Biology Unit

Ilaro, Nigeria

Biology Unit

Ilaro, Nigeria
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Gunnarsson J.,Biology Unit | Gunnarsson J.,Swedish National Police Academy | Eriksson H.,Biology Unit | Ansell R.,Biology Unit | Ansell R.,Linköping University
Z Zagadnien Nauk Sadowych | Year: 2010

In forensic biology, trace recovery by lifting traces for DNA typing using adhesive mini-tapes, is an efficient complement to traditional recovery methods such as swabbing or cutting. Here we present real crime case success rates for DNA sampling using mini-tapes based on a large data-set. The major findings are an increase in DNA mixtures compared to using conventional trace recovery techniques such as cutting, but in general with a significantly lower degree of inhibited DNA extracts and a higher proportion of usable DNA results. © by the Institute of Forensic Research.


News Article | November 16, 2015
Site: phys.org

As the 20th-century novelist Joseph Conrad famously wrote, "It's only those who do nothing that make no mistakes, I suppose," and Nature is very busy, so she makes lots of them. But as a genius, she can use them to advantage. Take for example whole genome duplication—an error in DNA replication, or mating between different species, that doubles the number of chromosomes, leading to a duplication of the vast majority of genes. Such grand mistakes turn out to be among the major forces accelerating evolution. Organisms with additional sets of genes can accumulate and test mutations much faster and with less selection pressure than organisms with just one set of genes. One of the copies of a gene can maintain normal functioning of the cells even if the other copy mutates to become harmful or useless. Other possible alternatives are when one of the genes acquires a completely new function, or both genes start to specialise, each taking over a certain part of the ancestral function. Redundancy is common in nature, for example many human genes exist in several copies. However, excessive redundancy can interfere with efficiency. Therefore, each whole genome duplication event is followed by the loss of duplicate genes. A new collaborative paper, published in Proceedings of the National Academy of Sciences (PNAS) by scientists from the Okinawa Institute of Science and Technology Graduate University (OIST), the University of the Ryukyus, Tohoku University, and Nihon University, proposes a two-phase mathematical model describing gene loss patterns over two differing time scales after a whole genome duplication. The research, started by Dr Jun Inoue, now a staff scientist in the OIST Mathematical Biology Unit, Assistant Prof. Yukuto Sato, now at Tohoku University, and Prof. Mutsumi Nishida, now Vice President of the University of the Ryukyus, while all three were working together at the University of Tokyo, focused on teleost fishes, the largest group of bony fishes (Fig. 1). These fishes underwent their own specific whole genome duplication approximately 300 million years ago. "By contrast, the last whole genome duplication in the human lineage happened about half a billion years ago, and it is extremely difficult to trace," explains Prof. Robert Sinclair, the head of the Mathematical Biology Unit. The work required the development of both new computational and also mathematical tools, each one adapted to the previously determined evolutionary history of the species involved. These tools, developed by the research group, can be applied to other cases of whole genome duplications in organisms of any kind, including humans. Comparison of the genomes of zebrafish and the common Japanese fish medaka—two distantly related species with 250 million years of independent evolution (Fig. 2A)—shows that they are very similar (Fig. 2B). "Their shapes, habitats, and reproductive patterns are very different, which suggests that the basic structure of the teleost genome was established before the major diversification of teleost species," says Dr Inoue. Genome analysis of seven other well-studied fishes supports this conclusion. The results of this study suggest that approximately 80% of the duplicate genes were lost in the first 60 million years after the whole genome duplication event (Fig. 2C). Considering that the first vertebrates appeared on Earth about 500 million years ago (Fig. 2A), 60 million years is a very short time. Dr Inoue states that it is possible that genome reduction happened even faster. "We are waiting for the eel genome to be fully decoded to check this hypothesis," he says. Eels and their relatives are one of the first groups separated from the majority of teleost fishes after the teleost-specific whole genome duplication. Comparison of eels with the other teleosts will eventually shed even more light on the evolution of all fishes. The idea of loss of redundant genes is not new; however, an important new result is that "we found evidence that genes are disposed of rapidly and in bulk after the whole genome duplication, and it leads to a rapid reshaping of the genome," says Prof. Sinclair. In the first phase, clusters of adjacent genes or even large chromosomal segments may have been deleted if they were useless or problematic. Interestingly, the diversification of many major lineages of living teleosts did not occur in this rapid phase (Fig. 2A). The second phase is characterised by slower gene loss (Fig. 2C). The scientists suggest that some paired genes are retained if each copy becomes essential. Other duplicate genes continue to be lost, but mostly one-by-one. This process continues to this day. Evolution never stops! The methods of genome analysis developed for this study will pave the road to a better understanding of evolution, including our own. Explore further: Paddlefish's doubled genome may question theories on limb evolution More information: Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling, PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1507669112


News Article | October 29, 2015
Site: phys.org

"This 'rotation model', which made the cover of BioEssays, represents a true paradigm shift in the membrane receptor field," stated Prof. Pierre De Meyts, a renowned researcher of insulin and receptor binding for almost half a century and one of the reviewers of the paper by Prof. Ichiro Maruyama, the head of the Information Processing Biology Unit at Okinawa Institute of Science and Technology Graduate University (OIST).


