Naturalistic Bladder Filling Reveals Subtypes in Overactive Bladder Syndrome That Differentially Engages Urinary Urgency-Related Brain Circuits: Results From the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN)

PURPOSE

Overactive bladder (OAB) may be attributed to dysfunction in supraspinal brain circuits. Overactive bladder participants enrolled in the LURN (Symptoms of Lower Urinary Tract Dysfunction Research Network) study reported sensations of urinary urgency during a bladder-filling paradigm while undergoing brain functional MRI to map supraspinal dysfunction.

MATERIALS AND METHODS

OAB participants and controls (CONs) completed 2 resting-state functional MRI scans following consumption of 350 mL water. Scans were conducted at fuller and emptier bladder states, interleaved with voiding. Urgency ratings (0-10) were assessed. Patterns of urgency during bladder filling were investigated using latent class trajectory models. Clusters of participants encompassing each pattern (ie, subtype) were derived from aggregated groups of OAB and CON independent of diagnosis.

RESULTS

Two distinct patterns of urgency trajectories were revealed: first subtype with OAB and CON who were unresponsive to bladder filling (OAB-1 and CON-1) and second highly responsive subtype predominantly containing OAB (OAB-2). OAB-2 participants scored significantly higher on urinary symptoms but not pain or psychosocial measures. Neuroimaging analyses showed change in urgency due to both bladder filling and voided volume related to multiple loci of brain network connectivity in OAB-2, and in some cases, different than OAB-1 and/or CON-1. Sensorimotor to dorsomedial/dorsolateral prefrontal connectivity mediated the relationship between stimulus (voided volume) and percept (urgency) in OAB-2.

CONCLUSIONS

Our results reveal different OAB subtypes with latent class trajectory models of urgency ratings during natural bladder filling. Functional MRI revealed differences in pathophysiology between subtypes, namely sensorimotor-prefrontal connectivity is a key locus in OAB patients with higher urinary symptoms.

Dynamic analysis of the individual patterns of intakes, voids, and bladder sensations reported in bladder diaries collected in the LURN study

The goal of this study was to develop the novel analytical approach and to perform an in-depth dynamic analysis of individual bladder diaries to inform which behavioral modifications would best reduce lower urinary tract symptoms, such as frequency and urgency. Three-day bladder diaries containing data on timing, volumes, and types of fluid intake, as well as timing, volumes, and bladder sensation at voids were analyzed for 197 participants with lower urinary tract symptoms. A novel dynamic analytic approach to bladder diary time series data was proposed and developed, including intra-subject correlations between time-varying variables: rates of intake, bladder filling rate, and urge growth rate. Grey-box models of bladder filling rate and multivariable linear regression models of urge growth rate were developed for individual diaries. These models revealed that bladder filling rate, rather than urine volume, was the primary determinant of urinary frequency and urgency growth rate in the majority of participants. Simulations performed with the developed models predicted that the most beneficial behavioral modifications to reduce the number of urgency episodes are those that smooth profiles of bladder filling rate, which might include behaviors such as exclusion of caffeine and alcohol and/or other measures, e.g., increasing number and decreasing volumes of intakes.

Dynamic analysis of the individual patterns of intakes, voids, and bladder sensations reported in bladder diaries collected in the LURN study

The goal of this study was to perform an in-depth dynamic analysis of individual bladder diaries to inform which behavioral modifications would best reduce lower urinary tract symptoms, such as frequency and urgency. Three-day bladder diaries containing data on timing, volumes, and types of fluid intake, as well as timing, volumes, and bladder sensation at voids were analyzed for 197 participants with lower urinary tract symptoms. A novel dynamic analytic approach to bladder diary time series data was proposed and developed, including intra-subject correlations between time-varying variables: rates of intake, bladder filling rate, and urge growth rate. Grey-box models of bladder filling rate and multivariable linear regression models of urge growth rate were developed for individual diaries. These models revealed that bladder filling rate, rather than urine volume, was the primary determinant of urinary frequency and urgency growth rate in the majority of participants. Simulations performed with the developed models predicted that the most beneficial behavioral modifications to reduce the number of urgency episodes are those that smooth profiles of bladder filling rate, which might include behaviors such as exclusion of caffeine and alcohol and/or other measures, e.g., increasing number and decreasing volumes of intakes.

Sublimation Enthalpies of Substituted Pyridine N-Oxides

The enthalpies of sublimation of five substituted pyridine N-oxides were determined by the Knudsen effusion method with mass spectrometric control of the vapor composition within the framework of the second law of thermodynamics. The sublimation enthalpy of mono-substituted compounds 4-X-PyO depends on the nature of the substituent X and increases in the order CH₃→NO₂→OCH₃. A difference is noted in the nature of dissociative ionization of disubstituted derivatives 2-CH₃-4-NO₂PyO and 3-CH₃-4-NO₂PyO. The relationship between the packing of molecules in crystals and the ΔH°_subl values is considered.

Symptom Based Clustering of Men in the LURN Observational Cohort Study

PURPOSE

Conventional classification of patients with lower urinary tract symptoms into diagnostic categories based on a predefined symptom complex or predominant symptom appears inadequate. This is due to the frequent presentation of patients with multiple urinary symptoms which could not be perfectly categorized into traditional diagnostic groups. We used a novel clustering method to identify subtypes of male patients with lower urinary tract symptoms based on detailed multisymptom information.

