Related Folds Research Articles

Marked up-regulation of anti inflammatory cytokine gene expression in the peripheral blood mononuclear cells of postpartum cows with endometritis

This study was designed to determine the mRNA expression profile of inflammatory and anti-inflammatory cytokines in peripheral blood mononuclear cells (PBMC) of endometritic and non-endometritic cows to find out a possible marker for diagnosis of endometritis. Cows (21) including 12 endometritic, and 9 normal (non-endometritic) that did not develop uterine diseases postpartum (pp) were selected. Expression profile (mRNA) of cytokines, viz. IL-1β, TNFα, IL-8 and IL-4 in endometritic cows relative to non-endometritic was studied in PBMC isolated from the blood of the cows collected within 4 to 5 weeks pp. Fold difference (n-fold) in cytokine gene expression in the PBMC of endometritic cows relative to normal was calculated using relative quantification method (2-ΔΔCt). The relative fold change in gene expression for IL-1 was significantly lower in endometritic animals (0.31) than in cows that did not develop endometritis. Significant up-regulation was noted for the proinflammatory cytokine TNFα (9.53 fold and anti-inflammatory cytokine IL-4 (90.09) in cows suffering from endometritis relative to nonendometritic cows. Up-regulation of chemokine IL-8 gene (6.25 fold; was also observed in endometritic compared to non-endometritic cows. Highest and significant up-regulation of mRNA expression for IL-4 followed by TNFα in PBMC of endometritic cows recorded in the study may indicate the development of endometritis in postpartum cows.

Role of Periodontal Bacteria, Viruses, and Placental mir155 in Chronic Periodontitis and Preeclampsia-A Genetic Microbiological Study.

Previous studies assessed the involvement and impact of periodontal bacteria in preeclamptic women with chronic periodontitis. To explore further, the current study aimed to associate periodontal viruses and bacteria with mir155 levels in placental tissues of preeclamptic women with generalized chronic periodontitis. Four-hundred 45 pregnant women, 18–35 years of age, were selected and divided into four groups (controls, A, B, and C) where the Controls included 145 systemically and periodontally healthy pregnant women Group A-100 systemically healthy pregnant women with chronic periodontitis, Group B- 100 preeclamptic women with chronic periodontitis, Group C- 100 preeclamptic women without chronic periodontitis. Age, BMI, SES, and periodontal parameters such as PI, BOP, PPD, and CAL were noted. Periodontal pathogens such as Tf, Td, Pg, Pi, Fn, HSV, EBV, and HCMV were tested in subgingival plaque, placental tissues, and mir155. We observed that PI, BOP, PPD, CAL, Tf, and EBV were highly significant in Group B. We found a higher number of periodontal bacteria, viruses, and mir 155 in Group B showing a higher risk of preeclampsia. More genetic studies in this field are advised to ascertain the role of periodontopathogens and mir 155 in preeclampsia and periodontal inflammation. What is already known on this subject? Periodontal diseases pose an increased risk of developing preeclampsia and delivering preterm and/or low-birth-weight babies. What do the results of this study add? Periodontal variables such as PI, pocket depth, BOP, and clinical attachment levels, were found to be increased in the preeclamptic women with chronic periodontitis. The significant difference was seen in the relative fold expression of mir155 with higher gene expression of mir155 in groups B and A as compared to group C and controls. What are the implications of these findings for clinical practice and/or further research? In our study, mir155 correlation with the periodontal parameters and periodontal pathogens further strengthen the evidence of periodontal inflammation as a risk of preeclampsia in pregnant women especially when associated with chronic periodontitis. mir155 can be considered to be one of the genetic biomarkers and can be used as a diagnostic tool for the early detection of PE.

