Functional Segregation of Overlapping Genes in HIV.

Overlapping genes pose an evolutionary dilemma as one DNA sequence evolves under the selection pressures of multiple proteins. Here, we perform systematic statistical and mutational analyses of the overlapping HIV-1 genes tat and rev and engineer exhaustive libraries of non-overlapped viruses to perform deep mutational scanning of each gene independently. We find a "segregated" organization in which overlapped sites encode functional residues of one gene or the other, but never both. Furthermore, this organization eliminates unfit genotypes, providing a fitness advantage to the population. Our comprehensive analysis reveals the extraordinary manner in which HIV minimizes the constraint of overlapping genes and repurposes that constraint to its own advantage. Thus, overlaps are not just consequences of evolutionary constraints, but rather can provide population fitness advantages.

Mitochondrial protein synthesis quality control.

Human mitochondrial DNA is one of the most simplified cellular genomes and facilitates compartmentalized gene expression. Within the organelle, there is no physical barrier to separate transcription and translation, nor is there evidence that quality control surveillance pathways are active to prevent translation on faulty mRNA transcripts. Mitochondrial ribosomes synthesize 13 hydrophobic proteins that require co-translational insertion into the inner membrane of the organelle. To maintain the integrity of the inner membrane, which is essential for organelle function, requires responsive quality control mechanisms to recognize aberrations in protein synthesis. In this review, we explore how defects in mitochondrial protein synthesis can arise due to the culmination of inherent mistakes that occur throughout the steps of gene expression. In turn, we examine the stepwise series of quality control processes that are needed to eliminate any mistakes that would perturb organelle homeostasis. We aim to provide an integrated view on the quality control mechanisms of mitochondrial protein synthesis and to identify promising avenues for future research.

A Massive Proteogenomic Screen Identifies Thousands of Novel Peptides From the Human "Dark" Proteome.

Although the human gene annotation has been continuously improved over the past 2 decades, numerous studies demonstrated the existence of a "dark proteome", consisting of proteins that were critical for biological processes but not included in widely used gene catalogs. The Genotype-Tissue Expression project generated more than 15,000 RNA-seq datasets from multiple tissues, which modeled 30 million transcripts in the human genome. To provide a resource of high-confidence novel proteins from the dark proteome, we screened 50,000 mass spectrometry runs from over 900 projects to identify proteins translated from the Genotype-Tissue Expression transcript model with proteomic support. We also integrated 3.8 million common genetic variants from the gnomAD database to improve peptide identification. As a result, we identified 170,529 novel peptides with proteomic evidence, of which 6048 passed the strictest standard we defined and were supported by PepQuery. We provided a user-friendly website (https://ncorf.genes.fun/) for researchers to check the evidence of novel peptides from their studies. The findings will improve our understanding of coding genes and facilitate genomic data interpretation in biomedical research.

Parametric information about eye movements is sent to the ears.

Eye movements alter the relationship between the visual and auditory spatial scenes. Signals related to eye movements affect neural pathways from the ear through auditory cortex and beyond, but how these signals contribute to computing the locations of sounds with respect to the visual scene is poorly understood. Here, we evaluated the information contained in eye movement-related eardrum oscillations (EMREOs), pressure changes recorded in the ear canal that occur in conjunction with simultaneous eye movements. We show that EMREOs contain parametric information about horizontal and vertical eye displacement as well as initial/final eye position with respect to the head. The parametric information in the horizontal and vertical directions can be modeled as combining linearly, allowing accurate prediction of the EMREOs associated with oblique (diagonal) eye movements. Target location can also be inferred from the EMREO signals recorded during eye movements to those targets. We hypothesize that the (currently unknown) mechanism underlying EMREOs could impose a two-dimensional eye-movement-related transfer function on any incoming sound, permitting subsequent processing stages to compute the positions of sounds in relation to the visual scene.

