Physicochemical Signatures Research Articles

PH dependent physicochemical signatures of amino acids in aqueous buffers: Thermodynamic analysis

The physicochemical signatures such as apparent molar volume (V2,Φ), isoentropic compressibilities (KS,2,φ), and dilution enthalpies of a series of amino acids (AAs) glycine (Gly), L-alanine (Ala), DL-α-amino-n-butyric acid (ABA), L-valine (Val) and L-leucine (Leu) have been measured at various pH values (pH = 2, 5 7 and 9) at a buffer molality of 0.1 mol kg−1 of water at 298.15 K. The data obtained from high sensitivity densimeter and sound analyser along with ultrasensitive isothermal titration calorimetry has been analyzed to evaluate the values of standard partial molar quantities such as for volume at infinite dilution (V2,m0), compressibility KS, 2,m0 and dilution enthalpy (ΔdilH0) of the AAs together with standard partial molar quantities of transfer of these solutes from water to aqueous buffer systems at these pH values. The linear correlation of V2,m0 for this series of AAs against number of carbon atoms in their alkyl chain has been used to evaluate the contribution of zwitterionic end groups (NH3+, COO–), the CH2 group, and other parts of alkyl chains of the AAs to the overall value of V2,m0. The results of standard partial molar transfer properties on volumes, compressibilities and enthalpies of dilution from water to aqueous buffer systems at various pH values have been connected and explained in terms of ion-polar, ion-hydrophilic, hydrophobic-hydrophobic and ion-hydrophobic interactions of the participating groups. These thermodynamic signatures when compared at different pH values suggest that at electrostriction of water dominates at pH 2. Such physicochemical properties of constituents of proteins such as amino acids have not been reported earlier. Thus, the results demonstrate that the interaction of individual amino acid residues with the buffer components does not lead to significant change in their physicochemical properties thereby permitting their use in obtaining mechanistic insights into systems of biological interest consisting of these constituents.

Local energetic frustration conservation in protein families and superfamilies

Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a methodology to analyze local frustration patterns within protein families and superfamilies that allows us to uncover constraints related to stability and function, and identify differential frustration patterns in families with a common ancestry. We analyze these signals in very well studied protein families such as PDZ, SH3, ɑ and β globins and RAS families. Recent advances in protein structure prediction make it possible to analyze a vast majority of the protein space. An automatic and unsupervised proteome-wide analysis on the SARS-CoV-2 virus demonstrates the potential of our approach to enhance our understanding of the natural phenotypic diversity of protein families beyond single protein instances. We apply our method to modify biophysical properties of natural proteins based on their family properties, as well as perform unsupervised analysis of large datasets to shed light on the physicochemical signatures of poorly characterized proteins such as the ones belonging to emergent pathogens.

HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation

BackgroundHIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner. Methods2253 sequences representing subtypes A1, B, C, and D were aligned and domains with known functional properties were scored based on amino acid physicochemical properties. Following feature generation, we used statistical pruning and evolved neural networks (ENNs) to determine if we could successfully classify subtypes. Next, we used ENNs to identify the top five key Nef physicochemical features applied to specific immunoregulatory domains that differentiated subtypes. A signature pattern analysis was performed to the assess amino acid diversity in sub-domains that differentiated each subtype. ResultsIn validation studies, ENNs successfully differentiated each subtype at A1 (87.2%), subtype B (89.5%), subtype C (91.7%), and subtype D (85.1%). Our feature-based domain scoring, followed by t-tests, and a similar ENN identified subtype-specific domain-associated features. Subtype A1 was associated with alterations in Nef CD4 binding domain; subtype B was associated with alterations with the AP-2 Binding domain; subtype C was associated with alterations in a structural Alpha Helix domain; and, subtype D was associated with alterations in a Beta-Sheet domain. ConclusionsRecent studies have focused on HIV Nef as a driver of immunoregulatory disease in those HIV infected and on ART. Nef acts through a complex mixture of interactions that are directly linked to the key features of the subtype-specific domains we identified with the ENN. The study supports the hypothesis that varied Nef subtypes contribute to subtype-specific disease progression.

