Functional characterization of the MSP-C6 promoter as a potential tool for mesocarp-preferential expression of transgenes.

Modification of lipid composition in the mesocarp tissue of oil palm involves genetic manipulation of multiple genes. More than one mesocarp-preferential promoter is necessary for the expression of individual transgenes in the same plant to obviate transcriptional gene silencing. This study aimed to identify genes that are preferentially expressed in the mesocarp tissue and characterize selected candidate mesocarp-preferential promoters. Ten transcripts that were preferentially expressed in the mesocarp tissue were identified from the analysis of 82 transcriptome datasets of 12 different oil palm tissues. The expression of two candidate genes, MSP-C1 and MSP-C6, was verified to be preferentially expressed in the mesocarp tissues and shown to have a low expression level in non-mesocarp tissues by reverse transcription quantitative real-time PCR (RT-qPCR). MSP-C6 promoter fragments of different lengths were transformed into tomato plants for further characterization. Both unripe and ripe fruits of transgenic tomato plants transformed with a construct harboring the MSP-C6-F1 (2014 bp) promoter were shown to have high beta-glucuronidase (GUS) activities. The findings of this study suggest the potential applications of the MSP-C6 promoter as a molecular tool for genetic engineering of novel traits in fruit crops.

First Report of Neopestalotiopsis clavispora causing Leaf Spot on Coconut Seedling in Malaysia.

Coconut (Cocos nucifera) is a high economic value cash crop in Malaysia. In December 2021, irregular spots with dotted rust-like appearance were observed mainly on the tip of the leaves of MATAG variety coconut seedlings at the nursery in Perak state. More than 90% of the coconut seedlings surveyed were infected with leaf spot symptoms. These symptoms could bring huge economic losses due to the downgrade value of the seedlings. 15 symptomatic leaves were obtained from the nursery, 10 mm2 of cut leaves were disinfected with 10% sodium hypochlorite for 10 minutes and rinsed with sterile distilled water before plated on potato dextrose agar (PDA). A total of 4 single-spore isolates were obtained and were observed morphologically. The isolates had white cotton-like appearance with undulate edge. Black acervuli were seen after 7 days of incubation at 26 °C. The conidia were fusiform and contained five cells with four septate and three versicolor cells in between the apical and basal cell. The conidia were 17.2 µm long and 5.9 µm wide (n=30). Conidia consisted of two to three apical appendages and one basal appendage. These morphological characters were consistent with the original description of Neopestalotiopsis clavispora (Santos et al., 2019; Abbas et al., 2022). Species identification was done by amplifying internal transcribed spacer (ITS) region using primers ITS 4 and ITS 5 (White et al., 1990) and beta-tubulin (TUB2) using primers Bt2a and Bt2b (Glass & Donaldson et al., 1995) of the representative isolate LKR1, then sequenced. The 488 bp ITS and 409 bp TUB2 sequences were deposited in GenBank under the accession numbers ON844193 and OP004810, respectively. Isolate LKR1 shares 99.8% identity with the ITS sequence (MH860736.1) of the reference pathogenic N. clavispora strain CBS:447.73 and 100% identity with the TUB2 sequence (KM199443.1) of the reference pathogenic N. clavispora strain CBS 447.73. The phylogenetic analysis confirmed that the isolate LKR1 belonged to N. clavispora when a supported clade is formed with 98% and 94% bootstrap support for ITS and TUB2 respectively with other related N. clavispora. Pathogenicity test was conducted by using five replicates of 8 month old seedlings, they were incubated under greenhouse condition and were watered daily. The leaves of the seedlings were injured with sterile needles and were sprayed with conidial suspension (1 x 10^6 conidia/ml). The control plants were also injured but sprayed with sterile distilled water. After a month, signature symptoms of spots on the leaves appear but none on the control seedling. N. clavispora was successfully re-isolated only from the inoculated symptomatic leaves and identified morphologically. No fungus was re-isolated from the control seedlings. The result was consistent even after repeating the test one more time. N. clavispora has been reported causing leaf spot on Macadamia integrifolia (Santos et al., 2019), Phoenix dactylifera L. (Basavand et al., 2020) and Musa acuminata (Qi et al., 2022). N. clavispora has also been reported causing rust-like appearance of leaves on strawberry (Fragaria × ananassa Duch.) (Obregón et al., 2018). To our knowledge, this is the first report of N. clavispora causing leaf spot disease on coconut seedlings in Malaysia. Through the identification of N. clavispora as the causal agent of leaf spot on coconut, this can help coconut growers to tackle the disease problem earlier thus, preventing the disease from spreading until the adult phase.

