An Improved Computational Prediction Model for Lysine Succinylation Sites Mapping on Homo sapiens by Fusing Three Sequence Encoding Schemes with the Random Forest Classifier

Background Lysine succinylation is one of the reversible protein post-translational modifications (PTMs), which regulate the structure and function of proteins. It plays a significant role in various cellular physiologies including some diseases of human as well as many other organisms. The accurate identification of succinylation site is essential to understand the various biological functions and drug development.Methods In this study, we developed an improved method to predict lysine succinylation sites mapping on Homo sapiens by the fusion of three encoding schemes such as binary, the composition of k-spaced amino acid pairs (CKSAAP) and amino acid composition (AAC) with the random forest (RF) classifier. The prediction performance of the proposed random forest (RF) based on the fusion model in a comparison of other candidates was investigated by using 20-fold cross-validation (CV) and two independent test datasets were collected from two different sources.Results The CV results showed that the proposed predictor achieves the highest scores of sensitivity (SN) as 0.800, specificity (SP) as 0.902, accuracy (ACC) as 0.919, Mathew correlation coefficient (MCC) as 0.766 and partial AUC (pAUC) as 0.163 at a false-positive rate (FPR) = 0.10 and area under the ROC curve (AUC) as 0.958. It achieved the highest performance scores of SN as 0.811, SP as 0.902, ACC as 0.891, MCC as 0.629 and pAUC as 0.139 and AUC as 0.921 for the independent test protein set-1 and SN as 0.772, SP as 0.901, ACC as 0.836, MCC as 0.677 and pAUC as 0.141 at FPR = 0.10 and AUC as 0.923 for the independent test protein set-2. It also outperformed all the other existing prediction models.Conclusion The prediction performances as discussed in this article recommend that the proposed method might be a useful and encouraging computational resource for lysine succinylation site prediction in the case of human population.     

Succession patterns of fungi associated to wound-induced agarwood in wild Aquilaria malaccensis revealed from quantitative PCR assay

Aquilaria malaccensis produces agarwood in response to wounding and fungal attack. However, information is limited regarding Aquilaria‘s interaction with its diverse fungal community. In this study, time-related changes of three natural fungal colonizers in two wounded wild A. malaccensis were tracked, beginning a few hours after wounding up to 12 months. Using species-specific primers derived from their nrITS sequences in quantitative real-time PCR (qPCR), we quantified the amount of Cunninghamella bainieri, Fusarium solani and Lasiodiplodia theobromae. Because time is a major factor affecting agarwood quantity and quality, 14 wood samples were collected at different time points, i.e., 0–18 h, 2–13 days, 2–18 weeks, and 6–12 months after wounding. qPCR data revealed that the abundance of the three species decreased over time. The fungi were detected in high numbers during the first few hours and days after wounding (40- to 25,000-fold higher levels compared with initial counts) and in low numbers (<1- to 3,200-fold higher than initially) many months later. Consistent with its role in defense response, the accumulation of secondary metabolites at the wounding site could have caused the decline in fungal abundance. Succession patterns of the two trees were not identical, indicating that fungal populations may have been affected by tree environment and wound microclimate. Our results are important for understanding the diversity of microbial community in wild Aquilaria species and their association to wound-induced agarwood formation. Fungi could be secondary triggers to agarwood production in situations where trees are wounded in attempt to induce agarwood.     

Tumor suppressor RecQL5 controls recombination induced by DNA crosslinking agents

RecQ family DNA helicases function in the maintenance of genome stability. Mice deficient in RecQL5, one of five RecQ helicases, show a cancer predisposition phenotype, suggesting that RecQL5 plays a tumor suppressor role. RecQL5 interacts with Rad51, a key factor in homologous recombination (HR), and displaces Rad51 from Rad51-single stranded DNA (ssDNA) filaments in vitro. However, the precise roles of RecQL5 in the cell remain elusive. Here, we present evidence suggesting that RecQL5 is involved in DNA interstrand crosslink (ICL) repair. Chicken DT40 RECQL5 gene knockout (KO) cells showed sensitivity to ICL-inducing agents such as cisplatin (CDDP) and mitomycin C (MMC) and a higher number of chromosome aberrations in the presence of MMC than wild-type cells. The phenotypes of RECQL5 KO cells resembled those of Fanconi anemia gene KO cells. Genetic analysis using corresponding gene knockout cells showed that RecQL5 is involved in the FANCD1 (BRCA2)-dependent ICL repair pathway in which Rad51-ssDNA filament formation is promoted by BRCA2. The disappearance but not appearance of Rad51-foci was delayed in RECQL5 KO cells after MMC treatment. Deletion of Rad54, which processes the Rad51-ssDNA filament in HR, in RECQL5 KO cells increased sensitivity to CDDP and further delayed the disappearance of Rad51-foci, suggesting that RecQL5 and Rad54 have different effects on the Rad51-ssDNA filament. Furthermore, the frequency and variation of CDDP-induced gene conversion at the immunoglobulin locus were increased in RECQL5 KO cells. These results suggest that RecQL5 plays a role in regulating the incidence and quality of ICL-induced recombination.     