MATERIALS AND METHODS

We analyzed baseline data on 503 care seeking men in the LURN (Symptoms of Lower Urinary Tract Dysfunction Research Network) Observational Cohort Study. Symptoms and symptom severity were assessed using the LUTS (Lower Urinary Tract Symptoms) Tool and the AUA SI (American Urological Association Symptom Index), which include a total of 52 questions. We used a resampling based consensus clustering algorithm to identify patient subtypes with distinct symptom signatures.

RESULTS

Four distinct symptom clusters were identified. The 166 patients in cluster M1 had predominant symptoms of frequency, nocturia, hesitancy, straining, weak stream, intermittency and incomplete bladder emptying suggestive of bladder outlet obstruction. The 93 patients in cluster M2 mainly endorsed post-micturition symptoms (eg post-void dribbling and post-void leakage) with some weak stream. The 114 patients in cluster M3 reported mostly urinary frequency without incontinence. The 130 patients in cluster M4 reported severe frequency, urgency and urgency incontinence. Most other urinary symptoms statistically differed between cluster pairs. Patient reported outcomes of bowel symptoms, mental health, sleep dysfunction, erectile function and urological pain significantly differed across the clusters.

CONCLUSIONS

We identified 4 data derived clusters among men seeking care for lower urinary tract symptoms. The clusters differed from traditional diagnostic categories. Further subtype refinement will be done to incorporate clinical data and nonurinary patient reported outcomes.

Longitudinal changes in symptom-based female and male LUTS clusters

AIMS

Lower urinary tract symptoms (LUTS) are diverse in type and variable in severity. We examined symptom change within the Symptoms of the Lower Urinary Tract Dysfunction Research Network (LURN) Observational Cohort study identified clusters over time and tested associations with treatments received.

METHODS

Patient-reported LUTS and treatment data were collected at multiple time points between baseline and 12 months from the LURN Observational Cohort study. LUTS severity scores were calculated to summarize changes in symptom reporting over time in previously identified LURN clusters. Repeated measures linear regression models tested adjusted associations between cluster membership and severity scores.

RESULTS

Four-hundred seventeen men and 396 women were classified into improved, unchanged, and worsened symptoms between baseline and 12 months (men: 44.1%, 40.5%, and 15.3%; women: 55.8%, 33.1%, 11.1%, respectively). Improvement in LUTS severity scores varied by cluster (estimated adjusted mean change from baseline range: -.04 change in standard deviations of severity scores (ΔSD) to -.67 ΔSD). Prostate surgery was associated with improved severity scores (-.63 ΔSD) in men, while stress incontinence surgery was associated with improved severity scores (-.88 ΔSD) in women.

CONCLUSION

Symptom improvement varied by cluster indicating response to therapy differs amongst subtypes of patients with LUTS. The differential improvement of patients in clusters suggests mechanistic differences between clusters and may aid in selecting more targeted treatments in the future.

Clustering of the structures by using "snakes-&-dragons" approach, or correlation matrix as a signal

Biological, ecological, social, and technological systems are complex structures with multiple interacting parts, often represented by networks. Correlation matrices describing interdependency of the variables in such structures provide key information for comparison and classification of such systems. Classification based on correlation matrices could supplement or improve classification based on variable values, since the former reveals similarities in system structures, while the latter relies on the similarities in system states. Importantly, this approach of clustering correlation matrices is different from clustering elements of the correlation matrices, because our goal is to compare and cluster multiple networks-not the nodes within the networks. A novel approach for clustering correlation matrices, named "snakes-&-dragons," is introduced and illustrated by examples from neuroscience, human microbiome, and macroeconomics.

The Distribution of Post-Void Residual Volumes in People Seeking Care in the Symptoms of Lower Urinary Tract Dysfunction Network Observational Cohort Study With Comparison to Asymptomatic Populations

OBJECTIVE

To describe the distribution of post-void residual (PVR) volumes across patients with and without lower urinary tract symptoms (LUTS) and examine relationships between self-reported voiding symptoms, storage symptoms, and PVR.

METHODS

PVR and demographic data were obtained from the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) observational cohort study. Self-reported symptoms were collected using the American Urological Association Symptom Index and the LUTS Tool. PVR values were obtained from 2 other cohorts: living kidney donors with unknown LUTS from the Renal and Lung Living Donors Evaluation Study (RELIVE), and continent women in the Establishing the Prevalence of Incontinence (EPI) study, a population-based study of racial differences in urinary incontinence prevalence.

RESULTS

Across the 3 studies, median PVRs were similar: 26 mL in LURN (n = 880, range 0-932 mL), 20 mL in EPI (n = 166, range 0-400 mL), and 14 mL in RELIVE (n = 191, range 0-352 mL). In LURN, males had 3.6 times higher odds of having PVR > 200 mL (95% CI = 1.72-7.48). In RELIVE, median PVR was significantly higher for males (20 mL vs 0 mL, P= .004). Among women, only the intermittency severity rating was associated with a probability of an elevated PVR. Among men, incomplete emptying and burning severity rating were associated with a higher odds of elevated PVR, but urgency severity ratings were associated with lower odds of elevated PVR.

