A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.

Drosophila melanogaster has a rich repertoire of innate and learned behaviors. Its 100,000-neuron brain is a large but tractable target for comprehensive neural circuit mapping. Only electron microscopy (EM) enables complete, unbiased mapping of synaptic connectivity; however, the fly brain is too large for conventional EM. We developed a custom high-throughput EM platform and imaged the entire brain of an adult female fly at synaptic resolution. To validate the dataset, we traced brain-spanning circuitry involving the mushroom body (MB), which has been extensively studied for its role in learning. All inputs to Kenyon cells (KCs), the intrinsic neurons of the MB, were mapped, revealing a previously unknown cell type, postsynaptic partners of KC dendrites, and unexpected clustering of olfactory projection neurons. These reconstructions show that this freely available EM volume supports mapping of brain-spanning circuits, which will significantly accelerate Drosophila neuroscience. VIDEO ABSTRACT.

Micrococcin cysteine-to-thiazole conversion through transient interactions between the scaffolding protein TclI and the modification enzymes TclJ and TclN.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase, and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, demonstrate complex formation between TclI, TclJ, and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core. IMPORTANCE: Thiopeptides are a family of antimicrobial peptides characterized for having sulfur-containing heterocycles and for being highly post-translationally modified. Numerous thiopeptides have been identified; almost all of which inhibit protein synthesis in gram-positive bacteria. These intrinsic antimicrobial properties make thiopeptides promising candidates for the development of new antibiotics. The thiopeptide micrococcin is synthesized by the ribosome and undergoes several post-translational modifications to acquire its bioactivity. In this study, we identify key interactions within the enzymatic complex that carries out cysteine to thiazole conversion in the biosynthesis of micrococcin.

Human tear film protein sampling using soft contact lenses.

BACKGROUND: Human tear protein biomarkers are useful for detecting ocular and systemic diseases. Unfortunately, existing tear film sampling methods (Schirmer strip; SS and microcapillary tube; MCT) have significant drawbacks, such as pain, risk of injury, sampling difficulty, and proteomic disparities between methods. Here, we present an alternative tear protein sampling method using soft contact lenses (SCLs). RESULTS: We optimized the SCL protein sampling in vitro and performed in vivo studies in 6 subjects. Using Etafilcon A SCLs and 4M guanidine-HCl for protein removal, we sampled an average of 60 ± 31 µg of protein per eye. We also performed objective and subjective assessments of all sampling methods. Signs of irritation post-sampling were observed with SS but not with MCT and SCLs. Proteomic analysis by mass spectrometry (MS) revealed that all sampling methods resulted in the detection of abundant tear proteins. However, smaller subsets of unique and shared proteins were identified, particularly for SS and MCT. Additionally, there was no significant intrasubject variation between MCT and SCL sampling. CONCLUSIONS: These experiments demonstrate that SCLs are an accessible tear-sampling method with the potential to surpass current methods in sampling basal tears.

Treatment Rates for Chlamydia trachomatis and Neisseria gonorrhoeae in a Metropolitan Area: Observational Cohort Analysis.

BACKGROUND: Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) are the 2 most common sexually transmitted infections (STIs) in the United States. The Centers for Disease Control and Prevention regularly publishes and updates STI Treatment Guidelines. The purpose of this study was to measure and compare treatment rates for CT and GC among public and private providers. METHODS: Data from multiple sources, including electronic health records and Medicaid claims, were linked and integrated. Cases observed during 2016-2020 were defined based on positive laboratory results. We calculated descriptive statistics and odd ratios based on characteristics of providers and patients, stratifying by public versus private providers. Univariate logistic regression models were used to examine the factors associated with recommended treatment. RESULTS: Overall, we found that 82.2% and 63.0% of initial CT and GC episodes, respectively, received Centers for Disease Control and Prevention-recommended treatment. The public STI clinic treated more than 90% of CT and GC cases consistently across the 5-year period. Private providers were significantly less likely to treat first episodes for CT (79.6%) and GC (53.3%; P < 0.01). Other factors associated with a higher likelihood of recommended treatment included being male, being HIV positive, and identifying as Black or multiracial. Among GC cases, 10.8% received nonrecommended treatment; all CT cases with treatment occurred per guidelines. CONCLUSIONS: Although these treatment rates are higher than previous studies, there remain significant gaps in STI treatment that require intervention from public health.

CHalf: Folding Stability Made Simple.

