Microbial Signatures in COVID-19: Distinguishing Mild and Severe Disease via Gut Microbiota.

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has significantly impacted global healthcare, underscoring the importance of exploring the virus's effects on infected individuals beyond treatments and vaccines. Notably, recent findings suggest that SARS-CoV-2 can infect the gut, thereby altering the gut microbiota. This study aimed to analyze the gut microbiota composition differences between COVID-19 patients experiencing mild and severe symptoms. We conducted 16S rRNA metagenomic sequencing on fecal samples from 49 mild and 43 severe COVID-19 cases upon hospital admission. Our analysis identified a differential abundance of specific bacterial species associated with the severity of the disease. Severely affected patients showed an association with Enterococcus faecium, Akkermansia muciniphila, and others, while milder cases were linked to Faecalibacterium prausnitzii, Alistipes putredinis, Blautia faecis, and additional species. Furthermore, a network analysis using SPIEC-EASI indicated keystone taxa and highlighted structural differences in bacterial connectivity, with a notable disruption in the severe group. Our study highlights the diverse impacts of SARS-CoV-2 on the gut microbiome among both mild and severe COVID-19 patients, showcasing a spectrum of microbial responses to the virus. Importantly, these findings align, to some extent, with observations from other studies on COVID-19 gut microbiomes, despite variations in methodologies. The findings from this study, based on retrospective data, establish a foundation for future prospective research to confirm the role of the gut microbiome as a predictive biomarker for the severity of COVID-19.

Evaluation of serum and urine biomarkers for severe COVID-19.

Introduction: The new coronavirus disease, COVID-19, poses complex challenges exacerbated by several factors, with respiratory tissue lesions being notably significant among them. Consequently, there is a pressing need to identify informative biological markers that can indicate the severity of the disease. Several studies have highlighted the involvement of proteins such as APOA1, XPNPEP2, ORP150, CUBN, HCII, and CREB3L3 in these respiratory tissue lesions. However, there is a lack of information regarding antibodies to these proteins in the human body, which could potentially serve as valuable diagnostic markers for COVID-19. Simultaneously, it is relevant to select biological fluids that can be obtained without invasive procedures. Urine is one such fluid, but its effect on clinical laboratory analysis is not yet fully understood due to lack of study on its composition. Methods: Methods used in this study are as follows: total serum protein analysis; ELISA on moderate and severe COVID-19 patients' serum and urine; bioinformatic methods: ROC analysis, PCA, SVM. Results and discussion: The levels of antiAPOA1, antiXPNPEP2, antiORP150, antiCUBN, antiHCII, and antiCREB3L3 exhibit gradual fluctuations ranging from moderate to severe in both the serum and urine of COVID-19 patients. However, the diagnostic value of individual anti-protein antibodies is low, in both blood serum and urine. On the contrary, joint detection of these antibodies in patients' serum significantly increases the diagnostic value as demonstrated by the results of principal component analysis (PCA) and support vector machine (SVM). The non-linear regression model achieved an accuracy of 0.833. Furthermore, PCA aided in identifying serum protein markers that have the greatest impact on patient group discrimination. The study revealed that serum serves as a superior analyte for describing protein quantification due to its consistent composition and lack of organic salts and drug residues, which can otherwise affect protein stability.

Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication.

Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA-DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA. For the leading PK-unfolding LNA and CPS oligonucleotide analogs, we also demonstrated dose-dependent RSF inhibition in dual luciferase assays (DLAs). Finally, we showed that the leading oligonucleotide analogs reduced SARS-CoV-2 replication at subtoxic concentrations in the nanomolar range in two human cell lines. Our findings highlight the promise of PK targeting, illustrate the advantages and limitations of various types of DNA modifications and may promote the future development of oligonucleotide-based antivirals.

Multicomponent Lipid Nanoparticles for RNA Transfection.

Despite the wide variety of available cationic lipid platforms for the delivery of nucleic acids into cells, the optimization of their composition has not lost its relevance. The purpose of this work was to develop multi-component cationic lipid nanoparticles (LNPs) with or without a hydrophobic core from natural lipids in order to evaluate the efficiency of LNPs with the widely used cationic lipoid DOTAP (1,2-dioleoyloxy-3-[trimethylammonium]-propane) and the previously unstudied oleoylcholine (Ol-Ch), as well as the ability of LNPs containing GM3 gangliosides to transfect cells with mRNA and siRNA. LNPs containing cationic lipids, phospholipids and cholesterol, and surfactants were prepared according to a three-stage procedure. The average size of the resulting LNPs was 176 nm (PDI 0.18). LNPs with DOTAP mesylate were more effective than those with Ol-Ch. Core LNPs demonstrated low transfection activity compared with bilayer LNPs. The type of phospholipid in LNPs was significant for the transfection of MDA-MB-231 and SW 620 cancer cells but not HEK 293T cells. LNPs with GM3 gangliosides were the most efficient for the delivery of mRNA to MDA-MB-231 cells and siRNA to SW620 cells. Thus, we developed a new lipid platform for the efficient delivery of RNA of various sizes to mammalian cells.

Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals.

The synthesis of most proteins begins at AUG codons, yet a small number of non-AUG initiated proteoforms are also known. Here we analyse a large number of publicly available Ribo-seq datasets to identify novel, previously uncharacterised non-AUG proteoforms using Trips-Viz implementation of a novel algorithm for detecting translated ORFs. In parallel we analyse genomic alignment of 120 mammals to identify evidence of protein coding evolution in sequences encoding potential extensions. Unexpectedly we find that the number of non-AUG proteoforms identified with ribosome profiling data greatly exceeds those with strong phylogenetic support suggesting their recent evolution. Our study argues that the protein coding potential of human genome greatly exceeds that detectable through comparative genomics and exposes the existence of multiple proteins encoded by the same genomic loci.

Elusive Trans-Acting Factors Which Operate with Type I (Poliovirus-like) IRES Elements.

The phenomenon of internal initiation of translation was discovered in 1988 on poliovirus mRNA. The prototypic cis-acting element in the 5' untranslated region (5'UTR) of poliovirus mRNA, which is able to direct initiation at an internal start codon without the involvement of a cap structure, has been called an IRES (Internal Ribosome Entry Site or Segment). Despite its early discovery, poliovirus and other related IRES elements of type I are poorly characterized, and it is not yet clear which host proteins (a.k.a. IRES trans-acting factors, ITAFs) are required for their full activity in vivo. Here we discuss recent and old results devoted to type I IRESes and provide evidence that Poly(rC) binding protein 2 (PCBP2), Glycyl-tRNA synthetase (GARS), and Cold Shock Domain Containing E1 (CSDE1, also known as UNR) are major regulators of type I IRES activity.

Ghrelin rapidly elevates protein synthesis in vitro by employing the rpS6K-eEF2K-eEF2 signalling axis.

Activated ghrelin receptor GHS-R1α triggers cell signalling pathways that modulate energy homeostasis and biosynthetic processes. However, the effects of ghrelin on mRNA translation are unknown. Using various reporter assays, here we demonstrate a rapid elevation of protein synthesis in cells within 15-30 min upon stimulation of GHS-R1α by ghrelin. We further show that ghrelin-induced activation of translation is mediated, at least in part, through the de-phosphorylation (de-suppression) of elongation factor 2 (eEF2). The levels of eEF2 phosphorylation at Thr56 decrease due to the reduced activity of eEF2 kinase, which is inhibited via Ser366 phosphorylation by rpS6 kinases. Being stress-susceptible, the ghrelin-mediated decrease in eEF2 phosphorylation can be abolished by glucose deprivation and mitochondrial uncoupling. We believe that the observed burst of translation benefits rapid restocking of neuropeptides, which are released upon GHS-R1α activation, and represents the most time- and energy-efficient way of prompt recharging the orexigenic neuronal circuitry.

Non-AUG translation initiation in mammals.

Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream-a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes.

Mitochondrial complex IV defects induce metabolic and signaling perturbations that expose potential vulnerabilities in HCT116 cells.

Mutations in genes encoding cytochrome c oxidase (mitochondrial complex IV) subunits and assembly factors [e.g., synthesis of cytochrome c oxidase 2 (SCO2)] are linked to severe metabolic syndromes. Notwithstanding that SCO2 is under transcriptional control of tumor suppressor p53, the role of mitochondrial complex IV dysfunction in cancer metabolism remains obscure. Herein, we demonstrate that the loss of SCO2 in HCT116 colorectal cancer cells leads to significant metabolic and signaling perturbations. Specifically, abrogation of SCO2 increased NAD+ regenerating reactions and decreased glucose oxidation through citric acid cycle while enhancing pyruvate carboxylation. This was accompanied by a reduction in amino acid levels and the accumulation of lipid droplets. In addition, SCO2 loss resulted in hyperactivation of the insulin-like growth factor 1 receptor (IGF1R)/AKT axis with paradoxical downregulation of mTOR signaling, which was accompanied by increased AMP-activated kinase activity. Accordingly, abrogation of SCO2 expression appears to increase the sensitivity of cells to IGF1R and AKT, but not mTOR inhibitors. Finally, the loss of SCO2 was associated with reduced proliferation and enhanced migration of HCT116 cells. Collectively, herein we describe potential adaptive signaling and metabolic perturbations triggered by mitochondrial complex IV dysfunction.