CONCLUSION

Care-seeking patients have PVRs similar to those in people with unknown history of LUTS (RELIVE) and without self-reported LUTS (EPI). Although PVR was correlated with voiding symptoms, the mean differences only explain ∼2% of the variance.

Are three-day voiding diaries feasible and reliable? Results from the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) cohort

AIMS

The aims of this study were to assess the completeness of voiding diaries in a research context and to correlate diary data with patient-reported questionnaires.

METHODS

Men and women enrolled in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) were given a 3-day voiding and fluid-intake diary to fill-out. Diaries were assessed for completeness and intake-output imbalances. They were assigned to one of four categories based on a percentage of missing data and fluid imbalance: no diary submitted, unusable (>40% missing void or intake volumes, or unphysiological fluid imbalance), usable but not complete, and complete.

RESULTS

A total of 1064 participants were enrolled and 85% (n = 902) returned the bladder diary. Of the diaries returned, 94% (n = 845) had data on three separate days, 87% (n = 786) had no missing intake volumes, 61% (n = 547) had no missing voided volumes, and 70% (n = 635) had a fluid imbalance within 3 L across the 3-day time period, resulting in 50% (n = 448) of participants with 100% complete diaries. Younger age was associated with a higher likelihood of not submitting a diary, or submitting an unusable diary. Women had a higher likelihood of submitting an unusable diary or a usable but incomplete diary.

CONCLUSION

Overall, 50% of LURN participants returned voiding diaries with perfectly complete data. Incomplete data for voided volumes was the most common deficiency. There was only a moderate correlation between diary data and questionnaire responses, indicating that diaries are a source of unique information.

A Novel Proteomics Approach to Identify Serum and Urinary Biomarkers and Pathways that Associate with Lower Urinary Tract Symptoms in Men and Women: Pilot Results of the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) Study

OBJECTIVES

To assess the feasibility of a novel proteomics approach to identify biomarkers associated with lower urinary tract symptoms (LUTS) within serum and urine, because many clinical factors contribute to LUTS in men and women. These factors confound clinicians' abilities to reliably evaluate and treat LUTS. Previous studies identified candidate LUTS biomarkers, but none are clinically utilized.

METHODS

Eighteen male and 18 female symptoms of lower urinary tract dysfunction research network (LURN) observational cohort study participants with LUTS (measured on the LUTS Tool questionnaire) were randomly selected. Twelve male and 12 female controls with minimal or no LUTS were recruited and matched for clinico-demographic characteristics. The SomaScan Assay (SomaLogic) was used to measure the abundance of 1305 proteins contained within urine and serum. Statistical analyses were performed to evaluate reproducibility of assays, compare protein abundances, and estimate effect size.

RESULTS

SomaScan assay results were more reproducible in serum than in urine. Within serum, there were many more differentially abundant proteins between cases and controls in males than in females. An enrichment/pathway analysis of the affected proteins in male and female subjects demonstrated that the enriched Gene Ontology processes were related to prostate morphogenesis in men and growth and inflammation in women.

CONCLUSION

The pilot study results support that the etiology and pathophysiologic mechanisms underlying LUTS may be sex-specific. While further studies involving larger numbers of subjects are warranted, our results support the feasibility of a novel proteomic approach to identify biomarkers for diagnostic classification of LUTS.

Accelerated coronary atherosclerosis not explained by traditional risk factors in 13% of young individuals

IMPORTANCE

Most individuals who die of sudden cardiac death (SCD) display very advanced lesions of atherosclerosis in their coronary arteries. Thus, we sought to identify and characterize a putative subpopulation of young individuals exhibiting accelerated coronary artery atherosclerosis.

OBJECTIVE

Our analysis of the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study-which examined 2651 individuals, obtaining quantitative measurements of traditional risk factors for coronary heart disease (CHD)-aimed to identify individuals with advanced coronary artery lesions, and to determine whether risk factors could account for such rapid disease progression, or not.

DESIGN

Using the cross-sectional PDAY study data, an exploratory de facto analysis stratified the population by age and observed number of coronary raised lesions and examined these groups via Poisson regression modeling. A separate de novo approach utilized Poisson mixture modeling to generate low- and high-growth groups based on measurements of traditional risk factors, and identified factors contributing to disease progression.

PARTICIPANTS

Participants, n = 2651 individuals aged 15-34, who had died of non-cardiac death, were recruited post mortem. Tissues and other samples were harvested for analysis (details in previously published PDAY studies). Main Outcome(s) and Measure(s). Using quantitative measurements of raised coronary lesions and traditional risk factors of CHD, we sought to identify which risk factors account for disease progression.

RESULTS

A group of ~13% of the PDAY population exhibits accelerated coronary atherosclerosis despite their young age. Several traditional risk factors were associated with increased odds of inclusion in this subgroup, reflecting current understanding of these markers of disease. However, only age was a significant contributing factor to the observed coronary lesion burden.

CONCLUSIONS

While a range of traditional risk factors contribute to an individual's inclusion to the identified subgroup with accelerated atherosclerosis, these factors, with the exceptions of age, are not able to predict an individual's lesion burden. Moreover, unattributed variances in observations indicate the need to study novel risk factors.

SHORT SUMMARY

Hypothesis The extent of coronary atherosclerotic disease is limited and homogeneous within youth, and its progression can be accounted for by traditional risk factors in this population.

