Mining human microbiomes reveals an untapped source of peptide antibiotics.

Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.

In Search of Lost Small Peptides.

A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.

Shedding Light on the Ghost Proteome.

Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to the identification of proteins translated from alternative open reading frames (AltORFs) in mRNAs. AltORFs are found in addition to predicted reference ORFs and noncoding RNA. Alternative proteins are not represented in the conventional protein databases, and this 'Ghost proteome' was not considered until recently. Some of these proteins are functional, and there is growing evidence that they are involved in central functions in physiological and physiopathological contexts. Here, we review how this Ghost proteome fills the gap in our understanding of signaling pathways, establishes new markers of pathologies, and highlights therapeutic targets.

Cortical activations associated with spatial remapping of finger touch using EEG.

The spatial coding of tactile information is functionally essential for touch-based shape perception and motor control. However, the spatiotemporal dynamics of how tactile information is remapped from the somatotopic reference frame in the primary somatosensory cortex to the spatiotopic reference frame remains unclear. This study investigated how hand position in space or posture influences cortical somatosensory processing. Twenty-two healthy subjects received electrical stimulation to the right thumb (D1) or little finger (D5) in three position conditions: palm down on right side of the body (baseline), hand crossing the body midline (effect of position), and palm up (effect of posture). Somatosensory-evoked potentials (SEPs) were recorded using electroencephalography. One early-, two mid-, and two late-latency neurophysiological components were identified for both fingers: P50, P1, N125, P200, and N250. D1 and D5 showed different cortical activation patterns: compared with baseline, the crossing condition showed significant clustering at P1 for D1, and at P50 and N125 for D5; the change in posture showed a significant cluster at N125 for D5. Clusters predominated at centro-parietal electrodes. These results suggest that tactile remapping of fingers after electrical stimulation occurs around 100-125 ms in the parietal cortex.

Effects of inter-stimulus and inter-trial intervals on somatosensory gating.

AIM OF THE STUDY: Sensory gating is a human higher cognitive function that serves to suppress excessive sensory information and prevent brain overactivity. To elucidate this function, a paired-pulse stimulation paradigm has been used while recording electroencephalography (EEG), and evaluated as an amplitude ratio of responses to a second stimulus (S2) over responses to the first stimulus (S1). The present study investigated the effects of the inter-stimulus interval (ISI) and inter-trial interval (ITI) on somatosensory gating using somatosensory-evoked potentials (SEPs). METHODS: In Experiment 1, ISI was set at five conditions: 200, 400, 600, 800, and 1000 ms. In Experiment 2, ITI was set at four conditions: 1, 2, 4, and 8 s. RESULTS: ISI affected the S2/S1 amplitude ratios of P22 and N27 at C3' and N30 at Fz, and these S2/S1 amplitude ratios decreased the most under the 200 and 400-ms conditions. ITI affected the S2/S1 amplitude ratios of P22, N27, and N60 at C3', and especially, the somatosensory gating did not work under the 1-s condition. These results suggest that not all SEP components are modulated in the same manner with changing ISI and ITI. The effects of ISI and ITI independently affected the somatosensory gating. CONCLUSIONS: Based on our findings, preferable parameters are 200-400 ms for ISI and 4 s or longer for ITI to evaluate the functional mechanisms on somatosensory gating in SEPs.

Sensorimotor integration and motor learning during a novel visuomotor tracing task in young adults with attention-deficit/hyperactivity disorder.

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder that has noted alterations to motor performance and coordination, potentially affecting learning processes and the acquisition of motor skills. This work will provide insight into the role of altered neural processing and sensorimotor integration (SMI) while learning a novel visuomotor task in young adults with ADHD. This work compared adults with ADHD (n = 12) to neurotypical controls (n = 16), using a novel visuomotor tracing task, where participants used their right-thumb to trace a sinusoidal waveform that varied in both frequency and amplitude. This learning paradigm was completed in pre, acquisition, and post blocks, where participants additionally returned and completed a retention and transfer test 24 h later. Right median nerve short latency somatosensory-evoked potentials (SEPs) were collected pre and post motor acquisition. Performance accuracy and variability improved at post and retention measures for both groups for both normalized (P < 0.001) and absolute (P < 0.001) performance scores. N18 SEP: increased in the ADHD group post motor learning and decreased in controls (P < 0.05). N20 SEP: increased in both groups post motor learning (P < 0.01). P25: increased in both groups post motor learning (P < 0.001). N24: increased for both groups at post measures (P < 0.05). N30: decreased in the ADHD group and increased in controls (P < 0.05). These findings suggest that there may be differences in cortico-cerebellar and prefrontal processing in response to novel visuomotor tasks in those with ADHD.NEW & NOTEWORTHY Alterations to somatosensory-evoked potentials (SEPs) were present in young adults with attention-deficit/hyperactivity disorder (ADHD), when compared with neurotypical controls. The N18 and N30 SEP peak had differential changes between groups, suggesting alterations to olivary-cerebellar-M1 processing and SMI in those with ADHD when acquiring a novel visuomotor tracing task. This suggests that short-latency SEPs may be a useful biomarker in the assessment of differential responses to motor acquisition in those with ADHD.

