Use of chromosome microdissection in fish molecular cytogenetics

Chromosome microdissection is a technique in which whole chromosomes or chromosomal segments are dissected under an inverted microscope yielding chromosome-specific sequences. Several protocol modifications introduced during the past 15 years reduced the number of chromosomes required for most applications. This is of particular interest to fish molecular cytogenetics, since most species present highly uniform karyotypes which make impossible the collection of multiple copies of the same chromosome. Probes developed in this manner can be used to investigate chromosome homologies in closely related species. Here we describe a protocol recently used in the gymnotiform species group Eigenmannia and review the major steps involved in the generation of these markers focusing on protocol modifications aiming to reduce the number of required chromosomes.

Hemigrammus arua, a new species of characid (Characiformes: Characidae) from the lower Amazon, Brazil

A new Hemigrammus species is described from tributaries of the igarapé Juruti Grande and rio Arapiuns, lower rio Amazonas, Pará State, Brazil. The new species can be easily diagnosed from all its congeners, except from Hemigrammus stictus (Durbin), by possessing a single, large humeral spot which extends longitudinally from the fifth or sixth to the posterior margin of eighth to tenth, lateral line scales. It can be distinguished from Hemigrammus stictus by possessing a pronounced upper, anteriorly-oriented extension in the humeral blotch, conferring an inverted-comma shape to it, and by displaying a distinct life color pattern.

Sources of variation of energy and nutrient intake among adolescents in São Paulo, Brazil

The aim of the current study was to describe the sources of variation of energy and nutrient intake and to calculate the number of repetitions of diet measurements to estimate usual intake in adolescents from São Paulo, Brazil. Data was collected using 24-hour dietary recalls (24hR) in 273 adolescents between 2007 and 2008. Individuals completed a repeat 24hR around two months later. The sources of variation were estimated using the random effect model. Variance ratios (within-person to between-person variance ratio) and the number of repetitions of 24hR to estimate usual intake were calculated. The principal source of variation was due to within-person variance. The contribution of day of week and month of year was less than 8%. Variations ranged from 1.15 for calcium to 7.31 for vitamin E. The number of 24hR repeats required to estimate usual intake varied according to nutrient and gender, numbering 15 for males and 8 for females.

Morfologia dos órgãos genitais masculinos e da cloaca da ema (Rhea americana americana)

As características morfológicas, macroscópicas e microscópicas, dos órgãos genitais masculinos e da cloaca foram analisados em 23 emas, quatro filhotes (duas semanas), sete jovens (de três a oito meses) e doze adultos (três anos), provenientes da Cooperativa Emas do Brasil, RS, e do CEMAS, Mossoró, RN. Os testículos da ema possuem formato alongado e localizam-se na cavidade celomática, na região intra-abdominal dorsal, com comprimento e larguras médias de 7,6±1,2cm e 2,6± 0,7cm nos adultos; 4,5±1,5cm e 0,9±0,4cm nos jovens; e 0,8±0,3cm, e 0,2±0,1cm nos filhotes. O testículo está envolto pela túnica albugínea e seu parênquima possui túbulos seminíferos irregulares, compostos por epitélio espermatogênico e por células de sustentação, e pelo tecido intersticial, com as células endócrinas intersticiais, tecido conjuntivo frouxo e vasos. Nos adultos observaram-se todas as células da linhagem espermatogênica, enquanto nos jovens com 3 meses, os testículos apresentaram túbulos seminíferos com luz reduzidas, espermatogônias e células de sustentação indiferenciadas. Os ductos eferentes possuem um epitélio cúbico ciliado, enquanto no ducto epididimário o epitélio é columnar. O epidídimo apresentou-se alongado e fusiforme junto a margem medial do testículo. O ducto deferentes apresentou trajeto sinuoso nos adultos, retilíneo nos jovens, convoluto na sua porção média, diminuindo seu formato sigmóide em sua porção caudal, próximo à cloaca. O epitélio é pseudoestratificado e reveste a luz irregular nos adultos e circular nos jovens, mantendo proximidade com o ureter. A cloaca dividiu-se em três segmentos: o coprodeu, o urodeo e o proctodeo. No urodeu os ductos deferentes desembocaram em papilas na parede ventro-lateral, próximo a inserção do falo fibroso. O falo é um órgão fibroso linfático, localizado na parede ventral, no assoalho da cloaca, e apresentou duas porções: uma rígida bifurcada e contorcida, e outra simples espiralada e flexível, a qual normalmente esteve invertida. Em exposição forçada, o falo teve 14 cm de comprimento. De forma geral os órgãos reprodutores das emas compartilharam da morfologia de outras aves, principalmente aquelas descritas para os avestruzes.

