Application of Aligned-UMAP to longitudinal biomedical studies

High-dimensional data analysis starts with projecting the data to low dimensions to visualize and understand the underlying data structure. Several methods have been developed for dimensionality reduction, but they are limited to cross-sectional datasets. The recently proposed Aligned-UMAP, an extension of the uniform manifold approximation and projection (UMAP) algorithm, can visualize high-dimensional longitudinal datasets. We demonstrated its utility for researchers to identify exciting patterns and trajectories within enormous datasets in biological sciences. We found that the algorithm parameters also play a crucial role and must be tuned carefully to utilize the algorithm's potential fully. We also discussed key points to remember and directions for future extensions of Aligned-UMAP. Further, we made our code open source to enhance the reproducibility and applicability of our work. We believe our benchmarking study becomes more important as more and more high-dimensional longitudinal data in biomedical research become available.

Antigenic specificity of human antibody to chlamydia in trachoma and lymphogranuloma venereum

An understanding of the molecular basis of the humoral immune response to chlamydial infections in man requires the identification of target antigens to which antibodies are directed. The antigenic specificity of antibody from patients with lymphogranuloma venereum (LGV) or trachoma was therefore assessed by Western blotting. Surface polypeptides were first identified using purified chlamydial outer membrane complex as antigen. Antibodies in sera from patients with LGV but not from control negative sera reacted with a wide range of chlamydial surface polypeptides with molecular masses of 19, 29, 41, 58, 63 and 65 kDa. The major component of the antibody response detected by both immunoblotting and immunoprecipitation assay was directed against the major outer membrane protein (MOMP). Antibody to MOMP was species-specific on Western blotting, whereas antibody to several other polypeptides recognized common immunodeterminants on polypeptides of C. psittaci Cal-10 of equivalent molecular mass. Immunologically C. psittaci Cal-10 was more closely related to LGV strains of C. trachomatis than a guinea pig inclusion conjunctivitis strain of C. psittaci. Trachoma sera collected from a village in southern Iran showed predominantly type-specific antibody on micro-immunofluorescence to serotype A or B trachoma agents. These sera showed a weak immune response to MOMP, a pronounced response to a polypeptide of 36 kDa and much less widespread reactivity with other chlamydial polypeptides. The lack of an immune response to SDS-stable immunodeterminants on MOMP might contribute to the susceptibility of trachoma patients to repeated cycles of ocular infection with chlamydiae.

How infectious is gonorrhoea?

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ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics

Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe , accompanied by a web interface.

Giant cell myocarditis causing sudden death in a patient with sarcoidosis

Giant cell myocarditis (GCM) is a rare and rapidly fatal cardiovascular condition most often seen in young adults. It is characterized microscopically by myocardial necrosis with multinucleated giant cells in the absence of well-defined granulomas. This disorder has typically been attributed to manifest as heart failure, but in some individuals, GCM may present as sudden cardiac death. Herein, we present a fatal case of GCM in a 36-year-old male with a history of autoimmune disorders. The decedent presented to the emergency room due to vomiting and was treated for nausea due to suspected dehydration. He was discharged that night and found dead on his bathroom floor the following day. Postmortem examination revealed psoriasis and granulomatous lesions in the lungs consistent with sarcoidosis, further supporting circumstantial evidence existing between GCM and autoimmune disorders. Additionally, this case provides an opportunity to distinguish GCM from the distinct clinical entity of cardiac sarcoidosis (CS), especially in the setting of systemic sarcoidosis. We hope to raise awareness of this rare disease process and its potential to cause sudden cardiac death so that it may be considered in a differential diagnosis as immunosuppression and early cardiac transplantation largely determine the prognosis.

ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes

Phase transitions of cellular proteins and lipids play a key role in governing the organisation and coordination of intracellular biology. The frequent juxtaposition of proteinaceous biomolecular condensates to cellular membranes raises the intriguing prospect that phase transitions in proteins and lipids could be co-regulated. Here we investigate this possibility in the ribonucleoprotein (RNP) granule-ANXA11-lysosome ensemble, where ANXA11 tethers RNP granule condensates to lysosomal membranes to enable their co-trafficking. We show that changes to the protein phase state within this system, driven by the low complexity ANXA11 N-terminus, induce a coupled phase state change in the lipids of the underlying membrane. We identify the ANXA11 interacting proteins ALG2 and CALC as potent regulators of ANXA11-based phase coupling and demonstrate their influence on the nanomechanical properties of the ANXA11-lysosome ensemble and its capacity to engage RNP granules. The phenomenon of protein-lipid phase coupling we observe within this system offers an important template to understand the numerous other examples across the cell whereby biomolecular condensates closely juxtapose cell membranes.

