Site-specific Differences Research Articles

Planning for success but facing uncertainty: lessons learned from a native oyster, Ostrea lurida, restoration project in the Salish Sea

Overexploitation and degradation of water quality nearly depleted Olympia oyster stocks in Puget Sound, Washington, USA by the early 1900s. With an intended goal of creating self-sustaining Olympia oyster populations in a target region in Puget Sound, the Swinomish Indian Tribal Community began reestablishing Olympia oysters at two different sites, Kiket and Lone Tree, from 2015-2017. One of our primary objectives was to quantify the biological successes or failures of our reestablished populations. Our results provide a guide for the evolution of project-specific, evidence-based restoration plans that could allow for further use of adaptive management and conservation aquaculture. Following the creation of experimental plots and restoration beds across two sites using 735 m² of shell habitat, including 245 m² of seeded cultch, we measured temporal change in oyster length and density as proxies for growth, recruitment, and survival. Significant growth was observed each year in each lagoon. Despite the known presence of brooding oysters and competent larvae in the region, we found no evidence of recruitment at either site through six years of monitoring. Survival decreased significantly each year and at each site. Thus, while we quantify evidence of growth and reproduction, we are not meeting the success metrics of recruitment or survival therefore hindering the chances of long-term success. We hypothesize that our restoration efforts are hampered by the relatively small population size within our restored areas, insufficient amounts of appropriate surrounding habitat, and lower water residence time. Our study suggests managers need to consistently monitor restoration projects due to site-specific differences and to determine if local failure is a possibility. Low survival and recruitment do not necessitate termination of projects. However, these measurements do suggest that projects like ours need to consider expanding use of conservation aquaculture as a tool or employing adaptive management by developing and implementing novel strategies to increase naturally-occurring adult populations and available habitat.

Post-Glacial Vegetation Trajectories on the Eastern Tibetan Plateau Reflect Millennial-Scale Migration Lags in Complex Mountain Terrain Based on Sedimentary Ancient DNA and Dynamic Dispersal Modeling.

Mountains with complex terrain and steep environmental gradients are biodiversity hotspots such as the eastern Tibetan Plateau (TP). However, it is generally assumed that mountain terrain plays a secondary role in plant species assembly on a millennial time-scale compared to climate change. Here, we investigate plant richness and community changes during the last 18,000 years at two sites: Lake Naleng and Lake Ximen on the eastern TP with similar elevation and climatic conditions but contrasting terrain. We applied plant DNA metabarcoding to lake sediments leveraging a new regional reference database for taxa identification. Furthermore, we developed a simplified species dispersal model named SMARC. This was used to simulate species migration along river valleys in response to past climate change at the taxonomic resolution of the sedimentary ancient DNA (sedaDNA) approach. Statistical analyses, including ordination-based ecological trajectory analysis, yielded a significant match between sedaDNA and simulated results at single taxon and community levels including certain site-specific differences. Steep terrain downstream of Lake Naleng enhances connectivity to glacial lowland refugia during postglacial warming. In contrast, gentle terrain over long distances implies weak connectivity to the lowland and thus resulted in a strong migration lag at Lake Ximen. Likewise, terrain differences among our sites defined the different connectivity to alpine refugia during late-Holocene cooling. Our consistent proxy- and model-based results, for the first time, indicate that dispersal related migration lags in complex mountain terrain lead to uneven vegetation trajectories at sites with similar climatic conditions mainly because of differences in connectivity to refugia. Ultimately our results indicate that connectivity to refugia is a first-order factor for species migration in addition to elevation-related climatic conditions shaping the postglacial vegetation trajectory in mountainous terrain. This has hitherto largely been ignored when forecasting mountain vegetation responses to climate change and related risk assessment.

