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At least 37 records · Page 2Linked to original sources

PubMed2026

Clinical and functional characterization of a novel homozygous non-canonical splice mutation (c.1910-15_1910-11delinsTTACA) in CEP290 causing Joubert syndrome.

BACKGROUND: Joubert syndrome (JS) is a rare, predominantly autosomal recessive neurodevelopmental disorder characterized by hypotonia, motor delay, intellectual disability, oculomotor apraxia, and the hallmark "molar tooth sign" on axial view of MRI. JS is genetically heterogeneous, with pathogenic variants identified in more than 40 genes involved in primary cilia function. Among these, CEP290 is one of the most frequently mutated genes. RESULTS: In this study, we investigated two children-an 11-year-old boy (the proband) and his 5-year-old sister-both presenting with a similar phenotype consistent with JS. The parents, who self-identified as Chechen, reported distant consanguinity. The family also included a healthy 13-year-old daughter. The proband had previously been evaluated by a neurologist and underwent whole-genome sequencing (WGS); however, no causative variants were identified initially. After phenotype reassessment by a clinical geneticist, we performed a reanalysis of the raw WGS data and identified a novel homozygous intronic variant of uncertain significance (VUS), c.1910-15_1910-11delinsTTACA in CEP290 (NM_025114.4). Sanger sequencing confirmed that both the proband and his affected sister were homozygous for this variant, which they inherited from their heterozygous parents. Their healthy sister did not carry the variant. mRNA-sequencing and targeted cDNA sequencing (read depth ~ 100,000x) demonstrated that this intronic variant causes completely aberrant splicing of CEP290 pre-mRNA. Predominantly this variant causes the skipping of exon 20 in the main CEP290 transcript. Alternatively, the variant results in partial inclusion of intron 19 into the mRNA, elongation of exon 20 by 58 nucleotides, and a homozygous substitution chr12:88114573 (ACTGTGTA> TTACAGTA). No canonical mRNA isoform was detected when the variant was homozygous. Both the predicted severe truncation and the likely degradation of aberrant transcripts through nonsense-mediated decay (NMD) would correspond to complete loss of CEP290 function. Following the reclassification of this VUS to likely pathogenic, the family was able to pursue in vitro fertilization (IVF) with preimplantation genetic testing for monogenic disorders (PGT-M). CONCLUSION: Our study highlights the critical importance of proper phenotyping prior to referral for WES/WGS as well as of combining NGS with functional mRNA studies to achieve a molecular diagnosis for patients with predicted splice-site mutations in JS-associated genes. It also emphasizes the need for functional reassessment of VUS when genomic data are expected to guide reproductive decision-making within affected families.

Humans↗

PubMed2025

APAV: An advanced pangenome analysis and visualization toolkit.

Traditional pangenome analysis focuses on gene presence/absence variations (gene PAVs). However, the current methods for gene PAV analysis are insensitive to detect small but valuable mutations within gene regions, and they overlook variations in intergenic regions. Additionally, the visual inspection of PAVs is an important but time-consuming step for pangenome analysis and result interpretation. To address these issues, we present APAV, an advanced toolkit designed for comprehensive PAV analysis and visualization. It integrates gene element-level PAV analysis and provides PAV analysis for arbitrary given regions in a genome. The resulted PAV profile can be visualized and investigated interactively with reports in HTML format, enabling researchers to conveniently verify sequencing read depth, target region coverage, and intervals of absence for each PAV. Furthermore, APAV offers various subsequent analysis and visualization functions based on the PAV profile table, including basic statistics, sample clustering, genome size estimation, and phenotype association analysis. We demonstrated the capability of APAV with pangenome analysis of tumor genomes and rice genomes. Performing PAV analysis at the element level not only provides more accurate information about the variations but also uncovers a larger number of variations for the phenotype-genotype association studies. In the rice genome analysis, we identified over twenty thousand distributed genes and more than fifty thousand distributed genetic elements. In the tumor genome analysis, element-level analysis revealed approximately three times as many phenotype-related genes as gene-level analysis. This indicates that altering the PAV unit from genes to smaller segments or elements can lead to more biological insights.

