Shallow Sites Research Articles

Influence of geostatistical interpolation method and cell-size resolution on CO2 storage capacity estimates: Application to saline aquifers with sparse data availability in Israel

The primary focus for future large-scale projects targeting the sequestration of CO2 lies in underground saline aquifers. In southern Israel, two such aquifers were identified as suitable for CO2 storage, however, the data available for these aquifers is limited and sparse. To confront this challenge, geostatistical interpolation techniques are often used to fill in the data gaps. In this study, we evaluate the impact of the interpolation method and cell size on the storage capacity of these two saline aquifers. Eight interpolation techniques are used to estimate three parameters of the aquifers (thickness, depth, and porosity), which serve as the basis for evaluating the CO2 storage capacity, utilizing the US-DOE-NETL equation. Our findings show that the choice of the interpolation method and cell size has a significant impact on the calculated CO2 storage capacity, and therefore stress the importance of documenting these parameters. Our evaluation also shows that shallow CO2 storage sites exhibit a greater sensitivity to depth relative to deeper storage sites. The results of our study are applicable to early-stage assessments of regional CO2 storage capacity in which data is limited. Calculated CO2 storage capacities for the two aquifers indicate their continued suitability for CO2 sequestration in Israel.

Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents.

Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans. The aim of this study was to characterize the subgingival bacteriome in Moroccan subjects with GCP positive to A. actinomycetemcomitans JP2 genotype. Subgingival plaque samples were collected from shallow and deep pockets of 8 subjects with GCP (17.2 ± 1.5 years) and from gingival sulci of 13 controls with no periodontitis (14.6 ± 1.1 years). Identification and genotyping of A. actinomycetemcomitans was performed using PCR analysis of the ltx operon, while bacteriome profiling was done by 16S rRNA gene sequencing (V1-V3 region). Groups were compared in terms of microbial diversity, abundances, and dysbiosis. The shallow and deep pocket sites from GCP cases had a significantly altered microbial composition compared to controls. Species associated with health included Haemophilus parainfluenzae, Lautropia mirabilis, Streptococcus spp., Gemella spp., and Rothia spp. While known periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema spp. and Fretibacterium spp., were significantly enriched in GCP, non-conventional taxa, including Pseudomonas oral taxon C61 and Enterobacter cloacae were more abundant and showed stronger association with the disease. Less significant differences in abundances of individual taxa were observed between shallow and deep pockets. Overall dysbiosis measured in terms of Subgingival Microbial Dysbiosis Index (SMDI) differentiated between GCP and no-periodontitis with 95% accuracy. The results suggest that several periodontal pathogens involved in the adult-type periodontitis also play a role in JP2 genotype-associated GCP. The potential role of non-conventional taxa in the pathogenesis of GCP warrants further investigation.

Quantifying links between topsoil depth, plant water use, and yield in a rainfed maize field in the U. S. Midwest

Agricultural production in highly variable soils is a challenge, especially when those soils are shallow. Precision agriculture techniques were developed to improve yields and minimize spatial and interannual variability in profit. In the Central Claypan region of the Midwest United States, many of the precision agriculture techniques were based on the assumption that topsoil depth controlled plant available water, and therefore yield. But this assumption has not been empirically tested. In this study, we use measurements of sap flow installed on maize plants with a gradient in topsoil depth, caused by a claypan layer. We hypothesize that plants with higher water use have higher yield, plants in areas with thicker topsoil have higher water use, and soils in the areas with thicker topsoil have higher soil water content. Sap flow sensors were installed on 5 plants each at three locations with topsoil depths of 19.6 cm (shallow), 21.6 cm (medium), and 30.5 cm (deep) from June – September, 2022. An ANOVA analysis demonstrates that the average total season transpiration at the deep site (279 mm) was significantly larger than at the shallow site (151 mm), while the medium site was in the middle with transpiration not significantly different from either shallow or deep sites (218 mm). At the end of the season, the plants were harvested and total biomass and grain yield were measured. Increase in plant transpiration was significantly related to both increases in biomass and yield. Finally, we measured volumetric soil water content at each location and found higher soil water content at the site with thicker topsoil. Our results demonstrate the link between topsoil depth, soil water content, plant transpiration, and yield. These findings will help improve precision agriculture techniques in areas with highly variable topsoil thickness.