Differential response of inner and outer zone meniscal cells to tensile load under non-inflammatory and inflammatory conditions

Differential response of inner and outer zone meniscal cells to tensile load under non-inflammatory and inflammatory conditions

Dinaric up-thrusts in the Pliocene evolution of the Central Apennines thrust belt of Italy: the Montagna dei Fiori structure

AbstractSeveral orogenic belts exhibit regional-scale anticlines characterized by prominent faults in their crestal/forelimb zone. These faults are also a common feature in the Neogene fold-and-thrust belt of the Apennines, where they have been contrastingly interpreted as younger-on-older thrust faults, large-scale strike-slip faults, and pre- or syn-thrusting normal faults. In this study, we analysed a NW–SE-trending fault (Montagna dei Fiori Fault) that affects the hinge-zone/forelimb of the Montagna dei Fiori Anticline. This fold is the outermost exposed contractional structure within the Pliocene–Quaternary antiformal stack of the outer Central Apennines. The integration of stratigraphic and structural data collected during a field geological survey enabled us to reconstruct a multiphase reactivation and deformation along the Montagna dei Fiori Fault. From the novel field data, a different interpretation for the evolution of the Montagna dei Fiori Fault is proposed. The fault originated as a Late Cretaceous – middle Miocene, NE-dipping, Dinaric up-thrust and was later reactivated, displaced and rotated during Pliocene Apennine thrusting and related folding, until assuming a present-day SW-dipping attitude with an apparent normal fault character. This newly proposed Dinaric origin of the Montagna dei Fiori structure is compared with an analogous subsurface example of a Palaeogene–Quaternary structure imaged by seismic reflection profile in the Adriatic foreland. The outcome of this combined field and subsurface investigation provides new elements to unravel the complex evolution of the Apennine thrust belt that developed at the expense of a previously deformed foreland, ahead of the advancing Dinaric chain.

Remote Homology Detection Identifies a Eukaryotic RPA DBD-C-like DNA Binding Domain as a Conserved Feature of Archaeal Rpa1-Like Proteins.

The eukaryotic single-stranded DNA binding factor replication protein A (RPA) is essential for DNA replication, repair and recombination. RPA is a heterotrimer containing six related OB folds and a winged helix-turn-helix (wH) domain. The OB folds are designated DBD-A through DBD-F, with DBD-A through DBD-D being directly involved in ssDNA binding. DBD-C is located at the C-terminus of the RPA1 protein and has a distinctive structure that includes an integral C4 zinc finger, while the wH domain is found at the C-terminus of the RPA2 protein. Previously characterised archaeal RPA proteins fall into a number of classes with varying numbers of OB folds, but one widespread class includes proteins that contain a C4 or C3H zinc finger followed by a 100–120 amino acid C-terminal region reported to lack detectable sequence or structural similarity. Here, the sequences spanning this zinc finger and including the C-terminal region are shown to comprise a previously unrecognised DBD-C-like OB fold, confirming the evolutionary relatedness of this group of archaeal RPA proteins to eukaryotic RPA1. The evolutionary relationship between eukaryotic and archaeal RPA is further underscored by the presence of RPA2-like proteins comprising an OB fold and C-terminal winged helix (wH) domain in multiple species and crucially, suggests that several biochemically characterised archaeal RPA proteins previously thought to exist as monomers are likely to be RPA1-RPA2 heterodimers.

