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An evaluation of the genus Amphidinium (Dinophyceae) combining evidence from morphology, phylogenetics, and toxin production, with the introduction of six novel species

Karafas S, Teng ST, Leaw CP, Alves-de-Souza C

Harmful Algae, 2017 09;68:128-151.
PMID: 28962975 DOI: 10.1016/j.hal.2017.08.001

The genus Amphidinium is an important group of athecated dinoflagellates because of its high abundance in marine habitats, its member's ability to live in a variety of environmental conditions and ability to produce toxins. Furthermore, the genus is of particular interest in the biotechnology field for its potential in the pharmaceutical arena. Taxonomically the there is a history of complication and confusion over the proper identities and placements of Amphidinium species due to high genetic variability coupled with high morphological conservation. Thirteen years has passed since the most recent review of the group, and while many issues were resolved, some remain. The present study used microscopy, phylogenetics of the 28S region of rDNA, secondary structure of the ITS2 region of rDNA, compensatory base change data, and cytotoxicity data from Amphidinium strains collected world-wide to elucidate remaining confusion. This holistic approach using multiple lines of evidence resulted in a more comprehensive understanding of the morphological, ecological, and genetic characteristics that are attributed to organisms belonging to Amphidinium, including six novel species: A. fijiensis, A. magnum, A. paucianulatum, A. pseudomassartii, A. theodori, and A. tomasii.

Matched MeSH terms: Species Specificity
Anaerobic Probiotics: The Key Microbes for Human Health

El Enshasy H, Malik K, Malek RA, Othman NZ, Elsayed EA, Wadaan M

Adv. Biochem. Eng. Biotechnol., 2016;156:397-431.
PMID: 26907552

Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.

Matched MeSH terms: Species Specificity
Analysis of Salmonella Agona and Salmonella Weltevreden in Malaysia by PCR fingerprinting and antibiotic resistance profiling

Learn-Han L, Yoke-Kqueen C, Salleh NA, Sukardi S, Jiun-Horng S, Chai-Hoon K, et al.

Antonie Van Leeuwenhoek, 2008 Oct;94(3):377-87.
PMID: 18548329 DOI: 10.1007/s10482-008-9254-y

Forty-eight strains of Salmonella enterica subsp. enterica serovar Agona and 33 strains of Salmonella enterica subsp. enterica serovar Weltevreden were characterized by random amplified polymorphic DNA (RAPD) fingerprinting using 3 different arbitrary primer, Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR) and antimicrobial susceptibility testing. By using RAPD, 81 strains (44 strains of S. Agona and 33 strains of S. Weltevreden) can be clustered into 14 groups and 6 single isolates whereas ERIC-PCR produced 7 clusters and 3 single isolates. Thirteen antimicrobial agents were used and all the isolates were resistant to erythromycin and showed Multiple Antimicrobial Resistance indexes, ranging from 0.08 to 0.62. Poultry still remain as the common reservoir for multi-drug-resistant Salmonella. On the other hand, vegetables contaminated with S. Weltevreden showed a gain in antimicrobial resistance. Besides that, consistent antibiograms were observed from S. Weltevreden isolated at Kajang wet market on 2000/08/02.

Matched MeSH terms: Species Specificity
Fulltext Analysis of the leprosy agents Mycobacterium leprae and Mycobacterium lepromatosis in four countries

Han XY, Aung FM, Choon SE, Werner B

Am J Clin Pathol, 2014 Oct;142(4):524-32.
PMID: 25239420 DOI: 10.1309/AJCP1GLCBE5CDZRM

To differentiate the leprosy agents Mycobacterium leprae and Mycobacterium lepromatosis and correlate them with geographic distribution and clinicopathologic features.

Matched MeSH terms: Species Specificity
Fulltext Analysis of viral diversity for vaccine target discovery

Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS, et al.

BMC Med Genomics, 2017 12 21;10(Suppl 4):78.
PMID: 29322922 DOI: 10.1186/s12920-017-0301-2

BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets.
RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis.
CONCLUSION: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

Matched MeSH terms: Species Specificity
Ancyronyx reticulatus and A. pulcherrimus, two new riffle beetle species from Borneo, and discussion about elmid plastron structures (Coleoptera: Elmidae)

Kodada J, Jäch MA, Ciampor F

Zootaxa, 2014;3760:383-95.
PMID: 24870088 DOI: 10.11646/zootaxa.3760.3.5

Two new species of Ancyronyx Erichson, 1847 (Coleoptera: Elmidae) are described from Borneo: A. pulcherrimus (Brunei) and A. reticulatus (Sabah). Habitus views, illustrations of important characters as well as plastron structures of Ancyronyx reticulatus are presented and discussed.