Emergence of two distinct spatial folds in a pair of plant virus proteins encoded by nested genes.

Virus genomes may encode overlapping or nested open reading frames that increase their coding capacity. It is not known whether the constraints on spatial structures of the two encoded proteins limit the evolvability of nested genes. We examine the evolution of a pair of proteins, p22 and p19, encoded by nested genes in plant viruses from the genus Tombusvirus. The known structure of p19, a suppressor of RNA silencing, belongs to the RAGNYA fold from the alpha+beta class. The structure of p22, the cell-to-cell movement protein from the 30K family widespread in plant viruses, is predicted with the AlphaFold approach, suggesting a single jelly-roll fold core from the all-beta class, structurally similar to capsid proteins from plant and animal viruses. The nucleotide and codon preferences impose modest constraints on the types of secondary structures encoded in the alternative reading frames, nonetheless allowing for compact, well-ordered folds from different structural classes in two similarly-sized nested proteins. Tombusvirus p22 emerged through radiation of the widespread 30K family, which evolved by duplication of a virus capsid protein early in the evolution of plant viruses, whereas lineage-specific p19 may have emerged by a stepwise increase in the length of the overprinted gene and incremental acquisition of functionally active secondary structure elements by the protein product. This evolution of p19 toward the RAGNYA fold represents one of the first documented examples of protein structure convergence in naturally occurring proteins.

slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.

Trans-splicing of a spliced leader (SL) to the 5' ends of mRNAs is used to produce mature mRNAs in several phyla of great importance to human health and the marine ecosystem. One of the consequences of the addition of SL sequences is the change or disruption of the open reading frames (ORFs) in the recipient transcripts. Given that most SL sequences have one or more of the trinucleotide NUG, including AUG in flatworms, trans-splicing of SL sequences can potentially supply a start codon to create new ORFs, which we refer to as slORFs, in the recipient mRNAs. Due to the lack of a tool to precisely detect them, slORFs were usually neglected in previous studies. In this work, we present the tool slORFfinder, which automatically links the SL sequences to the recipient mRNAs at the trans-splicing sites identified from SL-containing reads of RNA-Seq and predicts slORFs according to the distribution of ribosome-protected footprints (RPFs) on the trans-spliced transcripts. By applying this tool to the analyses of nematodes, ascidians and euglena, whose RPFs are publicly available, we find wide existence of slORFs in these taxa. Furthermore, we find that slORFs are generally translated at higher levels than the annotated ORFs in the genomes, suggesting they might have important functions. Overall, this study provides a tool, slORFfinder (https://github.com/songbo446/slORFfinder), to identify slORFs, which can enhance our understanding of ORFs in taxa with SL machinery.

Short open reading frame genes in innate immunity: from discovery to characterization.

Next-generation sequencing (NGS) technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to affect phenotype through sequence and structure and not via translated protein products despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs) translated from these transcripts are important contributors to diverse biological processes. Interest in SEPs is at an early stage and there is evidence for the existence of thousands of SEPs that are yet unstudied. We hope to pique interest in investigating this unexplored proteome by providing a discussion of SEP characterization generally and describing specific discoveries in innate immunity.

ORF3c is expressed in SARS-CoV-2-infected cells and inhibits innate sensing by targeting MAVS.

Most SARS-CoV-2 proteins are translated from subgenomic RNAs (sgRNAs). While the majority of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. One example is the ORF3a sgRNA that also encodes ORF3c, an enigmatic 41-amino-acid peptide. Here, we show that ORF3c is expressed in SARS-CoV-2-infected cells and suppresses RIG-I- and MDA5-mediated IFN-ß induction. ORF3c interacts with the signaling adaptor MAVS, induces its C-terminal cleavage, and inhibits the interaction of RIG-I with MAVS. The immunosuppressive activity of ORF3c is conserved among members of the subgenus sarbecovirus, including SARS-CoV and coronaviruses isolated from bats. Notably, however, the SARS-CoV-2 delta and kappa variants harbor premature stop codons in ORF3c, demonstrating that this reading frame is not essential for efficient viral replication in vivo and is likely compensated by other viral proteins. In agreement with this, disruption of ORF3c does not significantly affect SARS-CoV-2 replication in CaCo-2, CaLu-3, or Rhinolophus alcyone cells. In summary, we here identify ORF3c as an immune evasion factor of SARS-CoV-2 that suppresses innate sensing in infected cells.

