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Fulltext Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus

Spence RJ, Noune C, Hauxwell C

Genome Announc, 2016 Jun 30;4(3).
PMID: 27365355 DOI: 10.1128/genomeA.00633-16

Granuloviruses are widespread pathogens of Plutella xylostella L. (diamondback moth) and potential biopesticides for control of this global insect pest. We report the complete genomes of four Plutella xylostella granulovirus isolates from China, Malaysia, and Taiwan exhibiting pairs of noncoding, homologous repeat regions with significant sequence variation but equivalent length.
Fulltext Can Tumour Volume Percentage in Radical Prostatectomy Predict Cancer Biochemical Recurrence? Determining a Cut-off Point and Composite Risk Factors Approach

Alenezi A, Ismail M, Eden C

Res Rep Urol, 2021;13:445-455.
PMID: 34235101 DOI: 10.2147/RRU.S313455

BACKGROUND: Incidence of biochemical recurrence (BCR) after radical prostatectomy is relatively high and overall survival can be poor. Debate exists whether tumour volume predicts BCR and when treatments should be administered. In this study, we aimed to i) assess the impact of tumour volume percentage (TVP) as a predictor for BCR, ii) determine TVP cut-off point for BCR and iii) evaluate single and composite predictors of BCR.
METHODS: From March 2000 to December 2013, 1777 patients underwent laparoscopic radical prostatectomy for localized prostate cancer. None received neoadjuvant or adjuvant therapy. One hundred and forty-six patients experienced BCR (range 3 months-10 years). Using D'Amico classification, 146 matched controls without BCR were compared. Liu cut-point analysis was used to identify TVP with optimal sensitivity and specificity. Single and composite BCR risk predictors were analyzed using Cox hazards regression in cases and controls.
RESULTS: Median TVP was 10% (range 1-90%). Most of BCR peaked after 3 years of follow-up. TVP ≥8% was an independent predictor of BCR with HR 1.6 (p= 0.001, 95% CI= 1.11-2.48). TVP of 8% was associated with the highest accuracy: sensitivity 74% and specificity 53% (ROC curve= 0.7). At TVP ≥8%, pathological stage pT3 was associated with 1.7-fold higher risk of BCR compared to T2. Lymph node invasion was associated with 1.4-fold higher risk of BCR compared to no invasion. Combining TVP ≥8%, pT3 and lymph node invasion, HR jumped to 3.73 (p< 0.001, 95% CI= 2.27-6.14), whereas combining TVP ≥8%, positive surgical margin and lymph node invasion, HR was 2.68 (p= 001, 95% CI= 1.50-4.77).
CONCLUSION: TVP can be used as an independent predictor of BCR after radical prostatectomy for prostate cancer. TVP cut-point of ≥8% allows the best discrimination. TVP should be considered in combination with other clinico-pathological factors to improve prediction of long-term oncological outcomes and to stratify BCR risk.
Application of multilocus sequence analysis for molecular characterization of enterococci with virulence factors recovered from a tropical recreational beach

Ahmad A, Dada AC, Usup G

Southeast Asian J Trop Med Public Health, 2014 May;45(3):700-18.
PMID: 24974655

Partial gene sequences of phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA) were evaluated for species delineation and detection of recombination among enterococci populations recovered from a bathing beach impacted by low tide river flow. At inter-species level, a maximum similarity of 86.5% and 94.8% was observed among the enterococci pheS and rpoA sequence, respectively. A superimposed plot of delimited pairwise similarity values obtained for 266 pair-wise observations revealed that while there was a harmony between species identity obtained from both genes, pheS was more discriminatory than rpoA. The difference was more pronounced for inter-species comparison. A number of putative recombination events between indigenous and non-indigenous strains was detected based on a library of aligned sequences. Virulence genes cyl, esp, gelE and asa were detected in 7, 22, 100 and 63%, respectively among river isolates but at lower proportion of 0, 20, 67 and 42%, respectively among beach water isolates. Random amplified polymorphic DNA profiling presented evidence suggesting low tide river as a source of fecal enterococci entering the recreation beach water. Multilocus sequence typing analysis of a number of Enterococcus faecalis isolates presented four sequence types, ST59, 117, 181 and 474. The presence of genetically diverse fecal enterococci with associated virulence traits and a background of recombination events in surface recreational water could present a potential public health risk.
Fulltext Alum irrigation for the treatment of intractable haematuria