Matched MeSH terms: Species Specificity
Fulltext Anopheline mosquitos of northwest coastal Malaysia

Jaal Z, MacDonald WW

Southeast Asian J. Trop. Med. Public Health, 1992 Sep;23(3):479-85.
PMID: 1488703

Collections of adult anopheline mosquitos were made from a cow-baited trap in nine coastal villages located along nearly 160km of northwest peninsular Malaysia. Two collections, separated by 1.5 to 6 months, were made at each site. Nearly 6,000 anophelines of 19 species were collected. The dominant species were Anopheles peditaeniatus. An. sinensis, An. subpictus and An. lesteri paraliae. Small numbers of the malaria vectors An. maculatus (at one site) and An. campestris (at four sites) were collected, but no An. sundaicus were recorded.

Matched MeSH terms: Species Specificity
Anticandidal and antidermatophytic activity of Cinnamomum species essential oils

Mastura M, Nor Azah MA, Khozirah S, Mawardi R, Manaf AA

Cytobios, 1999;98(387):17-23.
PMID: 10490360
Matched MeSH terms: Species Specificity
Fulltext Antifungal, anti-inflammatory and cytotoxicity activities of three varieties of labisia pumila benth: from microwave obtained extracts

Karimi E, Jaafar HZ, Ahmad S

BMC Complement Altern Med, 2013;13:20.
PMID: 23347830 DOI: 10.1186/1472-6882-13-20

Labisia pumila, locally known as Kacip Fatimah, is a forest-floor plant that has tremendous potential in the herbal industry. It is one of the five herbal plants identified by the government as one of the national key economic areas to be developed for commercial purposes. There are three varieties of L. pumila namely, L. pumila var. pumila, L. pumila var. alata and L. pumila var. lanceolata and each has its own use.

Matched MeSH terms: Species Specificity
Fulltext Antioxidant, antityrosinase, anticholinesterase, and nitric oxide inhibition activities of three malaysian macaranga species

Mazlan NA, Mediani A, Abas F, Ahmad S, Shaari K, Khamis S, et al.

ScientificWorldJournal, 2013;2013:312741.
PMID: 24319356 DOI: 10.1155/2013/312741

The methanol extracts of three Macaranga species (M. denticulata, M. pruinosa, and M. gigantea) were screened to evaluate their total phenolic contents and activities as cholinesterase inhibitors, nitric oxide (NO) production inhibitors, tyrosinase inhibitors, and antioxidants. The bark of M. denticulata showed the highest total phenolic content (2682 mg gallic acid equivalent (GAE)/100 g) and free radical scavenging activity (IC50 = 0.063 mg/mL). All of the samples inhibited linoleic acid peroxidation by greater than 80%, with the leaves of M. gigantea exhibiting the highest inhibition of 92.21%. Most of the samples exhibited significant antioxidant potential. The bark of M. denticulata and the leaves of both M. pruinosa and M. gigantea exhibited greater than 50% tyrosinase inhibition, with the bark of M. denticulata having the highest percentage of inhibition (68.7%). The bark and leaves of M. denticulata exhibited greater than 50% inhibition (73.82% and 54.50%, resp.) of the acetylcholinesterase enzyme (AChE), while none of the samples showed any significant inhibition of butyrylcholinesterase (BChE). Only the bark of M. denticulata and M. gigantea displayed greater than 50% inhibition of nitric oxide production in cells (81.79% and 56.51%, resp.). These bioactivities indicate that some Macaranga spp. have therapeutic potential in medicinal research.

Matched MeSH terms: Species Specificity
Fulltext Ants (Hymenoptera: Formicidae) associated with pig carcasses in Malaysia

Heo CC, Mohamad AR, Rosli H, Nurul Ashikin A, Chen CD, John J, et al.