News Article | February 23, 2017
Site: www.eurekalert.org

New research supports a structure-based classification system for viruses which could help in the identification and treatment of emerging viruses. Professor Robert Sinclair at the Okinawa Institute of Science and Technology Graduate University (OIST) and Professor Dennis Bamford and Dr. Janne Ravantti from the University of Helsinki have found new evidence to support a classification system for viruses based on viral structure. The team developed a new highly-sensitive computational prototype tool, and used it to detect similarities in the genetic code of viruses with similar outer structures, that conventional tools have failed to detect, suggesting that they share a common ancestor. This is not what would have been expected if similarities in the structure of viruses were due to similar environmental pressures - a phenomenon known as convergence. The results, published in the Journal of Virology, suggest that viral structure could provide a means of categorizing viruses with their close relatives - a potentially superior approach to current classification systems. Application of this new structure-based classification system could make it easier to identify and treat newly emerging viruses that cannot easily be classified with existing classification systems. Viruses are notoriously difficult to classify due to their enormous diversity, high rates of change and tendency to exchange genetic material. They challenge the very concept of a clear distinction between the living and the dead, with many characteristics resembling those of living things, but lacking the ability to reproduce themselves, without the help of a host cell. As such, they do not fit neatly into the established biological classification system for cellular organisms. Existing classification systems are imperfect and often lead to very similar viruses being categorized as entirely different entities. These systems are also unable to account for the fact that viruses are constantly changing. If scientists could identify something that viruses are unable to change, it could provide a basis for a more meaningful approach to classification and enable the scientific community to tackle emerging viruses, such as HIV, SARS coronavirus and Zika virus, more easily. Previously observed similarities between the protein shell, or 'capsid', of viruses - that encloses and protects the genetic material - provide a basis for a classification system based on capsid structure, as previously proposed by Prof. Bamford. The few ways in which viruses package themselves are very similar, even between viruses that are likely to have had their common relative more than a billion years ago. Whether this conservation is due to convergence or common descent has been disputed. For a classification system based on virus capsid structure to be meaningful, the amino acids that provide the building blocks of the capsid proteins should be similar in related viruses. A seeming lack of sufficient amino acid sequence similarity picked up by conventional sequence analysis tools previously undermined capsid structure as a viable way to classify viruses. Using ideas from mathematics and computer science, Professor Sinclair from OIST's Mathematical Biology Unit worked with scientists at the University of Helsinki to reinvestigate whether the structure-based classification for viral capsids is in fact supported by previously undetected sequence similarity. "The conventional tools for detecting sequence similarity are very fast but they can miss things," says Professor Sinclair. "We used a more classical approach that takes longer but is much more sensitive." The team developed a computational prototype tool called the 'Helsinki Okinawa Sequence Similarity' or HOSS for short, to detect amino acid sequence similarity in viral coat proteins of icosahedral virus capsids - polyhedral capsids with 20 faces. The team also looked at nucleotide sequence similarity. "By randomly reshuffling the order of amino acids and nucleotides in pairs or triplets of viral sequences, we used statistics to find previously undetected similarities below 17% protein sequence identity, well below what conventional tools are capable of detecting," says Professor Dennis Bamford. The detection of extremely weak similarities in protein and coding sequences by HOSS suggests that viral capsid similarities are due to common descent, not convergence as previously suspected. This may reflect an aspect of viruses that is extremely difficult to change, and hence provide both a viable approach to classification and a potential therapeutic target. "Our work is the first to tie structural lineages to sequences so comprehensively," says Professor Sinclair. The team also demonstrated the power of their method by identifying a candidate capsid gene in the Pandoravirus salinus genome, something which no other team had been able to do. Now that the researchers have shown that there are similarities between viruses that were previously undetected, further work will focus on finding more efficient methods of data extraction, beyond the HOSS prototype. "We have also begun shifting our focus to RNA viruses, of which Zika virus and Ebola virus are examples. The genomes of RNA viruses tend to be more highly variable than DNA viruses, and are therefore even more challenging," says Professor Sinclair. "But with a refined method, it could well be possible."