Gene Expression of NLRP3 Inflammasome in Celiac Disease of Iraqi Children

Celiac disease (CD) is an autoimmune disorder characterized by chronic inflammation that essentially affects the small intestine and is caused by eating gluten-containing foods. This study sought to determine gene expression of NLRP3 Inflammasome in peripheral blood of Iraqi CD children using quantitative real-time PCR (qRT-PCR) assay. Thirty children with CD (12 males and 18 females) were enrolled in the study and their age range was 3-15 years. The diagnosis of the disease was confirmed by serological examinations and intestinal endoscopy. A control sample of 20 age-matched healthy children was also included. The children were stratified for age, gender, body max index (BMI), histological findings, and marsh classification. Further, the sera were examined for IgA anti-tissue transglutaminase (tTG) antibody, IgA anti-gliadin antibody, and interleukin-1 beta (IL-1β). Based on Marsh classification, the results revealed that the majority of patients (70%) had partial villous atrophy (Marsh Ш 3A), while children with subtotal and total villous atrophy (Marsh III: 3B/3C) were presented with a lower frequency (30.0%). Neither Marsh I nor Marsh II has been observed among the patients studied. Serum levels of anti-tTG and anti-gliadin IgA antibodies were significantly higher in CD children than in control children (73.8 and 31.8 vs. 0.8 U//ml, respectively; p < 0.001). Conversely, IL-1β serum level was decreased in CD children but the difference was not significant (35.5vs. 53.4 pg/ml; p = 0.285). In the case of NLRP3 inflammasome, the Relative Fold Change method (2-∆∆Ct) was used to assess the gene expression. The results revealed that the expression of NLRP3 inflammasome was decreased by 0.594 fold in CD children. In conclusion, the NLRP3 inflammasome was down-regulated in the present sample of CD children, and it was accompanied by a decreased serum level of IL-1β.

Caffeine Inhibits Growth of Temozolomide-Treated Glioma via Increasing Autophagy and Apoptosis but Not via Modulating Hypoxia, Angiogenesis, or Endoplasmic Reticulum Stress in Rats

Thirty rats with glioma were divided into control group, temozolomide (TMZ) group (TMZ 30 mg/kg once daily for 5 day), and TMZ plus Caffeine group (TMZ 30 mg/kg once daily for 5 day and caffeine 100 mg/kg once daily for 2 weeks). The relative tumor fold and expression of hypoxia-induced factor-1α (HIF-1α), vascular endothelial growth factor (VEGF), neuropilin-1 (NRP-1), CCAAT/enhancer-binding protein homologous protein (CHOP), LC-3A/B, apoptosis-inducing factor-1 (AIF-1), and cleaved caspase three were compared. The relative tumor fold of TMZ plus Caffeine group was lower significantly than that of TMZ group at day 14. HIF-1α, VEGF, NRP-1, and CHOP expressions were not significantly different in the three groups. The LC-3A/B expression of TMZ plus Caffeine group was higher significantly than that of the control group and TMZ group. The AIF expressions of TMZ group and TMZ plus Caffeine group were higher significantly than that of the control group. The caspase-3 expression of TMZ plus Caffeine group was higher significantly than that of the control group and TMZ group. In conclusions, the inhibitory effect of caffeine on TMZ-treated glioma might be associated with increasing expressions of autophagy- and apoptosis-related genes.

Proteomics Landscape of Host-Pathogen Interaction in Acinetobacter baumannii Infected Mouse Lung.

Acinetobacter baumannii is an important pathogen of nosocomial infection worldwide, which can primarily cause pneumonia, bloodstream infection, and urinary tract infection. The increasing drug resistance rate of A. baumannii and the slow development of new antibacterial drugs brought great challenges for clinical treatment. Host immunity is crucial to the defense of A. baumannii infection, and understanding the mechanisms of immune response can facilitate the development of new therapeutic strategies. To characterize the system-level changes of host proteome in immune response, we used tandem mass tag (TMT) labeling quantitative proteomics to compare the proteome changes of lungs from A. baumannii infected mice with control mice 6 h after infection. A total of 6,218 proteins were identified in which 6,172 could be quantified. With threshold p < 0.05 and relative expression fold change > 1.2 or < 0.83, we found 120 differentially expressed proteins. Bioinformatics analysis showed that differentially expressed proteins after infection were associated with receptor recognition, NADPH oxidase (NOX) activation and antimicrobial peptides. These differentially expressed proteins were involved in the pathways including leukocyte transendothelial migration, phagocyte, neutrophil degranulation, and antimicrobial peptides. In conclusion, our study showed proteome changes in mouse lung tissue due to A. baumannii infection and suggested the important roles of NOX, neutrophils, and antimicrobial peptides in host response. Our results provide a potential list of protein candidates for the further study of host-bacteria interaction in A. baumannii infection. Data are available via ProteomeXchange with identifier PXD020640.

