A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Length-weight relationship and the diets of Clarias lazera (Cuvier and Valenciennes), family Clariidae (Osteichthyes: Siluriformes) in Zaria, Nigeria

The length-weight relationship and the diets of Clarias lazera were investigated between July 1981 and June 1982. About 450 specimens were examined. The standard lengths of the fish ranged from 8.5 cm to 42.2 cm. Significant differences were found between the standard lengths of the males and females with the latter slightly shorter. Somatic weights varied between 10 g to 502 g. Length-weight regression analysis gave a "b" value of 3.02 for both males and females combined; thus indicating an isometric growth. Analysis of the food in the stomachs showed that the fish is an omnivore although, it fed more on insects and fish than other food items

Análisis crítico de la enseñanza de visualización en primer ciclo de universidad y propuesta alternativa de orientación constructivista

Este trabajo se ha ocupado de la problemática educativa que se presenta en el proceso de enseñanza/aprendizaje de la visualización de piezas en la asignatura de Expresión Gráfica en el primer curso de Universidad en estudios de Ingeniería Técnica. Se ha propuesto un modelo de resolución de problemas de visualización que integra tanto los contenidos conceptuales como los procedimentales implicados en el mismo. Se ha realizado un análisis crítico de la enseñanza habitual de la visualización de piezas, mostrando tanto deficiencias didácticas, como deficiencias y dificultades presentes en el aprendizaje de los alumnos. A continuación, se ha diseñado una propuesta alternativa de enseñanza de la visualización de orientación constructivista, desarrollando además un programa de actividades para su aprendizaje. Por último, se ha experimentado dicha propuesta, presentado las mejoras obtenidas en el aprendizaje logrado y los resultados obtenidos en la valoración de la propuesta alternativa.

Triploidy induction in Heterobranchus longifilis (Family: Clariidae) by cold shock

Triploid was induced in African Catfish (Heterobranchus longifilis) by cold shocking activated eggs at 5 degree C for forty minutes starting 3-4 minutes after fertilization. Triploidy was confirmed from mitotic chromosomes prepared from embryo which showed 100% triploidy in the cold shocking treatment and 100% diploidy in the control treatment

Effects of some environmental factors on the fecundity of Tilapia species (Family Cichlidae) in Kigera Reservoir, New Bussa

The effects of some environmental factors on the fecundity of Tilapia species (Family Cichilidae) was carried out at the Kigera dam. Four Tilapia species caught were Tilapia zilli, Hemichromis fasciatus, Sarotherodon galilaeus and Oreochromis niloticus while the environmental factors considered were water temperature, Dissolved Oxygen, pH value, level of rainfall and rate of sunshine and range of time. 43 fish comprising of 25 male with (58.1%) and 18 females having (41.9%) were studied with 74.42% been sexually matured. Both high levels of rainfall and dissolved oxygen favoured fecundity. The spawning peak occurred in (July), environmental factors monitored indicated that dissolved oxygen ranges from 3.7 to 4.45mg/lit rainfall ranges from (34.90mm to 237.80mm) sunshine ranges from (5hrs-8hrs) and pH ranges from (7.35-7.45). The spawning of these species in their natural or hatchery condition is therefore best achieved during the peak of raining season

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

In vivo analysis of interactions between trans-acting factors and their target genes

The investigations presented in this thesis use various in vivo techniques to understand how trans-acting factors control gene expression. The first part addresses the transcriptional regulation of muscle creatine kinase (MCK). MCK expression is activated during the course of development and is found only in differentiated muscle. Several in vivo footprints are observed at the enhancer of this gene, but all of these interactions are limited to cell types that express MCK. This is interesting because two of the footprints appear to represent muscle specific use of general transcription factors, while the other two correspond to sites that can bind the myogenic regulator, MyoD1, in vitro. MyoD1 and these general factors are present in myoblasts, but can bind to the enhancer only in myocytes. This suggests that either the factors themselves are post-translationally modified (phosphorylation or protein:protein interactions), or the accessibility of the enhancer to the factors is limited (changes in chromatin structure). The in vivo footprinting study of MCK was performed with a new ligation mediated, single-sided PCR (polymerase chain reaction) technique that I have developed.

The second half of the thesis concerns the regulation of mouse metallothionein (MT). Metallothioneins are a family of highly conserved housekeeping genes whose expression can be induced by heavy metals, steroids, and other stresses. By adapting a primer extension method of genomic sequencing to in vivo footprinting, I've observed both metal inducible and noninducible interactions at the promoter of MT-I. From these results I've been able to limit the possible mechanisms by which metal responsive trans-acting factors induce transcription. These interpretations correlate with a second line of experiments involving the stable titration of positive acting factors necessary for induction of MT. I've amplified the promoter of MT to 10^2-10^3 copies per cell by fusing the 5' and 3' ends of the MT gene to the coding region of DHFR and selecting cells for methotrexate resistance. In these cells, there is a metal-specific titration effect, and although it acts at the level of transcription, it appears to be independent of direct DNA binding factors.

Structure of the limbs and its significance for the ecology and systematics of the family Chydoridae. [Translation of: Voprosy Gidrobiologii, p385, 1965]

For an explanation of the dynamics of numbers of chydorids, appearing a massive group in the littoral of fresh water bodies, the structure of the limbs of 29 species was studied.