Anti-Diabetic Effect of Lactobacillus Paracasei Isolated from Malaysian Water Kefir Grains.

The prevalence of type 2 diabetes mellitus (T2DM) is alarming because it is always linked to the increase in chronic diseases, mortality, and socioeconomic burden. Water kefir has a wide range of functional and probiotic characteristics attributed to the microorganisms present in the kefir grains. The present study aims to evaluate the in vivo anti-diabetic potential of the isolated Lactobacillus paracasei from Malaysian water kefir grains (MWKG) which was reported to have excellent probiotic properties and high antioxidant activities as reported previously. High-fat diet/streptozotocin (HFD/STZ) induction was used to obtain a T2DM model followed by treatment with the isolated L. paracasei from MWKG. The levels of glucose, insulin, and in vivo liver antioxidants were quantified after 14 weeks. Gene expression analysis of the liver was also carried out using microarray analysis, and several genes were selected for validation using quantitative real-time PCR. Insulin tolerance test demonstrated that the L. paracasei isolated from the MWKG alleviated T2DM by improving the area under the curve of the insulin tolerance test whereby low-dose and high-dose concentrations treated groups showed 2424.50 ± 437.02 mmol/L·min and 2017.50 ± 347.09 mmol/L·min, respectively, compared to untreated diabetic mice which was 3884.50 ± 39.36 mmol/L·min. Additionally, treatment with the isolated L. paracasei from MWKG regulated the expression of several genes related to glucose homeostasis and lipid metabolism in diabetic mice. These results suggested that the isolated L. paracasei from MWKG could be a potential dietary supplement for T2DM.

Synergism: biocontrol agents and biostimulants in reducing abiotic and biotic stresses in crop.

In today's fast-shifting climate change scenario, crops are exposed to environmental pressures, abiotic and biotic stress. Hence, these will affect the production of agricultural products and give rise to a worldwide economic crisis. The increase in world population has exacerbated the situation with increasing food demand. The use of chemical agents is no longer recommended due to adverse effects towards the environment and health. Biocontrol agents (BCAs) and biostimulants, are feasible options for dealing with yield losses induced by plant stresses, which are becoming more intense due to climate change. BCAs and biostimulants have been recommended due to their dual action in reducing both stresses simultaneously. Although protection against biotic stresses falls outside the generally accepted definition of biostimulant, some microbial and non-microbial biostimulants possess the biocontrol function, which helps reduce biotic pressure on crops. The application of synergisms using BCAs and biostimulants to control crop stresses is rarely explored. Currently, a combined application using both agents offer a great alternative to increase the yield and growth of crops while managing stresses. This article provides an overview of crop stresses and plant stress responses, a general knowledge on synergism, mathematical modelling used for synergy evaluation and type of in vitro and in vivo synergy testing, as well as the application of synergism using BCAs and biostimulants in reducing crop stresses. This review will facilitate an understanding of the combined effect of both agents on improving crop yield and growth and reducing stress while also providing an eco-friendly alternative to agroecosystems.

