Ordovician klippen structures of the Sierra de Umango: New insights on Tectonic evolution of the Western Sierras Pampeanas, Argentina

The basement rock of the Pampean flat-slab (Sierras Pampeanas) in the Central Andes was uplifted and rotated in the Cenozoic era. The Western Sierras Pampeanas are characterised by meta-igneous rocks of Grenvillian Mesoproterozoic age and metasedimentary units metamorphosed in the Ordovician period. These rocks, known as the northern Cuyania composite terrane, were derived from Laurentia and accreted toward Western Gondwana during the Early Paleozoic. The Sierra de Umango is the westernmost range of the Western Sierras Pampeanas.This range is bounded by the Devonian sedimentary rocks of the Precordillera on the western side and Tertiary rocks from the Sierra de Maz and Sierra del Espinal on the eastern side and contains igneous and sedimentary rocks outcroppings from the Famatina System on the far eastern side. The Sierra de Umango evolved during a period of polyphase tectonic activity, including an Ordovician collisional event, a Devonian compressional deformation, Late Paleozoic and Mesozoic extensional faulting and sedimentation (Paganzo and Ischigualasto basins) and compressional deformation of the Andean foreland during the Cenozoic. A Nappe System and an important shear zone, La Puntilla-La Falda Shear Zone (PFSZ), characterise the Ordovician collisional event, which was related to the accretion of Cuyania Terrane to the proto-Andean margin of Gondwana. Three continuous deformational phases are recognised for this event: the D1 phase is distinguished by relics of 51 preserved as internal foliation within interkinematic staurolite por-phyroblasts and likely represents the progressive metamorphic stage; the D2 phase exhibits P-T conditions close to the metamorphic peak that were recorded in an 52 transposition or a mylonitic foliation and determine the main structure of Umango; and the D3 phase is described as a set of tight to recumbent folds with S3 axial plane foliation, often related to thrust faults, indicating the retrogressive metamorphic stage. The Nappe System shows a top-to-the S/SW sense direction of movement, and the PFSZ served as a right lateral ramp in the exhumation process. This structural pattern is indicative of an oblique collision, with the Cuyania Terrane subducting under the proto-Andean margin of Gondwana in the NE direction. This continental subduction and exhumation lasted at least 30 million years, nearly the entire Ordovician period, and produced metamorphic conditions of upper amphibolite-to-granulite facies in medium- to high-pressure regimes. At least two later events deformed the earlier structures: D4 and D5 deformational phases. The D4 deformational phase corresponds to upright folding, with wavelengths of approximately 10 km and a general N-S orientation. These folds modified the S2 surface in an approximately cylindrical manner and are associated with exposed, discrete shear zones in the Silurian Guandacolinos Granite. The cylindrical pattern and subhorizontal axis of the D4 folds indicates that the S2 surface was originally flat-lying. The D4 folds are responsible for preserving the basement unit Juchi Orthogneiss synformal klippen. This deformation corresponds to the Chanica Tectonic during the interval between the Devonian and Carboniferous periods. The D5 deformational phase comprehends cuspate-lobate shaped open plunging folds with E W high-angle axes (D5 folds) and sub-vertical spaced cleavage. The D5 folds and related spaced cleavage deformed the previous structures and could be associated with uplifting during the Andean Cycle. (C) 2012 Elsevier Ltd. All rights reserved.

Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment. Citation: Jimenez DJ, Andreote FD, Chaves D, Montana JS, Osorio-Forero C, et al. (2012) Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes. PLoS ONE 7(12): e52069. doi:10.1371/journal.pone.0052069

Research Blogging: Indexing and Registering the Change in Science 2.0

Increasing public interest in science information in a digital and 2.0 science era promotes a dramatically, rapid and deep change in science itself. The emergence and expansion of new technologies and internet-based tools is leading to new means to improve scientific methodology and communication, assessment, promotion and certification. It allows methods of acquisition, manipulation and storage, generating vast quantities of data that can further facilitate the research process. It also improves access to scientific results through information sharing and discussion. Content previously restricted only to specialists is now available to a wider audience. This context requires new management systems to make scientific knowledge more accessible and useable, including new measures to evaluate the reach of scientific information. The new science and research quality measures are strongly related to the new online technologies and services based in social media. Tools such as blogs, social bookmarks and online reference managers, Twitter and others offer alternative, transparent and more comprehensive information about the active interest, usage and reach of scientific publications. Another of these new filters is the Research Blogging platform, which was created in 2007 and now has over 1,230 active blogs, with over 26,960 entries posted about peer-reviewed research on subjects ranging from Anthropology to Zoology. This study takes a closer look at RB, in order to get insights into its contribution to the rapidly changing landscape of scientific communication.

