In the search for universal vaccine candidates for the prevention of avian influenza, the non-structural (NS)-1 protein of avian influenza virus (AIV) H5N1 has shown promising potential for its ability to effectively stimulate the host immunity. This study was aimed to produce a bacterial expression plasmid using pRSET B vector to harbour the NS1 gene of AIV H5N1 (A/Chicken/Malaysia/5858/2004 (H5N1)) for protein expression in Escherichia coli (E. coli). The NS1 gene (687 bp) was initially amplified by polymerase chain reaction (PCR) and then cloned into a pGEM-T Easy TA vector. The NS1 gene was released from pGEM-T-NS1 using EcoRI and XhoI restriction enzymes (RE). The pRSET B vector was also linearized using the same RE. The digested NS1 gene and linearized pRSET B were ligated using T4 DNA ligase to form the expression plasmid, pRSET B-NS1. The NS1 gene sequence in pRSET B-NS1 was confirmed by DNA sequencing. To prepare recombinant bacterial cells for protein expression in the future, pRSET B-NS1 was transformed into E. coli strain BL21 (DE3) by heat-shock. Colonies bearing the recombinant plasmid were screened using PCR. The DNA sequencing analysis revealed that the NS1 gene sequence was 97% homologous to that of AIV H5N1 A/Chicken/Malaysia/5858/2004 (H5N1). These results indicated that the NS1 gene of influenza A/Chicken/Malaysia/5858/2004 (H5N1) was successfully amplified and cloned into a pRSET B vector. Bacterial colonies carrying pRSET B-NS1 can be used for the synthesis of NS1-based influenza vaccine in the future and thereby aid in the prevention of avian influenza.
Cryptococcal meningitis is a central nervous system infection cause by Cryptococcus neoformans. Although Cryptococcus is found in bird droppings, it has never been reported for those ranchers involved in the niche swiftlet ranching industry despite having close proximity with the bird droppings. We present here a case of a 41-year-old healthy swiftlet rancher who presents with a history of prolonged fever, headache and altered behaviour of a month duration. Cerebral spinal fluid analysis revealed the presence of Cryptococcus. He was treated with intravenous amphotericin B and flucytosine and discharged well with fluconazole consolidation therapy for 8 weeks, followed by maintenance therapy for 1 year. We believe this is the first reported case of Cryptococcal meningitis (CM) occurring in an immunocompetent swiftlet rancher. This case should highlight the needs to wear a proper personal protective equipment inside a swiftlet ranch due to the constant exposure to the potential cryptococcal-rich environment. A high index of suspicion, careful history taking and physical examination focusing on neurologic assessment is key to early diagnosis and timely management of CM.
Malaysian edible bird’s nests (EBN) are from the swiflet species, Aerodromus fuciphagus. The objective of this study was to determine and compare the nutrient composition of EBN obtained from different parts of Peninsular Malaysia, collected at three different harvesting seasons, to four commercial brands. A total of 18 raw, unprocessed EBN samples from the North, South and East Coast zones of Peninsular Malaysia and duplicate samples of 4 commercial brands (processed) of EBN samples were analysed. The protein and mineral contents of unprocessed EBN samples between zones and harvesting seasons were comparable. Mean (± SEM) protein content of unprocessed EBN was 61.5 ± 0.6 g/100g and the top four minerals detected were calcium, sodium, magnesium and potassium with mean (± SEM) concentration of 553.1 ± 19.5 mg/100g, 187.9 ± 10.4 mg/100g, 92.9 ± 2.0 mg/100g and 6.3 ± 0.4 mg/100g respectively. Sialic acid content ranged between 0.7 to 1.5%, and remained comparable between samples from different zones and harvesting seasons. The commercial brands were found to contain higher amounts of calcium, sodium, magnesium, potassium and phosphorus compared to unprocessed EBN, warranting further investigation and verification with more samples. Since the nutrient contents of EBN may be affected by seasonal variations and even breeding sites, it is recommended that a more comprehensive study be conducted involving more samples and breeding sites as such data are important to ensure sustainability of the EBN industry in this country.
