MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues

BACKGROUND: Sequence alignment is one of the most important techniques to analyze biological systems. It is also true that the alignment is not complete and we have to develop it to look for more accurate method. In particular, an alignment for homologous sequences with low sequence similarity is not in satisfactory level. Usual methods for aligning protein sequences in recent years use a measure empirically determined. As an example, a measure is usually defined by a combination of two quantities (1) and (2) below: (1) the sum of substitutions between two residue segments, (2) the sum of gap penalties in insertion/deletion region. Such a measure is determined on the assumption that there is no an intersite correlation on the sequences. In this paper, we improve the alignment by taking the correlation of consecutive residues. RESULTS: We introduced a new method of alignment, called MTRAP by introducing a metric defined on compound systems of two sequences. In the benchmark tests by PREFAB 4.0 and HOMSTRAD, our pairwise alignment method gives higher accuracy than other methods such as ClustalW2, TCoffee, MAFFT. Especially for the sequences with sequence identity less than 15%, our method improves the alignment accuracy significantly. Moreover, we also showed that our algorithm works well together with a consistency-based progressive multiple alignment by modifying the TCoffee to use our measure. CONCLUSIONS: We indicated that our method leads to a significant increase in alignment accuracy compared with other methods. Our improvement is especially clear in low identity range of sequences. The source code is available at our web page, whose address is found in the section "Availability and requirements"

Identification of 2ndchromosome region translocated onto the W chromosome by RFLP with EST-cDNA clones in the Gensei-kouken strains of the mulberry silkworm, Bombyx mori L

In silkworms, sex-limited strains are either obtained spontaneously or induced by X-rays or gamma rays. When a fragment of an autosome carrying a dominant allele of those genes responsible for certain characters is translocated onto a W chromosome, the female of the successive generations will express these phenotypic characters and sex discrimination can be facilitated. Gensei-kouken strains are sex-limited strains of silkworms developed by irradiating the pupae with gamma rays, by which a portion of the second chromosome is translocated onto the W chromosome. In these improved strains, the females are yellow-blooded and spin yellow cocoons. By using the EST-cDNA clones mapped on the Z chromosome, we identified the sex according to the polymorphic banding pattern or intensity of the signals. Furthermore, by using the clones on the second chromosome, the region of the second chromosome translocated onto the W chromosome was also defined. In both the A95 and A 96 strains selected for the present study, only the mid-portion of the second chromosome was translocated. The differences in length of the fragments translocated in these strains are discussed

IMPEACHMENT E INTERVENÇÃO MILITAR – SIMILITUDES QUE MARCAM A HISTÓRIA RECENTE DE UM PAÍS REDEMOCRATIZADO HÁ 50 ANOS

A atual crise política, econômica e social do Brasil guarda muitas semelhanças com aquela que desaguou no golpe de 1964 e nos 21 anos de regime militar, do qual o país emergiu somente em 1985, com a eleição de Tancredo Neves no Colégio Eleitoral. Mas as semelhanças não chegam a desenhar uma intervenção militar, como exigem alguns manifestantes nas ruas e vários nas redes sociais da internet. Para compreender tais semelhanças é preciso relembrar e analisar, ainda uma vez, a história recente do país, o contexto mundial e local em que se deu a deposição de João Goulart. E, quanto a esse aspecto, é preciso cuidar o papel desempenhado pela imprensa – 50 anos atrás e agora. O presente artigo pretende promover essa recordação dos fatos e também a comparação entre o ontem e o hoje, como forma de criar condições para o pleno entendimento do que acontece no atual momento do país

Rearrangement of Variable Region T Cell Receptor y Genes in Acute Lymphoblastic Leukemia Vy Gene Usage Differs in Mature and Immature T Cells

Using probes recognizing variable regions (V gamma) and joining regions (J gamma) of the T cell receptor (TCR) gamma gene, we have analyzed the usage of V gamma genes in 24 patients with T cell acute lymphoblastic leukemia (ALL) and 36 patients with B-precursor ALL. In CD3- T-ALL derived from immature T cells, V gamma genes more proximal to J gamma were frequently rearranged; V gamma 8, V gamma 9, V gamma 10, and V gamma 11 were used in 19 of 24 rearrangements. In contrast, CD3+ T-ALL derived from a more mature stage of T cell ontogeny, showed a high frequency of rearrangements involving V gamma genes distal to J gamma; V gamma 2, V gamma 3, V gamma 4, and V gamma 5 were used in 17 of 25 rearrangements. In B-precursor ALL, no notable bias of V gamma gene usage was observed. This probably reflects the possibility that TCR genes may not rearrange according to a T cell hierarchy when under control of a B cell gene program. Furthermore, deletions of those V gamma genes located 3' to rearranged V gamma genes were observed in all patients analyzed. This supports the theory that loop deletion is a major mechanism for TCR-gamma gene rearrangement

A importância dos jogos educativos na aprendizagem da multiplicação com alunos que apresentam deficiência intelectual e cursam a 5ª série do Colégio Estadual Vítor Soares