The Cu–Pb–Zn-bearing veins of the Bou Skour deposit (Eastern Anti-Atlas, Morocco): structural control and tectonic evolution

In the central Saghro massif of the Moroccan Anti-Atlas belt, the Bou Skour polymetallic deposit is hosted within mafic to felsic rocks of the Ediacaran Saghro Group and the lower Ouarzazate Group together with Pan-African plutons and dykes. The mineralizations occur in a brittle-ductile shear zone as a vein-type system recently dated at 574.9±2.4Ma. In this contribution, a new multi-scale structural mapping and vein system analysis have been integrated to understand structural control and tectonic evolution of the Bou Skour deposit. The most important mineralized structures are known as “Filon Principal”, “Filon 1”, and “Filon 2” and are mainly hosted within NNW to NW transcrustal faults. They are represented as en-echelon tension gashes occasionally associated with horsetail satellite structures pointing to left-lateral strike-slip movement. The age and tectonic patterns are coherent with the NW–SE shortening of the last stage of the Pan-African orogeny rather than with post Pan-African events. Subsequent collapses and tilted blocks were accommodated by NE- to ENE normal and strike-slip faults in response to the Late Ediacaran–Cambrian extension events. Much later, probably during the Variscan or even Atlasic shortening, conjugated strike-slip reverse faults and related folds occurred, disrupting most of the rhyolitic dykes as well as the major mineralized structures.

Osteogenic Regulation by Graphene Nanoparticles in Human Mesenchymal Stem Cells

Background Degenerative bone diseases caused by trauma, cancer, or aging imposes a global health care burden every year. Treatment strategies include directing stem cell differentiation through osteogenesis, thereby creating new bone material for repairment. We previously identified that adult mesenchymal stem cells (MSCs) cultured on graphene nanoparticles spontaneously supports osteoblast development in vitro. However, the osteo-genetic signaling of MSCs in the presence of graphene is largely unknown. Therefore, this study sought to measure genetic expressions of MSCs cultured on graphene using focused PCR arrays. Methods MSCs were extracted from human adipose tissue (hAD-MSCs) and human bone marrow (hBM-MSCs) and expanded in growth media. For experimental conditions, hAD-MSCs and hBM-MSCs were seeded on a graphene surface and cultured for either 7 or 21 days. At each time point, cells were extracted for total RNA and reverse transcribed to cDNA before loading onto RT2 Profiler PCR Human Osteogenesis Array (Qiagen, Hilden, Germany). Gene expressions of both cell lines were compared either over time (day 7 as the control to day 21 as the treated group) or between both cell lines at each time point (hAD-MSCs to hBM-MSCs at day 7 or day 21). Results were analyzed using Qiagen Gene Globe software to determine the relative fold change in comparison to the control. Fold changes were considered statistically significant at p < 0.05. Results We examined expression of four transcriptional genes known to control stem cell fate: DLX5, RUNX2, SOX9, and SP7. In hAD-MSCs, RUNX2 was up-regulated while SOX9 and SP7 were down-regulated, suggesting RUNX2 to be a master regulator in hAD-MSCs. In contrast, all genes were down-regulated in hBM-MSCs. However, when hBM-MSCs were compared to hAD-MSCs, all genes were up-regulated at both time points. Interestingly, the fold changes at day 7 were more robust compared to that observed at day 21, suggesting transcriptional regulation of osteogenesis in hBM-MSCs occurs at an earlier time point. Secondly, we examined common markers of osteogenesis including ALPL, BGLAP, PHEX, and SPP1. In hAD-MSCs, ALPL, BGLAP, and PHEX were upregulated, while SPP1 was down-regulated.In hBM-MSCs, ALP, PHEX, and SPP1 were up-regulated, overall suggesting osteo-genetic signaling by graphene occurs in both cell types. Conclusion hAD-MSCs and hBM-MSCs cultured on graphene showed significant changes in osteogenic gene expressions. These cells were cultured in absence of any chemical inducers, suggesting graphene nanoparticles alone commits osteo-genetic signaling of MSCs. We also observed that osteogenesis of hBM-MSCs may occur at an earlier time point than hAD-MSCs. Lastly, we identified DLX5 as a novel osteogenic regulator supported by graphene. Overall, we show that MSCs isolated from two independent tissue sources spontaneously express osteogenic genes in the presence of graphene.