Comparative analysis of mangrove seedlings in natural, degraded, and restored ecosystems of Guyana

ABSTRACT Mangrove seedlings are exposed to several environmental stress factors, which frequently affect the current state of their ecosystems. We examined the density, diversity, distribution, survival rates, and biophysical parameters of over 900 naturally existing seedlings in natural, degraded, and restored coastline ecosystems in Guyana. Systematic sampling was conducted for 1 year following the point-centred quarter method (PCQM) during the wet and dry seasons. The restored ecosystems had greater seedling densities (1546.44–5506.303 individuals/ha), diversity (0.65–0.65), and richness (0.46–0.51) when compared to the natural and degraded ecosystems. Seedling survival rates [41.9–53.4%] were greater in the natural ecosystems, but short-term seasonal variations were prevalent in the restored ecosystems. Significant disparities were observed in seeding biophysical parameters [df = 8, p < 2.2e-16] which also exhibited positive correlations [p < 0.05, rs < 0.75] with their respective locations. The restored ecosystems showed taller seedlings (137.54 ± 4.68 cm) with a greater number of leaves (30.87 ± 1.51–107.30 ± 5.54), while the natural ecosystems showed seedlings with greater stem diameters (3.05 ± 0.11–11.38 ± 0.37 mm). Our findings show that mangrove seedlings can exhibit site-specific differences which may be influenced by ecosystem type and seasonality to some extent.

P88 Spatial transcriptomic profiling reveals body site-specific inflammatory differences in psoriasis lesions

Abstract Psoriasis is a common chronic inflammatory skin disease. A variety of treatment options lead to substantial improvement of most psoriasis plaques; however, recurrence of psoriasis in previously affected areas is common. Additionally, it can be challenging to reach disease resolution in certain hard-to-treat areas such as scalp and lower extremity (LE). Here, we map histologic and spatial transcriptomic differences between psoriasis lesions across different anatomical locations, to understand if differences in the inflammatory profile can be linked to plaque-site-specific treatment resistance. Quantitative immunohistochemical analysis and transcriptomic digital spatial profiling were performed on skin punch biopsies obtained from unaffected areas on the trunk, lesional areas of the scalp, upper extremity, and LE of 12 patients with psoriasis. Histological analysis showed no significant differences in epidermal thickness among lesional (LS) skin from different body locations. Immunohistochemical markers (CD3, CD4, CD8, CD103, CD207, RORγt, FOXP3 and MPO) were higher in LS skin compared with non-lesional (NL) skin but did not differ significantly between LS sites. Whole transcriptome spatial RNA profiling identified several differentially expressed genes that distinguished LS from NL skin and revealed site-specific transcriptomic differences. Notably, IL-23 signalling was significantly enriched in the LE epidermis, and IL-17 signalling was more pronounced in the epidermis of LS samples. These findings highlight minimal histological and immunohistochemical variation, yet significant transcriptomic and pathway differences between psoriasis body locations, suggesting potential future targets for site-specific therapeutic strategies.

Assessment of bioaerosol composition and public health implications in high-traffic urban areas of Southwest, Nigeria.

Bioaerosols, a significant yet underexplored component of atmospheric particulate matter, pose substantial public health risks, particularly in regions with poor air quality. This study investigates the composition of bioaerosols in public spaces, specifically two interstate motor parks and two marketplaces in Osun State, Nigeria, over six months. Air samples were collected, and bacterial and fungal species were identified, focusing on pathogenic organisms. The results revealed the presence of well-known pathogens, including Staphylococcus aureus, Escherichia coli, Klebsiella sp., Pseudomonas aeruginosa, Aspergillus sp., and Fusarium sp., which are associated with respiratory and gastrointestinal infections, as well as antimicrobial resistance. Site-specific differences in microbial diversity were observed, with higher bacterial diversity in motor parks and greater fungal occurrence in marketplaces influenced by environmental factors such as waste management. The findings highlight the urgent need for microbial air quality monitoring in public spaces, alongside improved sanitation practices. This study provides critical insights into the public health risks posed by bioaerosols and calls for local and global interventions to mitigate the impact of airborne pathogens in urban environments.

