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At least 1,207 records · Page 67Linked to original sources
PubMed2004

Genetic alterations in accelerated ageing syndromes. Do they play a role in natural ageing?

The molecular mechanisms leading to human senescence are still not known mostly because of the complexity of the process. Different research approaches are used to study ageing including studies of monogenic segmental progeroid syndromes. None of the known progerias represents true precocious ageing. Some of them, including Werner (WS), Bloom (BS), and Rothmund-Thomson syndromes (RTS) as well as combined xeroderma pigmentosa-Cockayne syndrome (XP-CS) are characterised by features resembling precocious ageing and the increased risk of malignant disease. Such phenotypes result from the mutations of the genes encoding proteins involved in the maintenance of genomic integrity, in most cases DNA helicases. Defective functioning of these proteins affects DNA repair, recombination, replication and transcription. Other segmental progeroid syndromes, such as Hutchinson-Gilford progeria (HGPS) and Cockayne syndrome are not associated with an increased risk of cancer. In this paper we present the clinical and molecular features of selected progeroid syndromes and describe the potential implications of these data for studies of ageing and cancer development.

Aging↗
PubMed2006

Amphiphilic porphyrin film on glass as a simple and selective solid-state chemosensor for aqueous Hg2+.

Deposition of amphiphilic porphyrin derivatives occurs spontaneously on silanised glass surfaces, in a controlled fashion. The resulting porphyrin films show appreciable fluorescence emission. This emission can be effectively quenched by immersion of the slides into a diluted solution of Hg(2+) (microM concentration). The initial intensity can be restored by washings with a solution of N,N,N',N'-tetrakis(2-pyridilmethyl)ethylenediammine with no loss of efficiency. A remarkable selectivity is featured toward the detection of Hg(2+) over Cu(2+), Cd(2+), Pb(2+) and Zn(2+) counterparts. This protocol can be extended to a flow-through apparatus. The presented results are of importance for the achievement of a solid-state chemosensor for mercuric ions, at micromolar concentration, in water.

Biosensing Techniques↗
PubMed2026

Machine learning-enabled multi-omics discovery of prognostic biomarkers and signaling targets in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains difficult to subtype using single omics layers. We conducted an exploratory investigation integrating reverse-phase protein array (RPPA) and DNA methylation data from the cancer genome atlas (TCGA)- pancreatic adenocarcinoma (PAAD) to assess the feasibility of multi-omics subtyping, alongside a supervised machine learning analysis of a small gene expression omnibus (GEO) transcriptomic cohort (n = 26) to identify candidate diagnostic genes. RPPA-based K-means clustering suggested a weak, possible two-subtype structure (silhouette ≈ 0.16) that remained unassociated with overall survival (log-rank p = 0.113) and lacked independent prognostic value. An independently performed similarity network fusion (SNF) analysis integrating RPPA and methylation data showed low concordance with RPPA-derived subtypes (Adjusted Rand Index (ARI) = 0.014), indicating limited convergence between molecular modalities. Supervised machine learning analysis of the GEO cohort using a fully nested leave-one-out cross-validation pipeline achieved a mean (area under the curve) AUC of 0.896 across four classifiers and identified four-fold-stable candidate genes (ESCO2, COL17A1, BCL2L14, and SOWAHB). However, this gene panel demonstrated limited external validity across two independent PDAC cohorts (log-rank p = 0.438 for both GSE62452 and GSE28735), indicating limited generalizability despite robust internal performance. Collectively, these findings provide limited evidence for a robust, prognostically significant multi-omics subtype or a validated diagnostic gene signature; instead, this study serves as a hypothesis-generating resource and highlights the importance of rigorous cross-validation and independent external validation in small-sample transcriptomic biomarker discovery.

Humans↗
PubMed2005

Tumour size is an important predictor for the outcome after liver transplantation for hepatocellular carcinoma.

