Unusual tumour-like pathologies caused by mysterious cells termed 'X-cells' have been reported from numerous fish groups worldwide. After nearly 100 years of research, the tumour-like growths have recently been shown to be caused by a protozoan parasite. In the present study, histopathology and small subunit ribosomal DNA (SSU rDNA) sequences are used to assess whether the X-cell parasite infecting Atlantic dab Limanda limanda L. is distinct from the X-cell parasite infecting Japanese flounder and goby, and to determine their systematic position within the protists. SSU rDNA from Scottish dab was 89.3% and 86.7% similar to Japanese X-cell sequences from flounder and goby respectively, indicating that the parasite infecting dab in the Atlantic is distinct from the Pacific species. Histological studies revealed significant gill pathology and demonstrated the precise location of the parasites within the gill tissues using specific in situ hybridization probes. Phylogenetic analyses showed that the X-cell parasites from Scotland and Japan form a monophyletic group within the Myzozoa, and are basal alveolates. However, ultrastructure of X-cells from dab fails to confirm this systematic placement.
A study was carried out to investigate correlation between presence of specific microalgal species and Leptoconops biting midge larvae in its breeding habitats. Sand samples containing microalgae were collected from the beach where the midges were most commonly biting and from sand beaches which are potential as breeding habitats of Leptoconops. The survey covered sand beaches from 12 seperate islands. At all sites, the Bacillariophyta constituted the largest representatives of the microalgae community with the majority from the Naviculaceae family. A total of 24 microalgal species were identified from the sand samples collected from the study sites. Sand samples from Kentot Kecil Island had the highest number of algal species (11.0) and the highest algae species diversity ( Shanon-Weiner Diversity Index, H' = 0.884). Besar Island (Johor) had the lowest number of algal species (2.0) whereas Tengol A Island had the lowest algae species diversity (H'=0.234). Highest similarity index was recorded between sand samples collected from Tengol A Island and Tengol B Island (75.0%) followed by Besar Island (Melaka) and Tengol B Island (62.0 %). The variation between other islands were relatively high. Virtually many kinds of algae were found where Leptoconops were breeding but Fragilaria intermedia, Mastigloia minuta and Navicula advena were particularly common.
The large intestine harbors microorganisms playing unique roles in host physiology. The beneficial or detrimental outcome of host-microbiome coexistence depends largely on the balance between regulators and responder intestinal CD4+ T cells. We found that ulcerative colitis-like changes in the large intestine after infection with the protist Blastocystis ST7 in a mouse model are associated with reduction of anti-inflammatory Treg cells and simultaneous expansion of pro-inflammatory Th17 responders. These alterations in CD4+ T cells depended on the tryptophan metabolite indole-3-acetaldehyde (I3AA) produced by this single-cell eukaryote. I3AA reduced the Treg subset in vivo and iTreg development in vitro by modifying their sensing of TGFβ, concomitantly affecting recognition of self-flora antigens by conventional CD4+ T cells. Parasite-derived I3AA also induces over-exuberant TCR signaling, manifested by increased CD69 expression and downregulation of co-inhibitor PD-1. We have thus identified a new mechanism dictating CD4+ fate decisions. The findings thus shine a new light on the ability of the protist microbiome and tryptophan metabolites, derived from them or other sources, to modulate the adaptive immune compartment, particularly in the context of gut inflammatory disorders.
Cage-cultured Asian redtail catfish Hemibagrus nemurus (Valenciennes, 1840), a popular food fish in Southeast Asia, proved to be infected by 3 myxozoan species. All the 3 species belonged to the genus Henneguya: 2 were identified as H. mystusia Sarkar, 1985 and H. hemibagri Tchang et Ma, 1993, while the other was described as H. basifilamentalis sp. n. All plasmodia were found in the gills and were characterised by a specific site selection. H. mystusia formed plasmodia in the multi-layered epithelium between the gill lamellae and in the non-lamellar edge of the gill filaments, while H. hemibagri developed in the capillary network of the lamellae. H. basifilamentalis sp. n. had large oval plasmodia located deep among the filaments just above the gill arch.
Any forms of valorization of microorganisms would require accurate identity recognition to ensure repeatability, reproducibility and quality assurance. This study aimed to evaluate the effectiveness of different primers for identifying cultured eukaryotic microalgae using a simple 18S rDNA approach. A total of 34 isolated microalgae and one culture collection were utilized in the search for an effective molecular identification method for microalgae. Ammonium formate was applied to marine microalgae prior to DNA extraction. The microalgal DNA was extracted using a commercial kit and subjected directly to PCR amplification using four different published 18S rDNA primers. The DNA sequences were analysed using Basic Local Alignment Search Tool (BLAST) and phylogenetic trees to determine the microalgae identity. The identity was further validated with conventional morphological taxonomic identification, and the relationship of microalgal morphology and genetic materials was also determined. The microalgal DNA was successfully amplified, including marine species without prior cleaning. In addition, the ss5 + ss3 primer pair was found to be an ideal primer set among the tested primers for identifying microalgae. Overall, molecular identification showed relative matching with morphological identification (82.86%). This study is important because it serves as a platform to develop a standardized eukaryotic microalgae identification method. In addition, this method could help to ease the eukaryotic microalgae identification process and enrich the current reference databases such as GenBank.
