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Phylogenetic relationships, morphological variation, and toxin patterns in the Alexandrium ostenfeldii (Dinophyceae) complex: implications for species boundaries and identities

Kremp A, Tahvanainen P, Litaker W, Krock B, Suikkanen S, Leaw CP, et al.

J Phycol, 2014 Feb;50(1):81-100.
PMID: 26988010 DOI: 10.1111/jpy.12134

Alexandrium ostenfeldii (Paulsen) Balech and Tangen and A. peruvianum (Balech and B.R. Mendiola) Balech and Tangen are morphologically closely related dinoflagellates known to produce potent neurotoxins. Together with Gonyaulax dimorpha Biecheler, they constitute the A. ostenfeldii species complex. Due to the subtle differences in the morphological characters used to differentiate these species, unambiguous species identification has proven problematic. To better understand the species boundaries within the A. ostenfeldii complex we compared rDNA data, morphometric characters and toxin profiles of multiple cultured isolates from different geographic regions. Phylogenetic analysis of rDNA sequences from cultures characterized as A. ostenfeldii or A. peruvianum formed a monophyletic clade consisting of six distinct groups. Each group examined contained strains morphologically identified as either A. ostenfeldii or A. peruvianum. Though key morphological characters were generally found to be highly variable and not consistently distributed, selected plate features and toxin profiles differed significantly among phylogenetic clusters. Additional sequence analyses revealed a lack of compensatory base changes in ITS2 rRNA structure, low to intermediate ITS/5.8S uncorrected genetic distances, and evidence of reticulation. Together these data (criteria currently used for species delineation in dinoflagellates) imply that the A. ostenfeldii complex should be regarded a single genetically structured species until more material and alternative criteria for species delimitation are available. Consequently, we propose that A. peruvianum is a heterotypic synonym of A. ostenfeldii and this taxon name should be discontinued.

Matched MeSH terms: Sequence Analysis
Fulltext InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia

Schönbach C, Tan TW, Kelso J, Rost B, Nathan S, Ranganathan S

BMC Genomics, 2011 Nov 30;12 Suppl 3:S1.
PMID: 22369160 DOI: 10.1186/1471-2164-12-S3-S1

In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.

Matched MeSH terms: Sequence Analysis, DNA
Genetic analysis of saffold virus-Penang in relation to other newly discovered saffold viruses

Voon K, Ng QM, Yu M, Wang LF, Chua KB

Southeast Asian J. Trop. Med. Public Health, 2012 Jul;43(4):917-26.
PMID: 23077814

Viruses in the family Picornaviridae are classified into nine genera. Within the family Picornaviridae, two species: Encephalomyocarditis virus and Theilovirus, are listed under the genus Cardiovirus. A novel Theilovirus, Saffold virus (SAFV), was first reported in 2007. Since then, numerous SAFV isolates have been detected around the world and genetic recombinations have been reported among them. In 2009, SAFV-Penang was isolated from a febrile child with influenza-like illness in Malaysia. SAFV-Penang is a genotype 3 SAFV. In this study we investigated the genome features of SAFV-Penang to exclude the possibility it is a recombinant variant. SAFV-Penang was found not to be a recombinant variant but to have three unique non-synonymous substitutions, alanine [A689], lysine [K708] and isoleucine [I724] in the VP1 protein.

Matched MeSH terms: Sequence Analysis, DNA
TRANSCRIPTOMIC ANALYSIS OF GRACILARIA CHANGII (RHODOPHYTA) IN RESPONSE TO HYPER- AND HYPOOSMOTIC STRESSES(1)

Teo SS, Ho CL, Teoh S, Rahim RA, Phang SM

J Phycol, 2009 Oct;45(5):1093-9.
PMID: 27032354 DOI: 10.1111/j.1529-8817.2009.00724.x

Osmotic stress is one of the most significant natural abiotic stresses that occur in the intertidal zones. Seaweeds may physiologically acclimate to changing osmolarity by altering their transcriptome. Here, we investigated the transcriptomic changes of Gracilaria changii (B. M. Xia et I. A. Abbott) I. A. Abbott, J. Zhang et B. M. Xia in response to hyper- and hypoosmotic stresses using a cDNA microarray approach. Microarray analysis revealed that 199 and 200 genes from ∼3,300 genes examined were up- and down-regulated by >2-fold in seaweed samples treated at 50 parts per thousand (ppt) artificial seawater (ASW) compared with those at 30 ppt ASW, respectively. The number of genes that were up- and down-regulated by >2-fold in seaweed samples treated at 10 ppt ASW compared with those at 30 ppt ASW were 154 and 187, respectively. A majority of these genes were only differentially expressed under hyper- or hypoosmotic conditions, whereas 67 transcripts were affected by both stresses. The findings of this study have shed light on the expression profiles of many transcripts during the acclimation of G. changii to hyperosmotic and hypoosmotic conditions. This information may assist in the prioritization of genes to be examined in future studies.

