Machine learning-aided protein identification from multidimensional signatures.

The ability to determine the identity of specific proteins is a critical challenge in many areas of cellular and molecular biology, and in medical diagnostics. Here, we present a macine learning aided microfluidic protein characterisation strategy that within a few minutes generates a three-dimensional fingerprint of a protein sample indicative of its amino acid composition and size and, thereby, creates a unique signature for the protein. By acquiring such multidimensional fingerprints for a set of ten proteins and using machine learning approaches to classify the fingerprints, we demonstrate that this strategy allows proteins to be classified at a high accuracy, even though classification using a single dimension is not possible. Moreover, we show that the acquired fingerprints correlate with the amino acid content of the samples, which makes it is possible to identify proteins directly from their sequence without requiring any prior knowledge about the fingerprints. These findings suggest that such a multidimensional profiling strategy can lead to the development of a novel method for protein identification in a microfluidic format.

Changing trends in Black-White racial differences in surgical menopause: a population-based study.

BACKGROUND: Bilateral oophorectomy before menopause, or surgical menopause, is associated with negative health outcomes, including an increased risk for stroke and other cardiovascular outcomes; however, surgical menopause also dramatically reduces ovarian cancer incidence and mortality rates. Because there are competing positive and negative sequelae associated with surgical menopause, clinical guidelines have not been definitive. Previous research indicates that White women have higher rates of surgical menopause than other racial groups. However, previous studies may have underestimated the rates of surgical menopause among Black women. Furthermore, clinical practice has changed dramatically in the past 15 years, and there are no population-based studies in which more recent data were used. Tracking actual racial differences among women with surgical menopause is important for ensuring equity in gynecologic care. OBJECTIVE: This population-based surveillance study evaluated racial differences in the rates of surgical menopause in all inpatient and outpatient settings in a large, racially diverse US state with historically high rates of hysterectomy. STUDY DESIGN: We evaluated all inpatient and outpatient surgeries in North Carolina from 2011 to 2014 for patients aged between 20 and 44 years. Surgical menopause was defined as a bilateral oophorectomy, with or without an accompanying hysterectomy, among North Carolina residents. International Classification of Diseases, Ninth Revision, and Current Procedural Terminology codes were used to identify inpatient and outpatient procedures, respectively, and diagnostic indications. We estimated age-, race-, and ethnicity-specific rates of surgical menopause using county-specific population estimates based on the 2010 United States census. We used Poisson regression with deviance-adjusted residuals to estimate the incidence rate ratios in the entire state population. We tested changes in surgery rates over time (reference year, 2011), differences by setting (reference, inpatient), and differences by race and ethnicity (reference, non-Hispanic White). We then described the surgery rates between non-Hispanic White and non-Hispanic Black patients. RESULTS: Between 2011 and 2014, 11,502 surgical menopause procedures for benign indications were performed in North Carolina among reproductive-aged residents. Most (95%) of these surgeries occurred concomitant with a hysterectomy. Over the 4-year study period, there was a 39% reduction in inpatient surgeries (incidence rate ratio, 0.61) and a 100% increase in outpatient surgeries (incidence rate ratio, 2.0). Restricting the analysis to surgeries among non-Hispanic White and Black patients, the increase in outpatient surgeries was significantly higher among non-Hispanic Black women (P<.01) for year-race interaction (reference, 2011 and non-Hispanic White). The overall rates of bilateral oophorectomy for non-Hispanic Black women rose more quickly than for non-Hispanic White women (P<.01). In 2011, the rate of surgical menopause was greater among White women than among Black women (17.7 vs 13.2 per 10,000 women). By 2014, the racial trends were reversed (rate, 24.8 per 10,000 for non-Hispanic White women and 28.4 per 10,000 for non-Hispanic Black women). CONCLUSION: Our findings suggest that the rates of surgical menopause increased in North Carolina in the early 2010s, especially among non-Hispanic Black women. By 2014, the rates of surgical menopause among non-Hispanic Black women had surpassed that of non-Hispanic White women. Given the long-term health consequences associated with surgical menopause, we propose potential drivers for the racially-patterned increases in the application of bilateral oophorectomy before the age of 45 years.

Douching or Perineal Talc Use and Prevalent Fibroids in Young African American Women.

Background: Black women are at an increased risk of developing fibroids, but the cause is unclear. Douching and perineal talc use are common lifestyle exposures among Black women, and may be risk factors for fibroid development. Materials and Methods: This cross-sectional study consisted of Black women 23-35 years of age in the metropolitan Detroit area (n = 1693) without prior diagnoses of fibroids and intact uteri. Main exposures were ever douching (yes/no) and any perineal talc use (ever/never). Main outcomes were prevalent fibroids at baseline (yes/no) and total fibroid volume at baseline (no fibroids/

The epidemiology of gynaecologic health: contemporary opportunities and challenges.