GRAPHICAL ABSTRACT

CRISPR interference to evaluate modifiers of C9ORF72-mediated toxicity in FTD

Treatments for neurodegenerative disease, including Frontotemporal dementia (FTD) and Amyotrophic lateral sclerosis (ALS), remain rather limited, underscoring the need for greater mechanistic insight and disease-relevant models. Our ability to develop novel disease models of genetic risk factors, disease modifiers, and other FTD/ALS-relevant targets is impeded by the significant amount of time and capital required to develop conventional knockout and transgenic mice. To overcome these limitations, we have generated a novel CRISPRi interference (CRISPRi) knockin mouse. CRISPRi uses a catalytically dead form of Cas9, fused to a transcriptional repressor to knockdown protein expression, following the introduction of single guide RNA against the gene of interest. To validate the utility of this model we have selected the TAR DNA binding protein (TDP-43) splicing target, stathmin-2 (STMN2). STMN2 RNA is downregulated in FTD/ALS due to loss of TDP-43 activity and STMN2 loss is suggested to play a role in ALS pathogenesis. The involvement of STMN2 loss of function in FTD has yet to be determined. We find that STMN2 protein levels in familial FTD cases are significantly reduced compared to controls, supporting that STMN2 depletion may be involved in the pathogenesis of FTD. Here, we provide proof-of-concept that we can simultaneously knock down Stmn2 and express the expanded repeat in the Chromosome 9 open reading frame 72 (C9ORF72) gene, successfully replicating features of C9-associated pathology. Of interest, depletion of Stmn2 had no effect on expression or deposition of dipeptide repeat proteins (DPRs), but significantly decreased the number of phosphorylated Tdp-43 (pTdp-43) inclusions. We submit that our novel CRISPRi mouse provides a versatile and rapid method to silence gene expression in vivo and propose this model will be useful to understand gene function in isolation or in the context of other neurodegenerative disease models.

Large structural variants in KOLF2.1J are unlikely to compromise neurological disease modelling

Gracia-Diaz and colleagues analysed high-density DNA microarray and whole genome sequencing (WGS) data from the KOLF2.1J 'reference' human induced pluripotent stem cell (hiPSC) line1, and report the presence of five high-confidence heterozygous copy number variants (CNVs) at least 100kbp in length2. Since three of these CNVs span coding genes, some of which have been associated with neurodevelopmental disease, the authors raise the concern that these CNVs may compromise the utility of KOLF2.1J for neurological disease modelling. We appreciate their thorough analysis and thoughtful interpretation, and agree that potential users of this line should be made aware of all cases where KOLF2.1J differs from the reference genome. However, we believe that the benefits from the widespread use of KOLF2.1J outweigh the potential risks that might arise from the identified CNVs.

Estimation of capitation expense for specialty services

Sources of financial uncertainty under capitation plans include not knowing the game rules, using the wrong game rules, basing financial decisions on incomplete data, or even being clueless about the factors that will determine financial risk. Financial risks under managed care can involve price, utilization, selection, and partner risks. Risks can vary by contract type. Controlling risk requires adequate information. Methods to manage risk include the modeling of risk implications; reliance on the law of large numbers; and the use of risk-sharing arrangements, stop-loss insurance, traditional insurance techniques, and various specific contracting techniques.

The association between deaths from myocardial infarction and household size in England and Wales

BACKGROUND

Chronic infection with organisms such as Chlamydia pneumoniae is thought to cause coronary heart disease. We investigated whether myocardial infarction deaths are associated with large household size and overcrowding, as these are factors that may facilitate the transmission of infection.

DESIGN

Ecological study of England and Wales.

METHODS

Population data were obtained from the 1991 National Census and mortality data were obtained from the Office of National Statistics. For various categories of household size and overcrowding, we calculated mortality rates standardized for age, sex and deprivation.

RESULTS

Standardized mortality rates for acute respiratory infections were associated with household size and overcrowding, while rates for myocardial infarction and gastric carcinoma, both putatively associated with chronic infection, were associated with household size. For combined deaths from causes other than myocardial infarction, there were small associations with household size and overcrowding. In the case of myocardial infarction, the association was generally strongest in the age group 45-54.9 years. For this age group, the standardized mortality rate ratio for the category of largest size household was 2.7 in the year 1991.

