Balanced polymorphism in bottlenecked populations: The case of the CCR5 5 ` cis-regulatory region in Amazonian Amerindians

The 5` cis-regulatory region of the CCR5 gene exhibits a strong signature of balancing selection in several human populations. Here we analyze the polymorphism of this region in Amerindians from Amazonia, who have a complex demographic history, including recent bottlenecks that are known to reduce genetic variability. Amerindians show high nucleotide diversity (pi = 0.27%) and significantly positive Tajima`s D, and carry haplotypes associated with weak and strong gene expression. To evaluate whether these signatures of balancing selection could be explained by demography, we perform neutrality tests based on empiric and simulated data. The observed Tajima`s D was higher than that of other world populations: higher than that found for 18 noncoding regions of South Amerindians, and higher than 99.6% of simulated genealogies, which assume nonequilibrium conditions. Moreover, comparing Amerindians and Asians, the Fst for CCR5 cis-regulatory region was unusually low, in relation to neutral markers. These findings indicate that, despite their complex demographic history, South Amerindians carry a detectable signature of selection on the CCR5 cis-regulatory region. (C) 2010 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Time-lag in biological responses to landscape changes in a highly dynamic Atlantic forest region

Time-lagged responses of biological variables to landscape modifications are widely recognized, but rarely considered in ecological studies. In order to test for the existence of time-lags in the response of trees, small mammals, birds and frogs to changes in fragment area and connectivity, we studied a fragmented and highly dynamic landscape in the Atlantic forest region. We also investigated the biological correlates associated with differential responses among taxonomic groups. Species richness and abundance for four taxonomic groups were measured in 21 secondary forest fragments during the same period (2000-2002), following a standardized protocol. Data analyses were based on power regressions and model selection procedures. The model inputs included present (2000) and past (1962, 1981) fragment areas and connectivity, as well as observed changes in these parameters. Although past landscape structure was particularly relevant for trees, all taxonomic groups (except small mammals) were affected by landscape dynamics, exhibiting a time-lagged response. Furthermore, fragment area was more important for species groups with lower dispersal capacity, while species with higher dispersal ability had stronger responses to connectivity measures. Although these secondary forest fragments still maintain a large fraction of their original biodiversity, the delay in biological response combined with high rates of deforestation and fast forest regeneration imply in a reduction in the average age of the forest. This also indicates that future species losses are likely, especially those that are more strictly-forest dwellers. Conservation actions should be implemented to reduce species extinction, to maintain old-growth forests and to favour the regeneration process. Our results demonstrate that landscape history can strongly affect the present distribution pattern of species in fragmented landscapes, and should be considered in conservation planning. (C) 2009 Elsevier Ltd. All rights reserved.

Iodide Transport Defect: Functional Characterization of a Novel Mutation in the Na(+)/I(-) Symporter 5 `-Untranslated Region in a Patient with Congenital Hypothyroidism

Context: Iodide transport defect (ITD) is an autosomal recessive disorder caused by impaired Na(+)/I(-) symporter (NIS)-mediated active iodide accumulation into thyroid follicular cells. Clinical manifestations comprise a variable degree of congenital hypothyroidism and goiter, and low to absent radioiodide uptake, as determined by thyroid scintigraphy. Hereditary molecular defects in NIS have been shown to cause ITD. Objective: Our objective was to perform molecular studies on NIS in a patient with congenital hypothyroidism presenting a clinical ITD phenotype. Design: The genomic DNA encoding NIS was sequenced, and an in vitro functional study of a newly identified NIS mutation was performed. Results: The analysis revealed the presence of an undescribed homozygous C to T transition at nucleotide -54 (-54C>T) located in the 5`-untranslated region in the NIS sequence. Functional studies in vitro demonstrated that the mutation was associated with a substantial decrease in iodide uptake when transfected into Cos-7 cells. The mutation severely impaired NIS protein expression, although NIS mRNA levels remained similar to those in cells transfected with wild-type NIS, suggesting a translational deficiency elicited by the mutation. Polysome profile analysis demonstrated reduced levels of polyribosomes-associated mutant NIS mRNA, consistent with reduced translation efficiency. Conclusions: We described a novel mutation in the 5`-untranslated region of the NIS gene in a newborn with congenital hypothyroidism bearing a clinical ITD phenotype. Functional evaluation of the molecular mechanism responsible for impaired NIS-mediated iodide concentration in thyroid cells indicated that the identified mutation reduces NIS translation efficiency with a subsequent decrease in protein expression and function. (J Clin Endocrinol Metab 96: E1100-E1107, 2011)