Early post-rift confined turbidite systems in a supra-detachment basin: Implications for the early to middle Miocene basin evolution and hydrocarbon exploration of the Pannonian Basin

Understanding the interplay of sedimentation and deformation style is essential to develop an adequate model of the evolutionary history of an extensional sedimentary basin. Due to their volume and temporal extent, late post-rift deposits are often in the focus of research; however, early post-rift deposits are less studied. The aim of the study is to reconstruct the tectono-sedimentary evolution of a syn -rift to early post-rift succession in the hanging wall of a low-angle detachment zone and to recognize the effects of this deformation style on turbidity current pathways and depocenters. The small Őri sub-basin of the western part of the Miocene Pannonian basin is used as a study area where the oldest early post-rift turbidites of ~15–12.8 Ma occurred. These sediments were deposited in a supradetachment setting, where inherited and actively forming structures controlled the sediment pathways and accommodation of both the distally and locally sourced marine turbidites. Seismic data, well logs and core information were integrated to identify and analyze unconformities, structural elements, and turbidite deposits. Syn-rift, early post-rift and late post-rift system tracts were identified. The syn -rift/post-rift unconformity is a result of combined eustatic sea level drop and the change in deformation intensity. The main low-angle detachment fault, orthogonal hanging wall transfer faults and related folds together controlled the complex synformal shape of the basin, which was related to major corrugations of the footwall detachment. Four turbidite phases were distinguished based on upward increasing sand content, areal extent, reservoir quality, and degree of confinement as the turbidity currents reached the basin margins. (1) Small fans deflected by transfer faults developed, followed by (2) an axial turbidite system that reached an anticline and was deflected by it. (3) Lateral confinement by the anticline increased significantly and thick sandstone bodies with abrupt pinch-outs formed, while the influence of smaller faults diminished. (4) The axial turbidite systems covered the basin floor and their interaction with basin margins created continuous sand bodies of confined character. The sand fairways and types of confinement of a supra-detachment basin differ from high-angle normal fault systems. The exhumed metamorphic rocks provided the sediment, and the extension-parallel antiformal and synformal corrugations acted as lateral confinement. The gentle back-tilt of the detachment hanging wall block exerted a frontal confinement for the extensive turbidite system at the distal part of the basin, but the gentle NE-ward dip over the detachment still permitted long run-out distances. • Combination of eustasy and tectonics leads to syn-rift-early post-rift unconformity. • Corrugation fold of a detachment creates an intricate topography for sediment flows. • Deformation activity decreases during deposition of early post-rift turbidites. • Lateral, frontal confinement of turbidity currents controls reservoirs quality. • Differences between sand fairways in high- and low-angle extensional systems.

