Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks.

The vast amount of available sequencing data allows the scientific community to explore different genetic alterations that may drive cancer or favor cancer progression. Software developers have proposed a myriad of predictive tools, allowing researchers and clinicians to compare and prioritize driver genes and mutations and their relative pathogenicity. However, there is little consensus on the computational approach or a golden standard for comparison.

PDBminer to Find and Annotate Protein Structures for Computational Analysis.

Computational methods relying on protein structure strongly depend on the structure selected for investigation. Typical sources of protein structures include experimental structures available at the Protein Data Bank (PDB) and high-quality model structures, such as those available at the AlphaFold Protein Structure Database. Either option has significant advantages and drawbacks, and exploring the wealth of available structures to identify the most suitable ones for specific applications can be a daunting task.

Disseminated infection in a patient with a history of sarcoidosis.

We present a case of infection in a man in his 60s with a history of sarcoidosis, treated for 24 years with systemic corticosteroids and later methotrexate as monotherapy. He presented with low grade fever, dyspnoea and right-sided thoracic pain and was admitted due to a treatment-refractory infection. After a prolonged period of symptoms and diagnostics, acid-fast bacilli were demonstrated in pleural fluid and PCR revealed The patient was treated with intravenous amikacin, peroral azithromycin, rifampicin and ethambutol for a total of 18 months, with a good clinical and radiological treatment response.

TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins.

S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1.

RosettaDDGPrediction for high-throughput mutational scans: From stability to binding.

Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein-protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods.

Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53.

The tumor protein 53 (p53) is involved in transcription-dependent and independent processes. Several p53 variants related to cancer have been found to impact protein stability. Other variants, on the contrary, might have little impact on structural stability and have local or long-range effects on the p53 interactome.

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles.

Mutations, which result in amino acid substitutions, influence the stability of proteins and their binding to biomolecules. A molecular understanding of the effects of protein mutations is both of biotechnological and medical relevance. Empirical free energy functions that quickly estimate the free energy change upon mutation (ΔΔG) can be exploited for systematic screenings of proteins and protein complexes.

T cell receptor sequence clustering and antigen specificity.

There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available.

Electromagnetic navigation bronchoscopy for lung nodule evaluation. Patient selection, diagnostic variables and safety.

Background: Electromagnetic navigation bronchoscopy (ENB) is a relatively new technique to diagnose pulmonary lesions in patients with reduced lung function. Several parameters have been shown to affect diagnostic yield including patient selection. We performed a prospective registration of data on one hundred patients who consecutively underwent electromagnetic navigation bronchoscopy.

New-onset asthma in a bilateral lung transplant patient.

We present a case of new-onset asthma in a 35-year-old man who had undergone bilateral lung transplantation 11 years before due to idiopathic bronchiectasis and pulmonary hypertension. He presented with recurrent episodes of breathlessness, wheezing and coughing. Spirometry demonstrated severe airway obstruction.

In Vivo Selection of a Unique Tandem Repeat Mediated Azole Resistance Mechanism (TR) in Aspergillus fumigatus cyp51A, Denmark.

We report a fatal aspergillosis case in which STRAf typing and whole-genome sequencing substantiated in vivo emergence of an azole-resistant Aspergillus fumigatus with a 120-bp tandem repeat in the promoter region of cyp51A. This event, previously restricted to the environment, challenges current understanding of azole resistance development in A. fumigatus.

Effect of intravenous infusion of exenatide (synthetic exendin-4) on glucose-dependent insulin secretion and counterregulation during hypoglycemia.

This study assessed whether glucose-dependent insulin secretion and overall counterregulatory response are preserved during hypoglycemia in the presence of exenatide. Twelve healthy fasted volunteers were randomized in a triple-blind crossover study to receive either intravenous exenatide (0.066 pmol.

One week's treatment with the long-acting glucagon-like peptide 1 derivative liraglutide (NN2211) markedly improves 24-h glycemia and alpha- and beta-cell function and reduces endogenous glucose release in patients with type 2 diabetes.

Glucagon-like peptide 1 (GLP-1) is potentially a very attractive agent for treating type 2 diabetes. We explored the effect of short-term (1 week) treatment with a GLP-1 derivative, liraglutide (NN2211), on 24-h dynamics in glycemia and circulating free fatty acids, islet cell hormone profiles, and gastric emptying during meals using acetaminophen. Furthermore, fasting endogenous glucose release and gluconeogenesis (3-(3)H-glucose infusion and (2)H(2)O ingestion, respectively) were determined, and aspects of pancreatic islet cell function were elucidated on the subsequent day using homeostasis model assessment and first- and second-phase insulin response during a hyperglycemic clamp (plasma glucose approximately 16 mmol/l), and, finally, on top of hyperglycemia, an arginine stimulation test was performed.

The insulin secretagogues glibenclamide and repaglinide do not influence growth hormone secretion in humans but stimulate glucagon secretion during profound insulin deficiency.

In vitro data have recently suggested that sulfonylureas (SUs) enhance GH secretion by modulating the effects of GHRH and somatostatin in pituitary cells. The present study was undertaken to explore in more detail a possible influence of a single dose of SU (glibenclamide) and a non-SU (repaglinide) insulin secretagogue on circulating GH dynamics. Ten C-peptide-negative type 1 diabetic individuals were examined on three occasions in random order.