The field of reproductive epidemiology has primarily focused on reproductive outcomes and gynaecologic cancers. The study of non-cancerous, gynaecologic conditions (eg, uterine fibroids, endometriosis) has not received serious treatment in existing epidemiology textbooks and reproductive epidemiology curricula. Further, these conditions do not neatly fit into the other common subdisciplines within epidemiology (eg, infectious disease, cardiovascular, injury and occupational epidemiology and so on). In this commentary, we identify and illustrate three critical challenges to advancing the epidemiologic research of non-cancerous, gynaecologic conditions. With greater investment and a patient-centred approach, epidemiology can advance knowledge about this critical area of human welfare.

Analysis of αB-crystallin polydispersity in solution through native microfluidic electrophoresis.

In recent years, significant advancements have been made in the understanding of the population distributions and dynamic oligomeric states of the molecular chaperone αB-crystallin and its core domain variants. In this work, we provide solution-phase evidence of the polydispersity of αB-crystallin using microfluidic methods, used for separating the oligomeric species present in solution according to their different electrophoretic mobilities on-chip in a matter of seconds. We in particular demonstrate that microfluidic high-field electrophoresis and diffusion can detect the oligomerisation of these highly dynamic molecular chaperones and characterise the dominant oligomeric species present. We thereby provide a robust microfluidic method for characterising the individual species within complex protein mixtures of biological relevance.

Cooperative Assembly of Hsp70 Subdomain Clusters.

Many molecular chaperones exist as oligomeric complexes in their functional states, yet the physical determinants underlying such self-assembly behavior, as well as the role of oligomerization in the activity of molecular chaperones in inhibiting protein aggregation, have proven to be difficult to define. Here, we demonstrate direct measurements under native conditions of the changes in the average oligomer populations of a chaperone system as a function of concentration and time and thus determine the thermodynamic and kinetic parameters governing the self-assembly process. We access this self-assembly behavior in real time under native-like conditions by monitoring the changes in the micrometer-scale diffusion of the different complexes in time and space using a microfluidic platform. Using this approach, we find that the oligomerization mechanism of the Hsp70 subdomain occurs in a cooperative manner and involves structural constraints that limit the size of the species formed beyond the limits imposed by mass balance. These results illustrate the ability of microfluidic methods to probe polydisperse protein self-assembly in real time in solution and to shed light on the nature and dynamics of oligomerization processes.

Real-Time Intrinsic Fluorescence Visualization and Sizing of Proteins and Protein Complexes in Microfluidic Devices.

Optical detection has become a convenient and scalable approach to read out information from microfluidic systems. For the study of many key biomolecules, however, including peptides and proteins, which have low fluorescence emission efficiencies at visible wavelengths, this approach typically requires labeling of the species of interest with extrinsic fluorophores to enhance the optical signal obtained - a process which can be time-consuming, requires purification steps, and has the propensity to perturb the behavior of the systems under study due to interactions between the labels and the analyte molecules. As such, the exploitation of the intrinsic fluorescence of protein molecules in the UV range of the electromagnetic spectrum is an attractive path to allow the study of unlabeled proteins. However, direct visualization using 280 nm excitation in microfluidic devices has to date commonly required the use of coherent sources with frequency multipliers and devices fabricated out of materials that are incompatible with soft lithography techniques. Here, we have developed a simple, robust, and cost-effective 280 nm LED platform that allows real-time visualization of intrinsic fluorescence from both unlabeled proteins and protein complexes in polydimethylsiloxane microfluidic channels fabricated through soft lithography. Using this platform, we demonstrate intrinsic fluorescence visualization of proteins at nanomolar concentrations on chip and combine visualization with micron-scale diffusional sizing to measure the hydrodynamic radii of individual proteins and protein complexes under their native conditions in solution in a label-free manner.

Biophysical approaches for the study of interactions between molecular chaperones and protein aggregates.

Molecular chaperones are key components of the arsenal of cellular defence mechanisms active against protein aggregation. In addition to their established role in assisting protein folding, increasing evidence indicates that molecular chaperones are able to protect against a range of potentially damaging aspects of protein behaviour, including misfolding and aggregation events that can result in the generation of aberrant protein assemblies whose formation is implicated in the onset and progression of neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The interactions between molecular chaperones and different amyloidogenic protein species are difficult to study owing to the inherent heterogeneity of the aggregation process as well as the dynamic nature of molecular chaperones under physiological conditions. As a consequence, understanding the detailed microscopic mechanisms underlying the nature and means of inhibition of aggregate formation remains challenging yet is a key objective for protein biophysics. In this review, we discuss recent results from biophysical studies on the interactions between molecular chaperones and protein aggregates. In particular, we focus on the insights gained from current experimental techniques into the dynamics of the oligomerisation process of molecular chaperones, and highlight the opportunities that future biophysical approaches have in advancing our understanding of the great variety of biological functions of this important class of proteins.