Ho CC, Md Zainuddin Z

Malays J Med Sci, 2009 Oct;16(4):66-8.
PMID: 22135514 MyJurnal

Managing intractable haematuria is a daunting task. One cause of this condition is radiationinduced haemorrhagic cystitis. Several treatments for the condition have been proposed and one non-invasive option is alum irrigation. Here, we report on a 65-year-old woman with intractable haematuria secondary to radiation cystitis who was successfully treated with alum irrigation. Alum irrigation is safe, well tolerated and relatively cheap. A review of the literature and a comprehensive discussion on alum irrigation as treatment for haematuria is discussed here to create an awareness regarding this treatment option.
Governance and networks for health co-benefits of climate change mitigation: Lessons from two Indian cities

Puppim de Oliveira JA, Doll CN

Environ Int, 2016 12;97:146-154.
PMID: 27665118 DOI: 10.1016/j.envint.2016.08.020

Health has been the main driver for many urban environmental interventions, particularly in cases of significant health problems linked to poor urban environmental conditions. This paper examines empirically the links between climate change mitigation and health in urban areas, when health is the main driver for improvements. The paper aims to understand how systems of urban governance can enable or prevent the creation of health outcomes via continuous improvements in the environmental conditions in a city. The research draws on cases from two Indian cities where initiatives were undertaken in different sectors: Surat (waste) and Delhi (transportation). Using the literature on network effectiveness as an analytical framework, the paper compares the cases to identify the possible ways to strengthen the governance and policy making process in the urban system so that each intervention can intentionally realize multiple impacts for both local health and climate change mitigation in the long term as well as factors that may pose a threat to long-term progress and revert back to the previous situation after initial achievements.
Differential effects of activated protein C on synovial fibroblasts in response to hypoxia and normoxia

Park YG, Choi J, Song I, Park SY, Seol JW, Jackson CJ

Sains Malaysiana, 2017;46:1895-1902.

Rheumatoid arthritis (RA) is a chronic disease characterized by inflammation of the joints and their lining or synovium. Previous studies showed that the synovium in RA patients is more hypoxic than normal synovium. Activated protein C (APC) has anticoagulant and anti-inflammatory effects and is highly expressed in the joints of RA patients. We examined the effect of APC on RA and normal synovial fibroblasts under hypoxic conditions. Human synovial fibroblasts were isolated from the synovial tissues of RA patients and normal controls and cells were exposed to recombinant APC under normoxic (21% oxygen) or hypoxic (1% oxygen) conditions. Cell proliferation was measured using MTT assays. Cell lysates and conditioned media were collected and assayed for matrix metalloproteinase (MMP)-2, MMP-9 and p38 using zymography and western blots. Proliferation of both normal and RA synovial fibroblasts dose-dependently increased after APC treatment in normoxic conditions. Under hypoxia, APC enhanced RA cell proliferation but had no effect on normal fibroblasts. MMP-2 production and activation were significantly augmented by APC in both cell types under normoxia and hypoxia conditions. However, activated MMP-2 was more reduced in cells under hypoxia than normoxia. APC substantially reduced the phosphorylation of p38 in normal and RA synovial fibroblasts under hypoxia. No difference in p38 phosphorylation was observed under normoxia. The receptor for APC, endothelial protein C receptor (EPCR), was elevated in normal fibroblasts under hypoxic conditions whereas in RA cells, EPCR was highly expressed under both normoxic and hypoxic conditions. We found that hypoxia enhanced the effect of APC on RA synovial fibroblasts through activation of MMP2 and inhibition of p38 phosphorylation. Our results suggested that APC may suppress joint destruction and progression of inflammation in a hypoxic RA environment.
Fulltext DEVELOPMENT OF ENTRY LOCATION ASSESSMENT CRITERIA (ELAC) MODEL FOR MALAYSIAN CONSTRUCTION FIRMS IN INTERNATIONAL MARKETS

