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At least 19 recordsLinked to original sources
PubMed1975

Genetic hybridization at the unlinked thy and str loci of Streptococcus.

The sanguis and pneumoniae species of Streptococcus were used as recipients in transformations from str+ to str-r and from thy- to thy+. The str-r mutations in the two species had been previously shown to be allelic. Homology of the thy- mutations in the two species was demonstrated in the similar phenotypic properties they conferred (death in the absence of thymidine, lack of thymidylate synthetase). The str and thy loci are unlinked in each species.--- When the two species are transformed by both homospecific and heterospecific DNA, the efficiency is always lower in the heterospecific cross. The efficiency of heterospecific transformation is considerably lower at the thy than at the str locus. DNA was extracted from recipients that had integrated markers of heterospecific origin. When such hybrid DNA is tested on the original recipient species, the heterospecific markers are usually as efficient as homospecific markers. When tested on the original donor species, however, the hybrid DNA is usually more efficient than heterospecific DNA. This is true for both thy and str transformation. -- -- Forty independent thy+ hybrids were obtained in the cross of sanguis thy- recipients with pneumoniae thy+ DNA. These hybrids fall into a number of classes based upon the relative efficiency with which their extracted DNA's are able to transfer the thy+ marker into pneumoniae thy- cells. The most efficient of these DNA's exhibits about 20% of the efficiency of homospecific pneumoniae thy+ DNA and three orders of magnitude greater efficiency than heterospecific sanguis thy+ DNA. Thus, very little of the inefficiency of heterospecific transformation of the thy locus is ascribable to a classic restriction mechanism. Rather, the wild-type thy+ loci in the two species appear to differ at multiple sites, and independent heterospecific transfers result in differential extents of integration of these sites. On this basis, the thy+ loci of the two species differ at a greater number of sites than do the respective str+ loci.

Alleles↗
PubMed2024

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗
PubMedDate not supplied

[Preparation of proteolytic enzymes from the thermophilous actinomycete Actinomyces thermovulgaris str. T-54].

A preparation with a high proteolytic activity has been obtained by acetone precipitation from the culture liquid filtrate of the thermophilous actinomycete Actinomyces thermovulgaris str. T-54. The proteolytic (caseinolytic), fibrinolytic and thrombolytic activity of the preparation is comparable with that of trypsin and far superior to that of fibrinolysine. The preparation is stable at pH 5.0=9.5 and inactivated in the acid zone. The study of pH dependent proteolytic activity has shown acid, neutral and alkaline proteases in the preparation. It is relatively thermostable, and is completely inactivated for 10 min at 90 degrees. It is suggested that the preparation contains four enzymes or four enzymic groups that are different in their temperature sensitivity.

Actinomyces↗
PubMed2026

Atypical short tandem repeat allelic patterns in a sexual assault case involving hematopoietic stem cell transplantation.

Short tandem repeat (STR) profiling is a cornerstone of forensic DNA analysis, particularly during criminal investigations. However, certain clinical conditions, such as bone marrow transplantation, can complicate interpretation. To illustrate the impact of allogeneic bone marrow transplantation on forensic STR analysis, this case report details a sexual assault investigation involving a female victim who had previously received a bone marrow transplant from a female donor. A female sexual assault victim underwent forensic examination, during which multiple biological swabs were collected. STR profiling was conducted on the victim's blood, fingernail, buccal, breast, hip, vulvar, vaginal, cervical samples, panty, and brassiere. As conflicting profiles were found, a detailed medical history was collected, and hair follicle analysis was performed to confirm the origin of the STR profiles. Blood STR profiling revealed a single female genotype, while multiple swabs, including vaginal and cervical samples, showed a second female STR profile alongside the first. Notably, the consistency and distribution of the mixed profile across samples reduced the likelihood of laboratory contamination. The medical history of the victim revealed a prior history of allogeneic bone marrow transplant. Hair follicle analysis identified the recipient's original genotype, confirming that the secondary STR profile originated from the donor. Bone marrow transplantation may result in a mixed STR profile, potentially leading to misidentification or misinterpretation of forensic evidence. Awareness of transplant history is crucial during forensic evaluations. However, such clinical history is currently not included in standard sexual-assault evidence forms, underscoring the need for procedural updates.

Female↗
PubMed2026

Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.