FINDINGS

A subpopulation (~13%) of the Pathobiological Determinants of Atherosclerosis in Youth cohort exhibited accelerated coronary artery atherosclerosis. While several traditional risk factors contribute to an individual's inclusion in this subgroup, these factors, with the exceptions of age, do not predict accurately an individual's lesions burden. Critically, unattributed variances in observations indicate the need for the identification of novel risk factors.

MEANING

Screening of the general population at a young age for high-risk group membership could provide opportunity for disease prevention and avoidance of the worse complications such as myocardial infarction and sudden cardiac death later in life.

Symptom Based Clustering of Women in the LURN Observational Cohort Study

PURPOSE

Women with lower urinary tract symptoms are often diagnosed based on a predefined symptom complex or a predominant symptom. There are many limitations to this paradigm as often patients present with multiple urinary symptoms which do not perfectly fit the preestablished diagnoses. We used cluster analysis to identify novel, symptom based subtypes of women with lower urinary tract symptoms.

MATERIALS AND METHODS

We analyzed baseline urinary symptom questionnaire data obtained from 545 care seeking female participants enrolled in the LURN (Symptoms of Lower Urinary Tract Dysfunction Research Network) Observational Cohort Study. Symptoms were measured with the LUTS (lower urinary tract symptoms) Tool and the AUA SI (American Urological Association Symptom Index), and analyzed using a probability based consensus clustering algorithm.

RESULTS

Four clusters were identified. The 138 women in cluster F1 did not report incontinence but experienced post-void dribbling, frequency and voiding symptoms. The 80 women in cluster F2 reported urgency incontinence as well as urgency and frequency but minimal voiding symptoms or stress incontinence. Cluster F3 included 244 women who reported all types of incontinence, urgency, frequency and mild voiding symptoms. The 83 women in cluster F4 reported all lower urinary tract symptoms at uniformly high levels. All but 2 of 44 LUTS Tool and 8 AUA SI questions significantly differed between at least 2 clusters (p <0.05). All clusters contained at least 1 member from each conventional group, including continence, and stress, urgency, mixed and other incontinence.

CONCLUSIONS

Women seeking care for lower urinary tract symptoms cluster into 4 distinct symptom groups which differ from conventional clinical diagnostic groups. Further validation is needed to determine whether management improves using this new classification.

The LURN Research Network Neuroimaging and Sensory Testing (NIST) Study: Design, protocols, and operations

The Neuroimaging and Sensory Testing (NIST) Study of the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) is a cross-sectional, case-control study designed to investigate whether disrupted brain connectivity and sensory processing are associated with abnormal lower urinary tract symptoms (LUTS) in patients with overactive bladder syndrome (OAB). The NIST Study tests the hypotheses that patients with urinary urgency will demonstrate: (1) abnormal functional and structural connectivity of brain regions involved in urinary sensation on magnetic resonance imaging (MRI), and (2) hypersensitivity to painful (pressure) and non-painful (auditory) sensory stimuli on quantitative sensory testing (QST), compared to controls. Male and female adults (18 years or older) who present at one of the six participating LURN clinical centers for clinical care of their LUTS, with symptoms of urinary urgency with or without urgency urinary incontinence, are eligible to participate. The NIST Study is the largest MRI and QST study of its kind, yielding a neuroimaging and sensory testing dataset unprecedented in OAB research. Advanced multi-modal techniques are used to understand brain functional and structural connectivity, including gray matter volume, and sensory function. Unlike previous MRI studies which involved invasive catheterization and repeated cycles of non-physiologic bladder filling and emptying via a catheter, we use a water ingestion protocol to mimic more physiological bladder filling through natural diuresis. Furthermore, these data will be used in concert with other phenotyping data to improve our understanding of clinically meaningful subtypes of patients with LUTS in order to improve patient care and management outcomes.

Baseline Lower Urinary Tract Symptoms in Patients Enrolled in LURN: A Prospective, Observational Cohort Study

PURPOSE

We described and compared the frequency and type of lower urinary tract symptoms reported by men and women at the time that they were recruited from urology and urogynecology clinics into the Symptoms of Lower Urinary Tract Dysfunction Research Network multicenter, prospective, observational cohort study.

MATERIALS AND METHODS

At 6 research sites treatment seeking men and women were enrolled who reported any lower urinary tract symptoms at a frequency more than rarely during the last month on the LUTS (Lower Urinary Tract Symptoms) Tool. At baseline the study participants underwent a standardized clinical evaluation and completed validated questionnaires. Urological tests were performed, including pelvic/rectal examination, post-void residual urine measurement and urinalysis.

RESULTS

A total of 545 women and 519 men were enrolled in the study. Mean ± SD age was 58.8 ± 14.1 years. At baseline nocturia, frequency and a sensation of incomplete emptying were similar in men and women but men experienced more voiding symptoms (90% vs 85%, p = 0.007) and women reported more urgency (85% vs 66%, p <0.001). Women also reported more of any type of urinary incontinence than men (82% vs 51% p <0.001), which was mixed incontinence in 57%. Only 1% of men reported stress incontinence but they had other urinary incontinence, including post-void dribbling in 44% and urgency incontinence in 46%. Older participants had higher odds of reporting symptoms of nocturia and urgency.