Matched MeSH terms: Oligonucleotide Array Sequence Analysis
Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing

Thai BT, Tan MH, Lee YP, Gan HM, Tran TT, Austin CM

Mol Biol Rep, 2016 May;43(5):391-6.
PMID: 26922181 DOI: 10.1007/s11033-016-3966-2

The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.

Matched MeSH terms: Sequence Analysis, DNA
Fulltext In vitro properties of designed antimicrobial peptides that exhibit potent antipneumococcal activity and produces synergism in combination with penicillin

Le CF, Yusof MY, Hassan H, Sekaran SD

Sci Rep, 2015;5:9761.
PMID: 25985150 DOI: 10.1038/srep09761

Antimicrobial peptides (AMPs) represent a promising class of novel antimicrobial agents owing to their potent antimicrobial activity. In this study, two lead peptides from unrelated classes of AMPs were systematically hybridized into a series of five hybrid peptides (DM1-DM5) with conserved N- and C-termini. This approach allows sequence bridging of two highly dissimilar AMPs and enables sequence-activity relationship be detailed down to single amino acid level. Presence of specific amino acids and physicochemical properties were used to describe the antipneumococcal activity of these hybrids. Results obtained suggested that cell wall and/or membrane targeting could be the principal mechanism exerted by the hybrids leading to microbial cell killing. Moreover, the pneumocidal rate was greater than penicillin (PEN). Combination treatment with both DMs and PEN produced synergism. The hybrids were also broad spectrum against multiple common clinical bacteria. Sequence analysis showed that presence of specific residues has a major role in affecting the antimicrobial and cell toxicity of the hybrids than physicochemical properties. Future studies should continue to investigate the mechanisms of actions, in vivo therapeutic potential, and improve rational peptide design based on the current strategy.

Matched MeSH terms: Sequence Analysis
Complete mitochondrial genomes of the tooth of a poached Bornean banteng (Bos javanicus lowi; Cetartiodactyla, Bovidae)

Ishige T, Gakuhari T, Hanzawa K, Kono T, Sunjoto I, Sukor JR, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 Jul;27(4):2453-4.
PMID: 26075477 DOI: 10.3109/19401736.2015.1033694

Here we report the complete mitochondrial genome of the Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae), which was determined using next-generation sequencing. The mitochondrial genome is 16,344 bp in length containing 13 protein-coding genes, 21 tRNAs and 2 rRNAs. It shows the typical pattern of bovine mitochondrial arrangement. Phylogenetic tree analysis of complete mtDNA sequences showed that Bornean banteng is more closely related to gaur than to other banteng subspecies. Divergence dating indicated that Bornean banteng and gaur diverged from their common ancestor approximately 5.03 million years ago. These results suggest that Bornean banteng might be a distinct species in need of conservation.

Matched MeSH terms: Sequence Analysis, DNA
Fulltext Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)

Liedigk R, Kolleck J, Böker KO, Meijaard E, Md-Zain BM, Abdul-Latiff MA, et al.

BMC Genomics, 2015 Mar 21;16:222.
PMID: 25887664 DOI: 10.1186/s12864-015-1437-0

BACKGROUND: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon's range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.
RESULTS: Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.
CONCLUSIONS: Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.

Matched MeSH terms: Sequence Analysis, DNA
Molecular cloning and sequence analysis of a cDNA encoding ornithine decarboxylase cDNA from chilli (Capsicum annuum)

Zainal Z, Sajari R, Ismail I

J. Biochem. Mol. Biol. Biophys., 2002 Dec;6(6):415-9.
PMID: 14972797

Ornithine decarboxylase (ODC) is an enzyme of one of the two pathways of putrescine biosynthesis in plants. The genes encoding ODC have previously been cloned from Datura stramonium and human. Using differential screening, we isolated ODC cDNA clone from a cDNA library of ripening Capsicum annuum fruit. The cDNA clone designated CUKM10 contains an insert of 1523 bp. The longest open reading frame potentially encodes a peptide of 345 amino acids with an estimated molecular mass of 47 kDa and exhibit striking similarity to other ODCs. Expression analysis showed that the capODC hybridised to a single transcript with a size of 1.7 kb. The capODC transcript was first observed in early ripening and increased steadily until it reached fully ripening stage. From the observation it is suggested that capODC is developmentally regulated especially during later stage of ripening.

