Long noncoding RNAs (lncRNAs) play diverse roles in biological processes. Aedes aegypti (Ae. aegypti), a blood-sucking mosquito, is the principal vector responsible for replication and transmission of arboviruses including dengue, Zika, and Chikungunya virus. Systematic identification and developmental characterisation of Ae. aegypti lncRNAs are still limited. We performed genome-wide identification of lncRNAs, followed by developmental profiling of lncRNA in Ae. aegypti. We identified a total of 4,689 novel lncRNA transcripts, of which 2,064, 2,076, and 549 were intergenic, intronic, and antisense respectively. Ae. aegypti lncRNAs share many characteristics with other species including low expression, low GC content, short in length, and low conservation. Besides, the expression of Ae. aegypti lncRNAs tend to be correlated with neighbouring and antisense protein-coding genes. A subset of lncRNAs shows evidence of maternal inheritance; hence, suggesting potential role of lncRNAs in early-stage embryos. Additionally, lncRNAs show higher tendency to be expressed in developmental and temporal specific manner. The results from this study provide foundation for future investigation on the function of Ae. aegypti lncRNAs.
Rafflesia possesses unique biological features and known primarily for producing the world's largest and existing as a single flower. However, to date, little is known about key regulators participating in Rafflesia flower development. In order to further understand the molecular mechanism that regulates Rafflesia cantleyi flower development, RNA-seq data from three developmental stages of floral bud, representing the floral organ primordia initiation, floral organ differentiation, and floral bud outgrowth, were analysed. A total of 89,890 transcripts were assembled of which up to 35% could be annotated based on homology search. Advanced transcriptome analysis using K-mean clustering on the differentially expressed genes (DEGs) was able to identify 12 expression clusters that reflect major trends and key transitional states, which correlate to specific developmental stages. Through this, comparative gene expression analysis of different floral bud stages identified various transcription factors related to flower development. The members of WRKY, NAC, bHLH, and MYB families are the most represented among the DEGs, suggesting their important function in flower development. Furthermore, pathway enrichment analysis also revealed DEGs that are involved in various phytohormone signal transduction events such as auxin and auxin transport, cytokinin and gibberellin biosynthesis. Results of this study imply that transcription factors and phytohormone signalling pathways play major role in Rafflesia floral bud development. This study provides an invaluable resource for molecular studies of the flower development process in Rafflesia and other plant species.
The richness of high-value bio-compounds derived from microalgae has made microalgae a promising and sustainable source of useful product. The present work starts with a review on the usage of open pond and photobioreactor in culturing various microalgae strains, followed by an in-depth evaluation on the common harvesting techniques used to collect microalgae from culture medium. The harvesting methods discussed include filtration, centrifugation, flocculation, and flotation. Additionally, the advanced extraction technologies using ionic liquids as extractive solvents applied to extract high-value bio-compounds such as lipids, carbohydrates, proteins, and other bioactive compounds from microalgae biomass are summarized and discussed. However, more work needs to be done to fully utilize the potential of microalgae biomass for the application in large-scale production of biofuels, food additives, and nutritive supplements.
Two lineages of stream toads in the genus Ansonia from Malaysian Borneo have long been suspected to be specifically distinct on the basis of molecular data. We assessed the taxonomic status of these lineages using morphological and additional genetic data. In mtDNA phylogeny, each lineage-one from Bario, Kelabit Highlands of Sarawak, the other from Mt. Mulu of Sarawak and the Crocker Range of Sabah-is separated from other congeners by large genetic distances, comparable with those observed between heterospecific species in the genus. These lineages are also morphologically distinguishable from other species, and are considered to represent valid, independently evolving species. We therefore describe them as A. kelabitensis sp. nov. and A. kanak sp. nov.
Matched MeSH terms: Bufonidae/growth & development
Urbanization has caused an increase in favorable habitats for Aedes aegypti (Diptera: Culicidae), given their ability to reproduce in small and often non-degradable artificial water-containers. While much work has been done on Ae. aegypti biology and ecology in urban landscapes, the role of shading on immature stages as an independent factor from temperature, and any possible interactions between these factors, remains unexamined. We assessed how temperature and shading affected egg hatch-rate, larval/pupal mortality, and larval development to adult stage under different factorial temperature (28; 31; 34; 37; 40° C) and shade (0%, 3,100 lux; 40%, 1,860 lux; 75%, 775 lux; 100%, 0 lux) regimes. Hatch-rate was significantly lower at 37° C (57 %), and no eggs hatched at 40° C. There was no significant effect caused by shading on hatchability. Larval and pupal mortality at 37° C was significantly higher (35%) compared to lower temperature groups, while the effects of shading were emergent at low temperatures. Developmental times from hatching to adult emergence were significantly reduced with increasing temperatures and with greater light exposures. The eco-physiological response of Ae. aegypti larvae to temperature and light regimes suggest a photosensitivity previously unstudied in this species.