Insights into the morphology of the Serra da Cangalha impact structure from geophysical modeling

Forward modeling is commonly applied to gravity field data of impact structures to determine the main gravity anomaly sources. In this context, we have developed 2.5-D gravity models of the Serra da Cangalha impact structure for the purpose of investigating geological bodies/structures underneath the crater. Interpretation of the models was supported by ground magnetic data acquired along profiles, as well as by high resolution aeromagnetic data. Ground magnetic data reveal the presence of short-wavelength anomalies probably related to shallow magnetic sources that could have been emplaced during the cratering process. Aeromagnetic data show that the basement underneath the crater occurs at an average depth of about 1.9 km, whereas in the region beneath the central uplift it is raised to 0.51 km below the current surface. These depths are also supported by 2.5-D gravity models showing a gentle relief for the basement beneath the central uplift area. Geophysical data were used to provide further constraints for numeral modeling of crater formation that provided important information on the structural modification that affected the rocks underneath the crater, as well as on shock-induced modifications of target rocks. The results showed that the morphology is consistent with the current observations of the crater and that Serra da Cangalha was formed by a meteorite of approximately 1.4 km diameter striking at 12 km s-1.

New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination

Crown ethers have the ability of solubilizing inorganic salts in apolar solvents and to promote chemical reactions by phase-transfer catalysis. However, details on how crown ethers catalyze ionic S(N)2 reactions and control selectivity are not well understood. In this work, we have used high level theoretical calculations to shed light on the details of phase-transfer catalysis mechanism of KF reaction with alkyl halides promoted by 18-crown-6. A complete analysis of the of the model reaction between KF(18-crown-6) and ethyl bromide reveals that the calculations can accurately predict the product ratio and the overall kinetics. Our results point out the importance of the K* ion and of the crown ether ring in determining product selectivity. While the K* ion favors the S(N)2 over the E2 anti pathway, the crown ether ring favors the S(N)2 over E2 syn route. The combination effects lead to a predicted 94% for the S(N)2 pathway in excellent agreement with the experimental value of 92%. A detailed analysis of the overall mechanism of the reaction under phase-transfer conditions also reveals that the KBr product generated in the nucleophilic fluorination acts as an inhibitor of the 18-crown-6 catalyst and it is responsible for the observed slow reaction rate. (C) 2012 Elsevier B.V. All rights reserved.

Structural insights regarding an insecticidal Talisia esculenta protein and its biotechnological potential for Diatraea saccharalis larval control

Talisin is a seed-storage protein from Talisia esculenta that presents lectin-like activities, as well as proteinase-inhibitor properties. The present study aims to provide new in vitro and in silico biochemical information about this protein, shedding some light on its mechanistic inhibitory strategies. A theoretical three-dimensional structure of Talisin bound to trypsin was constructed in order to determine the relative interaction mode. Since the structure of non-competitive inhibition has not been elucidated, Talisin-trypsin docking was carried out using Hex v5.1, since the structure of non-competitive inhibition has not been elucidated. The predicted non-coincidence of the trypsin binding site is completely different from that previously proposed for Kunitz-type inhibitors, which demonstrate a substitution of an Arg(64) for the Glu(64) residue. Data, therefore, provide more information regarding the mechanisms of non-competitive plant proteinase inhibitors. Bioassays with Talisin also presented a strong insecticide effect on the larval development of Diatraea saccharalis, demonstrating LD50 and ED50 of ca. 2.0% and 1.5%, respectively. (C) 2011 Elsevier Inc. All rights reserved.

Insights into Phosphate Cooperativity and Influence of Substrate Modifications on Binding and Catalysis of Hexameric Purine Nucleoside Phosphorylases

The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy) ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl-6 and Br-8 substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.

Considerations for Assessing Maximum Critical Temperatures in Small Ectothermic Animals: Insights from Leaf-Cutting Ants

