Common domain databases contain sequence motifs which belong to the ubiquitin fold family and are called Ras binding (RB) and Ras association (RalGDS/AF6 Ras associating) (RA) domains. The name ...implies that they bind to Ras (or Ras-like) GTP-binding proteins, and a few of them have been documented to qualify as true Ras effectors, defined as binding only to the activated GTP-bound form of Ras. Here we have expressed a large number of these domains and investigated their interaction with Ras, Rap and M-Ras. While their (albeit weak) sequence homology suggest that the domains adopt a common fold, not all of them bind to Ras proteins, irrespective of whether they are called RB or RA domains. We used fluorescence spectroscopy and isothermal titration calorimetry to show that the binding affinities vary over a large range, and are usually specific for either Ras or Rap. Moreover, the specificity is dictated by a set of key residues in the interface. Stopped-flow kinetic analysis showed that the association rate constants determine the different affinities of effector binding, while the dissociation rate constants are in a similar range. Manual sequence analysis allowed us to define positively charged sequence epitopes in certain secondary structure elements of the ubiquitin fold (β1, β2 and α1) which are located at similar positions and comprise the hot spots of the binding interface. These residues are important to qualify an RA/RB domain as a true candidate Ras or Rap effector.
Background
Immune‐checkpoint inhibitors (ICIs) are an effective therapeutic strategy, improving the survival of patients with lung cancer compared with conventional treatments. However, novel ...predictive biomarkers are needed to stratify which patients derive clinical benefit because the currently used and highly heterogenic histological PD‐L1 has shown low accuracy. Liquid biopsy is the analysis of biomarkers in body fluids and represents a minimally invasive tool that can be used to monitor tumor evolution and treatment effects, potentially reducing biases associated with tumor heterogeneity associated with tissue biopsies. In this context, cytokines, such as transforming growth factor‐β (TGF‐β), can be found free in circulation in the blood and packaged into extracellular vesicles (EVs), which have a specific delivery tropism and can affect in tumor/immune system interaction. TGF‐β is an immunosuppressive cytokine that plays a crucial role in tumor immune escape, treatment resistance, and metastasis. Thus, we aimed to evaluate the predictive value of circulating and EV TGF‐β in patients with non–small‐cell lung cancer receiving ICIs.
Methods
Plasma samples were collected in 33 patients with advanced non–small‐cell lung cancer before and during treatment with ICIs. EV were isolated from plasma by serial ultracentrifugation methods and circulating and EV TGF‐β expression levels were evaluated by enzyme‐linked immunosorbent assay.
Results
Baseline high expression of TGF‐β in EVs was associated with nonresponse to ICIs as well as shorter progression‐free survival and overall survival, outperforming circulating TGF‐β levels and tissue PD‐L1 as a predictive biomarker.
Conclusion
If validated, EV TGF‐β could be used to improve patient stratification, increasing the effectiveness of treatment with ICIs and potentially informing combinatory treatments with TGF‐β blockade.
Plain language summary
Treatment with immune‐checkpoint inhibitors (ICIs) has improved the survival of some patients with lung cancer. However, the majority of patients do not benefit from this treatment, making it essential to develop more reliable biomarkers to identify patients most likely to benefit.
In this pilot study, the expression of transforming growth factor‐β (TGF‐β) in blood circulation and in extracellular vesicles was analyzed.
The levels of extracellular vesicle TGF‐β before treatment were able to determine which patients would benefit from treatment with ICIs and have a longer survival with higher accuracy than circulating TGF‐β and tissue PD‐L1, which is the currently used biomarker in clinical practice.
Extracellular vesicle transforming growth factor‐β (TGF‐β) outperformed circulating TGF‐β and standard tissue PD‐L1 characterization for predicting treatment response and survival of patients with non–small cell lung cancer undergoing treatment with immune checkpoint inhibitors.
Context.
Future weak lensing surveys, such as the
Euclid
mission, will attempt to measure the shapes of billions of galaxies in order to derive cosmological information. These surveys will attain ...very low levels of statistical error, and systematic errors must be extremely well controlled. In particular, the point spread function (PSF) must be estimated using stars in the field, and recovered with high accuracy.
Aims.