Ligninolytic enzymes profiling in association with the aggressiveness of Ganoderma boninense isolates

Aims@#This study was designed to examine the enzyme activity of selected virulent isolates of Ganoderma boninense against oil palm. In a separate in vitro assessment, the effect of macronutrients on the mycelial growth of four selected Ganoderma spp. was also tested.@*Methodology and results@#The study involved a comparison of ligninolytic enzymes; lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac) profiling of eight isolates of G. boninense, categorized into three levels of aggressiveness, with two control isolates (G. boninense PER71 and G. tornatum NPG1) using solid-state fermentation (SSF). The Principal Component Analysis (PCA) revealed that the isolates had a significant production of ligninolytic enzymes on day 80. The most aggressive isolate, ET61 had the highest Lac production. As for the macronutrient test, mycelial growth for all the Ganoderma spp. was highly affected by potassium (K).@*Conclusion, significance and impact of study@#The findings of this study elucidated the characteristics of G. boninense in relation to enzyme production for the degradation of oil palm lignin and the identification of essential nutrients involved in the survival and growth of Ganoderma spp. The study provides vital information on the pathogenic characteristics of G. boninense isolates involved in biomass degradation along with the role of nutrient on the growth of Ganoderma spp. that may influence basal stem rot (BSR) management in the field.

Identification of drought responsive Elaeis guineensis WRKY transcription factors with sensitivity to other abiotic stresses and hormone treatments.

BACKGROUND: The ability of plants to withstand and thrive in an adverse environment is crucial to ensure their survivability and yield performance. The WRKY transcription factors (TFs) have crucial roles in plant growth, development and stress response, particularly drought stress. In oil palm, drought is recognized as one of the major yield limiting factors. However, the roles of WRKY TFs in the drought response of oil palm is unclear. RESULTS: Herein, we studied the transcriptome of drought treated oil palm leaf and identified 40 differentially expressed genes (DEGs) of WRKY TFs, of which 32 DEGs were upregulated and 8 DEGs were downregulated in response to drought stress in oil palm. They were categorized into Groups I to IV based on the numbers of WRKY domain and the structural difference in the zinc finger domain. Multiple stress- and hormone-responsive cis-regulatory elements were detected in the drought responsive oil palm EgWRKY (Dro-EgWRKY) genes. Fourteen of the 15 selected oil palm WRKY (EgWRKY) genes demonstrated a tissue-specific expression profile except for EgWRKY28 (Group I), which was expressed in all tissues tested. The expression levels of 15 candidate EgWRKYs were upregulated upon salinity and heat treatments, while several genes were also inducible by abscisic acid, methyl jasmonate, salicylic acid and hydrogen peroxide treatments. Members of the Group III WRKY TFs including EgWRKY07, 26, 40, 52, 59, 73 and 81 displayed multiple roles in drought- and salinity-response under the modulation of phytohormones. CONCLUSIONS: EgWRKY TFs of oil palm are involved in phytohormones and abiotic stress responses including drought, salinity and heat. EgWRKY07, 26, 59 and 81 from Group III maybe important regulators in modulating responses of different abiotic stresses. Further functional analysis is required to understand the underlying mechanism of WRKY TFs in the regulatory network of drought stress.

Ecological and evolutionary diversification of sulphated polysaccharides in diverse photosynthetic lineages: A review.

Sulphated polysaccharides (SPs) are carbohydrate macromolecules with sulphate esters that are found among marine algae, seagrasses, mangroves and some terrestrial plants. The sulphate concentration in the ocean (28 mM) since ancient time could have driven the production of SPs in marine algae. SPs have a gelatinous property that can protect marine algae against desiccation and salinity stress. Agar and carrageenan are red algal SPs that are widely used as gelling agents in the food and pharmaceutical industries. The information on the SPs from freshwater and land plants are limited. In this review, we reviewed the taxonomic distribution and composition of SPs in different photosynthetic lineages, and explored the association of SP production in these diversified photosynthetic organisms with evolution history and environmental stresses. We also reviewed the genes/proteins involved in SP biosynthesis. Insights into SP biosynthetic machinery may shed light on the evolution that accompanied adaptation to life on earth.

Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm.

Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.

Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root.