Bifunctional heterogeneous catalysts have a great potential to overcome the shortcomings of homogeneous and enzymatic catalysts and simplify the biodiesel production processes using low-grade, high-free-fatty-acid feedstock. In this study, we developed ZrO2-based bifunctional heterogeneous catalysts for simultaneous esterification and transesterification of microalgae to biodiesel. To avoid the disadvantage of the low surface area of ZrO2, the catalysts were prepared via a surfactant-assisted sol-gel method, followed by hydrothermal treatments. The response surface methodology central composite design was employed to investigate various factors, like the surfactant/Zr molar ratio, pH, aging time, and temperature on the ZrO2 surface area. The data were statistically analyzed to predict the optimal combination of factors, and further experiments were conducted for verification. Bi2O3 was supported on ZrO2 via the incipient wetness impregnation method. The catalysts were characterized by a variety of techniques, which disclosed that the surfactant-assisted ZrO2 nanoparticles possess higher surface area, better acid-base properties, and well-formed pore structures than bare ZrO2. The highest yield of fatty acid methyl esters (73.21%) was achieved using Bi2O3/ZrO2(CTAB), and the catalytic activity of the developed catalysts was linearly correlated with the total densities of the acidic and basic sites. The mechanism of the simultaneous reactions was also discussed.
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases.
Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.
Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of "functional redundancy" for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.
Cage-cultured sutchi catfish Pangasius hypophthalmus (Sauvage, 1878), a favourite food fish in Southeast Asia, proved to be infected by 6 myxozoan species. Three species belonged to the genus Hennegoides (H. berlandi, H. malayensis, and H. pangasii), 1 to Henneguya (H. shariffi) and 2 to Myxobolus (M. baskai, and M. pangasii). Five myxozoans infected the gills and 1 was found on the spleen. Myxozoans infecting the gills were characterised by a specific site selection. H. shariffi sp. n. and H. berlandi sp. n. formed plasmodia in the multi-layered epithelium of the gill filaments. Of the 2 vascular species H. pangasii sp. n. developed in the gill arteries, while M. baskai sp. n. infected the capillary network of the gill lamellae. Plasmodia of H. malayensis sp. n. were found inside the cartilaginous gill rays of the filaments. Large plasmodia of M. pangasii sp. n. were located in a groove of the spleen but they affected only the serosa layer covering the spleen.
A total of fifty anurans, comprising of Rana limnocharis and Bufo melanostictus were collected from Sungai Pinang, Balik Pulau, Penang. The prevalence, mean intensity and distribution of parasite species along the digestive tract were reported. Seven species of parasites were recorded. Blood parasites recovered were trypansomes and microfilariae.
Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.
Parasites and bacteria are reported in the faeces of birds in the current study. Fresh faecal samples of the large-billed crow (Corvus spp.) were collected from the study site at Bangsar, an urban setting in Kuala Lumpur, Malaysia. These samples were transported to laboratory and analysed for parasites and bacteria. Pre-prepared XLD agar plates were used for culturing the bacteria in the laboratory. Using the API 20ETM Test Strips, 9 different species of bacteria were identified belonging to the family Enterobacteriacea. They were Citrobacter freundii, Enterobacter cloacae, Proteus mirabilis, Klebsiella pneumoniae, Kluyvera ascorbata, Salmonella arizonae, Salmonella typhi, Shigella flexneri and Shigella sonnei. The protozoan parasites detected include Cryptosporidium spp., Cyclospora spp., Blastocystis spp., and Capillaria hepatica and Ascaris lumbricoidus ova. Environmental air samples collected on agar plates using an air sampler in the area only produced fungal colonies. Some of these pathogens found in the crows are of zoonotic importance, especially Cryptosporidium, Blastocystis, Cyclopsora, Salmonella, Shigella and Kluyvera. The finding of Kluyvera spp. in crows in our current study highlights its zoonotic potential in an urban setting.