CONCLUSIONS

In this large, treatment seeking cohort of men and women lower urinary tract symptoms varied widely by gender and age. Men reported more voiding symptoms and nonstress or urgency urinary incontinence while women reported more incontinence overall and urgency. Older participants had greater odds of urgency and nocturia.

Misclassification Errors in Unsupervised Classification Methods. Comparison Based on the Simulation of Targeted Proteomics Data

Unsupervised classification methods are gaining acceptance in omics studies of complex common diseases, which are often vaguely defined and are likely the collections of disease subtypes. Unsupervised classification based on the molecular signatures identified in omics studies have the potential to reflect molecular mechanisms of the subtypes of the disease and to lead to more targeted and successful interventions for the identified subtypes. Multiple classification algorithms exist but none is ideal for all types of data. Importantly, there are no established methods to estimate sample size in unsupervised classification (unlike power analysis in hypothesis testing). Therefore, we developed a simulation approach allowing comparison of misclassification errors and estimating the required sample size for a given effect size, number, and correlation matrix of the differentially abundant proteins in targeted proteomics studies. All the experiments were performed in silico. The simulated data imitated the expected one from the study of the plasma of patients with lower urinary tract dysfunction with the aptamer proteomics assay Somascan (SomaLogic Inc, Boulder, CO), which targeted 1129 proteins, including 330 involved in inflammation, 180 in stress response, 80 in aging, etc. Three popular clustering methods (hierarchical, k-means, and k-medoids) were compared. K-means clustering performed much better for the simulated data than the other two methods and enabled classification with misclassification error below 5% in the simulated cohort of 100 patients based on the molecular signatures of 40 differentially abundant proteins (effect size 1.5) from among the 1129-protein panel.

Cytoplasmic electric fields and electroosmosis: possible solution for the paradoxes of the intracellular transport of biomolecules

The objective of the paper is to show that electroosmotic flow might play an important role in the intracellular transport of biomolecules. The paper presents two mathematical models describing the role of electroosmosis in the transport of the negatively charged messenger proteins to the negatively charged nucleus and in the recovery of the fluorescence after photobleaching. The parameters of the models were derived from the extensive review of the literature data. Computer simulations were performed within the COMSOL 4.2a software environment. The first model demonstrated that the presence of electroosmosis might intensify the flux of messenger proteins to the nucleus and allow the efficient transport of the negatively charged phosphorylated messenger proteins against the electrostatic repulsion of the negatively charged nucleus. The second model revealed that the presence of the electroosmotic flow made the time of fluorescence recovery dependent on the position of the bleaching spot relative to cellular membrane. The magnitude of the electroosmotic flow effect was shown to be quite substantial, i.e. increasing the flux of the messengers onto the nucleus up to 4-fold relative to pure diffusion and resulting in the up to 3-fold change in the values of fluorescence recovery time, and therefore the apparent diffusion coefficient determined from the fluorescence recovery after photobleaching experiments. Based on the results of the modeling and on the universal nature of the electroosmotic flow, the potential wider implications of electroosmotic flow in the intracellular and extracellular biological processes are discussed. Both models are available for download at ModelDB.

[A new look at reactions with participation of metal-porphyrines]

Reactions ofnucleophilic substitution and enzymatic processes with participation of metal-porphyrins (MP) are considered from the point of view of Zn-tetraphenylporphin (Zn-TPhP) coordination with corresponding ligand/nucleophyl/substrate/base. Linear correlations perform between kinetic parameters of process of coordination of Zn-TPhP in chloroform (constants of stability) and reactions of nucleophilic substitution both in aqueous and organic solvents with participation ofpyridines, N-oxides ofpyridines, anilines, primary amines and oxidation of anilines by horseradish peroxidase in aqueous solutions (rate constants). Thermodynamic parameters of complexation and nucleophilic substitution mutually correlate linearly in the case of pyridines, anilines and primary amines.

Label-free quantitative LC-MS proteomics of Alzheimer's disease and normally aged human brains

Quantitative proteomics analysis of cortical samples of 10 Alzheimer's disease (AD) brains versus 10 normally aged brains was performed by following the accurate mass and time tag (AMT) approach with the high resolution LTQ Orbitrap mass spectrometer. More than 1400 proteins were identified and quantitated. A conservative approach of selecting only the consensus results of four normalization methods was suggested and used. A total of 197 proteins were shown to be significantly differentially abundant (p-values <0.05, corrected for multiplicity of testing) in AD versus control brain samples. Thirty-seven of these proteins were reported as differentially abundant or modified in AD in previous proteomics and transcriptomics publications. The rest to the best of our knowledge are new. Mapping of the discovered proteins with bioinformatic tools revealed significant enrichment with differentially abundant proteins of pathways and processes known to be important in AD, including signal transduction, regulation of protein phosphorylation, immune response, cytoskeleton organization, lipid metabolism, energy production, and cell death.