Characterizing the transitory groundwater-surface water interaction and its environmental consequence of a riverside karst pool

Exchange between groundwater (GW) and surface water (SW) is a common occurrence in karst water systems through sinking stream disappearance or groundwater emergence. However, the transitory GW-SW interaction caused by river backflowing into a spring is poorly observed and understood. In this study, we present an approach for characterizing the influence of GW-SW interaction in a karst spring by integrating high-resolution hydrology, carefully selected hydrochemistry monitoring and precise microbe measurements. The spring-fed pool water conditions can be distinguished as high, medium, and low-water level periods in a hydrological year. The high-water level accounts for <1 % in a year, while it is associated with the hydrological regimes of backflooding states. The inflow of river backflow was found to be 4.4 times that of the natural discharge of spring water during a rainfall event. The duration of river intrusion into the spring or karst conduit could be assessed by jointly interpreting hydrography and physicochemical signatures, while the lasting environmental consequences should be evaluated together with biotic factors such as Escherichia coli. The GW-SW interaction induced by river backflow has led to the retention of river water in a pool, spring, and karst conduit for 132, 94, and 56 h, respectively. Despite turbidity returning to normal levels after 56 h, E.coli continued to persist for an extended duration. Our study reveals that despite the transient nature of GW-SW induced by river backflow on the hydrograph, they present a lasting risk of contamination from heavy metals, organic matter, and microorganisms. This extended influence can persist within a karst aquifer lacking a hyporheic zone. This research contributes to the quantification of processes involved in transitory GW-SW interaction in a karst spring, and it highlights the underestimation of GW-SW interactions in karst water systems, which might negatively impact water resources management.

Land use scenarios, seasonality, and stream identity determine the water physicochemistry of tropical cloud forest streams.

Land use is a major factor determining stream water physicochemistry. However, most streams move from one land use type to another as they drain their watersheds. Here, we studied three land use scenarios in a tropical cloud forest zone in Mexico. We addressed three main goals, to: (1) assess how land use scenarios generate different patterns in stream physicochemical characteristics; (2) explore how seasonality (i.e., dry, dry-to-wet transition, and wet seasons) might result in changes to those patterns over the year; and (3) explore whether physicochemical patterns in different scenarios resulted in effects on biotic components (e.g., algal biomass). We studied Tropical Mountain Cloud Forest streams in La Antigua watershed, Mexico. Streams drained different three scenarios, streams with (1) an upstream section draining forest followed by a pasture section (F-P), (2) an upstream section in pasture followed by a forest section (P-F), and (3) an upstream forest section followed by coffee plantation (F-C). Physicochemistry was determined at the upstream and downstream sections, and at the boundary between land uses. Measurements were seasonal, including temperature, dissolved oxygen, conductivity, and pH. Water was analyzed for suspended solids, alkalinity, silica, chloride, sulfate, magnesium, sodium, and potassium. Nutrients included ammonium, nitrate, and phosphorus. We measured benthic and suspended organic matter and chlorophyll. Streams presented strong seasonality, with the highest discharge and suspended solids during the wet season. Scenarios and streams within each scenario had distinct physicochemical signatures. All three streams within each scenario clustered together in ordination space and remained close to each other during all seasons. There were significant scenario-season interactions on conductivity (F = 9.5, P < 0.001), discharge (F = 56.7, P < 0.001), pH (F = 4.5, P = 0.011), Cl- (F = 12.2, P < 0.001), SO42- (F = 8.8, P < 0.001) and NH4+ (F = 5.4, P = 0.005). Patterns within individual scenarios were associated with stream identity instead of land use. Both P-F and F-C scenarios had significantly different physicochemical patterns from those in F-P in all seasons (Procrustes analysis, m12 = 0.05-0.25; R = 0.86-0.97; P < 0.05). Chlorophyll was significantly different among scenarios and seasons (F = 5.36, P = 0.015, F = 3.81, P = 0.42, respectively). Concentrations were related to physicochemical variables more strongly during the transition season. Overall, land use scenarios resulted in distinctive water physicochemical signatures highlighting the complex effects that anthropogenic activities have on tropical cloud forest streams. Studies assessing the effect of land use on tropical streams will benefit from assessing scenarios, rather than focusing on individual land use types. We also found evidence of the importance that forest fragments play in maintaining or restoring stream water physicochemistry.