Singapore, an equatorial island in South East Asia, is influenced by a bi-annual reversal of wind directions which defines two monsoon seasons. We characterized the dynamics of the microbial communities of Singapore coastal waters by collecting monthly samples between February 2017 and July 2018 at four sites located across two straits with different trophic status, and sequencing the V6-V8 region of the small sub-unit ribosomal RNA gene (rRNA gene) of Bacteria, Archaea, and Eukaryota. Johor Strait, which is subjected to wider environmental fluctuations from anthropogenic activities, presented a higher abundance of copiotrophic microbes, including Cellvibrionales and Rhodobacterales. The mesotrophic Singapore Strait, where the seasonal variability is caused by changes in the oceanographic conditions, harboured a higher proportion of typically marine microbe groups such as Synechococcales, Nitrosupumilales, SAR11, SAR86, Marine Group II Archaea and Radiolaria. In addition, we observed seasonal variability of the microbial communities in the Singapore Strait, which was possibly influenced by the alternating monsoon regime, while no seasonal pattern was detected in the Johor Strait.
Thiocyanate (SCN-) forms as a by-product of cyanidation during gold ore processing and can be degraded by a variety of microorganisms utilizing it as an energy, nitrogen, sulphur and/or carbon source. In complex consortia inhabiting bioreactor systems, a range of metabolisms are sustained by SCN- degradation; however, despite the addition or presence of labile carbon sources in most bioreactor designs to date, autotrophic bacteria have been found to dominate key metabolic functions. In this study, we cultured an autotrophic SCN--degrading consortium directly from gold mine tailings. In a batch-mode bioreactor experiment, this consortium degraded 22 mM SCN-, accumulating ammonium (NH4+) and sulphate (SO42-) as the major end products. The consortium consisted of a diverse microbial community comprised of chemolithoautotrophic members, and despite the absence of an added organic carbon substrate, a significant population of heterotrophic bacteria. The role of eukaryotes in bioreactor systems is often poorly understood; however, we found their 18S rRNA genes to be most closely related to sequences from bacterivorous Amoebozoa. Through combined chemical and phylogenetic analyses, we were able to infer roles for key microbial consortium members during SCN- biodegradation. This study provides a basis for understanding the behaviour of a SCN- degrading bioreactor under autotrophic conditions, an anticipated approach to remediating SCN- at contemporary gold mines.
The objective was to estimate the prevalence of intestinal protozoa among the aborigines and to determine the problems regarding the infection. The study was carried out in January 2006 in Pos Senderut, Pahang, Malaysia. Samples of faeces were collected from children and adults and these were fixed in PVA and trichrome staining was carried out. From the 130 individuals studied, 94 (72.3%) were positive with at least one intestinal protozoa. Nine intestinal protozoa namely Blastocystis hominis, Giardia lamblia, Entamoeba histolytica, Entamoeba coli, Endolimax nana, Entamoeba hartmani, Entamoeba polecki, Iodamoeba butschlii and Chilomastix mesnili were detected. The prevalent species were B. hominis (52.3%), followed by G. lamblia (29.2%), E. coli (26.2%) and E. histolytica (18.5%). The other species ranged from 1.5 to 10.8%. Among the positive samples, mixed infection with E. histolytica and G. lamblia was 3.8%, E. histolytica and B. hominis was 15.4%, G. lamblia and B. hominis was 17.7%. Triple infection of E. histolytica, G. lamblia and B. hominis was 3.1%. The infection was more prevalent in children below 10 years age group (45.4%) and lowest in the age above 60 years (3.8%). The high prevalence was attributable to poor environmental management, poor personal hygiene and lack of health education.
Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.
Microsatellites or simple sequence repeats (SSRs) are tandem repeats of DNA of 1-6 bp long. They ubiquitously occur in both eukaryotic and prokaryotic genomes. Because of their abundance,
they have widespread applications in both animal and plant sciences; such as varietal identification, genetic mapping, QTL mapping, phylogenetic and diversity studies. Thus, SSRs have become valuable DNA markers for molecular biologists and geneticists. Microsatellites are markers
of choice for many molecular geneticists because of their hypervariability, codominant
inheritance, multi-allelism and PCR-based assaying of variations that are amenable to automation and high throughput assay. However, the utilization of microsatellite markers in the past was
hampered by its laborious de novo isolations and species-specific nature.
The telomere and telomerase hypothesis of aging and cancer is based on the findings that most human tumors have telomerase activity while almost all normal human somatic cells do not. Telomeres are nucleoprotein structure that located 100-300 kb from the end of linear eukaryotic chromosomes (Blackburn et al, 2001; Yoo & Robinson, 2000). Human telomeres consist of thousand repetitive sequences TTAGGG with ranging from 5 to 20 kb (Figure 1) (Martin, 2002). In human cell, there are 92 telomeres which have several functions including protecting chromosome ends, to maintain chromosome stability, serve as an attachment point to the nuclear matrix and also involve in the cell replication.