Protein-coding potential of non-canonical open reading frames in human transcriptome.

In recent years, proteogenomics and ribosome profiling studies have identified a large number of proteins encoded by noncoding regions in the human genome. They are encoded by small open reading frames (sORFs) in the untranslated regions (UTRs) of mRNAs and long non-coding RNAs (lncRNAs). These sORF encoded proteins (SEPs) are often <150AA and show poor evolutionary conservation. A subset of them have been functionally characterized and shown to play an important role in fundamental biological processes including cardiac and muscle function, DNA repair, embryonic development and various human diseases. How many novel protein-coding regions exist in the human genome and what fraction of them are functionally important remains a mystery. In this review, we discuss current progress in unraveling SEPs, approaches used for their identification, their limitations and reliability of these identifications. We also discuss functionally characterized SEPs and their involvement in various biological processes and diseases. Lastly, we provide insights into their distinctive features compared to canonical proteins and challenges associated with annotating these in protein reference databases.

Discovering microproteins: making the most of ribosome profiling data.

Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA sequencing and encoded translated regions inferred using sequence-based detection of start and stop combinations longer than 100 amino-acids to prevent false positives. This has led to small ORFs (smORFs) and their encoded proteins left un-annotated. Ribo-seq allows deciphering translated regions from untranslated irrespective of the length. In this review, we describe the power of Ribo-seq data in detection of smORFs while discussing the major challenge posed by data-quality, -depth and -sparseness in identifying the start and end of smORF translation. In particular, we outline smORF cataloguing efforts in humans and the large differences that have arisen due to variation in data, methods and assumptions. Although current versions of smORF reference sets can already be used as a powerful tool for hypothesis generation, we recommend that future editions should consider these data limitations and adopt unified processing for the community to establish a canonical catalogue of translated smORFs.

Has intraoperative neuromonitoring changed the surgery for unruptured middle cerebral artery aneurysms? A retrospective comparative study.

Intraoperative neurophysiological monitoring (IONM) represents one of the available technologies able to assess ischemia and aimed to improve surgical outcome reducing the treatment related morbidity in surgery for intracranial aneurysms. Many studies analyzing the impact of IONM are poised by the heterogeneity bias affecting the cohorts. We report our experience with IONM for surgery of unruptured middle cerebral artery (MCA) aneurysm in order to highlight its influence on functional and radiological outcome and surgical strategy. We retrospectively reviewed all MCA unruptured aneurysms treated between January 2013 and June 2021 by our institutional neurovascular team. Patients were divided into 2 groups according to the use of IONM. A total of 153 patients were included in the study, 52 operated on without IONM and 101 with IONM. The groups did not differ preoperatively regarding clinical status and aneurysm characteristics. Patients operated with IONM had better functional outcomes at discharge as well as at follow-up (p= 0.048, p=0.041) due to lower symptomatic ischemia and better radiological outcome due to lower rate of unexpected aneurysmal remnants (p= 0.0173). The introduction of IONM changed the use of temporary clipping (TeC), increasing its average duration (p= 0.01) improving the safety of dissecting and clipping the aneurysm. IONM in surgery for unruptured MCA aneurysm could improve the efficacy and safety of clipping strategy in the way it showed a role in changing the use of TeC and was associated to the reduction of unexpected aneurysmal remnants' rate and improvement in both short- and long-term patient's outcome.

Soluble extracellular polymeric substance (SEPS) of histo-blood group antigen (HBGA) expressing bacterium Sphingobacterium sp. SC015 influences the survival and persistence of norovirus on lettuce.