An integrated structural and geophysical approach to defining the structures of part of the Nangodi greenstone belt, northeastern Ghana

The application of integrated geophysical (aeromagnetic and airborne radiometric) and geological data has become more relevant in the investigation of subsurface geology with its inherent structures; this approach provides greater detail of structures and formations which are hidden beneath thick weathered zones. This approach was used to provide an in-depth study of the poly-deformational, structural and lithological character of parts of the Paleoproterozoic Nangodi Greenstone Belt in northeastern Ghana. The integrated method was specially chosen because of the paucity and lack of obvious lateral continuity of outcrops in much of the area. Processing and interpretation of aeromagnetic data led to the identification of structures and deformational features i.e. shear zones with related folds and faults. Combined with field evidence, three deformational events (D1-D3) were resolved within the study area. D1 is marked by NW-SE crustal shortening which was responsible for the production of macroscopic folds that imparted the regional NE-SW foliation observed in the rocks. D2, is a brittle-ductile deformational event mainly responsible for the production of a NE striking shear zone and some associated dextral strike slip faulting which were seen in the Gonzurudoug and Nangodi hills. D2 deformation is seen as an angularly hinged fold, described as an intramylonitic fold. D3 is responsible for the production of an ESE-WNW directed compressional force which produced folds with ENE striking axial planes as well as left lateral strike slip faults. Lithological boundaries were identified using ternary maps of radiometric data with confirmation from field observations.

Deformation history of a foredeep basin during the incorporation of its deposits within an advancing orogenic wedge: The case of the Oligocene-Early Miocene Macigno Costiero Formation, southern Tuscany, northern Apennines, Italy

The Upper Oligocene Macigno Formation cropping out in the coastal section of SW Tuscany represents the sedimentary fill of a foredeep basin developed during the collisional stages that led to the construction of the Apennine mountain belt of peninsular Italy. The stratigraphic sequence consists of alternating sandstones and siltstones, that are affected by km-scale contractional structures, namely SW-dipping thrusts and related NE-verging folds. An original field survey carried out along a superb coastal exposure, integrated with analysis of mesoscopic fabrics and their overprinting relationships, makes it possible to unravel a complex deformation history. Four main deformation stages are recognized: i) layer-parallel shortening A; ii) top-to-the-foreland shear B; iii) folding C, comprising the fold nucleation sub-stage C1 and the fold amplification sub-stage C2; and iv) thrust propagation D. The sequence of recognized stages indicates a progressive deformation history of the Macigno Formation as it was incorporated within the evolving Apennine orogenic system. The kinematic history inferred from deformation fabrics and their overprinting relationships within Macigno Fm. deposits in SW Tuscany shows remarkable analogies with the structural evolution of foredeep sediments from other fold-and-thrust belts, yet with little deviations mainly consisting of pureshear vs. simple shear fluctuations in the early history of accretion. These provide original information on the modes of accretion of foredeep deposits within evolving collisional belts, thus contributing to an enhanced understanding of orogenic dynamics during mountain building with a classical example whose evolution is unravelled in detail.

The evolutionary relationship of S15/NS1RNA binding domains with a similar protein domain pattern - A computational approach

Abstract RNA binding proteins are involved in many functions, though the majority of them are composed into small RNA binding domains. The S15/NS1 RNA binding domain is a ribosomal S15 and the non-structural NS1 protein. In this study, an attempt was made to find the evolutionarily related protein fold of the S15/NS1 RNA binding domain using structural and sequence-based analysis, and it was found that several protein domain folds similar to this fold. Apart from these, different support vector machine (SVM) based methods were also developed for the analysis of these folds. According to the results of the structure, sequence and SVM-based analysis, several domain folds are evolutionarily related to the S15/NS1 RNA binding domain fold.

A Comparative Study of ESTs Induced under Drought and Salinity Stress in Hyacinth Bean (&amp;lt;i&amp;gt;Lablab purpureus&amp;lt;/i&amp;gt;)

