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Gingival crevicular fluid: a new diagnostic aid in managing the periodontal patient.

On the whole, the studies on GCF have demonstrated that the flow of this fluid is sufficiently indicative of the inflammatory state that it can be used under a variety of clinical conditions to monitor and control gingival inflammation. Since gingivitis is extremely common, and since some cases of gingivitis presumably do not progress to periodontitis, the question could be posed whether or not a concerted effort to control inflammation (i.e. trying to achieve a GCF flow as near to zero as possible) would be clinically significant. Until there is evidence to the contrary, the answer must be "yes", since few cases are known where periodontitis occurs without being preceded by gingivitis. In other words, the control of all gingivitis, if feasible, should prevent most cases of periodontitis. Although control of all gingivitis would mean the treatment of many cases that would not progress to periodontal breakdown, such efforts would be worth-while if most periodontal destruction were prevented. Even the early destructive lesion exhibiting little or no inflammation may soon be identified, mainly because the minute volume of fluid collected from the gingival crevice can now be measured accurately. Accordingly, the concentration of various constituents in the GCF can be determined, which should lead to the development of tests to differentiate between pockets undergoing active destruction with minimal inflammation from the majority of active lesions that are intimately involved with frank inflammation. Thus, a clinician would measure sub-clinical gingival inflammation by measuring GCF flow, then differentiate destructive from quiescent lesions by analyzing the GCF sample for some constituent(s), chemical or microbial (Listgarten et al. 1975) indicative of the periodontal destructive process. Monitoring the flow of GCF might be of value in other clinical situations. For example, one could monitor the response of gingival tissues to various restorative and prosthetic procedures (Strauss et al. 1975) to ensure that these procedures do not aggravate the periodontal tissues and induce gingivitis or periodontitis. The education of the patient should be easier since patients can read their own numbers on the GCF meter at each examination and self-evaluate their personal periodontal condition and the effectiveness of their home care. Even the education of the dental student should be easier since he or she would have the means of self-evaluating the effectiveness of treatment, and not be as dependent upon the subjective assessment of his efforts by an instructor. Finally, monitoring GCF for various components could provide the dentist with a valuable means of easily screening patients for systemic disease. Obviously, this area of investigation is in its infancy, but does promise an exciting future for the oral diagnostician.

Ammonia

Estimation of carrier frequencies of autosomal and X-linked recessive genetic conditions based on gnomAD v4.0 data in different ancestries.

PURPOSE: Monogenic rare diseases contribute significantly to infant deaths and pediatric hospitalizations and cause burden to the patients and their families. The American College of Medical Genetics and Genomics recommended in 2021 that carrier screening of autosomal recessive and X-linked conditions with a carrier frequency of ≥1/200 and a severe or moderate phenotype should be offered when planning or during pregnancy. In November 2023 gnomAD v4.0 was released. It contains in total 807,162 individuals, being nearly 5× larger than previous versions, which have been used to estimate gene carrier frequencies (GCF). METHODS: We utilized gnomAD v4.0 (GRCh38) to calculate the GCFs for available genetic ancestry groups for variants having pathogenic or likely pathogenic classification (>80% of submissions) in ClinVar. We calculated GCF separately for exomes and genomes, combined data, and at-risk couple frequencies (ACF) per genetic ancestry group. RESULTS: In total, 324 genes had a GCF ≥1/200 in at least 1 ancestry subgroup. The number of genes with GCF ≥1/200 varied greatly between subgroups. ACFs were more similar, Ashkenazi Jewish having the highest ACF of 6.11%. CONCLUSION: Improved understanding of carrier risks and updated carrier screening content would allow patients to make more informed reproductive decisions.

Humans

Fine-grained structural classification of biosynthetic gene cluster-encoded products.

MOTIVATION: Biosynthetic gene clusters (BGCs) are responsible the biosynthesis of many natural products, including a multitude of effective therapeutics and their precursors. Advances in genomic data collection as well as computational techniques have made it possible to identify BGCs at scale. However, accurately determining the types of BGC-encoded products from genomic content remains elusive. RESULTS: Here, we introduce BGC annotation tool (BGCat), a machine learning method for fine-grained structural classification of BGC-encoded products, leveraging the NPClassifier natural product nomenclature. Our method leverages a pre-trained protein language model for creating meaningful gene representations and a deep neural network for class label prediction. We show the method outperforms state-of-the-art approaches in coarse-grained product classification and is effective for detailed classification. We implement a clustering-based augmentation strategy for BGC-product relationships, addressing a crucial gap in the available datasets. We then introduce the concept of product class profiles of gene cluster families (GCFs), associating each GCF with a probabilistic distribution of product types and offering a new perspective on GCF functions. Lastly, we use BGCat to provide new product class labels for over 100k BGCs in antiSMASH DB that presently have minimal information about their products. AVAILABILITY AND IMPLEMENTATION: The source code and trained model weights are freely available at https://github.com/HassounLab/BGCat.