The structure of a protein defines its function and integrity and correlates with the protein folding stability (PFS). Quantifying PFS allows researchers to assess differential stability of proteins in different disease or ligand binding states, providing insight into protein efficacy and potentially serving as a metric of protein quality. There are a number of mass spectrometry (MS)-based methods to assess PFS, such as Thermal Protein Profiling (TPP), Stability of Proteins from Rates of Oxidation (SPROX), and Iodination Protein Stability Assay (IPSA). Despite the critical value that PFS studies add to the understanding of mechanisms of disease and treatment development, proteomics research is still primarily dominated by concentration-based studies. We found that a major reason for the lack of PFS studies is the lack of a user-friendly data processing tool. Here we present the first user-friendly software, CHalf, with a graphical user interface for calculating PFS. Besides calculating site-specific PFS of a given protein from chemical denature folding stability assays, CHalf is also compatible with thermal denature folding stability assays. CHalf also includes a set of data visualization tools to help identify changes in PFS across protein sequences and in between different treatment conditions. We expect the introduction of CHalf to lower the barrier of entry for researchers to investigate PFS, promoting the usage of PFS in studies. In the long run, we expect this increase in PFS research to accelerate our understanding of the pathogenesis and pathophysiology of disease.

Quantifying In Situ Structural Stabilities of Human Blood Plasma Proteins Using a Novel Iodination Protein Stability Assay.

Many of the diseases that plague society today are driven by a loss of protein quality. One method to quantify protein quality is to measure the protein folding stability (PFS). Here, we present a novel mass spectrometry (MS)-based approach for PFS measurement, iodination protein stability assay (IPSA). IPSA quantifies the PFS by tracking the surface-accessibility differences of tyrosine, histidine, methionine, and cysteine under denaturing conditions. Relative to current methods, IPSA increases protein coverage and granularity to track the PFS changes of a protein along its sequence. To our knowledge, this study is the first time the PFS of human serum proteins has been measured in the context of the blood serum (in situ). We show that IPSA can quantify the PFS differences between different transferrin iron-binding states in near in vivo conditions. We also show that the direction of the denaturation curve reflects the in vivo surface accessibility of the amino acid residue and reproducibly reports a residue-specific PFS. Along with IPSA, we introduce an analysis tool Chalf that provides a simple workflow to calculate the residue-specific PFS. The introduction of IPSA increases the potential to use protein structural stability as a structural quality metric in understanding the etiology and progression of human disease. Data is openly available at Chorusproject.org (project ID 1771).

In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50-200 µm.

Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories to cost-effectively preserve valuable specimens for later study. With the rapid growth of spatial proteomics, FFPE tissues can serve as a more accessible alternative to more commonly used frozen tissues. However, extracting proteins from FFPE tissues is challenging due to cross-links formed between proteins and formaldehyde. Here, we have adapted the nanoPOTS sample processing workflow, which was previously applied to single cells and fresh-frozen tissues, to profile protein expression from FFPE tissues. Following the optimization of extraction solvents, times, and temperatures, we identified an average of 1312 and 3184 high-confidence master proteins from 10 µm thick FFPE-preserved mouse liver tissue squares having lateral dimensions of 50 and 200 µm, respectively. The observed proteome coverage for FFPE tissues was on average 88% of that achieved for similar fresh-frozen tissues. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. This modified nanodroplet processing in one pot for trace samples (nanoPOTS) and fully automated processing in one pot for trace sample (autoPOTS) workflows provides the greatest coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues. Data are available via ProteomeXchange with identifier PXD029729.

Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans.

The synthesis of new proteins and the degradation of old proteins in vivo can be quantified in serial samples using metabolic isotope labeling to measure turnover. Because serial biopsies in humans are impractical, we set out to develop a method to calculate the turnover rates of proteins from single human biopsies. This method involved a new metabolic labeling approach and adjustments to the calculations used in previous work to calculate protein turnover. We demonstrate that using a nonequilibrium isotope enrichment strategy avoids the time dependent bias caused by variable lag in label delivery to different tissues observed in traditional metabolic labeling methods. Turnover rates are consistent for the same subject in biopsies from different labeling periods, and turnover rates calculated in this study are consistent with previously reported values. We also demonstrate that by measuring protein turnover we can determine where proteins are synthesized. In human subjects a significant difference in turnover rates differentiated proteins synthesized in the salivary glands versus those imported from the serum. We also provide a data analysis tool, DeuteRater-H, to calculate protein turnover using this nonequilibrium metabolic 2H2O method.