Mechanisms of NMDA Receptor Inhibition by Sepimostat-Comparison with Nafamostat and Diarylamidine Compounds.

N-methyl-D-aspartate (NMDA) receptors are inhibited by many amidine and guanidine compounds. In this work, we studied the mechanisms of their inhibition by sepimostat-an amidine-containing serine protease inhibitor with neuroprotective properties. Sepimostat inhibited native NMDA receptors in rat hippocampal CA1 pyramidal neurons with IC50 of 3.5 ± 0.3 µM at -80 mV holding voltage. It demonstrated complex voltage dependence with voltage-independent and voltage-dependent components, suggesting the presence of shallow and deep binding sites. At -80 mV holding voltage, the voltage-dependent component dominates, and we observed pronounced tail currents and overshoots evidencing a "foot-in-the-door" open channel block. At depolarized voltages, the voltage-independent inhibition by sepimostat was significantly attenuated by the increase of agonist concentration. However, the voltage-independent inhibition was non-competitive. We further compared the mechanisms of the action of sepimostat with those of structurally-related amidine and guanidine compounds-nafamostat, gabexate, furamidine, pentamidine, diminazene, and DAPI-investigated previously. The action of all these compounds can be described by the two-component mechanism. All compounds demonstrated similar affinity to the shallow site, which is responsible for the voltage-independent inhibition, with binding constants in the range of 3-30 µM. In contrast, affinities to the deep site differed dramatically, with nafamostat, furamidine, and pentamidine being much more active.

Phosphorus mobilization in sulfidic sediments in the Baltic Sea

It is well-known that the geochemical behavior of phosphorus (P) in sediments is closely related to that of Fe and Mn, but their relations remain unclear in long-term sulfidic sediments such as those of the Gotland Basin in the Baltic Sea. Therefore, P mobilization in these sediments at both shallow and deep sites was investigated in relation to that of Fe, Mn, and S. To achieve that aim, classic sediment slicing and subsequent solid phase sequential extraction were combined with in situ DGT (Diffusive Gradients in Thin-films) sampling, DIFS (DGT induced flux in sediments) modelling, and Visual MINTEQ calculations. Correlations between total dissolved and labile dissolved concentrations of P, Mn, and Fe in porewater, and the associations between labile fractions of these elements in the solid phase suggested two kinds of sources for P: The dissolution of P-bearing Fe oxides and/or Mn carbonates was observed in the shallower sites, while P and Mn release from different solid sources was observed in the deepest sites. Although the formation of Fe sulfides leads to extremely low dissolved Fe level in porewater, the simultaneous release of P with Mn/Fe was confirmed by theoretical calculations with Visual MINTEQ. The DIFS model showed that the resupply ability of P from sediment solids is determined by labile pool size. The application of experimental and theoretical methods made it possible to clarify the relationships between P, Fe, Mn and S in sulfidic sediments which may contribute to a better understanding of the P cycle in other sulfidic regions.

Elevated internal phosphorus loading from shallow areas of eutrophic boreal lakes: Insights from porewater geochemistry