Software↗

PubMed2026

Two Bacillus PGPB Strains in Wheat and Soybean: Wheat Growth Promotion Without Detectable Rhizosphere Microbiome Restructuring.

Plant growth-promoting bacteria (PGPB) are increasingly deployed as biofertilizers, yet the link between an inoculant's genomic potential and its realized effect on the plant is rarely assessed within an integrative framework that jointly captures the rhizosphere microbiome, plant phenotype, and strain genome. Two Bacillus strains-B. halotolerans 1453 and B. pumilus 630-were applied to wheat and soybean in a factorial pot experiment (2 strains × 2 application methods × 3 frequencies + control, 3-4 replicates). Rhizosphere samples (n = 67 after filtering) were profiled by 16S rRNA sequencing with PICRUSt2 functional prediction and compositional validation (Aitchison PERMANOVA, ALDEx2, ANCOM-BC2). The PGPB gene repertoire was characterized by genome mining (481 marker genes, 14 categories). Wheat phenotype (six traits) and soybean height were analyzed with models appropriate for count data (Negative Binomial and binomial GLMs) for treatment-vs.-control comparisons, and with factorial ANOVA for decomposition into main effects and interactions. Crop identity was the dominant factor shaping both microbiome structure and function (PERMANOVA R2 = 14.7% taxonomically and R2 = 7.8% functionally, both p < 0.001), with biologically meaningful taxonomic differences between wheat and soybean; strain, application count and method had no significant effect on community composition (R2 < 4% each), and co-occurrence networks showed no reliable differences between crops once read depth and sample size were controlled for. Despite this neutrality at the microbiome level, inoculation significantly increased wheat spike count (NB-GLM, all 12 treatments vs. control, padj 0.0002-0.031), ear weight, and stem count, with application count the strongest source of variability and a pronounced strain × application count. Strain 1453 outperformed 630 in spike count (+23.1%, p = 0.012) and ear weight (+20.4%, p = 0.023); we hypothesize that this may be related to its more complete DNRA pathway (narGHI + nirB-nirD) and biocontrol genes (bacE, srfAA). Strain 630 produced a less pronounced effect than strain 1453 but was subject to smaller fluctuations across replicates (CV ≈ 16-21% vs. ≈24-26% for 1453), which may reflect better resilience to environmental fluctuations, possibly due to its confirmed rsbV/rsbW stress-tolerance regulon. Rhizosphere microbiome composition differed clearly by crop (wheat vs. soybean) but showed no detectable response to strain, application method, or application count. Despite this lack of a microbiome signal, inoculation significantly increased wheat spike count and ear weight, with the magnitude and stability of this effect differing by strain. We hypothesize that this strain-dependent difference relates to underlying genomic differences-particularly in nitrogen metabolism (DNRA pathway) and stress-tolerance genes-though this link has not been tested directly and remains a hypothesis for future work.

Triticum↗

PubMedDate not supplied

Improved diagnostics: clinical evaluation of a color-coded, polymeric periodontal probe.

The objective of this study was to compare the accuracy, reproducibility and patient comfort of a newly designed, color-coded, polymeric periodontal probe to a traditional, color-coded metal probe. Twenty-four adult subjects with varying degrees of periodontal disease (from slight to severe) reported for two visits, one week apart. A randomization schedule for probe use was adopted over the two visits so that the gingival crevices in two quadrants were probed with the same probe (metal or polymeric) providing reproducibility information for each probe, while the other two quadrants were probed first with one probe then the other for comparison data yielding information on accuracy. A bleeding index was obtained using the same schedule. Clinical scoring was performed by the same examiner. After probing each quadrant, subjects rated discomfort using a visual analog scale (VAS). Results showed no significant difference in depth readings greater than 2 mm between the polymeric and metal probes (3.41 +/- 0.37 mm vs. 3.38 +/- 0.32 mm, p = 0.55). Significantly less discomfort (assessed by VAS) was recorded by patients after polymeric probe use (3.70 +/- 2.40 cm vs. 4.44 +/- 2.49 cm, p = 0.015). The bleeding index indicated significantly less bleeding with the polymeric probe (0.80 +/- 0.56 vs. 1.24 +/- 0.65, p = 0.0001). Both the polymeric and metal probes were found to produce highly reproducible results in all measures across visits.