Norizzati Ibrahim, Atiqah Najwa, Che Maznah Mat Isa, Nur Kamaliah Mustaffa, Christopher Nigel Preece

Journal of Academia Universiti Teknologi MARA Negeri Sembilan, 2021;9(1):21-38.
MyJurnal

Malaysian construction firms have increasingly gained investment opportunities in foreign countries pushed by the competitive and saturated domestic market. However, the entry location decision involves complex factors to be considered by these firms prior to their international operations. Currently, based on a secondary data obtained from the Construction Industry Development Board (CIDB) Malaysia, there are twelve (12) firms that are actively operating in international markets. The main objective of this preliminary study is to develop an entry location assessment criteria (ELAC) model based on the performance of Malaysian construction firms in international markets. The ELAC formula was derived through a development of taxonomy criteria from previous studies. The construction firms’ performance was analyzed and ranked using a weightage score characterized under three (3) dimensions of country with the taxonomy criteria. First dimension involves entry location decision to countries in ASEAN, Non-ASEAN and both regions, while the second dimension involves entry location decision to ASEAN, Asia, Africa, United States of America and Europe while the third dimension involves entry location decision to countries categorized as Developing Countries (DLC); Least Developed Country (LDC); Newly Industrialized Countries (NIC); Developed Countries (DC); and Highly Developed Countries (HDC). The ELAC score shows that three (3) construction firms which are, Sapura Energy Berhad (66%), Gamuda Berhad (53%) and Sime Darby Berhad (50%) have sustained international operations in various locations by obtaining an ELAC score of more than 50% by venturing to ASEAN countries, developing countries and developed countries. Even though his study is limited to Malaysian construction firms, it provides significant information and contributes to the current knowledge in international market expansion. This ELAC model is useful especially for construction firms that are just beginning to explore foreign business opportunities or for the global players that are expanding geographically to new international markets.
Fulltext Microplastics - an emerging silent menace to public health

Li-Yin Pang, Shola Sonagara, Oreoluwatomide Oduwole, Christopher Gibbins, Ting Kang Nee

Life Sciences, Medicine and Biomedicine, 2021;5(1):0-0.
MyJurnal

Over the past few decades, microplastics have become increasingly ubiquitous in the environment and now contaminate the bodies of many living organisms, including humans. Microplastics, as defined here, are plastics within the size range 0.1 μm and 5 mm and are a worrying form of pollution due to public health concerns. This mini-review aims to summarise the route of entry of microplastics into humans and explore the potential detrimental health effects of microplastics. Trophic transfer is an important pathway for microplastic to be transferred across different groups of organisms, with ingestion is regarded as one of the major routes of exposure for humans. Other pathways include inhalation and dermal contact. The health consequences of microplastics manifest because these materials can translocate into the circulatory system and accumulate in the lungs, liver, kidney, and even brain, regardless of the route of entry. Health effects include gastrointestinal disturbances such as inflammation and gut microbiota disruption, respiratory conditions, neurotoxicity and potential cancers. Overall, while it is apparent that microplastics are causing adverse effects on different biological groups and ecosystems, current research is largely focused on marine organisms and aquaculture. Therefore, more studies are needed to investigate specific effects in mammalian cells and tissues, with more long-term epidemiological studies needed on human population considered to be at high-risk due to socioeconomic or other circumstance. Knowledge of the toxicity and long-term health impacts of microplastics is currently limited and requires urgent attention.
Fulltext Asian men’s health: gender disparity and life expectancy

Ho, Christopher C.K., Teo, C.H., Ng, C.J., Zulkifli, M.Z., Tan, M.H.

Journal of Surgical Academia, 2014;4(2):5-8.
MyJurnal

The aim of this review was to analyze the gender disparities found as well as the life expectancies in Asia. An analysis of the data on gender disparities as well as life expectancies of the different Asian countries was done based on the World Health Organization (WHO) Global Health Observatory Data Repository as well as the regional government databases. Middle Eastern countries have the highest male to female population ratio. The results show that in terms of population pyramid, Asia is moving towards a more geriatric population. Qatar has the highest life expectancy for men and is the only country in Asia where men live longer than women (difference of 2 years). In general, women in Asia live longer than men. High income countries like Hong Kong, Japan and Singapore have higher life expectancies as compared to those on the lower income nations. The life expectancy of Asian men still lags women. Men’s health care needs to be addressed urgently. The disparity in income-status reflecting the lifespan of men is an impetus for us to narrow the gap of health in Asian countries.
Fulltext Postnatal urinary incontinence: prevalence and factors associated with it in a Malaysian population

Dariah, M.Y., Paterson, J., Se, Ho, Ho, Christopher CK, Lily, X., Belan, I.

