A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Metamaterial adhesives for programmable adhesion through reverse crack propagation.

Adhesives are typically either strong and permanent or reversible with limited strength. However, current strategies to create strong yet reversible adhesives needed for wearable devices, robotics and material disassembly lack independent control of strength and release, require complex fabrication or only work in specific conditions. Here we report metamaterial adhesives that simultaneously achieve strong and releasable adhesion with spatially selectable adhesion strength through programmed cut architectures. Nonlinear cuts uniquely suppress crack propagation by forcing cracks to propagate backwards for 60× enhancement in adhesion, while allowing crack growth in the opposite direction for easy release and reusability. This mechanism functions in numerous adhesives on diverse substrates in wet and dry conditions and enables highly tunable adhesion with independently programmable adhesion strength in two directions simultaneously at any location. We create these multifunctional materials in a maskless, digital fabrication framework to rapidly customize adhesive characteristics with deterministic control for next-generation adhesives.

Spectroelectrochemical Studies of CTAB Adsorbed on Gold Surfaces in Perchloric Acid.

The behaviour of CTAB adsorbed on polycrystalline gold electrodes has been studied using a combination of spectroelectrochemical methods. The results indicate that the formation of the layer is the consequence of the precipitation of the CTAB micelles on the electrode surface as bromide ions, which stabilize the micelles, are replaced by perchlorate anions. This process leads to the formation of CTA+ layers in which perchlorate ions are intercalated, in which the adlayer suffers a continuous rearrangement that leads to the formation of micro-dominions of different types of hydrogen-bonded water populations throughout the adlayer. After prolonged cycling, a stable situation is reached. Under these conditions, water molecules permeate through the adlayer toward the electrode surface at potentials positive of the potential of zero charge, due to the repulsion between the CTA+ layer and the positive charge of the electrode.

Recent Advances in the Catalytic Synthesis of the Cyclopentene Core.

Five-membered carbocycles are ubiquitously found in natural products, pharmaceuticals, and other classes of organic compounds. Within this category, cyclopentenes deserve special attention due to their prevalence as targets and as well as key intermediates for synthesizing more complex molecules. Herein, we offer an overview summarizing some significant recent advances in the catalytic assembly of this structural motif. A great variety of synthetic methodologies and strategies are covered, including transition metal-catalyzed or organocatalyzed processes. Both inter- and intramolecular transformations are documented. On this ground, our expertise in the application of C-H functionalization reactions oriented towards the formation of this ring and its subsequent selective functionalization is embedded.

MiRNA Differences Related to Treatment-Resistant Schizophrenia.

Schizophrenia (SZ) is a serious mental disorder that is typically treated with antipsychotic medication. Treatment-resistant schizophrenia (TRS) is the condition where symptoms remain after pharmacological intervention, resulting in long-lasting functional and social impairments. As the identification and treatment of a TRS patient requires previous failed treatments, early mechanisms of detection are needed in order to quicken the access to effective therapy, as well as improve treatment adherence. In this study, we aim to find a microRNA (miRNA) signature for TRS, as well as to shed some light on the molecular pathways potentially involved in this severe condition. To do this, we compared the blood miRNAs of schizophrenia patients that respond to medication and TRS patients, thus obtaining a 16-miRNA TRS profile. Then, we assessed the ability of this signature to separate responders and TRS patients using hierarchical clustering, observing that most of them are grouped correctly (~70% accuracy). We also conducted a network, pathway analysis, and bibliography search to spot molecular pathways potentially altered in TRS. We found that the response to stress seems to be a key factor in TRS and that proteins p53, SIRT1, MDM2, and TRIM28 could be the potential mediators of such responses. Finally, we suggest a molecular pathway potentially regulated by the miRNAs of the TRS profile.

Treated and highly diluted, but wastewater still impacts diversity and energy fluxes of freshwater food webs.