BACKGROUND: Short tandem repeats (STRs) are repetitive DNA sequences with 1–6 nucleotide repeat units, exhibiting high polymorphism due to varying repeat counts. STRs are more variable than SNPs and can cause genetic disorders. With population-scale cattle whole-genome sequencing data available, whole-genome STR identification has attracted new interest, but challenges remain due to the lack of standardized methods, sequencing data limitations, and the diversity of STR-calling tools. This study compared six STR-calling tools: HipSTR, GangSTR, and ExpansionHunter for short-read data, and Straglr, RepeatHMM, and LongTR for Oxford Nanopore (ONT) long-read data—using sequences from five Holstein cattle (two parent–offspring trios with a shared sire). This is the first cattle study to evaluate short- and long-read STR callers using both data types from the same animals. RESULTS: In short-read data, ExpansionHunter identified the highest number of polymorphic STRs (pSTRs) (327,690), followed by HipSTR (205,900) and GangSTR (110,680), with 93,023 loci detected by all three tools. In long-read data, LongTR detected 470,250 pSTRs, RepeatHMM 224,185, and Straglr 90,275, with only 33,253 loci shared among them. Mendelian consistency of STR genotypes in the trio offspring was high (> 0.8) for all short-read tools, with HipSTR and GangSTR highest at 0.98. LongTR was the only long-read tool with high consistency (0.88). Short-read tools also showed higher concordance in STR genotypes among themselves than was observed among long-read tools. However, long-read tools had a clear advantage in detecting large STRs. Relative to computational efficiency, HipSTR and GangSTR (short-reads), and LongTR (long-reads) required less memory and shorter runtimes than the other tools. CONCLUSIONS: Tool selection is critical for accurate whole-genome STR identification in cattle. For short-read data, HipSTR showed relatively high Mendelian consistency and concordance compared to the other tools, while ExpansionHunter was able to detect longer STRs but with lower Mendelian consistency. For long-read data, LongTR demonstrated higher consistency and computational efficiency relative to the other tools. Based on these results, HipSTR and LongTR are suggested as preferred options for short-read and ONT long-read datasets, respectively, in cattle STR analysis. These recommendations are based on the metrics observed in this study, and confirmatory analyses across additional breeds, larger sample sizes, and validated truth sets are encouraged.

Animals↗
PubMed1977

A comparison of the genetic and physical size of the streptomycin resistance locus in Pneumococcus.

Polyacrylamide gel electrophoresis of the 30S ribosomal proteins derived from six streptomycin resistant strains indicates that each mutation alters the same ribosomal protein (str-r protein). Preliminary data utilizing SDS gels indicates that the str-r protein has a molecular weight between 10,000 and 20,000 daltons. No significant differences could be detected between the molecular weight of the str-r protein when it is derived either from a sensitive or from a resistant strain, including those derived from strains carrying multisite mutations of different genetic size. We have estimated the size of the multisite str-r mutations to be less than 30 base pairs. Two factor crosses with str-r markers in the trans position demonstrate recombination frequencies expected of closely linked, intragenic markers although cotransfer frequencies, of these same markers from the cis position, are very low. It is concluded that the cotransfer frequencies represent a marker effect and possible explanations are discussed. A reinterpretation of the genetic map of the pneumococcal str-r locus is presented.

Bacterial Proteins↗
PubMed2026

[Empirical Classification of Tri-Allelic Genotype Cases and Parentage Index Calculation].

OBJECTIVES: To standardize the calculation method of the parentage index (PI) for short tandem repeat (STR) tri-allelic genotypes, thereby ensuring the accuracy and reliability of parentage tes‑ ting conclusions. METHODS: A systematic analysis of 160 real cases was conducted. A classification system was constructed based on the occurrence mechanisms and inheritance patterns of STR tri-alleles, and the PI calculation method was optimized by integrating previous research findings with empirical data. RESULTS: A mechanism-based classification system for STR tri-allelic genotypes was established, comprising Type I (2 subtypes), Type II (6 subtypes), and the trisomic type (2 subtypes). On this basis, a standardized PI calculation method covering all categories of STR tri-allelic genotypes was developed. CONCLUSIONS: This study provides methodological guidance for the scientific and standardized calculation of PI for STR tri-allelic genotypes and offers an important reference for the formulation and refinement of relevant industry standards.

