Protein sequences classification based on weighting scheme

We present a new technique to recognize remote protein homologies that rely on combining probabilistic modeling and supervised learning in high-dimensional feature spaces. The main novelty of our technique is the method of constructing feature vectors using Hidden Markov Model and the combination of this representation with a classifier capable of learning in very sparse high-dimensional spaces. Each feature vector records the sensitivity of each protein domain to a previously learned set of sub-sequences (strings). Unlike other previous methods, our method takes in consideration the conserved and non-conserved regions. The system subsequently utilizes Support Vector Machines (SVM) classifiers to learn the boundaries between structural protein classes. Experiments show that this method, which we call the String Weighting Scheme-SVM (SWS-SVM) method, significantly improves on previous methods for the classification of protein domains based on remote homologies. Our method is then compared to five existing homology detection methods

Mandelate dehydrogenases from Rhodotorula graminis

Rhodotorula graminis is a yeast with the ability to utilise mandelate as a source of carbon and energy. Mandelate exists in two enantiomeric forms; D-mandelate and L-mandelate. R. graminis possesses both D(-)-mandelate dehydrogenase and L(+)-mandelate dehydrogenases which enable this organism to use both forms of mandelate. The L(+)- mandelate dehydrogenase (LMDH) is a soluble component of the mitochondrial intermembrane space and is similar to L(+)-lactate dehydrogenase (LLDH) from S. cerevisiae and H. anomala which is a flavocytochrome b2. The D(-)-mandelate dehydrogenase is an unrelated enzyme which is a soluble NAD-dependent enzyme.In order to study these two proteins the genes encoding LMDH and DMDH were isolated, sequenced and expressed. An 81 bp fragment was amplified by RT-PCR and used to probe the gene encoding the LMDH from R. graminis.The genomic DNA was isolated from a genomic library and then the cDNA was amplified by RT- PCR. Comparison of the genomic DNA and the cDNA sequences reveals the presence of eleven introns in the genomic DNA encoding LMDH. The conserved intron sequences of LMDH in R. graminis are similar to the intron sequences from the phenylalanine- ammonia lyase (PAL) gene in Rhodosporidium toruloides and Rhodotorula rubra. The LMDH from R. graminis is predicted to contain a 74 amino acid extension at the N- terminus. This presequence is highly basic and contains a long stretch of non -polar amino acids, typical of a subclass of mitochondrial targeting sequences. The 1479 bp cDNA specifies a mature LMDH of 492 amino acids including the incorporated N- terminal methionine. The calculated Mr is 54,604. Computer search with other proteins in the database shows similarity with other FMN- dependent 2- hydroxyacid oxidising enzymes. LMDH is very closely related to flavocytochrome b2 from S. cerevisiae and H. anomala. Based on the crystal structure and the amino acid sequence comparison with L(+)-lactate dehydrogenase from S. cerevisiae, LMDH from R. graminis could be divided into two domains, the haem binding domain and the flavin binding domain. The amino acid sequence of the predicted cytochrome domain shows high similarity with microsomal b5. Comparison of the amino acid sequence of LMDH and LLDH from S. cerevisiae shows that all the residues important in catalysis and substrate binding of the enzyme are highly conserved. Amino acid sequence comparison also reveals that Leu230 in LLDH from S. cerevisiae, which determins the substrate specificities of the enzyme, is replaced by a smaller glycine in LMDH from R. graminis.The genomic DNA and the cDNA of D(-)-mandelate dehydrogenase have been isolated and amplified respectively. Comparison of the genomic DNA and the cDNA revealed the presence of three introns. All the introns start with GT, have the sequence of CAG at the 3' end and have an internal consensus sequence of CTGAC. The entire 1053 bp sequence of the amplified cDNA specifies a protein (DMDH) of 351 amino acids with the calculated Mr of 38,591. A computer search with other proteins in the database shows that DMDH from R. graminis belongs to the D-isomer-2 hydroxyacid dehydrogenase family. Based on the crystal structure and amino acid sequence from D-glycerate dehydrogenase from Hyphomicrobium methylovorum it is predicted that the polypeptide chain of DMDH is divided into two domains, the catalytic domain which is formed by approximately residues 1 to 111 and 308 to 351 and the second coenzyme-binding domain which is located in the middle of the polypeptide chain approximately between residue 111 to 307. Arg259 in DMDH is believed to be important in substrate binding as in the other D- isomer specific dehydrogenases. His304 acts as an acid/base catalyst. The highly conserved sequence G-X-G-X-X-G-17X-D which is common to the NAD-binding domain is conserved in DMDH except that the third glycine is replaced by glutamine. The function of glutamine here is not clear and can only be determined when the DMDH crystal structure becomes available.Both LMDH and DMDH were succesfully expressed by using the expression vector pRC23 which is thermoinducible. The calculated kcal and Km of the partially purified recombinant LMDH is 350 s⁻¹ and 0.35 mM respectively. The specific activity for DMDH is 0.0528 units /mg