News Article | February 23, 2017
Site: phys.org

The team developed a new highly-sensitive computational prototype tool, and used it to detect similarities in the genetic code of viruses with similar outer structures, that conventional tools have failed to detect, suggesting that they share a common ancestor. This is not what would have been expected if similarities in the structure of viruses were due to similar environmental pressures - a phenomenon known as convergence. The results, published in the Journal of Virology, suggest that viral structure could provide a means of categorizing viruses with their close relatives - a potentially superior approach to current classification systems. Application of this new structure-based classification system could make it easier to identify and treat newly emerging viruses that cannot easily be classified with existing classification systems. Viruses are notoriously difficult to classify due to their enormous diversity, high rates of change and tendency to exchange genetic material. They challenge the very concept of a clear distinction between the living and the dead, with many characteristics resembling those of living things, but lacking the ability to reproduce themselves, without the help of a host cell. As such, they do not fit neatly into the established biological classification system for cellular organisms. Existing classification systems are imperfect and often lead to very similar viruses being categorized as entirely different entities. These systems are also unable to account for the fact that viruses are constantly changing. If scientists could identify something that viruses are unable to change, it could provide a basis for a more meaningful approach to classification and enable the scientific community to tackle emerging viruses, such as HIV, SARS coronavirus and Zika virus, more easily. Previously observed similarities between the protein shell, or 'capsid', of viruses - that encloses and protects the genetic material - provide a basis for a classification system based on capsid structure, as previously proposed by Prof. Bamford. The few ways in which viruses package themselves are very similar, even between viruses that are likely to have had their common relative more than a billion years ago. Whether this conservation is due to convergence or common descent has been disputed. For a classification system based on virus capsid structure to be meaningful, the amino acids that provide the building blocks of the capsid proteins should be similar in related viruses. A seeming lack of sufficient amino acid sequence similarity picked up by conventional sequence analysis tools previously undermined capsid structure as a viable way to classify viruses. Using ideas from mathematics and computer science, Professor Sinclair from OIST's Mathematical Biology Unit worked with scientists at the University of Helsinki to reinvestigate whether the structure-based classification for viral capsids is in fact supported by previously undetected sequence similarity. "The conventional tools for detecting sequence similarity are very fast but they can miss things," says Professor Sinclair. "We used a more classical approach that takes longer but is much more sensitive." The team developed a computational prototype tool called the 'Helsinki Okinawa Sequence Similarity' or HOSS for short, to detect amino acid sequence similarity in viral coat proteins of icosahedral virus capsids - polyhedral capsids with 20 faces. The team also looked at nucleotide sequence similarity. "By randomly reshuffling the order of amino acids and nucleotides in pairs or triplets of viral sequences, we used statistics to find previously undetected similarities below 17% protein sequence identity, well below what conventional tools are capable of detecting," says Professor Dennis Bamford. The detection of extremely weak similarities in protein and coding sequences by HOSS suggests that viral capsid similarities are due to common descent, not convergence as previously suspected. This may reflect an aspect of viruses that is extremely difficult to change, and hence provide both a viable approach to classification and a potential therapeutic target. "Our work is the first to tie structural lineages to sequences so comprehensively," says Professor Sinclair. The team also demonstrated the power of their method by identifying a candidate capsid gene in the Pandoravirus salinus genome, something which no other team had been able to do. Now that the researchers have shown that there are similarities between viruses that were previously undetected, further work will focus on finding more efficient methods of data extraction, beyond the HOSS prototype. "We have also begun shifting our focus to RNA viruses, of which Zika virus and Ebola virus are examples. The genomes of RNA viruses tend to be more highly variable than DNA viruses, and are therefore even more challenging," says Professor Sinclair. "But with a refined method, it could well be possible." Explore further: VirusDetect, a new bioinformatics pipeline for virus identification released More information: Robert M. Sinclair et al, Nucleic and amino acid sequences support structure-based viral classification, Journal of Virology (2017). DOI: 10.1128/JVI.02275-16


Jusot J.-F.,Epidemiology Health Environment Climate Unit | Tohon Z.,University of Kentucky | Yazi A.A.,Epidemiology Unit | Collard J.-M.,Biology Unit
BMC Infectious Diseases | Year: 2013