Trop Biomed, 2009 Apr;26(1):106-9.
PMID: 19696735

An observational study was conducted in an oil palm plantation in Tanjung Sepat, Selangor, Malaysia on August until September 2007 to note the decomposition process of pigs and their related faunal succession. We collected six species of ants (Formicidae) from 3 subfamilies: Formicinae (Oecophylla smaragdina and Anoplolepis gracilipes), Myrmicinae (Tetramorium sp. and Pheidologeton sp.) and Ponerinae (Odontoponera sp. and Diacamma sp.) that were associated with pig carcasses placed on the ground. Oecophylla smaragdina, Pheidologeton sp. and Tetramorium sp. were found on a partially burnt pig carcass whereas the other species were recovered from unburned pig carcass. These ants predated on fly eggs, larvae, pupae and adults. Ants could be found at all stages of decomposition starting from fresh until dry stage. Predatory ants can reduce fly population and thus may affect the rate of carcass decomposition but this was not seen in our study. Even though O. smaragdina was seen at all stages of decomposition of the burnt pig, this did not alter much the decomposition process by fly larvae.

Matched MeSH terms: Species Specificity
Apoptosis in Blastocystis spp. is related to subtype

Dhurga DB, Suresh KG, Tan TC, Chandramathi S

Trans R Soc Trop Med Hyg, 2012 Dec;106(12):725-30.
PMID: 23141370 DOI: 10.1016/j.trstmh.2012.08.005

Previous studies have shown that apoptosis-like features are observed in Blastocystis spp., an intestinal protozoan parasite, when exposed to the cytotoxic drug metronidazole (MTZ). This study reports that among the four subtypes of Blastocystis spp. investigated for rate of apoptosis when treated with MTZ, subtype 3 showed the highest significant increase after 72h of in vitro culture when treated with MTZ at 0.1mg/ml (79%; p<0.01) and 0.0001mg/ml (89%; p<0.001). The close correlation between viable cells and apoptotic cells for both dosages implies that the pathogenic potential of these isolates has been enhanced when treated with MTZ. This suggests that there is a mechanism in Blastocystis spp. that actually regulates the apoptotic process to produce higher number of viable cells when treated. Apoptosis may not just be programmed cell death but instead a mechanism to increase the number of viable cells to ensure survival during stressed conditions. The findings of the present study have an important contribution to influence chemotherapeutic approaches when developing drugs against the emerging Blastocystis spp. infections.

Matched MeSH terms: Species Specificity
Application of multivariate statistical techniques for differentiation of ripe banana flour based on the composition of elements

Alkarkhi AF, Ramli SB, Easa AM

Int J Food Sci Nutr, 2009;60 Suppl 4:116-25.
PMID: 19115121 DOI: 10.1080/09637480802609368

Major (sodium, potassium, calcium, magnesium) and minor elements (iron, copper, zinc, manganese) and one heavy metal (lead) of Cavendish banana flour and Dream banana flour were determined, and data were analyzed using multivariate statistical techniques of factor analysis and discriminant analysis. Factor analysis yielded four factors explaining more than 81% of the total variance: the first factor explained 28.73%, comprising magnesium, sodium, and iron; the second factor explained 21.47%, comprising only manganese and copper; the third factor explained 15.66%, comprising zinc and lead; while the fourth factor explained 15.50%, comprising potassium. Discriminant analysis showed that magnesium and sodium exhibited a strong contribution in discriminating the two types of banana flour, affording 100% correct assignation. This study presents the usefulness of multivariate statistical techniques for analysis and interpretation of complex mineral content data from banana flour of different varieties.

Matched MeSH terms: Species Specificity
Fulltext Assessment of antiproliferative and antiplasmodial activities of five selected Apocynaceae species

Wong SK, Lim YY, Abdullah NR, Nordin FJ

BMC Complement Altern Med, 2011;11:3.
PMID: 21232161 DOI: 10.1186/1472-6882-11-3

Studies have shown that the barks and roots of some Apocynaceae species have anticancer and antimalarial properties. In this study, leaf extracts of five selected species of Apocynaceae used in traditional medicine (Alstonia angustiloba, Calotropis gigantea, Dyera costulata, Kopsia fruticosa and Vallaris glabra) were assessed for antiproliferative (APF) and antiplasmodial (APM) activities, and analysed for total alkaloid content (TAC), total phenolic content (TPC) and radical-scavenging activity (RSA). As V. glabra leaf extracts showed wide spectrum APF and APM activities, they were further screened for saponins, tannins, cardenolides and terpenoids.