Growth, feed intake and diet selection in pigs: theory and experiments

A theory of growth and feed intake in the pig is proposed and the results of five experiments to test it are reported here. An attempt is first made to describe the potential growth in pigs, that is, growth under non-limiting conditions; the conditions needed to allow potential growth to be retained are then considered. Two ways of providing non-limiting feeding conditions are discussed: a single balanced feed and a set of feeds given as a choice. In addition, a model which predicts the voluntary feed intake of pigs is also developed and tested in experiments. The results from pigs offered single feeds in the first two experiments were consistent with the predictions of the model, which were that the rate of feed intake would increase as the protein content of the feeds was decreased. The size of the increase depended on the ability of the pig to lose heat. In these experiments, when pigs were offered a pair of feeds as a choice, a combination of which was non-limiting, the results suggested that this method cannot be successfully used to attain the potential growth of pigs. The diet selection results were characterised by a considerable variation in the diets selected by individual pigs, and only some pigs achieved what was estimated to be their potential rate of growth. It was suggested that pigs which failed to select a non-limiting diet did not have the necessary chance to choose. Experiment 3 evaluated a simple method of ensuring that pigs are given both the necessary choice, and the chance to choose. This was achieved by giving them the opportunity to sample the single feeds, which were to be offered as a choice, alone on alternate days for a short period of six days. Subsequently, pigs given a choice between two feeds were able to select a non-limiting diet. Experiment 4 incorporated the method established previously and consisted of a severe investigation into the rules of diet selection. It was concluded that pigs are able to avoid excess of nutrient, in this case protein, intake or to select the best possible diet in less favourable conditions, ie. a choice between two limiting feeds. The last experiment consisted of an extended test of the theory that a pig will select a diet which is a reflection of its degree of maturity, state and sex. Pigs made fat and delayed in growth in one period were subsequently given the opportunity to recover on a pair of feeds offered as a choice. The diets selected by the fat pigs satisfied their requirements for compensatory protein gain allowing only a slow rate of lipid gain. In addition, they met the different growth and fattening requirements by the two sexes. All these findings are discussed in relation to the use of choice-feeding as an independent test of other estimates of resource requirements, as a feeding technique when the potential growth of pigs is to be observed and as a help in predicting the feeding behaviour in pigs

An APOS analysis of the understanding of vector space concepts by Zimbabwean in-service Mathematics teachers.

Doctoral Degree. University of KwaZulu-Natal. Durban.University mathematics students often find the content of linear algebra difficult because of the abstract and highly theoretical nature of the subject as well as the formal logic required to carry out proofs. This study explored some specific difficulties experienced by students when negotiating the various vector space concepts. The participants were 73 Zimbabwean mathematics teachers who were enrolled in an in-service programme and who were studying for a Bachelor of Science Education Honours Degree in Mathematics. The Zimbabwean mathematics in-service teachers who were studying these concepts were also teaching some of the concepts at high school. The study was qualitative in nature and it was strengthened by the interpretivist paradigm. Data were generated from the teachers’ written responses to three tasks based on the various vector space concepts. The items in the activity sheets probed the participants on the concepts on vector space, subspace, linear combination, linear independence, basis and dimension. Follow-up interviews on the written work were conducted to identify the participants’ ways of understanding. Thirteen students volunteered to be interviewed and were probed further about the vector space concepts so as to elicit more information on the way they understood the various vector space concepts, and the connection they seemed to make between these concepts. An APOS (action–process–object–schema) theory was used to unpack the structure of the concepts. The main aim of the study was to identify the mental constructions that the students made when learning the various vector space concepts and the extent to which they concurred with a preliminary genetic decomposition.. The study also employed another theoretical framework, Sfard theory, which was used to describe the in-service teachers cognitive difficulties in the learning of linear algebra which were identified as errors and misconceptions with particular reference to the study of vector space concepts. The errors were categorised in terms of conceptual (deeply seated misunderstandings) procedural (related to using related procedures) and technical (calculation or interpretation) errors. In terms of APOS theory, the responses revealed that most in-service teachers were operating at the action and process levels, with a few students using some aspects of object level reasoning for some of the questions. Findings revealed that the teachers struggled with the vector space and subspace concepts, mainly because of prior non-encapsulation of prerequisite concepts of sets and binary operations, and difficulties with understanding the role of counter-examples in showing that a set is not a vector subspace. Most of the students operated at the action level of understanding. The findings revealed that across the items on the concepts on linear combinations, linear independence, basis and dimension, students were comfortable in answering problems that required the use of algorithms, for example carrying out the Gaussian elimination method. However a major hurdle that hindered them from interiorising the actions into a process for the items on linear combination, linear independence and basis was their failure to interpret the solutions to the systems of equations and providing insufficient argumentation in relation to the posed questions. Fifty students struggled with concepts on linear combination and did not provide any evidence in their written responses of moving past an action conception.The results on understanding linear independence revealed that 17 (23%) students were able to make arguments based on the use of theorems that given vectors are linearly dependent without showing the step by step procedures and giving precise descriptions of the procedures used to determine linear independence. There were 46 students who represented their understanding in a manner described as the action conception as they were engaged in a step by step manner in an attempt to show that given vectors are linearly independent. The major drawback that hindered the students to develop their understanding of the concept of linear independence was a failure to distinguish the two terms linear independence/dependence, application of inappropriate theorems and inappropriate methods when solving the problems. Furthermore, the results on understanding of basis and dimension also revealed that the in-service teachers were able to cope with the procedures of row reduction, but struggled to justify whether given vectors formed a basis or not; they also struggled to find the basis of the solution space. Only 9 (12%) of the students were able to develop their mental construction at the process conception of basis of a vector space as they were able to coordinate the two processes of establishing that a given set span the particular vector space and that the set is linearly independent. On cognitive challenges, the study revealed the distribution pattern of the conceptual errors, technical errors and procedural errors varied across the items. The most errors manifested were the conceptual and technical. It is hoped that the identification of such errors and misconceptions will assist other educators in modifying their planning so that long term learning will take place