SDHC phaeochromocytoma and paraganglioma: A UK-wide case series.

OBJECTIVE: Phaeochromocytomas and paragangliomas (PPGL) are rare, but strongly heritable tumours. Variants in succinate dehydrogenase (SDH) subunits are identified in approximately 25% of cases. However, clinical and genetic information of patients with SDHC variants are underreported. DESIGN: This retrospective case series collated data from 18 UK Genetics and Endocrinology departments. PATIENTS: Both asymptomatic and disease-affected patients with confirmed SDHC germline variants are included. MEASUREMENTS: Clinical data including tumour type and location, surveillance outcomes and interventions, SDHC genetic variant assessment, interpretation, and tumour risk calculation. RESULTS: We report 91 SDHC cases, 46 probands and 45 non-probands. Fifty-one cases were disease-affected. Median age at genetic diagnosis was 43 years (range: 11-79). Twenty-four SDHC germline variants were identified including six novel variants. Head and neck paraganglioma (HNPGL, n = 30, 65.2%), extra-adrenal paraganglioma (EAPGL, n = 13, 28.2%) and phaeochromocytomas (PCC) (n = 3, 6.5%) were present. One case had multiple PPGLs. Malignant disease was reported in 19.6% (9/46). Eight cases had non-PPGL SDHC-associated tumours, six gastrointestinal stromal tumours (GIST) and two renal cell cancers (RCC). Cumulative tumour risk (95% CI) at age 60 years was 0.94 (CI: 0.79-0.99) in probands, and 0.16 (CI: 0-0.31) in non-probands, respectively. CONCLUSIONS: This study describes the largest cohort of 91 SDHC patients worldwide. We confirm disease-affected SDHC variant cases develop isolated HNPGL disease in nearly 2/3 of patients, EAPGL and PCC in 1/3, with an increased risk of GIST and RCC. One fifth developed malignant disease, requiring comprehensive lifelong tumour screening and surveillance.

Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus.

Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system-the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.

Quality of Life in Post-Surgical Hypoparathyroidism (PoSH) in Thyroid and Parathyroid Surgery.

BACKGROUND: Post-surgical hypoparathyroidism (PoSH) is often long term, with significant associated morbidity and ongoing treatment. A recent systematic review found impaired quality of life (QoL) in patients with PoSH, despite stable treatment. Most studies did not include an appropriate control arm and further studies were recommended, taking into account underlying disease and comorbidities. This study aims to compare QoL in patients with PoSH with appropriate control groups. METHODS: This was a cross-sectional observational study using the general quality of life SF-36 tool and a hypocalcaemia symptom score (HcSS) to assess QoL in patients with PoSH and controls (who had similar surgery but without PoSH). Participants were identified from two patient groups (the Butterfly Thyroid Cancer Trust and the Association for Multiple Endocrine Neoplasia Disorders) and a single tertiary centre in the UK. RESULTS: Four hundred and thirty-nine responses (female n = 379, PoSH n = 89) were included with a median (range) age of 52 (19-92) years. Reported dates of surgery ranged from 1973 to 2019. HcSS scores showed significantly more associated symptoms in patients with PoSH than those without (p < 0.001). Although there was no overall difference in QoL between groups, patients with PoSH consistently had lower scores (p = 0.008) in the energy/fatigue subdomain of the SF-36. CONCLUSION: Patients with PoSH reported significantly more fatigue and loss of energy compared to appropriately matched controls, but overall QoL was not significantly different. Standardised QoL measures may not be sensitive enough to highlight the impact on QoL in these patients. A disease-specific tool may be required.

Changing the name of diabetes insipidus: a position statement of The Working Group for Renaming Diabetes Insipidus.

"What's in a name? That which we call a rose/By any other name would smell as sweet." (Juliet, from Romeo and Juliet by William Shakespeare). Shakespeare's implication is that a name is nothing but a word and it therefore represents a convention with no intrinsic meaning. Whilst this may be relevant to romantic literature, disease names do have real meanings, and consequences, in medicine. Hence, there must be a very good rational for changing the name of a disease that has a centuries-old historical context. A working group of representatives from national and international endocrinology and pediatric endocrine societies now proposes changing the name of "diabetes insipidus" to "Arginine Vasopressin Deficiency (AVP-D)" for central etiologies, and "Arginine Vasopressin Resistance (AVP-R)" for nephrogenic etiologies. This editorial provides both the historical context and the rational for this proposed name change.

Top 10 research priorities for people living with pulmonary fibrosis, their caregivers, healthcare professionals and researchers.

