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At least 19 recordsLinked to original sources
PubMed2026

Naturally Occurring CodY Variants Alter Ligand Binding, DNA Target Affinity, and Virulence in Clostridioides difficile.

Clostridioides difficile is an important nosocomial pathogen and is the major cause of antibiotic-associated diarrhea and colitis. CodY is a global transcriptional regulator that coordinates metabolism and virulence in Gram-positive pathogens by sensing branched-chain amino acids and GTP. In C. difficile, CodY represses toxin production by inhibiting transcription of tcdR and by influencing c-di-GMP turnover. Here, we characterized two naturally occurring CodY variants, CodY(Y146N) and CodY(V58A), whose substitutions lie near the GTP- and ILV-binding sites, respectively. GTP-binding by CodY(Y146N) was severely compromised, while leucine binding was enhanced; CodY(V58A) showed reduced leucine binding. Both variants exhibited reduced ligand-dependent binding to the tcdR promoter and failed to repress toxin production as effectively as CodY(WT). Expression of virulence-associated genes (tcdR, pdcB) was elevated in strains producing either variant. In a hamster infection model, both variant-producing strains were significantly more virulent than the CodY(WT) strain. These findings demonstrate that single amino acid substitutions in this global regulator can alter ligand affinity and promoter binding, potentially rewiring gene regulatory networks to enhance the pathogenic potential of C. difficile.

Clostridioides difficile↗
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

Staphylococcus aureus urease is controlled by a complex regulatory network to promote dissemination during CAUTI.

UNLABELLED: Catheter-associated urinary tract infections (CAUTIs) are one of the most common hospital-associated infections in the United States, accounting for >1 million cases annually. One CAUTI pathogen, Staphylococcus aureus, is commonly found persisting asymptomatically in the bladder of catheterized individuals, increasing these individuals' risk of developing infection. Importantly, S. aureus is not only associated with severe symptoms during CAUTI, including bacteremia and septic shock, but it also produces a common uropathogen-associated virulence factor, urease. Despite its importance, urease has only been well-studied in another uropathogen, Proteus mirabilis. While previous studies identified three S. aureus urease regulators, including CodY, CcpA, and Agr, the environmental signals required for expression and activity, and the enzyme's contribution to CAUTI have not been explored. In this study, we demonstrate that post-exponential growth and growth in the urinary tract environment significantly induce S. aureus urease expression and activity. Additionally, we identify SigB, SaeR, and SrrA as novel regulators of urease, and further explore the role of CodY, CcpA, and Agr-previously implicated in urease expression-in urease regulation in the urinary tract environment. Impactfully, we found that the urease promoters of clinical isolates contain genomic changes that enhance urease expression. Furthermore, urease contributes to biofilm formation under catheterized urinary tract-like conditions in vitro and dissemination from the bladder to the kidneys in a mouse CAUTI model. Together, our data not only provide insight into the regulatory pathway controlling S. aureus urease but also emphasize the importance of studying these mechanisms in a model that mimics the urinary environment. IMPORTANCE: In this study, we investigate how regulatory pathways coordinate the expression and activity of urease in response to environmental signals present within the catheterized urinary tract. We show that growth during the post-exponential phase and in conditions that mimic the urinary tract increases urease expression and activity. This finding challenges the dogma that Staphylococcus aureus is a "weak" urease producer. We also identified three novel regulators of S. aureus urease-SigB, SrrA, and SaeR-and show that their respective activation signals can modulate urease expression. Additionally, single-nucleotide changes identified in the urease regulatory pathway of clinical urinary catheter-associated isolates enhance urease expression. Finally, urease promotes biofilm formation under conditions that mimic the catheterized urinary tract and dissemination during catheter-associated urinary tract infections (CAUTIs). Our study provides insight into the complex regulatory mechanisms controlling urease in the urinary tract and highlights the role urease plays in S. aureus CAUTI.

Urease↗
PubMed1992

Does frequency-dependent selection optimize fitness?