Internal phosphorus (P) loading is widely recognized as a major cause of lake eutrophication. One conventional paradigm states that the magnitude of internal loading through P diffusion is constrained by the presence of iron (Fe) oxides in surface sediments under oxic conditions near the sediment-water interface (SWI). However, biogeochemical P dynamics in Fe-rich sedimentary systems are still not fully understood, especially in eutrophic lakes where intensively coupled organic matter (OM) remineralization and reductive dissolution of Fe-bound P (Fe-P) exist concurrently. Here, we assess the diagenetic processes that govern sedimentary P cycling in two eutrophic Fe-rich lakes in southern Finland, Lake Hiidenvesi and Lake Kytäjärvi, using a combination of porewater and solid-phase analyses. Coupled reductive dissolution of Fe-P and OM remineralization controlled P regeneration in both lakes, with Fe-P acting as the dominant source for porewater P. Vivianite formation likely immobilized sedimentary P in the deepest basin of Hiidenvesi. Elevated P diffusion rates were observed at shallow sites under oxic bottom water conditions in summer in both lakes, stimulated by enhanced remineralization of both freshly- (mostly phytoplankton-origin) and earlier-deposited OM under elevated temperatures. Areas overlain by oxic bottom water contributed more benthic P fluxes to the water column compared to anoxic/hypoxic areas in both lakes during all sampling seasons. Our study suggests that in shallow eutrophic settings with high OM deposition and elevated temperatures, remineralization in upper sediments regenerates P efficiently enough to support a significant amount of P release to the water column even under sedimentary molar Fe/P ratios >20. We also discuss the implication of our findings for lake restoration strategies.

Structural basis for the hydrolytic activity of the transpeptidase-like protein DpaA to detach Braun's lipoprotein from peptidoglycan.

Cross-linking reaction of Braun's lipoprotein (Lpp) to peptidoglycan (PG) is catalyzed by some members of the YkuD family of transpeptidases. However, the exact opposite reaction of cleaving the Lpp-PG cross-link is performed by DpaA, which is also a YkuD-like protein. In this work, we determined the crystal structure of DpaA to provide the molecular rationale for the ability of the transpeptidase-like protein to cleave, rather than form, the Lpp-PG linkage. Our findings also revealed the structural features that distinguish the different functional types of the YkuD family enzymes from one another.

Experimental comparison of active seismic surface wave tests on shallow and deep bedrock sites

Active seismic surface wave tests are tests during which signals are generated by artificial sources such as sledgehammers, drop weights and fixed or variable frequency shakers. A number of active seismic surface wave tests have become popular in the geotechnical industry. Interestingly, different surface wave tests are popular in different regions of the world, presumably because the tests require different equipment, expertise and numerical analysis techniques. Few studies have been done to compare seismic surface wave tests directly. This study investigated the performance of three active seismic surface wave tests, namely the spectral analysis of surface waves (SASW), multi-channel analysis of surface waves (MASW) and continuous surface wave (CSW) tests. This paper reports the performance of the three tests with regard to repeatability, susceptibility to near-field effects, and maximum and minimum measurement depths at both a shallow and a deep bedrock site.

Calibration of Sr/Ca Ratio and In Situ Temperature Using Hawaiian Corals

AbstractThe Sr/Ca ratio of modern coral skeletons can record local seawater temperature (T) and is an important tool for reconstructing past environments. However, site‐specific calibrations are required to ensure accurate temperature reconstructions. Here, we examine three modern coral skeletons collected at contrasting sites on the island of Oahu, Hawaii to establish the first accurate calibrations for this region and investigate site specific influences on the calibration process. Satellite T data, which is used for many calibrations, may not be able to derive an accurate thermometer. For our shallow lagoonal sites, satellite T had smaller seasonal T ranges, which resulted in significantly higher slopes of Sr/Ca‐T compared to using in situ T. The traditional age model based on aligning only min/max values can lead to errors in the Sr/Ca‐T calibration due to variable growth rates. An enhanced age model which adds midpoint alignments between the min/max peak values can account for seasonal changes in growth rate and reduce the error. On the same island, site‐ and time period specific conditions can cause notable differences in the Sr/Ca‐T calibrations. The coral from an estuarine embayment showed a high Sr/Ca offset, likely due to high Sr/Ca in ambient seawater. For corals which experienced thermal stress, lower slopes were observed probably due to elevated Sr/Ca values during the period of thermal stress.