Introduction: Heavy metals and other contaminants in food have been a concern to food industries, consumers and governing authorities. The purpose of this study was to determine the levels of heavy metals and other elements in edible bird nests (EBNs). Methods: Raw and processed (commercial) EBNs were used in the study. Raw EBNs were collected directly from five house farms in Peninsular Malaysia - Kuala Sanglang (Kedah), Pantai Remis (Perak), Kluang Gohor), Kota Bharu (Kelantan) and Kajang (Selangor). Processed EBNs were pmchased from five Chinese traditional medicinal shops located in Peninsular Malaysia. The levels of 32 elements were determined by inductively coupled plasma-mass spectrometry and findings of the study were compared to the maximum regulatory limits set by the Standards and Industrial Research Institute of Malaysia (SIRIM) for EBNs. Results: Of the seven elements with maximum regulatory limits (As, Cd, Pb, Hg, Sn, Cu, Fe), one raw EBN was detected with mercury level of 70.180 ppb which was above the SIRIM permissible limit of 50 ppb. All the EBNs had iron levels above the SIRIM permissible limit of 30 ppb. The levels of the other 25 elements with no maximum regulatory limits (Ca, Mg, Na, K, P, Co, Cr, Mn, Mo, Se, Zn, Ag, Ba, Be, Bi, B, Li, Ni, Sb, Sr, Ti, U, V, Al, Zr) were also determined. Conclusion: The data obtained for the 25 elements with no permissible limits can serve as baseline data for further studies to establish their maximum regulatory limits.
Though several AI-based models have been established for COVID-19 diagnosis, the machine-based diagnostic gap is still ongoing, making further efforts to combat this epidemic imperative. So, we tried to create a new feature selection (FS) method because of the persistent need for a reliable system to choose features and to develop a model to predict the COVID-19 virus from clinical texts. This study employs a newly developed methodology inspired by the flamingo's behavior to find a near-ideal feature subset for accurate diagnosis of COVID-19 patients. The best features are selected using a two-stage. In the first stage, we implemented a term weighting technique, which that is RTF-C-IEF, to quantify the significance of the features extracted. The second stage involves using a newly developed feature selection approach called the improved binary flamingo search algorithm (IBFSA), which chooses the most important and relevant features for COVID-19 patients. The proposed multi-strategy improvement process is at the heart of this study to improve the search algorithm. The primary objective is to broaden the algorithm's capabilities by increasing diversity and support exploring the algorithm search space. Additionally, a binary mechanism was used to improve the performance of traditional FSA to make it appropriate for binary FS issues. Two datasets, totaling 3053 and 1446 cases, were used to evaluate the suggested model based on the Support Vector Machine (SVM) and other classifiers. The results showed that IBFSA has the best performance compared to numerous previous swarm algorithms. It was noted, that the number of feature subsets that were chosen was also drastically reduced by 88% and obtained the best global optimal features.
Avian influenza, an infectious disease of birds, is caused by type A strain of the influenza virus. The disease, which was first identified in Italy more than 100 years ago, occurs worldwide. Avian influenza viruses are mainly distributed by migratory birds. Various animals like birds, pigs, horses, sea mammals and, finally, humans are susceptible to influenza A viruses. The high possibility of genomic changes like gene shift and drift are caused by the segmented RNA genome.
Matched MeSH terms: Birds; Influenza in Birds/mortality; Influenza in Birds/epidemiology; Influenza in Birds/prevention & control; Influenza in Birds/transmission*; Influenza in Birds/virology
Subtype-specific multiplex reverse transcription-polymerase chain reaction (RT-PCR) was developed to simultaneously detect three subtypes (H5, H7 and H9) of avian influenza virus (AIV) type A. The sensitivity of the multiplex RT-PCR was evaluated and compared to that of RT-PCR-enzyme-linked immunosorbent assay (ELISA) and conventional RT-PCR. While the sensitivity of the multiplex RT-PCR is as sensitive as the conventional RT-PCR, it is 10 times less sensitive than RT-PCR-ELISA. The multiplex RT-PCR is also as sensitive as the virus isolation method in detecting H9N2 from tracheal samples collected at day 3 and 5 post inoculation. Hence, the developed multiplex RT-PCR assay is a rapid, sensitive and specific assay for detecting of AIV subtypes.
