Assignment of Putative Functions to Membrane "Hypothetical Proteins" from the Trypanosoma cruzi Genome

Protozoan parasites cause thousands of deaths each year in developing countries. The genome projects of these parasites opened a new era in the identification of therapeutic targets. However, the putative function could be predicted for fewer than half of the protein-coding genes. In this work, all Trypanosoma cruzi proteins containing predicted transmembrane spans were processed through an automated computational routine and further analyzed in order to assign the most probable function. The analysis consisted of dissecting the whole predicted protein in different regions. More than 5,000 sequences were processed, and the predicted biological functions were grouped into 19 categories according to the hits obtained after analysis. One focus of interest, due to the scarce information available on trypanosomatids, is the proteins involved in signal-transduction processes. In the present work, we identified 54 proteins belonging to this group, which were individually analyzed. The results show that by means of a simple pipeline it was possible to attribute probable functions to sequences annotated as coding for "hypothetical proteins.'' Also, we successfully identified the majority of candidates participating in the signal-transduction pathways in T. cruzi.

Disentangling social networks from spatiotemporal dynamics: the temporal structure of a dolphin society

Social networks are static illustrations of dynamic societies, within which social interactions are constantly changing. Fundamental sources of variation include ranging behaviour and temporal demographic changes. Spatiotemporal dynamics can favour or limit opportunities for individuals to interact, and then a network may not essentially represent social processes. We examined whether a social network can embed such nonsocial effects in its topology, whereby emerging modules depict spatially or temporally segregated individuals. To this end, we applied a combination of spatial, temporal and demographic analyses to a long-term study of the association patterns of Guiana dolphins, Sotalia guianensis. We found that association patterns are organized into a modular social network. Space use was unlikely to reflect these modules, since dolphins' ranging behaviour clearly overlapped. However, a temporal demographic turnover, caused by the exit/entrance of individuals (most likely emigration/immigration), defined three modules of associations occurring at different times. Although this factor could mask real social processes, we identified the temporal scale that allowed us to account for these demographic effects. By looking within this turnover period (32 months), we assessed fission-fusion dynamics of the poorly known social organization of Guiana dolphins. We highlight that spatiotemporal dynamics can strongly influence the structure of social networks. Our findings show that hypothetical social units can emerge due to the temporal opportunities for individuals to interact. Therefore, a thorough search for a satisfactory spatiotemporal scale that removes such nonsocial noise is critical when analysing a social system. (C) 2012 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Priorização de pacientes em emergências médicas: uma análise ética

Objetivo: Identificar e analisar, à luz de referencial ético, as escolhas e justificativas de profissionais de saúde pública em situações hipotéticas de priorização de pacientes em casos de limitações de recursos no atendimento de emergências médicas. Métodos: Pesquisa qualiquantitativa, mediante entrevistas com 80 profissionais de saúde pública, pós-graduandos (mestrado e doutorado) em Saúde Pública, aos quais foram apresentadas situações hipotéticas, envolvendo os critérios de sexo, idade e responsabilidade, sendo requeridos que escolhessem entre alternativas que se referiam à existência de pessoas, correndo risco igual de vida, que necessitam de atendimento em um serviço de emergência. Resultados: As escolhas priorizaram crianças, jovens, mulheres e casadas, com a tomada de decisão invocando os princípios éticos de vulnerabilidade, utilidade social e equidade. Conclusão: A pesquisa mostra clara tendência de justificativas das escolhas feitas, orientadas pela ética utilitarista.

Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

Background: Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results: Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome). B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4). The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions: Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly.

The remarkable solar twin HIP 56948: a prime target in the quest for other Earths

