Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms

Background

Multiple protein templates are commonly used in manual protein structure prediction. However, few automated algorithms of selecting and combining multiple templates are available.

Results

Here we develop an effective multi-template combination algorithm for protein comparative modeling. The algorithm selects templates according to the similarity significance of the alignments between template and target proteins. It combines the whole template-target alignments whose similarity significance score is close to that of the top template-target alignment within a threshold, whereas it only takes alignment fragments from a less similar template-target alignment that align with a sizable uncovered region of the target. We compare the algorithm with the traditional method of using a single top template on the 45 comparative modeling targets (i.e. easy template-based modeling targets) used in the seventh edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7). The multi-template combination algorithm improves the GDT-TS scores of predicted models by 6.8% on average. The statistical analysis shows that the improvement is significant (p-value < 10^-4). Compared with the ideal approach that always uses the best template, the multi-template approach yields only slightly better performance. During the CASP7 experiment, the preliminary implementation of the multi-template combination algorithm (FOLDpro) was ranked second among 67 servers in the category of high-accuracy structure prediction in terms of GDT-TS measure.

Conclusion

We have developed a novel multi-template algorithm to improve protein comparative modeling.     

Cytochrome c-mediated oxidation of hydroethidine and mito-hydroethidine in mitochondria: identification of homo- and heterodimers

Here we report that ferricytochrome c (cyt c(3+)) induces oxidation of hydroethidine (HE) and mitochondria-targeted hydroethidine (Mito-HE or MitoSOX Red) forming highly characteristic homo- and heterodimeric products. Using an HPLC-electrochemical (EC) method, several products were detected from cyt c(3+)-catalyzed oxidation of HE and Mito-HE and characterized by mass spectrometry and NMR techniques as follows: homodimers (HE-HE, E(+)-E(+), Mito-HE-Mito-HE, and Mito-E(+)-Mito-E(+)) and heterodimers (HE-E(+) and Mito-HE-Mito-E(+)), as well as the monomeric ethidium (E(+)) and mito-ethidium (Mito-E(+)). Similar products were detected when HE and Mito-HE were incubated with mitochondria. In contrast, mitochondria depleted of cyt c(3+) were much less effective in oxidizing HE or Mito-HE to corresponding dimeric products. Unlike E(+) or Mito-E(+), the dimeric analogs (E(+)-E(+) and Mito-E(+)-Mito-E(+)) were not fluorescent. Superoxide (O(2)(*-)) or Fremy's salt reacts with Mito-HE to form a product, 2-hydroxy-mito-ethidium (2-OH-Mito-E(+)) that was detected by HPLC. We conclude that HPLC-EC but not the confocal and fluorescence microscopy is a viable technique for measuring superoxide and cyt c(3+)-dependent oxidation products of HE and Mito-HE in cells. Superoxide detection using HE and Mito-HE could be severely compromised due to their propensity to undergo oxidation.     

Effect of desiccation on physiological and biochemical indicators associated with the germination and vigor of cryopreserved seeds of <Emphasis Type="Italic">Nicotiana tabacum</Emphasis> L. cv. Sancti Spíritus 96

Cryopreservation is a valuable technique for the long-term conservation of plant germplasm and complementary to traditional seed storage methods. However, critical factors such as seed moisture content should be optimized before using this technique as a safe strategy for storing seeds such as those of Nicotiana spp. This study aimed to determine the effect of desiccation on physiological and biochemical indicators associated with germination and vigor in cryopreserved seeds of Nicotiana tabacum cv. Sancti Spíritus 96 (SS-96). The germination and vigor of seeds with a range of moisture content were assessed using electrolyte leakage and accelerated aging tests. In addition, these physiological indicators were related to the oxidative state of the seeds, in terms of the rate of O₂ ^·? generation and the H₂O₂ content, and the activity of enzymatic antioxidants superoxide dismutase and catalase. The cryopreserved seeds of N. tabacum SS-96 with a moisture content of 2.1% exhibited higher vigor probably due to the retention of membrane integrity, reflected by lower levels of lipid peroxidation and electrolyte leakage associated with the absence of oxidative stress. The results suggest 2.1% as the optimal moisture content for the storage of seeds of this cultivar, both at cryogenic temperatures and at 5°C.     

cDNA sequence and molecular modeling of a nerve growth factor from Bothrops jararacussu venomous gland