INTRODUCTION: People with pulmonary fibrosis (PF) experience a high symptom burden, reduced quality of life and a shortened lifespan. Treatment options are limited and little is known about what patients, caregivers and healthcare professionals (HCPs)/researchers consider as the most important research priorities. This study aimed to identify the top 10 research priorities for PF across all stakeholders. METHODS: Participants included people with PF, caregivers and HCPs/researchers involved with PF. The research priority setting exercise involved three stages: (1) identifying priorities using an open-ended questionnaire and thematic analysis, (2) development of specific research questions at a face-to-face workshop, and (3) online ranking of research questions to identify the top 10 research priorities using nominal group ranking method. RESULTS: 196 participants completed stage 1 generating 560 questions and 14 research themes were identified. Stage 2 involved 32 participants and generated 53 indicative questions from which 39 were used for the final ranking. Stage 3 was completed by 270 participants. The top ranked priorities focussed on medications to reverse scarring in the lungs (ranked 1st), improving lung function (ranked 2nd, 6th and 8th), interventions aimed at alleviating symptoms (ranked 5th and 7th), prevention of PF (ranked 3rd and 4th) and the best exercise programme for PF (ranked 10th). There was good consensus among patients/carers and HCPs/researchers on the top 10 priorities, however, causes of acute exacerbations and early diagnosis for improving survival, was ranked higher by HCPs/researchers. CONCLUSION: Interventions for preserving lung health and alleviation of symptom burden were top research priorities for PF stakeholders.

Measurements of lethal and nonlethal inbreeding depression inform the de novo domestication of Silphium integrifolium.

PREMISE: Inbreeding depression, or the reduction in fitness of progeny with related parents, has the potential to adversely affect the long-term viability of both wild and captive plant populations. Silphium integrifolium, a prairie plant native to the central United States, has been identified as a potential candidate for domestication as a perennial oilseed crop. Little is known about the potential for inbreeding depression in this species, but it is expected to be nonnegligible because S. integrifolium is both perennial and self-incompatible. Here, we measure lethal inbreeding depression expressed through embryo deaths, and nonlethal inbreeding depression expressed through changes in vigor and fitness phenotypes of progeny. METHODS: First, we made controlled crosses among related and unrelated individuals to determine the effect of two different levels of inbreeding on seed production. Then, we grew inbred and outbred progeny from this population to reproductive maturity and measured 11 key traits. RESULTS: We found that within an improved S. integrifolium population, individuals carried an average of slightly less than one lethal allele per gamete. In progeny, significant inbreeding depression was observed in at least one family for eight of the 11 measured traits. CONCLUSIONS: Inbreeding depression is likely to be an important challenge to S. integrifolium domestication, reducing overall population fecundity and values for important phenotypes. These effects may grow worse as selection reduces effective population size. We recommend several strategies for S. integrifolium breeding to help mitigate these problems.

Long-term safety of gamma knife radiosurgery (SRS) for acromegaly.

PURPOSE: Acromegaly has high morbidity and mortality when growth hormone secretion remains uncontrolled. Stereotactic radiosurgery (SRS) may be used when pituitary surgery is not suitable or unsuccessful, but there are few very long-term safety data available, especially for significant adverse events such as stroke. METHODS: 118 patients with acromegaly were treated with SRS between 1985 and 2015, at the National Centre for Stereotactic Radiosurgery, Sheffield, UK. Data were gathered from case notes, hospital databases, and patient questionnaires. Stroke incidence in comparison to the normal population was quantified using the standardised incidence ratio (SIR), and visual complications assessed. RESULTS: 88% (104/118) had complete morbidity follow up data for analysis. The mean follow-up was 134 months, and median SRS dose was 30 Gy. 81% of tumours had cavernous sinus invasion. There was no excess stroke rate relative to that seen in two age- and sex-matched large population studies (SIR = 1.36, 95% CI 0.27-3.96; SIR = 0.52, 95% CI 0.06-1.89). In 68/104 patients who had MRI-guided SRS with no further radiation treatment (SRS or fractionated radiotherapy) there was no loss of visual acuity and 3% developed ophthalmoplegia. There was a positive correlation between > 1 radiation treatment and both ophthalmoplegia and worsening visual acuity. CONCLUSION: Stroke rate is not increased by SRS for acromegaly. Accurate MRI-based treatment planning and single SRS treatment allow the lowest complication rates. More than one radiation treatment (SRS or fractionated radiotherapy) was associated with increased visual complications.