Abiotic stressors like drought and salinity are major causes for loss of agricultural productivity. Comparison of expressed sesquence tags (ESTs) under different abiotic stresses provides insight into underlying mechanism of stress response, and candidate genes to improve tolerance to abiotic and biotic stresses via breading and transgenic methods. In order to identify and compare stress-specific ESTs from drought and salinity stressed Hyacinth Bean, ten days old seedlings were subjected to respective stresses and RNA was extracted from control and stressed leaves for EST identification. 31 and 12 ESTs, respectively, were characterized from leaves of drought and salinity stressed seedlings of Hyacinth Bean, Lablab purpureus by differential display RT-PCR using identical combinations of 48 primers and validated using quantitative RT-PCR. Relative fold expression was higher under salt stress than drought stress. Whereas 19 EST overexpressed under drought, 12 EST were down regulated. Of the 12 EST under salinity, 9 EST were downregulated and 3 EST upregulated. Putative functions predicted from sequence homology indicated that 11 drought specific EST corresponded to metabolic functions, and 4 of them corresponded to transcription regulation. Under salinity, 4 and 2 EST, respectively, corresponded to metabolic and RNA associated functions. Under both stresses, there were ESTs associated with unknown functions, whose characterization may throw light on the regulatory mechanism. Differing number of ESTs differentially expressed under drought and salt stress, and their predicted functionalities, suggested distinct set of response genes involved under these two stresses, despite a good number of physiological players being common. From the predicted functions of ESTs, the paper attempts to explain the possible mechanism of response of Hyacinth Bean to these two stresses.

CHARACTERIZATION OF PUTATIVE HEAT SHOCK TRANSCRIPTION FACTOR (Hsf2) GENE INVOLVED IN REGULATING THE EXPRESSION OF HSP90 IN WHEAT UNDER TERMINAL HEAT STRESS

Wheat, being staple food grain crop, is highly sensitive to heat stress. The effect is more evident under present threat of global climate change. Very limited information about heat-responsive transcription factor is known in wheat. A putative Heat Shock Factor (HSF) was cloned from wheat under HS. The gene was titled as Hsf2 (acc No. KP063542). The nucleotide sequence was found to be 1551 bp long with open reading frame (ORF) of 1125 bp (5’UTR of 213bp and 3’UTR of 213bp). The amino acid sequence showed the presence of HSF_ DNA binding domain having high degree of similarity (homology) with other HSF coding gene of related species (Aegilops tauschii with 95% homology and 100% homology with Chinese spring cultivar of Triticum aestivum). The protein was observed to be localized in the nucleus. Phosphorylation study showed the presence of phosphorylated threonine at seventeen sites in amino acid sequence. Expression analysis of Hsf2 showed maximum relative fold expression (2.04fold) in the leaves of HD2967 under HS, as compared to control. The transcript abundance was observed maximum in thermotolerant cv., as compared to thermo susceptible. Current study established positive correlation between the expression of Hsf2 and HSP90 under HS. Hsf2, being regulator of HSPs can be used as potential molecular marker for screening wheat germplasm for thermo tolerance. It will pave the way for the development of ‘climate-smart’ wheat crop.

Principles that rule the calculation of dihedral angles in secondary structures: the cases of an α-helix and a β-sheet

The folding process has been described as the output of main mechanical forces which generate from the specific chemical interplay among residues of an amino acid chain. Recently, we have reported that dihedral angle values in (poly)peptides can be calculated by means of a newly defined parameter referred as folding factor. This physical measure is directly linked to the determination of the degrees of freedom (η), namely the number of possible interactions that can occur between atoms (on the base of changes in interatomic distances). Precise rules to accurately define the degrees of freedom and, in turn, the related folding factors, have not been reported to date. We propose here an empirical analysis of possible physico-chemical principles for a careful evaluation of the degrees of freedom, as well as the threshold distances for the chemical interactions to occur. To validate our systematic approach, we have applied these rules to the calculation of dihedral angles of the α-helix Vps27p and the beta-sheet U(1–17)T9D, highlighting wide agreement between predicted and experimental values.