The aims of this paper are twofold. Firstly, we took steps toward a nonparametric method to address the issue of recovering the PSF field, namely that of finding the correct PSF at the position of any galaxy in the field, applicable to
Euclid
. Our approach relies solely on the data, as opposed to parametric methods that make use of our knowledge of the instrument. Secondly, we studied the impact of imperfect PSF models on the shape measurement of galaxies themselves, and whether common assumptions about this impact hold true in an
Euclid
scenario.
Methods.
We extended the recently proposed resolved components analysis approach, which performs super-resolution on a field of under-sampled observations of a spatially varying, image-valued function. We added a spatial interpolation component to the method, making it a true 2-dimensional PSF model. We compared our approach to
PSFEx
, then quantified the impact of PSF recovery errors on galaxy shape measurements through image simulations.
Results.
Our approach yields an improvement over
PSFEx
in terms of the PSF model and on observed galaxy shape errors, though it is at present far from reaching the required
Euclid
accuracy. We also find that the usual formalism used for the propagation of PSF model errors to weak lensing quantities no longer holds in the case of an
Euclid
-like PSF. In particular, different shape measurement approaches can react differently to the same PSF modeling errors.
Chagas disease (CD) is caused by the protozoan Trypanosoma cruzi, which leads to a spectrum of clinical presentations that range from asymptomatic to severe cardiac involvement. The host immune ...response plays a pivotal role in disease progression. Ig isotypes may contribute to disease pathogenesis. Investigating these components can provide insights into the immunopathogenic mechanisms underlying CD. This cross-sectional study aims to establish a correlation between the Ig profile of individuals infected with T. cruzi with the clinical forms of chronic CD. Serum samples were collected from partner institutions in different states of Brazil. Individuals diagnosed with chronic CD were categorized based on the clinical form of the disease. The indirect ELISA method using the recombinant chimeric Molecular Biology Institute of Paraná membrane protein 8.4 as the antigen was used to determine the Ig profile, including total IgG, IgG1, IgG2, IgG3, and IgG4. Ninety-seven serum samples from patients classified as negative (NEG, n = 38), indeterminate (IND, n = 24), mild cardiac (MC, n = 20), and severe cardiac (SC, n = 15) forms were analyzed. IgG1 exhibited greater levels compared with the other isotypes, showing a significant difference between the MC and IND groups. IgG3 levels were greater in individuals from the MC group compared with the SC group. IgG1 and IgG3 isotypes can serve as biomarkers to evaluate the progression of CD because they exhibit variations across clinical groups. Additional longitudinal studies are necessary to explore the relationship between antibody kinetics and the development of tissue damage.
Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening ...rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.
Concomitant trisomy 2q3 and monosomy 4q3 have been rarely reported. Pure trisomy 2q3 has been associated with microcephaly, hypertelorism, low-set ears, micrognathia, visceral abnormalities, and ...growth retardation. Monosomy 4q3 includes a wide variety of dysmorphic features such an abnormal skull shape, hypertelorism, Pierre Robin sequence, short nose with abnormal bridge, fifth finger clinodactyly, congenital heart, and genitourinary defects, in addition to intellectual disability, developmental delay, and hypotonia, but more distal deletions involving 4q34-qter may result in milder phenotypes. Here, we present a child with a mild dysmorphic syndrome, resulted of a duplication 2q34-qter and a deletion 4q35.2-qter inherited of his father.
We report a child, who at birth presented hypotonia, dysmorphism, and bilateral cryptorchidism. At 2 years and 9 month of age he showed brachycephaly, narrow forehead, bilateral frontoparietal hypertrichosis, down slanting palpebral fissures, sparse eyebrows, sparse short eyelashes, hypertelorism, depressed nasal root, broad nasal bridge, bulbous nasal tip, prominent colummela, broad nasal ala, smooth filtrum, high arched palate, thin upper lips, and ears rotated backwards. He also showed telethelia, hypertrichosis from dorsal to the sacral region, hands with clinodactyly and hypoplasia of the terminal phalanx of the fifth finger, and broad thumbs, broad first toes, and right cryptorchidism. A chromosomal study revealed a karyotype 46,XY,der(4)t(2;4)(q34;q35.2), while an array comparative genomic hybridization showed a 31.12 Mb duplication of the chromosome 2q34-q37.3 and a 1.49 Mb deletion in the chromosome 4q35.2.