CONCLUSIONS

There is an association between household size and mortality from myocardial infarction. Chronic infection is a possible cause.

Investigations of dynamic amyloid-like structures of the Wnt signalling pathway by solid-state NMR

We report solid-state Nuclear Magnetic Resonance (ssNMR) studies on amyloid-like protein complexes formed by DIX domains that mediate key protein interactions in the Wnt signalling pathway. Our results provide insight into the 3D fold of the self-associated Axin-DIX domain and identify a potential lipid cofactor.

Anaesthesia for the neonatal pig--'the micropig'

The use of spontaneous respiration of oxygen, nitrous oxide, and halothane via Jackson Rees's modification of Ayre's T-piece and a flexible 'snout' mask proved to be a simple and effective way of anaesthetizing neonatal pigs--'micropigs'--in the first few days of life without resorting to endotracheal intubation. No airway obstruction occurred as long as the head was extended with firm traction on the jaw and provided the nostrils were not pressed up against the wall of the mask. The anaesthetic technique described provided adequate muscle relaxation and analgesia for extensive abdominal surgery. The animals recovered rapidly and there were no postoperative complications.

[Species-specific monoclonal antibodies against the major outer membrane protein (MOMP) of Chlamydia trachomatis]

The synthesized one quarter N-terminal MOMP of C. trachomatis was used for primary immunization of three male BALB/c mice (8 weeks of age), and the boost with C. trachomatis L1/440/Bu elementary bodies (EBs) was followed on day 14. Spleen cells from one mouse with good response of immunization were fused with murine myeloma NS-1 cells on day 24. The hybrid cell suspension was seeded into the wells of 96-well microtest plates which contained macrophage feeder layers. Anti-chlamydial antibodies in culture fluids were screened by ELISA with 1/4 MOMP & L1 EBs coated 96-well trays. Positive wells were cloned by limiting dilution. Four clones which secreted immunoglobulin G1 & G2a class were obtained after elimination of those clones that produced antibodies to C. psittaci strain EAE, C. pneumoniae strain ATCC VR1310 and uninfected BGMK cells. In micro-IF test, we found that the all four clones of MAbs reacted with our laboratory prepared L1, L2, A, B, C, E EBs, L2 tissue culture inclusions, as well as the EBs of all 15 standard serovars of C. trachomatis. The titers of their ascites were more than 1:12,800 in micro-IF test. It was shown that the four clones of MAbs reacted predominantly with 40,000 MOMP of C. trachomatis L1 in Western blot.

FTLD targets brain regions expressing recently evolved genes

In frontotemporal lobar degeneration (FTLD), pathological protein aggregation is associated with a decline in human-specialized social-emotional and language functions. Most disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD targets brain regions that express genes containing human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution. To this end, we used structural neuroimaging from patients with FTLD and normative human regional transcriptomic data to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions expressing recently evolved genes. In addition, we asked whether genes expressed in FTLD-targeted brain regions are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired. We found that FTLD-TDP and FTLD-tau subtypes target brain regions that express overlapping and distinct genes, including many linked to neuromodulatory functions. Genes whose normative brain regional expression pattern correlated with FTLD cortical atrophy were strongly associated with HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes. Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary specialization and provide intriguing potential leads regarding the transcriptomic basis for selective vulnerability in distinct FTLD molecular-anatomical subtypes.

HDGFL2 cryptic proteins report presence of TDP-43 pathology in neurodegenerative diseases

This letter demonstrates the potential of novel cryptic proteins resulting from TAR DNA-binding protein 43 (TDP-43) dysfunction as markers of TDP-43 pathology in neurodegenerative diseases.

Chlamydial urethral infection in male students in Chiang Mai: a screening test of urine deposits by enzyme immunoassay (EIA)

Adolescent males are considered to be an important genital chlamydial reservoir. However, there has been little information on urethral chlamydial infection in Thai adolescent males. About one fourth of males who are genital chlamydial reservoirs are asymptomatic. An appropriate means of defining the extent of chlamydial infection in adolescent males would be a non-invasive screening survey, instead of the conventional method of a deep swab cell culture, which is painful. The objectives of this study were to estimate the prevalence and to determine what factors should indicate the use of a screening test for urethral chlamydial infection in adolescent males residing in Chiang Mai. Chlamydial urethritis was detected by examining urine deposits for chlamydial antigen by enzyme immunoassay (EIA).