Humans↗
PubMed2026

Application efficacy evaluation of the STRSeqTyper122 kit and the FASTASeq 300 second generation sequencer in kinship identification.

Forensic DNA technology is the method of choice for kinship identification. However, existing standard methods still have certain limitations in accurately determining the range of kinship relationships. China's independently developed second generation sequencing technology and equipment are expected to enhance the capability of forensic DNA kinship identification. In this study, we utilized the STRSeqTyper122 second generation sequencing STR typing kit and the FASTASeq 300 second generation sequencer to analyze 107 real kinship samples. The analysis included 63 autosomal STR loci, 42 Y-STR loci, 16 X-STR loci, and one gender-determining locus, Amel. The samples covered various kinship relationships, including 113 parent-child pairs, 48 full-sibling pairs, 76 uncle-nephew pairs, 66 grandparent-grandchild pairs, and 4 half-sibling pairs. Combined with simulated data, the ITO method was applied to calculate the cumulative likelihood ratio (CLR) for different levels of kinship based on the length polymorphism and sequence polymorphism of autosomal STR loci, systematically evaluating the practical application performance of this system in kinship identification. The results showed that, using log10CLR values of 4 and -4 as thresholds, the system achieved 100% efficiency in identifying real parent-child and full-sibling relationships. For second degree kinship identification, the system efficiency based on simulated length polymorphism data was 55.2%, while sequence polymorphism improved it to 75.11%. For real sample data, length polymorphism based efficiency was 54.45%, and sequence polymorphism based efficiency reached 76.71%. The findings indicate that the STRSeqTyper122 kit holds significant value in first degree kinship identification. Sequence polymorphism can improve second degree kinship identification efficiency to over 75%.

Humans↗
PubMed2026

An avuncular relationship generating a parent-offspring signal in forensic familial DNA searching: a case report.

In 2019, a series of vehicle burglaries occurred near the Dead Sea, Israel. DNA profiles obtained from six crime scenes were concordant, but no direct match was found in the national forensic DNA database. A CODIS familial search identified a male candidate as the highest-ranked potential relative. Pairwise kinship analysis based on 15 shared autosomal STR loci yielded the highest likelihood ratio under the parent-offspring (PO) hypothesis (LR = 530,300). However, Y-STR analysis performed in parallel with the familial search excluded a shared paternal lineage. Full mitochondrial genome sequencing subsequently demonstrated an identical haplotype, supporting a shared maternal lineage. Investigative inquiries identified a maternal uncle of the candidate whose reference STR profile fully matched the evidentiary profile.Population-based simulations of 100,000 second-degree relative pairs and 100,000 unrelated pairs showed that 2.05% of simulated second-degree pairs produced LRs equal to or greater than the observed second-degree LR (CODIS HS LR = 5,538), demonstrating that the observed similarity, although within the upper tail, remained within the expected second-degree distribution. In a retrospective expanded-marker analysis, increasing the shared autosomal STR loci from 15 to 20 excluded the PO hypothesis (LR = 0), while close-relationship hypotheses remained supported.This case illustrates how stochastic allele sharing across a limited number of autosomal STR loci can produce overlap between relationship categories and how additional markers can substantially alter relationship inference. Integrating sufficiently informative autosomal markers, lineage-specific markers, statistical evaluation, and investigative information is therefore important when interpreting familial DNA search results.

Autosomal STRs↗
PubMed2026

pSTRminer: integrated bioinformatic software for genome-wide identification and population-scale evaluation of polymorphic short tandem repeats.

Animal forensic genetics plays a critical role in criminal investigations by providing crucial evidence through domestic animal individualization and wildlife species identification. While human forensic genetics benefits from standardized short tandem repeats (STR) genotyping systems, animal forensic applications encounter significant challenges, including the limited availability of validated STR markers, the prevalence of error-prone dinucleotide STRs (di-STRs), and insufficient integration of population data. To address these challenges, we developed pSTRminer, an integrated bioinformatic tool that automates genome-wide STR mining and polymorphism evaluation. By applying pSTRminer to domestic cattle (Bos taurus), we identified 775,444 STRs de novo from the reference genome and genotyped them using whole-genome sequencing data from 60 Chinese and 111 African cattle to evaluate polymorphism across diverse genetic backgrounds. This led to the development of the cattle STR database (CSDB), comprising loci with a genotyping success rate&#x2009;&#x2265;&#x2009;40% and polymorphism information content (PIC)&#x2009;&#x2265;&#x2009;0.5. Experimental validation of 30 randomly selected tetranucleotide STRs (tetra-STRs) and 33 di-STRs via next-generation sequencing in a local Chinese cattle population (n&#x2009;=&#x2009;145) confirmed marker reliability. Although tetra-STRs had lower average polymorphism levels, they exhibited significantly lower stutter ratios (p&#x2009;<&#x2009;0.05), providing a viable path for identifying discriminative markers with fewer artifacts. Systematic screening revealed that certain tetra-STRs could surpass di-STRs in polymorphism. In conclusion, pSTRminer provides a scalable framework for developing standardized STR panels, facilitating the identification of robust and informative markers in forensic applications.