Structural style and evolution of the offshore portion of the Sinu Fold Belt (South Caribbean Deformed Belt) and adjacent part of the Colombian Basin

The Sinu fold belt, located in northwestern Colombia, is the southwesternmost part of the South Caribbean Deformed Belt, which has been interpreted as an accretionary wedge resulting from the subduction of the Caribbean Plate under the South American Plate. The geological interpretation of 2D seismic surveys and bathymetric maps, with the aid of a few exploration wells, has been the basis to construct a structural map and several geological sections to illustrate the offshore part of the Sinu Fold Belt and the portion of the Colombian Basin adjacent to the belt. Their analysis has allowed us to characterize different structural styles (thrusts and related folds in the outer part of the belt, and normal faults and shale diapirs in the inner one), the timing of the structures, as well as the kinematic evolution from a Cretaceous-Paleocene extensional event responsible for the Colombian Basin structure to the Pliocene-Quaternary contractional event which caused the Sinu Fold Belt.

An evaluation of single-sample tumor subtype classification methods

Large efforts have been made to divide bladder cancer into prognostic or predictive subtypes by unsupervised or semi-supervised clustering of mRNA data. To validate and make use of subtypes, classifiers must be constructed that accurately predicts subtypes in new samples. Variations of nearest centroid classification is commonly used, where each class is represented as a vector of mean fold changes of selected genes. The similarity to these vectors is then used to predict the class of a new sample. Using relative fold change values means that classification becomes related to both the composition of the training cohort and the cohort the new sample originates from. Without thorough data preprocessing, this can result in major classification errors. Optimally, we want to classify a new sample in isolation in a manner robust to preprocessing, sample purity, and mRNA measurement technology. We evaluated single sample classification methods based on using sets of gene-pair rules (e.g. Gene A>Gene B indicates Subtype X), using the R packages AIMS and SwitchBox, and a custom iterative RandomForest (RF) approach, as well as the single sample centroid approach used by Kamoun et. el. These were tested on Lund, TCGA, and IMvigor210 data. Rule-based and centroid based single sample classifiers were able to achieve similar accuracy in predicting LundTaxonomy subtypes in the datasets. The single sample centroid classifier based on raw expression values suffered from poor separation between predictions (delta between best and second-best prediction), which becomes worse as more genes were included. Rule-based methods, particularly RF, had much more distinct subtype calls. The custom RF approach outperformed the published AIMS and SwitchBox methods. Each single sample classifier method had strengths and limitations. The RF based approach emerged as a promising new method, being robust even when using very few genes, while also allowing for evaluation of class stability and putative incorrect reference labels during training. The main challenge is how to select which gene-rules to use in the classifier. An R package (“multiclassPairs”) for building SwitchBox and RandomForest classifier models is currently being prepared.

ReconCNV: interactive visualization of copy number data from high-throughput sequencing.

Copy number variation (CNV) is an important category of unbalanced structural rearrangement. While methods for detecting CNV in high-throughput targeted sequencing have become increasingly sophisticated, dedicated tools for interactive and dynamic visualization of CNV from these data are still lacking. We describe reconCNV, a tool that produces an interactive and annotated web-based dashboard for viewing and summarizing CNVs detected in next-generation sequencing (NGS) data. reconCNV is designed to work with delimited result files from most NGS CNV callers with minor adjustments to the configuration file. The reconCNV output is an HTML file that is viewable on any modern web browser, requires no backend server, and can be readily appended to existing analysis pipelines. In addition to a standard CNV track for visualizing relative fold change and absolute copy number, the tool includes an auxiliary variant allele fraction track for visualizing underlying allelic imbalance and loss of heterozygosity. A feature to mask assay-specific technical artifacts and a direct HTML link out to the UCSC Genome Browser are also included to augment the reviewer experience. By providing a light-weight plugin for interactive visualization to existing NGS CNV pipelines, reconCNV can facilitate efficient NGS CNV visualization and interpretation in both research and clinical settings. The source code and documentation including a tutorial can be accessed athttps://github.com/rghu/reconCNV as well as a Docker image at https://hub.docker.com/repository/docker/raghuc1990/reconcnv. Supplementary data are available at Bioinformatics online.