Matched MeSH terms: Sequence Analysis, DNA/methods*; Sequence Analysis, Protein/methods*
Fulltext Hepatitis C virus genotyping methods: evaluation of AmpliSens(®) HCV-1/2/3-FRT compared to sequencing method

Mohamed NA, Rashid ZZ, Wong KK

J Clin Lab Anal, 2014 May;28(3):224-8.
PMID: 24478138 DOI: 10.1002/jcla.21670

BACKGROUND: Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective of this study was to evaluate the performance of AmpliSens(®) HCV-1/2/3-FRT kit in comparison to sequencing method for genotyping.
METHODS: A total of 17 samples collected from December 2009 to January 2011 were analyzed. Reverse transcriptase polymerase chain reaction (PCR) was performed, followed by sequencing technique. Results were analyzed based on sequence information in GenBank. A second genotyping method (AmpliSens(®) HCV-1/2/3-FRT) was done, which differentiates HCV genotypes by means of real-time hybridization-fluorescence detection.
RESULTS: From 17 samples, four were untypeable by AmpliSens(®) HCV-1/2/3-FRT. Eleven of 13 (84.6%) results showed concordant genotypes. A specimen that was determined as genotype 3a by sequencing was genotype 1 by the AmpliSens(®) HCV-1/2/3-FRT. Another specimen that was genotype 1 by sequencing was identified as genotype 3 by AmpliSens(®) HCV-1/2/3-FRT.
CONCLUSION: HCV genotyping with AmpliSens(®) HCV-1/2/3-FRT using real-time PCR method provides a much simpler and more feasible workflow with shorter time compared to sequencing method. There was good concordance compared to sequencing method. However, more evaluation studies would be required to show statistical significance, and to troubleshoot discordant results. AmpliSens(®) HCV-1/2/3-FRT does differentiate between genotype but not until subtype level.

Matched MeSH terms: Sequence Analysis, RNA
Occurrence of zoonotic Cryptosporidium and Giardia duodenalis species/genotypes in urban rodents

Tan TK, Low VL, Ng WH, Ibrahim J, Wang D, Tan CH, et al.

Parasitol Int, 2019 Apr;69:110-113.
PMID: 30590124 DOI: 10.1016/j.parint.2018.12.007

This report describes the detection of zoonotic Cryptosporidium muris, C. parvum subgenotype IIa and Giardia duodenalis genotype B in urban rodents in Malaysia. A rare occurrence of C. meleagridis was also reported suggesting a role of rodents in mechanical transmission of this pathogen. Utilization of DNA sequencing and subtyping analysis confirmed the presence of zoonotic C. parvum subtypes IIaA17G2R1 and IIaA16G3R1 for the first time in rodents.

Matched MeSH terms: Sequence Analysis, DNA
Presbytis neglectus or P. femoralis, Colobine Molecular Phylogenies, and GenBank Submission of Newly Generated DNA Sequences

Nijman V

Folia Primatol., 2020;91(3):228-239.
PMID: 31578029 DOI: 10.1159/000502093

Great progress has been made in unravelling the evolutionary history of Asian colobines, largely through the use of dated molecular phylogenies based on multiple markers. The Presbytis langurs are a case in point, with more allopatric species being identified, recognition of Presbytis thomasi from Sumatra rather than P. potenziani from the Mentawai Islands as being the most basal species of the group, and the discovery that P. rubicunda from Borneo is nested among the Sumatran species and only made it to Borneo in the last 1.3 million years. Based on variation in mitochondrial d-loop, it has recently been argued that Malaysia's P. femoralis femoralis is actually P. neglectus neglectus. Unfortunately, despite being available, sequences from the type locality, Singapore, were excluded from the analysis, and none of the newly generated sequences was deposited in GenBank. I manually reconstructed these sequences, which allowed me to present a molecular phylogeny that includes 8 additional sequences from West Malaysia and Singapore. P. neglectus from Malaysia and P. femoralis from Singapore form one monophyletic clade, with minimal divergence. I conclude that recognition of P. neglectus is erroneous and the name is a junior synonym of P. femoralis. Colobine taxonomy and systematics have advanced, and continue to advance, mostly by considering evidence from a wide range of individuals, species and data sets (molecular, behavioural and morphological) rather than focusing on single molecular markers from 1 or 2 species from one small geographic area. For an orderly taxonomic debate where evidence can be evaluated and reinterpreted it is essential that newly generated sequences are deposited in public repositories.