AIMS: Recently, there is a tendency to expand tumour sizes qualifying for OLT. The present study re-evaluates tumour size and histopathological features as selection criteria for OLT. METHODS: Retrospective analysis of 93 adult HCC patients underwent OLT between June 1985 and December 2003. Median follow-up was 28 months (1-222 months). The Milan criteria were routinely applied since 1994. RESULTS: Five year survival rate of HCC patients was significantly lower than in patients transplanted for benign diseases, 41 and 71%, respectively (p<0.0001). Multivariate analysis revealed that the presence of vascular invasion represents the most significant predictor (p<0.001) affecting the survival rate. Survival was also significantly impaired when the tumour size was >5 cm (p<0.05), whereas the number of nodules had no significant effect on survival. Consequently, the survival rate for HCC fulfilling the Milan criteria histologically improved to 70% since 1994. CONCLUSION: Tumour size has been shown to be the most important pre-operatively detectable predictor for patient survival after OLT.

Adolescent↗
PubMed2005

Cell cycle and/or proliferation markers: what is the best method to discriminate cervical high-grade lesions?

The aim of this study on a series of biopsies diagnosed as normal, metaplastic, low-grade squamous intraepithelial lesions (LSILs), and high-grade squamous intraepithelial lesions (HSILs) was dual: to determine the chronology of cell cycle and proliferation abnormalities after human papillomavirus infection during the development of squamous intraepithelial lesions and to determine the best diagnostic indicator(s) linked to the appearance of an HSIL. Ninety-nine cervical biopsies, 18 normal, 9 with metaplastic changes, 29 LSIL, and 43 HSIL (23 cervical intraepithelial neoplasia 2 and 20 cervical intraepithelial neoplasia 3), were analyzed by image cytometry for DNA ploidy and p16INK4A determination, AgNOR counting, MIB-1, and ICBP90 immunostaining quantification. The human papillomavirus status had been previously determined on corresponding cytological smears with the Hybrid Capture II test. Suspect DNA profile and p16INK4A staining were the first significant events that preceded the increase of cell proliferation. Indeed, these markers were the best tests for the detection of a lesion, whatever its grade (positive predictive values of 90% and 100%, respectively). The presence of MIB-1- or ICBP90-positive cells in the upper two thirds of the epithelium was a very accurate feature to select HSIL (sensitivity, 100% for MIB-1) but with a low specificity. The sensitivity of a suspect DNA profile associated with a positive MIB-1 or ICPB90 immunostaining for the detection of an HSIL was, respectively, 92.8% and 92.7%; their specificities were 54.2% and 44%; their positive predictive values were 78% and 73%; their negative predictive values were 81.2% and 78.6%; and the global values were 78.8% and 74.3%. Thus, the most accurate test to distinguish an LSIL from an HSIL was the association of a suspect DNA profile and the presence of MIB-1- or ICBP90-positive cells in the upper two thirds of the epithelium.

Antibodies, Antinuclear↗
PubMed2026

Hierarchical modeling of tumor subtypes in cell lines using large-scale genomic datasets.

Cancer cell lines (CLs) are widely used to study tumor biology and drug response, yet their translational relevance is often limited by inaccurate subtype annotations. Existing CL-tumor matching approaches are frequently constrained by flat classification schemes, weak subtype definitions, and the exclusion of normal tissue references, leading to potential confounding of tumor-specific and tissue-of-origin signals. To address these limitations, a hierarchical classification (HC) framework is presented in which CLs are aligned with patient tumors across biological resolutions, from organ to molecular subtype. Gene expression profiles from 802 CLs, 5,612 tumors from The Cancer Genome Atlas (TCGA) , and 8,939 non-cancerous tissues were integrated to separate oncogenic signals from tissue-specific signals. Node-specific features were selected using maximum relevance minimum redundancy, and balanced accuracies of 89% in cross-validation and 75%, and 80% on external datasets were achieved. Through the framework, 43 CLs were reassigned, and clinically relevant underrepresented subtypes were identified.

cancer cell lines↗
PubMed2005

Selective identification and quantitative analysis of methionine containing peptides by charge derivatization and tandem mass spectrometry.