Dynamics of plasma proteome during leptin-replacement therapy in genetically based leptin deficiency

The effects of leptin-replacement therapy on the plasma proteome of three unique adults with genetically based leptin deficiency were studied longitudinally during the course of recombinant human leptin-replacement treatment. Quantitative proteomics analysis was performed in plasma samples collected during four stages: before leptin treatment was initiated, after 1.5 and 6 years of leptin-replacement treatment, and after 7 weeks of temporary interruption of leptin-replacement therapy. Of 500 proteins reliably identified and quantitated in those four stages, about 100 were differentially abundant twofold or more in one or more stages. Synchronous dynamics of abundances of about 90 proteins was observed reflecting both short- and long-term effects of leptin-replacement therapy. Pathways and processes enriched with overabundant synchronous proteins were cell adhesion, cytoskeleton remodeling, cell cycle, blood coagulation, glycolysis, and gluconeogenesis. Plausible common regulators of the above synchronous proteins were identified using transcription regulation network analysis. The generated network included two transcription factors (c-Myc and androgen receptor) that are known to activate each other through a double-positive feedback loop, which may represent a potential molecular mechanism for the long-term effects of leptin-replacement therapy. Our findings may help to elucidate the effects of leptin on insulin resistance.

Deconvolution of insulin secretion, insulin hepatic extraction post-hepatic delivery rates and sensitivity during 24-hour standardized meals: time course of glucose homeostasis in leptin replacement treatment

Minimally invasive methodology, mathematical model, and software for analysis of glucose homeostasis by deconvolution of insulin secretion, hepatic extraction, post-hepatic delivery, and sensitivity from 24-hour standardized meals test have been developed and illustrated by the study of glucose homeostasis of a genetically based leptin-deficient patient before and after leptin replacement treatment. The only genetically leptin-deficient adult man identified in the world was treated for 24 months with recombinant methionyl human leptin. Blood was collected every 7 minutes for 24 hours, with standardized meals consumed during the 4 visits: at baseline, one-week, 18-months, and 24-months after initiation of the treatment. Concentrations of insulin, C-peptide, and plasma glucose were measured. Insulin secretion was obtained by deconvolution of C-peptide data. Hepatic insulin extraction was determined based on our modifications of the insulin kinetics model . Insulin sensitivity for each of the four meals was calculated by using the minimal glucose model approach. Hepatic extraction of insulin was the first element of glucose homeostasis to respond to leptin replacement treatment and increased 2-fold after one week of treatment. Insulin secretion and delivery rates decreased more than 2-fold and insulin sensitivity increased 10-fold after 24 months of treatment. Computer programs for analysis of 24-hour insulin secretion, extraction, delivery, and action are available upon request.

A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS

A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQ-FT MS mass spectrometer (or other high-resolution mass spectrometers, such as a Q-TOF MS). The strategy, termed "cross-assignment", is introduced to increase substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC-MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of Escherichia coli samples spiked with known amounts of non-E. coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC-MS data sets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication.

An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics

Methanosarcina acetivorans produces acetate, formate, and methane when cultured with CO as the growth substrate [Rother M, Metcalf WW (2004) Proc Natl Acad Sci USA 101:], which suggests novel features of CO metabolism. Here we present a genome-wide proteomic approach to identify and quantify proteins differentially abundant in response to growth on CO versus methanol or acetate. The results indicate that oxidation of CO to CO2 supplies electrons for reduction of CO2 to a methyl group by steps and enzymes of the pathway for CO2 reduction determined for other methane-producing species. However, proteomic and quantitative RT-PCR results suggest that reduction of the methyl group to methane involves novel methyltransferases and a coenzyme F420H2:heterodisulfide oxidoreductase system that generates a proton gradient for ATP synthesis not previously described for pathways reducing CO2 to methane. Biochemical assays support a role for the oxidoreductase, and transcriptional mapping identified an unusual operon structure encoding the oxidoreductase. The proteomic results further indicate that acetate is synthesized from the methyl group and CO by a reversal of initial steps in the pathway for conversion of acetate to methane that yields ATP by substrate level phosphorylation. The results indicate that M. acetivorans utilizes a pathway distinct from all known CO2 reduction pathways for methane formation that reflects an adaptation to the marine environment. Finally, the pathway supports the basis for a recently proposed primitive CO-dependent energy-conservation cycle that drove and directed the early evolution of life on Earth.

New Algorithm for 15N/14N Quantitation with LC−ESI−MS Using an LTQ-FT Mass Spectrometer

A new algorithm (QN) for the (15)N /(14)N quantitation of relative protein abundances in complex proteomic samples is described. QN takes advantage of the high resolution, mass accuracy and throughput of the hybrid mass spectrometer LTQ-FT MS. Peptide quantitation is based on MS peak intensity (measured in the FT MS), while peptide identification is performed in the MS/MS mode (measured in the LTQ linear ion trap). Accuracy of the protein abundance is enhanced by a novel scoring procedure, allowing filtering of less reliable measurements of peptide abundances. The performance of QN is illustrated in the relative quantitative analysis of M. acetivorans C2A cultures grown with carbon monoxide vs methanol as substrate. Roughly 1,000 proteins were quantitated with an average CV of 9% for the protein abundance ratios. QN performs quantitation without manual intervention, does not require high processing power, and generates files compatible with the Guidelines for Proteomic Data Publication.