The thermal limits of individual animals were originally proposed as a link between animal physiology and thermal ecology. Although this link is valid in theory, the evaluation of physiological tolerances involves some problems that are the focus of this study. One rationale was that heating rates shall influence upper critical limits, so that ecological thermal limits need to consider experimental heating rates. In addition, if thermal limits are not surpassed in experiments, subsequent tests of the same individual should yield similar results or produce evidence of hardening. Finally, several non-controlled variables such as time under experimental conditions and procedures may affect results. To analyze these issues we conducted an integrative study of upper critical temperatures in a single species, the ant Atta sexdens rubropiosa, an animal model providing large numbers of individuals of diverse sizes but similar genetic makeup. Our specific aims were to test the 1) influence of heating rates in the experimental evaluation of upper critical temperature, 2) assumptions of absence of physical damage and reproducibility, and 3) sources of variance often overlooked in the thermal-limits literature; and 4) to introduce some experimental approaches that may help researchers to separate physiological and methodological issues. The upper thermal limits were influenced by both heating rates and body mass. In the latter case, the effect was physiological rather than methodological. The critical temperature decreased during subsequent tests performed on the same individual ants, even one week after the initial test. Accordingly, upper thermal limits may have been overestimated by our (and typical) protocols. Heating rates, body mass, procedures independent of temperature and other variables may affect the estimation of upper critical temperatures. Therefore, based on our data, we offer suggestions to enhance the quality of measurements, and offer recommendations to authors aiming to compile and analyze databases from the literature.

Field and Laboratory Studies Provide Insights into the Meaning of Day-Time Activity in a Subterranean Rodent (Ctenomys aff. knighti), the Tuco-Tuco

South American subterranean rodents (Ctenomys aff. knighti), commonly known as tuco-tucos, display nocturnal, wheel-running behavior under light-dark (LD) conditions, and free-running periods >24 h in constant darkness (DD). However, several reports in the field suggested that a substantial amount of activity occurs during daylight hours, leading us to question whether circadian entrainment in the laboratory accurately reflects behavior in natural conditions. We compared circadian patterns of locomotor activity in DD of animals previously entrained to full laboratory LD cycles (LD12:12) with those of animals that were trapped directly from the field. In both cases, activity onsets in DD immediately reflected the previous dark onset or sundown. Furthermore, freerunning periods upon release into DD were close to 24 h indicating aftereffects of prior entrainment, similarly in both conditions. No difference was detected in the phase of activity measured with and without access to a running wheel. However, when individuals were observed continuously during daylight hours in a semi-natural enclosure, they emerged above-ground on a daily basis. These day-time activities consisted of foraging and burrow maintenance, suggesting that the designation of this species as nocturnal might be inaccurate in the field. Our study of a solitary subterranean species suggests that the circadian clock is entrained similarly under field and laboratory conditions and that day-time activity expressed only in the field is required for foraging and may not be time-dictated by the circadian pacemaker.

Structural Insights into Human Peroxisome Proliferator Activated Receptor Delta (PPAR-Delta) Selective Ligand Binding

Peroxisome proliferator activated receptors (PPARs delta, alpha and gamma) are closely related transcription factors that exert distinct effects on fatty acid and glucose metabolism, cardiac disease, inflammatory response and other processes. Several groups developed PPAR subtype specific modulators to trigger desirable effects of particular PPARs without harmful side effects associated with activation of other subtypes. Presently, however, many compounds that bind to one of the PPARs cross-react with others and rational strategies to obtain highly selective PPAR modulators are far from clear. GW0742 is a synthetic ligand that binds PPAR delta more than 300-fold more tightly than PPAR alpha or PPAR gamma but the structural basis of PPAR delta: GW0742 interactions and reasons for strong selectivity are not clear. Here we report the crystal structure of the PPAR delta:GW0742 complex. Comparisons of the PPAR delta:GW0742 complex with published structures of PPARs in complex with alpha and gamma selective agonists and pan agonists suggests that two residues (Val312 and Ile328) in the buried hormone binding pocket play special roles in PPAR delta selective binding and experimental and computational analysis of effects of mutations in these residues confirms this and suggests that bulky substituents that line the PPAR alpha and gamma ligand binding pockets as structural barriers for GW0742 binding. This analysis suggests general strategies for selective PPAR delta ligand design.

New insights about host response to smallpox using microarray data

Abstract Background Smallpox is a lethal disease that was endemic in many parts of the world until eradicated by massive immunization. Due to its lethality, there are serious concerns about its use as a bioweapon. Here we analyze publicly available microarray data to further understand survival of smallpox infected macaques, using systems biology approaches. Our goal is to improve the knowledge about the progression of this disease. Results We used KEGG pathways annotations to define groups of genes (or modules), and subsequently compared them to macaque survival times. This technique provided additional insights about the host response to this disease, such as increased expression of the cytokines and ECM receptors in the individuals with higher survival times. These results could indicate that these gene groups could influence an effective response from the host to smallpox. Conclusion Macaques with higher survival times clearly express some specific pathways previously unidentified using regular gene-by-gene approaches. Our work also shows how third party analysis of public datasets can be important to support new hypotheses to relevant biological problems.