Expanded endoscopic transnasal odontoidectomy and posterior stabilization: a combined approach.

BACKGROUND: Lesions of the craniovertebral junction are difficult to access, which is due to the anatomical features and high concentration of vital structures in the area. The transoral access has been most used for anterior approach to treat craniovertebral junction pathology. This method has consistently shown a high complication rate and difficulties in-patient rehabilitation. In this study we analyzed the benefits of surgical treatment of the craniovertebral junction area pathology with the transnasal approach. METHODS: Four patients with C2 odontoid process invagination and brain stem compression were treated with the transnasal endoscopic resection of the pathological process combined with simultaneous occipital-cervical stabilization (OCS). Surgical procedure, anatomical findings, complications, and rehabilitation period were assessed. RESULTS: Transnasal treatment of C2 odontoid process lesions was applied successfully in all four cases. A modified extended transnasal approach was used. This approach is characterized by an increased operating time (238 minutes), lower complication rate, safer access (less traumatization of oropharyngeal tissue), better patient rehabilitation (no need for tracheostomy or feeding tube), better recovery and higher patient satisfaction (quick regression of the symptomatic patients). CONCLUSIONS: The extended transnasal access to the craniovertebral junction is a safer, more comfortable technique, which facilitates more radical treatment of lesions in this area. For brain stem compression due to C2 odontoid process invagination, a combination of transnasal resection and OCS shows excellent preliminary results. This method should be favorable over the transoral approach in certain cases, as it provides a better direct access to lesion of the craniovertebral junction and allows for more complex combined procedures.

Modifications of Ribosome Profiling that Provide New Data on the Translation Regulation.

Ribosome profiling (riboseq) has opened the possibilities for the genome-wide studies of translation in all living organisms. This method is based on deep sequencing of mRNA fragments protected by the ribosomes from hydrolysis by ribonucleases, the so-called ribosomal footprints (RFPs). Ribosomal profiling together with RNA sequencing allows not only to identify with a reasonable accuracy translated reading frames in the transcriptome, but also to track changes in gene expression in response to various stimuli. Notably, ribosomal profiling in its classical version has certain limitations. The size of the selected mRNA fragments is 25-35 nts, while RFPs of other sizes are usually omitted from analysis. Also, ribosomal profiling "averages" the data from all ribosomes and does not allow to study specific ribosomal complexes associated with particular translation factors. However, recently developed modifications of ribosomal profiling provide answers to a number of questions. Thus, it has become possible to analyze not only elongating, but also scanning and reinitiating ribosomes, to study events associated with the collision of ribosomes during mRNA translation, to discover new ways of cotranslational assembly of multisubunit protein complexes during translation, and to selectively isolate ribosomal complexes associated with certain protein factors. New data obtained using these modified approaches provide a better understanding of the mechanisms of translation regulation and the functional roles of translational apparatus components.

Primary Sellar Abscesses: A Systematic Review and 2 Rare Observations.

BACKGROUND: Abscesses of the chiasmatic-sellar region are quite rare and are often a result of surgical intervention, trauma, or tumor growth. Primary abscesses are extremely rare and represent a group of abscesses the occur because of internal microbial seeding. Primary abscesses are rarely reported. We present 2 clinical cases featuring primary abscesses of the chiasmal-sellar region. To put into perspective the rarity of these findings, we performed a systematic review of existing clinical reports regarding this pathology. METHODS: A systematic review of literature was conducted to gather existing clinical reports on primary abscesses of the chiasmatic-sellar region. Two personal findings are added to the literature review, including a 13-year-old girl and a 58-year-old man who presented with chiasmal-sellar region primary abscesses. The diagnostic aspects, treatment strategy, and outcomes are discussed. RESULTS: Both patients included in the report had positive outcome. The pediatric patient developed a recurrence of the abscess and was treated accordingly. Overall, 41 cases of primary abscesses of this region have been reported in literature, of which 6 are in children under 18 years of age. The main nonspecific clinical manifestations include headaches, visual impairment, and endocrine pathology. Acute inflammatory responses are rarely seen, despite infectious genesis. Transnasal endoscopic surgical treatment offers diagnostic and treatment advantages. CONCLUSIONS: Proper diagnostic procedures can aid in correct treatment strategy and improve overall outcome.