Helicobacter pylori colonizes the gastric epithelial cells of at least half of the world's population, and it is the strongest risk factor for developing gastric complications like chronic gastritis, ulcer diseases, and gastric cancer. To successfully colonize and establish a persistent infection, the bacteria must overcome harsh gastric conditions. H. pylori has a well-developed mechanism by which it can survive in a very acidic niche. Despite bacterial factors, gastric environmental factors and host genetic constituents together play a co-operative role for gastric pathogenicity. The virulence factors include bacterial colonization factors BabA, SabA, OipA, and HopQ, and the virulence factors necessary for gastric pathogenicity include the effector proteins like CagA, VacA, HtrA, and the outer membrane vesicles. Bacterial factors are considered more important. Here, we summarize the recent information to better understand several bacterial virulence factors and their role in the pathogenic mechanism.
Matched MeSH terms: Helicobacter pylori/growth & development
Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.
Chlorella is a popular microalga with robust physiological and biochemical characteristics, which can be cultured under various conditions. The exploration of the small RNA content of Chlorella could improve strategies for the enhancement of metabolite production from this microalga. In this study, stress was introduced to the Chlorella sorokiniana culture to produce high-value metabolites such as carotenoids and phenolic content. The small RNA transcriptome of C. sorokiniana was sequenced, focusing on microRNA (miRNA) content. From the analysis, 98 miRNAs were identified in cultures subjected to normal and stress conditions. The functional analysis result showed that the miRNA targets found were most often involved in the biosynthesis of secondary metabolites, followed by protein metabolism, cell cycle, and porphyrin and chlorophyll metabolism. Furthermore, the biosynthesis of secondary metabolites such as carotenoids, terpenoids, and lipids was found mostly in stress conditions. These results may help to improve our understanding of regulatory mechanisms of miRNA in the biological and metabolic process of Chlorella species. It is important and timely to determine the true potential of this microalga species and to support the potential for genetic engineering of microalgae as they receive increasing focus for their development as an alternative source of biofuel, food, and health supplements.
Matched MeSH terms: Chlorella/growth & development
KEY MESSAGE: Three tau class MaGSTs responded to abiotic stress, MaGSTF1 and MaGSTL1 responded to signaling molecules, they may play an important role in the growth of banana plantlet. Glutathione S-transferases (GST) are multifunctional detoxification enzymes that participate in a variety of cellular processes, including stress responses. In this study, we report the molecular characteristics of five GST genes (MaGSTU1, MaGSTU2, MaGSTU3, MaGSTF1 and MaGSTL1) cloned from banana (Musa acuminate L. AAA group, cv. Cavendish) using a RACE-PCR-based strategy. The predicted molecular masses of these GSTs range from 23.4 to 27.7 kDa and their pIs are acidic. At the amino acid level, they share high sequence similarity with GSTs in the banana DH-Pahang (AA group) genome. Phylogenetic analysis showed that the deduced amino acid sequences of MaGSTs also have high similarity to GSTs of other plant species. Expression analysis by semi-quantitative RT-PCR revealed that these genes are differentially expressed in various tissues. In addition, their expression is regulated by various stress conditions, including exposure to signaling molecules, cold, salinity, drought and Fusarium oxysporum f specialis(f. Sp) cubense Tropical Race 4 (Foc TR4) infection. The expression of the tau class MaGSTs (MaGSTU1, MaGSTU2 and MaGSTU3) mainly responded to cold, salinity and drought while MaGSTF1 and MaGSTL1 expressions were upregulated by signaling molecules. Our findings suggest that MaGSTs play a key role in both development and abiotic stress responses.