To enable the development of a tandem mass spectrometry (MS/MS) based methodology for selective protein identification and differential quantitative analysis, a novel derivatization strategy is proposed, based on the formation of a "fixed-charge" sulfonium ion on the side-chain of a methionine amino acid residue contained within a protein or peptide of interest. The gas-phase fragmentation behavior of these side chain fixed charge sulfonium ion containing peptides is observed to result in exclusive loss of the derivatized side chain and the formation of a single characteristic product ion, independently of charge state or amino acid composition. Thus, fixed charge containing peptide ions may be selectively identified from complex mixtures, for example, by selective neutral loss scan mode MS/MS methods. Further structural interrogation of identified peptide ions may be achieved by subjecting the characteristic MS/MS product ion to multistage MS/MS (MS3) in a quadrupole ion trap mass spectrometer, or by energy resolved "pseudo" MS3 in a triple quadrupole mass spectrometer. The general principles underlying this fixed charge derivatization approach are demonstrated here by MS/MS, MS3 and "pseudo" MS3 analysis of side chain fixed-charge sulfonium ion derivatives of peptides containing methionine formed by reaction with phenacylbromide. Incorporation of "light" and "heavy" isotopically encoded labels into the fixed-charge derivatives facilitates the application of this method to the quantitative analysis of differential protein expression, via measurement of the relative abundances of the neutral loss product ions generated by dissociation of the light and heavy labeled peptide ions. This approach, termed "selective extraction of labeled entities by charge derivatization and tandem mass spectrometry" (SELECT), thereby offers the potential for significantly improved sensitivity and selectivity for the identification and quantitative analysis of peptides or proteins containing selected structural features, without requirement for extensive fractionation or otherwise enrichment from a complex mixture prior to analysis.

Amino Acid Sequence↗
PubMed2004

beta2-microglobulin H31Y variant 3D structure highlights the protein natural propensity towards intermolecular aggregation.

beta2-Microglobulin (beta2m) is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). The natural turnover of MHC-I gives rise to the release of beta2m into plasmatic fluids and to its catabolism in the kidney. beta2m dissociation from the heavy chain of the complex is a severe complication in patients receiving prolonged hemodialysis. As a consequence of renal failure, the increasing beta2m concentrations can lead to deposition of the protein as amyloid fibrils. Here we characterize the His31-->Tyr human beta2m mutant, a non-natural form of beta2m that is more stable than the wild-type protein, displaying a ten-fold acceleration of the slow phase of folding. We report the 2.9A resolution crystal structure and the NMR characterization of the mutant beta2m, focussing on selected structural features and on the molecular packing observed in the crystals. Juxtaposition of the four mutant beta2m molecules contained in the crystal asymmetric unit, and specific hydrogen bonds, stabilize a compact protein assembly. Conformational heterogeneity of the four independent molecules, some of their mutual interactions and partial unpairing of the N-terminal beta-strand in one protomer are in keeping with the amyloidogenic properties displayed by the mutant beta2m.

Amino Acid Substitution↗
PubMed2025

Properties Governing Native State Entanglements and Relationships to Protein Function.

Non-covalent lasso entanglements are structural motifs found in a majority of globular proteins, and their misfolding has been linked to a range of biological consequences. Here, we characterize these motifs' structural and physicochemical properties, sequence biases, functional site correlations, and universal features across E. coli, S. cerevisiae, and H. sapiens. We find that the crossing residues, which pierce the plane of the entanglement loop, are 11-times more likely to be a &#x3b2;-strand than an &#x3b1;-helix or random coil, and that around this position the protein sequence is 2.5-times more likely to be composed of a stretch of all hydrophobic residues (most often Val, Ile, or Phe) compared to other sequence motifs. Functionally, crossing residues are enriched at enzyme active sites in S. cerevisiae and small molecule binding residues across all species to degrees greater than expected by random chance. Metal binding residues are enriched in these entanglements in H. sapiens. Increasing statistical power by pooling together these species data, we find RNA-binding residues are enriched in these entanglement components. On the other hand, there is a spatial depletion of crossing residues at sites involved in protein binding. Using machine learning, we identified eight robust features predictive of these entanglements, achieving AUROC scores of 0.8 across species. These results are significant because they suggest a direct role for components of native entanglements in particular protein functions, as well as identifying strong secondary structure and sequence preferences in native entanglements.