A Universal Denoising and Peak Picking Algorithm for LC−MS Based on Matched Filtration in the Chromatographic Time Domain

A new denoising and peak picking algorithm (MEND, matched filtration with experimental noise determination) for analysis of LC-MS data is described. The algorithm minimizes both random and chemical noise in order to determine MS peaks corresponding to sample components. Noise characteristics in the data set are experimentally determined and used for efficient denoising. MEND is shown to enable low-intensity peaks to be detected, thus providing additional useful information for sample analysis. The process of denoising, performed in the chromatographic time domain, does not distort peak shapes in the m/z domain, allowing accurate determination of MS peak centroids, including low-intensity peaks. MEND has been applied to denoising of LC-MALDI-TOF-MS and LC-ESI-TOF-MS data for tryptic digests of protein mixtures. MEND is shown to suppress chemical and random noise and baseline fluctuations, as well as filter out false peaks originating from the matrix (MALDI) or mobile phase (ESI). In addition, MEND is shown to be effective for protein expression analysis by allowing selection of a large number of differentially expressed ICAT pairs, due to increased signal-to-noise ratio and mass accuracy.

Computer simulation of affinity capillary electrophoresis

A computer-simulated model of affinity capillary electrophoresis is developed. Unlike existing models, it is able to describe the situation where the concentrations of sample molecules and ligand molecules are commensurable, or even the situation where the zones occupied by these molecules are not mixed initially. The model permits to study the dependence of the spatial and temporal distributions of sample molecules on various parameters such as reaction rate constants, concentrations of sample and reagent, electromigration velocities of sample and reagent and sample injection volume. A collection of peak shapes for different values of parameters is presented. The dependence of peak variance on the ratio of the time of analysis to the characteristic time of reaction is studied.

Hydrodynamics and mass transfer of the coaxial jet mixer in flow injection analysis

A coaxial jet mixer that was previously proposed for rapid and efficient mixing under laminar flow conditions has been studied both theoretically and experimentally. A mathematical model that consists of a set of Navie-Stokes equations that determine the flow velocities and three diffusion-convection reaction equations that determine the reactant and product concentrations has been developed. Equations are solved with the help of finite difference techniques for different flow conditions. The quality of sample and reagent mixing is characterized by the mean product concentration and the amount of product produced. Theoretical results are compared with experimental ones for the mixing of bromothymol blue (a pH indicator) in the outer capillary with NaOH in the inner capillary of the jet mixer.

[The use of ocular drug films of propolis in the sequelae of ophthalmic herpes]

There was studied the therapeutic efficiency of ocular medical propolis films (OMF) in 35 patients with postherpetic trophic keratitis and in 20 with postherpetic nebula. OMF were applied behind the lower eyelid at bedtime during 10-15 days. All the patients endured the propolis films well. OMF accelerated the cornea epithelization. Epitheliopathy and micropoint edema of cornea epithelium rapidly disappeared. Time of patients recovery reduced nearly twice (P,001) in comparison with the control group--from 14.1 to 7.6 days. On the average their visual acuity increased in two times--from 0.12 to 0.27 (P > 0.001).

Investigation of the electroosmotic flow effect on the efficiency of capillary electrophoresis

The influence of the electroosmotic flow profile on the efficiency and resolution of capillary electrophoresis is studied. The mathematical model is formulated and the set of equations is solved numerically. The results of the analysis are applicable to a wide range of buffer concentrations and capillary diameters. The temperature dependence of electrophoretic mobility, viscosity and thermal conductivity and the dependence of electrical conductivity on temperature and ion concentration in the double layer are taken into account. It is shown that there exists a region of buffer concentrations and capillary diameters where the influence of the electroosmotic flow profile on the efficiency and resolution is much greater than that of the temperature dependence of the electrophoretic mobility. The results are especially essential for small buffer concentrations or capillary diameters comparable with the double electrical layer thickness.

[Characteristics of recovery process in kidney tubule epithelium of white rats with advanced mercuric chloride-induced necrotic nephrosis]

Paraffin and semithin sections were used to study the peculiarities of recovery process in kidney tubules of white rats at various intervals (3 days to 5 months). Koss reaction for evaluation of calcium saline level was used after subcutaneous injection of large doses of sublimate (0.6 mg/100 g of b.w.). The study revealed the expressed destruction of tubules to be followed by rapid (3 days after nephrotoxin injection) calcification of cellular detritus.

[Changes in the nucleoli of epithelial cells of the kidney tubules in mercuric chloride-induced experimental kidney tubular necrosis]

Electron-microscopic studies of epithelial cells of uric tubules in white rat kidneys after i.m. injections of mercury dichloride (0.4 mg/100 of body weight) given every 24, 48 and 72 hours showed the affected epithelial cells to have nonspecific changes in tubule ultrastructure, i.e. dissociation and segregation of tubule components as well as degranulation, fragmentation and hypertrophy. The dissociation of nucleolus components is followed by the damage of an essential part of cell mitochondrial apparatus and becomes irreversible. In some damaged cells degranulation is accompanied by the nucleolus decay into separate solid fragments formed of fibrous tissue. The enlargement of nucleolus fragments in the absence of proribosomes speaks in favour of the depression of proribosome formation process while the ability to synthesize p-RNA in comparatively slight.

[Correlations of intracellular and cellular regeneration of the epithelium of the kidney tubules in necronephrosis]

The study of radioautographs in ultrathin and semithin sections extracted from animal tissues and following the impulsive as well as long-term injection of 3H-thymidine was made. Intracellular regeneration processes (external cell membrane synthesis, DNA reparation, restoration of the lost albumin-synthesizing complex and cytoskeleton) turned to develop in proximal canals of epithelial cells. The processes were aimed at the liquidation of distortions preventing cell from entering mitosis.