Bioinformatic software↗
PubMed1978

Use of pyruvate fermentation compared with tetrazolium reduction in the differentiation of group D streptococci.

The reduction of 2, 3, 5 triphenyltetrazolium chloride in the original medium of Barnes (Journal of General Microbiology, 14, 57, 1956), and in a modified medium, was compared with the ability to ferment pyruvate as a means of separating Streptococcus faecalis from all other group D streptococci. The tetrazolium reduction test gave an occasional negative reaction with Str. faecalis strains. In addition, a number of strains gave a weakly positive reaction in the test, as did some strains of Str. faecium and Str. bovis. With some batches of tetrazolium, these weak reactions with Str. faecalis were so frequent that interpretation of the results was difficult. On the other hand, all Str. faecalis strains, and no other group D streptococci, gave a positive pyruvate-fermentation reaction in 48 hours.

Bacteriological Techniques↗
PubMed2026

A novel relationship between time offsets in capillary electrophoresis and DNA sequence variations in short tandem repeats.

Next-generation sequencing (NGS) provides increased discriminatory power in forensic DNA analysis due to the detection of isoalleles. Differences in sequences between alleles allow for a second layer of differentiation between DNA contributors beyond the number of short tandem repeat (STR) repeat units. However, because NGS is a more time and resource-intensive analysis than conventional capillary electrophoresis (CE), laboratories may benefit from indicators that suggest NGS is likely to provide added value. This study examined whether CE migration offsets, measured as residuals in the OSIRIS analysis software, can differ significantly among STR isoalleles. Residuals represent the time offset between a sample allele peak and its corresponding allelic ladder peak. Paired CE and NGS data from 95 single source samples were analyzed for CE-based residual differences, as the NGS data provided the sequence information of the corresponding isoalleles. Residual values differed significantly among isoalleles at several STR loci. Statistically significant differences were identified at D16S539 and D3S1358, as well as at specific allele lengths within D12S391, D13S317, and D8S1179. These findings demonstrate that CE residual variation can reflect underlying STR sequence differences between contributors. In practice, residual-based metrics could help laboratories to identify casework reference samples where NGS is likely to provide additional discrimination, without the need for processing outside of a routine CE workflow. Due to the potentially large number of isoalleles, community wide efforts to aggregate CE residual differences versus isoallele sequences may be useful in the validation and implementation of this approach to add value to forensic DNA analyses.

Electrophoresis, Capillary↗
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

A rare and atypical case of long-distance indirect DNA transfer: Contamination from an investigator never present at the scene.

To maximize the usefulness of DNA obtained from biological samples in forensic genetics, it is crucial to avoid DNA contamination throughout all procedures, from sample collection at crime scenes to STR profile generation in DNA laboratories. This study reports a rare and atypical case of DNA contamination in a forensic setting. During the analysis of biological evidence from a cold case preserved for 18 years, the STR profile obtained from the surface of a plastic bag matched that of an investigator, identified through the DNA elimination database. Case reconstruction confirmed that the investigator-who was located 80&#x202f;km from the DNA laboratory and had never entered the crime scene or the sample storage room-was not a suspect and that the obtained STR profile originated from contamination. The most plausible explanation for the contamination was indirect transfer: investigator's DNA had adhered to a colleague's clothing and was subsequently dislodged and deposited onto the surface of the plastic bag as the colleague approached the sample pretreatment area. This study integrates trace DNA profiling of challenged samples with rapid contamination investigation and proposes prevention and control measures. This case underscores that, although DNA is widely regarded as the "gold standard" in forensic genetics, its interpretation must be considered within the context of the entire case. Conclusions should not be drawn based solely on a single DNA result.