Abstract 4141486: Site-Specific Transcriptomic Patterns and Cell Types Associated with Hypertension

Introduction: The biology of early human hypertensive heart disease (HHD) is largely unexplored due to limited cardiac tissue access. Site-specific transcriptomics of human cardiac tissue before development of overt HHD offers a unique vantage to understand the biology of HHD in human cardiac tissue. Hypothesis: We hypothesize that transcriptomic signatures and cell subtype proportions differ in human heart tissue from HTN donors compared to normotensive (NTN) donors in a site-specific manner. Methods: We performed bulk RNA-seq on rRNA-depleted libraries from left (LV) and right (RV) mid-ventricular-wall tissue (average depth 114 million reads/sample) collected postmortem from HTN (n=3, 67% Black/Latinx) and NTN (n=2, 50% Black/Latinx) donors. We performed single-nucleus RNA-seq (snRNA-Seq) on cardiac tissue from the same donors (average of 4,062 LV nuclei). Differential gene expression, lineage identification, and Gene Set Enrichment Analysis (GSEA) were performed with publicly available software. Results: All donors were female with matched postmortem intervals (time from death to tissue preservation; HTN 19±9 hours, NTN 18±6 hours). HTN donors were older (65±7 years) than NTN donors (36±16 years). A total of 416 genes were associated with HTN (Wald test, FDR q &lt;0.05) across both ventricles (correcting for site). When tested separately, 72 (LV) or 83 (RV) genes were associated with HTN (FDR q &lt;0.05), with 13 common genes, indicating site-specific differences. GSEA of genes ranked by Wald statistic computed across both ventricles showed that transcripts involved in single-stranded DNA helicase activity, branched-chain amino acid catabolism, and NAD-dependent deacetylase activity were coordinately associated with HTN (FDR q &lt;0.05). snRNA-seq revealed 9 cell types in these samples, including immune cells and chamber-specific cardiomyocytes (CMs) with higher proportions of LV CMs and lymphocytes associated with HTN compared to NTN. MYH6 and MYL7 expression was unchanged with respect to HTN by RNA-seq but lower in LV HTN CMs compared to NTN by snRNA-seq, suggesting dysregulation of contractile programming in HTN LV CMs. Conclusion: HTN is associated with altered cardiomyocyte/lymphocyte ratios, and site-specific differential expression of cardiac contractile elements. Further study is required to validate these findings with additional samples and elucidate mechanisms driving transcriptional program differences in the hypertensive human heart.

Land snail Δ47 thermometry using cultured and European natural populations of Clausilia pumila, Succinella oblonga and Trochulus hispidus

Clumped isotope composition (Δ47) of aragonitic shells of terrestrial molluscs allow the quantitative reconstructions of continental paleotemperatures from loess-paleosol records of the last 2.5 million years, but it needs testing the method under controlled laboratory conditions and using natural populations. In this study the stable carbon, oxygen and clumped isotope compositions of cultured individuals and field-collected specimens of three species (Clausilia pumila, Succinella oblonga and Trochulus hispidus), widespread in Quaternary loess deposits in Europe, were measured in the Debrecen (ATOMKI) and ETH Zürich laboratories. Our data of cultured snails demonstrate that shells of the three species record Δ47 signatures close to equilibrium conditions with mostly positive (C. pumila), both positive/negative (T. hispidus), and mostly negative (S. oblonga) offsets on the order of 0.0158 ± 0.0105 ‰ (mean offset±1 SD) compared to the Anderson et al. (2021) unified calibration. Calcification temperatures (TΔ47) derived from C. pumila shells were found to be in excellent agreement with chamber temperatures of 12, 18 and 24 °C, especially in the ATOMKI laboratory (mean T offset: 2.1 ± 2.2 °C, 1 SD), while the other two species exhibited larger discrepancies on the order of 5–8 °C (mean offset). Single shell-based mean TΔ47 values of field-collected molluscs indicated growth temperatures spanning values from the frost-free period to summer season, or even above summer maxima. The sites of natural populations, characterized by different climate conditions, could be grouped using the aridity index (AI) with values of 0.96–1.06 representing mean temperature of the frost-free period (TFFP), and AI ranging either from 0.85 to 0.91 or 1.14 to 1.51 reflecting mean summer season or July temperatures (TJJA/TJ). Multi-shell TΔ47, obtained by homogenizing the material of 3–5 shells of C. pumila and T. hispidus, reflect TJJA in most cases. We observed a dependence of the shell oxygen isotope compositions of the three species on oceanity/continentality with more negative/positive values characteristic for more continental/oceanic sites, likely due to moisture source distance and depletion of rainfall in 18O towards the continental interior. In addition, deviation of body fluid δ18O values (derived from δ18Oshell and Δ47shell) from seasonal precipitation δ18O is also controlled by an additional temperature effect, being independent of the climate zone of the collection site, but co-varying with the site-specific difference between single shell TΔ47 and TJJA.