Adult↗

PubMed1988

Correlation between electronic and visual readings of pocket depths with a newly developed constant force probe.

The purpose of this study was to compare probing measurements obtained using a newly developed constant force electronic probe, which eliminates errors of visual reading and variable force, to those obtained using a standard periodontal probe. The probe was connected to a digital readout through a linear variable differential transformer; the digital readout was connected to a printer and a foot switch. When the probe was in position and the foot switch depressed, the pocket depth was printed to the nearest 0.1 mm. 12 subjects with minimal to early periodontitis were selected for the study. The pocket depths of each patient were recorded electronically utilizing a constant force of 25 g, and conventionally using the same instrument in a "locked" position and visual reading. Probings were performed on each subject by 3 different examiners, on 3 separate occasions 2-3 days apart. The results showed a high correlation between manual and electronic probing. The average correlations for the 3 investigators between examinations were consistently higher for the electronic probings. In comparing the 3 examiners to each other, consistently higher correlations were found for the electronic pocket readings. Correlations for single-rooted teeth were lower for all 3 examiners. The pocket depth measurements recorded when using the manual probe with visual readings were consistently deeper than those obtained using the electronic probe with computer readings. It was concluded that the reproducibility of measurements obtained with the electronic probe was significantly superior to that obtained with a manual probe.

Adult↗

PubMed2026

esloco: simulation-based estimation of local coverage in long-read DNA sequencing.

SUMMARY: Long-read DNA sequencing is increasingly applied for whole-genome studies, yet experimental planning often lacks reliable estimates of target region coverage, leading to costly and time-consuming pilot studies and replicates. We present esloco, a Monte Carlo-based simulation framework for estimating local coverage in long-read sequencing experiments, including scenarios with unknown target regions (e.g. viral integration, CRISPR-Cas9) or PCR-free designs (e.g. base modifications). By modeling coverage as a function of sequencing depth and read length distribution, esloco enables informed predictions of local sequencing outcomes. Benchmarking across a 45-gene panel demonstrated close agreement with empirical data, underscoring the framework's reliability. AVAILABILITY AND IMPLEMENTATION: esloco is a Python package available on PyPI (https://pypi.org/project/esloco/), GitHub (https://github.com/aweich/esloco), and Zenodo (https://doi.org/10.5281/zenodo.17776161).

Sequence Analysis, DNA↗

PubMed2026

Whole metagenome sequencing: not deep enough for complete microbial function recovery.

BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality. RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed. CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.

Humans↗

PubMed2025

UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.

MOTIVATION: One of the key applications of Unique Molecular Identifiers (UMIs) in high-throughput sequencing is to correct for PCR amplification bias and removal of PCR duplicates, thereby improving quantification in DNA-seq and RNA-seq applications. Accurately grouping error-bearing UMIs that originate from the same input molecule through a UMI deduplication method is a critical step in this process. However, many existing UMI deduplication tools rely on simple Hamming distance comparisons or suboptimal clustering algorithms, often resulting in erroneous UMI groupings, particularly in error-prone long-read sequencing or ultra-high-depth short-read sequencing. RESULTS: We introduce UMI-nea, a tool that utilizes Levenshtein distance comparisons and a novel clustering approach to optimize multithreading workflows. Compared against three other indel-aware UMI deduplication tools, UMI-nea achieves more accurate UMI groupings with efficient run time. It demonstrates robust performance across diverse sequencing platforms, depths, and UMI lengths. Additionally, UMI-nea incorporates a data-guided adaptive UMI filter, further enhancing quantification accuracy. AVAILABILITY AND IMPLEMENTATION: UMI-nea is available on github https://github.com/Qiaseq-research/UMI-nea.git or Zenodo https://doi.org/10.5281/zenodo.16745758. Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.