Foodborne norovirus (NoV) outbreaks linked to leafy greens are common due to a lack of efficient strategies to prevent NoV spread from contaminated surfaces. We previously found that Sphingobacterium sp. SC015 in lettuce phyllosphere expresses histo-blood group antigen (HBGA)-like substances in soluble extracellular polymeric substances (SEPS) that contribute to NoV adherence on lettuce. Here, we extracted SEPS from bacterium SC015 (SEPS-SC015), analyzed their chemical composition, and examined their roles in the survival and protection of NoV and surrogates [murine norovirus (MNV-1) and Tulane virus (TuV)] on lettuce. Presence of SEPS-SC015 significantly increased survival and persistence of human NoV (HuNoV), MNV-1, and TuV at days 7 and 14, compared with virus alone. HuNoV, TuV, and MNV-1 seeded with SEPS-SC015 were more resistant to heat (70 °C, 2 min) than these viruses alone. SEPS-SC015 also increased viral resistance to sodium hypochlorite inactivation by treatment with 30 and 300 ppm bleach at 26 °C for 10 min. However, SEPS-SC015 was not effective at protecting these viruses under UV inactivation. Binding of TuV to SC015 bacteria and SEPS-SC015, visualized using transmission electron microscopy, suggests that protection might be related to direct interaction between SEPS-SC015 and viral particles. This study provides important insights that will help inform strategies to improve food safety.

Immune-related effects of compound astragalus polysaccharide and sulfated epimedium polysaccharide on newborn piglets.

This study aimed to evaluate the immune effects of compound astragalus polysaccharide and sulfated epimedium polysaccharide (APS-sEPS) on the peripheral blood lymphocyte and intestinal mucosa in newborn piglets. A total of 40 newborn piglets were randomly divided into four groups during a 25-day experiment, including APS-sEPS, APS, sEPS and control group. The results showed that supplementation with APS-sEPS to newborn piglets remarkably increased the physiological parameters, especially the WBC. In peripheral blood, piglets that received APS-sEPS showed the highest proliferation of T lymphocytes, the percentage of CD3 + CD4+ and CD3 + CD8+ cells were the highest on days 15 and 25 (p < 0.05). The serum concentrations of IFN-γ on days 7 and 15, and IL-4, IL-10, sIgA on days 7, 15 and 25 in APS-sEPS group were significantly higher than those in the control group (p < 0.05). Furthermore, the villus length and the ratio of villus length to crypt depth in APS-sEPS group were both significantly increased compared to that of control group (p < 0.05). In the duodenum, jejunum and illume, the concentrations of IFN-γ, IL-10, total IgG and sIgA in APS-sEPS group were all significantly higher than that in control group (p < 0.05). In intestinal mucosa, APS-sEPS significantly increased the expression of NF-κB and IRF-3 mRNA in each section of small intestine of piglets. Nevertheless, in the illume segment, the effect of APS-sEPS was more significant than that of APS and sEPS (p < 0.05). The expression of TLR4 was more significant than that of control group in duodenum only. The results from the present research provide evidence that the suckling piglets administered with APS-sEPS supplement exhibited enhanced immune function of peripheral blood lymphocyte and expression of specific antibodies, and ameliorated intestinal morphological development and increased activities of humoral immune response in the small intestine, which would be related to the activation of the TLR4-NF-κB signaling pathway and IRF3.

Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.

Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or "transcriptional noise". However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids. The vigorous development of computational algorithms, ribosome profiling, and peptidome has facilitated the prediction and identification of many new SEPs. These SEPs were revealed to be involved in a wide range of basic biological processes, such as gene expression regulation, embryonic development, cellular metabolism, inflammation, and even carcinogenesis. To effectively understand the potential biological functions of SEPs, we discuss the history and development of the newly emerging research on sORFs and SEPs. In particular, we review a range of recently discovered bioinformatics tools for identifying, predicting, and validating SEPs as well as a variety of biochemical experiments for characterizing SEP functions. Lastly, this review underlines the challenges and future directions in identifying and validating sORFs and their encoded micropeptides, providing a significant reference for upcoming research on sORF-encoded peptides.

Systematic Identification of Microproteins during the Development of Drosophila melanogaster.

Short open reading frame-encoded peptides (SEPs) are microproteins with less than 100 amino acids that play an essential role in the growth and development of organisms. There are plenty of short open reading frames in Drosophila melanogaster that potentially code polypeptides. We chose 11 time points during the life cycle of Drosophila to investigate microproteins, particularly those related to development. Finally, we identified a total of 410 microproteins, of which 27 were noncoding RNA-encoded proteins. Of the 410 microproteins, 74 were expressed in all stages from embryo to adults, whereas 300 microproteins were only found in one or two time points. Approximately, one-third of the microproteins were not reported previously and 44 were obtained from de novo sequencing, validated by synthetic peptides. These microproteins are related to the main bioprocesses of growth and development, such as multicellular organism reproduction, postmating behavior, and oviposition. Over half of the microproteins have predicted functional domains and are conserved across species, suggesting that these microproteins have critical functions in fly development. This work enriches the D. melanogaster proteome and provides a significant data resource for growth and development research.