Species diversity of Leishmania (Viannia) parasites circulating in an endemic area for cutaneous leishmaniasis located in the Atlantic rainforest region of northeastern Brazil

OBJECTIVES To identify the aetiological agents of cutaneous leishmaniasis and to investigate the genetic polymorphism of Leishmania (Viannia) parasites circulating in an area with endemic cutaneous leishmaniasis (CL) in the Atlantic rainforest region of northeastern Brazil. METHODS Leishmania spp. isolates came from three sources: (i) patients diagnosed clinically and parasitologically with CL based on primary lesions, secondary lesions, clinical recidiva, mucocutaneous leishmaniasis and scars; (ii) sentinel hamsters, sylvatic or synanthropic small rodents; and (iii) the sand fly species Lutzomyia whitmani. Isolates were characterised using monoclonal antibodies, multilocus enzyme electrophoresis (MLEE) and polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region rDNA locus. RESULTS Seventy-seven isolates were obtained and characterised. All isolates were identified as Leishmania (Viannia) braziliensis serodeme 1 based on reactivity to monoclonal antibodies. MLEE identified 10 zymodemes circulating in the study region. Most isolates were classified as zymodemes closely related to L. (V.) braziliensis, but five isolates were classified as Leishmania (Viannia) shawi. All but three of the identified zymodemes have so far been observed only in the study region. Enzootic transmission and multiclonal infection were observed. CONCLUSIONS Our results confirm that transmission cycle complexity and the co-existence of two or more species in the same area can affect the level of genetic polymorphism in a natural Leishmania population. Although it is not possible to make inferences as to the modes of genetic exchange, one can speculate that some of the zymodemes specific to the region are hybrids of L. (V.) braziliensis and L. (V.) shawi.

Diversity of Somatic Coliphages in Coastal Regions with Different Levels of Anthropogenic Activity in Sao Paulo State, Brazil

Bacteriophages are the most abundant and genetically diverse viruses on Earth, with complex ecology in both quantitative and qualitative terms. Somatic coliphages (SC) have been reported to be good indicators of fecal pollution in seawater. This study focused on determining the concentration of SC and their diversity by electron microscopy of seawater, plankton, and bivalve samples collected at three coastal regions in Sao Paulo, Brazil. The SC counts varied from < 1 to 3.4 x 103 PFU/100 ml in seawater (73 samples tested), from < 1 to 4.7 x 10(2) PFU/g in plankton (46 samples tested), and from < 1 to 2.2 x 10(1) PFU/g in bivalves (11 samples tested). In seawater samples, a relationship between the thermotolerant coliforms and Escherichia coli and SC was observed at the three regions (P = 0.0001) according to the anthropogenic activities present at each region. However, SC were found in plankton samples from three regions: Baixada Santista (17/20), Canal de Sao Sebastiao (6/14), and Ubatuba (3/12). In seawater samples collected from Baixada Santista, four morphotypes were observed: A1 (4.5%), B1 (50%), C1 (36.4%), and D1 (9.1%). One coliphage, Siphoviridae type T1, had the longest tail: between 939 and 995 nm. In plankton samples, Siphoviridae (65.8%), Podoviridae (15.8%), Microviridae (15.8%), and Myoviridae (2.6%) were found. In bivalves, only the morphotype B1 was observed. These SC were associated with enteric hosts: enterobacteria, E. coli, Proteus, Salmonella, and Yersinia. Baixada Santista is an area containing a high level of fecal pollution compared to those in the Canal de Sao Sebastiao and Ubatuba. This is the first report of coliphage diversity in seawater, plankton, and bivalve samples collected from Sao Paulo coastal regions. A better characterization of SC diversity in coastal environments will help with the management and evaluation of the microbiological risks for recreation, seafood cultivation, and consumption.

Search for Salmonella spp. in ostrich productive chain of Brazilian southeast region

We analyzed ostriches from an equipped farm located in the Brazilian southeast region for the presence of Salmonella spp. This bacterium was investigated in 80 samples of ostrich droppings, 90 eggs, 30 samples of feed and 30 samples of droppings from rodents. Additionally, at slaughter-house this bacterium was investigated in droppings, caecal content, spleen, liver and carcasses from 90 slaughtered ostriches from the studied farm. Also, blood serum of those animals were harvested and submitted to serum plate agglutination using commercial Salmonella Pullorum antigen. No Salmonella spp. was detected in any eggs, caecal content, liver, spleen, carcass and droppings from ostriches and rodents. However, Salmonella Javiana and Salmonella enterica subsp. enterica 4, 12: i:- were isolated from some samples of feed. The serologic test was negative for all samples. Good sanitary farming management and the application of HACCP principles and GMP during the slaughtering process could explain the absence of Salmonella spp. in the tested samples.