Soundscapes of the central Red Sea mesophotic reef zones

Despite covering a large amount of seafloor & representing a significant percentage of coral reef ecosystem biomass, Mesophotic Coral Ecosystems (MCEs) globally have been largely understudied in comparison to their shallow counterparts. The Red Sea is a unique and biodiverse tropical ecosystem, where few mesophotic coral reefs have been studied. To define spatiotemporal activity of marine life and characterize the soundscapes of the MCE in the Central Red Sea, two locations were surveyed at 70–80 m, as well as at two adjacent shallow reef sites at ∼10 m depth, respectively, during the winter (Jan 2022) and summer (Jul–Aug 2022) seasons. The results of this study, the first of its kind in the Red Sea, show a clear shift in the soundscape between seasons, as well as between the shallow and mesophotic zones, driven mainly by a change in fish and invertebrate chorusing. During the study periods, temperature and oxygen levels in the mesophotic zone remained relatively stable, in comparison to the shallow reef zone which saw a steep temperature increase and large diel fluctuations in oxygen in the summer. Chronic exposure to shipping noise is evident across Red Sea MCE soundscapes and the resulting potential effects are discussed.

Combining heterointerface/surface oxygen vacancies engineering of bismuth oxide to synergistically improve its solar water splitting performance

Solar-powered photoelectrochemical (PEC) water splitting is recognized as a strategy for addressing fossil resource and global warming concerns. The purpose of this paper is to demonstrate for the first time a facile method to fabricate dendritic nanostructured (DN) Bi:Bi2O3 heterointerface engineering junctions that possess abundant surface oxygen vacancies (OVs, DN Bi:Bi2O3-OVs/FTO), with outstanding PEC performance. The surface OVs serve as shallow donors and active reaction sites, whereas the Bi-metal bridges are used for fast electron transport. Furthermore, surface OVs can enhance the surface features of Bi:Bi2O3 heterointerfaces and boost their electrical conductivity and donor density. This greatly enhances electrolyte ion and electron mobility, resulting in rapid water oxidation reactions at the Bi:Bi2O3/electrolyte interfaces. By combining the Bi:Bi2O3 heterointerface junction and surface OVs, we are able to create an effective photoanode with 95 % charge injection efficiency, applied bias photon-to-current efficiency (ABPE) of 0.112 %, and a photocurrent response of 0.334 mA.cm−2 at 1.23 V vs. the reversible hydrogen electrode (RHE), which represents improvements of about 4.5 and 10 folds over that of pure DN Bi2O3 photoanode. It is possible to construct a variety of unique nanostructured electrodes with adjustable optical and electronic properties to be used in solar cells, energy storage, and PEC applications.

Soil water dynamics and biomass production of young rooibos (Aspalathus linearis) plants

Rooibos (Aspalathus linearis) is endemic to certain regions of the Western- and Northern Cape of South Africa, where it is also commercially grown. Being low-rainfall regions, information on the soil water balance of rooibos is essential, but such data is limited. Consequently, the effect of inorganic fertilisation and soil depth on soil water dynamics in a young rooibos plantation at Nardouwsberg, Western Cape were studied. Soil water content of plots planted to unfertilised and fertilised plants as well as that of bare soil were determined over the duration of the 2016/17 season. All treatments were replicated on shallow and deep soils sites and plant growth was determined at the end of the season. At the end of the study, the profile soil water content and evapotranspiration of the bare and planted plots were similar which prove that fallowing (water harvesting) is not an option in the sandy soils of this region. With the exception of the 20−30 cm root zone of the planted plots at the deep site, the water content decreased to levels below the permanent wilting point in the soil profile during summer. It was concluded that rooibos plants could survive through an adapted root system. A further survival method was proposed, involving moisture moved through evaporation from the deeper soil layers into the drying-front in the ~ 10−30 cm soil layer where a condensation-evaporation cycle enables rooibos to harvest small amounts of water. The highest shoot biomass with the longest taproot resulted from the unfertilised treatment on the deep soil thanks to higher soil water content, whereas the shoot and root biomass of the fertilised treatment at both sites were low due to high P soil concentration. This study revealed that unfertilised plants on deeper soils result in higher rooibos production under drought conditions.

