Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics.

Many liquid chromatography-mass spectrometry (LC-MS) studies have compared formalin-fixed paraffin-embedded (FFPE) tissues with matched fresh-frozen (FF) tissues to examine the effect of preservation techniques on the proteome; however, few studies have included the phosphoproteome. A high degree of overlap and correlation between the two preservation techniques would demonstrate the importance of FFPE tissues as a valuable biomedical resource. Our aim was to quantitatively compare the proteome and phosphoproteome of matched FFPE and FF tissues using data-independent acquisition LC-MS.

Accelerating Heritability, Genetic Correlation, and Genome-Wide Association Imaging Genetic Analyses in Complex Pedigrees.

National and international biobanking efforts led to the collection of large and inclusive imaging genetics datasets that enable examination of the contribution of genetic and environmental factors to human brains in illness and health. High-resolution neuroimaging (~10 voxels) and genetic (10 single nucleotide polymorphic [SNP] variants) data are available in statistically powerful (N = 10) epidemiological and disorder-focused samples. Performing imaging genetics analyses at full resolution afforded in these datasets is a formidable computational task even under the assumption of unrelatedness among the subjects.

Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics.

Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs).

High-Throughput Proteomics and Phosphoproteomics of Rat Tissues Using Microflow Zeno SWATH.

High-throughput tissue proteomics has great potential in the advancement of precision medicine. Here, we investigated the combined sensitivity of trap-elute microflow liquid chromatography with a ZenoTOF for DIA proteomics and phosphoproteomics. Method optimization was conducted on HEK293T cell lines to determine the optimal variable window size, MS2 accumulation time and gradient length.

Motivation, inclusivity, and realism should drive data science education.

Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the individuals entering data science, but also increases the field's innovation and potential impact as a whole. Education is the most scalable solution to meet these needs, but many data science educators lack formal training in education.

Predicting Heterogeneity in Patient Response to Morphine Treatment for Neonatal Opioid Withdrawal Syndrome.

Infants with neonatal opioid withdrawal syndrome commonly receive morphine treatment to manage their withdrawal signs. However, the effectiveness of this pharmacotherapy in managing the infants' withdrawal signs vary widely. We sought to understand how information available early in infant monitoring can anticipate this treatment response, focusing on early modified Finnegan Neonatal Abstinence Scoring System (FNASS) scores, polygenic risk for opioid dependence (polygenic risk score (PRS)), and drug exposure.

There is no F in APC: Using physiological fluoride-free solutions for high throughput automated patch clamp experiments.

Fluoride has been used in the internal recording solution for manual and automated patch clamp experiments for decades because it helps to improve the seal resistance and promotes longer lasting recordings. In manual patch clamp, fluoride has been used to record voltage-gated Na (Na) channels where seal resistance and access resistance are critical for good voltage control. In automated patch clamp, suction is applied from underneath the patch clamp chip to attract a cell to the hole and obtain a good seal.

Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder.

Bipolar disorder is an often-severe mental health condition characterized by alternation between extreme mood states of mania and depression. Despite strong heritability and the recent identification of 64 common variant risk loci of small effect, pathophysiological mechanisms remain unknown. Here, we analyzed genome sequences from 41 multiply-affected pedigrees and identified variants in 741 genes with nominally significant linkage or association with bipolar disorder.

How can we improve information for people affected by cancer? A national survey exploring gaps in current information provision, and challenges with accessing cancer information online.

Objective: Despite improved recognition regarding the importance and association between provision of high quality information for people affected by cancer and improved outcomes and experiences; gaps and unmet needs are still reported. As oncology health information provision increasingly moves online, understanding how service users experience and manage misinformation is important. Determining patient and carer preferences regarding cancer provision is needed to address outstanding gaps.

Multiple dimensions of stress vs. genetic effects on depression.

Many psychiatric disorders including depression involve complex interactions of genetics and environmental stressors. Environmental influence is challenging to measure objectively and account for in genetic studies because the necessary large population samples in these studies involve individuals with varying cultures and life experiences, clouding genetic findings. In a unique population with relative sociocultural homogeneity and a narrower range of types of stress experiences, we quantitatively assessed multiple stress dimensions and measured their potential influence in biasing the heritability estimate of depression.

Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty.

Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 330,759) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5x10-8), of which eight have not been reported previously in the peer-reviewed literature. We investigated the regulatory and cell specific expression for these loci by generating mRNA-seq, ATAC-seq, and single-cell RNA-seq from cells in the mouse cochlea.

Publisher Correction: Cross-site and cross-platform variability of automated patch clamp assessments of drug effects on human cardiac currents in recombinant cells.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Quantitative proteomics characterization of acutely isolated primary adult rat cardiomyocytes and fibroblasts.