Matched MeSH terms: Sequence Analysis, DNA
Fulltext Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo

Geml J, Morgado LN, Semenova-Nelsen TA, Schilthuizen M

New Phytol, 2017 Jul;215(1):454-468.
PMID: 28401981 DOI: 10.1111/nph.14566

The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges. We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect). Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model. We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect.

Matched MeSH terms: Sequence Analysis, DNA
Fulltext Pathogenic mutations in ARX, CDKL5and STXBP1genes are not associated with the early-onset epileptic encephalopathy in Malaysian pediatricpatients: A pilot study

Ameerah Jaafar, Feizel Alsiddiq, Ling, King-Hwa

Neuroscience Research Notes, 2018;1(3):5-17.
MyJurnal

Gene mutation is one of the etiologies of early-onset epileptic encephalopathy (EOEE), an age-dependent seizure in infants, which leads to brain defects. Previous studies have shown that several genes namely, aristalessrelated homeobox (ARX), cyclindependent kinaselike 5 (CDKL5) and syntaxinbinding protein 1 (STXBP1) are responsible for the pathophysiology of the syndrome. Thestudy involved 20 EOEE patients and 60 control subjects, which aimed toinvestigatethe clinical association of Malaysian EOEE subjects with 13 known pathogenic mutations in the genes of interest. In addition, the entire ARX exonic region was also sequenced for known and novel mutations. PCR specificity and efficiency were optimized using conventional PCR and High Resolution Melting Analysis (HRMA). All cases and approximately 10% of control amplicon samples were purified and subjected to DNA sequencing. All known mutations reported previously were not found in control subjects and Malaysian EOEE patients with 100% confirmation by sequencing results. Sequencing of ARX exonic regionsof patient samplesdid not find any mutation in all exons. The preliminary study indicates that selected known pathogenic mutations of ARX, CDKL5and STXBP1are not associated with EOEE in Malaysian paediatric patients.

Matched MeSH terms: Sequence Analysis, DNA
Enhanced secretion of cyclodextrin glucanotransferase (CGTase) by Lactococcus lactis using heterologous signal peptides and optimization of cultivation conditions

Mahmud H, Ismail A, Abdul Rahim R, Low KO, Md Illias R

J Biotechnol, 2019 Apr 20;296:22-31.
PMID: 30878516 DOI: 10.1016/j.jbiotec.2019.02.013

In previous studies of Lactococcus lactis, the levels of proteins secreted using heterologous signal peptides were observed to be lower than those obtained using the signal peptide from Usp45, the major secreted lactococcal protein. In this study, G1 (the native signal peptide of CGTase) and the signal peptide M5 (mutant of the G1 signal peptide) were introduced into L. lactis to investigate the effect of signal peptides on lactococcal protein secretion to improve secretion efficiency. The effectiveness of these signal peptides were compared to the Usp45 signal peptide. The highest secretion levels were obtained using the G1 signal peptide. Sequence analysis of signal peptide amino acids revealed that a basic N-terminal signal peptide is not absolutely required for efficient protein export in L. lactis. Moreover, the introduction of a helix-breaking residue in the H-region of the M5 signal peptide caused a reduction in the signal peptide hydrophobicity and decreased protein secretion. In addition, the optimization of cultivation conditions for recombinant G1-CGTase production via response surface methodology (RSM) showed that CGTase activity increased approximately 2.92-fold from 5.01 to 16.89 U/ml compared to the unoptimized conditions.

Matched MeSH terms: Sequence Analysis
Fulltext Cloning and expression of a subfamily 1.4 lipase from Bacillus licheniformis IBRL-CHS2

Reddy, Nidyaletchmy Subba, Rashidah Abdul Rahim, Darah Ibrahim, Kumar, K. Sudesh

Trop Life Sci Res, 2016;27(11):145-150.
MyJurnal

We report on the cloning of the lipase gene from Bacillus licheniformis IBRLCHS2
and the expression of the recombinant lipase. DNA sequencing analysis of the
cloned lipase gene showed that it shares 99% identity with the lipase gene from
B. licheniformis ATCC 14580 and belongs to subfamily 1.4 of true lipases based on amino
acid sequence alignment of various Bacillus lipases. The 612 bp lipase gene was then
cloned into the pET-15b(+) expression vector and the construct was transformed into
E. coli BL21 (DE3) for bulk expression of the lipase. Expression was analysed by SDSPAGE
where the lipase was found to have a molecular weight of about 23 kDa.