The Neighbourhood Method for Measuring Differences in Maternal Mortality,Infant Mortality and Other Rare Demographic Events

In the absence of reliable systems for registering rare types of vital events large surveys are required to measure changes in their rates. However some events such as maternal deaths are widely known about in the community. This study examined the utility of asking respondents about events in their neighbourhood as an efficient method for measuring relative rates of rare health events such as maternal and infant deaths. A survey was conducted in the health and demographic surveillance system (HDSS) in Matlab, Bangladesh, which includes two areas with different health care regimes. Adult women were asked about any maternal deaths; multiple births; infant deaths, live births and some other events they knew of in a small specified area around their home. Agreement between HDSS records and survey responses was moderate or better (kappa≥0.44) for all the events and greatest for maternal deaths (kappa = 0.77) with 84% being reported. Most events were more likely to be reported if they were recent (p<0.05). Infant mortality rate in one area was 0.56 times that in the other which was well reflected by the ratio of survey results (0.53). Simulations were used to study the ability of the method to detect differences in maternal mortality ratio. These suggested that a sample size around 5000 would give 80% power to detect a 50% decrease from a baseline of 183 which compared well with an estimated sample size around 10 times larger using the direct sisterhood method. The findings suggest that the Neighbourhood Method has potential for monitoring relative differences between areas or changes over time in the rates of rare demographic events, requiring considerably smaller sample sizes than traditional methods. This raises the possibility for interventions to demonstrate real effects on outcomes such as maternal deaths where previously this was only feasible by indirect methods.     

Screening and Characterization of RAPD Markers in Viscerotropic Leishmania Parasites

Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5′ end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents.     

Distribution of detritivores in tropical forest streams of peninsular Malaysia: role of temperature,canopy cover and altitude variability

The diversity and abundance of macroinvertebrate shredders were investigated in 52 forested streams (local scale) from nine catchments (regional scale) covering a large area of peninsular Malaysia. A total of 10,642 individuals of aquatic macroinvertebrates were collected, of which 18.22 % were shredders. Biodiversity of shredders was described by alpha (α_average ), beta (β) and gamma diversity (γ) measures. We found high diversity and abundance of shredders in all catchments, represented by 1,939 individuals (range 6–115 and average per site of 37.29?±?3.48 SE) from 31 taxa with 2–13 taxa per site (α_average?=?6.98?±?0.33 SE) and 10–15 taxa per catchment (γ?=?13.33?±?0.55 SE). At the local scale, water temperature, stream width, depth and altitude were correlated significantly with diversity (Adj-R ²?=?0.205). Meanwhile, dissolved oxygen, stream velocity, water temperature, stream width and altitude were correlated to shredder abundance (Adj-R ²?=?0.242). At regional scale, however, water temperature was correlated negatively with β and γ diversity (r ²?=?0.161 and 0.237, respectively) as well as abundance of shredders (r ²?=?0.235). Canopy cover was correlated positively with β diversity (r ²?=?0.378) and abundance (r ²?=?0.266), meanwhile altitude was correlated positively with β (quadratic: r ²?=?0.175), γ diversity (quadratic: r ²?=?0.848) as well as abundance (quadratic: r ²?=?0.299). The present study is considered as the first report describing the biodiversity and abundance of shredders in forested headwater streams across a large spatial scale in peninsular Malaysia. We concluded that water temperature has a negative effect while altitude showed a positive relationship with diversity and abundance of shredders. However, it was difficult to detect an influence of canopy cover on shredder diversity.     

Distributed shared arrays: A distributed virtual machine with mobility support for reconfiguration