Small peptides: could they have a big role in metabolism and the response to exercise?

Exercise is a powerful non-pharmacological intervention for the treatment and prevention of numerous chronic diseases. Contracting skeletal muscles provoke widespread perturbations in numerous cells, tissues and organs, which stimulate multiple integrated adaptations that ultimately contribute to the many health benefits associated with regular exercise. Despite much research, the molecular mechanisms driving such changes are not completely resolved. Technological advancements beginning in the early 1960s have opened new avenues to explore the mechanisms responsible for the many beneficial adaptations to exercise. This has led to increased research into the role of small peptides (<100 amino acids) and mitochondrially derived peptides in metabolism and disease, including those coded within small open reading frames (sORFs; coding sequences that encode small peptides). Recently, it has been hypothesized that sORF-encoded mitochondrially derived peptides and other small peptides play significant roles as exercise-sensitive peptides in exercise-induced physiological adaptation. In this review, we highlight the discovery of mitochondrially derived peptides and newly discovered small peptides involved in metabolism, with a specific emphasis on their functions in exercise-induced adaptations and the prevention of metabolic diseases. In light of the few studies available, we also present data on how both single exercise sessions and exercise training affect expression of sORF-encoded mitochondrially derived peptides. Finally, we outline numerous research questions that await investigation regarding the roles of mitochondrially derived peptides in metabolism and prevention of various diseases, in addition to their roles in exercise-induced physiological adaptations, for future studies.

Microproteins transitioning into a new Phase: Defining the undefined.

Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.

Cortical Correlates of Visuospatial Switching Processes Between Egocentric and Allocentric Frames of Reference: A fNIRS Study.

Human beings represent spatial information according to egocentric (body-to-object) and allocentric (object-to-object) frames of reference. In everyday life, we constantly switch from one frame of reference to another in order to react effectively to the specific needs of the environment and task demands. However, to the best of our knowledge, no study to date has investigated the cortical activity of switching and non-switching processes between egocentric and allocentric spatial encodings. To this aim, a custom-designed visuo-spatial memory task was administered and the cortical activities underlying switching vs non-switching spatial processes were investigated. Changes in concentrations of oxygenated and deoxygenated haemoglobin were measured using functional near-infrared spectroscopy (fNIRS). Participants were asked to memorize triads of geometric objects and then make two consecutive judgments about the same triad. In the non-switching condition, both spatial judgments considered the same frame of reference: only egocentric or only allocentric. In the switching condition, if the first judgment was egocentric, the second one was allocentric (or vice versa). The results showed a generalized activation of the frontal regions during the switching compared to the non-switching condition. Additionally, increased cortical activity was found in the temporo-parietal junction during the switching condition compared to the non-switching condition. Overall, these results illustrate the cortical activity underlying the processing of switching between body position and environmental stimuli, showing an important role of the temporo-parietal junction and frontal regions in the preparation and switching between egocentric and allocentric reference frames.

The potential role of occupational therapy in the treatment of avoidant/restrictive food intake disorder.