Matched MeSH terms: Sequence Analysis, DNA
Fulltext Psychrophilic lipase from arctic bacterium

Zakiah Ramle, Rashidah Abdul Rahim

Trop Life Sci Res, 2016;27(11):151-157.
MyJurnal

A lipase producer psychrophilic microorganism isolated from Arctic sample was
studied. The genomic DNA of the isolate was extracted using modified CTAB method.
Identification of the isolate by morphological and 16S rRNA sequence analysis revealed
that the isolate is closely related to Arthrobacter gangotriensis (97% similarity).
A. gangotriensis was determined as positive lipase producer based on the plate screening
using specific and sensitive plate assay of Rhodamine B. The PCR result using
Arthrobacter sp.’s full lipase gene sequence as the template primers emphasised a
possible lipase gene at 900 bp band size. The gene is further cloned in a suitable vector
system for expression of lipase.

Matched MeSH terms: Sequence Analysis
Surface plasmon resonance biosensor for real-time detection of genetically modified organisms

Yoke-Kqueen, C., Son, R.

International Food Research Journal, 2010;17(2):477-483.
MyJurnal

Application of surface plasmon resonance (SPR) biosensor in detection of genetically modified organism (GMO) is demonstrated. A total of four biotinylated probes namely Tnosb, P35Sb, LECb and TSQb were successfully immobilized onto the SA chip. Results analysis indicated that the SPR system with the sensor chip immobilized with the Tnosb, P35Sb, LECb and TSQb biotinylated probes potentially detect complementary standard fragments as low as 1 nM. Biospecific interaction analysis (BIA), employing surface plasmon resonance (SPR) and biosensor technologies provide easy, rapid and automatable approach in detection of GMOs. Short assay times, label free DNA hybridization reaction and no toxic compounds are required, i.e. ethidium bromide, and the reusability of the sensor surface are some of the factors that contribute to the general advantages of the surface plasmon resonance (SPR) biosensor system in detection of GMOs.

Matched MeSH terms: Oligonucleotide Array Sequence Analysis
Systematics of the combtooth blenny clade Omobranchus (Blenniidae: Omobranchini), with notes on early life history stages

Gibbs S, Hundt PJ, Nelson A, Egan JP, Tongnunui P, Simons AM

Zootaxa, 2018 Jan 03;4369(2):270-280.
PMID: 29689891 DOI: 10.11646/zootaxa.4369.2.7

The combtooth blenny (Blenniidae) genus Omobranchus contains small, cryptobenthic fishes common to nearshore habitats throughout the Indo-West Pacific. Recent molecular systematic studies have resolved Omobranchus as monophyletic but little research has been done to resolve species-level relationships. Herein, phylogenetic analyses of one mitochondrial (CO1) and four nuclear (ENC1, myh6, sreb2, and tbr1) genes provide evidence for the monophyly of Omobranchus and support for the elongatus and banditus species group. Sampling of multiple individuals from widespread species (O. ferox, O. punctatus, and O. elongatus) suggested that the Thai-Malay Peninsula is a phylogeographic break that may be a historic barrier to gene flow. Additionally, common meristics and other morphological characters are used to describe an early life history stage of O. ferox and O. punctatus.

Matched MeSH terms: Sequence Analysis, DNA
End of an enigma: Aenigmopteris belongs in Tectaria (Tectariaceae: Polypodiopsida)

Chen CW, Rothfels CJ, Mustapeng AMA, Gubilil M, Karger DN, Kessler M, et al.

J Plant Res, 2018 Jan;131(1):67-76.
PMID: 28741041 DOI: 10.1007/s10265-017-0966-9

The phylogenetic affinities of the fern genus Aenigmopteris have been the subject of considerable disagreement, but until now, no molecular data were available from the genus. Based on the analysis of three chloroplast DNA regions (rbcL, rps16-matK, and trnL-F) we demonstrate that Aenigmopteris dubia (the type species of the genus) and A. elegans are closely related and deeply imbedded in Tectaria. The other three species of genus are morphologically very similar; we therefore transfer all five known species into Tectaria. Detailed morphological comparison further shows that previously proposed diagnostic characters of Aenigmopteris fall within the range of variation of a broadly circumscribed Tectaria.

Matched MeSH terms: Sequence Analysis, DNA

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