Prevalência de anticorpos anti-Chlamydophila spp. em propriedades rurais com histórico de aborto bovino no estado do Paraná

Chlamydophila abortus é o agente etiológico do aborto epizoótico bovino, cujas manifestações clínicas mais freqüentes são aborto, nascimento de bezerros prematuros e de animais fracos, natimorto e repetição de cio em intervalos irregulares. O objetivo deste trabalho foi estimar a prevalência de anticorpos anti-Chlamydophila spp. em fêmeas bovinas de propriedades rurais com histórico de aborto, selecionadas dentro do delineamento amostral do Plano Nacional de Controle e Erradicação da Brucelose e Tuberculose no estado do Paraná. Foram testadas pela prova de fixação de complemento 3.102 amostras de soro de fêmeas bovinas (idade > 24 meses), provenientes de 373 propriedades. Ao total, 44 (1,42%) animais foram positivos com títulos > 32. A prevalência de focos foi de 8,82% (6,15%-12,17%). Animais confinados ou semi-confinados (OR=3.339, P=0.004), propriedade com menos de 35 matrizes (OR=3.339, P=0.017), presença de produtos do aborto na pastagem (OR=2.372, P=0.037) e aluguel de pasto (OR=3.398, P=0.006) foram considerados fatores de risco para Chlamydophila spp. A infecção por Chlamydophila spp. acometeu um número pequeno de animais, oriundos de propriedades com histórico de aborto. A importância deste agente como causa de aborto em bovinos no estado do Paraná, se existir, é muito pequena.

Dose-response effects of systemic anandamide administration in mice sequentially submitted to the open field and elevated plus-maze tests

The endocannabinoid system is involved in the control of many physiological functions, including the control of emotional states. In rodents, previous exposure to an open field increases the anxiety-like behavior in the elevated plus-maze. Anxiolytic-like effects of pharmacological compounds that increase endocannabinoid levels have been well documented. However, these effects are more evident in animals with high anxiety levels. Several studies have described characteristic inverted U-shaped dose-response effects of drugs that modulate the endocannabinoid levels. However, there are no studies showing the effects of different doses of exogenous anandamide, an endocannabinoid, in animal models of anxiety. Thus, in the present study, we determined the dose-response effects of exogenous anandamide at doses of 0.01, 0.1, and 1.0 mg/kg in C57BL/6 mice (N = 10/group) sequentially submitted to the open field and elevated plus-maze. Anandamide was diluted in 0.9% saline, ethyl alcohol, Emulphor® (18:1:1) and administered ip (0.1 mL/10 g body weight); control animals received the same volume of anandamide vehicle. Anandamide at the dose of 0.1 mg/kg (but not of 0.01 or 1 mg/kg) increased (P < 0.05) the time spent and the distance covered in the central zone of the open field, as well as the exploration of the open arms of the elevated plus-maze. Thus, exogenous anandamide, like pharmacological compounds that increase endocannabinoid levels, promoted a characteristic inverted U-shaped dose-response effect in animal models of anxiety. Furthermore, anandamide (0.1 mg/kg) induced an anxiolytic-like effect in the elevated plus-maze (P < 0.05) after exposing the animals to the open field test.

Fontes de variação da ingestão de energia e nutrientes entre adolescentes do Município de São Paulo, Brasil

Este estudo propôs-se a descrever as fontes de variação da ingestão de energia e nutrientes e calcular o número de dias necessários para a estimativa da ingestão habitual em adolescentes do Município de São Paulo, Brasil. Foi aplicado um recordatório alimentar de 24 horas (R24h) em 273 adolescentes, durante os anos de 2007 e 2008, e posteriormente cada indivíduo foi convidado a responder a outro R24h. Foram estimadas as fontes de variação da ingestão utilizando-se modelo de efeitos aleatórios. A variância intrapessoal foi o componente de variância que mais contribuiu para a variabilidade da ingestão de energia e nutrientes, ao passo que a contribuição do dia da semana e mês do ano foi pequena (< 8por cento ) para a variabilidade total da ingestão. As razões de variância variaram de 1,15 para o cálcio a 7,31 para a vitamina E. O número de R24h necessário para estimar a ingestão habitual variou de acordo com o nutriente: em torno de 15 para o sexo masculino e 8 para o feminino

Relationship of autonomic imbalance and circadian disruption with obesity and type 2 diabetes in resistant hypertensive patients