Surgical Correction of a Clivus Cerebrospinal Fluid Fistula: A Technical Report.

BACKGROUND: Cerebrospinal fistulas of the clivus region often result from previous surgical intervention at the skull base. The localization and size of the fistula determine the appropriate treatment strategy. When flap closure is not possible, the microsuture technique with autograft placement provides a favorable outcome. METHODS: We present a technical report on the application of the microsuture technique for clivus region cerebrospinal fluid fistula closure in a patient with previous chordoma treatment and nonspecific coronavirus disease 2019 complications. RESULTS: The application of the microsuture technique resulted in stable remission of the fistula and complete regression of the clinical manifestations. CONCLUSIONS: The microsuture technique for clivus region fistula closure is a potentially valuable alternative to vascularized flap closure.

Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF.

While near-cognate codons are frequently used for translation initiation in eukaryotes, their efficiencies are usually low (<10% compared to an AUG in optimal context). Here, we describe a rare case of highly efficient near-cognate initiation. A CUG triplet located in the 5' leader of POLG messenger RNA (mRNA) initiates almost as efficiently (∼60 to 70%) as an AUG in optimal context. This CUG directs translation of a conserved 260-triplet-long overlapping open reading frame (ORF), which we call POLGARF (POLG Alternative Reading Frame). Translation of a short upstream ORF 5' of this CUG governs the ratio between POLG (the catalytic subunit of mitochondrial DNA polymerase) and POLGARF synthesized from a single POLG mRNA. Functional investigation of POLGARF suggests a role in extracellular signaling. While unprocessed POLGARF localizes to the nucleoli together with its interacting partner C1QBP, serum stimulation results in rapid cleavage and secretion of a POLGARF C-terminal fragment. Phylogenetic analysis shows that POLGARF evolved ∼160 million y ago due to a mammalian-wide interspersed repeat (MIR) transposition into the 5' leader sequence of the mammalian POLG gene, which became fixed in placental mammals. This discovery of POLGARF unveils a previously undescribed mechanism of de novo protein-coding gene evolution.

Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context.

Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scanning takes place during which a fraction of ribosomes continues the mRNA probing. We explored the relationship between the context of AUG codons annotated as starts of protein-coding sequences and the next AUG codon occurrence. We found that AUG codons downstream from weak starts occur in the same frame more frequently than downstream from strong starts. We suggest that evolutionary selection on in-frame AUGs downstream from weak start codons is driven by the advantage of the reduction of wasteful out-of-frame product synthesis and also by the advantage of producing multiple proteoforms from certain mRNAs. We confirmed translation initiation downstream from weak start codons using ribosome profiling data. We also tested translation of alternative start codons in 10 specific human genes using reporter constructs. In all tested cases, initiation at downstream start codons was more productive than at the annotated ones. In most cases, optimization of Kozak context did not completely abolish downstream initiation, and in the specific example of CMPK1 mRNA, the optimized start remained unproductive. Collectively, our work reveals previously uncharacterized forces shaping the evolution of protein-coding genes and points to the plurality of translation initiation and the existence of sequence features influencing start codon selection, other than Kozak context.

Anatomical Aspects of the Transnasal Endoscopic Access to the Craniovertebral Junction.

OBJECTIVE: Interest in endoscopic transnasal access has increased with continued technological advances in endoscopic technology. The goals of this study were to review the normal anatomy in transnasal endoscopic neurosurgery and outline the anatomical basis for an expanded surgical approach. Defining anatomical aspects of surgical endoscopy helps guide the surgeon by defining normal anatomy of the access vector. METHODS: This anatomic study was conducted on 15 adult male cadaver specimens using various microsurgical tools and endoscopic instruments and 1 intraoperative case. The vasculature was injected with colored silicone to aid visualization. Different transnasal approach techniques were used, with angles of endoscope access at 0°, 30°, 45°, and 70° accordingly for extensive anatomical mapping. RESULTS: The proximity of critical structures is different in each approach degree. A full understanding of the possible structures to be met during transnasal access is described. As a result of the study, anatomical aspects and important structures were outlined, and a surgical protocol was defined for minimal risk access in respect to normal anatomy of the area. CONCLUSIONS: Thorough knowledge of topographic anatomy of the craniovertebral junction is required for performing minimal-risk surgical intervention in this region. It is important to know all anatomical aspects of the transnasal approach in order to reduce the risk of damage to vital structures. Transnasal endoscopic surgery of the craniovertebral junction is a relatively new direction in neurosurgery; therefore, anatomical studies such as the one described in this article are extremely important for the development of this access method.

Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.

TMA20 (MCT-1), TMA22 (DENR) and TMA64 (eIF2D) are eukaryotic translation factors involved in ribosome recycling and re-initiation. They operate with P-site bound tRNA in post-termination or (re-)initiation translation complexes, thus participating in the removal of 40S ribosomal subunit from mRNA stop codons after termination and controlling translation re-initiation on mRNAs with upstream open reading frames (uORFs), as well as de novo initiation on some specific mRNAs. Here we report ribosomal profiling data of S.cerevisiae strains with individual deletions of TMA20, TMA64 or both TMA20 and TMA64 genes. We provide RNA-Seq and Ribo-Seq data from yeast strains grown in the rich YPD or minimal SD medium. We illustrate our data by plotting differential distribution of ribosomal-bound mRNA fragments throughout uORFs in 5'-untranslated region (5' UTR) of GCN4 mRNA and on mRNA transcripts encoded in MAT locus in the mutant and wild-type strains, thus providing a basis for investigation of the role of these factors in the stress response, mating and sporulation. We also document a shift of transcription start site of the APC4 gene which occurs when the neighboring TMA64 gene is replaced by the standard G418-resistance cassette used for the creation of the Yeast Deletion Library. This shift results in dramatic deregulation of the APC4 gene expression, as revealed by our Ribo-Seq data, which can be probably used to explain strong genetic interactions of TMA64 with genes involved in the cell cycle and mitotic checkpoints. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039).

Endoscopic Transsphenoidal Approach in Treatment of Germinomas of the Chiasmosellar Region.

INTRODUCTION: Germinogenic central nervous system (CNS) tumors represent a heterogeneous group of tumors, constituting approximately 0.4% of all primary brain tumors. Removal of the tumor has no prognostic value. In "pure" primary germinomas of the CNS, the alpha-fetoprotein and human chorionic gonadotropin levels are within normal limits, and no specific biochemical tumor markers currently exist for this tumor type, making histological verification crucial for the choice of treatment tactics. When the tumor is located in the chiasmosellar region, one of the possible verification methods is endoscopic endonasal transsphenoidal biopsy. OBJECTIVE: The main objective of the study is to demonstrate the feasibility and safety of endoscopic transsphenoidal approach for histological verification of primary germinomas of the CNS with chiasmosellar localization. MATERIALS AND METHODS: The current study includes 13 patients with "pure" germinomas of the chiasmosellar region who underwent endoscopic endonasal surgical interventions with subsequent treatment according to the "Germinoma 2008" protocol. RESULTS: The extent of surgical intervention ranged from biopsy (4) to partial (5) and total (4) removal of the tumor. In all cases, histological verification of the diagnosis was achieved and none of the patients presented with cerebrospinal fluid leaks and/or meningitis in the postoperative period, allowing to evaluate endoscopic intervention in our patient series as safe and effective. Two out of 13 patients were lost to follow-up. CONCLUSION: The endoscopic endonasal approach for histological verification and removal of chiasmosellar region germinomas is safe, and in some cases, less traumatic for the patient than transcranial and transventricular approaches.

Endoscopic Endonasal Transclival Approach to Tumors of the Clivus and Anterior Region of the Posterior Cranial Fossa (Results of Surgical Treatment of 136 Patients).

INTRODUCTION: With the introduction into the neurosurgical practice of minimally invasive methods using endoscopic techniques, it became possible to effectively remove hard-to-reach tumors, including central tumors of the anterior region of the posterior cranial fossa. OBJECTIVE: To analyze the results of surgical treatment of patients with various centrally located tumors of the base of the skull that extend into the anterior region of the posterior cranial fossa using the endoscopic endonasal transclival approach. METHODS: The personal surgical experience of the first author is 136 patients with various tumors (e.g., chordomas, meningiomas, pituitary adenomas, and fibrous dysplasia). RESULTS: Radicality of tumor removal was total 61.03%; subtotal 25%; partial 13.23%; and insufficient removal 0.74%. Postoperative cerebrospinal fluid leaks occurred in 9 cases (6.62%) and meningitis in 13 cases (9.56%). In 2 cases, surgical treatment had a lethal outcome (1.47%). CONCLUSIONS: The endoscopic endonasal transclival approach can be used to obtain access to centrally located skull base tumors. This approach allows for a radical and low-risk removal of various skull base tumors of central localization that, until recently, were considered to be almost inoperable.