584P Genomic and transcriptomic characterization of peritoneal, lung and liver metastases of colorectal carcinoma reveals site-specific differences

584P Genomic and transcriptomic characterization of peritoneal, lung and liver metastases of colorectal carcinoma reveals site-specific differences

Invasive knotweed (Polygonum spp.) movement in a northern New Hampshire (USA) stream system

AbstractNon-native plants negatively impact ecosystems via a variety of mechanisms, including in forested riparian areas. Japanese knotweed [Polygonum cuspidatum Siebold &amp; Zucc.] and its hybrids (referred to as Polygonum spp. hereafter) are widely spread throughout North America and can impact flora and fauna of riparian habitats. Thus, information improving our ability to understand and predict the potential spread and colonization of Polygonum spp. is valuable. One dispersal mechanism is hydrochory (i.e., dispersal by water), including the downstream dispersal of viable stems that can facilitate rapid invasion within a watershed. We used passive integrated transponder (PIT) telemetry in experimental releases of Polygonum spp. stems to track the downstream transport of Polygonum spp. in a small (second-order) stream in northern New Hampshire, USA, in the summers of 2021 and 2022. A total of 180 (90 each year) Polygonum spp. stems were released at three sites within the stream reach, with 185 (∼98%) being recaptured at least once, with a total of 686 recaptures. Individual relocated stems moved a maximum distance of 30 to 875 m downstream in 2021 and 13 to 1,233 m in 2022 during regular flows; however, a high-streamflow event in July 2021 flushed out all remaining stems downstream of the study area. Generalized additive mixed models (GAMMs) identified site-specific differences in stem movement rates and a general reduction in movement rates with increased duration of time elapsed since post-release. In general, Polygonum spp. stems moved farther downstream in sites with lower channel sinuosity, although other fine-scale habitat factors (e.g., water depth, habitat type, and presence of wood and debris jams) likely contribute to the ability for Polygonum spp. to further disperse or otherwise be retained within the channel. Thus, stream morphology and stream flow are likely to affect where Polygonum spp. stems will be retained and potentially reestablish. Predictive tools identifying areas of higher probability of hydrochory-based dispersal could help to focus removal efforts when employed or to identify riparian habitats at highest risk for spread.

Predictive Functional Profiling Reveals Putative Metabolic Capacities of Bacterial Communities in Drinking Water Resources and Distribution Supply in Mega Manila, Philippines

Assessing bacterial communities across water resources is crucial for understanding ecological dynamics and improving water quality management. This study examines the functional profiles of bacterial communities in drinking water resources in Mega Manila, Philippines, including Laguna Lake tributaries, pre-treatment plant sites, groundwater sources, and post-treatment plant sites. Using eDNA sequencing, flux balance analysis, and taxonomy-to-phenotype mapping, we identified metabolic pathways involved in nutrient metabolism, pollutant degradation, antibio- tic synthesis, and nutrient cycling. Despite site variations, there are shared metabolic pathways, suggesting the influence of common ecological factors. Site-specific differences in pathways like ascorbate, aldarate, and phenylalanine metabolism indicate localized environmental adaptations. Antibiotic synthesis pathways, such as streptomycin and polyketide sugar unit biosynthesis, were detected across sites. Bacterial communities in raw and pre-treatment water showed potential for pollutant degradation such as for endocrine-disrupting chemicals. High levels of ammonia-oxidizing and sulfate-reducing bacteria in pre- and post-treatment water suggest active nitrogen removal and pH neutralization, indicating a need to reassess existing water treatment approaches. This study underscores the adaptability of bacterial communities to environmental factors, as well as the importance of considering their functional profiles in assessing drinking water quality resources in urban areas.