Background: Hypertension, diabetes and obesity are not isolated findings, but a series of interacting interactive physiologic derangements. Taking into account genetic background and lifestyle behavior, AI (autonomic imbalance) could be a common root for RHTN (resistant hypertension) or RHTN plus type 2 diabetes (T2D) comorbidity development. Moreover, circadian disruption can lead to metabolic and vasomotor impairments such as obesity, insulin resistance and resistant hypertension. In order to better understand the triggered emergence of obesity and T2D comorbidity in resistant hypertension, we investigated the pattern of autonomic activity in the circadian rhythm in RHTN with and without type 2 diabetes (T2D), and its relationship with serum adiponectin concentration. Methods: Twenty five RHTN patients (15 non-T2D and 10 T2D, 15 males, 10 females; age range 34 to 70 years) were evaluated using the following parameters: BMI (body mass index), biochemical analysis, serum adiponectinemia, echocardiogram and ambulatory electrocardiograph heart rate variability (HRV) in time and frequency domains stratified into three periods: 24 hour, day time and night time. Results: Both groups demonstrated similar characteristics despite of the laboratory analysis concerning T2D like fasting glucose, HbA1c levels and hypertriglyceridemia. Both groups also revealed disruption of the circadian rhythm: inverted sympathetic and parasympathetic tones during day (parasympathetic > sympathetic tone) and night periods (sympathetic > parasympathetic tone). T2D group had increased BMI and serum triglyceride levels (mean 33.7 +/- 4.0 vs 26.6 +/- 3.7 kg/m(2) - p = 0.00; 254.8 +/- 226.4 vs 108.6 +/- 48.7 mg/dL - p = 0.04), lower levels of adiponectin (6729.7 +/- 3381.5 vs 10911.5 +/- 5554.0 ng/mL - p = 0.04) and greater autonomic imbalance evaluated by HRV parameters in time domain compared to non-T2D RHTN patients. Total patients had HRV correlated positively with serum adiponectin (r = 0.37 [95% CI - 0.04 - 1.00] p = 0.03), negatively with HbA1c levels (r = -0.58 [95% CI -1.00 - -0.3] p = 0.00) and also adiponectin correlated negatively with HbA1c levels (r = -0.40 [95% CI -1.00 - -0.07] p = 0.02). Conclusion: Type 2 diabetes comorbidity is associated with greater autonomic imbalance, lower adiponectin levels and greater BMI in RHTN patients. Similar circadian disruption was also found in both groups indicating the importance of lifestyle behavior in the genesis of RHTN.

Placentation in Sigmodontinae: a rodent taxon native to South America

Background: Sigmodontinae, known as ""New World rats and mice,"" is a large subfamily of Cricetidae for which we herein provide the first comprehensive investigation of the placenta. Methods: Placentas of various gestational ages ranging from early pregnancy to near term were obtained for five genera, i.e. Necromys, Euryoryzomys, Cerradomys, Hylaeamys, and Oligoryzomys. They were investigated by means of histology, immunohistochemistry, a proliferation marker, DBA-lectin staining and transmission electron microscopy. Results: The chorioallantoic placenta was organized in a labyrinthine zone, spongy zone and decidua and an inverted yolk sac persisted until term. The chorioallantoic placenta was hemotrichorial. The interhemal barrier comprised fetal capillary endothelium and three layers of trophoblast, an outermost, cellular layer and two syncytial ones, with interspersed trophoblast giant cells (TGC). In addition, accumulations of TGC occurred below Reichert's membrane. The junctional zone contained syncytial trophoblast, proliferative cellular trophoblast, glycogen cells and TGC that were situated near to the maternal blood channels. In three of the genera, TGC were also accumulated in distinct areas at the placental periphery. PAS-positive glycogen cells derived from the junctional zone invaded the decidua. Abundant maternal uNK cells with positive response to PAS, vimentin and DBA-lectin were found in the decidua. The visceral yolk sac was completely inverted and villous. Conclusion: The general aspect of the fetal membranes in Sigmodontinae resembled that found in other cricetid rodents. Compared to murid rodents there were larger numbers of giant cells and in some genera these were seen to congregate at the periphery of the placental disk. Glycogen cells were found to invade the decidua but we did not identify trophoblast in the walls of the deeper decidual arteries. In contrast these vessels were surrounded by large numbers of uNK cells. This survey of wild-trapped specimens from five genera is a useful starting point for the study of placentation in an important subfamily of South American rodents. We note, however, that some of these rodents can be captive bred and recommend that future studies focus on the study of time dated pregnancies.

Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli

Background: Leifsonia xyli is a xylem-inhabiting bacterial species comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp. cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in sugarcane commercial fields and Lxc colonizes the xylem of several grasses causing either mild or no symptoms of disease. The completely sequenced genome of Lxx provided insights into its biology and pathogenicity. Since IS elements are largely reported as an important source of bacterial genome diversification and nothing is known about their role in chromosome architecture of L. xyli, a comparative analysis of Lxc and Lxx elements was performed. Results: Sample sequencing of Lxc genome and comparative analysis with Lxx complete DNA sequence revealed a variable number of IS transposable elements acting upon genomic diversity. A detailed characterization of Lxc IS elements and a comparative review with IS elements of Lxx are presented. Each genome showed a unique set of elements although related to same IS families when considering features such as similarity among transposases, inverted and direct repeats, and element size. Most of the Lxc and Lxx IS families assigned were reported to maintain transposition at low levels using translation regulatory mechanisms, consistent with our in silico analysis. Some of the IS elements were found associated with rearrangements and specific regions of each genome. Differences were also found in the effect of IS elements upon insertion, although none of the elements were preferentially associated with gene disruption. A survey of transposases among genomes of Actinobacteria showed no correlation between phylogenetic relatedness and distribution of IS families. By using Southern hybridization, we suggested that diversification of Lxc isolates is also mediated by insertion sequences in probably recent events. Conclusion: Collectively our data indicate that transposable elements are involved in genome diversification of Lxc and Lxx. The IS elements were probably acquired after the divergence of the two subspecies and are associated with genome organization and gene contents. In addition to enhancing understanding of IS element dynamics in general, these data will contribute to our ongoing comparative analyses aimed at understanding the biological differences of the Lxc and Lxx.

New constraints on muon-neutrino to electron-neutrino transitions in MINOS

This paper reports results from a search for nu(mu) -> nu(e) transitions by the MINOS experiment based on a 7 x 10(20) protons-on-target exposure. Our observation of 54 candidate nu(e) events in the far detector with a background of 49.1 +/- 7.0(stat) +/- 2.7(syst) events predicted by the measurements in the near detector requires 2sin(2)(2 theta(13))sin(2)theta(23) < 0.12(0.20) at the 90% C.L. for the normal (inverted) mass hierarchy at delta(CP) = 0. The experiment sets the tightest limits to date on the value of theta(13) for nearly all values of delta(CP) for the normal neutrino mass hierarchy and maximal sin(2)(2 theta(23)).

Testing for large extra dimensions with neutrino oscillations

We consider a model where sterile neutrinos can propagate in a large compactified extra dimension giving rise to Kaluza-Klein (KK) modes and the standard model left-handed neutrinos are confined to a 4-dimensional spacetime brane. The KK modes mix with the standard neutrinos modifying their oscillation pattern. We examine former and current experiments such as CHOOZ, KamLAND, and MINOS to estimate the impact of the possible presence of such KK modes on the determination of the neutrino oscillation parameters and simultaneously obtain limits on the size of the largest extra dimension. We found that the presence of the KK modes does not essentially improve the quality of the fit compared to the case of the standard oscillation. By combining the results from CHOOZ, KamLAND, and MINOS, in the limit of a vanishing lightest neutrino mass, we obtain the stronger bound on the size of the extra dimension as similar to 1.0(0.6) mu m at 99% C.L. for normal (inverted) mass hierarchy. If the lightest neutrino mass turns out to be larger, 0.2 eV, for example, we obtain the bound similar to 0.1 mu m. We also discuss the expected sensitivities on the size of the extra dimension for future experiments such as Double CHOOZ, T2K, and NO nu A.

Evidence for zero-differential resistance states in electronic bilayers

We observe zero-differential resistance states at low temperatures and moderate direct currents in a bilayer electron system formed by a wide quantum well. Several regions of vanishing resistance evolve from the inverted peaks of magneto-intersubband oscillations as the current increases. The experiment, supported by a theoretical analysis, suggests that the origin of this phenomenon is based on instability of homogeneous current flow under conditions of negative differential resistivity, which leads to formation of current domains in our sample, similar to the case of single-layer systems.

Transport in disordered two-dimensional topological insulators

The transport properties of the ""inverted"" semiconductor HgTe-based quantum well, recently shown to be a two-dimensional topological insulator, are studied experimentally in the diffusive regime. Nonlocal transport measurements are performed in the absence of magnetic field, and a large signal due to the edge states is observed. This shows that the edge states can propagate over a long distance, similar to 1 mm, and therefore, there is no difference between local and nonlocal electrical measurements in a topological insulator. In the presence of an in-plane magnetic field a strong decrease of the local resistance and complete suppression of the nonlocal resistance is observed. We attribute this behavior to an in-plane magnetic-field-induced transition from the topological insulator state to a conventional bulk metal state.

Lossless filter for multiple repeats with bounded edit distance

Background: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. Results: The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment. Conclusion: To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.