To our knowledge, only four families with translocation t(2;4) have been reported, two of them involving t(2q;4q), but the breakpoints involved in our patient have not been previously observed. The genomic imbalance in this patient was a duplication of 318 genes of the region 2q34-q37.3 and a deletion of 7 genes of 4q35.2. We discuss difficulty to assign specific congenital abnormalities to these duplicated/deleted regions and include some cases with terminal deletions of 4q with normal or just mildly detectable phenotypic effects.
Abstract
The vacuolar H+-ATPase is an enzymatic complex that functions in an ATP-dependent manner to pump protons across membranes and acidify organelles, thereby creating the proton/pH gradient ...required for membrane trafficking by several different types of transporters. We describe heterozygous point variants in ATP6V0C, encoding the c-subunit in the membrane bound integral domain of the vacuolar H+-ATPase, in 27 patients with neurodevelopmental abnormalities with or without epilepsy. Corpus callosum hypoplasia and cardiac abnormalities were also present in some patients. In silico modelling suggested that the patient variants interfere with the interactions between the ATP6V0C and ATP6V0A subunits during ATP hydrolysis. Consistent with decreased vacuolar H+-ATPase activity, functional analyses conducted in Saccharomyces cerevisiae revealed reduced LysoSensor fluorescence and reduced growth in media containing varying concentrations of CaCl2. Knockdown of ATP6V0C in Drosophila resulted in increased duration of seizure-like behaviour, and the expression of selected patient variants in Caenorhabditis elegans led to reduced growth, motor dysfunction and reduced lifespan. In summary, this study establishes ATP6V0C as an important disease gene, describes the clinical features of the associated neurodevelopmental disorder and provides insight into disease mechanisms.
Mattison et al. identify ATP6V0C variants in patients with a neurodevelopmental syndrome. Using computational modelling and studies in Drosophila, yeast and worms, they show that the variants result in decreased V-ATPase function, providing evidence for their pathogenicity as well as insights into the underlying disease mechanisms.
Considering the large number of putative Ras effector proteins, it is highly desirable to develop computational methods to be able to identify true Ras binding molecules. Based on a limited sequence ...homology among members of the Ras association (RA) and Ras binding (RB) sub-domain families of the ubiquitin super-family, we have built structural homology models of Ras proteins in complex with different RA and RB domains, using the FOLD-X software. A critical step in our approach is to use different templates of Ras complexes, in order to account for the structural variation among the RA and RB domains. The homology models are validated by predicting the effect of mutating hot spot residues in the interface, and residues important for the specificity of interaction with different Ras proteins. The FOLD-X calculated energies of the best-modelled complexes are in good agreement with previously published experimental data and with new data reported here. Based on these results, we can establish energy thresholds above, or below which, we can predict with 96% confidence that a RA/RB domain will or will not interact with Ras. This study shows the importance of in depth structural analysis, high quality force-fields and modelling for correct prediction. Our work opens the possibility of genome-wide prediction for this protein family and for others, where there is enough structural information.
This paper presents an estimation of the quantity of carbon fixed in trees in a one hectare (ha) plot at the Cerro Pelado-Gamboa Hydrology Tropical Observatory, which is located in the province of ...Colon, Panama. The estimation of carbon fixed in trees may provide significant information on carbon flux due to water circulation, which may ultimately enable evaluation of the carbon cycle. All trees larger than 10 cm diameter at breast height (DBH) in the plot were investigated. Carbon fixed within these trees was estimated using a parameterized formula. Tree biomass estimations for the plot were 97.21 Mg ha-1. We identified a rare arboreal pear species (Euphorbiaceous) with higher carbon density than other trees in the plot. The presence of this apparently unique species may be due to specific soil characteristics. The method was evaluated by comparing the results with a second study performed in 2011, which resulted in an estimate of net new carbon (biomass) increment (NNCI), which gives 3.88 Mg ha-1 year-1. In general, the estimation of the biomass and associated carbon content found in this investigation are useful comparative data for economic evaluation of tropical forests in terms of capacity to capture carbon.
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