BACKGROUND: Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application of phosphate rock, a non-renewable resource has been the common practice to increase Pi accessibility and maintain crop productivity in Malaysia. However, high fixation rate of Pi in the native acidic tropical soils has led to excessive utilization of P fertilizers. This has caused serious environmental pollutions and cost increment. Even so, the Pi deficiency response mechanism in oil palm as one of the basic prerequisites for crop improvement remains largely unknown. RESULTS: Using total RNA extracted from young roots as template, we performed a comparative transcriptome analysis on oil palm responding to 14d and 28d of Pi deprivation treatment and under adequate Pi supply. By using Illumina HiSeq4000 platform, RNA-Seq analysis was successfully conducted on 12 paired-end RNA-Seq libraries and generated more than 1.2 billion of clean reads in total. Transcript abundance estimated by fragments per kilobase per million fragments (FPKM) and differential expression analysis revealed 36 and 252 genes that are differentially regulated in Pi-starved roots at 14d and 28d, respectively. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, hormonal signaling and gene transcription were found among the differentially expressed genes. CONCLUSIONS: Our results showed that the molecular response mechanism underlying Pi starvation in oil palm is complexed and involved multilevel regulation of various sensing and signaling components. This contribution would generate valuable genomic resources in the effort to develop oil palm planting materials that possess Pi-use efficient trait through molecular manipulation and breeding programs.

Expression of Genes Encoding Manganese Peroxidase and Laccase of Ganoderma boninense in Response to Nitrogen Sources, Hydrogen Peroxide and Phytohormones.

Ganoderma produces lignolytic enzymes that can degrade the lignin component of plant cell walls, causing basal stem rot to oil palms. Nitrogen sources may affect plant tolerance to root pathogens while hydrogen peroxide (H2O2), salicylic acid (SA) and jasmonic acid (JA) play important roles in plant defense against pathogens. In this study, we examined the expression of genes encoding manganese peroxidase (MnP) and laccase (Lac) in Ganoderma boninense treated with different nitrogen sources (ammonium nitrate, ammonium sulphate, sodium nitrate and potassium nitrate), JA, SA and H2O2. Transcripts encoding MnP and Lac were cloned from G. boninense. Of the three GbMnP genes, GbMnP_U6011 was up-regulated by all nitrogen sources examined and H2O2 but was down-regulated by JA. The expression of GbMnP_U87 was only up-regulated by JA while GbMnP_35959 was up-regulated by ammonium nitrate but suppressed by sodium nitrate and down-regulated by H2O2. Among the three GbLac genes examined, GbLac_U90667 was up-regulated by ammonium nitrate, JA, SA and H2O2; GbLac_U36023 was up-regulated by JA and H2O2 while GbLac_U30636 was up-regulated by SA but suppressed by ammonium sulphate, sodium nitrate, JA and H2O2. Differential expression of these genes may be required by their different functional roles in G. boninense.

Transcriptome analysis of chicken intraepithelial lymphocyte natural killer cells infected with very virulent infectious bursal disease virus.

The infectious bursal disease (IBD) is an acute immunosuppressive viral disease that significantly affects the economics of the poultry industry. The IBD virus (IBDV) was known to infect B lymphocytes and activate macrophage and T lymphocytes, but there are limited studies on the impact of IBDV infection on chicken intraepithelial lymphocyte natural killer (IEL-NK) cells. This study employed an mRNA sequencing approach to investigate the early regulation of gene expression patterns in chicken IEL-NK cells after infection with very virulent IBDV strain UPM0081. A total of 12,141 genes were expressed in uninfected chicken IEL-NK cells, and most of the genes with high expression were involved in the metabolic pathway, whereas most of the low expressed genes were involved in the cytokine-cytokine receptor pathway. A total of 1,266 genes were differentially expressed (DE) at 3 day-post-infection (dpi), and these DE genes were involved in inflammation, antiviral response and interferon stimulation. The innate immune response was activated as several genes involved in inflammation, antiviral response and recruitment of NK cells to the infected area were up-regulated. This is the first study to examine the whole transcriptome profile of chicken NK cells towards IBDV infection and provides better insight into the early immune response of chicken NK cells.

