Designing primers for loop-mediated isothermal amplifi cation (LAMP) for detection of Ganoderma boninense

Basal Stem Rot (BSR) caused by Ganoderma boninense is one of the most serious diseases of South East Asia’s oil palm industry. The losses due to this disease were reported up to RM 1.5 billion a year in Malaysia. Typical methodologies currently used for detection of BSR infection, usually involved visual observation followed by detection of the pathogen using invasive and/or time consuming and expensive instruments. This includes the use of molecular DNA based technique, Ganoderma Selective Media (GSM), molecular techniques. However, most of these methods cannot be performed in situ. Samples need to be sent to the laboratory for testing. In this paper, a diagnostic tool using loop-mediated isothermal reaction (LAMP) is presented for detection of G. boninense. LAMP reaction which consist of a set of four primers, two outer and two inner, was designed specifi cally to recognize the manganese superoxide gene (MnSOD) obtained from NCBI Genbank (Accession no: U56128) of G. boninense, the causal pathogen of BSR. The assay was conducted in the thermal block with temperature 65°C for 50 min and the LAMP products were viewed on agarose gel electrophoresis. This technique removes the need to perform the reaction in thermal cycler as it can be done in a heat block. Results show the ladder-like pattern of bands sizes from 683 bp specifi cally to the gene MnSOD was amplifi ed. Thus, the chosen set of primers can be used for detection of G. boninense in oil palm estates subjected to sensitivity and specifi city

Gene silencing by microrna in pineapple: discovery, involvement in the control of fruit development and its application as artificial gene regulators

MicroRNAs (miRNAs) are a class of small RNAs, usually 19-24 nt in length, which are found endogenously within the cell and do not code for any protein. However, they participate in regulating the level of mRNA transcripts through cleavage or translational inhibition, creating an effect called gene silencing. MicroRNAs have been shown to be essential for major biological and physiological development in plants, including pineapple. A hundred and fifty-three miRNAs, regulating many aspects of plant growth, have been described in pineapple to date. Reports of the existence of this natural gene silencing system have led to the development of a similar system at a synthetic level. Artificial microRNA (amiRNA) is a unique custom-designed molecule of RNA, approximately 21 nt in length, with the sole function of silencing the expression of its target gene by mimicking the action of miRNA in the RNA interference (RNAi) pathway. In pineapple, target genes have not only been silenced using this technique but the silencing has occurred in a specific manner, i.e., the target genes were silenced without affecting the expression of other, unrelated genes. This technique has addressed the limitations of conventional breeding techniques, as amiRNA silencing can be performed rapidly and is time-consuming and occurs in a specific manner

Isolation of Alkalophilic Pectinolytic Bacteria and their Bio Retting Effect on Kenaf Fiber Compositions

Retting is the most limiting process of high-quality cellulosic kenaf bast fiber production which facilitating the separation of useable fiber from the plants' cell wall matrix. Existing traditional water retting approach confronts ineptitude and eutrophication related complications. Aiming to enhance the kenaf bio-retting process, sixty-seven alkalophilic bacterial colonies were isolated from paddy land soil sediments and kenaf retting water. These isolates were subsequently screened, of that two isolates were selected based on hyper qualitative and quantitative pectinolytic enzymatic measures. 16s rDNA gene sequence analysis revealed that both two strains were closely related to Bacillus pumilus species and designated as KRB56 and KRB22. These strains were applied in augmented non-sterile kenaf tank retting to investigate their kenaf retting efficiency and yielded fiber were analyzed for chemical compositions. Results revealed that, stains KRB56 and KRB22 significantly improve the retting process by degradation of 82.78% and 75.28% non-cellulosic gums, respectively comparing with uninoculated treatment niche (62.12%). These bacterial treated fiber samples showed thinner, smooth, and cleaner fibers surface morphology by SEM indicates sufficient non-cellulosic gums (NCGs) removal comparing with URKF. Moreover, yielded fibers were examined for chemical composition, FTIR, XRD test. Results revealed that compare to un retted and un inoculated kenaf fiber, bacterial treated kenaf fiber increases cellulose portions, and their crystallinity index increases 35.50-41.30 % due to sufficient NCGs removal. This study's findings indicate that isolated alkalophilic bacterial strains KRB56 and KRB22 were effectively to be used as kenaf bio retting agents to produce quality kenaf fiber