The complete nucleotide sequence of a nerve growth factor precursor from Bothrops jararacussu snake (Bj-NGF) was determined by DNA sequencing of a clone from cDNA library prepared from the poly(A) + RNA of the venom gland of B. jararacussu. cDNA encoding Bj-NGF precursor contained 723 bp in length, which encoded a prepro-NGF molecule with 241 amino acid residues. The mature Bj-NGF molecule was composed of 118 amino acid residues with theoretical pI and molecular weight of 8.31 and 13,537, respectively. Its amino acid sequence showed 97%, 96%, 93%, 86%, 78%, 74%, 76%, 76% and 55% sequential similarities with NGFs from Crotalus durissus terrificus, Agkistrodon halys pallas, Daboia (Vipera) russelli russelli, Bungarus multicinctus, Naja sp., mouse, human, bovine and cat, respectively. Phylogenetic analyses based on the amino acid sequences of 15 NGFs separate the Elapidae family (Naja and Bungarus) from those Crotalidae snakes (Bothrops, Crotalus and Agkistrodon). The three-dimensional structure of mature Bj-NGF was modeled based on the crystal structure of the human NGF. The model reveals that the core of NGF, formed by a pair of beta-sheets, is highly conserved and the major mutations are both at the three beta-hairpin loops and at the reverse turn.     

Role of thyroid hormones in renal tubule acidification

Renal tubule acidification was studied in thyroparathyroidectomized rats which had the parathyroids reimplanted into cervical muscle tissue, by stopped-flow microperfusion using ion-exchange resin microelectrodes. Hypothyroid rats had decreased rates of proximal and late distal bicarbonate reabsorption. This reduction occurred in the absence of changes in pH gradients, and was due mostly to decreases in acidification half-times, that is, of the rate of bicarbonate exit from the tubule lumen. H⁺ back-flux from the lumen measured during luminal perfusion with solutions at pH 6 (below stationary pH) was decreased in proximal tubule of hypothyroid rats, showing that the acidification defect was not due to an increased H⁺ shunt across the epithelium. These data indicate that in hypothyroid rats the proximal tubule luminal density of Na⁺/H⁺ exchangers or their turnover is decreased in the absence of alterations in the driving force (H⁺ and Na⁺ gradients across the luminal membrane) for H⁺ secretion. The effect observed in distal tubule may be due to action on Na⁺/H⁺ exchangers that are present also on this site, or to an impairment of the action of other H⁺ transporters such as H⁺-ATPases, including the provision of energy for them.This paper is dedicated to Prof. Carlos Chagas Filho, founder of the Institute of Biophysics, on the occasion of its 50th anniversary.     

Distinct serum proteome profiles associated with collagen‐induced arthritis and complete Freund's adjuvant‐induced inflammation in CD38−/− mice: The discriminative power of protein species or proteoforms

Collagen‐type‐II‐induced arthritis (CIA) is an autoimmune disease, which involves a complex host systemic response including inflammatory and autoimmune reactions. CIA is milder in CD38^?/? than in wild‐type (WT) mice. ProteoMiner‐equalized serum samples were subjected to 2D‐DiGE and MS‐MALDI‐TOF/TOF analyses to identify proteins that changed in their relative abundances in CD38^?/? versus WT mice either with arthritis (CIA⁺), with no arthritis (CIA^?), or with inflammation (complete Freund's adjuvant (CFA)‐treated mice). Multivariate analyses revealed that a multiprotein signature (n = 28) was able to discriminate CIA⁺ from CIA^? mice, and WT from CD38^?/? mice within each condition. Likewise, a distinct multiprotein signature (n = 16) was identified which differentiated CIA⁺ CD38^?/? mice from CIA⁺ WT mice, and lastly, a third multiprotein signature (n = 18) indicated that CD38^?/? and WT mice could be segregated in response to CFA treatment. Further analyses showed that the discriminative power to distinguish these groups was reached at protein species level and not at the protein level. Hence, the need to identify and quantify proteins at protein species level to better correlate proteome changes with disease processes. It is crucial for plasma proteomics at the low‐abundance protein species level to apply the ProteoMiner enrichment. All MS data have been deposited in the ProteomeXchange with identifiers PXD001788, PXD001799 and PXD002071 ( http://proteomecentral.proteomexchange.org/dataset/PXD001788 , http://proteomecentral.proteomexchange.org/dataset/PXD001799 and http://proteomecentral.proteomexchange.org/dataset/PXD002071 ).     