The sound of geological targets on Mars from the absolute intensity of laser-induced sparks shock waves

Inspection of geological material is one of the main goals of the Perseverance rover during its journey across the landscape of the Jezero crater in Mars. NASA's rover integrates SuperCam, an instrument capable of performing standoff characterization of samples using a variety of techniques. Among those tools, SuperCam can perform laser-induced breakdown spectroscopy (LIBS) studies to elucidate the chemical composition of the targets of interest. Data from optical spectroscopy can be supplemented by simultaneously-produced laser-produced plasma acoustics in order to expand the information acquired from the probed rocks thanks to the SuperCam's microphone (MIC) as it can be synchronized with the LIBS laser. Herein, we report cover results from LIBS and MIC during Perseverance's first 380 sols on the Martian surface. We study the correlation between both recorded signals, considering the main intrasample and environmental sources of variation for each technique, to understand their behavior and how they can be interpreted together towards complimenting LIBS with acoustics. We find that louder and more stable acoustic signals are recorded from rock with compact surfaces, i.e., low presence loose particulate material, and harder mineral phases in their composition. Reported results constitute the first description of the evolution of the intensity in the time domain of shockwaves from laser-produced plasmas on geological targets recorded in Mars. These signals are expected contain physicochemical signatures pertaining to the inspected sampling positions. As the dependence of the acoustic signal recorded on the sample composition, provided by LIBS, is unveiled, the sound from sparks become a powerful tool for the identification of mineral phases with similar optical emission spectra.

Combined use of in-reservoir geological records for oil-reservoir destruction identification: A case study in the Jingbian area (Ordos Basin, China)

Rapid identification of reservoir destruction is critical to avoid exploration failure. More indicators of reservoir destruction are urgently needed to be developed besides the evaluation methods of trap effectiveness based on structural analysis. Here, we provide a case study in the Ordos Basin to show that the combined use of in-reservoir geological records is a robust tool to rapidly identify oil-reservoir destruction. The sandstones within the Yanchang Formation in the oil-depleted Jingbian area were investigated by petrological and geochemical analysis. The results show that 1) the oils with increased density and viscosity occur in the low permeability sandstones, whereas the high permeability sandstones were occupied by water, 2) abundant solid bitumen occur in the intergranular pores, 3) the n-alkanes with carbon numbers less than 19 are significantly lost from the original oils, and 4) the majority of paleo oil layers have evolved into present water layers. All these in-reservoir physicochemical signatures unravel the same geological event (i.e., oil-reservoir destruction) in the Jingbian area. This oil-reservoir destruction was likely caused by the uplift-induced erosion and the fault activities after oil accumulation during the Late Early Cretaceous.

Physicochemical models of protein–DNA binding with standard and modified base pairs

DNA-binding proteins play important roles in various cellular processes, but the mechanisms by which proteins recognize genomic target sites remain incompletely understood. Functional groups at the edges of the base pairs (bp) exposed in the DNA grooves represent physicochemical signatures. As these signatures enable proteins to form specific contacts between protein residues and bp, their study can provide mechanistic insights into protein-DNA binding. Existing experimental methods, such as X-ray crystallography, can reveal such mechanisms based on physicochemical interactions between proteins and their DNA target sites. However, the low throughput of structural biology methods limits mechanistic insights for selection of many genomic sites. High-throughput binding assays enable prediction of potential target sites by determining relative binding affinities of a protein to massive numbers of DNA sequences. Many currently available computational methods are based on the sequence of standard Watson-Crick bp. They assume that the contribution of overall binding affinity is independent for each base pair, or alternatively include dinucleotides or short k-mers. These methods cannot directly expand to physicochemical contacts, and they are not suitable to apply to DNA modifications or non-Watson-Crick bp. These variations include DNA methylation, and synthetic or mismatched bp. The proposed method, DeepRec, can predict relative binding affinities as function of physicochemical signatures and the effect of DNA methylation or other chemical modifications on binding. Sequence-based modeling methods are in comparison a coarse-grain description and cannot achieve such insights. Our chemistry-based modeling framework provides a path towards understanding genome function at a mechanistic level.

PP 1.18 – 00105 Machine learning identifies differentiating physicochemical signatures between HIV subtypes in Nef domains associated with host-cell regulation

PP 1.18 – 00105 Machine learning identifies differentiating physicochemical signatures between HIV subtypes in Nef domains associated with host-cell regulation

Estimating grapevine-relevant physicochemical soil zones using apparent electrical conductivity and in-phase data from EMI methods

This study explores the ability of the frequency domain electromagnetic induction (EMI) method to produce physicochemical soil maps with relevance to grapevine vigor. The study was conducted in the Médoc area of the Bordeaux wine region in France. A flexible clustering approach was used with both the apparent electrical conductivity and the in-phase components of EMI measurements. Soil zones with distinct physicochemical signatures were successfully identified, primarily due to the inclusion of in-phase data in the clustering method. Importantly, this approach does not use prior information to guide zone classification and does not require calibration of EMI measurements. Extensive soil texture and physicochemical measurements were used to compare the different zones identified by the clustering approach. Grapevine vigor was assessed using normalized vegetation index (NDVI) data to help conceptualize the critical physicochemical variables of the soil. It was evident that NDVI and EMI data were correlated to organic matter, nitrogen, CEC, pH, CaO, and copper concentration in one of the investigated sites. Unlike previous work in other Bordeaux soil viticulture areas, soil texture at these sites was relatively homogenous and consequently did not influence plant vigor substantially. This work demonstrates the value of the in-phase component of EMI measurements to estimate soil zonation. More generally, this work demonstrates the ability of coupled EMI and NDVI surveys to inform viticulture at scales relevant to management decisions.

Mining Residues Characterization and Sentinel-2A Mapping for the Valorization and Efficient Resource Use by Multidisciplinary Strategy

Raw materials are essential for all sectors of the economy as well as for all innovative technologies. Currently, industry is largely dependent on imports and consumption of these materials, and in the future, following the global energy transition, this trend will drastically increase. For this reason, it is necessary to develop new strategies to meet the supply–demand of raw materials by strategic sectors and technologies. To this end, mining residues are turning into viable raw materials sources as they represent reliable access to valuable resource supply. This work aims to validate a methodology providing more in-depth quali-quantitative information about 100 samples of mining residues collected in the Joda West mine (India) by multidisciplinary strategy in order to valorize and promote efficient resource use. In this paper, physicochemical and mineralogical characterization and hyperspectral signatures have been integrated with satellite Sentinel-2A data. In particular, the X-ray powder diffraction (XRPD), X-ray fluorescence (XRF), and scanning electron microscopy with energy dispersive spectroscopy (SEM-EDS) analyses indicated the presence of mining residues samples rich in raw materials that were possible to spectrally distinguish in order to use them as input for the object-oriented classification of a satellite image. The satellite resulting map highlighted four different classes of mining residues with mean concentrations of around 36% for hematite, 23.5% for quartz, 9% for kaolinite and 5% for pyrolusite. These results represent the possibility of transforming an environmental problem (mining residues) into a resource potentially exploitable by industries knowing their composition and position in the study area. Moreover, by doing so, it will be possible to ensure sustainable consumption of the raw materials and to build resilient economies and societies, minimizing environmental degradation.

Characterization of physicochemical markers for homeopathic medicines and biological supernatant samples

Introduction: Solvatochromic dyes are probes to detect variations on the dipole moment of solvents after the insertion of homeopathic potencies. Recent studies have shown they can be useful tools in laboratory and field studies to detect the activity of homeopathic remedies. Objective: Determine whether solvatochromic dyes can be a diagnostic tool for cells infected by different agents and/or markers to identify the activity of homeopathic medicines. Methods: Ethilicum 1cH, Silicea terra 6, 30, 200cH; Zincum metallicum 6, 30, 200cH and Phosphorus 6, 30 and 200cH were analyzed by pouring the samples (in a 1:60 rate) into a series of seven dyes (rhodamine, ET 33, ET 30, coumarin 7, NN DMIA, Nile red, methylene violet) diluted in absolute ethanol using pre-established working concentrations. Oscillations of dye absorbance were observed at visible light spectrophotometry according to the remedy and potency. Water and succussed water were used as controls. In a second moment, the absorbance profile of the remedies will be compared with those of biological samples (supernatants) and checked with the biological effect previously obtained from each treatment. Supernatants of RAW 264.7 macrophages stimulated by Calmette-Guérin bacilli (BCG) or infected with Encephalitozoon cuniculi will be analyzed. Results: Preliminary results have shown that Silicea terra 6cH, Phosphorus 30 and 200cH and Zincum metallicum 6, 30 and 200cH reduced the absorbance of methylene violet (p=0.01). Repetitions and analysis of supernatants are expected to be performed in the next steps of the study. Future perspectives: Establish a pattern of reactivity of the studied medicines with different dyes and the putative relation with the corresponding supernatants, as an attempt to obtain a “physicochemical signature” for each kind of infection and/or treatment.

How do turbidite systems behave from the hydrogeological point of view? New insights and open questions coming from an interdisciplinary work in southern Italy.

Turbidite successions can behave either as aquitards or aquifers depending on their lithological and hydraulic features. In particular, post-depositional processes can increase rock permeability due to fracture development in the competent layers. Thus, at a local scale, turbidite systems warrant further detailed investigations, aimed at reconstructing reliable hydrogeological models. The objective of this work was to investigate from the hydrogeological perspective a turbiditic aquifer located in southern Italy, where several perennial and seasonal springs were detected. Considering the complex hydrodynamics of these systems at the catchment scale, to reach an optimal characterization, a multidisciplinary approach was adopted. The conceptual framework employed microbial communities as groundwater tracers, together with the physicochemical features and isotopic signature of springs and streams from water samples. Meanwhile, geophysical investigations coupled with the geological survey provided the contextualization of the hydrogeological data into the detailed geological reconstruction of the study area. This modus operandi allowed us to typify several differences among the samples, allowing identification of sources and paths of surface water and groundwater, along with diffuse groundwater outflow along streams. As a final result, a hydrogeological conceptual model was reconstructed, underlining how at a very local scale the lithologic, hydraulic, and geomorphological heterogeneity of the studied relief can lead to an improved hydrogeological conceptual model compared to that of other turbidite systems. These results open new questions about the hydrogeological behavior of turbiditic aquifers, which could be pivotal in future research. In fact, these systems could support relevant ecosystems and anthropic activities, especially where climate change will force the research of new (and probably less hydrogeologically efficient) water sources.

A comparative evaluation of automated recession extraction methods to determine the late-time recession characteristics of karst spring hydrographs

Recession Curve Analysis is a common method to characterize karstic aquifers and their discharge dynamics. Although this technique provides crucial information on quantifying system hydrodynamic properties, the manually selected recession curves analysis is neither a practical technique to cover all candidate recession curves, nor it allows extracting the entire hydrological diversity of the recession behavior. This study aimed to comparatively evaluate the applicability of automated recession selection procedures to the late-time recession analysis of karst spring hydrograph. For the comparative evaluation of the three automated recession extraction methods (Vogel Method, Brutsaert Method, and Aksoy and Wittenberg Method), we quantified the late-time recession parameters of spring hydrographs by combining three extraction methods with four recession analysis methods (Maillet, 1905; Boussinesq, 1904; Coutagne, 1948; and Wittenberg, 1999). By applying our experimental design into the five karst springs located in Austria, we identified the possible weaknesses of the automated recession extraction procedures for the late-time recession analysis for spring hydrographs. To explore the value of the karst spring’s physicochemical data (electrical conductivity and water temperature) as a completion data for the recession curve analysis, we carried out the hydro-chemograph analysis to examine the recession time and its duration. The research provides a research direction as to how the automated recession extraction procedures for the karst spring hydrographs could be improved by the physicochemical signatures of karst springs.

Karst aquifer characterization by inverse application of MODFLOW-2005 CFPv2 discrete-continuum flow and transport model

This research presents the first application of a distributed discrete-continuum numerical model for simultaneous inversion of long-term spring flow in conjunction with solute- and heat-transport signatures, in a large-scale karst system. The MODFLOW-2005 CFPv2 code was adopted for this reason, utilizing PEST for automated inversion. Taking the principal of model parsimony into account, simulations were performed at two stages, testing likely conceptual models based on the hydro-geological understandings. At the first stage, simple yet realistic conceptual models were setup considering different probable variants of conduit geometries. Results of this stage highlights the importance of sinkhole-spring dynamics, in the recorded spring signatures; such that, successful simultaneous calibration of all spring signatures could not be obtained unless high linkage of conduits to the sinkholes all over the catchment was adopted. Subsequently, some additional rational complexity was added in order to achieve a more demonstrable model of the karst system, as the second stage. Model selection criteria, fitting statistics and reasonableness of calibrated parameters were assessed, at this stage. Although one of the model variants could statistically represent all observations with reasonable parameter values and high agreement with catchment hydrogeological perspective, it still cannot be approved as a predictive tool, unless field measurements on conduit system characteristics and matrix hydraulic parameters, as well as long-term observation of aquifer physicochemical signatures be collected for further validation/improvement of conceptual and numerical model. Achieved simultaneous inversion results can serve as a proof of concept for applicability of physically based discrete-continuum modeling approach for flow and transport modeling in karst.

Ultraspecific live imaging of the dynamics of zebrafish neutrophil granules by a histopermeable fluorogenic benzochalcone probe.

Neutrophil granules (NGs) are key components of the innate immune response and mark the development of neutrophilic granulocytes in mammals. However, there has been no specific fluorescent vital stain up to now to monitor their dynamics within a whole live organism. We rationally designed a benzochalcone fluorescent probe (HAB) featuring high tissue permeability and optimal photophysics such as elevated quantum yield, pronounced solvatochromism and target-induced fluorogenesis. Phenotypic screening identified HAB as the first cell- and organelle-specific small-molecule fluorescent tracer of NGs in live zebrafish larvae, with no labeling of other cell types or organelles. HAB staining was independent of the state of neutrophil activation, labeling NGs of both resting and phagocytically active neutrophils with equal specificity. By high-resolution live imaging, we documented the dynamics of HAB-stained NGs during phagocytosis. Upon zymosan injection, labeled NGs were rapidly recruited to the forming phagosomes. Despite being a reversible ligand, HAB could not be displaced by high concentrations of pharmacologically relevant competing chalcones, indicating that this specific labeling was the result of the HAB's precise physicochemical signature rather than a general feature of chalcones. However, one of the competitors was discovered as a promising interstitial fluorescent tracer illuminating zebrafish histology, similarly to BODIPY-ceramide. As a yellow-emitting histopermeable vital stain, HAB functionally and spectrally complements most genetically incorporated fluorescent tags commonly used in live zebrafish biology, holding promise for the study of neutrophil-dependent responses relevant to human physiopathology such as developmental defects, inflammation and infection. Furthermore, HAB intensely labeled isolated live human neutrophils at the level of granulated subcellular structures consistent with human NGs, suggesting that the labeling of NGs by HAB is not restricted to the zebrafish model but also relevant to mammalian systems.