Matched MeSH terms: Species Specificity
Assessment of articular cartilage and subchondral bone using EPIC-microCT in Labrador retrievers with incipient medial coronoid disease

Lau SF, Wolschrijn CF, Siebelt M, Vernooij JC, Voorhout G, Hazewinkel HA

Vet J, 2013 Oct;198(1):116-21.
PMID: 23846028 DOI: 10.1016/j.tvjl.2013.05.038

The aetiopathogenesis of medial coronoid disease (MCD) remains obscure, despite its high prevalence. The role of changes to subchondral bone or articular cartilage is much debated. Although there is evidence of micro-damage to subchondral bone, it is not known whether this is a cause or a consequence of MCD, nor is it known whether articular cartilage is modified in the early stages of the disease. The aim of the present study was to use equilibrium partitioning of an ionic contrast agent with micro-computed tomography (microCT) to investigate changes to both the articular cartilage and the subchondral bone of the medial coronoid processes (MCP) of growing Labrador retrievers at an early stage of the disease and at different bodyweights. Of 14 purpose-bred Labrador retrievers (15-27 weeks), six were diagnosed with bilateral MCD and one was diagnosed with unilateral MCD on the basis of microCT studies. The mean X-ray attenuation of articular cartilage was significantly higher in dogs with MCD than in dogs without MCD (P<0.01). In all dogs, the mean X-ray attenuation of articular cartilage was significantly higher at the lateral (P<0.001) than at the proximal aspect of the MCP, indicating decreased glycosaminoglycan content. Changes in parameters of subchondral bone micro-architecture, namely the ratio of bone volume to tissue volume (BV/TV), bone surface density (BS/TV), bone surface to volume ratio (BS/BV), trabecular thickness (Tb.Th; mm), size of marrow cavities described by trabecular spacing (Tb.Sp; mm), and structural model index (SMI), differed significantly by litter (P<0.05) due to the difference in age and weight, but not by the presence/absence of MCD (P>0.05), indicating that subchondral bone density is not affected in early MCD. This study demonstrated that cartilage matrix and not subchondral bone density is affected in the early stages of MCD.

Matched MeSH terms: Species Specificity
Fulltext Association of some Campylobacter jejuni with Pseudomonas aeruginosa biofilms increases attachment under conditions mimicking those in the environment

Teh AHT, Lee SM, Dykes GA

PLoS One, 2019;14(4):e0215275.
PMID: 30970009 DOI: 10.1371/journal.pone.0215275

Campylobacter jejuni is a microaerophilic bacterial species which is a major food-borne pathogen worldwide. Attachment and biofilm formation have been suggested to contribute to the survival of this fastidious bacteria in the environment. In this study the attachment of three C. jejuni strains (C. jejuni strains 2868 and 2871 isolated from poultry and ATCC 33291) to different abiotic surfaces (stainless steel, glass and polystyrene) alone or with Pseudomonas aeruginosa biofilms on them, in air at 25°C and under static or flow conditions, were investigated using a modified Robbins Device. Bacteria were enumerated and scanning electron microscopy was carried out. The results indicated that both C. jejuni strains isolated from poultry attached better to Pseudomonas aeruginosa biofilms on abiotic surfaces than to the surfaces alone under the different conditions tested. This suggests that biofilms of other bacterial species may passively protect C. jejuni against shear forces and potentially oxygen stress which then contribute to their persistence in environments which are detrimental to them. By contrast the C. jejuni ATCC 33291 strain did not attach differentially to P. aeruginosa biofilms, suggesting that different C. jejuni strains may have alternative strategies for persistence in the environment. This study supports the hypothesis that C. jejuni do not form biofilms per se under conditions they encounter in the environment but simply attach to surfaces or biofilms of other species.

Matched MeSH terms: Species Specificity
Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin

Hendrickson WA, Ward KB

Biochem Biophys Res Commun, 1975 Oct 27;66(4):1349-56.
PMID: 5
Matched MeSH terms: Species Specificity
Attenuation of virulence of flaviviruses following passage in HeLa cells

Dunster LM, Gibson CA, Stephenson JR, Minor PD, Barrett AD

J Gen Virol, 1990 Mar;71 ( Pt 3):601-7.
PMID: 2155996

The ability of passage in HeLa cells to attenuate flaviviruses was investigated for three different strains of the mosquito-borne West Nile (WN) virus and two tick-borne viruses, louping-ill and Langat. One strain of WN virus, Sarawak, was attenuated 4000-fold for adult mice by intraperitoneal or intranasal challenge after six HeLa passages. The HeLa-passaged virus was also found to be antigenically different and temperature-sensitive in its growth characteristics compared with the parent. After six HeLa cell passages the Egypt 101 and Smithburn strains of WN virus lost their ability to infect monkey kidney cells and no longer killed adult mice, although inoculated animals became sick for several days. In contrast, two tick-borne flaviviruses remained as virulent for mice after six HeLa passages as the parent non-HeLa-passaged virus. Neither of the tick-borne viruses exhibited characteristics associated with temperature sensitivity. The results, therefore, indicate that the mosquito-borne, but not tick-borne, flaviviruses can be attenuated by very few passages in HeLa cells. This observation may provide a model system with which to analyse the molecular basis of attenuation and/or virulence of mosquito-borne flaviviruses.