Most individuals with avoidant/restrictive food intake disorder (ARFID) never receive treatment, and treatment needs far exceed the current capacity of mental health services. Occupational therapy (OT) focuses on enhancing function in daily activities, including eating and feeding. Given OT's rich history in mental health and pediatric feeding disorder treatment, we spotlight the potential role of OT in ARFID treatment, current knowledge, and opportunities for future research. Through a preliminary exploratory inquiry involving a review of current literature and clinical practice, we investigated OT's current involvement, knowledge, and interprofessional collaborative practice gaps in ARFID treatment. While many occupational therapy practitioners (OTPs) engage in ARFID treatment, interventions lack rigorous evaluation, and there is limited evidence defining OT's distinct role in interprofessional ARFID treatment. OTPs are uniquely positioned to provide interventions for individuals with ARFID across the lifespan, though research is needed to evaluate the efficacy of OT interventions. Future research suggestions include standardizing OT approaches to ARFID treatment and conducting single-case experiments and randomized controlled trials to compare OT approaches with alternative methods. Recommendations to address practice gaps include enhancing ARFID education for OT students and practitioners and fostering a greater understanding of OT's role on the interprofessional team. PUBLIC SIGNIFICANCE: Individuals with ARFID face barriers to eating that impact their health and function. On a multidisciplinary team, OTPs can treat diverse client populations by identifying and addressing barriers to daily participation, such as physical impairments, trauma history, and environmental barriers. More research is needed to evaluate the efficacy of OT practices in ARFID treatment.

A deep learning pipeline for automated classification of vocal fold polyps in flexible laryngoscopy.

PURPOSE: To develop and validate a deep learning model for distinguishing healthy vocal folds (HVF) and vocal fold polyps (VFP) on laryngoscopy videos, while demonstrating the ability of a previously developed informative frame classifier in facilitating deep learning development. METHODS: Following retrospective extraction of image frames from 52 HVF and 77 unilateral VFP videos, two researchers manually labeled each frame as informative or uninformative. A previously developed informative frame classifier was used to extract informative frames from the same video set. Both sets of videos were independently divided into training (60%), validation (20%), and test (20%) by patient. Machine-labeled frames were independently verified by two researchers to assess the precision of the informative frame classifier. Two models, pre-trained on ResNet18, were trained to classify frames as containing HVF or VFP. The accuracy of the polyp classifier trained on machine-labeled frames was compared to that of the classifier trained on human-labeled frames. The performance was measured by accuracy and area under the receiver operating characteristic curve (AUROC). RESULTS: When evaluated on a hold-out test set, the polyp classifier trained on machine-labeled frames achieved an accuracy of 85% and AUROC of 0.84, whereas the classifier trained on human-labeled frames achieved an accuracy of 69% and AUROC of 0.66. CONCLUSION: An accurate deep learning classifier for vocal fold polyp identification was developed and validated with the assistance of a peer-reviewed informative frame classifier for dataset assembly. The classifier trained on machine-labeled frames demonstrates improved performance compared to the classifier trained on human-labeled frames.

How best to support parents in the management of standing frame usage in home settings: A mixed methods study.

BACKGROUND: An improved understanding of the current practice of standing frame use may have implications for supporting parents in managing standing frames. We aimed to investigate how parents of children with cerebral palsy perceive and manage standing frame use in home settings. METHODS: We conducted a mixed methods study with an explanatory sequential design, first collecting and analysing quantitative questionnaire data and then using these results to inform a qualitative follow-up phase to explain them. The questionnaire was answered by 103 parents of children with cerebral palsy across five countries, Denmark, Norway, Great Britain, Canada and the United States, and 12 Danish families participated in the subsequent interviews. A descriptive analysis was conducted using the questionnaire data. The qualitative data were analysed using a directed content analysis, enabling integration of the quantitative and qualitative data. RESULTS: The quantitative analysis showed that 89% of the parents felt confident with their child's standing frame, and 82% felt they had sufficient knowledge about how their child's standing frame could/should be used. However, the qualitative analysis showed that even when feeling confident, the parents experienced insecurity regarding whether their child was positioned correctly, and being responsible for positioning was challenging. CONCLUSION: Our study implies a need for providing educational materials to assist the parents in ensuring optimal positioning of their child in the standing frame to decrease insecurity. Additionally, our study suggests a need to provide more thorough information about the benefits of using a standing frame and ensure alignment of expectations in relation to the child's prognosis of functional independence.