Physicochemical property based computational scheme for classifying DNA sequence elements of Saccharomyces cerevisiae

GenerationE of huge “omics” data necessitates the development and application of computational methods to annotate the data in terms of biological features. In the context of DNA sequence, it is important to unravel the hidden physicochemical signatures. For this purpose, we have considered various sequence elements such as promoter, ACS, LTRs, telomere, and retrotransposon of the model organism Saccharomyces cerevisiae. Contributions due to di-nucleotides play a major role in studying the DNA conformation profile. The physicochemical parameters used are hydrogen bonding energy, stacking energy and solvation energy per base pair. Our computational study shows that all sequence elements in this study have distinctive physicochemical signatures and the same can be exploited for prediction experiments. The order that we see in a DNA sequence is dictated by biological regions and hence, there exists role of dependency in the sequence makeup, keeping this in mind we are proposing two computational schemes (a) using a windowing block size procedure and (b) using di-nucleotide transitions. We obtained better discriminating profile when we analyzed the sequence data in windowing manner. In the second novel approach, we introduced the di-nucleotide transition probability matrix (DTPM) to study the hidden layer of information embedded in the sequences. DTPM has been used as weights for scanning and predictions. This proposed computational scheme incorporates the memory property which is more realistic to study the physicochemical properties embedded in DNA sequences. Our analysis shows that the DTPM scheme performs better than the existing method in this applied region. Characterization of these elements will be a key to genome editing applications and advanced machine learning approaches may also require such distinctive profiles as useful input features.

Computational identification of physicochemical signatures for host tropism of influenza A virus.

Avian influenza viruses from migratory birds have managed to cross host species barriers and infected various hosts like human and swine. Epidemics and pandemics might occur when influenza viruses are adapted to humans, causing deaths and enormous economic loss. Receptor-binding specificity of the virus is one of the key factors for the transmission of influenza viruses across species. The determination of host tropism and understanding of molecular properties would help identify the mechanism why zoonotic influenza viruses can cross species barrier and infect humans. In this study, we have constructed computational models for host tropism prediction on human-adapted subtypes of influenza HA proteins using random forest. The feature vectors of the prediction models were generated based on seven physicochemical properties of amino acids from influenza sequences of three major hosts. Feature aggregation and associative rules were further applied to select top 20 features and extract host-associated physicochemical signatures on the combined model of nonspecific subtypes. The prediction model achieved high performance ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mtext>Accuracy</mml:mtext><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo><mml:mn>9</mml:mn><mml:mn>4</mml:mn><mml:mn>8</mml:mn></mml:math> , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mtext>Precision</mml:mtext><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo><mml:mn>9</mml:mn><mml:mn>5</mml:mn><mml:mn>4</mml:mn></mml:math> , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mtext>MCC</mml:mtext><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo><mml:mn>9</mml:mn><mml:mn>2</mml:mn><mml:mn>2</mml:mn></mml:math> ). Support and confidence rates were calculated for the host class-association rules. The results indicated that secondary structure and normalized Van der Waals volume were identified as more important physicochemical signatures in determining the host tropism.

Assessment of the physicochemical characteristics of surface waterbodies in a region earmarked for shale gas exploration (Eastern Cape Karoo, South Africa)

The proposed drilling for shale gas resources in the Eastern Cape Karoo region of South Africa has triggered much debate over the potential effects of hydraulic fracturing on water resources. Herein we present results on some limnological aspects of surface waterbodies in this water-scarce region before shale gas exploration. Thirty-three waterbodies (nine dams, 13 depression wetlands and 11 rivers) were sampled in November 2014 and April 2015. Principal component analysis revealed that depression wetlands and rivers had distinct physicochemical signatures, whereas dams were highly variable in their physicochemical attributes and exhibited characteristics similar to those of either rivers or depression wetlands. Non-parametric multivariate regressions and permutational multivariate analysis of variance (MANOVA) indicated that landscape variables such as underlying geology, altitude and land use poorly explained the physicochemical characteristics of the sampled waterbodies. Waterbody type was the only factor that explained a significant amount of the variation in physicochemistry during both sampling events. These data need to be supplemented by water quality information from additional sites and over longer time periods, as well as supporting data relating to other aspects, such as algae and invertebrates, before they can be used as a baseline for the long-term monitoring of freshwater ecosystems in the region.

Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures.

BackgroundThe microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion.ResultsHere we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape.ConclusionTogether this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1920-7) contains supplementary material, which is available to authorized users.