No abstract

Infectious bronchitis virus (IBV) is a major economic problem in commercial chicken farms with acute multiple-system infection, especially in respiratory and urogenital systems. A live-attenuated and killed vaccine is currently immunized to control IBV infection; however, repeated outbreaks occur in both unvaccinated and vaccinated birds due to the choice of inadequate vaccine candidates and continuous emergence of novel infectious bronchitis (IB) variants and failure of vaccination. However, similar clinical signs were shown in different respiratory diseases that are essential to improving the diagnostic assay to detect IBV infections. Various risk factors involved in the failure of IB vaccination, such as various routes of application of vaccination, the interval between vaccinations, and challenge with various possible immunosuppression of birds are reviewed. The review article also highlights and updates factors affecting the diagnosis of IBV disease in the poultry industry with differential diagnosis to find the nature of infections compared with non-IBV diseases. Therefore, it is essential to monitor the common reasons for failed IBV vaccinations with preventive action, and proper diagnostic facilities for identifying the infective stage, leading to earlier control and reduced economic losses from IBV disease.

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Dengue fever is an arthropod-borne viral disease caused by the Dengue virus (genus Falvivirus, family Flaviviridae). It has rapidly spread all over the world affecting approximately 400 million people annually. Human dengue infection is caused by four types of closely related viruses (also called serotypes) namely DENV-1, DENV-2, DENV-3, and DENV-4, all of which can be all found in Sabah, Malaysia. Each serotype can then be divided into unique groups based on its genotypes. In Malaysia, dengue has been reported as the most prevalent disease of the country with a ratio of 328.3 cases per 100,000 populations. Exacerbating this further, it was also recently reported in 2017 of the emergence of a newly identified Asian lineage dengue virus i.e. type 3 genotype II (D3GII) in Malaysia. We have aimed, through this study, to examine the serotypes and the genotypes of dengue virus circulating in Sabah. This study was conducted for a period of 8 months i.e. from January to August 2017. A total of 52 NS1 (50.9% were males and 49.1% were females) positive dengue patient serum samples were genotyped. Viral RNA was extracted from serum using QIAamp viral RNA mini kit and DNA sequencing was done on Applied Biosystems 3730xl DNA analyzer. The results showed that serotype DENV-3 was the most predominant dengue circulating virus in Sabah with 23 cases detected. These were further grouped under three genotypes namely D3GI (1 case), D3GII (14 cases) and D3GIII (8 cases). Serotype DENV-1 was the second most common circulating virus in Sabah with 17 cases and grouped under two genotypes, D1Gia (15 cases) and D1Gic (2 cases), respectively. On the other hand, only one genotype (D4GII) was detected for DENV-4 (9 cases), and two genotypes (D2 Cosmopolitan Clade I and D2 Cosmopolitan Clade Ib) for DENV-2, each with one case per genotype, respectively. Understanding of genotype diversity will be useful in designing strategies for dengue management in epidemiological surveillance and vaccine design.

High-quality RNA is an important genetic study as it has minimal contaminants that can affect gene discovery including degraded RNAs, chemical, and biological residues. Hence, it is a prerequisite for genetic analysis using Next Generation Sequencing (NGS) for accurate and reliable data mining. Despite its importance, extracting high-quality RNA from different samples is often a challenge, as every tissue has a different biochemical composition, thus requiring different protocols. This paper reports protocols for the extraction of high-quality RNA from two type of pineapple tissues, which are thickly lignified hard tissue (tillers, inflorescence, flowers) and watery soft tissue (mature fruit, ripe fruit, and overripe fruit) via modified Kim and Hamada (2005) method. Total RNA was extracted in all six tissues, which showed two distinctive 25S and 18S band on agarose gel. The total RNA in this study was considered high-quality as the minimum concentration was 50 ng/μl, the absorbance ratio (A260:A280) was more than 1.8 and RNA integrity number (RIN) was greater than 7. The obtained results showed that the modified Kim and Hamada (2005) method was effective in extracting high-quality RNA from the challenging MD2 pineapple tissue, which is suitable for subsequent molecular analysis, including the highly sensitive NGS.

Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.

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Microorganisms have acquired both common and unique abilities to withstand cold stress on Earth. Many studies on bacterial cold shock have been conducted, however, the majority of the studies were focused on mesophiles and psychrophiles. To date, limited information is available on the response of thermophilic bacteria to cold stress and therefore, it is not known how thermophilic bacteria would respond to different cold shocks. To address this question, the cold shock responses of a thermophilic Parageobacillus caldoxylosilyticus ER4B which has an optimal growth temperature at 64 °C were determined using Real-Time PCR (RT-qPCR). When the bacterium was exposed to mild cold shock at 54 °C, the expressions of gene encoding for pyruvate kinase and acetolactate synthase were significantly upregulated, suggesting that more pyruvate molecules were produced to synthesize branched-chain amino acids that could alter the fatty acid profile on the cell membrane. Accumulation of pyruvate in the bacterium could also help to scavenge cold-induced reactive oxygen species (ROS). Meanwhile, exposing the bacterium to extreme cold shock at 10 °C resulted in significant upregulation of genes encoding for γ-glutamylcyclotransferase, cold shock protein B and competence protein ComEA. An increase in these enzymes expression indicated more extreme measures including apoptosis and transformation were adopted during extreme cold shock.