Light-Sensitive Open Channel Block of Ionotropic Glutamate Receptors by Quaternary Ammonium Azobenzene Derivatives.

Glutamate ionotropic receptors mediate fast excitation processes in the central nervous system of vertebrates and play an important role in synaptic plasticity, learning, and memory. Here, we describe the action of two azobenene-containing compounds, AAQ (acrylamide-azobenzene-quaternary ammonium) and QAQ (quaternary ammonium-azobenzene-quaternary ammonium), which produced rapid and fully reversible light-dependent inhibition of glutamate ionotropic receptors. The compounds demonstrated voltage-dependent inhibition with only minor voltage-independent allosteric action. Calcium-impermeable AMPA receptors had weaker sensitivity compared to NMDA and calcium-permeable AMPA receptors. We further revealed that the compounds bound to NMDA and calcium-permeable AMPA receptors in different modes. They were able to enter the wide selectivity filter of AMPA receptors, and strong negative voltages caused permeation into the cytoplasm. The narrow selectivity filter of the NMDA receptors did not allow the molecules to bypass them; therefore, QAQ and AAQ bound to the shallow channel site and prevented channel closure by a foot-in-the-door mechanism. Computer simulations employing available AMPA and NMDA receptor structures readily reproduced the experimental findings, allowing for the structure-based design of more potent and selective drugs in the future. Thus, our work creates a framework for the development of light-sensitive blockers of calcium-permeable AMPA receptors, which are desirable tools for neuroscience.

Predicting Turbulent Vertical Velocity in the Ocean Surface Layer under Mixed Convective and Wind/Wave Forcing

Abstract Turbulence in the ocean surface layer is forced by a mixture of buoyancy, wind, and wave processes that evolves over time scales from the diurnal scale of buoyancy forcing, through storm time scales, to the annual cycle. This study seeks a predictor for root-mean-square w (rmsw), a time and surface layer average of turbulent vertical velocity w measured by bottom-mounted vertical-beam acoustic Doppler current profilers, in terms of concurrently measured surface forcing fields. Data used are from two coastal sites, one shallow (LEO, 15-m depth) and one deeper (R2, 26-m depth). The analysis demonstrates that it is possible to predict observed rmsw with a simple linear combination of two scale velocities, one the convective scale velocity familiar from the atmospheric literature, the other a scale velocity wS representing combined wind and wave effects. Three variants are considered for this latter scale velocity, the wind stress velocity alone and two forms using both and US, a Stokes velocity characteristic of the surface wave field. At both sites, the two-parameter fit using alone is least accurate, while fits using the other two variants are essentially indistinguishable. At both sites, the coefficient multiplying is the same, within error bounds, and within the range of previous observations. At the deeper site, the coefficient multiplying the wind/wave scale velocity wS is approximately half that at the shallow site, a difference here attributed to difference in wave character.

Profiling of the β-glucosidases identified in the genome of Penicillium funiculosum: insights from genomics, transcriptomics, proteomics, and homology-modeling studies.