Aspergillus flavus is the predominant species that produce aflatoxins in stored peanuts under favourable conditions. This study aimed to describe the growth and aflatoxin production by two A. flavus strains isolated from imported raw peanuts and to model the effects of temperature and aw on their colony growth rate as a function of temperature and aw in Peanut Meal Extract Agar (PMEA). A full factorial design with seven aw levels (0.85-0.98 aw) and five temperature levels (20-40 °C) was used to investigate the growth and aflatoxin production. Colony diameter was measured daily for 28 days while AFB1 and total aflatoxin were determined on day 3, 7, 14, and 21. The maximum colony growth rate, μmax (mm/day) was estimated by using the primary model of Baranyi, and the μmax was then fitted to the secondary model; second-order polynomial and linear Arrhenius-Davey to describe the colony growth rate as a function of temperature and aw. The results indicated that both strains failed to grow at temperature of 20 °C with aw <0.94 and aw of 0.85 for all temperatures except 30 °C. The highest growth rate was observed at 30 °C, with 0.98 aw for both strains. The analysis of variance showed a significant effect of strain, temperature, and aw on the fungal growth and aflatoxin production (p
Anguillid eels of the genus Anguilla, which have a unique catadromous life history, are widely distributed across many parts of the world. However, little research has been conducted on the behavioural mechanisms of habitat segregation between sympatric species in tropical anguillid eels. To understand the ecological and behavioural mechanisms involved in the life history and migration of tropical anguillid eels, strontium (Sr):calcium (Ca) ratios were examined in otoliths of A. bengalensis bengalensis (41 specimens) and A. bicolor bicolor (130 specimens) collected from ten rivers in northwestern Peninsular Malaysia. The otolith Sr:Ca ratios revealed different habitat use between the two species. The broad range of otolith Sr:Ca ratios and habitat shift found in A. bicolor bicolor suggested that its habitat utilization was opportunistic in environments of varying salinity. A. bicolor bicolor prefers to live in the midstream to downstream areas with tidal influences. A. bengalensis bengalensis, however, was found to only reside in freshwater environments throughout their continental growth. A. bengalensis bengalensis tends to live in upstream area with no tidal influence. Their habitat use, migratory history, and habitat distribution indicate that habitat segregation occurs between the two species, leading to the different habitat preferences in tropical river systems.
Carnivorous pitcher plants produce specialised pitcher organs containing secretory glands, which secrete acidic fluids with hydrolytic enzymes for prey digestion and nutrient absorption. The content of pitcher fluids has been the focus of many fluid protein profiling studies. These studies suggest an evolutionary convergence of a conserved group of similar enzymes in diverse families of pitcher plants. A recent study showed that endogenous proteins were replenished in the pitcher fluid, which indicates a feedback mechanism in protein secretion. This poses an interesting question on the physiological effect of plant protein loss. However, there is no study to date that describes the pitcher response to endogenous protein depletion. To address this gap of knowledge, we previously performed a comparative RNA-sequencing experiment of newly opened pitchers (D0) against pitchers after 3 days of opening (D3C) and pitchers with filtered endogenous proteins (>10 kDa) upon pitcher opening (D3L). Nepenthes ampullaria was chosen as a model study species due to their abundance and unique feeding behaviour on leaf litters. The analysis of unigenes with top 1% abundance found protein translation and stress response to be overrepresented in D0, compared to cell wall related, transport, and signalling for D3L. Differentially expressed gene (DEG) analysis identified DEGs with functional enrichment in protein regulation, secondary metabolism, intracellular trafficking, secretion, and vesicular transport. The transcriptomic landscape of the pitcher dramatically shifted towards intracellular transport and defence response at the expense of energy metabolism and photosynthesis upon endogenous protein depletion. This is supported by secretome, transportome, and transcription factor analysis with RT-qPCR validation based on independent samples. This study provides the first glimpse into the molecular responses of pitchers to protein loss with implications to future cost/benefit analysis of carnivorous pitcher plant energetics and resource allocation for adaptation in stochastic environments.
Matched MeSH terms: Sarraceniaceae/growth & development
Nearly 20% of tropical forests are within 100 m of a nonforest edge, a consequence of rapid deforestation for agriculture. Despite widespread conversion, roughly 1.2 billion ha of tropical forest remain, constituting the largest terrestrial component of the global carbon budget. Effects of deforestation on carbon dynamics in remnant forests, and spatial variation in underlying changes in structure and function at the plant scale, remain highly uncertain. Using airborne imaging spectroscopy and light detection and ranging (LiDAR) data, we mapped and quantified changes in forest structure and foliar characteristics along forest/oil palm boundaries in Malaysian Borneo to understand spatial and temporal variation in the influence of edges on aboveground carbon and associated changes in ecosystem structure and function. We uncovered declines in aboveground carbon averaging 22% along edges that extended over 100 m into the forest. Aboveground carbon losses were correlated with significant reductions in canopy height and leaf mass per area and increased foliar phosphorus, three plant traits related to light capture and growth. Carbon declines amplified with edge age. Our results indicate that carbon losses along forest edges can arise from multiple, distinct effects on canopy structure and function that vary with edge age and environmental conditions, pointing to a need for consideration of differences in ecosystem sensitivity when developing land-use and conservation strategies. Our findings reveal that, although edge effects on ecosystem structure and function vary, forests neighboring agricultural plantations are consistently vulnerable to long-lasting negative effects on fundamental ecosystem characteristics controlling primary productivity and carbon storage.
