NetCleave: An Open-Source Algorithm for Predicting C-Terminal Antigen Processing for MHC-I and MHC-II.

T cell epitopes presented on the surface of mammalian cells are subjected to a complex network of antigen processing and presentation. Among them, C-terminal antigen processing constitutes one of the main bottlenecks for the generation of epitopes, as it defines the C-terminal end of the final epitope and delimits the peptidome that will be presented downstream. Previously (Amengual-Rigo and Guallar, Sci Rep 111(11):1-8, 2021), we demonstrated that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, which in its turn can be crucial to design peptide-based vaccination strategies.

CDK6 is activated by the atypical cyclin I to promote E2F-mediated gene expression and cancer cell proliferation.

Cyclin-dependent kinases (CDKs), together with their cyclin partners, are the master cell cycle regulators. Remarkably, the cyclin family was extended to include atypical cyclins, characterized by distinctive structural features, but their partner CDKs remain elusive. Here, we conducted a yeast two-hybrid screen to identify new atypical cyclin-CDK complexes.

Peroxygenase-Catalysed Selective Oxidation of Silanes to Silanols.

A peroxygenase-catalysed hydroxylation of organosilanes is reported. The recombinant peroxygenase from Agrocybe aegerita (AaeUPO) enabled efficient conversion of a broad range of silane starting materials in attractive productivities (up to 300 mM h ), catalyst performance (up to 84 s and more than 120 000 catalytic turnovers). Molecular modelling of the enzyme-substrate interaction puts a basis for the mechanistic understanding of AaeUPO selectivity.

Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein.

Domain swapping is a mechanism of protein oligomerization by which two or more subunits exchange structural elements to generate an intertwined complex. Numerous studies support a diversity of swapping mechanisms in which structural elements can be exchanged at different stages of the folding pathway of a subunit. Here, we used single-molecule optical tweezers technique to analyze the swapping mechanism of the forkhead DNA-binding domain of human transcription factor FoxP1.

SBMOpenMM: A Builder of Structure-Based Models for OpenMM.

Molecular dynamics (MD) simulations have become a standard tool to correlate the structure and function of biomolecules and significant advances have been made in the study of proteins and their complexes. A major drawback of conventional MD simulations is the difficulty and cost of obtaining converged results, especially when exploring potential energy surfaces containing considerable energy barriers. This limits the wide use of MD calculations to determine the thermodynamic properties of biomolecular processes.

Dynamic chromatin association of IκBα is regulated by acetylation and cleavage of histone H4.

IκBs exert principal functions as cytoplasmic inhibitors of NF-kB transcription factors. Additional roles for IκB homologues have been described, including chromatin association and transcriptional regulation. Phosphorylated and SUMOylated IκBα (pS-IκBα) binds to histones H2A and H4 in the stem cell and progenitor cell compartment of skin and intestine, but the mechanisms controlling its recruitment to chromatin are largely unknown.

Assessing disease experience across the life span for individuals with osteogenesis imperfecta: challenges and opportunities for patient-reported outcomes (PROs) measurement: a pilot study.

Background: Patient reported outcome (PRO) information is crucial for establishing better patient-provider communication, improving shared decision-making between clinicians and patients, assessing patient responses to therapeutic interventions, and increasing satisfaction with care. We used the Brittle Bones Disease Consortium (BBDC) Contact Registry for People with OI, managed by the Rare Disease Clinical Research Network (RDCRN) to (1) to evaluate the construct validity of the Patient-Reported Outcome Measurement Information System® (PROMIS®) to record important components of the disease experience among individuals with OI; and (2) explore the feasibility of using a registry to recruit individuals with OI to report on health status. Our long-term goal is to enhance communication of health and disease management findings back to the OI community, especially those who do not have access to major OI clinical centers.

Incorporating the patient perspective in the study of rare bone disease: insights from the osteogenesis imperfecta community.

Unlabelled: There is limited research which examines health concerns of individuals with osteogenesis imperfecta (OI). Discussion groups with leaders of the adult OI community identified a broad range of medical priorities beyond fractures and brittle bones. Our work underscores the need to include patient-reported outcomes in rare bone disease research.

Author Correction: The energy cost of polypeptide knot formation and its folding consequences.

The original version of this article contained an error in the spelling of the author Christian A.M. Wilson, which was incorrectly given as Christian M.

The energy cost of polypeptide knot formation and its folding consequences.

Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain-an event that can potentially impair its folding-and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.

Proteoliposomal formulations of an HIV-1 gp41-based miniprotein elicit a lipid-dependent immunodominant response overlapping the 2F5 binding motif.

The HIV-1 gp41 Membrane Proximal External Region (MPER) is recognized by broadly neutralizing antibodies and represents a promising vaccine target. However, MPER immunogenicity and antibody activity are influenced by membrane lipids. To evaluate lipid modulation of MPER immunogenicity, we generated a 1-Palmitoyl-2-oleoylphosphatidylcholine (POPC)-based proteoliposome collection containing combinations of phosphatidylserine (PS), GM3 ganglioside, cholesterol (CHOL), sphingomyelin (SM) and the TLR4 agonist monophosphoryl lipid A (MPLA).