Medicine & Health, 2014;9(1):22-32.
MyJurnal

The aim of this study was to investigate the prevalence of postnatal urinary incontinence (PNUI), the risk factors associated with it and postnatal women’s (PN) level of engagement in practicing traditional Malay confinement care (TMCC) in Kelantan, Malaysia. A cross-sectional survey was conducted among 362 postnatal women aged between 18 – 45 years and who were between three to five months post-delivery. Participants were selected through convenience sampling at six Maternal and Child Health Clinics located in comparatively similar districts. Descriptive and inferential analyses including, factor analysis, Pearson chi-square, Mann-Whitney U test and logistic regressions analysis were used for data analysis. Overall, PNUI was reported by 80 women (22.1%). Vaginal delivery was associated with PNUI. All PN women within the study context practiced TMCC. The findings revealed that women who had PNUI were more likely to engage in a higher level of the ‘Body care’ component of TMCC. UI is prevalent among PN women in Kelantan, Malaysia. Further research into the impact of the ‘body care’ component of TMCC on PNUI is required.
Inflamatory pseudotumor of the bladder: a histopathological diagnostic challenge from its malignant variant

Muhammad Akbar, Praveen, S., Christopher, H.C.K., Goh, E.H., Swaminathan, Zulkifli, M.Z.

Journal of Surgical Academia, 2012;2(1):46-49.
MyJurnal

Inflammatory Pseudotumor (IP) of bladder is one of a variety of lesions which may arise from spindle cell lesions in the bladder. It is benign in nature compared to the other end of the spectrum of spindle cell lesions, such as sarcoma, sarcomatoid carcinoma and leiomyosarcoma. The diagnosis of IP and its differentiation from a malignant pathology is a diagnostic dilemma for Urologist and Pathologist as both entities share certain similar morphological and histo-pathological appearance as well as immuno-histo chemistry staining. It is however crucial to avoid misdiagnosis as the treatment option varies significantly between a radical or partial cystectomy with future surveillance cystoscopes. Hereby, we highlight a case of a benign variant of spindle cell tumour of bladder which needed second pathology review for confirmation and thus avoiding a radical cystectomy. We also review the literature on its presentation and emphasis characteristics differentiating a benign from a malignant pathology
Individual factors and perceptions of organization safety level: evidence from a manufacturing organization in Malaysia

Shah Rollah Abdul Wahab, Durrishah Idrus, Christopher J. Rees, Ishak Mad Shah

Journal of Occupational Safety and Health, 2011;8(1):33-48.
MyJurnal

Individual factors have been considered to be a key issue to organizations’ performance and survival. Specifically, previous studies provide evidence that individual factors are closely associated with accidents in the workplace. Therefore, this study seeks to investigate the relationship between individual factors and workplace safety. 50 respondents have been randomly chosen from a manufacturing company in Johor Bahru, Malaysia. Data are collected using a survey and are analyzed using SPSS version 16.0. A descriptive statistic, cross tabulation, independent sample t-test and one-way between groups ANOVA are employed to interpret findings of the study. Findings show that employees’ perception on safety performance is at high level (Mean= 115, Standard Deviation= 17.73). Furthermore, the results of cross tabulation demonstrate that individual factors play a key role to determine the organization safety performance level. Another significant finding reveals that there is a significant difference of safety performance mean to two of individual factors namely gender and tenure of service. Individual factors namely gender, age, tenure of service and academic qualification give a significant impact to employees’ perception on safety performance.
Fulltext Extra-gonadal germ cell tumour – what about the testis!

Johann, F.K., Praveen, S., Christopher, C.K.H., Goh, E.H., Razman, J., Zulkifli, M.Z.