In evolutionary biology, the axiom that natural selection tends ideally to maximize inclusive fitness of the individual or some other suitable quantity is often advanced (Cody, 1974; Maynard Smith, 1978; Krebs & McCleery, 1984; Houston et al., 1988). Moreover, the evolutionists generally distinguish two situations (Dawkins, 1980; Maynard Smith, 1982): one in which fitness is independent of the frequency of the phenotypes present in the population (frequency-independent selection), and one in which it does depend on this frequency (frequency-dependent selection). This led some authors such as Parker (1984), and more recently Parker & Maynard Smith (1990), to consider "a 2-speed optimization": frequency-independent selection should lead to a "simple optimum" at the end of the selective process, since all the individuals should have the same strategy and the mean fitness of the population should be maximized; frequency-dependent selection, formulated in terms of the theory of games, should lead to a "competitive optimum" even though the "evolutionary stable strategy" (or "ESS"; Maynard Smith & Price, 1973) characterizing the equilibrium "is not the strategy that maximizes fitness in a population sense" (Parker & Maynard Smith, 1990: 30). Our aim in this short communication is to criticize the concept of "competitive optimum" by Parker & Maynard Smith, as well as the general ability of natural selection to "maximize fitness", even in "phenotypic models" (Lloyd, 1977). These models, devoid of genetic constraints since each strategist is assumed to reproduce its own kind, are especially suitable for examining the ideal effect of natural selection.

Animals↗
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↗
PubMed2026

Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.

Recent advances in large language models have extended to genomic applications, yet model robustness relative to context is unclear. Here, we demonstrate two intrinsic biases (input sequence length and nucleotide position) affecting SegmentNT results, a model included with the Nucleotide Transformer that provides nucleotide-level predictions of biological features. We demonstrate that nucleotide position within the input sequence (beginning, middle, or end) alters the nature of SegmentNT's raw prediction probabilities, which can be standardized to improve prediction consistency. While longer input sequence length improves model performance, diminishing returns suggest a surprisingly small input length of ∼3072 nucleotides might be sufficient for many applications. We further identify a 24-nucleotide periodic oscillation in SegmentNT's prediction probabilities, revealing an intrinsic bias potentially linked to the model's training tokenization (6-mers) and architecture. We identify potential approaches to account for these biases and provide generalizable insights for utilizing nucleotide-resolution functional prediction models.

Nucleotides↗
PubMed1977

Stapedius reflex decay in myasthenia gravis.

Stapedius reflex decay, in response to a one-minute sound stimulus of 500 Hz occurred in six patients with myasthenia gravis. This decay is analagous to the decremental response of muscle action potentials to rapid nerve stimulation. Edrophonium chloride decreases the degree of decay. This represents a useful test in the diagnosis of myasthenia gravis.

Acoustic Stimulation↗
PubMed1992

Absolute configuration and conformation of the pure opioid antagonist (+)-2,9 alpha-dimethyl-5-(m-hydroxyphenyl)morphan.

(+)-2,9 alpha-Dimethyl-5-(m-hydroxyphenyl)morphan is the only phenylmorphan analog whose affinity for opioid kappa-receptors is greater than its affinity for opioid mu-receptors. Pharmacologically, the compound is a pure opioid antagonist devoid of agonist activity in in vivo assays of antinociception. The absolute configuration of the compound has been determined to be (1R,5S,9R) from an X-ray crystallographic study of the chloride salt. Thus, the absolute configuration corresponds to that of the atypical opioid agonist (-)-phenylmorphan while the weak atypical agonist (-)-2,9 alpha-dimethyl-5-(m- hydroxyphenyl)morphan corresponds to the potent morphine-like (+)-phenylmorphan. The preferred orientations of the phenyl ring for the two stereoisomers were determined using the molecular mechanics program MM2-87 and found to vary from that of the two parent compounds. The atypical properties of the two 9 alpha-methyl analogs is consistent with an opioid ligand model which proposes that morphine-like properties require a particular range of phenyl orientations. There was good agreement between the structure obtained from X-ray crystallography and computed with the MM2-87 program.

Chemical Phenomena↗
PubMed1979

Development of antinuclear antibodies during acebutolol therapy.