Genotoxicity and composition of particulate matter from biomass burning in the eastern Brazilian Amazon region

In the present study Tradescantia pallida micronucleus (Trad-MCN) bioassay was used to assess the genotoxicity of particulate matter with a mass median aerodynamic diameter less than 10 pm (PM(10)) in Tangara da Serra (MT), a Brazilian Amazon region that suffers the impact of biomass burning. The levels of PM (coarse and fine size fractions) and black carbon (BC) collected were also measured. Furthermore, the alkanes and polycyclic aromatic hydrocarbons (PAHs) were identified and quantified in the samples taken during the burning period by gas chromatography with flame ionization detection (GC-FID). The PM and BC results for both fractions indicate a strong correlation (p < 0.001). The analysis of alkanes indicates an anthropic influence. Retene was the most abundant PAH found, an indicator of biomass burning, and 12 other PAHs considered to be potentially mutagenic and/or carcinogenic were identified in this sample. The Trad-MCN bioassay showed a significant increase in micronucleus frequency during the period of most intense burning, possibly related to the mutagenic PAHs that were found in such extracts. This study demonstrated that Trad-MCN was sensitive and efficient in evaluating the genotoxicity of organic compounds from biomass burning. It further emphasizes the importance of performing chemical analysis, because changes in chemical composition generally have a negative effect on many living organisms. This bioassay (ex situ), using T. pallida with chemical analysis, is thus recommended for characterizing the genotoxicity of air pollution. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Evaluation of trace element levels in muscles, liver and gonad of fish species from Sao Francisco River of the Parana Brazilian state by using SR-TXRF technique

This study is focused on the analysis of an accumulation of inorganic elements in muscles, liver and gonad of seven fish species from Sao Francisco River located in the Parana state of Brazil. Concentrations of the elements were determined using the SR-TXRF technique. In the muscles of fish species, negative length dependent relationships were observed for chromium and zinc ion absorption. The obtained results showed that accumulated Cr ions values are above the limits defined in the Brazilian legislative norm on food. (C) 2010 Elsevier Ltd All rights reserved.

Tectonic fabric revealed by AARM of the proterozoic mafic dike swarm in the Salvador city (Bahia state): Sao Francisco Craton, NE Brazil

Magnetic fabric and rock magnetism studies were performed on 25 unmetamorphosed mafic dikes of the Meso-Late Proterozoic (similar to 1.02 Ga) dike swarm from Salvador (Bahia State, NE Brazil). This area lies in the north-eastern part of the Sao Francisco Craton, which was dominantly formed/reworked during the Transamazonian orogeny (2.14-1.94 Ga). The dikes crop out along the beaches and in quarries around Salvador city, and cut across both amphibolite dikes and granulites. Their widths range from a few centimeters up to 30 m with an average of similar to 4 m, and show two main trends N 140-190 and N 100-120 with vertical dips. Magnetic fabrics were determined using both anisotropy of low-field magnetic susceptibility (AMS) and anisotropy of anhysteretic remanent magnetization (AARM). The magnetic mineralogy was investigated by many experiments including remanent magnetization measurements at variable low temperatures (10-300 K), Mossbauer spectroscopy, high temperature magnetization curves (25-700 degrees C) and scanning electron microscopy (SEM). The rock magnetism study suggests pseudo-single-domain magnetite grains carrying the bulk magnetic susceptibility and AARM fabrics. The magnetite grains found in these dikes are large and we discard the presence of single-domain grains. Its composition is close to stoichiometric with low Ti substitution, and its Verwey transition occurs around 120 K. The main AMS fabric recognized in the swarm is so-called normal, in which the K(max)-K(int) plane is parallel to the dike plane and the magnetic foliation pole K(min)) is perpendicular to it. This fabric is interpreted as due to magma flow, and analysis of the K m inclination permitted to infer that approximately 80% of the dikes were fed by horizontal or sub-horizontal flows (K(max) < 30 degrees). This interpretation is supported by structural field evidence found in five dikes. In addition, based on the plunge of K(max), two mantle sources could be inferred; one of them which fed about 80% of the swarm would be located in the southern part of the region, and the other underlied the Valeria quarry. However, for all dikes the AARM tensors are not coaxial with AMS fabrics and show a magnetic lineation (AARM(max)) oriented to N30-60E, suggesting that magnetite grains were rotated clockwise from dike plane. The orientation of AARM lineation is similar to the orientation of a system of faults in which the Salvador normal fault is the most important. These faults were formed during Cretaceous rifting in the Reconcavo-Tucano-jatoba assemblage that corresponds to an aborted intra-continental rift formed during the opening of the South Atlantic. Therefore, the AARM fabric found for the Salvador dikes is probably tectonic in origin and suggests that the dike swarm was affected by the important tectonic event responsible for the break-up of the Gondwanaland. (C) 2008 Elsevier B.V. All rights reserved.