Developmental changes in brain structure and function following exposure to oral LSD during adolescence

LSD is a hallucinogen with complex neurobiological and behavioral effects. Underlying these effects are changes in brain neuroplasticity. This is the first study to follow the developmental changes in brain structure and function following LSD exposure in periadolescence. We hypothesized LSD given during a time of heightened neuroplasticity, particularly in the forebrain, would affect cognitive and emotional behavior and the associated underlying neuroanatomy and neurocircuitry. Female and male mice were given vehicle, single or multiple treatments of 3.3 µg of LSD by oral gavage starting on postnatal day 51. Between postnatal days 90–120 mice were imaged and tested for cognitive and motor behavior. MRI data from voxel-based morphometry, diffusion weighted imaging, and BOLD resting state functional connectivity were registered to a mouse 3D MRI atlas with 139 brain regions providing site-specific differences in global brain structure and functional connectivity between experimental groups. Motor behavior and cognitive performance were unaffected by periadolescent exposure to LSD. Differences across experimental groups in brain volume for any of the 139 brain areas were few in number and not focused on any specific brain region. Multiple exposures to LSD significantly altered gray matter microarchitecture across much of the brain. These changes were primary associated with the thalamus, sensory and motor cortices, and basal ganglia. The forebrain olfactory system and prefrontal cortex and hindbrain cerebellum and brainstem were unaffected. The functional connectivity between forebrain white matter tracts and sensorimotor cortices and hippocampus was reduced with multidose LSD exposure. Does exposure to LSD in late adolescence have lasting effects on brain development? The bulk of our significant findings were seen through changes is DWI values across 74 brain areas in the multi-dose LSD group. The pronounced changes in indices of anisotropy across much of the brain would suggest altered gray matter microarchitecture and neuroplasticity. There was no evidence of LSD having consequential effects on cognitive or motor behavior when animal were evaluated as young adults 90–120 days of age. Neither were there any differences in the volume of specific brain areas between experimental conditions. The reduction in connectivity in forebrain white matter tracts with multidose LSD and consolidation around sensorimotor and hippocampal brain areas requires a battery of tests to understand the consequences of these changes on behavior.

Patient selection for nonoperating room anesthesia.

Given the rapid growth of nonoperating room anesthesia (NORA) in recent years, it is essential to review its unique challenges as well as strategies for patient selection and care optimization. Recent investigations have uncovered an increasing prevalence of older and higher ASA physical status patients in NORA settings. Although closed claim data regarding patient injury demonstrate a lower proportion of NORA cases resulting in a claim than traditional operating room cases, NORA cases have an increased risk of claim for death. Challenges within NORA include site-specific differences, limitations in ergonomic design, and increased stress among anesthesia providers. Several authors have thus proposed strategies focusing on standardizing processes, site-specific protocols, and ergonomic improvements to mitigate risks. Considering the unique challenges of NORA settings, meticulous patient selection, risk stratification, and preoperative optimization are crucial. Embracing data-driven strategies and leveraging technological innovations (such as artificial intelligence) is imperative to refine quality control methods in targeted areas. Collaborative efforts led by anesthesia providers will ensure personalized, well tolerated, and improved patient outcomes across all phases of NORA care.

Comparative analysis of the mutational landscape and evolutionary patterns of pancreatic ductal adenocarcinoma metastases in the liver or peritoneum

BackgroundPancreatic ductal adenocarcinoma (PDAC) often presents with liver or peritoneal metastases at diagnosis. Despite similar treatment approaches, patient outcomes vary between these metastatic sites. To improve targeted therapies for metastatic PDAC, a comprehensive analysis of the genetic profiles and evolutionary patterns at these distinct metastatic locations is essential. MethodsWe performed whole exome sequencing on 44 tissue samples from 27 PDAC patients, including primary tumours and matched liver or peritoneal metastases. We analysed somatic mutation profiles, signatures, and affected pathways for each group, and examined clonal evolution using subclonal architectures and phylogenetic trees. ResultsKRAS mutations remained the predominant driver alteration, with a prevalence of 89 % across all tumours. Notably, we observed site-specific differences in mutation frequencies, with KRAS alterations detected in 77.8 % (7/9) of peritoneal metastases and 87.5 % (7/8) of liver metastases. TP53 mutations exhibited a similar pattern, occurring in 55.6 % (5/9) of peritoneal and 37.5 % (3/8) of liver metastases. Intriguingly, we identified site-specific alterations in DNA repair pathway genes, including ATM and BRCA1, with distinct mutational profiles in liver versus peritoneal metastases. Furthermore, liver metastases demonstrated a significantly higher tumor mutational burden (TMB) compared to peritoneal metastases (median [IQR]: 2.14 [1.77–2.71] vs. 1.29 [1.21–1.69] mutations/Mb; P = 0.048). ConclusionsIn conclusion, metastasis of pancreatic cancer may be influenced by variables other than KRAS mutations, such as TP53. PDAC peritoneal and liver metastases may differ in potential therapeutic biomarkers. Further inquiry is needed on the biological mechanisms underlying metastasis and the treatment of diverse metastases.

