each pixel size has a dimension of 10μm × 10μm. The pixel's frame rate is targeted to be 120 frames per second (fps) working in a QVGA picture format (320× 240 pixels). From simulation, the illumination range of 0.01 lux to 0.25 lux has been tested and shows only a 2.8% error from the ideal output linearity

Quantitative detection and characterization of Shiga toxin-producing Escherichia coli O157 and non-O157 in raw vegetables by MPN-PCR in Malaysia

Foodborne diseases are mainly caused by bacterial contamination which can lead to severe diarrhea. This study aimed to detect the presence of Shiga toxin-Producing Escherichia coli O157, Escherichia coli non-O157 and virulence gene in raw vegetables. The samples were purchased from wet market and hypermarket in Selangor. The detections were carried out by using the combination methods of Most Probable Number-Polymerase Chain Reaction (MPN- PCR). A total of 37(18.5%) samples were found to be contaminated by STEC. Out of these 37 isolates, four (10.8%) of the isolates were E. coli O157 while 33(89.2%) were E. coli non- O157. However, there was no E. coli O157:H7 detected in all the samples. The occurrence of Shiga toxin-Producing E. coli in edible raw vegetables samples suggests the importance of this pathogen in vegetables. Therefore, more studies are required to remove this pathogen from vegetables

Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations

BackgroundRecent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated.ResultsWe analyzed the whole-genome deep sequencing data (30x) of five native trios from Peninsular Malaysia and North Borneo, and characterized the genomic variants, including single nucleotide variants (SNVs), small insertions and deletions (indels) and copy number variants (CNVs). We discovered approximately 6.9 million SNVs, 1.2 million indels, and 9000 CNVs in the 15 samples, of which 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify de novo variants and estimated the autosomal mutation rates to be 0.81x10(-8) - 1.33x10(-8), 1.0x10(-9) - 2.9x10(-9), and 0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example is a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples.ConclusionOur study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia

Detection of Klebsiella pneumoniae in raw vegetables using most probable number-polymerase chain reaction (MPN-PCR)

Klebsiella pneumoniae (K. pneumoniae) is one of the most important members of Klebsiella genus in Enterobacteriacae family, which is responsible for pneumonia (the destructive lung inflammation disease). Vegetables are known as source of contamination with K. pneumonia. Raw vegetables are usually consumed in salads and other dishes. The aim of this study was to investigate the occurrence of K. pneumoniae in raw vegetables marketed in Malaysia. Two hundred commonly used salad vegetables (lettuces, parsley, cucumber, tomato and carrot) from hypermarkets and wet markets were investigated for presence of K. pneumoniae using Most Probable Number-Polymerase Chain Reaction (MPN-PCR). K. pneumoniae was found to be significantly more frequent (100%) and (82.5%) in lettuce and cucumbers, respectively. K. pneumoniae contamination was lowest in carrot samples (30%). All samples were contaminated with K. pneumoniae ranging from <3 to 1100 MPN/g. Results showed the high health risk associated with consumption of raw vegetables

Risk assessment of acquiring listeriosis from consumption of chicken offal in Selangor, Malaysia

Listeria monocytogenes (L. monocytogenes) is an important foodborne pathogen which can cause foodborne listeriosis with high mortality rates especially in susceptible population groups such as pregnant women, elderly and immunocompromised individuals. The biosafety level of L. monocytogenes in chicken offal has becomes a great concern as chicken offal is a cheap source of protein and it is often served as side dishes in South East Asian countries. In Malaysia, the consumption of chicken offal has almost doubled from 5 g per capita per day in the early 1980s to 9 g per capita per day in 2009. In this study, risk assessment was conducted to estimate the risk of acquiring listeriosis from consumption of chicken offal in Malaysia. A microbial survey on the prevalence and concentration of L. monocytogenes in chicken offal were carried out in Selangor, Malaysia over a one-year period (November 2010 to October 2011). It was assumed that there were no seasonal changes in the prevalence and consumption pattern all year round. Assuming that 5.6 million people in Selangor, Malaysia consume a single serving (125 g) of chicken offal per week, it is estimated that in a year there could be 0.61 cases and 1.98 × 10-4 cases of listeriosis per 100,000 population of pregnant woman and immunocompromised individual, respectively. However, the potential for getting listeriosis among the healthy population was very low, only 1.39 × 10-8 cases per 100,000 population. This study demonstrated risk assessment model not only used as a tool to estimate the risk of acquiring illness but it can influence public health surveillance and providing data in setting appropriate level of protection

Risk of Escherichia coli O157:H7 transmission linked to the consumption of raw milk

E. coli O157:H7 is associated with life threatening diseases such as hemorrhagic colitis (HC), hemolytic uremic syndrome (HUS) and thrombotic thrombocytopenic purpura (TTP). Raw milk is considered a high risk food as it is highly nutritious and serves as an ideal medium for bacterial growth. The aim of this study was to investigate the prevalence of E. coli O157:H7 in raw cow, goat and buffalo milk samples. MPN-PCR method targeting the major virulence rfbE gene and fliCH 7 gene of E. coli O157:H7 was used. Total of 177 raw milk samples were collected from local dairy farms in the state of Selangor, Malaysia. The highest prevalence of E. coli O157:H7 was found in raw cow milk (8.75%) followed by raw goat milk (7.32%) and raw buffalo milk (1.79%). The estimated quantity of E. coli O157:H7 in raw cow, goat and buffalo milk ranged from <30 MPN/g to 120 MPN/g. In raw cow and goat milk samples examined contain E. coli O157:H7 microbial load ranged from 30 to 120 MPN/g and 30 to 36 MPN/g, respectively. E. coli O157:H7 microbial load in buffalo milk samples was found to be the lowest, only 30 MPN/g. Results of this research provide useful information on biosafety of E. coli O157:H7 in raw milk marketed in Malaysia

The impact of using recycled culture medium to grow Chlorella vulgaris in a sequential flow system: Evaluation on growth, carbon removal, and biochemical compositions

Excessive of carbon dioxide (CO2) emission and water pollution have been identified as the two primary challenges to humans and environment. Hence, biological carbon sequestration by microalgae is recommended as an environmentally friendly approach to capture and convert this CO2 into value-added products. However, research related to the development of efficient system to concurrently overcome low CO2 solubility in water and reduction of water footprint in microalgae cultivation is still limited in the literature. In this study, the CO2 capture by Chlorella vulgaris in a recycled cultivation medium was exploited using a sequential flow photobioreactor system. The study revealed that nutrient replenished recycled medium did not significantly affect the growth performance and lipid content of C. vulgaris. It was also observed that the CO2 capture efficiency and protein content were gradually increased from the first (SFB-RWN1) to the third (SFB-RWN3) cycle of cultivation due to the increment of carbon and nitrogen content in the microalgae cell. Besides, the lipid profile of C. vulgaris cultivated in the recycled medium comprised of high concentration of saturated (up to 32.41%) and polyunsaturated (up to 43.21%) fatty acid methyl ester (FAME). The present study suggested that growing C. vulgaris in a recycled medium is a feasible solution to fix CO2 from the atmosphere and help to reduce water footprint in the microalgae cultivation system

Genetic Relatedness of Indigenous Ethic Groups in Northern Borneo to Neighboring Populations from Southeast Asia, as inferred from Genome-wide SNP Data

The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s)