Background: Beside high mortality, acute bacterial meningitis may lead to a high frequency of neuropsychological sequelae. The Sahelian countries belonging to the meningitis belt experience approximately 50% of the meningitis cases occurring in the world. Studies in Africa have shown that N. meningitidis could cause hearing loss in up to 30% of the cases, exceeding sometimes measles. The situation is similar in Niger which experiences yearly meningitis epidemics and where rehabilitation wards are rare and hearing aids remain unaffordable. The aim of this study was to estimate the frequency of neuropsychological sequelae after acute bacterial meningitis in four of the eight regions of Niger.Methods: Subjects exposed to acute bacterial meningitis were enrolled into a cohort with non exposed subjects matched on age and gender. Consenting subjects were interviewed during inclusion and at a control visit two months later. If clinical symptoms or psychological troubles persisted at both visits among the exposed subjects with a frequency significantly greater than that observed among the non exposed subjects, a sequelae was retained. The comparison of the frequency of sequelae between non exposed and exposed subjects to bacterial meningitis was also calculated using the Fisher exact test.Results: Three persisting functional symptoms were registered: headaches, asthenia, and vertigo among 31.3, 36.9, and 22.4% respectively of the exposed subjects. A significant motor impairment was retrieved among 12.3% of the exposed versus 1.6% of the non exposed subjects. Hearing loss significantly disabled 31.3% of the exposed subjects and 10.4% exhibited a serious deafness.Conclusions: This study carried out in Niger confirms two serious neurological sequelae occurring at high frequencies after bacterial meningitis: severe and profound hearing loss and motor impairment. Cochlear implantation and hearing aids are too expensive for populations living in developing countries. Neurological sequelae occurring after meningitis should sensitize African public health authorities on the development of rehabilitation centers. All these challenges can be met through existing strategies and guidelines. © 2013 Jusot et al.; licensee BioMed Central Ltd.


Hefke G.,University of the Western Cape | Hefke G.,Biology Unit | Davison S.,University of the Western Cape | D'Amato M.E.,University of the Western Cape
Electrophoresis | Year: 2015

The utilization of binary markers in human individual identification is gaining ground in forensic genetics. We analyzed the polymorphisms from the first commercial indel kit Investigator DIPplex (Qiagen) in 512 individuals from Afrikaner, Indian, admixed Cape Colored, and the native Bantu Xhosa and Zulu origin in South Africa and evaluated forensic and population genetics parameters for their forensic application in South Africa. The levels of genetic diversity in population and forensic parameters in South Africa are similar to other published data, with lower diversity values for the native Bantu. Departures from Hardy-Weinberg expectations were observed in HLD97 in Indians, Admixed and Bantus, along with 6.83% null homozygotes in the Bantu populations. Sequencing of the flanking regions showed a previously reported transition G>A in rs17245568. Strong population structure was detected with Fst, AMOVA, and the Bayesian unsupervised clustering method in STRUCTURE. Therefore we evaluated the efficiency of individual assignments to population groups using the ancestral membership proportions from STRUCTURE and the Bayesian classification algorithm in Snipper App Suite. Both methods showed low cross-assignment error (0-4%) between Bantus and either Afrikaners or Indians. The differentiation between populations seems to be driven by four loci under positive selection pressure. Based on these results, we draw recommendations for the application of this kit in SA. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Faparusi F.,Biology Unit | Bello-Akinosho M.M.,Biology Unit | Oyede R.T.,Chemistry Unit | Adewole A.,Biology Unit | And 2 more authors.
Research Journal of Phytochemistry | Year: 2012

Brillantaisia patula is a medicinal plant used for different ailments in Africa. Phytochemical constituents and antibacterial potential of the plant were investigated. In vitro antibacterial activity using agar-well diffusion method was carried out against Staphylococcus aureus (ATCC 25923), Enterococcus faecalis (ATGC 24212), Proteus hauseri (ATCG 13315), Pseudomonas aeruginosa ATCC 27853 and Escherichia coli (ATCC 38218). The phytochemistry of both methanol and ethanol extracts of Brillantaisia patula leaf revealed the presence of alkaloids, glycosides, terpenoids, steroids, flavonoids, tannins, steroids, flavonoids and saponins. Terpenoids and flavonoids were found in the methanolic extract but not in the ethanolic extract while steroid was found in the ethanolic extract but not in the methanolic extract. The ethanolic extract was active against all the five pathogenic bacteria while the methanolic extract inhibited all the test bacteria but Staphylococcus aureus. Ethanolic extract zones of inhibition ranged from 15.3±0.6 to 20.7±0.6 mm, whereas methanolic extract zones of inhibition ranged from 18.0±1.0 to 30.0±1.0 mm. The Minimum Inhibitory Concentration (MIC) of ethanolic extract ranged from 25 to 200 mg mL -1 while that of methanolic extract was from 50 to 100 mg mL -1. The Minimum Bactericidal Concentration (MBC) of methanolic extract ranged from 100 to 200 mg mL -1. The least MBC value (50 mg mL -1) of ethanolic extract was against Escherichia coli while the highest value (>200 mg mL -1) was against Proteus hauseri. Leaf of Brillantaisia patula could be a novel source of antibacterial agent (s) that might have broad spectrum activity. © 2012 Academic Journals Inc.

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