Humans↗
PubMed2007

Discovery of morphological subgroups that correlate with severity of symptoms in interstitial cystitis: a proposed biopsy classification system.

PURPOSE: We identified morphologically distinct subgroups in interstitial cystitis using cluster analysis and investigated the associations between cluster membership and urinary symptoms. MATERIALS AND METHODS: Of 637 patients enrolled in the Interstitial Cystitis Data Base Study 203 (32%) provided bladder biopsies at baseline screening, representing the focus of this analysis. A cluster analysis algorithm implemented in SAS PROC CLUSTER using standardized distances to measure the dissimilarity of each pair of patients with respect to select histopathological features was used to construct subgroups of these patients. Multivariate regression models for baseline nighttime and 24-hour voiding frequency, urinary urgency and pain were developed, incorporating indicator variables for cluster membership as predictors. Longitudinal urinary symptom profiles during 3 years of followup were also compared among the morphology clusters. RESULTS: Three morphology clusters were identified, corresponding to unique pathological groupings. In cluster C2 7 patients showed multiple pathological features of parenchymal damage, including several inflammatory features. In cluster C1 17 patients was characterized by complete denudation of the urothelium and variable edema. In cluster C0 in 179 patients none of the pathological features were present above the specified thresholds for C2. Cluster membership was significantly associated with baseline nighttime and 24-hour frequency (p <0.001, and with urinary urgency (p = 0.03). These significant increases in baseline symptom severity among clusters from C0 to C1 to C2 persisted throughout the 3 years of followup. CONCLUSIONS: These results suggest an important role for histopathological features in the predictive modeling of interstitial cystitis symptoms.

Adult↗
PubMed2004

De-novo design of complementary (antisense) peptide mini-receptor inhibitor of interleukin 18 (IL-18).

Complementary (antisense) peptide mini-receptor inhibitors are complementary peptides designed to be receptor-surrogates that act by binding to selected surface features of biologically important proteins thereby inhibiting protein-cognate receptor interactions and subsequent biological effects. Previously, we described a complementary peptide mini-receptor inhibitor of interleukin-1beta (IL-1beta) that was designed to bind to an external surface loop (beta-bulge) of IL-1beta (Boraschi loop) clearly identified in the X-ray crystal structure of this cytokine. Here, we report the de-novo design and rational development of a complementary peptide mini-receptor inhibitor of cytokine interleukin-18 (IL-18), a protein for which there is no known X-ray crystal structure. Using sequence homology comparisons with IL-1beta, putative IL-18 surface loops are identified and used as a starting point for design, including a loop region 1 thought to be equivalent with the Boraschi loop of IL-1beta. Only loop region 1 complementary peptides are found to be promising leads as mini-receptor inhibitors of IL-18 but these are prevented from being properly successful owing to solubility problems. The application of "M-I pair mutagenesis" and inclusion of a C-terminal arginine residue are then sufficient to solve this problem and convert one lead peptide into a functional complementary peptide mini-receptor inhibitor of IL-18. This suggests that the biophysical and biological properties of complementary peptides can be improved in a rational and logical manner where appropriate, further strengthening the potential importance of complementary peptides as inhibitors of protein-protein interactions, even when X-ray crystal structural information is not readily available.

Drug Design↗
PubMed2005

Computational and in vitro studies of persistent activity: edging towards cellular and synaptic mechanisms of working memory.

Persistent neural activity selective to features of an extinct stimulus has been identified as the neural correlate of working memory processes. The precise nature of the physiological substrate for this self-sustained activity is still unknown. In the last few years, this problem has gathered experimental together with computational neuroscientists in a quest to identify the cellular and network mechanisms involved. I introduce here the attractor theory framework within which current persistent activity computational models are built, and I then review the main physiological mechanisms that have been linked thereby to persistent activity and working memory. Open computational and physiological issues with these models are discussed, together with their potential experimental validation in current in vitro models of persistent activity.