Wastewater treatment plants (WWTPs) have greatly improved water quality globally. However, treated effluents still contain a complex cocktail of pollutants whose environmental effects might go unnoticed, masked by additional stressors in the receiving waters or by spatiotemporal variability. We conducted a BACI (Before-After/Control-Impact) ecosystem manipulation experiment, where we diverted part of the effluent of a large tertiary WWTP into a small, unpolluted stream to assess the effects of a well-treated and highly diluted effluent on riverine diversity and food web dynamics. We sampled basal food resources, benthic invertebrates and fish to search for changes on the structure and energy transfer of the food web with the effluent. Although effluent toxicity was low, it reduced diversity, increased primary production and herbivory, and reduced energy fluxes associated to terrestrial inputs. Altogether, the effluent decreased total energy fluxes in stream food webs, showing that treated wastewater can lead to important ecosystem-level changes, affecting the structure and functioning of stream communities even at high dilution rates. The present study shows that current procedures to treat wastewater can still affect freshwater ecosystems and highlights the need for further efforts to treat polluted waters to conserve aquatic food webs.

C-H Activation of Unbiased C(sp3 )-H Bonds: Gold(I)-Catalyzed Cycloisomerization of 1-Bromoalkynes.

Selective functionalization of non-activated C(sp3 )-H bonds is a major challenge in chemistry, so functional groups are often used to enhance reactivity. Here, we present a gold(I)-catalyzed C(sp3 )-H activation of 1-bromoalkynes without any sort of electronic, or conformational bias. The reaction proceeds regiospecifically and stereospecifically to the corresponding bromocyclopentene derivatives. The latter can be readily modified, comprising an excellent library of diverse 3D scaffolds for medicinal chemistry. In addition, a mechanistic study has shown that the reaction proceeds via a so far unknown mechanism: a concerted [1,5]-H shift / C-C bond formation involving a gold-stabilized vinylcation-like transition state.

Mahalanobis distance tractometry (MaD-Tract) - a framework for personalized white matter anomaly detection applied to TBI.

Imaging-based quantitative measures from diffusion-weighted MRI (dMRI) offer the ability to non-invasively extract microscopic information from human brain tissues. Group-level comparisons of such measures represent an important approach to investigate abnormal brain conditions. These types of analyses are especially useful when the regions of abnormality spatially coincide across subjects. When this is not true, approaches for individualized analyses are necessary. Here we present a framework for single-subject multidimensional analysis based on the Mahalanobis distance. This is conducted along specific white matter pathways represented by tractography-derived streamline bundles. A definition for abnormality was constructed from Wilk's criterion, which accounts for normative sample size, number of features used in the Mahalanobis distance, and multiple comparisons. One example of a condition exhibiting high heterogeneity across subjects is traumatic brain injury (TBI). Using the Mahalanobis distance computed from the three eigenvalues of the diffusion tensor along the cingulum, uncinate, and parcellated corpus callosum tractograms, 8 severe TBI patients were individually compared to a normative sample of 49 healthy controls. For all TBI patients, the analyses showed statistically significant deviations from the normative data at one or multiple locations along the analyzed bundles. The detected anomalies were widespread across the analyzed tracts, consistent with the expected heterogeneity that is hallmark of TBI. Each of the controls subjects was also compared to the remaining 48 subjects in the control group in a leave-one-out fashion. Only two segments were identified as abnormal out of the entire analysis in the control group, thus the method also demonstrated good specificity.

Prepolarized MRI of hard tissues and solid-state matter.

Prepolarized MRI (PMRI) is a long-established technique conceived to counteract the loss in signal-to-noise ratio (SNR) inherent to low-field MRI systems. When it comes to hard biological tissues and solid-state matter, PMRI is severely restricted by their ultra-short characteristic relaxation times. Here we demonstrate that efficient hard-tissue prepolarization is within reach with a special-purpose 0.26 T scanner designed for ex vivo dental MRI and equipped with suitable high-power electronics. We have characterized the performance of a 0.5 T prepolarizer module, which can be switched on and off in 200 µs. To this end, we have used resin, dental and bone samples, all with T1 times of the order of 20 ms at our field strength. The measured SNR enhancement is in good agreement with a simple theoretical model, and deviations in extreme regimes can be attributed to mechanical vibrations due to the magnetic interaction between the prepolarization and main magnets.