Identification and characterisation of thiamine pyrophosphate (TPP) riboswitch in Elaeis guineensis.

The oil palm (Elaeis guineensis) is an important crop in Malaysia but its productivity is hampered by various biotic and abiotic stresses. Recent studies suggest the importance of signalling molecules in plants in coping against stresses, which includes thiamine (vitamin B1). Thiamine is an essential microelement that is synthesized de novo by plants and microorganisms. The active form of thiamine, thiamine pyrophosphate (TPP), plays a prominent role in metabolic activities particularly as an enzymatic cofactor. Recently, thiamine biosynthesis pathways in oil palm have been characterised but the search of novel regulatory element known as riboswitch is yet to be done. Previous studies showed that thiamine biosynthesis pathway is regulated by an RNA element known as riboswitch. Riboswitch binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. TPP binds specifically to TPP riboswitch to regulate thiamine biosynthesis through a variety of mechanisms found in archaea, bacteria and eukaryotes. This study was carried out to hunt for TPP riboswitch in oil palm thiamine biosynthesis gene. Riboswitch detection software like RiboSW, RibEx, Riboswitch Scanner and Denison Riboswitch Detector were utilised in order to locate putative TPP riboswitch in oil palm ThiC gene sequence that encodes for the first enzyme in the pyrimidine branch of the pathway. The analysis revealed a 192 bp putative TPP riboswitch located at the 3' untranslated region (UTR) of the mRNA. Further comparative gene analysis showed that the 92-nucleotide aptamer region, where the metabolite binds was conserved inter-species. The secondary structure analysis was also carried out using Mfold Web server and it showed a stem-loop structure manifested with stems (P1-P5) with minimum free energy of -12.26 kcal/mol. Besides that, the interaction of riboswitch and its ligand was determined using isothermal titration calorimetry (ITC) and it yielded an exothermic reaction with 1:1 stoichiometry interaction with binding affinities of 0.178 nM, at 30°C. To further evaluate the ability of riboswitch to control the pathway, exogenous thiamine was applied to four months old of oil palm seedlings and sampling of spear leaves tissue was carried out at days 0, 1, 2 and 3 post-treatment for expression analysis of ThiC gene fragment via quantitative polymerase chain reaction (qPCR). Results showed an approximately 5-fold decrease in ThiC gene expression upon application of exogenous thiamine. Quantification of thiamine and its derivatives was carried out via HPLC and the results showed that it was correlated to the down regulation of ThiC gene expression. The application of exogenous thiamine to oil palm affected ThiC gene expression, which supported the prediction of the presence of TPP riboswitch in the gene. Overall, this study provides the first evidence on the presence, binding and the functionality of TPP riboswitch in oil palm. This study is hoped to pave a way for better understanding on the regulation of thiamine biosynthesis pathway in oil palm, which can later be exploited for various purposes especially in manipulation of thiamine biosynthesis pathways in combating stresses in oil palm.

Identification of Reference Genes in Chicken Intraepithelial Lymphocyte Natural Killer Cells Infected with Very-virulent Infectious Bursal Disease Virus.

Due to the limitations in the range of antibodies recognising avian viruses, quantitative real-time PCR (RT-qPCR) is still the most widely used method to evaluate the expression of immunologically related genes in avian viruses. The objective of this study was to identify suitable reference genes for mRNA expression analysis in chicken intraepithelial lymphocyte natural killer (IEL-NK) cells after infection with very-virulent infectious bursal disease virus (vvIBDV). Fifteen potential reference genes were selected based on the references available. The coefficient of variation percentage (CV%) and average count of these 15 genes were determined by NanoString technology for control and infected samples. The M and V values for shortlisted reference genes (ACTB, GAPDH, HMBS, HPRT1, SDHA, TUBB1 and YWHAZ) were calculated using geNorm and NormFinder. GAPDH, YWHAZ and HMBS were the most stably expressed genes. The expression levels of three innate immune response related target genes, CASP8, IL22 and TLR3, agreed in the NanoString and RNA sequencing (RNA-Seq) results using one or two reference genes for normalisation (not HMBS). In conclusion, GAPDH and YWHAZ could be used as reference genes for the normalisation of chicken IEL-NK cell gene responses to infection with vvIBDV.