Rational development of functional hydrophilic polymer to characterize site-specific glycan differences between bovine milk and colostrum

As vastly modified on secreted proteins, N-glycosylation is found on milk proteins and undergo dynamic changes during lactation, characterizing milk protein glycosylation would benefit the elucidation of glycosylation pattern differences between samples. However, their low abundance required specific enrichment. Herein, through rational design and controllable synthesis, we developed a novel multi-functional polymer for the isolation of protein glycosylation. It efficiently separated glycopeptides from complex background inferences with mutual efforts of hydrophilic interaction chromatography (HILIC), metal ion affinity and ion exchange. By fine-tuning Ca2+ as regulators of aldehyde hyaluronic acid (HA) conformation, the grafting density of HA was remarkably improved. Moreover, grafting Ti4+ further enhanced the enrichment performance. Application of this material to characterize bovine milk and colostrum proteins yields 479 and 611 intact glycopeptides, respectively. Comparative analysis unraveled the distinct glycosylation pattern as well the different distribution of glycoprotein abundances between the two samples, offering insights for functional food development.

Diversity, virulence and antibiotic resistance of Vibrio Harveyi clade species associated with bivalve aquaculture within marine protected areas

The aim of the present study was to investigate the diversity, distribution of virulence factor genes and antimicrobial resistance phenotypes of Vibrio Harveyi clade species from two distinct and spatially distant near-shore bivalve farming environments located in protected marine reserves of the eastern Adriatic. Tissues of farmed Mediterranean mussel Mytilus galloprovincialis and European flat oyster Ostrea edulis, seawater and sediment samples were collected during six bi-monthly sampling events conducted over one year from farming locations in Lim Bay and Mali Ston Bay, Croatia. Eight distinctive Harveyi subclades, namely, V. harveyi, V. alginolyticus, V. diabolicus, V. jasicida, V. parahaemolyticus, V. rotiferianus, V. campbellii and V. communis, were detected by Phylogenetic Multilocus Sequence Analysis (MLSA) based on rpoD, toxR and rctB concatenated genes sequences. Genomic fingerprinting of MLSA-classified samples revealed substantial diversity of environmental isolates. The virulence-related genes considered typical for the Harveyi clade and their homologues were represented in all subclades with varying frequencies. Of twelve antibiotics commonly used in human and veterinary medicine, the most frequent resistance phenotypes were resistance to ampicillin (90%), erythromycin (39%), imipenem (29%) and streptomycin (22%). >60% of isolates were resistant to at least two classes of antibiotics. Seasonal or site-specific differences were found in the proportion of isolates carrying virulence genes and displaying specific antibiotic resistance phenotype.This study is the first to provide a broader perspective on the properties of Vibrio Harveyi clade species associated with ecosystems under presumably low anthropogenic pressures, such as marine protected areas. New data on virulence and antibiotic resistance are presented of Harveyi clade species coexisting in different environmental compartments, including those that have been largely overlooked or understudied in the context of bivalve aquaculture. Taken together, these results highlight the importance of monitoring the presence of potentially pathogenic strains in the natural Vibrio population of bivalve farming areas to reduce the risk to seafood consumers.

Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs.

