AlphaFold predictions of fold-switched conformations are driven by structure memorization.

Recent work suggests that AlphaFold (AF)-a deep learning-based model that can accurately infer protein structure from sequence-may discern important features of folded protein energy landscapes, defined by the diversity and frequency of different conformations in the folded state. Here, we test the limits of its predictive power on fold-switching proteins, which assume two structures with regions of distinct secondary and/or tertiary structure. We find that (1) AF is a weak predictor of fold switching and (2) some of its successes result from memorization of training-set structures rather than learned protein energetics.

AlphaFold2 has more to learn about protein energy landscapes.

Recent work suggests that AlphaFold2 (AF2)-a deep learning-based model that can accurately infer protein structure from sequence-may discern important features of folded protein energy landscapes, defined by the diversity and frequency of different conformations in the folded state. Here, we test the limits of its predictive power on fold-switching proteins, which assume two structures with regions of distinct secondary and/or tertiary structure. Using several implementations of AF2, including two published enhanced sampling approaches, we generated >280,000 models of 93 fold-switching proteins whose experimentally determined conformations were likely in AF2's training set.

Disordered proteins mitigate the temperature dependence of site-specific binding free energies.

Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story.

The cellular function of ROP GTPase prenylation is important for multicellularity in the moss Physcomitrium patens.

A complete picture of how signaling pathways lead to multicellularity is largely unknown. Previously, we generated mutations in a protein prenylation enzyme, GGB, and showed that it is essential for maintaining multicellularity in the moss Physcomitrium patens. Here, we show that ROP GTPases act as downstream factors that are prenylated by GGB and themselves play an important role in the multicellularity of P.

Development and optimization of an in vivo electrocardiogram recording method and analysis program for adult zebrafish.

Clinically pertinent electrocardiogram (ECG) data from model systems, such as zebrafish, are crucial for illuminating factors contributing to human cardiac electrophysiological abnormalities and disease. Current zebrafish ECG collection strategies have not adequately addressed the consistent acquisition of high-quality traces or sources of phenotypic variation that could obscure data interpretation. Thus, we developed a novel platform to ensure high-quality recording of in vivo subdermal adult zebrafish ECGs and zebrafish ECG reading GUI (zERG), a program to acquire measurements from traces that commercial software cannot examine owing to erroneous peak calling.

Oocytes for Eukaryotic In-Cell NMR.

Understanding how the crowded and complex cellular milieu affects protein stability and dynamics has only recently become possible by using techniques such as in-cell nuclear magnetic resonance. However, the combination of stabilizing and destabilizing interactions makes simple predictions difficult. Here we show the potential of oocytes as an in-cell nuclear magnetic resonance model that can be widely used to measure protein stability and dynamics.

Pulmonary MTBVAC vaccination induces immune signatures previously correlated with prevention of tuberculosis infection.

To fight tuberculosis, better vaccination strategies are needed. Live attenuated -derived vaccine, MTBVAC, is a promising candidate in the pipeline, proven to be safe and immunogenic in humans so far. Independent studies have shown that pulmonary mucosal delivery of Bacillus Calmette-Guérin (BCG), the only tuberculosis (TB) vaccine available today, confers superior protection over standard intradermal immunization.

Stronger induction of trained immunity by mucosal BCG or MTBVAC vaccination compared to standard intradermal vaccination.

BCG vaccination can strengthen protection against pathogens through the induction of epigenetic and metabolic reprogramming of innate immune cells, a process called trained immunity. We and others recently demonstrated that mucosal or intravenous BCG better protects rhesus macaques from infection and TB disease than standard intradermal vaccination, correlating with local adaptive immune signatures. In line with prior mouse data, here, we show in rhesus macaques that intravenous BCG enhances innate cytokine production associated with changes in H3K27 acetylation typical of trained immunity.

The TB vaccine development pathway - An innovative approach to accelerating global TB vaccine development.