The enzymatic conversion of lignocellulosic biomass to bioethanol depends on efficient enzyme systems with β-glucosidase as one of the key components. In this study, we performed in-depth profiling of the various β-glucosidases present in the genome of the hypercellulolytic fungus Penicillium funiculosum using genomics, transcriptomics, proteomics, and molecular dynamics simulation approaches. Of the eight β-glucosidase genes identified in the P. funiculosum genome, three were predicted to be extracellular based on signal peptide prediction and abundance in the secretome. Among the three secreted β-glucosidases, two belonged to the GH3 family and one belonged to the GH1 family. Homology models of these proteins predicted a deep and narrow active site for the GH3 β-glucosidases (PfBgl3A and PfBgl3B) and a shallow open active site for the GH1 β-glucosidase (PfBgl1A). The enzymatic assays indicated that P. funiculosum-secreted proteins showed high β-glucosidase activities with prominent bands on the 4-methylumbelliferyl β-D-glucopyranoside zymogram. To understand the contributory effects of each of the three secreted β-glucosidases (PfBgls), the corresponding gene was deleted separately, and the effect of the deletion on the β-glucosidase activity of the secretome was examined. Although not the most abundant, PfBgl3A was found to be one of the most important β-glucosidases, as evidenced by a 42% reduction in β-glucosidase activity in the ΔPfBgl3A strain. Our results advance the understanding of the genetic and biochemical nature of all β-glucosidases produced by P. funiculosum and pave the way to design a superior biocatalyst for the hydrolysis of lignocellulosic biomass. IMPORTANCE Commercially available cellulases are primarily produced from Trichoderma reesei. However, external supplementation of the cellulase cocktail from this host with exogenous β-glucosidase is often required to achieve the desired optimal saccharification of cellulosic feedstocks. This challenge has led to the exploration of other cellulase-producing strains. The nonmodel hypercellulolytic fungus Penicillium funiculosum has been studied in recent times and identified as a promising source of industrial cellulases mainly due to its ability to produce a balanced concoction of cellulolytic enzymes, including β-glucosidases. Various genetic interventions targeted at strain improvement for cellulase production have been performed; however, the β-glucosidases of this strain have remained largely understudied. This study, therefore, reports profiling of all eight β-glucosidases of P. funiculosum via molecular and computational approaches. The results of this study provide useful insights that will establish the background for future engineering strategies to transform this fungus into an industrial workhorse.

Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study.

STAT3 belongs to a family of seven transcription factors. It plays an important role in activating the transcription of various genes involved in a variety of cellular processes. High levels of STAT3 are detected in several types of cancer. Hence, STAT3 inhibition is considered a promising therapeutic anti-cancer strategy. However, since STAT3 inhibitors bind to the shallow SH2 domain of the protein, it is expected that hydration water molecules play significant role in ligand-binding complicating the discovery of potent binders. To remedy this issue, we herein propose to extract pharmacophores from molecular dynamics (MD) frames of a potent co-crystallized ligand complexed within STAT3 SH2 domain. Subsequently, we employ genetic function algorithm coupled with machine learning (GFA-ML) to explore the optimal combination of MD-derived pharmacophores that can account for the variations in bioactivity among a list of inhibitors. To enhance the dataset, the training and testing lists were augmented nearly a 100-fold by considering multiple conformers of the ligands. A single significant pharmacophore emerged after 188ns of MD simulation to represent STAT3-ligand binding. Screening the National Cancer Institute (NCI) database with this model identified one low micromolar inhibitor most likely binds to the SH2 domain of STAT3 and inhibits this pathway.

Optimizing Ocean Bottom Seismometers for Shallow Water Using Shielding and Horizontal Pressure Gradient Data

AbstractWe show large “shields” can significantly reduce horizontal component noise levels for ocean bottom seismometers by shielding the seismic sensors from shaking due to ocean currents. However, at short period (<1 s) some noise from vibration or rocking of the shield under current can partly couple through the ground causing peaks in the noise spectra. Deformation of the seafloor under ocean wave loading (“compliance”) raises noise levels at long period (>5 s) for both vertical and horizontal components at shallow water sites. Pressure gauge data is now routinely used to predict and remove this source of noise on vertical component data. We have developed horizontal pressure gradient (HPG) gauges to measure and remove this source of noise from horizontal component data. The combination of HPG data and shielding enables low noise long period seismic observations at otherwise very noisy shallow seafloor sites.

First detection and genome analysis of simple nosed bat polyomaviruses in Central Europe.