Temporary Central Vision Blindness After Oseltamivir Administration in a 15-Year-Old Pediatric Male Positive for Influenza A.

Objective: A 15-year-old pediatric male patient was influenza A positive and started on oseltamivir at an outpatient clinic. Method: The next morning the patient presented to the emergency department (ED) with a chief complaint of visual disturbances including decreased central vision. Prior to presenting to the ED the patient was evaluated by his optometrist and his eye exam tested 20/400 bilaterally. His previous year's eye exam was normal, 20/25 bilaterally. Results: In the ED, the patient had an MRI which showed a normal appearing optic nerve, chiasm, and optic tracts. The oseltamivir therapy was discontinued, and the patient followed up with an ophthalmologist outpatient. Conclusion: At a 10-week follow-up visit the patient had 90% recovery of his vision.

Detailed protocol for optimised expression and purification of functional monomeric human Heat Shock Factor 1.

Heat Shock Factor 1 (HSF1) is the master regulator of the heat shock response, a universal survival mechanism throughout eukaryotic species used to buffer potentially lethal proteotoxic conditions. HSF1's function in vivo is regulated by several factors, including post translational modifications and elevated temperatures, whereupon it forms trimers to bind with heat shock elements in DNA. Unsurprisingly, HSF1 is also extremely sensitive to elevated temperatures in vitro, which poses specific technical challenges when producing HSF1 using a recombinant expression system. Although there are several useful publications which outline steps taken for HSF1 expression and purification, studies that describe specific strategies and detailed protocols to overcome HSF1 trimerisation and degradation are currently lacking. Herein, we have reported our detailed experimental protocol for the expression and purification of monomeric human HSF1 (HsHSF1) as a major species. We also propose a refined method of inducing HsHSF1 activation in vitro, that we consider more accurately mimics HsHSF1 activation in vivo and is therefore more physiologically relevant.

Peer Connect Service for people with pulmonary fibrosis in Australia: Participants' experiences and process evaluation.

BACKGROUND AND OBJECTIVE: People living with pulmonary fibrosis (PF) report unmet needs for information and support. Lung Foundation Australia (LFA) have developed the Peer Connect Service to facilitate telephone support for people with PF across Australia. This project documented the experiences of participants and the resources required to support the service. METHODS: Consenting participants took part in semi-structured interviews by telephone. Primary peers (peers who agreed to initiate contact) and secondary peers (eligible patients who sought a peer match) were interviewed. Thematic analysis was undertaken by two independent researchers. Data were collected on the number of matches and contacts required to establish each match. RESULTS: Interviews were conducted with 32 participants (16 primary peers, 15 secondary peers and 1 who was both), aged from 53 to 89 years with 56% being male. Major themes included the value of shared experiences, providing mutual support and the importance of shared personal characteristics (e.g. gender and hobbies) in allowing information and emotional support needs to be met. Participants saw face-to-face contact with peers as highly desirable whilst acknowledging the practical difficulties. Primary peers were cognizant that their role was not to provide medical advice but to listen and share experiences. In the 12-month period, 60 peer matches were made, each match requiring a minimum of seven staff contacts. CONCLUSION: The Peer Connect Service provides a unique opportunity for people with PF to share experiences and offer mutual support. This telephone matching model may be useful in providing peer support for individuals with rare diseases who are geographically dispersed.

Ischemic Stroke Symptoms After Warfarin Reversal With 4-Factor Prothrombin Complex Concentrate Case Report.

Objective: An 83-year-old woman with atrial fibrillation on chronic warfarin therapy was given 4-factor prothrombin complex concentrate to reverse her warfarin for surgery. She had fallen off a step stool at home and fractured her left wrist which initially the surgeon was going to repair surgically. Method: The day after she received 4-factor prothrombin complex concentrate, she developed stroke-like symptoms, National Institutes of Health Stroke Scale (NIHSS) was 14, and met criteria for tissue plasminogen activator (tPA) administration. Tissue plasminogen activator was administered and she was transferred to the intensive care unit (ICU), per hospital protocol. Results: She remained in the ICU for 24 hours for follow-up and monitoring. Her warfarin was restarted and bridged with enoxaparin. She was not a candidate for antiplatelet therapy due to her history of a gastrointestinal (GI) bleed. Conclusion: At discharge, she had no residual effects from her stroke-like symptoms and a magnetic resonance imaging (MRI) of her brain was negative for an acute cerebrovascular accident (CVA).