Exponential Fusion of Interpolated Frames Network (EFIF-Net): Advancing Multi-Frame Image Super-Resolution with Convolutional Neural Networks.

Convolutional neural networks (CNNs) have become instrumental in advancing multi-frame image super-resolution (SR), a technique that merges multiple low-resolution images of the same scene into a high-resolution image. In this paper, a novel deep learning multi-frame SR algorithm is introduced. The proposed CNN model, named Exponential Fusion of Interpolated Frames Network (EFIF-Net), seamlessly integrates fusion and restoration within an end-to-end network. Key features of the new EFIF-Net include a custom exponentially weighted fusion (EWF) layer for image fusion and a modification of the Residual Channel Attention Network for restoration to deblur the fused image. Input frames are registered with subpixel accuracy using an affine motion model to capture the camera platform motion. The frames are externally upsampled using single-image interpolation. The interpolated frames are then fused with the custom EWF layer, employing subpixel registration information to give more weight to pixels with less interpolation error. Realistic image acquisition conditions are simulated to generate training and testing datasets with corresponding ground truths. The observation model captures optical degradation from diffraction and detector integration from the sensor. The experimental results demonstrate the efficacy of EFIF-Net using both simulated and real camera data. The real camera results use authentic, unaltered camera data without artificial downsampling or degradation.

The EU as a Political Determinant of Global Health: The Case of Research and Development Incentives for Orphan Medicines and Biotechnology.

CONTEXT: The European Union (EU) governs global health through its constituent laws, institutions, actors and policies. However, it is unclear whether or how these political factors interact to position the Union as a political determinant of global health. METHODS: A case study of the political factors (Rushton and Williams, 2012) influencing the adoption of the EU's Biotechnology Directive 98/44/EC and Orphan Medicines Regulation 141/2000. FINDINGS: The European Commission (EC) generally framed both of its proposals around economical and biomedical paradigms aligned with the needs of the EU's industry and patients, whereas the European Parliament (EP) contested some of these frames and proposed amendments supporting global access to medical products. The political factors influencing the adoption (in the Directive) or rejection (in the Regulation) of the EP's amendments include: the complementarity between the EP and EC proposals; the EP's power in the intra- and inter-institutional negotiating process; the existence and support of civil society; and the alignment with Member State(s)' priorities in the Council. CONCLUSIONS: In the late 1990s, the EU was an internally fragmented and politicised player concerning global health matters. These political factors should be considered for a coherent post-2022 EU strategy on global health.

(Re)Construction of Quantum Space-Time: Transcribing Hilbert into Configuration Space.

Space-time in quantum mechanics is about bridging Hilbert and configuration space. Thereby, an entirely new perspective is obtained by replacing the Newtonian space-time theater with the image of a presumably high-dimensional Hilbert space, through which space-time becomes an epiphenomenon construed by internal observers.

Framing Unions and Nurses.

Union communication and framing are important for how union members, as well as how unions as organizations, are represented. In the context of declining union density and therefore fewer direct union members, unions' daily communication material on social media may be one of the most common interactions people have with unions. This case study focuses on United Nurses of Alberta, the union for most registered nurses in Alberta, Canada, where unionization rates are among the lowest in Canada. This case study shows how United Nurses of Alberta uses two collective action frames, nurses-as-distinct and nurses-as-advocates, in their daily communication to members and the public. In creating and promoting these frames, United Nurses of Alberta draws from and pushes against the industrial relations framework under which they operate and the historical narrative of nurses as caring and self-sacrificing, which may reinforce common understandings of nursing and also limit United Nurses of Alberta's ability to represent their members.

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project.

The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

Small open reading frames: a comparative genetics approach to validation.

Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease.