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At least 19 recordsLinked to original sources
PubMed2026

Using high-dimensional environmental covariates to study genotype by environment interaction for reproductive traits in Duroc boars.

We investigated the potential of incorporating grid-cell-based environmental covariates (ECs) in the genetic evaluation of total sperm count (TSC), sperm motility (MOT), and sperm morphology (MOR) for Duroc boars. A total of 188,665 records derived from 3,684 genotyped boars, born between December 2018 and October 2024 and raised in three stud farms located in different U.S. states, were analyzed using multi-trait linear-threshold repeatability models. To account for genotype by environment interactions (GE), we constructed an interaction matrix as the Hadamard product of the genomic relationship matrix and an environmental (co)variance matrix. The environmental groups were defined in three ways: farm, farm-season, and farm-year-season. The (co)variance matrix was constructed based on daily ECs obtained from the NASA POWER database for each environmental group. Of all available ECs, those significantly associated with TSC, MOT, and MOR (temperature, relative humidity, atmospheric pressure, and wind speed and direction) were retained. We evaluated five models with different GE structures: M1 represented the baseline without accounting for GE, in M2 the GE included farm as environmental groups, in M3 the GE included farm-season as environmental groups, in M4 the GE included farm-year-season as environmental groups, and M5 involved M3 with an additional random effect of the farm-season. Estimates of heritability for TSC, MOT, and MOR ranged from 0.03 to 0.04, 0.05 to 0.08, and 0.04 to 0.08, respectively. Corresponding repeatability ranged from 0.15 to 0.23, 0.28 to 0.49, and 0.28 to 0.49. The proportion of phenotypic variance attributed to GE variance ranged from 0.00 to 0.32, 0.00 to 0.44, and 0.00 to 0.44. Lastly, estimates of genetic correlation, TSC-MOT, TSC-MOR, and MOT-MOR ranged from 0.27 to 0.31, 0.24 to 0.31, and 0.98 to 0.99, respectively, with minor differences across models. We assessed the predictive ability of models using the linear regression validation. Across traits and models, bias ranged from -0.05 to 0.02 standard deviations, slope varied from 0.88 to 0.99, the correlation ranged from 0.75 to 0.84, and accuracy from 0.41 to 0.53. Overall, building the GE matrix considering grid-cell-based ECs helped to account for GE, thereby reducing the proportion of phenotypic variance attributed to genetic components; however, it did not improve the validation metrics. Additional on-farm records for ECs may improve the model performance.

Animals↗
PubMed2026

Thermal analysis techniques for microplastic mass quantification: Methodological challenges and standardization needs.

Microplastics (MPs, 1 &#x3bc;m-5 mm) and nanoplastics (NPs, <1&#x202f;&#x3bc;m) are ubiquitous contaminants requiring standardized quantification methods. This systematic review evaluates thermal analysis techniques for mass-based MP detection, including pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS), thermogravimetry-MS (TGA-MS), thermal extraction desorption-GC-MS (TED-GC-MS), and differential scanning calorimetry (DSC). Database searches (Web of Science, from inception to December 1, 2025) following PRISMA guidelines identified studies across seven environmental matrices (water, soil/sediment, atmosphere, biota, human tissues). We identify critical standardization gaps: inconsistent marker ion selection, unvalidated conversion factors for tire and road wear particles (TRWPs), and the absence of certified reference materials for complex matrices. Py-GC-MS demonstrates versatility but suffers from lipid interference in biological samples; TED-GC-MS offers superior sensitivity (sample capacity &#x223c;200&#xd7; Py-GC-MS) but lacks real-time chromatographic monitoring. To advance data comparability, we propose: (i) harmonized ion selection hierarchies based on specificity-sensitivity balance, (ii) matrix-specific TRWP quantification protocols, and (iii) inter-laboratory validation using environmental reference materials. This review provides a methodological roadmap for standardizing thermal analysis in MP research.

Humans↗
PubMed1979

A multivariate twin analysis of within-family environmental influences in infants' social responsiveness.

Observational measures of social responsiveness were obtained for twin infants. The structure of within-family environmental influences was assessed by correlating identical twin pair differences for 13 behaviors in seven social settings. Factor analysis of the difference score matrix yielded one interpretable factor. This factor indicated that within-family environmental influences were not completely random but may exert a systematic effect on social behavior in several situations.

Child, Preschool↗
PubMed2026

Effects of CRISPR technology on agricultural sustainability: global applications and turkish perspective.

This review evaluates CRISPR/Cas applications in agriculture from a global perspective with explicit reference to T&#xfc;rkiye. Using a literature gap-matrix approach organised around four analytical dimensions-environmental, economic, social and policy, and scientific and technological-we synthesize the primary evidence on water and input use, productivity, disease resistance, and product quality. The literature concentrates on water and fertilizer use, productivity, and off-target accuracy, whereas soil health, biodiversity, consumer acceptance, ethical considerations and regulatory frameworks remain systematically under-represented. Global deployment of CRISPR is already delivering measurable advantages in food security, shelf life and nutritional value, while in T&#xfc;rkiye the research base is at an early stage but has clear potential in wheat, barley, tomato and olive. Translating CRISPR into Turkish agricultural sustainability requires (i) a domestic biosafety framework aligned with the emerging European New Genomic Techniques approach, (ii) sustained investment in multi-location primary field trials, and (iii) inclusive deployment mechanisms-particularly through producer cooperatives-that allow smallholder farmers to benefit from edited varieties.

Plants, Genetically Modified↗
PubMed2026

Meta-analysis of source identification and apportionment in soil: A systematic review of analytical procedures, receptor modeling, and environmental applications.

Soil pollution poses significant risks to ecosystems and human health, necessitating accurate source identification and apportionment to guide mitigation strategies. This systematic review evaluates the application of Positive Matrix Factorization (PMF) and other receptor models in soil pollution studies, focusing on analytical procedures, tracer indicators, and environmental applications. This review aims to provide a comprehensive framework for conducting soil source apportionment studies, aiding policymakers in designing effective, region-specific environmental management strategies by compiling global trends and methodological insights. The study addresses sampling protocols, emphasizing representativeness and quality control. Data from 500 peer-reviewed publications highlight the dominance of research in China, Eastern Europe, and South Asia, with agricultural soils being the most frequently studied. Key findings reveal that traffic emissions (20.8 %) and industrial activities (19.4 %) are the primary global contributors to soil contamination, with regional variations such as coal combustion in cold climates and agricultural inputs in developing regions. Policy recommendations include stricter industrial regulations, sustainable agricultural practices, and targeted remediation efforts based on source-specific risks.

Soil Pollutants↗
PubMed1977

Chemical evaluation of the beeswax pellet implantation bioassay model for studies of environmental carcinogens.

The release properties of a number of constituents of cigarette smoke condensate in a condensate--beeswax matrix were characterized by an in vitro study. Eighteen compounds that were representative of several classes of condenate components were tested. Equal quantities of condensate and beeswax, mixed with tracer quantities of the 14C-labeled test compounds, were formed into rod-shaped pellets similar to those used for trachea implant studies, and the rate at which the 14C was removed from the pellet by a flowing saline stream was monitored. Results indicated a wide range in the rates of which the test compounds were released from the pellets. The smaller and water-soluble molecules were released rapidly; about 90% of the nicotine and phenol were leached out in the first 24 hours. Larger and less soluble molecules were released slowly or not at all. Only about 10% of the stearic acid and essentially none of the benzo[a]pyrene was released in 28 days. The effects of such an uneven release of components from an implantation of biologically active material in an inert carrier matrix are discussed with regard to bioassay systems.

Animals↗
PubMed1977

A photoacoustic study of newborn rat stratum corneum.

We have applied photoacoustic spectroscopy, a new spectroscopic technique, to the study of intact stratum corneum, a translucent membrane with high ultraviolet light scattering, and have obtained clear spectra in the 220-450 nm region. The photoacoustic technique has been used to study the effects of hydration and chemical alteration of the stratum corneum. Newborn rat stratum corneum shows marked spectral changes during the initial 60 h maturation period. These changes are attributed partly to the environmental and conformational changes occurring within the stratum corneum matrix during this time period. We also postulate the possibility of a novel molecular change within the keratin protein to account for our results.

Aging↗
PubMed1977

Paths of association in epidemiological analysis: application to health effects of environmental exposures.

Conventional regression analysis is based on assumptions of bidirectional associations between pairs of independent variables. In a number of circumstances these assumptions are not plausible. Structural representation in conventional regression is based on a set of parallel paths between independent and dependent variables; when the implausible assumptions are excluded, a different structrual relation between the independent and dependent variables is found. It permits a series associative path between independent variables. Two criteria for modification of conventional multivariate analysis are presented. They are when bilateral symmetry among independent variables is implausible on the basis of a priori information, and when there are significant differences between zero order and first order partial correlation coefficients. When these criteria are applied, there may result a series-parallel matrix of associations. For analysis of such a matrix, the procedures of path analysis are appropriate. The concepts are illustrated with environmental examples, and path analytical computations are worked out for a set of data on social and environmental factors which affected infant mortality in England and Wales between 1928-1938.

England↗
PubMed1977

Calcite growth under controlled diffusion.

The growth of calcite was studied in a gelatin-gel medium under variable environmental conditions by 2 different methods. The results suggest that the organic matrix, the temperature, the diffusion fluctuation depending on ionic concentrations, and the presence of additives exert a fine control on the evolution of single crystals, polycrystalline aggregates, and highly structured concretions of calcite.

Calcification, Physiologic↗
PubMed2026

Disruption of efflux activity reduces biofilm formation through multiple pathways.

Free-swimming bacteria must undergo large-scale changes in gene expression to form structured, aggregated biofilm communities. These regulatory changes are susceptible to environmental stimuli such as exposure to antimicrobials, which can affect adhesion, biofilm matrix production, pathogenicity and multidrug susceptibility. Previously, we found that genetic or chemical inactivation of efflux activity in Escherichia coli and Salmonella Typhimurium disrupts biofilm formation with a wide range of pathways sensitive to efflux inhibition, including reduced expression of csgD, a major regulator of biofilm matrix production. How the regulatory networks controlling efflux activity and biofilm formation overlap and how perturbing efflux impacts biofilm formation is still unclear. To address this, we used a combination of directed evolution experiments and large-scale functional genomics screens (TraDIS-Xpress) to identify the genes and pathways affecting efflux activity and biofilm formation in Salmonella enterica serovar Typhimurium and E. coli. This work describes the landscape of pathways linking efflux activity and biofilm formation. Whilst no singular gene or pathway was found to control the link between the two phenotypes, we propose changes in membrane potential following efflux inactivation are sensed through multiple response regulators that each in turn contribute to repression of biofilm development. These include the two-component signal transduction system EnvZ-OmpR and AraC/XylS family transcriptional regulators, RamA and MarA, which have extensive overlapping regulons and demonstrate high degrees of functional redundancy. This work deepens our understanding of the regulatory networks governing efflux activity and biofilm formation in Enterobacteriaceae and highlights the level of overlapping regulation and functional redundancy between them.

Salmonella typhimurium↗
PubMed2025

Impact of the ECM on the Mechanical Memory of Cancer Cells.

Besides genomic and proteomic analyses of bulk and individual cancer cells, cancer research focuses on the mechanical analysis of cancers, such as cancer cells. Throughout the oncogenic evolution of cancer, mechanical inputs are stored as epigenetic memory, which ensures versatile coding of malignant characteristics and a quicker response to external environmental influences in comparison to solely mutation-based clonal evolutionary mechanisms. Cancer's mechanical memory is a proposed mechanism for how complex details such as metastatic phenotypes, treatment resistance, and the interaction of cancers with their environment could be stored at multiple levels. The mechanism appears to be similar to the formation of memories in the brain and immune system like epigenetic alterations in individual cells and scattered state changes in groups of cells. Carcinogenesis could therefore be the outcome of physiological multistage feedback mechanisms triggered by specific heritable oncogenic alterations, resulting in a tumor-specific disruption of the integration of the target site/tissue into the overall organism. This review highlights and discusses the impact of the ECM on cancer cells' mechanical memory during their metastatic spread. Additionally, it demonstrates how the emergence of a mechanical memory of cancer can give rise to new degrees of individuality within the host organism, and a connection to the cancer entity is established by discussing a connection to the metastasis cascade. The aim is to identify common mechanical memory mechanisms of different types of cancer. Finally, it is emphasized that efforts to identify the malignant potency of tumors should go way beyond sequencing approaches and include a functional diagnosis of cancer physiology and a dynamic mechanical assessment of cancer cells.

Humans↗
PubMed1976

Pattern-analytic approach to analysis of accidents due to human error: an application of the ortho-oblique-type binary data decomposition.

An ortho-oblique-type binary data decomposition based on data matrices providing relevant conditions of accidents is proposed as a means of classifying patterns of human error, and the computing procedures are described. The usefulness of the technique is shown by a numerical example of accidents in freight-car classification yard work. Forty-two severely injured victims were interviewed by psychologists and the contents of case reports were rearranged into a reliable binary data matrix which indicated the presence or absence of an interrelationship between each sample and each of 42 items of operational, environmental, and psychological conditions. Three patterns of error leading to an accident were identified by interpreting the orthogonally rotated results. They were 1) failure of strenuous performance in relation to fatigue and poor communication, 2) veterans' mistakes in teamwork, possibly due to hasty operation or distractions, and 3) errors caused by certain defects of machines or inappropriate work space. Recommendations were thus made on training plans for beginners. The importance of using non-scaled accidental data in binary form and allowing rotation for data decomposition is discussed.

Accidents, Occupational↗
PubMed2025

Biofilms in clinical infection: pathophysiology, diagnosis, and the evolving therapeutic landscape.

Biofilms are structured communities of microorganisms encased in a self-produced polymeric matrix that typically adhere to surfaces. Recent research, however, has revealed that non-attached aggregates share many common traits with the surface-dependent biofilms. This mode of bacterial growth provides enhanced protection against antibiotics and resistance to host immune defenses. Biofilms require higher antibiotic concentrations than those needed to inhibit planktonic bacteria, necessitating prolonged high-dose and combination therapies to achieve effective eradication. This increased resistance is attributed to multiple factors, including the protective extracellular matrix, reduced metabolic activity of bacteria within the biofilm, and also the ability of bacterial genomes to rapidly adjust in response to environmental changes. Diagnostic modalities such as sonication, tissue culture, and polymerase chain reaction-based assays currently dominate clinical diagnostics of biofilm infections due to their practicality, cost-effectiveness, and proven reliability. Recent research has led to innovative treatment strategies that target biofilm structure, enhance drug delivery, and modulate host-pathogen interactions. This review summarizes our current knowledge of biofilm formation, explores the current techniques for detecting microbial biofilms, and discusses future perspectives for advancing diagnostic and therapeutic strategies.

Biofilms↗
PubMed2025

Oocyte surface proteins EGG-1 and EGG-2 are required for eggshell integrity in Caenorhabditis elegans.

Metazoan eggs are surrounded by a specialized coat of extracellular matrix that mediates sperm-egg interactions. This coat is rapidly remodeled after fertilization to form a barrier that prevents polyspermy, protects against environmental insults, and provides structural support to the developing embryo. In C. elegans several oocyte surface proteins have been identified that mediate these events. However, whether two of these proteins, EGG-1 and EGG-2, are required for fertilization or downstream events has been unclear. Here, we address this question using more recent advances in genome editing tools through the creation of egg-1 egg-2 deletions of the endogenous loci. We found that egg-1 egg-2 oocytes are fertilization competent and form rudimentary eggshells. While the integrity of the egg-1 egg-2 eggshells are compromised and often rupture within the uterus, surprisingly, some embryos are capable of undergoing several rounds of cell division. Overall, our findings demonstrate that EGG-1 and EGG-2 are not required for fertilization but are involved in post-fertilization processes.

Caenorhabditis elegans↗
PubMed1976

A complex control circuit. Regulation of immunity in temperate bacteriophages.

Temperate bacteriophages can display in a stable way two essentially different behaviours. In the immune state, a gene (cI) produces a repressor which prevents expression of all the other viral genes; in the non-immune state the typically viral functions are expressed. The choice between the two pathways and the establishment of one of them have much in common with cell determination and differentiation. This choice depends on a complex control system, in fact one of the most intricate nets of regulation known in some detail. Our paper provides a formal description and partial analysis of this regulatory net. It is shown that even for relatively simple known models, this kind of analysis uncovers predictions which had previously remained hidden. Some of these predictions were checked experimentally. The experimental part chiefly deals with the efficiency of lysogenization by thermoinducible lambda phage carrying mutations in one or more of the regulatory genes, N, cro and cII. Although N- mutations are widely known for preventing efficient integration, and both N- and cII mutations for preventing efficient establishment of immunity, it is shown that, as predicted by a simple model, both N- and cII- phage efficiently lysogenize at low temperature if they are in addition cro-. In contrast with lambda N- cro+, lambda N- cro- is not propagated as a plasmid at low temperature, precisely because it establishes immunity too efficiently. Genetic control circuits are described in terms of sets of logic equations, which relate the state of expression of genes or of chemical reactions (functions) to input (genetic and environmental) variables and to the presence of gene and reaction products (internal, or memorization varibles). From the set of equations, one derives a matrix which shows the stable stationary states (if any) of the system, and from which one can derive the pathways (temporal sequences of states) consistent with the model. This kind of analysis is complementary to the more widely used analysis based on differential equations; it allows one to analyze in less detail more complex systems. The language might be used as well, mutatis mutandis, in fields very different from genetics. The last part of the discussion deals with the role of positive feedback loops in our specific problem (establishment and maintenance of immunity in temperate bacteriophages) and in developmental genetics in general. As a generalization of an old idea, it is suggested that cell determination (for a given character) depends on a set of genes whose interaction constitutes a positive feedback loop. Such a system has two stable stationary states: which one is chosen will usually depend on additional controls grafted on the loop.

Bacteriophages↗
PubMed2026

Proteomic profiling of bone for the estimation of post-mortem interval and post-mortem submersion interval: a systematic review.

Accurate estimation of the Post-Mortem Interval (PMI) and Post-Mortem Submersion Interval (PMSI) remains a persistent challenge in forensic science, especially when traditional morphological and entomological methods fail due to advanced decomposition or in aquatic environments. Proteomic profiling of bone tissues has recently emerged as a promising approach, leveraging the predictable degradation patterns of bone proteins to estimate time since death more reliably. This systematic review, conducted in accordance with PRISMA guidelines, analyzed 24 peer-reviewed studies focusing on the application of proteomic techniques to bone tissue for PMI and PMSI estimation. The included studies were evaluated based on sample type, analytical techniques used, identified biomarkers, environmental conditions assessed, and the overall reliability and reproducibility of the findings. The review found that specific bone proteins, particularly collagen, osteocalcin, fetuin-A, etc. exhibited consistent degradation patterns that correlated strongly with elapsed post-mortem time. Cortical bone was identified as a more stable and informative matrix compared to trabecular bone. Mass spectrometry, especially LC-MS/MS, emerged as the predominant analytical technique due to its high sensitivity and accuracy in detecting low-abundance proteins over extended PMIs and PMSIs. However, protein degradation rates were significantly influenced by environmental variables such as temperature, humidity, soil pH, and microbial activity. This review also emphasizes the transformative role of bone proteomics in advancing forensic science while identifying key gaps that must be addressed to achieve global standardization and practical implementation in diverse forensic contexts. The integration of proteomics with other emerging technologies, such as machine learning algorithms and computational modeling, may further enhance the precision of PMI and PMSI estimation in future applications.

Postmortem Changes↗