Context. The Sun shows abundance anomalies relative to most solar twins. If the abundance peculiarities are due to the formation of inner rocky planets, that would mean that only a small fraction of solar type stars may host terrestrial planets. Aims. In this work we study HIP 56948, the best solar twin known to date, to determine with an unparalleled precision how similar it is to the Sun in its physical properties, chemical composition and planet architecture. We explore whether the abundances anomalies may be due to pollution from stellar ejecta or to terrestrial planet formation. Methods. We perform a differential abundance analysis (both in LTE and NLTE) using high resolution (R similar to 100 000) high S/N (600-650) Keck HIRES spectra of the Sun (as reflected from the asteroid Ceres) and HIP 56948. We use precise radial velocity data from the McDonald and Keck observatories to search for planets around this star. Results. We achieve a precision of sigma less than or similar to 0.003 dex for several elements. Including errors in stellar parameters the total uncertainty is as low as sigma similar or equal to 0.005 dex (1%), which is unprecedented in elemental abundance studies. The similarities between HIP 56948 and the Sun are astonishing. HIP 56948 is only 17 +/- 7 K hotter than the Sun, and log g, [Fe/H] and microturbulence velocity are only +0.02 +/- 0.02 dex, +0.02 +/- 0.01 dex and +0.01 +/- 0.01 km s(-1) higher than solar, respectively. Our precise stellar parameters and a differential isochrone analysis shows that HIP 56948 has a mass of 1.02 +/- 0.02 M-circle dot and that it is similar to 1 Gyr younger than the Sun, as constrained by isochrones, chromospheric activity, Li and rotation. Both stars show a chemical abundance pattern that differs from most solar twins, but the refractory elements (those with condensation temperature T-cond greater than or similar to 1000 K) are slightly (similar to 0.01 dex) more depleted in the Sun than in HIP 56948. The trend with T-cond in differential abundances (twins -HIP 56948) can be reproduced very well by adding similar to 3 M-circle plus of a mix of Earth and meteoritic material, to the convection zone of HIP 56948. The element-to-element scatter of the Earth/meteoritic mix for the case of hypothetical rocky planets around HIP 56948 is only 0.0047 dex. From our radial velocity monitoring we find no indications of giant planets interior to or within the habitable zone of HIP 56948. Conclusions. We conclude that HIP 56948 is an excellent candidate to host a planetary system like our own, including the possible presence of inner terrestrial planets. Its striking similarity to the Sun and its mature age makes HIP 56948 a prime target in the quest for other Earths and SETI endeavors.

Lsa30, a novel adhesin of Leptospira interrogans binds human plasminogen and the complement regulator C4bp

Pathogenic Leptospira is the etiological agent of leptospirosis, a life-threatening disease that affects populations worldwide. Surface proteins have the potential to promote several activities, including adhesion. This work aimed to study the leptospiral coding sequence (CDS) LIC11087, genome annotated as hypothetical outer membrane protein. The LIC11087 gene was cloned and expressed in Escherichia coil BL21 (DE3) strain by using the expression vector pAE. The recombinant protein tagged with N-terminal 6XHis was purified by metal-charged chromatography and characterized by circular dichroism (CD) spectroscopy. The recombinant protein has the ability to mediate attachment to the extracellular matrix (ECM) components, laminin and plasma fibronectin, and was named Lsa30 (Leptospiral surface adhesin of 30 kDa). Lsa30 binds to laminin and to plasma fibronectin in a dose-dependent and saturable manner, with dissociation equilibrium constants (K-D) of 292 +/- 24 nM and 157 +/- 35 nM, respectively. Moreover, the Lsa30 is a plasminogen (PLC) receptor, capable of generating plasmin, in the presence of activator. This protein may interfere with the complement cascade by interacting with C4bp regulator. The Lsa30 is probably a new surface protein of Leptospira as revealed by immunofluorescence assays with living organisms and the reactivity with antibodies present in serum samples of experimentally infected hamsters. Thus, Lsa30 is a novel versatile protein that may play a role in mediating adhesion and may help pathogenic Leptospira to overcome tissue barriers and to escape the immune system. (C) 2012 Elsevier Ltd. All rights reserved.

Cost-effectiveness and budget impact of saxagliptine as additional therapy to metformin for the treatment of diabetes mellitus type 2 in the Brazilian private health system

Cost-effectiveness and budget impact of saxagliptine as additional therapy to metformin for the treatment of diabetes mellitus type 2 in the Brazilian private health system Objectives: To compare costs and clinical benefits of three additional therapies to metformin (MF) for patients with diabetes mellitus type 2 (DM2). Methods: A discrete event simulation model seas built to estimate the cost-utility ratio (cost per quality-adjusted life years [QALY)) of saxagliptine as an additional therapy to MF when compared to rosiglitazone or pioglitazone. A budget impact model (BIM) was built to simulate the economic impact of saxagliptine use in the context of the Brazilian private health system. Results: The acquiring medication costs for the hypothetical patient group analyzed in a time frame of three years, were R$ 10,850,185, R$ 14,836,265 and R$ 14,679,099 for saxagliptine, pioglitazone and rosiglitazone, respectively. Saxagliptine showed lower costs and greater effectiveness in both comparisons, with projected savings for the first three years of R$ 3,874 and R$ 3,996, respectively. The BIM estimated cumulative savings of R$ 417,958 with the repayment of saxagliptine in three years from the perspective of a health plan with 1,000,000 covered individuals. Conclusion: From the perspective of private paying source, the projection is that adding saxagliptine with MF save costs when compared with the addition of rosiglitazone or pioglitazone in patients with DM2 that have not reached the HbA1c goal with metformin monotherapy. The BIM of including saxagliptine in the reimbursement lists of health plans indicated significant savings on the three-year horizon.