Multigene Family

Genetic polymorphism of the vitamin D binding protein and another post-albumin protein in horse serum.

Horizontal polyacrylamide gel electrophoreses, on 10% separation gel, of horse serum revealed polymorphism of the vitamin D binding protein (Gc protein) and another post-albumin protein (Pa). Family data supported the hypothesis that Gc and Pa types were controlled by autosomal codominant alleles. For both Gc and Pa proteins, the homozygous types showed a single fraction while the heterozygous type had two fractions. Pa types were found to be identical to the post-albumin types reported earlier by starch gel electrophoresis. Two Gc alleles, GcF and GcS, and three Pa alleles, Pa D, Pa F and Pa S, were observed in samples from Swedish (four breeds), Lipizzaner and Arab horses. The frequency of the more common allele at the two loci, i.e. GcF and PaF, ranged from 0.72-0.93 and from 0.58-0.99, respectively, in the different breeds studied. Plasma samples showed an extra protein fraction near the GcS fraction and thus were found unsuitable for Gc typing.

Alpha-Globulins

Comparison of gingival health and gingival crevicular fluid flow in children with and without diabetes.

GCF flow measurements and a clinical scoring of gingival health were both recorded for a group of 56 children with diabetes and 41 children without diabets. The children with diabetes had significantly more gingival disease than the children without diabetes when compared with either measure. A small but significant correlation was found between the GCF flow and the clinical scores with the children with diabetes but not with the children without diabetes.

Adolescent

MicroRNAs in Oral Bio-Fluids as Predictive Biomarkers of Orthodontic Tooth Movement: A Systematic Review.

This systematic review was designed to assess scientific evidence of the association of microRNA expression during orthodontic tooth movement through various time points. A systematic review was performed in accordance with the PRISMA checklist. A search strategy was developed in electronic databases including Med Line, Scopus, EBSCO Host and ProQuest Dissertations & Theses Global until June 2025. Eligibility criteria included studies that investigated microRNA expression in saliva/GCF during orthodontic treatment. The risk of bias of the included studies was analysed using the QUADAS-2 and RoB-2 tools. The search retrieved 2800 records, of which nine studies were selected. Minor variations in GCF collection were noted, while stimulated saliva was collected in one study. RT-PCR and the Fluro meter accounted for the majority of miRNA estimation. Thirteen miRNAs were identified as target biomarkers for OTM regulation. Despite the high risk of bias, the evidence from the current systematic review indicates that microRNAs can be considered as potential biomarkers of orthodontic tooth movement in oral biofluids. Trial Registration: Prospero ID-CRD420251153064.

Humans

Precision periodontology in clinical practice: bridging omics and clinical decision-making.

BACKGROUND: Precision periodontology integrates molecular diagnostics, genomics, and advanced imaging into clinical decision-making. Despite major advances in microbiome characterisation, host genetics, and inflammatory biomarkers, their translation into routine care remains limited. OBJECTIVES: To critically appraise current evidence on microbiome-based profiling, genetic and epigenetic markers, host-response biomarkers, and three-dimensional imaging in periodontology, and to propose a conceptual decision-support framework linking diagnostic outputs to potential therapeutic actions and future implementation research. MATERIALS AND METHODS: A narrative review searching PubMed/MEDLINE, Scopus, Embase, and the Cochrane Library (2010-2025) using terms related to precision periodontology, subgingival microbiome, periodontitis genetics and epigenetics, salivary and GCF biomarkers, aMMP-8, CBCT, risk assessment, and artificial intelligence. Priority was given to meta-analyses, systematic reviews, longitudinal studies, and guideline documents. RESULTS: Microbiological testing has defined but narrow indications; single-SNP genotyping has not demonstrated clinical utility commensurate with cost; aMMP-8 point-of-care testing is among the most extensively investigated host-response tools and may have adjunctive value in selected monitoring and peri-implant scenarios; however, current evidence remains insufficient to support routine diagnostic implementation. CBCT may directly influence surgical decision-making through defect morphology characterisation. AI-based models show promise but lack prospective clinical validation. These conclusions are consistent with the 20th EFP Workshop Consensus Report. CONCLUSIONS: Precision periodontology currently operates in addition to, rather than in replacement of, conventional staging and grading. We propose a conceptual decision-threshold framework for the selective consideration of molecular and advanced imaging tools when their additive contribution may meaningfully inform management. This framework should be regarded as a research-oriented decision-support model rather than a validated clinical algorithm. CLINICAL RELEVANCE: Clinicians are provided with a structured, evidence-based framework that identifies specific clinical scenarios where molecular diagnostics, host-response biomarkers, and three-dimensional imaging may meaningfully modify periodontal treatment decisions, supporting the operationalisation of precision approaches in daily practice.