Action Potentials↗
PubMed2004

Photodynamic therapy with verteporfin in ocular histoplasmosis: uncontrolled, open-label 2-year study.

OBJECTIVE: To evaluate the safety, effect on visual function, and fluorescein angiographic appearance of subfoveal choroidal neovascularization (CNV) through 2 years after photodynamic therapy with verteporfin (Visudyne; Novartis AG, Basel, Switzerland) in patients with ocular histoplasmosis syndrome (OHS). DESIGN: Open-label, 3-center, uncontrolled clinical study. PARTICIPANTS: Ocular histoplasmosis syndrome patients with subfoveal CNV (N = 26) with a greatest linear dimension no larger than 5400 microm with classic or occult CNV extending under the geometric center of the fovea, and best-corrected visual acuity letter score of approximately 20/40 to 20/200. METHODS: The methods were similar to those described in the 1-year results with follow-up examinations every 3 months continuing through the second year. During the second year, additional therapy was recommended if fluorescein angiography showed leakage at a scheduled visit. MAIN OUTCOME MEASUREMENTS: Visual function measurements included the changes from baseline in visual acuity and contrast sensitivity scores. Lesion size and leakage from classic and occult CNV were assessed at month 12 and month 24. Safety assessments also were made. RESULTS: A 24-month examination was completed in 22 of the 26 enrolled participants (85%). At the 24-month examination, median improvement from baseline in visual acuity of the 22 patients evaluated was 6 letters; median contrast sensitivity improved by 3.5 letters. At the 24-month examination, 10 patients (45%) gained 7 or more letters of visual acuity from baseline, whereas 4 patients (18%) lost 8 or more letters, including 2 patients (9%) who lost at least 15 letters. There was absence of fluorescein angiographic leakage from classic CNV in 17 of the 20 evaluable lesions (85%), and leakage from occult CNV was absent in all eyes. No serious ocular adverse events were reported, and no serious systemic event was considered to be associated with treatment. CONCLUSIONS: Median visual acuity improved and fluorescein angiographic leakage decreased after verteporfin therapy in this small, uncontrolled clinical study of patients with subfoveal CNV resulting from OHS. Verteporfin therapy seemed to be relatively safe in these patients. The selected cases feature fluorescein angiographic examples of CNV that are important in determining when to apply verteporfin therapy.

Adult↗
PubMedDate not supplied

Clinical features in the management of selected hypertensive emergencies.

A hypertensive emergency is a clinical diagnosis that is appropriate when marked hypertension is associated with acute target-organ damage; in this setting, lowering of blood pressure (BP) is typically begun within hours of diagnosis. For hypertensive urgency with no acute target-organ damage, BP lowering may occur over hours to days. A hypertensive emergency may present with cardiac, renal, neurologic, hemorrhagic, or obstetric manifestations, but prompt recognition of the condition and institution of rapidly acting parenteral therapy to lower BP (typically in an intensive care unit) are widely recommended. For aortic dissection, the systolic BP target is lower than 120 mm Hg, to be achieved during the first 20 minutes using a beta-blocker (typically esmolol) and a vasodilator to reduce both shear stress on the aortic tear and the BP, respectively. Otherwise, sodium nitroprusside is the agent with the lowest acquisition cost and longest record of successful use in hypertensive emergencies; however, it is metabolized to toxic thiocyanate and cyanide. Other attractive agents include fenoldopam mesylate, nicardipine, and labetalol; in pregnant women, magnesium and nifedipine are used commonly. Most authors suggest a reduction in mean arterial pressure of approximately 10% during the first hour and a further 10% to 15% during the next 2 to 4 hours; hypoperfusion can result if the BP is lowered too suddenly or too far (eg, into the range of <140/90 mm Hg). Oral antihypertensive therapy can usually be instituted after 6 to 12 hours of parenteral therapy, and the patient moved out of the intensive care unit, when consideration should be given to screening for secondary causes of hypertension. Long-term follow-up to ensure adequate control of hypertension is necessary to prevent further target-organ damage and recurrence of another hypertensive emergency.