High-Throughput Nucleotide Sequencing↗

PubMed1992

Load dependency and reliability of microhardness measurements on acid-etched enamel surfaces.

The load dependency of hardness measurements was investigated on sound and demineralized enamel samples. For all samples investigated, the Knoop hardness number (KHN) varied as a function of the applied load. Higher loads enhanced indenter penetration into the test surface. The variation in KHN values observed in demineralized enamel, both surface-softened and surface-etched, was explained by a decrease in porosity as a function of depth. The reading error for indentations made on surface enamel etched with 37% phosphoric acid gel for 30 s was found to be slightly elevated compared to indentations made on a polished sound enamel surface. It was concluded that the surface microhardness technique can be used for the longitudinal investigation of etched surface enamel.

Acid Etching, Dental↗

PubMed1976

A successful method for development of voluntary alcohol intoxication in mice.

Eight strains of male mice, C57BL, C3H SWM, SW, KK, KSB, KR and DBA, were fed on a standard pelletized diet and offered a choice of water or 10% sake solution (sake containing 10% alcohol). Both young (3 months of age) and old (8 months of age) groups were studied simultaneously. The degree of intoxication was measured by recording the drinking behavior on a pulse recorder, by calculating gaschromatographically the blood alcohol concentration, by taking depth electroencephalogram readings and so on. Intoxication, shown by lack of coordination such as grossly impaired gait, was observed only in the older mice of strain with a moderate natural alcohol preference such as C3H, SWM, SW, KK and KSB. In general, the intoxicated mice were over 9 months of age, tended to consume fluids regardless of the time of day or night and suffered a loss of body weight. The blood alcohol levels of them were over 4.6%. The threshold elevation of the ascending reticular activating system on electroencephalogram in a intoxicated mouse reached about 167%. The present study provides a successful method for the development of voluntary alcohol intoxication in mice.

Age Factors↗

PubMed1990

[Alcohol drinking behaviors--physiological and sociomedical factors].

Alcohol drinking behavior is usually studied from two perspectives, factors leading to drinking behavior and the behavioral effects of alcohol drinking. Many detailed medicolegal, pharmacological and psychiatric studies have been conducted on the behavioral effects of alcohol drinking. Few studies have considered the biological aspects of a desire for alcohol. However, these issues can not be ignored. The role of genetic, environmental and nutritional factors in alcohol preference has extensively debated. Recently, biochemical, physiological and pharmacological studies have also been performed to elucidate the mechanism of the desire for alcohol. In this study, the biological aspects of drinking behavior and alcohol preference have been studied using inbred strains of mice as an animal model on alcoholism. In addition, factors affecting drinking behavior of human beings are discussed based on the results obtained from a medico-legal study of alcohol-related cases. 1. Alcohol preference in several animal species The alcohol preference expressed as a ratio (%) of the volume taken (water and 10% (v/v) alcohol solution), was not constant in several animal species. The preference ratio was observed to be 2.7 +/- 0.7, 3.7 +/- 0.8, 22.0 +/- 19.8 and 39.6 +/- 5.4 in male inbred strains of SAMP2, DBA/2cr, B10.Br/Sg and C57BL/6J mice respectively, and 10.7 +/- 7.6, 15.9 +/- 13.6, 31.3 +/- 22.6 and 32.4 +/- 16.7 in male Donryu, DA, Wistar and Buffalo rats respectively, and 91.3 +/- 9.1 in male Golden hamster, and 2.1 +/- 0.3 in Hartley guinea pigs. Rabbits and Japanese monkeys do not demonstrate high alcohol preference. By comparison, the alcohol preference of a Japanese people was estimated to be approximately 11-35% on the basis of data obtained by questionnaire. 2. Development of alcohol dependence and withdrawal by voluntary alcohol intake in mice Eight strains of male mice, C57BL, C3H, SWM, SW, KK, KSB, KR and DBA, were offered a choice of water or 10% sake solution (sake containing 10% alcohol). Both young (3 months of age) and old (8 months of age) groups were studied simultaneously. The degree of intoxication was measured by recording the drinking behavior on a pulse recorder, by measuring gas-chromatographically the blood alcohol concentration, by taking depth electroencephalogram readings and so on. Intoxication, shown by lack of coordination such as grossly impaired gait, was observed only in the older mice of a strain with a moderate natural alcohol preference such as C3H, SWM, SW, KK and KSB.(ABSTRACT TRUNCATED AT 250 WORDS)