Distributed Shared Arrays (DSA) is a distributed virtual machine that supports Java-compliant multithreaded programming with mobility support for system reconfiguration in distributed environments. The DSA programming model allows programmers to explicitly control data distribution so as to take advantage of the deep memory hierarchy, while relieving them from error-prone orchestration of communication and synchronization at run-time. The DSA system is developed as an integral component of mobility support middleware for Grid computing so that DSA-based virtual machines can be reconfigured to adapt to the varying resource supplies or demand over the course of a computation. The DSA runtime system also features a directory-based cache coherence protocol in support of replication of user-defined sharing granularity and a communication proxy mechanism for reducing network contention. System reconfiguration is achieved by a DSA service migration mechanism, which moves the DSA service and residing computational agents between physical servers for load balancing and fault resilience. We demonstrate the programmability of the model in a number of parallel applications and evaluate its performance by application benchmark programs, in particular, the impact of the coherence granularity and service migration overhead. Song Fu received the BS degreee in computer science from Nanjing University of Aeronautics and Astronautics, China, in 1999, and the MS degree in computer science from Nanjing University, China, in 2002. He is currently a PhD candidate in computer engineering at Wayne State University. His research interests include the resource management, security, and mobility issues in wide-area distributed systems. Cheng-Zhong Xu received the BS and MS degrees in computer science from Nanjing University in 1986 and 1989, respectively, and the Ph.D. degree in computer science from the University of Hong Kong in 1993. He is an Associate Professor in the Department of Electrical and Computer Engineer of Wayne State University. His research interests lie in distributed are in distributed and parallel systems, particularly in resource management for high performance cluster and grid computing and scalable and secure Internet services. He has published more than100 peer-reviewed articles in journals and conference proceedings in these areas. He is the author of the book Scalable and Secure Internet Services and Architecture (CRC Press, 2005) and a co-author of the book Load Balancing in Parallel Computers: Theory and Practice (Kluwer Academic, 1997). He serves on the editorial boards of J. of Parallel and Distributed Computing, J. of Parallel, Emergent, and Distributed Systems, J. of High Performance Computing and Networking, and J. of Computers and Applications. He was the founding program co-chair of International Workshop on Security in Systems and Networks (SSN), the general co-chair of the IFIP 2006 International Conference on Embedded and Ubiquitous Computing (EUC06), and a member of the program committees of numerous conferences. His research was supported in part by the US National Science Foundation, NASA, and Cray Research. He is a recipient of the Faculty Research Award of Wayne State University in 2000, the Presidents Award for Excellence in Teaching in 2002, and the Career Development Chair Award in 2003. He is a senior member of the IEEE. Brian A. Wims was born in Washington, DC in 1967. He received the Bachelor of Science in Electrical Engineering from GMI-EMI (now called Kettering University) in 1990; and Master of Science in Computer Engineering from Wayne State University in 1999. His research interests are primarily in the fields of parallel and distributed systems with applications in Mobile Agent technologies. From 1990–2001 he worked in various Engineering positions in General Motors, including Electrical Analysis, Software Design, and Test and Development. In 2001, he joined the General Motors IS&S department where he is currently a Project Manager in the Computer Aided Test group. Responsibilities include managing the development of test automation applications in the Electrical, EMC, and Safety Labs. Ramzi Basharahil was born in Aden, Yemen in 1972. He received the Bachelor of Science degree in Electrical Engineering from the United Arab Emirates University. He graduated top of his engineering graduated class of 1997. He obtained Master of Science degree in 2001 from Wayne State University in the Department of Electrical and Computer Engineering. His main research interests are primarily in the fields of parallel and distributed systems with applications to distributed processing across cluster of servers. From 1997 to 1998, he worked as a Teaching Assistant in the Department of Electrical Engineering at the UAE University. In 2000, he joined Internet Security Systems as a security software engineer. He later joined NetIQ Corporation in 2002 and still working since then. He is leading the security events trending and events management software development where he is involved in designing and the implementing event/log managements products.     

Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans

Admixed populations such as African Americans and Hispanic Americans present both challenges and opportunities in genetic epidemiologic research. Because of variation in admixture levels among individuals, case-control association studies may be subject to stratification bias. On the other hand, admixed populations also present special opportunities both for examining the role of genetic and environmental factors for observed racial/ethnic differences, and for possibly mapping alleles that contribute to such differences. Here we examined the distribution and relationship of individual admixture (IA) estimates with BMI and three measures of blood pressure in two admixed populations in the NHLBI Family Blood Pressure Program (FBPP): African Americans and Mexican Americans. For the African Americans, we observed modest but significant differences in average African IA among four recruitment sites. We observed a slight excess of African IA among hypertensives compared to normotensives, and a positive (non-significant) regression of African IA on blood pressure in untreated participants. Within Mexican Americans, we found no difference in average IA between hypertensives and normotensives, but a positive (marginally significant) regression of African IA on diastolic blood pressure. We also observed a significant positive regression of Caucasian IA (and negative regression of Native American IA) on BMI. Our results are suggestive of genetic differences between Africans and non-Africans that influence blood pressure, but such effects are likely to be modest compared to environmental ones. Excess obesity among Native Americans compared to whites is not consistent with a simple genetic explanation.     

Desmids of Bangladesh

214 taxa under 21 genera of desmids have been described and illustrated from Bangladesh, of which 3 species and 8 varieties are new to science.