Nucleotide variations of 9-cis-epoxycarotenoid dioxygenase 2 (NCED2) and pericarp coloration genes (Rc and Rd) from upland rice varieties.

In this study, we analyzed the Rc and Rd genes that are responsible for the coloration of rice pericarps from six upland rice varieties. We also examined the association of pericarp coloration to the single nucleotide polymorphism in 9-cis-epoxycarotenoid dioxygenase 2 (NCED2), a key gene involved in abscisic acid (ABA) biosynthesis. Our findings demonstrated that all the upland rice varieties analyzed have a Rd gene which encodes a complete dihydroflavonol-4-reductase without early translational termination codon irrespective of their pericarp colors. However, the upland rice varieties with white pericarps were found to have a defective Rc gene with a 14-base deletion at exon 7 which could disrupt the function of a positive regulator of proanthocyanidin biosynthesis. In addition, the NCED2 genes from the upland rice varieties with white pericarps in this study have a C-allele while the NCED2 genes from Pandasan Red, Tomou and Taragang varieties that bear red pericarps were found to have a T-allele which was reported to be associated with a higher ABA level in upland rice. A better understanding of the gene sequences of upland rice varieties with red pericarp may provide important information for rice breeding programs.

Comparative genomics reveals differences in algal galactan biosynthesis and related pathways in early and late diverging red algae.

Red algae are a major source of marine sulfated galactans. In this study, orthologs and inparalogs from seven red algae were analyzed and compared with the aim to discover differences in algal galactan biosynthesis and related pathways of these algae. Red algal orthologs for putative carbohydrate sulfotransferases were found to be prevalent in Porphyridium purpureum, Florideophytes and Bangiophytes, while red algal orthologs for putative chondroitin sulfate synthases, sulfurylases, and porphyranases /carrageenases were found exclusively in Florideophytes and Bangiophytes. The acquirement of these genes could have happened after the divergence from Cyanidiales red algae. Cyanidiales red algae were found to have more number and types of putative sulfate permeases, suggesting that these genes could have been acquired in adaptation to the environmental stresses and biogeochemistry of respective habitats. The findings of this study shed lights on the evolution of different homeostasis mechanisms by the early and late diverging red algal orders.

Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice.

The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene's expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some-but not all-CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.

Isolation and Characterization of Lactobacillus spp. from Kefir Samples in Malaysia.

Kefir is a homemade, natural fermented product comprised of a probiotic bacteria and yeast complex. Kefir consumption has been associated with many advantageous properties to general health, including as an antioxidative, anti-obesity, anti-inflammatory, anti-microbial, and anti-tumor moiety. This beverage is commonly found and consumed by people in the United States of America, China, France, Brazil, and Japan. Recently, the consumption of kefir has been popularized in other countries including Malaysia. The microflora in kefir from different countries differs due to variations in culture conditions and the starter media. Thus, this study was aimed at isolating and characterizing the lactic acid bacteria that are predominant in Malaysian kefir grains via macroscopic examination and 16S ribosomal RNA gene sequencing. The results revealed that the Malaysian kefir grains are dominated by three different strains of Lactobacillus strains, which are Lactobacillus harbinensis, Lactobacillusparacasei, and Lactobacillus plantarum. The probiotic properties of these strains, such as acid and bile salt tolerances, adherence ability to the intestinal mucosa, antibiotic resistance, and hemolytic test, were subsequently conducted and extensively studied. The isolated Lactobacillus spp. from kefir H maintained its survival rate within 3 h of incubation at pH 3 and pH 4 at 98.0 ± 3.3% and 96.1 ± 1.7% of bacteria growth and exhibited the highest survival at bile salt condition at 0.3% and 0.5%. The same isolate also showed high adherence ability to intestinal cells at 96.3 ± 0.01%, has antibiotic resistance towards ampicillin, penicillin, and tetracycline, and showed no hemolytic activity. In addition, the results of antioxidant activity tests demonstrated that isolated Lactobacillus spp. from kefir G possessed high antioxidant activities for total phenolic content (TPC), total flavonoid content (TFC), ferric reducing ability of plasma (FRAP), and 1,1-diphenyl-2-picryl-hydrazine (DPPH) assay compared to other isolates. From these data, all Lactobacillus spp. isolated from Malaysian kefir serve as promising candidates for probiotics foods and beverage since they exhibit potential probiotic properties and antioxidant activities.