Polymorphisms in Plasmodium vivax Circumsporozoite Protein (CSP) Influence Parasite Burden and Cytokine Balance in a Pre-Amazon Endemic Area from Brazil

Mechanisms involved in severe P. vivax malaria remain unclear. Parasite polymorphisms, parasite load and host cytokine profile may influence the course of infection. In this study, we investigated the influence of circumsporozoite protein (CSP) polymorphisms on parasite load and cytokine profile in patients with vivax malaria. A cross-sectional study was carried out in three cities: São Luís, Cedral and Buriticupu, Maranhão state, Brazil, areas of high prevalence of P. vivax. Interleukin (IL)-2, IL-4, IL-10, IL-6, IL-17, tumor necrosis factor alpha (TNF-α, interferon gamma (IFN-γ and transforming growth factor beta (TGF-β were quantified in blood plasma of patients and in supernatants from peripheral blood mononuclear cell (PBMC) cultures. Furthermore, the levels of cytokines and parasite load were correlated with VK210, VK247 and P. vivax-like CSP variants. Patients infected with P. vivax showed increased IL-10 and IL-6 levels, which correlated with the parasite load, however, in multiple comparisons, only IL-10 kept this association. A regulatory cytokine profile prevailed in plasma, while an inflammatory profile prevailed in PBMC culture supernatants and these patterns were related to CSP polymorphisms. VK247 infected patients showed higher parasitaemia and IL-6 concentrations, which were not associated to IL-10 anti-inflammatory effect. By contrast, in VK210 patients, these two cytokines showed a strong positive correlation and the parasite load was lower. Patients with the VK210 variant showed a regulatory cytokine profile in plasma, while those infected with the VK247 variant have a predominantly inflammatory cytokine profile and higher parasite loads, which altogether may result in more complications in infection. In conclusion, we propose that CSP polymorphisms is associated to the increase of non-regulated inflammatory immune responses, which in turn may be associated with the outcome of infection.     

Climate and fishing steer ecosystem regeneration to uncertain economic futures

Overfishing of large predatory fish populations has resulted in lasting restructurings of entire marine food webs worldwide, with serious socio-economic consequences. Fortunately, some degraded ecosystems show signs of recovery. A key challenge for ecosystem management is to anticipate the degree to which recovery is possible. By applying a statistical food-web model, using the Baltic Sea as a case study, we show that under current temperature and salinity conditions, complete recovery of this heavily altered ecosystem will be impossible. Instead, the ecosystem regenerates towards a new ecological baseline. This new baseline is characterized by lower and more variable biomass of cod, the commercially most important fish stock in the Baltic Sea, even under very low exploitation pressure. Furthermore, a socio-economic assessment shows that this signal is amplified at the level of societal costs, owing to increased uncertainty in biomass and reduced consumer surplus. Specifically, the combined economic losses amount to approximately 120 million € per year, which equals half of today''s maximum economic yield for the Baltic cod fishery. Our analyses suggest that shifts in ecological and economic baselines can lead to higher economic uncertainty and costs for exploited ecosystems, in particular, under climate change.     

Reef‐building coralline algae from the Southwest Atlantic: filling gaps with the recognition of Harveylithon (Corallinaceae,Rhodophyta) on the Brazilian coast

The Southwest Atlantic is notable for having extensive reef areas cemented by nongeniculate coralline red algae. Based on an analysis of four genetic markers and morpho‐anatomical features, we clarify the species of Harveylithon in the tropical and warm temperate Southwest Atlantic. Species delimitation methods (mBGD, ABGD, SPN, and PTP), using three markers (psbA, rbcL, and COI), support the recognition of three new species: H. catarinense sp. nov., H. maris‐bahiensis sp. nov., and H. riosmenum sp. nov., previously incorrectly called Hydrolithon samoënse. Our findings highlight the importance of using an approach with several lines of evidence to solve the taxonomic status of the cryptic species.     

Molecular profiling of drug resistant isolates of Mycobacterium tuberculosis in the state of Santa Catarina,southern Brazil

Drug resistance is a global threat and one of the main contributing factors to tuberculosis (TB) outbreaks. The goal of this study was to analyse the molecular profile of multidrug-resistant TB (MDR-TB) in the state of Santa Catarina in southern Brazil. Fifty-three MDR Mycobacterium tuberculosisclinical isolates were analysed by spoligotyping and a partial region of therpoB gene, which is associated with rifampicin resistance (RMP-R), was sequenced. Some isolates were also distinguished by their mycobacterial interspersed repetitive units (MIRU). S531L was the most prevalent mutation found within rpoB in RMP-R isolates (58.5%), followed by S531W (20.8%). Only two MDR isolates showed no mutations withinrpoB. Isolates of the Latin American Mediterranean (LAM) family were the most prevalent (45.3%) found by spoligotyping, followed by Haarlem (9.4%) and T (7.5%) families. SIT106 was found in 26.4% of isolates and all SIT106 isolates typed by MIRU-12 (5 out of 14) belong to MIT251. There was a high correlation between the S531W mutation and the LAM family mainly because all SIT2263 (LAM9) isolates carry this mutation. Among isolates with the S531W mutation in rpoB MIRU demonstrates a cluster formed by four isolates (SIT2263 and MIT163) and very similar profiles were observed between eight of the nine isolates. Better characterisation of TB isolates may lead to new ways in which to control and treat TB in this region of Brazil.