Comparative, dose-dependent analysis of interactions between small molecule drugs and their targets, as well as off-target interactions, in complex proteomes is crucial for selecting optimal drug candidates. The affinity of small molecules for targeted proteins is largely dictated by interactions between amino acid side chains and these drugs. Thus, studying drug-protein interactions at an amino acid resolution provides a comprehensive understanding of the drug selectivity and efficacy. In this study, we further refined the site-specific activity-based protein profiling strategy (ABPP), PhosID-ABPP, on a timsTOF HT mass spectrometer. This refinement enables dual dose-dependent competition of inhibitors within a single cellular proteome. Here, a comparative analysis of two activity-based probes (ABPs), developed to selectively target the epidermal growth factor receptor (EGFR), namely, PF-06672131 (PF131) and PF-6422899 (PF899), facilitated the simultaneous identification of ABP-specific binding sites at a proteome-wide scale within a cellular proteome. Dose-dependent probe-binding preferences for proteinaceous cysteines, even at low nanomolar ABP concentrations, could be revealed. Notably, in addition to the intrinsic affinity of the electrophilic probes for specific sites in targeted proteins, the observed labeling intensity is influenced by several other factors. These include the efficiency of cellular uptake, the stability of the probes, and their intracellular distribution. While both ABPs showed comparable labeling efficiency for EGFR, PF131 had a broader off-target reactivity profile. In contrast, PF899 exhibited a higher labeling efficiency for the ERBB2 receptor and bound to catalytic cysteines in several other enzymes, which is likely to disrupt their catalytic activity. Notably, PF131 effectively labeled ADP/ATP translocase proteins at a concentration of just 1 nm, and we found this affected ATP transport. Analysis of the effect of PF131 and its parent inhibitor Afatinib on murine translocase SLC25A4 (ANT1)-mediated ATP transport strongly indicated that PF131 (10 μM) partially blocked ATP transport. Afatinib was less efficient at inhibiting ATP transport by SLC25A4 than PF131, and the reduction of ATP transport by Afatinib was not significant. Follow-up analysis is required to evaluate the affinity of these inhibitors for ADP/ATP translocase SLC25A4 in more detail. Additionally, the analysis of different binding sites within the EGF receptor and the voltage-dependent anion channel 2 revealed secondary binding sites of both probes and provided insights into the binding poses of inhibitors on these proteins. Insights from the PhosID-ABPP analysis of these two ABPs serve as a valuable resource for understanding drug on- and off-target engagement in a dose- and site-specific manner.

Leveraging multi-site electronic health data for characterization of subtypes: a pilot study of dementia in the N3C Clinical Tenant.

To provide a foundational methodology for differentiating comorbidity patterns in subphenotypes through investigation of a multi-site dementia patient dataset. Employing the National Clinical Cohort Collaborative Tenant Pilot (N3C Clinical) dataset, our approach integrates machine learning algorithms-logistic regression and eXtreme Gradient Boosting (XGBoost)-with a diagnostic hierarchical model for nuanced classification of dementia subtypes based on comorbidities and gender. The methodology is enhanced by multi-site EHR data, implementing a hybrid sampling strategy combining 65% Synthetic Minority Over-sampling Technique (SMOTE), 35% Random Under-Sampling (RUS), and Tomek Links for class imbalance. The hierarchical model further refines the analysis, allowing for layered understanding of disease patterns. The study identified significant comorbidity patterns associated with diagnosis of Alzheimer's, Vascular, and Lewy Body dementia subtypes. The classification models achieved accuracies up to 69% for Alzheimer's/Vascular dementia and highlighted challenges in distinguishing Dementia with Lewy Bodies. The hierarchical model elucidates the complexity of diagnosing Dementia with Lewy Bodies and reveals the potential impact of regional clinical practices on dementia classification. Our methodology underscores the importance of leveraging multi-site datasets and tailored sampling techniques for dementia research. This framework holds promise for extending to other disease subtypes, offering a pathway to more nuanced and generalizable insights into dementia and its complex interplay with comorbid conditions. This study underscores the critical role of multi-site data analyzes in understanding the relationship between comorbidities and disease subtypes. By utilizing diverse healthcare data, we emphasize the need to consider site-specific differences in clinical practices and patient demographics. Despite challenges like class imbalance and variability in EHR data, our findings highlight the essential contribution of multi-site data to developing accurate and generalizable models for disease classification.

ADP-ribosylome analysis reveals homogeneous DNA-damage-induced serine ADP-ribosylation across wild-type and BRCA-mutant breast cancer cell lines

ADP-ribosylation (ADPr) signaling plays a crucial role in DNA damage response. Inhibitors against the main enzyme catalyzing ADPr after DNA damage, poly(ADP-ribose) polymerase 1 (PARP1), are used to treat patients with breast cancer harboring BRCA1/2 mutations. However, resistance to PARP inhibitors (PARPi) is a major obstacle in treating patients. To understand the role of ADPr in PARPi sensitivity, we use liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze ADPr in six breast cancer cell lines exhibiting different PARPi sensitivities. We identify 1,632 sites on 777 proteins across all cell lines, primarily on serine residues, with site-specific overlap of targeted residues across DNA-damage-related proteins across all cell lines, demonstrating high conservation of serine ADPr-signaling networks upon DNA damage. Furthermore, we observe site-specific differences in ADPr intensities in PARPi-sensitive BRCA mutants and unique ADPr sites in PARPi-resistant BRCA-mutant HCC1937 cells, which have low poly(ADP-ribose) glycohydrolase (PARG) levels and longer ADPr chains on PARP1.

Multi-resolution remote sensing for flark area detection in boreal aapa mires

ABSTRACT Peatlands have suffered significant degradation globally due to human impacts, which has increased the need to monitor the condition and changes in peatland ecosystems. With remote sensing, point-based in-situ observations can be upscaled to larger areas but there is a need to develop scalable monitoring methods. We predicted wet flark area extent, a key ecological indicator for patterned flark fens, in five sites in central Finland. Our primary aim was to test how the spatial and spectral resolution of different optical satellite image products (Landsat 8–9, Sentinel-2, PlanetScope) affect flark area coverage prediction. We also tested if there were seasonal or site-specific differences in prediction accuracy. Lastly, we upscaled the flark area coverage to entire mire areas. We used unmanned aerial vehicle (UAV)-derived flark area classification as a ground reference data to compare satellite sensors’ prediction accuracies. We predicted flark area coverage using spectral bands and indices as predictor variables using random forest regression. All sensors provided accurate results with some differences between Landsat (pseudo-R2 32−84%, root-mean squared error (RMSE) 10 − 18%), Sentinel-2 (R2 61−92%, RMSE 6−14%), and PlanetScope (R2 46 − 92%, RMSE 6 − 17%). The shortwave infrared bands of Landsat and Sentinel-2 did not increase the prediction accuracy. There were notable site-specific variations in prediction accuracy despite all the sites having typical open aapa mire wet flark – dry string patterns. With single-site models, the prediction accuracies were similar for early and late summer data, but when transferring the models to the other sites, performance significantly decreased, especially with the models using the late-summer imagery. Finally, we successfully upscaled the flark area coverage across entire mire areas. Our results demonstrate that the combination of UAV and satellite imagery can be used successfully to monitor peatland conditions and changes in them.

Mapping the geographical distribution of the mucosa-associated gut microbiome in GI-symptomatic children with autism spectrum disorder.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by cognitive, behavioral, and communication impairments. In the past few years, it has been proposed that alterations in the gut microbiota may contribute to an aberrant communication between the gut and brain in children with ASD. Consistent with this notion, several studies have demonstrated that children with ASD have an altered fecal microbiota compared with typically developing (TD) children. However, it is unclear where along the length of the gastrointestinal (GI) tract these alterations in microbial communities occur. In addition, the variation between specific mucosa-associated communities remains unknown. To address this gap in knowledge of the microbiome associated with ASD, biopsies from the antrum, duodenum, ileum, right colon, and rectum of children with ASD and age- and sex-matched TD children were examined by 16S rRNA sequencing. We observed an overall elevated abundance of Bacillota and Bacteroidota and a decreased abundance of Pseudomonadota in all GI tract regions of both male and female children with ASD compared with TD children. Further analysis at the genera level revealed unique differences in the microbiome in the different regions of the GI tract in children with ASD compared with TD children. We also observed sex-specific differences in the gut microbiota composition in children with ASD. These data indicate that the microbiota of children with ASD is altered in multiple regions of the GI tract and that different anatomic locations have unique alterations in mucosa-associated bacterial genera.NEW & NOTEWORTHY Analysis in stool samples has shown gut microbiota alterations in children with autism spectrum disorder (ASD) compared with typically developing (TD) children. However, it is unclear which segment(s) of the gut exhibit alterations in microbiome composition. In this study, we examined microbiota composition along the gastrointestinal (GI) tract in the stomach, duodenum, ileum, right colon, and rectum. We found site-specific and sex-specific differences in the gut microbiota of children with ASD, compared with controls.