Squamous Cell Carcinoma of Mammary Gland in Domestic Cat

Background: In the feline species, 80% to 93% of neoplasias in the mammary gland are malignant, being the majority carcinomas. Among them, there is the mammary squamous cell carcinoma, which amounts to a very rare neoplasm in the domestic cat, with considerable potential for malignancy. This study aimed to report a case of squamous cell mammary carcinoma in the feline species. Case: A female cat, mixed breed, ten years old, presented history of skin lesion. The cat had been spayed two years before, but with previous administration of contraceptives. At the physical examination, it was observed ulcer between the caudal abdominal mammary glands. The occurrence of skin or mammary neoplasia was conceived. The following complementary tests were requested: complete blood count, serum biochemical profile (renal and hepatic), chest radiographs, abdominal ultrasound, and incisional biopsy of the ulcerated region periphery, followed by classic histopathology. The lesion histopathology was compatible with squamous cell carcinoma of the mammary gland. Due to such a diagnosis, bilateral mastectomy was recommended. The material obtained during the surgical procedure was sent for anatomopathological analysis. Microscopically, surgical margins infiltration and a regional lymph node were verified. The owner was advised of the need for complementary therapies and medical monitoring of the cat. However, there was no return. It is noteworthy that the animal's physical and laboratory examinations showed no neoplasia in other regions, being the squamous cell carcinoma of the mammary gland considered primary. Discussion: The malignant mammary neoplasia genesis in feline species, in general, seems to be related to steroid hormones. The ovariectomized females are less likely to develop the disease when compared to intact cats, but there is no protective effect of surgery on those spayed after two years of age regarding the appearance of the neoplasia. Thus, at the time the reported patient was ovariectomized, this effect no longer occurred. The synthetic progestins regularly used to prevent estrus increase by three times the risk of breast carcinomas onset. In humans, there is no clear definition of the etiology and pathogenesis of mammary squamous cell carcinoma. However, it has been suggested its association with extreme forms of squamous metaplasia present in pre-existing mammary adenocarcinoma, besides cysts, chronic inflammations, abscesses and mammary gland adenofibromas. In a hypothetical way, this etiology could also be related to the feline mammary carcinoma, although, for the case at issue, the exogenous and endogenous hormonal influence should not be excluded. It has been reported that mammary squamous cell carcinomas in cats are classified in grades II and III (ie, moderately and poorly differentiated, respectively). Thus, they are considered tumors with more unfavorable prognosis. However, the monitoring of the clinical course, in order to evaluate possible recurrence of the neoplasia and metastases to distant sites, was not possible as the animal under discussion did not return. The squamous cell carcinoma is the most common skin tumor in feline species, despite the primary location in the mammary gland. It is, therefore, important to differentiate squamous cell carcinoma originated in the breast from histological types derived from skin. The description of this special and rare feline mammary carcinoma is important due to its particular characteristics and potential for malignancy.

Criteria for the request of preoperative tests among oral and maxillofacial surgeons

Objective: The aim of this study was to analyze the criteria employed for the requesting of preoperative tests among maxillofacial surgeons. Materials and methods: Thirty maxillofacial surgeons working in Aracaju (Brazil) received a questionnaire to fill out. The study inquired about the practice of requesting preoperative tests for healthy patients scheduled to undergo elective surgery. Results: Most of the surgeons interviewed requested tests that are not recommended for the case in question. The highest frequency of requests was a complete blood count, coagulation test, blood glucose test and chest radiograph. Conclusion: The absence of strict rules for the requesting of preoperative tests causes uncertainty and a lack of criteria regarding pre-surgical conduct. It was not possible to clearly define the criteria used by surgeons for requesting such tests, as the clinical characteristics of the hypothetical case presented suggest a smaller number of tests. (C) 2011 European Association for Cranio-Maxillo-Facial Surgery.