Initial report of the osteogenesis imperfecta adult natural history initiative.

Background: A better understanding of the natural history of osteogenesis imperfecta (OI) in adulthood should improve health care for patients with this rare condition.

Methods: The Osteogenesis Imperfecta Foundation established the Adult Natural History Initiative (ANHI) in 2010 to give voice to the health concerns of the adult OI community and to begin to address existing knowledge gaps for this condition. Using a web-based platform, 959 adults with self-reported OI, representing a wide range of self-reported disease severity, reported symptoms and health conditions, estimated the impact of these concerns on present and future health-related quality of life (QoL) and completed a Patient-Reported Outcomes Measurement Information System (PROMIS®) survey of health issues.

Hypertension after renal transplantation. Calcium channel or converting enzyme blockade?

We compared the effects of 4 weeks of calcium channel blockade (amlodipine) or converting enzyme inhibition (lisinopril) on blood pressure and renal hemodynamics in a double-blind crossover trial in a group of 20 hypertensive cyclosporine-treated renal transplant patients. Amlodipine (10 mg) was more effective than the same dose of lisinopril in controlling hypertension (mean 24-hour arterial pressure, 111 +/- 9 and 115 +/- 9 mm Hg, respectively; P < .05).

Effect of loracarbef and amoxicillin on the oropharyngeal and intestinal microflora of patients with bronchitis.

The effect on the oropharyngeal and intestinal microflora and the efficacy and tolerance of loracarbef (200 mg b.i.d.

Comparison of three days' therapy with cefcanel or amoxicillin for the treatment of acute uncomplicated urinary tract infection.

The clinical and bacteriologic efficacy of 3 days of cefcanel daloxate therapy, compared with 3 days of amoxicillin for the treatment of acute uncomplicated urinary tract infection was compared in a prospective randomized double-blind multicentre study. 400 subjects were randomized to receive cefcanel daloxate and 199 to receive amoxicillin. 166 (77%) of 215 evaluable cefcanel daloxate subjects and 72 (77%) of 94 evaluable amoxicillin subjects evidenced bacteriologic elimination at short-term follow-up, while in 149 (69%) and 67 (71%), respectively, clinical symptoms disappeared.

Fecal bile acid excretion and composition in response to changes in dietary wheat bran, fat and calcium in the rat.

The effect and possible interactive influence of different dietary amounts of wheat bran, fat and calcium on the fecal excretion, concentration and composition of bile acids was studied in Fischer-344 rats. The fecal bile acids were analyzed using gas-liquid chromatography. Dietary wheat bran increased both total bile acid excretion and fecal weight without changes in fecal bile acid concentration.

Magnesium and calcium absorption in Fischer-344 rats influenced by changes in dietary fibre (wheat bran), fat and calcium.

Magnesium and calcium absorption were affected by changes in dietary wheat bran fibre and calcium, but not fat, in Fischer-344 rats when studied in a full factorial study which was a portion of a larger study of diet and colon carcinogenesis. For four weeks, nine-week-old rats were fed experimental purified diets to which had been added: wheat bran 0, 2.5 10, or 20%; fat 1, 5 or 10%; and calcium 0.

Serum gastrin increases with increasing dietary calcium but not with increasing dietary fat or fiber in Fischer-344 rats.

We studied the effects of dietary calcium, fat and fiber on serum gastrin in Fischer-344 rats in a full factorial experiment as part of a larger study of diet and colon cancer risk factors. Nine- to 10-wk-old male rats were fed standard or experimental diets for 4 wk. Wheat bran was the sole source of fiber.

Stability and expression of transferred DNA in F1 tobacco transformants studied at various states of differentiation.

Grafts from the SR1 tobacco crown-gall lines NT1 (having a deletion eliminating part of the transferred (TL)-DNA auxin locus) and NT2 (having an IS60 insertion in gene 2 of this auxin locus) were cross-pollinated with pollen from nontransformed SR1 tobacco plants. One half of the resulting F1 progeny resembled the female parent ("transformed" NT1-like and NT2-like seedlings respectively) and one half resembled the male parent ("non-transformed" SR1-like seedlings). For three states of differentiation (callus, shoot, graft) all phenotypic markers of the transformed seedlings studied were identical to those of the transformed female parent.

Transformation of plant protoplasts with DNA: cotransformation of non-selected calf thymus carrier DNA and meiotic segregation of transforming DNA sequences.

With the DNA transformation procedure developed in our laboratory (13) several transformed tobacco SR1 tissues were obtained which, apart from selected and non-selected pTi sequences (T(+)), also had acquired non-selected calf thymus carrier DNA sequences (C(+)), being integrated in their nuclear genomes. From one such tissue (cNT4), with a shooty crown gall phenotype and expressing mannopine synthesis activity (Mas(+)), shoots were grafted and mature, flowering plants (gNT4) were obtained. After cross pollination with wild type SR1 tobacco pollen 49% of the seedlings obtained, had the maternal NT4-like crown gall phenotype and 51% showed wild type (SR1) features.