Our heart is comprised of many different cell types that all contribute to cardiac function. An important step in deciphering the molecular complexity of our heart is to decipher the molecular composition of the various cardiac cell types. Here we set out to delineate a comprehensive protein expression profile of the two most prevalent cell types in the heart: cardiomyocytes and cardiac fibroblasts.

Cross-site and cross-platform variability of automated patch clamp assessments of drug effects on human cardiac currents in recombinant cells.

Automated patch clamp (APC) instruments enable efficient evaluation of electrophysiologic effects of drugs on human cardiac currents in heterologous expression systems. Differences in experimental protocols, instruments, and dissimilar site procedures affect the variability of IC values characterizing drug block potency. This impacts the utility of APC platforms for assessing a drug's cardiac safety margin.

A systematic strategy for estimating hERG block potency and its implications in a new cardiac safety paradigm.

Introduction: hERG block potency is widely used to calculate a drug's safety margin against its torsadogenic potential. Previous studies are confounded by use of different patch clamp electrophysiology protocols and a lack of statistical quantification of experimental variability. Since the new cardiac safety paradigm being discussed by the International Council for Harmonisation promotes a tighter integration of nonclinical and clinical data for torsadogenic risk assessment, a more systematic approach to estimate the hERG block potency and safety margin is needed.

Short- and long-term outcomes of selective pelvic exenteration surgery in a low-volume specialized tertiary setting.

Background: Most published data on pelvic exenteration comes from high-volume quaternary units, with limited data available from outside of this setting. This study reports outcomes of selective pelvic exenteration performed in a low-volume tertiary unit with multidisciplinary support.

Methods: A retrospective review of consecutive patients who underwent pelvic exenteration surgery for rectal/anal carcinoma, or gynaecological malignancy at Royal Adelaide Hospital between June 2008 and September 2018.

In-silico guided discovery of novel CCR9 antagonists.

Antagonism of CCR9 is a promising mechanism for treatment of inflammatory bowel disease, including ulcerative colitis and Crohn's disease. There is limited experimental data on CCR9 and its ligands, complicating efforts to identify new small molecule antagonists. We present here results of a successful virtual screening and rational hit-to-lead campaign that led to the discovery and initial optimization of novel CCR9 antagonists.

Marine Antifouling Behavior of Lubricant-Infused Nanowrinkled Polymeric Surfaces.

A new family of polymeric, lubricant-infused, nanostructured wrinkled surfaces was designed that effectively retains inert nontoxic silicone oil, after draining by spin-coating and vigorous shear for 2 weeks. The wrinkled surfaces were fabricated using three different polymers (Teflon AF, polystyrene, and poly(4-vinylpyridine)) and two shrinkable substrates (Polyshrink and shrinkwrap), and Teflon on Polyshrink was found to be the most effective system. The volume of trapped lubricant was quantified by adding Nile red to the silicone oil before infusion and then extracting the oil and Nile red from the surfaces in heptane and measuring by fluorimetry.

Calcium/calmodulin-dependent kinase 2 mediates Epac-induced spontaneous transient outward currents in rat vascular smooth muscle.

Key Points: The Ca and redox-sensing enzyme Ca /calmodulin-dependent kinase 2 (CaMKII) is a crucial and well-established signalling molecule in the heart and brain. In vascular smooth muscle, which controls blood flow by contracting and relaxing in response to complex Ca signals and oxidative stress, surprisingly little is known about the role of CaMKII. The vasodilator-induced second messenger cAMP can relax vascular smooth muscle via its effector, exchange protein directly activated by cAMP (Epac), by activating spontaneous transient outward currents (STOCs) that hyperpolarize the cell membrane and reduce voltage-dependent Ca influx.

Germline Mutations in ATM and BRCA1/2 Distinguish Risk for Lethal and Indolent Prostate Cancer and are Associated with Early Age at Death.

Background: Germline mutations in BRCA1/2 and ATM have been associated with prostate cancer (PCa) risk.

Objective: To directly assess whether germline mutations in these three genes distinguish lethal from indolent PCa and whether they confer any effect on age at death.

Design, Setting, And Participants: A retrospective case-case study of 313 patients who died of PCa and 486 patients with low-risk localized PCa of European, African, and Chinese descent.

Correlating early motor skills to white matter abnormalities in preterm infants using diffusion tensor imaging.

Purpose: Diffusion tensor imaging (DTI) can detect injury to specific white matter (WM) tracts involved with sensorimotor processing and may provide sensitive measures for latent or nascent motor skills. We hypothesized that DTI measures of WM fractional anisotropy (FA) could predict early motor scores on a standardized assessment in a cohort of preterm infants at risk for WM injury.

Methods: In this prospective study, preterm infants (n= 26, 11 female, 15 male, mean gestational age 29.