Alcohol Drinking↗

PubMed1989

Research in physical medicine and rehabilitation. II. The conceptual review of the literature or how to read more articles than you ever want to see in your entire life.

The purpose of the literature review is to place your research question in the context of the existing scientific literature. This article will help you to develop an overall conceptual framework to allow you to sort through the mass of published material in a focused way. The conceptual review differs from the individual article review in that it is guided by your understanding of the basic issues rather than by your knowledge of research methodology. The goal of this paper is to help you develop a conceptual framework starting from your clinical knowledge. A specific search strategy is presented to help you determine which articles are highly relevant to your topic and to locate all of these published within the past 5 years. Articles are classified into three types: those that are obviously highly relevant, other less relevant articles and articles that are potentially relevant. Guidelines are given on how to start looking, when to stop looking, how to organize the articles you find so that you can review them in a reasonable amount of time and how to read in depth the most pertinent ones you find.

Abstracting and Indexing↗

PubMed1978

Panum's area explained in terms of known acuity mechanism.

Comparisons between the various types of binocular and monocular visual acuity thresholds are made in this study. The results obtained in monocular resolution and binocular diplopia experiments support LeGrand's view regarding Panum's area. Thus the physiological mechanism which appears to account for both monocular resolution and binocular diplopia thresholds could also account for a spatial tolerance which gives rise to Panum's area.

Depth Perception↗

PubMed1992

1991 Federal Nursing Service Award recipient. The effect of increased atmospheric pressure on glucose reagent strip accuracy.

Hyperbaric oxygen (HBO) is currently being used throughout the world as an adjunctive therapy for non-healing diabetic wounds. Anecdotal accounts of diabetic patients experiencing hypoglycemic reactions with HBO necessitated glucose testing by fingerstick during treatment dives to 2.4 atmospheres absolute. This study looked at four glucose testing methods and the accuracy of their readings using high and low control solutions at both sea level and at depth. A one-way analysis of variance showed significant differences with all of the high and 75% of the low control solutions when comparing sea level readings to depth readings. The significance varied between reaction rate and end point reading methods, with the reaction rate technology performing better.

Air Pressure↗

PubMed1991

The identification of periodontal attachment loss from clinical measurements.

Clinical readings of pocket depth and loss of periodontal attachment were recorded on the approximal sites of 21 teeth scheduled for extraction. Corresponding laboratory measurements of pocket depth and loss of periodontal attachment were made on the teeth after extraction. Clinical measurements were within 1mm of their corresponding laboratory values on 95% of occasions. Clinical readings of loss of periodontal attachment of 0 or 1mm showed poor agreement with corresponding laboratory measurements. It was concluded that the presence of loss of periodontal attachment can only be reliably identified where a clinical reading of 2mm or greater is recorded.

Adult↗

PubMed2025

Polygenic variants in DNA repair genes are associated with neurodevelopmental disorders, regression and increased burdens of somatic variants and short tandem repeat expansions.