Proteome of rice roots treated with exogenous proline.

Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expressed proteins were identified by mass spectrometry. Proline-treated rice roots showed up-regulation and down-regulation of nine and eight proteins, respectively, when compared to those in the control. Among the differentially expressed proteins, the down-regulation of glutathione reductase and peroxidase could be involved in the regulation of cellular hydrogen peroxide and reactive oxygen species levels that modulate the root cell wall structure. Differentially expressed proteins identified as pathogenesis-related proteins might be related to stress adaptive mechanisms in response to exogenous proline treatment. In addition, differentially expressed protein identified as the fructose-bisphosphate aldolases and cytochrome c oxidase might be associated with energy metabolism, which is needed during root developmental process. This is the first attempt to study the changes in rice root proteome treated with proline. The acquired information could open new avenues for further functional studies on the involvement of proline in modulating root development and its relation to stress adaptation of plants.

EgRBP42 from oil palm enhances adaptation to stress in Arabidopsis through regulation of nucleocytoplasmic transport of stress-responsive mRNAs.

Abiotic stress reduces plant growth and crop productivity. However, the mechanism underlying posttranscriptional regulations of stress response remains elusive. Herein, we report the posttranscriptional mechanism of nucleocytoplasmic RNA transport of stress-responsive transcripts mediated by EgRBP42, a heterogeneous nuclear ribonucleoprotein-like RNA-binding protein from oil palm, which could be necessary for rapid protein translation to confer abiotic stress tolerance in plants. Transgenic Arabidopsis overexpressing EgRBP42 showed early flowering through alteration of gene expression of flowering regulators and exhibited tolerance towards heat, cold, drought, flood, and salinity stresses with enhanced poststress recovery response by increasing the expression of its target stress-responsive genes. EgRBP42 harbours nucleocytoplasmic shuttling activity mediated by the nuclear localization signal and the M9-like domain of EgRBP42 and interacts directly with regulators in the nucleus, membrane, and the cytoplasm. EgRBP42 regulates the nucleocytoplasmic RNA transport of target stress-responsive transcripts through direct binding to their AG-rich motifs. Additionally, EgRBP42 transcript and protein induction by environmental stimuli are regulated at the transcriptional and posttranscriptional levels. Taken together, the posttranscriptional regulation of RNA transport mediated by EgRBP42 may change the stress-responsive protein profiles under abiotic stress conditions leading to a better adaptation of plants to environmental changes.

Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales).

Agar and agarose have wide applications in food and pharmaceutical industries. Knowledge on the genome of red seaweeds that produce them is still lacking. To fill the gap in genome analyses of these red algae, we have sequenced the nuclear and organellar genomes of an agarophyte, Gracilaria changii. The partial nuclear genome sequence of G. changii has a total length of 35.8Mb with 10,912 predicted protein coding sequences. Only 39.4% predicted proteins were found to have significant matches to protein sequences in SwissProt. The chloroplast genome of G. changii is 183,855bp with a total of 201 open reading frames (ORFs), 29 tRNAs and 3 rRNAs predicted. Five genes: ssrA, leuC and leuD CP76_p173 (orf139) and pbsA were absent in the chloroplast genome of G. changii. The genome information is valuable in accelerating functional studies of individual genes and resolving evolutionary relationship of red seaweeds.