Matched MeSH terms: Birds; Influenza in Birds/diagnosis; Influenza in Birds/virology*
Biotechnology-based detection systems and sensors are in use for a wide range of applications in biomedicine, including the diagnostics of viral pathogens. In this review, emerging detection systems and their applicability for diagnostics of viruses, exemplified by the case of avian influenza virus, are discussed. In particular, nano-diagnostic assays presently under development or available as prototype and their potentials for sensitive and rapid virus detection are highlighted.
Matched MeSH terms: Birds/virology; Influenza in Birds/diagnosis; Influenza in Birds/virology*
Cryptococcus albidus and C. laurentii were the predominant non-neoformans cryptococci isolated during an environmental sampling study for C. gattii at Klang Valley, Malaysia. Cryptococcus gattii was not isolated from any of the environmental samples. Cryptococcus albidus and C. laurentii were isolated mainly from vegetative samples of Eucalyptus trees and bird droppings. Upon testing on canavanine-glycine-bromothymol blue (CGB) agar, all the C. albidus isolates remained unchanged. Interestingly, a total of 29 (76.3%) C. laurentii isolates formed blue colours on the CGB agar. Sequence analysis of ITS1-5.8rDNA-ITS2 gene sequences (468 bp) of four CGB-blue C. laurentii isolates demonstrated the closest match (99%) with that of C. laurentii CBS 7140. This study demonstrated the diverse environmental niche of C. albidus and C. laurentii in Malaysia.
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests.
The spatial scaling of stability is key to understanding ecological sustainability across scales and the sensitivity of ecosystems to habitat destruction. Here we propose the invariability-area relationship (IAR) as a novel approach to investigate the spatial scaling of stability. The shape and slope of IAR are largely determined by patterns of spatial synchrony across scales. When synchrony decays exponentially with distance, IARs exhibit three phases, characterized by steeper increases in invariability at both small and large scales. Such triphasic IARs are observed for primary productivity from plot to continental scales. When synchrony decays as a power law with distance, IARs are quasilinear on a log-log scale. Such quasilinear IARs are observed for North American bird biomass at both species and community levels. The IAR provides a quantitative tool to predict the effects of habitat loss on population and ecosystem stability and to detect regime shifts in spatial ecological systems, which are goals of relevance to conservation and policy.
Biogeographic history can lead to variation in biodiversity across regions, but it remains unclear how the degree of biogeographic isolation among communities may lead to differences in biodiversity. Biogeographic analyses generally treat regions as discrete units, but species assemblages differ in how much biogeographic history they share, just as species differ in how much evolutionary history they share. Here, we use a continuous measure of biogeographic distance, phylobetadiversity, to analyze the influence of biogeographic isolation on the taxonomic and functional diversity of global mammal and bird assemblages. On average, biodiversity is better predicted by environment than by isolation, especially for birds. However, mammals in deeply isolated regions are strongly influenced by isolation; mammal assemblages in Australia and Madagascar, for example, are much less diverse than predicted by environment alone and contain unique combinations of functional traits compared to other regions. Neotropical bat assemblages are far more functionally diverse than Paleotropical assemblages, reflecting the different trajectories of bat communities that have developed in isolation over tens of millions of years. Our results elucidate how long-lasting biogeographic barriers can lead to divergent diversity patterns, against the backdrop of environmental determinism that predominantly structures diversity across most of the world.