Selenoprotein S: A versatile disordered protein.

Selenoprotein S (selenos) is a small, intrinsically disordered membrane protein that is associated with various cellular functions, such as inflammatory processes, cellular stress response, protein quality control, and signaling pathways. It is primarily known for its contribution to the ER-associated degradation (ERAD) pathway, which governs the extraction of misfolded proteins or misassembled protein complexes from the ER to the cytosol for degradation by the proteasome. However, selenos's other cellular roles in signaling are equally vital, including the control of transcription factors and cytokine levels. Consequently, genetic polymorphisms of selenos are associated with increased risk for diabetes, dyslipidemia, and cardiovascular diseases, while high expression levels correlate with poor prognosis in several cancers. Its inhibitory role in cytokine secretion is also exploited by viruses. Since selenos binds multiple protein complexes, however, its specific contributions to various cellular pathways and diseases have been difficult to establish. Thus, the precise cellular functions of selenos and their interconnectivity have only recently begun to emerge. This review aims to summarize recent insights into the structure, interactome, and cellular roles of selenos.

Middle meningeal artery embolization with subdural evacuating port system for primary management of chronic subdural hematomas.

Optimal treatment for chronic subdural hematomas remains controversial and perioperative risks and comorbidities may affect management strategies. Minimally invasive procedures are emerging as alternatives to the standard operative treatments. We evaluate our experience with middle meningeal artery (MMA) embolization combined with Subdural Evacuating Port System (SEPS) placement as a first-line treatment for patients with cSDH. A single institution retrospective review was performed of all patients undergoing intervention. Patients were stratified by treatment with MMA embolization and SEPS placement, MMA embolization and surgery, SEPS placement only, and surgery only for cSDH from 2017 to 2020, and cohorts were compared against each other. Patients treated with MMA/SEPS were more likely to be older, be on anticoagulation, have significant comorbidities, have shorter length of stay, and less likely to have symptomatic recurrence compared to SEPS only cohort. Thus, MMA/SEPS appears to be a safe and equally effective minimally invasive treatment for cSDH patients with significant comorbidities who are poor surgical candidates.

Recovery of structural extracellular polymeric substances (sEPS) from aerobic granular sludge: Insights on biopolymers characterization and hydrogel properties for potential applications.

Nowadays, wastewater treatment plants (WWTPs) are transforming into water resource recovery facilities (WRRFs) where the resource recovery from waste streams is pivotal. Aerobic granular sludge (AGS) is a novel technology applied for wastewater treatment. Extracellular polymeric substances (EPS) secreted by microorganisms promote the aggregation of bacterial cells into AGS and the structural fraction of EPS (sEPS) is responsible for the mechanical properties of AGS. sEPS can be extracted and recovered from waste AGS by physico-chemical methods and its characterization is to date of relevant concern to understand the properties in the perspective of potential applications. This study reports on: characterization of sEPS extracted and recovered from AGS; - formation and characterization of sEPS-based hydrogels. Briefly, sEPS were extracted by a thermo-alkaline process followed by an acidic precipitation. sEPS-based hydrogels were formed by a cross-linking process with a 2.5% w/w CaCl2 solution. The following key-findings can be drawn: i) hydrogels can be formed starting from 1% w/w sEPS on, by diffusion of Ca2+ into sEPS network; ii) the Ca/C molar ratio of hydrogels decreased with increasing concentration of sEPS from 1 to 10% w/w; iii) the thermogravimetric and spectroscopic behaviours of sEPS show that the cross-linking reaction mainly involves the polysaccharidic fraction of biopolymers; iv) water-holding capacity up to 99 gH2O/gsEPS was registered for 1% w/w sEPS-based hydrogels, suggesting applications in several industrial sectors (i.e. chemical, paper, textile, agronomic, etc.); v) rheological results highlighted a solid-like behaviour (G'≫G") of sEPS-based hydrogels. The power-law fitting of G' vs. sEPS concentration suggests that the expansion of the sEPS network during cross-linking occurs through a percolative mechanism involving the initial formation of sEPS oligomers clusters followed by their interconnection towards the formation of 3D network. These findings provide additional information about the mechanisms of sEPS-based hydrogel formation and reveal the peculiar physico-chemical characteristics of sEPS which nowadays are increasingly gaining interest in the context of resource recovery.