PURPOSE: Developmental regression, characterized by the loss of acquired milestones, occurs in some individuals with neurodevelopmental disorders (NDDs); yet, its molecular basis remains unclear. Studies suggest that DNA damage repair (DDR) genes, such as FAN1, may protect against neurological dysfunction by modulating the somatic stability of short tandem repeats (STRs). This study explores the contribution of DDR gene variants in NDD cases presenting with regression. METHODS: We analyzed 1087 NDD patients, focusing on those carrying variants in DDR genes and presenting regression. We assessed the sensitivity to DNA damage using mitomycin C on lymphoblastoid cells. Somatic variants and STR expansions were evaluated through high-depth short-read genome sequencing. To further investigate the pathogenetic role of STR expansions, we performed long-read genome sequencing on the most severely affected proband. RESULTS: Probands with regression carried multiple DDR gene variants, several within the Fanconi anemia pathway. Their lymphoblastoid cells showed increased sensitivity to mitomycin C-induced cytotoxicity compared with parental and control samples. Probands with severe phenotypes and regression exhibited an accumulation of somatic variants and STR instability, enriched in neurodevelopmental genes. CONCLUSION: Our findings suggest that polygenic DDR gene variants may contribute to developmental regression in NDDs by promoting the accumulation of somatic variants and STR expansions.

Humans↗

PubMed2026

Sperm subpopulations differing in mitochondrial abundance show divergent nuclear allele frequencies.

Mammalian ejaculates contain heterogeneous sperm subpopulations that differ in subcellular architecture and developmental history, despite appearing morphologically uniform. The extent to which this cellular heterogeneity reflects underlying nuclear genomic structure within a sire remains largely unexplored. Mitochondrial architecture in sperm is established during spermatogenesis, with final assembly and organization occurring during spermiogenesis under nuclear genomic control, positioning variation in mitochondrial abundance and organization as a potential phenomic indicator of within-sire allelic segregation. Here, we tested whether sperm subpopulations defined by differing mitochondrial abundance exhibit systematic differences in nuclear allele representation. Boar sperm were resolved into low and high mitochondrial subpopulations using fluorescence-activated cell sorting based on MitoTracker™ Green fluorescence while excluding debris, doublets, and non-viable cells. Epifluorescence microscopy confirmed that high MitoTracker™ Green fluorescence sperm possessed longer mitochondrial sheaths, validating a structural distinction between subpopulations. Whole-genome sequencing of paired mitochondrial subpopulations from three boars was performed, and allelic ratio distortion was evaluated relative to heterozygous baseline populations. Analyses across heterozygous loci genome-wide identified candidate allele frequency shifts between mitochondrial-defined subpopulations, suggesting non-random segregation of alleles within ejaculates. Using a minimum sequencing depth of 30 reads in both sorted fractions, 182 candidate SNPs were identified with evidence of allele-frequency differences between mitochondrial fluorescence-defined subpopulations. These findings suggest that sperm mitochondrial abundance can potentially serve as an indirect, high-throughput marker of nuclear genomic heterogeneity within sires. This proof-of-concept framework establishes a foundation for future studies integrating sperm phenotyping, genome-wide allele-frequency analysis and functional validation to better characterize gamete-level heterogeneity.

Male↗

PubMed1992

Evaluation of the interprobe electronic periodontal probe.

The Interprobe is designed to provide measurements of pocket depths and attachment loss. Investigators involved in a clinical study on dental implants being conducted by the Dental Implant Clinical Research Group participated in an in vitro evaluation of the variability of repeated measurements made with the Interprobe. Measurements were made on holes drilled to predetermined depths in metal blocks. Three readings by investigators for each of nine test holes were in agreement 75.2 percent of the time. At least two of three readings were in agreement in 98.1 percent of the attempts. Either two of three or three of three readings were within 0.5 mm of the actual depth of the holes over 99 percent of the time. No correlation was noted for accuracy of measurements with hole depth or present clinical duties of the investigators. Although slight initial improvement in measurement accuracy was observed, it was not statistically significant in time over the three measurement sequence.

Analysis of Variance↗