Journal of Surgical Academia, 2011;1(1):28-31.
MyJurnal

Extra-gonadal germ cell tumours (EGGCT) are rare. Therefore further investigations of the testis is aimed at sourcing a possible primary origin of gonadal tumour. Over the years, various case series on EGGCT have been reported questioning its true nature as in a majority of them, a primary source is found in the testis, thus representing a metastatic gonadal tumour. The testis pathology could be either a true germ cell foci, an intra-tubular epithelial neoplasia or an area of fibrosis, indicating a ‘burnt out tumour’. We report a 39-year-old male who underwent laparotomy and excision of a retroperitoneal tumour. Histopathological examination revealed retroperitoneal lymph node of mixed germ cell tumour origin. Clinical and ultrasound examination of bilateral testis was normal. The patient refused orchidectomy or a testicular biopsy. He underwent four cycles of bleomycin, cisplatin, and etoposide with no evidence of tumour recurrence on follow up and remains disease free after 12 months of diagnosis. A literature review of EGGCT, its relation and factors relating with future testicular tumour is presented.
Fulltext Nephrectomy for a case of intrarenal dermoid cyst: was it an appropriate decision?

Christopher, C.K.H., Praveen, S., Goh, E.H., Tan, G.H., Rozman, Z., Zulkifli, M.Z., et al.

Journal of Surgical Academia, 2011;1(1):25-27.
MyJurnal

Dermoid cyst in a kidney is rarely seen. We report a case of intrarenal dermoid cyst which mimics malignant renal tumour and discuss the dilemma in managing this disease.
Fulltext Structured education programme on patient controlled analgesia (PCA) for orthopaedic patients

Ho, S.E., Ho, Christopher C.K., Zainah, M., Indra, Jaafar, M.Z., Choy, Y.C., et al.

Medicine & Health, 2016;11(1):62-71.
MyJurnal

Patient-controlled analgesia (PCA) via an infusion pump enables patient to
administer their own analgesia. The aim of this study was to evaluate the effect
of an educational programme in managing post-operative pain and satisfaction
on PCA following orthopedic surgery. A pre-test and post-test interventional study
design with implementation of patient education programme on PCA was provided
to 54 respondents. The control group received conventional PCA briefing from
the Acute Pain Service protocol. Pain intensity was measured at 2 hrs, 6 hrs and
24 hrs following surgery and pre-test and post-test of the Revised American Pain
Society Patient Outcome Questionnaire (APS-POQ-R) was administered. There
was difference in respondents’ level of pain score among the study respondents’
medians for control group at 2 hrs, 6 hrs and 24 hrs following surgery and they were
7.00 (IQR=3.00), 5.00 (IQR=2.00) and 3.00 (IQR=2.00); intervention group at 2 hrs,
6 hrs and 24 hrs following surgery were 6.00 (IQR=2.00), 3.00 (IQR=1.00) and
1.00 (IQR=1.00) respectively. There were significant differences in median of pain
score between intervention and control group at 2 (U=142.0, p
Fulltext Factors associated with poor nutritional status among hemodialysis patients in Malaysia

Chan Yoke Mun, Zalilah Mohd Shariff, Christopher Lim Thiam Seong, Goh Bak Leong

Malaysian Journal of Medicine and Health Sciences, 2019;15(201):77-83.
MyJurnal

Introduction: Poor nutritional status is prevalent among hemodialysis patients, with limited studies available on how it is being influenced by other factors in the local context. The current study aimed to determine the nutritional sta- tus and its associated factors among hemodialysis patients. Methods: This was a study undertaken in a total of 455 hemodialysis patients (256 men and 199 women). The main outcome measure was Malnutrition Inflammation Score (MIS), which was utilized to identify nutritional and inflammatory status of the hemodialysis patients. Other evalu- ation tools included anthropometry and biochemical measurements as well as dietary assessment. Results: A high proportion of hemodialysis patients were malnourished (64.4%) and presented with inflammation (67.5%). Using multiple linear regression analysis, factors contributing to malnutrition were older age, lower lean body mass, higher interdialytic weight gain (IDWG), inadequate intakes of energy and protein, as well as presence of comorbidities and inflammation. Conclusion: The presence of malnutrition and inflammation were prevalent among hemodialysis patients. Several determinants of poor nutritional status of hemodialysis patients were modifiable and should be rec- ognized while formulating and implementing appropriate intervention plans for this vulnerable group.
Trends in Self-Harm in Kuala Lumpur, 2005-2011