Eleven patients were studied while taking the beta blocker acebutolol for a period ranging from 12 to more than 24 wk. Control titers for fluorescent antinuclear antibody (ANA) were obtained in all. Serial testing was performed over the duration of the therapy and following its discontinuation. Additional immunologic testing was performed in most patients. The patients were observed closely for the development of clinical autoimmune disease. Using a sensitive assay, fluorescent ANA developed in 8 of 9 patients with negative values in the control period. In no patient has evidence of clinical autoimmune disease developed. In general, the titers of ANA tended to rise with increasing duration of therapy and decline after its discontinuation. Positive lupus erythematosus cell preparations were also observed in several patients. These data suggest that autoantibodies are frequently induced by acebutolol and, although no evidence of clinical autoimmune disease has been reported, immunologic surveillance is warranted.

Acebutolol↗
PubMed1992

Purification and crystallization of insecticidal delta-endotoxin CryIIIB2 from Bacillus thuringiensis.

CryIIIB2, an insecticidal protein from Bacillus thuringiensis has been crystallized from 0.6 M NaBr and HEPES buffer at pH 7.0 and X-ray diffraction data collected on a native crystal to 2.4 A. The insecticidal protein was obtained from a Bacillus thuringiensis (Bt) strain EG7231. Crystals of the endotoxin are orthorhombic, space group C2221, with unit cell dimensions of a = 122.44, b = 131.81, and c = 105.37 A. A unit cell contains one molecule of the 67,000 Da endotoxin per asymmetric unit.

Bacillus thuringiensis↗
PubMed1976

NMR-studies of triiodothyropropionic acid in ethanol-HCl.

The barrier to rotation in the N-acetyl methyl ester of the thyroxine was found to be 8.6 kcal mol-1. Previous experiments determining the barrier to rotation in triiodothyropropionic acid in HCl-ethanol were shown to be in error.

Ethanol↗
PubMedDate not supplied

Phenotypic differences between Syrian hamster embryo cells cultured at pH 6.7 or 7.3.

We have investigated the molecular phenotypic differences between Syrian hamster embryo (SHE) cells cultured at pH 6.7 or 7.3. Multiple pH-sensitive phenotypic differences were noted including changes in cellular morphology, a unique charge differential in a major cellular protein, nine uniquely expressed proteins, two unique phosphoserine/threonine phosphoproteins, one unique phosphotyrosine phosphoprotein, and the pH dependent mRNA level of a gap junctional gene (connexin 43). These differences, combined with previously described pH-specific differences (differential transformation rates and gap junctional communication), illustrate that culturing SHE cells in media that differ by 0.6 pH units (0.3 units on either side of pH 7.0) can have a profound influence on the cellular phenotype.

Animals↗
PubMed1991

Exercise-induced secretion of atrial natriuretic factor and its relation to hemodynamic and sympathetic stimulation in untreated essential hypertension.

This study evaluates the release of atrial natriuretic factor (ANF) during maximal exercise in 7 patients with untreated moderate to severe hypertension with invasive monitoring of hemodynamic characteristics in relation to sympathetic activity. Peripheral venous ANF (fmol/ml) was determined at rest and maximal exercise producing a respiratory exchange ratio of 1.14 +/- 0.10. In 5 of 7 patients, simultaneous right ventricular and peripheral venous ANF samples could be obtained to assess exercise myocardial secretion of ANF. With exercise, mean blood pressure increased from 150 +/- 26 to 192 +/- 29 mm Hg (p less than 0.001), pulmonary wedge pressure increased from 7 +/- 3 to 18 +/- 10 mm Hg (p less than 0.05) and ANF increased from 11.7 +/- 8.2 to 25.7 +/- 15.9 (p less than 0.02). This ANF response correlated weakly with pulmonary wedge pressure (r = 0.497, p = not significant), since patients without an increase in pulmonary wedge pressure had no increase in ANF. However, changes in pulmonary wedge pressure and plasma norepinephrine during exercise were inversely correlated (r = -0.811, p less than 0.02), with the greatest increase in norepinephrine occurring with a minimal increase in pulmonary wedge pressure. Similarly, ANF and plasma norepinephrine were inversely correlated during exercise (r = -0.869, p less than 0.05). A significant increase in right ventricular ANF indicated myocardial secretion. Plasma ANF therefore increased because of active myocardial production during exercise in patients with moderate to severe hypertension. These findings further suggest a directionally opposing relation between ANF release resulting from increased atrial tension and sympathetic nervous system influence on cardiac performance during exercise.