Geochemistry of natural chromium occurrence in a sandstone aquifer in Bauru Basin, Sao Paulo State, Brazil

Anomalous concentrations of Cr(VI) occur in groundwaters of the Adamantina Aquifer, in a large region in the western state of Sao Paulo, sometimes exceeding the potability limit (0.05 mg L(-1)). To identify the possible geochemical reactions responsible for the occurrence of Cr in groundwater in Urania, borehole rock samples were collected in order to carry out mineralogical and chemical analyses. In addition, multilevel monitoring wells were installed and groundwater samples were analyzed. Analyses of the borehole rock samples show the occurrence of a geochemical anomaly of Cr in the quartzose sandstones (average concentrations of 221 ppm). Chrome-diopside is one of the main minerals contributing to this anomaly, having an average Cr content of 1505 ppm. Sequential extraction experiments indicated weakly adsorbed Cr in the order of 0.54 ppm, and this quantity is enough to provide the Cr concentrations observed in groundwater. Groundwaters from the monitoring wells proved to be stratified, with the highest concentrations of Cr(VI) (0.13 mg L(-1)) being associated with high redox and pH values (over 10) and high concentrations of Na. Geochemical reactions that may explain the release of Cr from the solid phase to groundwater involve the release of Cr(III) from minerals (like chrome-diopside and Cr-Fe hydroxide), followed by oxidation of Cr(III) to Cr(VI), probably related to the reduction of Mn oxides present in the aquifer. Then cation exchange occurs and dissolution of carbonates which increases the pH of groundwater, resulting in the desorption and mobilization of Cr(VI) into groundwater. (C) 2011 Elsevier Ltd. All rights reserved.

Lycopodiopsis derbyi Renault from the Corumbatai Formation in the state of Sao Paulo (Guadalupian of Parana Basin, Southern Brazil): New data from compressed silicified stems

Lycopodiopsis derbyi Renault was analyzed on the basis of compressed silicified stems from four Guadalupian outcrops of the Parana Basin (Corumbatai Formation) in the State of Sao Paulo, Southern Brazil. Dichotomous stems have been recorded, and three different branch regions related to apoxogenesis are described. The most proximal region has larger, clearly rhomboidal leaf cushions, with protruding upper edges; the intermediate transitional region also has rhombic leaf cushions, but they are smaller and less elongated than the lower in the same axis; finally, the most distal region reveals only incipient cushions, with inconspicuous infrafoliar bladders; interspersed microphylls were still attached. A well preserved branch representative of this most distal region was sectioned; it has a siphonostelic cylinder similar to that previously described for L derbyi. The cortex, however, shows new traits, such as a short portion of elongated cells between the periderm and the external cortex (or leaf cushion tissue). The stems were apparently silicified prior to their final burial but were probably not transported for long distances. Their final burial may have taken place during storm events, which were common during the deposition of the Corumbatai Formation. These stems are commonly deformed due to compression, mainly because the internal cortical portions rapidly decayed prior to silicification due to their thin-walled tissue, and are therefore not preserved. The common alkalinity of a shallow marine environment such as that in which the Corumbatai Formation was deposited, should mobilize the silica and favors petrifaction. Based on the new data, an emended diagnosis is proposed and a modification of the identification key published by Thomas and Meyen in 1984 for Upper Paleozoic Lycopsida is suggested. (C) 2009 Elsevier B.V. All rights reserved.

Anomalous content of chromium in a Cretaceous sandstone aquifer of the Bauru Basin, state of Sao Paulo, Brazil

Anomalous and natural concentrations of Cr(6+), occasionally exceeding the permitted limit for human consumption (0.05 mg/L), have been detected in groundwater in the northwestern region of the state of Sao Paulo. As part of a water-rock interaction investigation, this article describes the chemical and mineralogical characterization of rock samples taken from boreholes in the municipality of Urania, with the objective of identifying Cr-bearing minerals and determining how chromium is associated with these minerals. Rock sample analysis were performed using X-ray Fluorescence, X-ray Diffraction, Scanning Electron Microscopy, electron microprobe and sequential extraction techniques. Chemical analyses indicated that the quartzose sandstones show a geochemical anomaly of chromium, with an average content of 221 ppm, which is higher than the reported chromium content of generic sandstones (35 ppm). Diopside was identified as the primary Cr-bearing mineral potentially subject to weathering processes, with a chromium content of up to 1.2% as Cr(2)O(3). Many of the diopside grains showed dissolution features, confirming the occurrence of weathering. Sequential extraction experiments indicated that 99.3% of the chromium in samples is tightly bonded to minerals, whereas 0.24% is weakly bonded via adsorption. Assuming hypothetically that all adsorbed chromium is released via desorption, the theoretical Cr concentration in water would be one order of magnitude higher than the concentrations of Cr(6+) detected in groundwater. (C) 2010 Elsevier Ltd. All rights reserved.