Edible bird's nest (EBN) is constructed from saliva of swiftlets birds and consumed largely by Southeast and East Asians for its nutritional value and anti-aging properties. Although the neuroprotection of EBN in animals has been reported, there has not been yet systemically summarized. Thus, this review systemically outlined the evidence of the neuroprotective activity of EBN in modulating the cognitive functions of either healthy or with induced-cognitive dysfunction animals as compared to placebos. The related records from 2010 to 2020 were retrieved from PubMed, Scopus, Web of Science and ScienceDirect using pre-specified keywords. The relevant records to the effect of EBN on cognition were selected according to the eligibility criteria and these studies underwent appraisal for the risk of bias. EBN improved the cognitive functions of induced-cognitive dysfunction and enhanced the cognitive performance of healthy animals as well as attenuated the neuroinflammations and neuro-oxidative stress in the hippocampus of these animals. Malaysian EBN could improve the cognitive functions of experimental animals as a treatment in induced cognitive dysfunction, a nutritional cognitive-enhancing agent in offspring and a prophylactic conservative effect on cognition against exposure to subsequent noxious cerebral accidents in a dose-depended manner through attenuating neuroinflammation and neuro-oxidative stress. This systemic review did not proceed meta-analysis.
Tropical rainforest disturbance and conversion are critical drivers of biodiversity loss. A key knowledge gap is understanding the impacts of habitat modification on mechanisms of community assembly, which are predicted to respond differently between taxa and across spatial scales. We use a null model approach to detect trait assembly of species at local- and landscape-scales, and then subdivide communities with different habitat associations and foraging guilds to investigate whether the detection of assembly mechanisms varies between groups. We focus on two indicator taxa, dung beetles and birds, across a disturbance gradient of primary rainforest, selectively logged rainforest, and oil palm plantations in Borneo, Southeast Asia. Random community assembly was predominant for dung beetles across habitats, whereas trait convergence, indicative of environmental filtering, occurred across the disturbance gradient for birds. Assembly patterns at the two spatial scales were similar. Subdividing for habitat association and foraging guild revealed patterns hidden when focusing on the overall community. Dung beetle forest specialists and habitat generalists showed opposing assembly mechanisms in primary forest, community assembly of habitat generalists for both taxa differed with disturbance intensity, and insectivorous birds strongly influenced overall community assembly relative to other guilds. Our study reveals the sensitivity of community assembly mechanisms to anthropogenic disturbance via a shift in the relative contribution of stochastic and deterministic processes. This highlights the need for greater understanding of how habitat modification alters species interactions and the importance of incorporating species' traits within assessments.
West Nile virus (WNV) is a zoonotic mosquito-borne flavivirus that is harbored and amplified by wild birds via the enzootic transmission cycle. Wide range of hosts are found to be susceptible to WNV infection including mammals, amphibians and reptiles across the world. Several studies have demonstrated that WNV was present in the Malaysian Orang Asli and captive birds. However, no data are available on the WNV prevalence in wild birds found in Malaysia. Therefore this study was conducted to determine the serological and molecular prevalence of WNV in wild birds in selected areas in the West Coast of Peninsular Malaysia. Two types of wild birds were screened, namely migratory and resident birds in order to explore any possibility of WNV transmission from the migratory birds to the resident birds. Thus, a cross-sectional study was conducted at the migratory birds sanctuary located in Kuala Gula, Perak and Kapar, Selangor by catching 163 migratory birds, and 97 resident birds from Kuala Gula and Parit Buntar, Perak at different time between 2016 and 2017 (Total, n = 260). Blood and oropharyngeal swabs were collected for serological and molecular analysis, respectively. Serum were screened for WNV antibodies using a commercial competitive ELISA (c-ELISA) (ID Screen® West Nile Competition Multi-species ELISA, ID VET, Montpellier, France) and cross-reactivity towards Japanese Encephalitis virus (JEV) was also carried out using the JEV-double antigen sandwich (DAS) ELISA. Oropharyngeal swabs were subjected to one-step RT-PCR to detect WNV RNA, in which positive reactions were subsequently sequenced. WNV seropositive rate of 18.71% (29/155) at 95% CI (0.131 to 0.260) and molecular prevalence of 15.2% (16/105) at 95% CI (0.092 to 0.239) were demonstrated in migratory and resident wild birds found in West Coast Malaysia. Phylogenetic analyses of the 16 WNV isolates found in this study revealed that the local strains have 99% similarity to the strains from South Africa and were clustered under lineage 2. Evidence of WNV infection in resident and migratory birds were demonstrated in this study. As a summary, intervention between migratory birds, resident birds and mosquitoes might cause the introduction and maintenance of WNV in Malaysia, however the assumption could be further proven by studying the infection dynamics in the mosquitoes present in the studied areas.