Two proof of concept clinical trials with TB vaccines demonstrate that new approaches can prevent sustained TB infection in adolescents (BCG revaccination) and TB disease in adults (M72/ASO1) (Nemes et al., 2018; Tait et al., 2019) [1,2].

Rarity among the rare-large and invasive thymoma, a case report and review.

Thymomas are rare tumors of the thymic epithelium with an incidence of 1.5 cases in a million, with a wide spectrum of morphological, pathologic characteristics, and clinical presentations. Despite its benign histological appearance, it can invade nearby structures or metastasize hence clinicians need to have a high index of suspicion for early diagnosis.

Live-attenuated Mycobacterium tuberculosis vaccine MTBVAC versus BCG in adults and neonates: a randomised controlled, double-blind dose-escalation trial.

Background: Infants are a key target population for new tuberculosis vaccines. We assessed the safety and immunogenicity of the live-attenuated Mycobacterium tuberculosis vaccine candidate MTBVAC in adults and infants in a region where transmission of tuberculosis is very high.

Methods: We did a randomised, double-blind, BCG-controlled, dose-escalation trial at the South African Tuberculosis Vaccine Initiative site near Cape Town, South Africa.

Nitric oxide maintains endothelial redox homeostasis through PKM2 inhibition.

Decreased nitric oxide (NO) bioavailability and oxidative stress are hallmarks of endothelial dysfunction and cardiovascular diseases. Although numerous proteins are S-nitrosated, whether and how changes in protein S-nitrosation influence endothelial function under pathophysiological conditions remains unknown. We report that active endothelial NO synthase (eNOS) interacts with and S-nitrosates pyruvate kinase M2 (PKM2), which reduces PKM2 activity.

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.

The progressive loss of midbrain (MB) dopaminergic (DA) neurons defines the motor features of Parkinson disease (PD), and modulation of risk by common variants in PD has been well established through genome-wide association studies (GWASs). We acquired open chromatin signatures of purified embryonic mouse MB DA neurons because we anticipated that a fraction of PD-associated genetic variation might mediate the variants' effects within this neuronal population. Correlation with >2,300 putative enhancers assayed in mice revealed enrichment for MB cis-regulatory elements (CREs), and these data were reinforced by transgenic analyses of six additional sequences in zebrafish and mice.

Survey of Human Chromosome 21 Gene Expression Effects on Early Development in .

Trisomy for human chromosome 21 (Hsa21) results in Down syndrome (DS), one of the most genetically complex conditions compatible with human survival. Assessment of the physiological consequences of dosage-driven overexpression of individual Hsa21 genes during early embryogenesis and the resulting contributions to DS pathology in mammals are not tractable in a systematic way. A recent study looked at loss-of-function of a subset of orthologs of Hsa21 genes and identified ten candidates with behavioral phenotypes, but the equivalent over-expression experiment has not been done.

TBVAC2020: Advancing Tuberculosis Vaccines from Discovery to Clinical Development.

TBVAC2020 is a research project supported by the Horizon 2020 program of the European Commission (EC). It aims at the discovery and development of novel tuberculosis (TB) vaccines from preclinical research projects to early clinical assessment. The project builds on previous collaborations from 1998 onwards funded through the EC framework programs FP5, FP6, and FP7.

Status of vaccine research and development of vaccines for tuberculosis.

TB is now the single pathogen that causes the greatest mortality in the world, at over 1.6 million deaths each year. The widely used the 90 year old BCG vaccine appears to have minimal impact on the worldwide incidence despite some efficacy in infants.

Application of Microwave Irradiation and Heat to Improve Gliadin Detection and Ricin ELISA Throughput with Food Samples.