Profiling of MicroRNA expression in obese and diabetic-induced mice for biomarker discovery

MicroRNAs (miRNAs) are short (-22 nucleotides) regulatory RNAs involved in many fundamental biological processes. They are involved in post-transcriptional regulation of gene expression. Dysregulated expression of microRNAs has been associated with a variety of diseases, including obesity and diabetes. Obesity is a potential risk factor contributing to the development of type 2 diabetes. Meanwhile, diabetes is one of the most prevalent chronic diseases, affecting 6.4% of the world’s adult population. The aim of this study is to identify microRNAs that are differentially expressed in obese, diabetic and control C57BL/6 mice by using small RNA sequencing. Total RNAs were extracted from the serum of the target groups of animals. Next, the small RNAs were sequenced using the TruSeq small RNA Library Prep Kit in a MiSeq Illumina sequencer. A total of 52 up-regulated and 54 down-regulated miRNAs were identified based on the comparison of the log2 fold change of obese and diabetic (with normal mice as control; FC ≥ 2). The obese groups showed 22 up-regulated and 25 down-regulated microRNAs. Meanwhile, in the diabetic group, 32 microRNAs were up-regulated and 29 were down-regulated. This finding will help better understand the mechanism of metabolic disorders and may influence future approaches for the diagnosis and treatment of obesity and diabetes

Evidence of chelonid herpesvirus 5 (ChHV5) in green turtles (chelonia mydas) from Sabah, Borneo

Fibropapillomatosis (FP) is characterized by cutaneous tumours and is associated with Chelonid herpesvirus 5 (ChHV5), an alphaherpesvirus from the family Herpesviridae. Here, we provide the first evidence of ChHV5-associated FP in endangered Green turtles (Chelonia mydas) from Sabah, which is located at the northern region of Malaysian Borneo. The aims of this study were firstly, to determine the presence of ChHV5 in both tumour exhibiting and tumour-free turtles using molecular techniques and secondly, to determine the phylogeography of ChHV5 in Sabah. We also aim to provide evidence of ChHV5 infection through histopathological examinations. A total of 115 Green turtles were sampled from Mabul Island, Sabah. We observed three Green turtles that exhibited FP tumours and were positive for ChHV5.In addition, six clinically healthy turtles were also positive for the virus based on Polymerase Chain Reaction of three viral genes (Capsid protein gene UL18, Glycoprotein H gene UL22 and Glycoprotein B gene UL27). The prevalence of the ChHV5 was 5.22% in asymptomatic Green turtles. Epidermal intranuclear inclusions were identified in tumour lesions upon histopathological examination. Thus, the emergence of ChHV5 in Green turtle in the waters of Sabah could indicate a possible threat to sea turtle populations in the future and requires further monitoring of the populations along the Bornean coast

Critical factors for optimum biodegradation of bast fiber’s gums in bacterial retting

Bast fiber plants require a post-harvest process to yield useable natural cellulosic fibers, denoted as retting or degumming. It encompasses the degradation of the cell wall’s non-cellulosic gummy substances (NCGs), facilitating fibers separations, setting the fiber’s quality, and determining downstream usages. Due to the inconvenience of traditional retting practices, bacterial inoculum and enzyme applications for retting gained attention. Therefore, concurrent changes of agroclimatic and socioeconomic conditions, the conventional water retting confront multiple difficulties, bast industries become vulnerable, and bacterial agents mediated augmented bio-retting processes trying to adapt to sustainability. However, this process’s success demands a delicate balance among substrates and retting-related biotic and abiotic factors. These critical factors were coupled to degrade bast fibers NCGs in bacterial retting while holistically disregarded in basic research. In this study, a set of factors were defined that critically regulates the process and requires to be comprehended to achieve optimum retting without failure. This review presents the bacterial strain characteristics, enzyme potentials, specific bast plant cell wall’s structure, compositions, solvents, and interactions relating to the maximum NCGs removal. Among plants, associated factors pectin is the primary biding material that determines the process’s dynamics, while its degree of esterification has a proficient effect through bacterial enzymatic degradation. The accomplished bast plant cell wall’s structure, macerating solvents pH, and temperature greatly influence the bacterial retting process. This article also highlights the remediation process of water retting pollution in a biocompatible manner concerning the bast fiber industry’s endurance