Humans↗
PubMed1978

Lactostrepcins--acid bacteriocins produced by lactic streptococci.

All 47 non-nisin producing strains of Streptococcus lactis and 12/13 strains of Str. lactis subsp. diacetylactis examined produced bacteriocins, for which the term lactostrepcins is suggested. Seven strains of Str. cremoris examined produced no bacteriocins active against 3 lactic streptococci strains used as indicators. The strains examined were divided into 3 groups: I, those producing lactostrepcins active against only one streptomycin resistant mutant of Str. lactis 60 indicator strain; II, those producing lactostrepcins active against all 3 indicator strains; III, those not producing lactostrepcins active against the indicator strains employed. The lactostrepcins were sensitive to various proteolytic enzymes and to phospholipase D, but retained full or partial activity after dialysis. Most of the bacteriocins studied were fully active only within the pH range 4.2--5.0 and were reversibly inactivated at pH 7.0 or 8.0. Results suggested occurrence of 4 different lactostrepcins. The lactostrepcins produced by all group I strains were the same, but there were differences among the lactostrepcins produced by group II strains. Lactostrepcins killed some beta-haemolytic streptococci and some strains of Lactobacillus helveticus. One of the lactostrepcins was also active against certain Leuconostoc strains, but not against other Leuconostoc strains, nor against L. helveticus or other Gram-positive bacteria.

Bacteriocins↗
PubMed2026

Evaluation of bone preparation approaches using length-based analysis and targeted sequencing for forensic human identification of historic skeletal remains.

Advances in DNA technology have significantly enhanced the forensic community's ability to develop genetic profiles from unidentified human skeletal remains. However, sampling requires mechanical grinding of hard tissues before DNA isolation. This processing can compromise genetic profiles, particularly in aged bones. We compared the industry-standard pulverization method with an alternative powder-free preparation involving prolonged demineralization and subsequent slicing of 19th-century cortical bone. Data from DNA quantification, STR genotyping, and targeted SNP sequencing were used to evaluate powdered samples versus demineralized slices from paired human bones. Average human DNA yields for pulverized samples and demineralized slices were 0.032&#x2009;ng and 0.692&#x2009;ng, respectively. Demineralized slices recovered more amplifiable DNA than traditional homogenization methods (p&#x2009;<&#x2009;0.05). No pulverized samples produced STR profiles, whereas demineralized slices from the same bone samples yielded partial profiles. Samples underwent DNA repair, library preparation, and hybridization capture using the FORensic Capture Enrichment (FORCE) panel. Applying low-coverage (1X) analysis of high-throughput sequencing (HTS) data, demineralized slices outperformed those prepared by traditional pulverization methods (p&#x2009;<&#x2009;0.05) and substantially increased the information recovered compared with conventional STR analysis methods. Based on HTS data from pulverized samples, DNA fragment length ranged from 27 to 95&#x2009;bp, and FORCE SNP recovery was 33.23%. In contrast, for demineralized slices, DNA fragment length ranged from 85 to 114&#x2009;bp, and FORCE SNP recovery was 83.24%. The required reagents and equipment are typically available in forensic labs, and the workflow outlined herein significantly increases the success of DNA recovery from challenging skeletal samples.

Humans↗
PubMed2026

Invasive Wickerhamomyces anomalus Infections among Injecting Drug Users, France, 2012-20241.

Wickerhamomyces anomalus is a yeast rarely involved in human invasive fungal diseases (IFD). We retrospectively analyzed 44 episodes of W. anomalus IFD in France during 2012-2024. Injecting drug use (IDU) was the main risk factor among 26/35 (74.3%) incident cases. Most infections were community acquired; overall 3-month mortality rate was 1/30 (3.3%). Short tandem repeat (STR) genotyping and whole-genome sequencing analyses revealed substantial genetic diversity among isolates. However, 1 STR genotype was shared by 2 IDU patients, suggesting common exposure. In addition, 1 isolate obtained from a cotton filter used for drug preparation was identical by STR genotyping to the bloodstream isolate from the same patient, indicating direct inoculation via contaminated material or poor injection practices. Our findings highlight the increased risk for W. anomalus IFD among IDU patients and emphasize the importance of targeted preventive measures within that population.

Humans↗