[Isolation of viruses of antigenic complexes of California encephalitis and Bunyamwera (Bunyaviridae, Bunuavirus) from mosquitoes in northeast Asia]

Studies in suckling mice and by direct solid-phase enzyme immunoassay were carried out with 111,1 thousand Aedes mosquitoes collected in July, 1986, in tundra, forest-tundra, and northern taiga of Kamchatka region and Chukotka autonomous district of Magadan region (North-Pacific natural area within 69 degrees-53 degrees North and 156 degrees-177 degrees East). Eleven strains were isolated of which 7 were classified as members of the California encephalitis complex (Tahyna-like strains) and 4 as members of the Bunyamwera complex (Batai-like strains). According to electron-microscopic studies of 2 strains (one from each antigenic complex), both were classified as belonging to the family of Bunyaviridae. Strains of both complexes were isolated in all landscape zones examined--tundra, forest-tundra, northern taiga. Virus-neutralizing antibodies to them were found in human and reindeer sera also in all the landscape zones, to Tahyna virus in 11%-61%, to Batain virus in 2%-6% blood specimens. No antibody to Uukuniemi virus was found.

[Electron microscopic-radioautographic study of RNA synthesis in the epithelial cells of the kidney urinary tubules of white rats in corrosive sublimate poisoning]

Radioautographic study of ultrathin selections of proximal white rat renal canals labeled with 3H-uridine revealed diffuse transition of peripheral and paranuclear heterochromatin to be observed in nuclei of undamaged epithelia cells and those affected by partial necrosis in case of sublimate nephrosis. Nucleus degranulation as well as decrease in its size accompanied by inhibition of RNA synthesis is also observed. Nucleus reparation being observed 48 hours after subcutaneous injection of 0.4/0.1 kg corrosive sublimate in some cells and characterized by the appearance of granular component as well as the increase of nucleolar vacuole count is usually revealed in case of decondensation form of peripheral and paranuclear chromatin in the enlarged nuclei.

[Autoradiographic research on RNA biosynthesis in renal tissue in the early period of corrosive sublimate-induced necronephrosis]

Study of 3H-uridine autoradiographs in semithin methacrylate renal sections of white rats showed pronounced decrease of uridine mark in all cellular types of renal tissue following 24 hours after the administration of 0.5 mg corrosive sublimate per 100 g bw. The period was marked by the development of anuria in animals. 48 hours later increase of uridine mark level in renal cortical substance was observed. Epithelial cells being contiguous with necrosed zone of non- and partially damaged but kept-alive urinary small canals became hypertrophic and synthesized RNA actively preceding their mitotic division.

[Electron microscopic and radioautographic study of DNA synthesis in kidney tubule epithelial cells in white rats with sublimate-induced necronephrosis]

Electron microscopic analysis of 3H-thymidine radioautographs of ultrathin sections from the white rat kidney has revealed that 72 hours after subcutaneous injection of 0.5 mg per 100 g body weight of mercury bichloride, the damaged and partially necrotized epithelial cell became capable of DNA synthesis. However, due to the reduction of cellular organelle count the process was less intensive, as compared to that in insignificantly damaged cells. The presence in the cytoplasm of many damaged epithelial cells capable of DNA synthesis and free ribosomes demonstrates that the RNA and free ribosome biogenesis is an earlier cell regenerative reaction than DNA synthesis.

[Autoradiographic study of DNA synthesis in epithelial cells of albino rat kidney tubules as affected by corrosive sublimate nephrosis]

The analysis of 3H-thymidine radioautographs of semithin (0.5 micron) methacrylate sections of white rat kidney has shown that 72 h after corrosive sublimate injection in a dose of 0.5 mg/100 g bw, pronounced heterogeneity of impulse thymidine mark distribution stipulated by asynchronous DNA replication in damaged nephrocytes was noted. Thymidine mark is to be observed in some heavily damaged nephrocytes, retaining around the nucleus a negligible amount of cytoplasm. Thymidine mark concentration in the peripheral zone of nuclei typical only of nephrocytes with increased cytoplasm amount testifies to the fact that during S-period repairing processes take place in the damaged nephrocytes, leading to normalization of nuclear-cytoplasmic shifts.

[Characteristics of destructive-regenerative processes in the kidneys of albino rats in conditions of necronephrosis caused by corrosive sublimate]

Study of serial semi-thin (0.5 micron) metacrylate and paraffinic (8 microns) of rat kidney sections 6, 12, 24 and 48 h after subcutaneous injection of mercury bichloride at a dose of 0.6 mg/100 g bw has revealed that injury to different parts of the canalicular nephron is of heterogeneous character. The proximal part of the nephron demonstrates both complete and partial necrosis of nephrocyte cytoplasm. The distal parts of the nephron and collecting tubules are characterized by partial necrosis of the apical cytoplasm. Within the period between 12 and 24 h after the mercury bichloride injection, intracellular reparative processes are observed, in addition to destruction, in partially damaged but viable nephrocytes, which is confirmed by the enlargement of the nucleolic size. Regeneration of the tubular epithelium due to cellular restoration was unmarked 24 h after the mercury bichloride injection.