Adult↗
PubMed1992

Maintenance of forearm vasodilator action of atrial natriuretic factor in congestive heart failure secondary to ischemic or idiopathic dilated cardiomyopathy.

Infusions of atrial natriuretic factor (ANF) are frequently associated with attenuated natriuretic and diuretic responses in patients with congestive heart failure. However, ANF infusions result in systemic vasodilation, suggesting that end organ responsiveness to ANF may not be uniformly decreased. To determine if the vasodilator effects of ANF were altered in heart failure, strain-gauge plethysmography was utilized to measure forearm blood flow responses to the intraarterial infusion of ANF using a dose range that was low enough to avoid systemic effects. In 9 control subjects, ANF infusions of 0.5, 1.0, 2.0 and 4.0 micrograms/min/100 ml forearm volume significantly increased forearm blood flow from 3.21 +/- 1.71 to 5.69 +/- 3.14, 6.20 +/- 2.57, 6.64 +/- 2.53 and 6.97 +/- 2.49 ml/min/100 ml forearm volume, respectively (all p less than 0.01). In 7 patients with heart failure, ANF infusion significantly increased forearm blood flow from 2.19 +/- 0.98 to 3.18 +/- 1.70, 3.76 +/- 2.0 and 4.42 +/- 2.80 ml/min/100 ml forearm volume for the 0.5, 1.0 and 2.0 micrograms doses, respectively (all p less than 0.05). By analysis of variance, the forearm blood flow responses pooled over all doses were not significantly different between the 2 groups. At the 2.0 micrograms dose, the peak increase in forearm blood flow in normal subjects represented a 107% increase over baseline compared with a 102% increase in patients with heart failure. In summary, these data demonstrate that intraarterial administration of ANF in patients with heart failure resulted in dose-related increases in forearm blood flow. The responses were not significantly different from normal subjects expressed both as an absolute response and as a percent increase.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗
PubMed1992

Management of refractory congestive heart failure.

Despite recent advances in the treatment of congestive heart failure (CHF), many patients continue to present with symptoms refractory to digoxin, diuretic, and vasodilatory therapy. Since it is unlikely that this population will decrease in the near future, practical approaches to management of refractory CHF are reviewed. Refractory CHF here is defined as New York Heart Association (NYHA) functional class III-IV heart failure, despite maximal drug therapy. Before such a diagnosis is made, the patient should be treated with digoxin, diuretics, and a vasodilator. Approach to therapy requires assessment of changing clinical status and pathophysiology, optimizing oral drug treatment, and providing temporary parenteral support when indicated. Specific attention should be given to factors that influence the optimal response to each of these 3 treatment classes. A theoretical, but unproven, concept suggests that combined vasodilatory therapy may be appropriate as long as excessive hypotension is avoided. In the course of management, a decision is required as to whether further optimization of therapy can be achieved on an outpatient basis. Hospital-based intravenous inotropic support given for 2-4 days will often provide the opportunity to restructure patient therapy.

Administration, Oral↗
PubMed1992

Cellulitis after axillary lymph node dissection for carcinoma of the breast.

We present a series of patients who developed cellulitis following axillary lymph node dissection for carcinoma of the breast. Bacterial cultures were not helpful in making a diagnosis for the majority of the cases. The clinical scenario of upper extremity cellulitis after axillary dissection mimics the presentation of cellulitis in the lower extremity. Until diagnostic methods or treatment advances can eliminate the indications for axillary lymphadenectomy, many women treated for breast cancer will be at long-term risk for the development of cellulitis due to localized immune impairment. Patient and physician awareness of this syndrome is the best available tool to prevent secondary exacerbation of lymphedema. Prompt treatment with appropriate antibiotics appears universally successful. Antistreptococcal antibiotics should not be withheld pending results of blood or tissue cultures, since in only a few cases will a pathogen be isolated. Although there are no studies confirming the concept, it is likely that appropriate treatment for lymphedema may reduce the risk of infection.

Adult↗