Key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae of the fauna of the USSR. [Translation from: Larvae and pupae of midges of the subfamily Orthocladiinae of the fauna of the USSR (Diptera, Chironomidae = Tendipedidae) (ed. Pankratova V.Ya.), 51-55. Leningrad, Nauka, 1970. ]

A key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae. Parts of the key refer to the rest of the publication which is not included in this partial translation.

Family: Cladophora Kutzing 1843. identification key. [ Translation from: Flora Slodkowodna Polski 10, 227-263, 1972.]

A description of the algal genus Cladophora from Vol 10 of the ”Freshwater Flora of Poland”. Illustrations are included.

The family of chironomids or midges - Chironomidae. Keys to larvae and pupae [Translation from: Guide to the freshwater invertebrates of the European area of the USSR (Plankton and benthos) (ed. L. A. Kutikova and Ya. I. Starobogatov), p.371-431. Leningrad, Gidrometeoizdat, 1977]

The translation of this section of the larger publication ”Opredelitel' presnovodnykh bespozvonochnykh evropeiskoi chasti SSSR. (Plankton i bentos)” provides identification keys to the larvae and pupae of chironomids that occur in the Soviet Union. The morphology of the larvae of Chironomidae is described in the introductory part.

Efeito de um primer autocondicionante na resistência ao cisalhamento de bráquetes com compósito pré-incorporado

O uso de primers autocondicionantes e de bráquetes com compósito pré-incorporado tem sido apresentado como uma alternativa para a redução de passos clínicos. O propósito deste estudo foi avaliar o efeito de um primer autocondicionante (Transbond Plus Self-Etching Primer - SEP) na resistência ao cisalhamento de bráquetes com compósito pré-incorporado colados in vivo. A amostra consistiu de 92 dentes obtidos de 23 pacientes com indicação prévia de extração de 4 pré-molares. Os dentes foram divididos em 4 grupos, sendo os bráquetes colados pelo mesmo operador, alternando os quadrantes em cada paciente: Grupo 1 (controle) - Ácido fosfórico à 37% + primer (Transbond XT Primer) + compósito (Transbond XT Adhesive Paste) + bráquete convencional; Grupo 2 - Ácido fosfórico à 37% + primer + bráquete com compósito pré-incorporado; Grupo 3 SEP + compósito + bráquete convencional; Grupo 4 - SEP + bráquete com compósito pré-incorporado. Após 30 dias os pré-molares foram extraídos, sendo submetidos ao teste de resistência ao cisalhamento através da uma Máquina de Ensaios Universal, com velocidade de 0,5mm/min. Os dados obtidos pelos grupos foram analisados com 2-way ANOVA (p<0,05). As forças médias e desvios padrão obtidos foram os seguintes: Grupo 1 = 11,35 (2,36) MPa; Grupo 2 = 9,77 (2,49) MPa; Grupo 3 = 10,89 (2,60) MPa; e Grupo 4 = 10,16 (2,75) MPa. Não foi observada diferença significativa entre o uso do SEP e o de condicionador e primer tradicionais (p = 0,948). De qualquer modo, diferenças significativas na força de adesão foram observadas quando utilizados bráquetes com compósito pré-incorporado (p = 0,032). Pode ser concluído que a combinação do primer autocondicionante com o bráquete com compósito pré-incorporado apresentou valores de força de adesão adequados, sendo promissora para uso clínico.

Estudo aleatório e controlado do uso clínico de um primer autocondicionante na colagem de bráquetes ortodônticos

O uso de primers autocondicionantes tem sido proposto como uma alternativa para a redução de passos clínicos. O objetivo deste estudo clínico aleatório e controlado foi avaliar a performance de um sistema autocondicionante (Transbond Plus Self-Etching Primer, 3M Unitek - SEP) comparado a um sistema multipasso convencional (Transbond XT, 3M Unitek - TBXT) de colagem ortodôntica, durante um período de 12 meses. Vinte e oito pacientes participaram deste estudo, sendo estes alocados aos grupos SEP ou TBXT de forma aleatória, através de randomização em bloco. Um total de 548 bráquetes metálicos (Micro-Arch, prescrição Alexander, GAC International, Bohemia, NY) foram colados com uso da pasta adesiva Transbond XT (3M Unitek), sendo todos os produtos manuseados de acordo com as recomendações dos fabricantes. Foram totalizados 276 bráquetes no grupo controle e 272 no segundo. Curvas de sobrevivência Kaplan-Meier e o teste log-rank (p<0,05) foram utilizados para comparar o percentual de falhas adesivas para as duas técnicas. Ao final do período foram verificadas trinta e duas falhas adesivas (bráquetes descolados), sendo 19 (6,98%) falhas quando utilizado o primer autocondicionante (SEP) e 13 (4,71%) quando usado o primer convencional (TBXT). Não houve diferença significante entre a sobrevivência dos bráquetes entre os dois grupos avaliados (log-rank test, p=0,311). Quando a influência de gênero do paciente, arco dentário e tipo dentário (anterior ou posterior) foram analisados, somente o tipo dentário foi achado significante. Bráquetes de dentes posteriores apresentaram uma maior probabilidade de falha adesiva que os colados em dentes anteriores (p=0,013) Os autores concluem que o primer autocondicionante pode ser utilizado para colagem direta de bráquetes ortodônticos sem que sua sobrevivência clínica seja afetada.