Antihypertensive Agents↗
PubMed2024

Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts.

Chronic inflammation is a hallmark of age-related disease states. The effectiveness of inflammatory proteins including C-reactive protein (CRP) in assessing long-term inflammation is hindered by their phasic nature. DNA methylation (DNAm) signatures of CRP may act as more reliable markers of chronic inflammation. We show that inter-individual differences in DNAm capture 50% of the variance in circulating CRP (N&#xa0;= 17,936, Generation Scotland). We develop a series of DNAm predictors of CRP using state-of-the-art algorithms. An elastic-net-regression-based predictor outperformed competing methods and explained 18% of phenotypic variance in the Lothian Birth Cohort of 1936 (LBC1936) cohort, doubling that of existing DNAm predictors. DNAm predictors performed comparably in four additional test cohorts (Avon Longitudinal Study of Parents and Children, Health for Life in Singapore, Southall and Brent Revisited, and LBC1921), including for individuals of diverse genetic ancestry and different age groups. The best-performing predictor surpassed assay-measured CRP and a genetic score in its associations with 26 health outcomes. Our findings forge new avenues for assessing chronic low-grade inflammation in diverse populations.

Humans↗
PubMed2005

Role of poly(A) tail length in Alu retrotransposition.

Alu are mobile noncoding Short INterspersed Elements (SINEs) present at a million copies in the human genome. Using marked Alu sequences in an ex vivo assay, we previously showed that they are mobilized through diversion of the LINE (Long INterspersed Elements) retrotransposition machinery, with the poly(A) tail of the Alu being required for their mobility. Here we show that other homopolymeric tracts cannot functionally replace the Alu poly(A) tail, and that the Alu transposition rate varies over a two-log range depending on the poly(A) tail length. Variation is according to a sigmoid-shaped curve with a lag observed for tails shorter than 15 nt and a plateau reached for tails longer than 50 nt, consistent with the binding of a limited number of a protein component requiring multiple contacts for a productive interaction with the poly(A) stretch. This analysis indicates that most of the naturally occurring genomic Alu, owing to their pA tail length, should be poor substrates for the LINE machinery, a feature possibly "selected" for the host sake.

Alu Elements↗
PubMed1997

Physiologic responses to sensory stimulation by food: nutritional implications.

The importance of sensory factors (both the sensory properties of foods and sensory abilities of consumers) in food selection is widely accepted. Less recognized and understood are the effects of sensory stimulation on physiologic processes. Mere exposure to the sight, smell, taste, and textural attributes of foods elicits myriad digestive, endocrinologic, thermogenic. cardiovascular, and renal responses. The responses are rapid (generally occurring within minutes of sensory stimulation), small (relative to the magnitude achieved when food is actually being metabolized), and transient (returning to near-baseline levels within minutes). Nevertheless, they have been hypothesized to prime the body to better absorb and use ingested nutrients. They are termed preabsorptive or cephalic phase responses. This review summarizes current knowledge of stimuli that trigger cephalic phase responses and selected response features (eg, magnitude and type of enzymes or hormones released). Mechanisms by which cephalic phase responses may influence nutrient absorption and use are proposed. Current knowledge of the behavioral and physiologic importance of cephalic phase responses is limited, thereby hampering development of dietary recommendations for preventive or therapeutic interventions. Further study of several identified promising areas of application and other easily proposed situations may provide a basis for expanded medical nutrition therapy.

Animals↗
PubMedDate not supplied

Dysmorphology and mental retardation: molecular cytogenetic studies in dysmorphic mentally retarded patients.

In an institutionalised population of 471 mentally retarded adult residents (436 males and 35 females), 18 patients (16 males and 2 females) with dysmorphic features were selected to perform FISH studies by using subtelomeric probes to discover cryptic terminal deletions or duplications, undetectable with standard banding techniques. In the 13 investigated patients, no abnormalities were found with a selected battery of subtelomeric probes. The results of cryptic chromosomal rearrangement studies are variable but the frequency of positive diagnostic findings seems to be lower than previously expected.

Adolescent↗