Structural analysis of the Itapucumi Group in the Vallemi region, northern Paraguay: Evidence of a new Brasiliano/Pan-African mobile belt

The Neoproterozoic (Ediacaran) Itapucumi Group in northern Paraguay is composed of carbonate and siliciclastic rocks, including ooid grainstones, marls, shales and sandstones, containing Cloudina fossils in the eastern region. It is almost undeformed over the Rio Apa Cratonic Block but shows a strong deformational pattern at its western edge. A detailed structural analysis of the Itapucumi Group was conducted in the Vallemi Mine, along with a regional survey in other outcrops downstream in the Paraguay River and in the San Alfredo, Cerro Paiva and Sargent Jose E. Lopez regions. In the main Vallemi quarry, the structural style is characterized by an axial-plane slaty cleavage in open to isoclinal folds, sometimes overturned, associated with N-S trending thrust faults and shear zones of E-vergence and with a low-grade chlorite zone metamorphism. The structural data presented here are compatible with the hypothesis of a newly recognized mobile belt on the western side of the Rio Apa Cratonic Block, with opposite vergence to that of the Paraguay Mobile Belt in Brazil. Both belts are related to the Late Brasiliano/Pan-African tectonic cycle with a Lower Cambrian deformation and metamorphism age. The deformation could be due to the late collision of the Amazonian Craton with the remainder of Western Gondwana or to the western active plate boundary related to the Pampean Belt. The structural and lithologic differences between the western Itapucumi Group in the Vallemi and Paraguay River region and the eastern region, near San Alfredo and Cerro Paiva, suggest that this group could be divided into two lithostratigraphic units, but more stratigraphic and geochronological analyses are required to confirm this possibility. (C) 2010 Elsevier Ltd. All rights reserved.

Fluoride in the groundwater of the Tubarao and Crystaline aquifers, Salto-Indaiatuba region (SP)

Anomalous concentrations of fluoride in groundwater were identified in 19 drilling wells in the Salto-Indaiatuba region, Sao Paulo State, with an average concentration of 3.03 mg dm(-3) and a maximum of 6.95 mg dm(-3), which constitute a restriction for the water`s usage in terms of human consumption. The wells exploit water from the Tubarao Aquifer (sedimentary, granular) and Crystalline Aquifer (granitic, fractured), used for sanitary or industrial purposes. These groundwaters are typically HCO(3) and HCO(3)-SO(4) types, with high concentrations of HCO(3) -and Na(+) and high pH-values between 7.5 and 10.0. The highest concentrations of F-are associated to the Tubarao and Tubarao/Crystalline aquifer drilling wells. The presence of F-in groundwater is controlled by these high pH-values, alkalinity, and fluorine availability. The source of fluoride in the Tubarao and Crystalline Aquifers can be related to the percolation of hydrothermal fluids associated with Mesozoic lava flow, emplaced due to the opening of Atlantic Ocean and/or hydrolysis of fluorine-rich minerals and clay minerals.

Fine needle aspiration biopsy in the oral cavity and head and neck region

The objective of the current study was to evaluate the sensitivity, specificity and accuracy of fine needle aspiration biopsy (FNAB) of submucous nodules from the oral cavity and head and neck region as an auxiliary diagnostic tool. Fifty patients with nodule lesions in the oral cavity and the head and neck region were selected. All of them were submitted to FNAB and to either incisional or excisional biopsy. The diagnoses from the FNABs were compared with the biopsy diagnosis as the gold standard. All the cases of FNAB were analyzed by a single oral pathologist prior to the biopsy diagnosis. The results showed that the sensitivity of FNAB was 75%, its specificity was 96% and its accuracy was 58.8%. The false positive and false negative rates were 6.7% and 13.3%, respectively. The positive predictive value was 86% and the negative predictive value was 93%. The inconclusive rate was 16/50. FNAB displayed a high success rate for identifying both malignant and benign lesions, but a low accuracy for making a final diagnosis.