An Analysis of the Factors Affecting House Prices in Malaysia – An Econometric Approach

The housing price in Malaysia remains an issue that makes a significant concern to the government as well as potential house buyers at large. The trend has portrayed discernable expansion of housing prices over the years. The study intends to expand on a previous research that only found Gross Domestic Product to have a significant impact on house prices in Malaysia. The results from the study were only able to explain merely 15% of the variations in house pricing. Further research in this study intends to determine other possible factors which could significantly impact the housing price in Malaysia. Variables selected include gross domestic product, inflation, unemployment rate and population. This study covers a period of 23 years from 1988 to 2010 using Multiple Regression method. The aim of the study is to develop a significant econometric model that can be used to forecast Malaysian housing price. By determining the significant factors that could affect housing prices in Malaysia, this study would outline concerns on the factors that contribute to volatile housing prices and hence assist the government in making significant policies in controlling the price of residential properties from escalating uncontrollably which can potentially invite financial disaster such as the subprime crisis that occurred in the USA recently

La médecine alternative et complémentaire: quelle place dans le traitement des hémopathies en Afrique?

Lettre aux éditeurs du Journal Pan Africain de Médecine.Pan African Medical Journal 2012; 12:2

Cloning and expression of pullulanase gene from locally isolated bacillus SP

Bacterial pullulanase represents one of th e starch-degrading enzymes that are widely used in the starch processing indu stry along with amylases. Amylases hydrolyze a -(1,4 )-glycosidic linkage in starch to produce a mixture of glucose , maltooligo sacchari de and limited a-dextrin. All the remaining a -(1,6)-glycosid ic branches in the products are hydrolyzed by p ullulanase. This is an advantage t o improve glucose production by coupling pullulanase and amylase in the p rocess. As such, many pullulana e enzyme has been isolated and one has been showing optimum pH of 10-10.5 which is suitable for use in dishwasher detergent additive in removal of star ch stain. We have recently iso lated a few bacterias that have shown potentially pullulanase producers by the holo-zone in pullulan-plate assay. One of them, we named Bacillus –1 sho ws a bigger holo-zone among others, Bacillus- 1 is highly active in pH more than 7. The enzyme also shows a mo derate activity to wards starch that may be indicates be side hydrolyzes a -(1,6)-glycosidic linkage in starch, it also hydrolyzes a -(1,4)- glycosidi c simi lar to a -amylase. Unfortunately the enzyme from wild-type bacteria is in lower yield an d in this studies, we intend to clone and sequence the pullulanase gene and also expressed the gene in a high expression system to be able to produce in a high yield before characterizing expressed protein

South European Populism as a Consequence of the Multidimensional Crisis? The Cases of SYRIZA, PODEMOS and M5S

The occurrence of the financial crisis in Europe has offered enough space for the growth of populist alternatives in the public speech. Thus, the aim of this study is to connect the socio-economic consequences of the crisis with the populist rhetoric of SYRIZA (Radical Left Coalition), M5S (5 Star Movement) and PODEMOS (We Can) parties in Greece, Italy and Spain respectively. A comparative analysis will be conducted in order to identify their main characteristics as well as the differences and the commonalities of the three cases. Taking into account as analytical tools, the specificities of the South European area and the old and new theories of populism, this paper aims to offer lucrative incentives to the scientific discussion about the rise of populism in this region

Optimization of medium for the production of β-cyclodextrin glucanotransferase using Central Composite Design (CCD)

Production of cyclodextrin glucanotransferase (CGTase) from Bacillus G 1, a new bacterial isolate was optimized in shake-flask cultures using statistical design approach. An efficient fermentation medium producing CGTase with high activity (54.9U/ml) was determined: A 2(5) Central Composite Design (CCD; half fraction) has been chosen to elucidate the combined effect of five process variables; tapioca starch, peptone, yeast extract, magnesium sulphate and potassium phosphate concentration. Concentrations of 4% tapioca starch, 2% peptone, 0.04% magnesium sulphate and 1 % sodium carbonate have been shown to be optimum for the production of CGTase