Menopause causes cognitive and memory dysfunction due to impaired neuronal plasticity in the hippocampus. Sirtuin-1 (SIRT1) downregulation in the hippocampus is implicated in the underlying molecular mechanism. Edible bird's nest (EBN) is traditionally used to improve general wellbeing, and in this study, we evaluated its effects on SIRT1 expression in the hippocampus and implications on ovariectomy-induced memory and cognitive decline in rats. Ovariectomized female Sprague-Dawley rats were fed with normal pellet alone or normal pellet + EBN (6, 3, or 1.5%), compared with estrogen therapy (0.2 mg/kg/day). After 12 weeks of intervention, Morris water maze (four-day trial and one probe trial) was conducted, and serum estrogen levels, toxicity markers (alanine transaminase, alkaline phosphatase, urea, and creatinine), and hippocampal SIRT1 immunohistochemistry were estimated after sacrifice. The results indicated that EBN and estrogen enhanced spatial learning and memory and increased serum estrogen and hippocampal SIRT1 expression. In addition, the EBN groups did not show as much toxicity to the liver as the estrogen group. The data suggested that EBN treatment for 12 weeks could improve cognition and memory in ovariectomized female rats and may be an effective alternative to estrogen therapy for menopause-induced aging-related memory loss.
Extinction rates in the Anthropocene are three orders of magnitude higher than background and disproportionately occur in the tropics, home of half the world's species. Despite global efforts to combat tropical species extinctions, lack of high-quality, objective information on tropical biodiversity has hampered quantitative evaluation of conservation strategies. In particular, the scarcity of population-level monitoring in tropical forests has stymied assessment of biodiversity outcomes, such as the status and trends of animal populations in protected areas. Here, we evaluate occupancy trends for 511 populations of terrestrial mammals and birds, representing 244 species from 15 tropical forest protected areas on three continents. For the first time to our knowledge, we use annual surveys from tropical forests worldwide that employ a standardized camera trapping protocol, and we compute data analytics that correct for imperfect detection. We found that occupancy declined in 22%, increased in 17%, and exhibited no change in 22% of populations during the last 3-8 years, while 39% of populations were detected too infrequently to assess occupancy changes. Despite extensive variability in occupancy trends, these 15 tropical protected areas have not exhibited systematic declines in biodiversity (i.e., occupancy, richness, or evenness) at the community level. Our results differ from reports of widespread biodiversity declines based on aggregated secondary data and expert opinion and suggest less extreme deterioration in tropical forest protected areas. We simultaneously fill an important conservation data gap and demonstrate the value of large-scale monitoring infrastructure and powerful analytics, which can be scaled to incorporate additional sites, ecosystems, and monitoring methods. In an era of catastrophic biodiversity loss, robust indicators produced from standardized monitoring infrastructure are critical to accurately assess population outcomes and identify conservation strategies that can avert biodiversity collapse.
Theories of tropical tree diversity emphasize dispersal limitation as a potential mechanism for separating species in space and reducing competitive exclusion. We compared the dispersal morphologies, fruit sizes, and spatial distributions of 561 tree species within a fully mapped, 50-hectare plot of primary tropical forest in peninsular Malaysia. We demonstrate here that the extent and scale of conspecific spatial aggregation is correlated with the mode of seed dispersal. This relationship holds for saplings as well as for mature trees. Phylogenetically independent contrasts confirm that the relationship between dispersal and spatial pattern is significant even after controlling for common ancestry among species. We found the same qualitative results for a 50-hectare tropical forest plot in Panama. Our results provide broad empirical evidence for the importance of dispersal mode in establishing the long-term community structure of tropical forests.