Armitage CJ, Abdul Rahim W, Rowe R, O'Connor RC

Arch Suicide Res, 2016;20(1):22-8.
PMID: 26649775 DOI: 10.1080/13811118.2015.1004493

Acts of self-harm are not routinely tracked in Malaysia. The present study investigates the prevalence of self-harm in Kuala Lumpur, Malaysia, over a 7-year period. The aims were to: (a) assess the prevalence of self-harm; (b) examine any changes over a period of 7 years, and (c) identify correlates of methods of self-harm. Data were extracted from the hospital records of Kuala Lumpur Hospital to review trends in self-harm between 2005 and 2011. There were 918 episodes of self-harm across the 7-year period, with a significant peak in 2007-2009. The average rate of self-harm (7.7 per 100,000 population per year) was similar or lower than the rate of suicide (6-8 or 8-13 per 100,000) suggesting that genuine cases of self-harm are often attributed to other causes. Nevertheless, over-representation of young people, women and Indians suggest areas in which resources to prevent self-harm might usefully be targeted. Estimating rates of self-harm are fraught with problems and further research is needed to understand the economic and cultural barriers around seeking treatment for self-harm, reporting self-harm and classifying self-harm.
Fulltext Two Monthly Continuous Dynamic Model Based on Nash Bargaining Theory for Conflict Resolution in Reservoir System

Homayounfar M, Zomorodian M, Martinez CJ, Lai SH

PLoS One, 2015;10(12):e0143198.
PMID: 26641095 DOI: 10.1371/journal.pone.0143198

So far many optimization models based on Nash Bargaining Theory associated with reservoir operation have been developed. Most of them have aimed to provide practical and efficient solutions for water allocation in order to alleviate conflicts among water users. These models can be discussed from two viewpoints: (i) having a discrete nature; and (ii) working on an annual basis. Although discrete dynamic game models provide appropriate reservoir operator policies, their discretization of variables increases the run time and causes dimensionality problems. In this study, two monthly based non-discrete optimization models based on the Nash Bargaining Solution are developed for a reservoir system. In the first model, based on constrained state formulation, the first and second moments (mean and variance) of the state variable (water level in the reservoir) is calculated. Using moment equations as the constraint, the long-term utility of the reservoir manager and water users are optimized. The second model is a dynamic approach structured based on continuous state Markov decision models. The corresponding solution based on the collocation method is structured for a reservoir system. In this model, the reward function is defined based on the Nash Bargaining Solution. Indeed, it is used to yield equilibrium in every proper sub-game, thereby satisfying the Markov perfect equilibrium. Both approaches are applicable for water allocation in arid and semi-arid regions. A case study was carried out at the Zayandeh-Rud river basin located in central Iran to identify the effectiveness of the presented methods. The results are compared with the results of an annual form of dynamic game, a classical stochastic dynamic programming model (e.g. Bayesian Stochastic Dynamic Programming model, BSDP), and a discrete stochastic dynamic game model (PSDNG). By comparing the results of alternative methods, it is shown that both models are capable of tackling conflict issues in water allocation in situations of water scarcity properly. Also, comparing the annual dynamic game models, the presented models result in superior results in practice. Furthermore, unlike discrete dynamic game models, the presented models can significantly reduce the runtime thereby avoiding dimensionality problems.
MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes

Tan MH, Gan HM, Schultz MB, Austin CM

Mol Phylogenet Evol, 2015 Apr;85:180-8.
PMID: 25721538 DOI: 10.1016/j.ympev.2015.02.009

The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phylogenetic analysis. Hence, we present MitoPhAST, an automated tool that (1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to undertake an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evolutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogenome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogenome information. MitoPhAST is available for download at https://github.com/mht85/MitoPhAST.
The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3981-3982.
PMID: 25541307

The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.

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