Trypanosoma cruzi Gene Expression in Response to Gamma Radiation

Trypanosoma cruzi is an organism highly resistant to ionizing radiation. Following a dose of 500 Gy of gamma radiation, the fragmented genomic DNA is gradually reconstructed and the pattern of chromosomal bands is restored in less than 48 hours. Cell growth arrests after irradiation but, while DNA is completely fragmented, RNA maintains its integrity. In this work we compared the transcriptional profiles of irradiated and non-irradiated epimastigotes at different time points after irradiation using microarray. In total, 273 genes were differentially expressed; from these, 160 were up-regulated and 113 down-regulated. We found that genes with predicted functions are the most prevalent in the down-regulated gene category. Translation and protein metabolic processes, as well as generation of precursor of metabolites and energy pathways were affected. In contrast, the up-regulated category was mainly composed of obsolete sequences (which included some genes of the kinetoplast DNA), genes coding for hypothetical proteins, and Retrotransposon Hot Spot genes. Finally, the tyrosyl-DNA phosphodiesterase 1, a gene involved in double-strand DNA break repair process, was up-regulated. Our study demonstrated the peculiar response to ionizing radiation, raising questions about how this organism changes its gene expression to manage such a harmful stress.

Influence of caffeine on the survival of leaf-cutting ants Atta sexdens rubropilosa and in vitro growth of their mutualistic fungus

BACKGROUND: Leaf-cutting ants collect plant fresh material for the cultivation of their mutualistic fungus. Atta sexdens rubropilosa Forel (Hymenoptera: Formicidae) cause great economic losses through their foraging activity, mainly in agriculture. The main control method is the application of granulated toxic baits incorporated with an active ingredient (AI). The present goal is to evaluate the effect of caffeine on in vitro growth of the mutualistic fungus and on the survival of the leaf-cutting ants, aiming to verify the potential toxicity of this secondary metabolite over these organisms. RESULTS: Three distinct patterns of fungal growth correlated with caffeine concentration were observed: (1) no effect (0.01% caffeine); (2) intermediate growth reduction (0.05% caffeine); (3) drastic growth reduction (0.10 and 0.50% caffeine). The highest caffeine concentration causes fungus death in the first week. As for insect survival, caffeine does not seem to exert any effect. The treatments with diet containing caffeine showed similar values of M50, irrespective of caffeine concentration. CONCLUSION: As caffeine was shown to reduce growth of the mutualistic fungus of Atta sexdens rubropilosa, but with no conclusive effect on insect survival, a hypothetical explanation for the selection of different Coffea species by this leaf-cutting ant species might be associated with caffeine toxicity to the fungus. Copyright (C) 2011 Society of Chemical Industry

THE ROLE OF TURBULENT MAGNETIC RECONNECTION IN THE FORMATION OF ROTATIONALLY SUPPORTED PROTOSTELLAR DISKS

The formation of protostellar disks out of molecular cloud cores is still not fully understood. Under ideal MHD conditions, the removal of angular momentum from the disk progenitor by the typically embedded magnetic field may prevent the formation of a rotationally supported disk during the main protostellar accretion phase of low-mass stars. This has been known as the magnetic braking problem and the most investigated mechanism to alleviate this problem and help remove the excess of magnetic flux during the star formation process, the so-called ambipolar diffusion (AD), has been shown to be not sufficient to weaken the magnetic braking at least at this stage of the disk formation. In this work, motivated by recent progress in the understanding of magnetic reconnection in turbulent environments, we appeal to the diffusion of magnetic field mediated by magnetic reconnection as an alternative mechanism for removing magnetic flux. We investigate numerically this mechanism during the later phases of the protostellar disk formation and show its high efficiency. By means of fully three-dimensional MHD simulations, we show that the diffusivity arising from turbulent magnetic reconnection is able to transport magnetic flux to the outskirts of the disk progenitor at timescales compatible with the collapse, allowing the formation of a rotationally supported disk around the protostar of dimensions similar to 100 AU, with a nearly Keplerian profile in the early accretion phase. Since MHD turbulence is expected to be present in protostellar disks, this is a natural mechanism for removing magnetic flux excess and allowing the formation of these disks. This mechanism dismisses the necessity of postulating a hypothetical increase of the ohmic resistivity as discussed in the literature. Together with our earlier work which showed that magnetic flux removal from molecular cloud cores is very efficient, this work calls for reconsidering the relative role of AD in the processes of star and planet formation.

Global transcriptional response of Caulobacter crescentus to iron availability

Abstract Background In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. Results In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility. Conclusions Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms.

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks

The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical behavior displaying the degree of robustness typical of the biological cell cycle. The structure of our PGN model was inspired in well-established biological facts such as the existence of integrator subsystems, negative and positive feedback loops, and redundant signaling pathways. Our model represents genes interactions as stochastic processes and presents strong robustness in the presence of moderate noise and parameters fluctuations. A recently published deterministic yeast cell-cycle model does not perform as well as our PGN model, even upon moderate noise conditions. In addition, self stimulatory mechanisms can give our PGN model the possibility of having a pacemaker activity similar to the observed in the oscillatory embryonic cell cycle.