Polyomaviruses (PyVs) are known to infect a diverse range of vertebrate host species. We report the discovery of PyVs in vesper bats (family Vespertilionidae) from sampling in Central Europe. Seven partial VP1 sequences from different PyVs were detected in samples originating from six distinct vesper bat species. Using a methodology based on conserved segments within the major capsid virus protein 1 (VP1) among known PyVs, the complete genomes of two different novel bat PyVs were determined. The genetic distances of the large T antigen coding sequences from these PyVs compared to previously-described bat PyVs exceeded 15% meriting classification as representatives of two novel PyV species: Alphapolyomavirus epserotinus and Alphapolyomavirus myodaubentonii. Phylogenetic analysis revealed that both belong to the genus Alphapolyomavirus and clustered together with high confidence in clades including other bat alphapolyomaviruses reported from China, South America and Africa. In silico protein modeling of the VP1 subunits and capsid pentamers, and electrostatic surface potential comparison of the pentamers showed significant differences between the reference template (murine polyomavirus) and the novel bat PyVs. An electrostatic potential difference pattern between the two bat VP1 pentamers was also revealed. Disaccharide molecular docking studies showed that the reference template and both bat PyVs possess the typical shallow sialic acid-binding site located between two VP1 subunits, with relevant oligosaccharide-binding affinities. The characterisation of these novel bat PyVs and the reported properties of their capsid proteins will potentially contribute in the elucidation of the conditions creating the host-pathogen restrictions associated with these viruses.

SiteFerret: Beyond Simple Pocket Identification in Proteins.

We present a novel method for the automatic detection of pockets on protein molecular surfaces. The algorithm is based on an ad hoc hierarchical clustering of virtual probe spheres obtained from the geometrical primitives used by the NanoShaper software to build the solvent-excluded molecular surface. The final ranking of putative pockets is based on the Isolation Forest method, an unsupervised learning approach originally developed for anomaly detection. A detailed importance analysis of pocket features provides insight into which geometrical (clustering) and chemical (amino acidic composition) properties characterize a good binding site. The method also provides a segmentation of pockets into smaller subpockets. We prove that subpockets are a convenient representation to pinpoint the binding site with great precision. SiteFerret is outstanding in its versatility, accurately predicting a wide range of binding sites, from those binding small molecules to those binding peptides, including difficult shallow sites.

Parkinson's disease is positively associated with periodontal inflammation.

Parkinson's disease (PA) affects 1% of the global population above 60 years. PA pathogenesis involves severe neuroinflammation that impacts systemic and local inflammatory changes. We tested the hypothesis that PA is associated with periodontal tissue inflammation promoting a greater systemic inflammatory burden. We recruited 60 patients with Stage III, Grade B periodontitis (P) with and without PA (n=20 for each). We also included systemically and periodontally healthy individuals as controls (n=20). Clinical periodontal parameters were recorded. Serum, saliva, and gingival crevicular fluid (GCF) samples were collected to measure the inflammatory and neurodegenerative targets (YKL-40, fractalkine, S100B, alpha-synuclein, tau, vascular cell adhesion protein-1 (VCAM-1), brain-derived neurotrophic factor (BDNF), neurofilament light chain (NfL). Parkinson's patients in this study had mild to moderate motor dysfunctions, which did not prevent them from performing optimal oral hygiene control. Periodontal parameters and GCF volume were significantly higher in the P and P+PA groups than in the control group. PA was associated with significantly increased bleeding on probing (BOP) compared to P-alone (p<0.05), while other clinical parameters were similar between P and P+PA groups. In saliva and serum, YKL-40 levels were higher in the P+PA group than in P and C groups (p<0.001). GCF NfL levels from shallow sites were significantly higher in the P+PA group compared to the C group (p=0.0462). GCF S100B levels from deep sites were higher in the P+PA group than in healthy individuals (p=0.0194). The data suggested that PA is highly associated with increased periodontal inflammatory burden-bleeding upon probing and inflammatory markers-in parallel with PA-related neuroinflammation.