Matched MeSH terms: Species Specificity
B-cell development: one problem, multiple solutions

Alitheen NB, McClure S, McCullagh P

Immunol Cell Biol, 2010 01 19;88(4):445-50.
PMID: 20084079 DOI: 10.1038/icb.2009.119

Interspecies variations in the processes of B-cell development and repertoire generation contrast with the greater consistency of T-cell development. B-cell development in mice and humans, with postnatal B-cell generation of new repertoire in the bone marrow throughout life, is regarded as the 'standard' pattern. In contrast, accounts of B cells in birds, sheep, cattle, rabbits and pigs (the 'other' species) describe cessation of gene diversification in the perinatal period, with the gut-associated lymphoid tissue (GALT) functioning as the primary lymphoid organ thereafter. It has become customary to regard the developmental pathways of T and B cells within any individual species as being as dissimilar as the functions of the two mature cell types. Reinterpretation of B-cell development patterns in different species is overdue in response to two types of reports. The first of these describe T-B 'crossover', specifically the intrathymic production of B cells and the extrathymic production of T cells. The second attests to the extent of sharing of B-cell developmental features across the two groups of species. We propose that, as is a feature of other haematopoietic cells, a menu of alternative B- and T-cell pathways has been retained and shared across species. A single pathway usually predominates in any species, masking alternatives. The observed predominance of any pathway is determined by factors such as placental permeability, extent of maturation of the immune system by birth and the feasibility of direct experimental intervention in development.

Matched MeSH terms: Species Specificity
Bacterial communities in Haemaphysalis, Dermacentor and Amblyomma ticks collected from wild boar of an Orang Asli Community in Malaysia

Lim FS, Khoo JJ, Tan KK, Zainal N, Loong SK, Khor CS, et al.

Ticks Tick Borne Dis, 2020 03;11(2):101352.
PMID: 31866439 DOI: 10.1016/j.ttbdis.2019.101352

Ticks are hematophagous vectors of arthropod-borne disease agents globally. In Malaysia, despite seroprevalence studies indicating the presence of tick-borne diseases among the indigenous people, the etiological agents of these diseases are still unclear. These indigenous people, also known as the Orang Asli, still live in forested areas with frequent contact with wildlife. Wild boar are ubiquitously found in the forested areas where the Orang Asli communities are located and are commonly hunted as a food supplement. In this study, we aim to determine the tick species parasitizing wild boar from an Orang Asli community, and explore the tick-associated bacterial communities using 16 s rRNA amplicon sequencing on the Ion Torrent PGM™ platform. A total of 72 ticks were collected from three wild boar and were morphologically identified as Haemaphysalis hystricis (n = 32), Dermacentor compactus (n = 15), Amblyomma testudinarium (n = 13), Dermacentor steini (n = 10) and Dermacentor atrosignatus (n = 2). Across all tick samples, 910 bacterial taxa were identified. Although the bacterial communities were not significantly distinct between tick species in beta-diversity analyses, Coxiella, Rickettsia and Francisella were detected at high relative abundance in H. hystricis, D. compactus and D. steini respectively. Many other bacterial genera, including those that have been described in many different tick species, were also identified, including Pseudomonas, Acinetobacter, Staphylococcus and Corynebacterium. Beta-diversity analyses also showed that the bacterial communities were separated based on the animal host from which the ticks were collected from, suggesting that the bacterial communities here may be influenced by the animal skin microflora, host blood or the environment. PCR screening confirmed the presence of Rickettsia sp. related to spotted fever group Rickettsia in some of the ticks. This study provides baseline knowledge of the microbiome of H. hystricis, D. atrosignatus, D. compactus, D. steini and A. testudinarium parasitizing wild boar in this region. The information gained in this study provides the basis to target our efforts in H. hystricis, D. compactus and D. steini for the future investigation of vector competence and the zoonotic potential for the Coxiella, Rickettsia and Francisella detected here, as well as their implications for the risks of tick-borne diseases among the Orang Asli communities.

Matched MeSH terms: Species Specificity

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