Matched MeSH terms: Plant Leaves/growth & development
Gastrointestinal (GI) or gut microbiotas play essential roles in host development and physiology. These roles are influenced partly by the microbial community composition. During early developmental stages, the ecological processes underlying the assembly and successional changes in host GI community composition are influenced by numerous factors, including dispersal from the surrounding environment, age-dependent changes in the gut environment, and changes in dietary regimes. However, the relative importance of these factors to the gut microbiota is not well understood. We examined the effects of environmental (diet and water sources) and host early ontogenetic development on the diversity of and the compositional changes in the gut microbiota of a primitive teleost fish, the lake sturgeon (Acipenser fulvescens), based on massively parallel sequencing of the 16S rRNA gene. Fish larvae were raised in environments that differed in water source (stream versus filtered groundwater) and diet (supplemented versus nonsupplemented Artemia fish). We quantified the gut microbial community structure at three stages (prefeeding and 1 and 2 weeks after exogenous feeding began). The diversity declined and the community composition differed significantly among stages; however, only modest differences associated with dietary or water source treatments were documented. Many taxa present in the gut were over- or underrepresented relative to neutral expectations in each sampling period. The findings indicate dynamic relationships between the gut microbiota composition and host gastrointestinal physiology, with comparatively smaller influences being associated with the rearing environments. Neutral models of community assembly could not be rejected, but selectivity associated with microbe-host GI tract interactions through early ontogenetic stages was evident. The results have implications for sturgeon conservation and aquaculture production specifically and applications of microbe-based management in teleost fish generally.IMPORTANCE We quantified the effects of environment (diet and water sources) and host early ontogenetic development on the diversity of and compositional changes in gut microbial communities based on massively parallel sequencing of the 16S rRNA genes from the GI tracts of larval lake sturgeon (Acipenser fulvescens). The gut microbial community diversity declined and the community composition differed significantly among ontogenetic stages; however, only modest differences associated with dietary or water source treatments were documented. Selectivity associated with microbe-host GI tract interactions through early ontogenetic stages was evident. The results have implications for lake sturgeon and early larval ecology and survival in their natural habitat and for conservation and aquaculture production specifically, as well as applications of microbe-based management in teleost fish generally.
Almost 50 species of Ophiorrhiza plants were reviewed in this work and the main objective is to critically analyse their distribution, phytochemical content, biological activity, and propagation. Moreover, the information would be useful in promoting the relevant uses of the plant, especially in the medicinal fields based on in vitro and in vivo studies. To this end, scientific sources, including theses, PubMed, Google Scholar, International Islamic University Malaysia IIUM EBSCO, PubChem, and Elsevier, were accessed for publications regarding the Ophiorrhiza genus in this review. Scientific literature regarding the Ophiorrhiza plants revealed their wide distribution across Asia and the neighbouring countries, whereby they were utilised as traditional medicine to treat various diseases. In particular, various active compounds, such as alkaloids, flavonoids, and terpenoids, were reported in the plant. Furthermore, the Ophiorrhiza species showed highly diverse biological activities, such as anti-cancer, antiviral, antimicrobial, and more. The genus propagation reported could produce a high quality and quantity of potent anticancer compound, namely camptothecin (CPT). Hence, it is believed that the relevant uses of natural compounds present in the plants can replace the existing crop of synthetic anticancer drugs associated with a multitude of unbearable side effects. Additionally, more future studies on the Ophiorrhiza species should be undertaken to establish the links between its traditional uses, active compounds, and pharmacological activities reported.
Matched MeSH terms: Rubiaceae/growth & development
Palm kernel cake (PKC) has been largely produced in Malaysia as one of the cheap and abundant agro-waste by-products from the palm oil industry and it contains high fiber (mannan) content. The present study aimed to produce β-mannanase by Bacillus subtilis ATCC11774 via optimization of the medium composition using palm kernel cake as substrate in semi-solid fermentation. The fermentation nutrients such as PKC, peptone, yeast extract, sodium chloride, magnesium sulphate (MgSO2), initial culture pH and temperature were screened using a Plackett-Burman design. The three most significant factors identified, PKC, peptone and NaCl, were further optimized using central composite design (CCD), a response surface methodology (RSM) approach, where yeast extract and MgSO2 were fixed as a constant factor. The maximum β-mannanase activity predicted by CCD under the optimum medium composition of 16.50 g/L PKC, 19.59 g/L peptone, 3.00 g/L yeast extract, 2.72 g/L NaCl and 0.2 g/L MgSO2 was 799 U/mL. The validated β-mannanase activity was 805.12 U/mL, which was close to the predicted β-mannanas activity. As a comparison, commercial media such as nutrient broth, M9 and Luria bertani were used for the production of β-mannanase with activities achieved at 204.16 ± 9.21 U/mL, 50.32 U/mL and 88.90 U/mL, respectively. The optimized PKC fermentation medium was four times higher than nutrient broth. Hence, it could be a potential fermentation substrate for the production of β-mannanase activity by Bacillus subtilis ATCC11774.
Matched MeSH terms: Bacillus subtilis/growth & development
Endolysins have been studied intensively as an alternative to antibiotics. In this study, endolysin derived from a phage which infects methicillin-resistant Staphylococcus aureus (MRSA) was cloned and expressed in Escherichia coli pET28a. Initially, the endolysin was cloned using BamHI/XhoI, resulting in expression of a recombinant endolysin which was expressed in inclusion bodies. While solubilization was successful, the protein remained nonfunctional. Recloning the endolysin using NcoI/XhoI resulted in expression of soluble and functional proteins at 18°C. The endolysin was able to form halo zones on MRSA plates and showed a reduction in turbidity of MRSA growth. Therefore, cloning strategies should be chosen carefully even in an established expression system as they could greatly affect the functionality of the expressed protein.
Matched MeSH terms: Methicillin-Resistant Staphylococcus aureus/growth & development
Microbes in groundwater play a key role in determining the drinking water quality of the water. The study aims to interpret the sources of microbes in groundwater and its relationship to geochemistry. The study was carried out by collecting groundwater samples and analyzed to obtain various cations and anions, where HCO3-, Cl- and NO3- found to be higher than permissible limits in few samples. Microbial analysis, like total coliform (TC), total viable counts (TVC), fecal coliforms (FC), Vibrio cholera (V. cholerae) and total Streptococci (T. streptococci) were analyzed, and the observations reveal that most of the samples were found to be above the permissible limits adopted by EU, BIS, WHO and USEPA standards. Correlation analysis shows good correlation between Mg2+-HCO3-, K+-NO3-, TVC- V. cholerae and T. streptococci-FC. Major ions like Mg+, K+, NO3, Ca2+ and PO4 along with TS and FC were identified to control the geochemical and microbial activities in the region. The magnesium hardness in the groundwater is inferred to influence the TVC and V. cholerae. The mixing of effluents from different sources reflected the association of Cl with TC. Population of microbes T. streptococci and FC was mainly associated with Ca and Cl content in groundwater, depicting the role of electron acceptors and donors. The sources of the microbial population were observed with respect to the land use pattern and the spatial distribution of hydrogeochemical factors in the region. The study inferred that highest microbial activity in the observed in the residential areas, cultivated regions and around the landfill sites due to the leaching of sewage water and fertilizers runoff into groundwater. The concentrations of ions and microbes were found to be above the permissible limits of drinking water quality standards. This may lead to the deterioration in the health of particular coastal region.
The eucheumatoids Kappaphycus and Eucheuma are cultivated in tropical or subtropical regions for the production of carrageenan, a hydrocolloid widely used in the food and cosmetic industries. Kappaphycus alvarezii is a highly valued economic crop in the Coral Triangle, with the Philippines, Indonesia and Malaysia ranked among the largest producers. In the absence of measures to mitigate climate change, extreme events including heatwaves, typhoons, severe El Niño and La Niña, are expected to increase in frequency and magnitude. This inadvertently brings adverse effects to the seaweed cultivation industry, especially in the tropics. Temperatures are rapidly reaching the upper limit of biologically tolerable levels and an increase in reports of ice-ice and pest outbreaks is attributable to these shifts of environmental parameters. Nevertheless, few reports on the response of eucheumatoids to a changing environment, in particular global warming, are available. Understanding the responses and possible mechanisms for acclimation to warming is crucial for a sustainable seaweed cultivation industry. Here, the physiological and biochemical responses of K. alvarezii to acute warming indicated that the strain used in the current study is unlikely to survive sudden increases in temperature above 36°C. As temperature increased, the growth rates, photosynthetic performance, phycocolloid quality (carrageenan yield, gel strength and gel viscosity) and pigment content (chlorophyll-a, carotenoid and phycobiliproteins) were reduced while the production of reactive oxygen species increased indicating the occurrence of stress in the seaweeds. This study provides a basis for future work on long term acclimation to elevated temperature and mesocosm-based multivariate studies to identify heat-tolerant strains for sustainable cultivation.
Matched MeSH terms: Rhodophyta/growth & development