The utility of microwave irradiation to accelerate the onset of equilibrium and improve ELISA performance was examined using ELISAs for the detection of the plant toxin ricin and gliadin. The ricin ELISA normally requires several one hour incubations at 37 °C, a total assay time of approximately five hours, and employs a complex buffer containing PBS, Tween-20®, and non-fat milk. Different energy levels and pulse designs were compared to the use of abbreviated incubation times at 37 °C for the detection of ricin in food.

Next-generation sequencing as a tool to quickly identify causative EMS-generated mutations.

The advent of next generation sequencing has influenced every aspect of biological research. Many labs are now using whole genome sequencing in Arabidopsis thaliana as a means to quickly identify EMS-generated mutations present in isolated mutants. Following identification of these mutations, examination of T-DNA insertional alleles defective in candidate genes or complementation of the mutant phenotype with a wild type copy of candidate genes can be used to verify which mutation is causative for the phenotype of interest.

TRANSVAC workshop on standardisation and harmonisation of analytical platforms for HIV, TB and malaria vaccines: 'how can big data help?'.

High-throughput analyses of RNA and protein expression are increasingly used for better understanding of vaccine-induced immunity and protection against infectious disease. With an increasing number of vaccine candidates in clinical development, it is timely to consider standardisation and harmonisation of sample collection, storage and analysis to ensure results of highest quality from these precious samples. These challenges were discussed by a group of international experts during a workshop organised by TRANSVAC, a European Commission-funded Research Infrastructure project.

Abscisic acid regulates root elongation through the activities of auxin and ethylene in Arabidopsis thaliana.

Abscisic acid (ABA) regulates many aspects of plant growth and development, including inhibition of root elongation and seed germination. We performed an ABA resistance screen to identify factors required for ABA response in root elongation inhibition. We identified two classes of Arabidopsis thaliana AR mutants that displayed ABA-resistant root elongation: those that displayed resistance to ABA in both root elongation and seed germination and those that displayed resistance to ABA in root elongation but not in seed germination.

Prenylation is required for polar cell elongation, cell adhesion, and differentiation in Physcomitrella patens.

Protein prenylation is required for a variety of growth and developmental processes in flowering plants. Here we report the consequences of loss of function of all known prenylation subunits in the moss Physcomitrella patens. As in Arabidopsis, protein farnesyltransferase and protein geranylgeranyltransferase type I are not required for viability.

Preventive vaccines for tuberculosis.

There are nearly ten million new cases and 1.4 million deaths from tuberculosis (TB) each year, and the 90-year old bacille calmette-guérin (BCG) vaccine in widespread use appears to have minimal impact on the worldwide incidence, despite demonstrating reasonable efficacy against complications of infant TB and death. Novel vaccine development has accelerated in the past ten years, with at least 16 candidates entering human trials, and a few vaccines have entered into Phase 2b efficacy studies.

Detection and treatment of subclinical tuberculosis.

Reduction of active disease by preventive therapy has the potential to make an important contribution towards the goal of tuberculosis (TB) elimination. This report summarises discussions amongst a Working Group convened to consider areas of research that will be important in optimising the design and delivery of preventative therapies. The Working Group met in Cape Town on 26th February 2012, following presentation of results from the GC11 Grand Challenges in Global Health project to discover drugs for latent TB.

ClgR regulation of chaperone and protease systems is essential for Mycobacterium tuberculosis parasitism of the macrophage.

Chaperone and protease systems play essential roles in cellular homeostasis and have vital functions in controlling the abundance of specific cellular proteins involved in processes such as transcription, replication, metabolism and virulence. Bacteria have evolved accurate regulatory systems to control the expression and function of chaperones and potentially destructive proteases. Here, we have used a combination of transcriptomics, proteomics and targeted mutagenesis to reveal that the clp gene regulator (ClgR) of Mycobacterium tuberculosis activates the transcription of at least ten genes, including four that encode protease systems (ClpP1/C, ClpP2/C, PtrB and HtrA-like protease Rv1043c) and three that encode chaperones (Acr2, ClpB and the chaperonin Rv3269).