Prospective bioremediation of toxic heavy metals in water by surfactant exopolysaccharide of Ochrobactrum pseudintermedium using cost-effective substrate.

Globally, the underlying peril of cumulative toxicity of heavy metals in water bodies contaminated by industrial effluents is a matter of great concern to the environmentalists. Heavy metals like lead, cadmium, and nickel are particularly liable for this. Such toxic water is not only hazardous to human health but also harmful to aquatic animals. Remedial measures are being taken by physico-chemical techniques, but most of them are neither eco-friendly nor cost-effective. Biological means like bioaccumulation of heavy metals by viable bacteria are often tedious. In the present study, biosorption of heavy metals is successfully expedited by surfactant exopolysaccharide (SEPS) of Ochrobactrum pseudintermedium C1 as a simple, safe, and economically sustainable option utilizing an easily available and cost-effective substrate like molasses extract. Its efficacy in bioremediation of toxic heavy metals like cadmium, nickel, and lead have been studied by UV-Vis spectrophotometry and verified by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). FTIR and zeta potential studies have also been carried out to explore this novel biosorption potential. Results are conclusive and promising. Moreover, this particular SEPS alone can remediate all these three toxic heavy metals in water. For futuristic applications, it might be a prospective and cost-effective resource for bioremediation of toxic heavy metals in aqueous environment.

The microproteome of cancer: From invisibility to relevance.

Recent findings have revealed that many genomic regions previously annotated as non-protein coding actually contain small open reading frames, smaller that 300 bp, that are transcribed and translated into evolutionary conserved microproteins. To date, only a small subset of them have been functionally characterized, but they play key functions in fundamental processes such as DNA repair, RNA processing and metabolism regulation. This emergent field seems to hide a new category of molecular regulators with clinical potential. In this review, we focus on its relevance for cancer. Following Hanahan and Weinberg's classification of the hallmarks of cancer, we provide an overview of those microproteins known to be implicated in cancer or those that, based on their function, are likely to play a role in cancer. The resulting picture is that while we are at the very early times of this field, it holds the promise to provide crucial information to understand cancer biology.

Optimized Proteomics Workflow for the Detection of Small Proteins.

Small open reading frame encoded proteins (SEPs) gained increasing interest during the last few years because of their broad range of important functions in both prokaryotes and eukaryotes. In bacteria, signaling, virulence, and regulation of enzyme activities have been associated with SEPs. Nonetheless, the number of SEPs detected in large-scale proteome studies is often low as classical methods are biased toward the identification of larger proteins. Here, we present a workflow that allows enhanced identification of small proteins compared to traditional protocols. For this aim, the steps of small protein enrichment, proteolytic digest, and database search were reviewed and adjusted to the special requirement of SEPs. Enrichment by the use of small-pore-sized solid-phase material increased the number of identified SEPs by a factor of 2, and utilization of alternative proteases to trypsin reduced the spectral counts for larger proteins. The application of the optimized protocol allowed the detection of 210 already annotated proteins up to 100 amino acids (aa) length, including 16 proteins below 51 aa in the Gram-positive model organism Bacillus subtilis. Moreover, 12% of all identified proteins were up to 100 aa, which is a significantly larger fraction than that reported in studies involving traditional proteomics workflows. Finally, the application of an integrated proteogenomics search database and extensive subsequent validation resulted in the confident identification of three novel, not yet annotated, SEPs, which are 21, 26, and 42 aa long.

Anti-chemotactic activity in the secretory/excretory products of Lepeophtheirus salmonis.

The ectoparasite, Lepeophtheirus salmonis (Kroyer 1837), is effective at avoiding elimination from its host, Atlantic salmon, Salmo salar L., by inhibiting the recruitment of immune cells to the site of attachment. In other ectoparasitic arthropods, numerous factors have been identified that bind or neutralize chemokines preventing their interaction with receptors on the surfaces of immune cells. To determine if L. salmonis is utilizing a similar mechanism of immune modulation, the chemotactic activity of peripheral blood leukocytes (PBL) to leukotriene B4 (LTB4) and the secreted/excreted products (SEPs) of the sea louse were investigated in vitro. The results showed that incubation of LTB4 with SEPs reduced leukocyte migration compared to LTB4 immune stimulation alone. Data suggests that one of the mechanisms L. salmonis may be using to regulate immune cell recruitment in Atlantic salmon is by inhibiting or neutralizing the activity of chemokines.