Humans

TNF-NF-κB signaling mediates immune-biomineralization crosstalk during shell repair under ocean acidification in Mytilus edulis.

Ocean acidification (OA) impairs biomineralization in bivalves, but its effects on immune-biomineralization crosstalk during shell repair remain unknown. Here, we exposed adult Mytilus edulis bearing standardized shell perforations to three pH levels (8.1, 7.9, and 7.7) for up to 40 days. OA slowed early repair and caused microstructural disorganization and an approximately 87% reduction of compressive strength at pH 7.7, yet the damaged area appeared largely closed by day 15, suggesting a decoupling between morphological closure and functional recovery. In addition, transcriptomic profiling of hemocytes and mantle tissue, based on an average of 6.5 Gb of clean reads per sample mapped to the M. edulis reference genome (NCBI Assembly GCF_000511035.1), revealed that these shell-level defects were accompanied by coordinated immune and metabolic reprogramming. Hemocytes, the primary immune effector cells of bivalves, exhibited pH- and time-dependent shifts with moderate acidification (pH 7.9) promoting inflammatory transcripts, whereas severe acidification (pH 7.7) suppressed these signals while upregulating stress-associated pathways; both treatments consistently downregulated lysosomal proteases and NF-κB negative regulators. The mantle, a primarily mineralizing organ, paradoxically upregulated immune-related genes while suppressing oxidative phosphorylation and extracellular matrix pathways. This tissue-level imbalance, with hemocytes recruited but functionally constrained and mantle metabolically suppressed yet immunologically activated, points to TNF-NF-κB pathway modulation as a key mediator of shell repair under acidification. Our findings demonstrate that visible shell closure masks underlying structural and mechanical failure, and that immune regulation, rather than simple suppression or activation, critically shapes the repair outcome. These results advocate for multifunctional indicators beyond closure area to assess shell integrity in acidified marine environments.

Animals

Gene model for the ortholog of Pi3K21B in Drosophila eugracilis.

Gene model for the ortholog of Phosphatidylinositol 3-kinase 21B (Pi3K21B) in the D. eugracilis May 2021 (Stanford ASM1815383v1/DeugRefSeq2) Genome Assembly (GenBank Accession: GCF_018153835.1) of Drosophila eugracilis. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Journal Article

Equine markers genes. Polymorphism for group-specific component (Gc).

Polymorphism of equine Gc protein was demonstrated by immunofixation electrophoresis with a goat anti-human Gc antibody. Three different phenotypes, F, FS and S, were found. Family data supported the genetic theory of two autosomal codominant alleles, GcF and GcS. Both alleles occurred in Standardbred, Thoroughbred and Arabian horses and in Shetland ponies. A frequency of 0.23 for GcS in the American Standardbred horse indicates the system should be useful for problems of identification and parentage.

Alleles

The use of extracted teeth to evaluate clinical measurements of periodontal disease.

Clinical indicators of periodontal disease, Gingivitis Index, Gingival crevicular fluid and pocket depth measurements were obtained from the gingiva surfaces of 30 teeth. The gingival margins were marked on the surfaces of the teeth prior to extraction. The extracted teeth were stained with hematoxylin and air dried, and the distances from the groove to the base of the calculus, plaque, and connective tissue attachment were obtained. The plaque-free zone was also measured. Comparisons were made between clinical and tooth surface measurements. A high correlation was found between clinical pocket depth measurements and tooth surface parameters. The correlations between all tooth surface parameters and GCF were statistically significant. The G.I. was significantly correlated only with the penetration of calculus into the pocket. The clinical pocket depth was statistically the same as the distance from the gingival groove to the coronal connective tissue attachment. The plaque-free zone appeared to represent the junctional epithelium.

Dental Calculus