Este artigo foi elaborado como Trabalho de Conclusão de Curso da Especialização em Atendimento Educacional Especializado (AEE). O estudo foi realizado no Colégio Estadual Vítor Soares, na cidade de Salvador. Pelo fato desta unidade escolar promover a inclusão de alunos com deficiência, foi implantada pela Secretaria de Educação do Estado da Bahia, através da Coordenação de Educação Especial, equipada com recursos do Ministério da Educação (MEC), uma Sala de Recursos Multifuncionais que oferece o AEE, no turno oposto, ao dos alunos matriculados no ensino regular que apresentam algum tipo de deficiência. Teve como público alvo quatro alunos com deficiência intelectual que frequentam a 5ª série do referido colégio. Por ser esta sala um espaço organizado com materiais pedagógicos, equipamentos e profissionais que atendem às necessidades educacionais desse aluno, por meio do desenvolvimento de estratégias que permitam a construção do conhecimento, o jogo torna-se uma ferramenta fundamental nesse processo de aprendizagem. O resultado foi muito satisfatório, pois é evidente o interesse e a participação dos alunos na atividade, além de dar a oportunidade ao professor de presenciar a construção do pensamento lógico dos mesmos.Palavras-chave: Deficiência intelectual. Jogos. Inclusão

High Excess Risk of Heart Disease Mortality among Hiroshima Atomic Bomb Male Survivors Exposed Near the Hypocenter

Heart disease (HD) mortality is the second leading cause of death in Japan. The HD mortality risk among Atomic bomb survivors is slightly positive but shows a statistically significant dose-response relationship with initial radiation dose, as reported by the Radiation Effects Research Foundation. In that report, dosimetry was based on initial radiation only, with the effect of indirect radiation dose not taken into consideration. The atomic bomb radiation, however, consisted of both initial and residual radiation. We reevaluated the dose-response relationship for HD mortality using exposure distance (ground distance between the location where exposed and the hypocenter) as a surrogate indicator of radiation dose. At Hiroshima University, a cohort study has been conducted with Hiroshima Atomic Bomb Survivors (ABS) since 1970. We selected 29605 subjects from the ABS who were exposed at 3.5 km or less from the hypocenter and alive on January 1, 1970. These subjects, referred to as “Hiroshima hibakusha” in this paper, were followed until December 31, 2010. We stratified the cohort data with respect to sex and age at the time of bombing (ATB) into 10-year age groups. For each stratum, by applying an extended Cox regression model with time-dependent covariates, we analyzed the risk of HD mortality using either initial radiation dose or exposure distance as an explanatory variable. The results indicate a high excess risk in males and older age ATB females who were exposed near the hypocenter. This difference may be explained by the effect of female sex hormone on the circulatory system among young age ATB females. Some unknown risk factor related to exposure distance was also implicated in the elevated risk of HD among the Hiroshima hibakusha, especially in males. This necessitates further study.This research was supported in part by Grants-in-Aid for Scientific Research (A) 24249039 (2012–2014), and the Joint Usage/Research Center (RIRBM), Hiroshima University

Anatomical characteristics of the rectus abdominis and transversus abdominis muscles related to ultrasound-guided rectus sheath block for analgesia around the umbilicus in healthy adult Japanese volunteers

Background: The rectus abdominis muscle partially overlaps with the transversus abdominis muscle belly when following cephalad. This study aimed to evaluate the overlapping properties between the rectus abdominis muscle and the transversus abdominis muscle belly in relation to the performance of ultrasound-guided rectus sheath block for analgesia around the umbilicus.Methods: After obtaining institutional approval and written informed consent, ultrasound examinations of bilateral abdominal walls were performed in healthy adult Japanese volunteers. The craniocaudal distance from the level of the umbilicus to the point where the rectus abdominis muscle and the transversus abdominis muscle belly begin to overlap on the ultrasound image was measured.Results: Sixty hemi-abdominal walls were examined in 30 volunteers (15 males, 32±6 years old, and 15 females, 31±5 years old). The craniocaudal distance from the level of the umbilicus to the point where the rectus abdominis muscle and the transversus abdominis muscle belly begin to overlap on the ultrasound image (left side/right side) was 17.4±11.8/18.8±13.3 mm in male subjects and 19.5±11.5/21.2±12.4 mm in female subjects, respectively. At the level of the umbilicus, overlapping of the two muscles was observed only in 2 of 60 subjects. At 45 mm cephalad from the level of the umbilicus, the two muscles began to overlap in 58 of 60 subjects (96.7%).Conclusions: The position where the rectus abdominis muscle and transversus abdominis muscle belly begin to overlap as detected by ultrasound imaging is approximately 20 mm cephalad to the umbilicus

看護学生の老人のイメージについて

本研究は、老年人口割合の高い地域における看護学生の老人イメージを明らかにすること、それによって老人看護の学習を進めていくための示唆を得ようとするものである。調査の結果、学生の身体機能に関する老人イメージは否定的イメージが多かったが、社会的存在としての老人イメージは老人が生き生きと活動しているものが多く、また老人の自己決定を尊重し、老人を受け入れる態度があった。これは三世帯家族の割合の高さや老人と日頃身近にふれあう体験によるものと考えられる

Macrophage centripetal migration drives spontaneous healing process after spinal cord injury.

Traumatic spinal cord injury (SCI) brings numerous inflammatory cells, including macrophages, from the circulating blood to lesions, but pathophysiological impact resulting from spatiotemporal dynamics of macrophages is unknown. Here, we show that macrophages centripetally migrate toward the lesion epicenter after infiltrating into the wide range of spinal cord, depending on the gradient of chemoattractant C5a. However, macrophages lacking interferon regulatory factor 8 (IRF8) cannot migrate toward the epicenter and remain widely scattered in the injured cord with profound axonal loss and little remyelination, resulting in a poor functional outcome after SCI. Time-lapse imaging and P2X/YRs blockade revealed that macrophage migration via IRF8 was caused by purinergic receptors involved in the C5a-directed migration. Conversely, pharmacological promotion of IRF8 activation facilitated macrophage centripetal movement, thereby improving the SCI recovery. Our findings reveal the importance of macrophage centripetal migration via IRF8, providing a novel therapeutic target for central nervous system injury