PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information.

The dynamic evolution of the severe acute respiratory syndrome coronavirus 2 virus is primarily driven by mutations in its genetic sequence, culminating in the emergence of variants with increased capability to evade host immune responses. Accurate prediction of such mutations is fundamental in mitigating pandemic spread and developing effective control measures. This study introduces a robust and interpretable deep-learning approach called PRIEST. This innovative model leverages time-series viral sequences to foresee potential viral mutations. Our comprehensive experimental evaluations underscore PRIEST's proficiency in accurately predicting immune-evading mutations. Our work represents a substantial step in utilizing deep-learning methodologies for anticipatory viral mutation analysis and pandemic response.

Short telomeres in alveolar type II cells associate with lung fibrosis in post COVID-19 patients with cancer.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) pandemic. The severity of COVID-19 increases with each decade of life, a phenomenon that suggest that organismal aging contributes to the fatality of the disease. In this regard, we and others have previously shown that COVID-19 severity correlates with shorter telomeres, a molecular determinant of aging, in patient's leukocytes. Lung injury is a predominant feature of acute SARS-CoV-2 infection that can further progress to lung fibrosis in post-COVID-19 patients. Short or dysfunctional telomeres in Alveolar type II (ATII) cells are sufficient to induce pulmonary fibrosis in mouse and humans. Here, we analyze telomere length and the histopathology of lung biopsies from a cohort of alive post-COVID-19 patients and a cohort of age-matched controls with lung cancer. We found loss of ATII cellularity and shorter telomeres in ATII cells concomitant with a marked increase in fibrotic lung parenchyma remodeling in post- COVID-19 patients compared to controls. These findings reveal a link between presence of short telomeres in ATII cells and long-term lung fibrosis sequel in Post-COVID-19 patients.

Proteomic analysis defines the interactome of telomerase in the protozoan parasite, Trypanosoma brucei.

Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long non-coding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in parasitic protozoa, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.

The RRM-mediated RNA binding activity in T. brucei RAP1 is essential for VSG monoallelic expression.

Trypanosoma brucei is a protozoan parasite that causes human African trypanosomiasis. Its major surface antigen VSG is expressed from subtelomeric loci in a strictly monoallelic manner. We previously showed that the telomere protein TbRAP1 binds dsDNA through its 737RKRRR741 patch to silence VSGs globally. How TbRAP1 permits expression of the single active VSG is unknown. Through NMR structural analysis, we unexpectedly identify an RNA Recognition Motif (RRM) in TbRAP1, which is unprecedented for RAP1 homologs. Assisted by the 737RKRRR741 patch, TbRAP1 RRM recognizes consensus sequences of VSG 3'UTRs in vitro and binds the active VSG RNA in vivo. Mutating conserved RRM residues abolishes the RNA binding activity, significantly decreases the active VSG RNA level, and derepresses silent VSGs. The competition between TbRAP1's RNA and dsDNA binding activities suggests a VSG monoallelic expression mechanism in which the active VSG's abundant RNA antagonizes TbRAP1's silencing effect, thereby sustaining its full-level expression.

A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry.

The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.

Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data.

Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, for a combination of reasons (ranging from sampling biases to more biological causes, as in gene birth and loss), gene trees are often incomplete, meaning that not all species of interest have a common set of genes. Incomplete gene trees can potentially impact the accuracy of phylogenomic inference. We, for the first time, introduce the problem of imputing the quartet distribution induced by a set of incomplete gene trees, which involves adding the missing quartets back to the quartet distribution. We present Quartet based Gene tree Imputation using Deep Learning (QT-GILD), an automated and specially tailored unsupervised deep learning technique, accompanied by cues from natural language processing, which learns the quartet distribution in a given set of incomplete gene trees and generates a complete set of quartets accordingly. QT-GILD is a general-purpose technique needing no explicit modeling of the subject system or reasons for missing data or gene tree heterogeneity. Experimental studies on a collection of simulated and empirical datasets suggest that QT-GILD can effectively impute the quartet distribution, which results in a dramatic improvement in the species tree accuracy. Remarkably, QT-GILD not only imputes the missing quartets but can also account for gene tree estimation error. Therefore, QT-GILD advances the state-of-the-art in species tree estimation from gene trees in the face of missing data.

Phylogenetic Analyses of SARS-CoV-2 Strains Reveal Its Link to the Spread of COVID-19 Across the Globe.

This study leveraged the phylogenetic analysis of more than 10K strains of novel coronavirus (SARS-CoV-2) from 67 countries. Due to the requirement of high-end computational power for phylogenetic analysis, we leverage a fast yet highly accurate alignment-free method to develop the phylogenetic tree out of all the strains of novel coronavirus. K-Means clustering and PCA-based dimension reduction technique were used to identify a representative strain from each location. The resulting phylogenetic tree was able to highlight evolutionary relationships of SARS-CoV-2 genome and, subsequently, linked to the interpretation of facts and figures across the globe for the spread of COVID-19. Our analysis revealed that the geographical boundaries could not be explained by the phylogenetic analysis of novel coronavirus as it placed different countries from Asia, Europe and the USA in very close proximity in the tree. Instead, the commute of people from one country to another is the key to the spread of COVID-19. We believe our study will support the policymakers to contain the spread of COVID-19 globally.

In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei.

Telomerase is a unique ribonucleoprotein (RNP) reverse transcriptase that utilizes its cognate RNA molecule as a template for telomere DNA repeat synthesis. Telomerase contains the reverse transcriptase protein, TERT and the template RNA, TR, as its core components. The 5'-half of TR forms a highly conserved catalytic core comprising of the template region and adjacent domains necessary for telomere synthesis. However, how telomerase RNA folding takes place in vivo has not been fully understood due to low abundance of the native RNP. Here, using unicellular pathogen Trypanosoma brucei as a model, we reveal important regional folding information of the native telomerase RNA core domains, i.e. TR template, template boundary element, template proximal helix and Helix IV (eCR4-CR5) domain. For this purpose, we uniquely combined in-cell probing with targeted high-throughput RNA sequencing and mutational mapping under three conditions: in vivo (in WT and TERT-/- cells), in an immunopurified catalytically active telomerase RNP complex and ex vivo (deproteinized). We discover that TR forms at least two different conformers with distinct folding topologies in the insect and mammalian developmental stages of T. brucei. Also, TERT does not significantly affect the RNA folding in vivo, suggesting that the telomerase RNA in T. brucei exists in a conformationally preorganized stable structure. Our observed differences in RNA (TR) folding at two distinct developmental stages of T. brucei suggest that important conformational changes are a key component of T. brucei development.

Paraganglioma of Urinary Bladder: An Uncommon Entity in Uropathology.

Paraganglioma of the urinary bladder is a rare neoplasm. It may be functional, secreting catecholamines, or nonfunctional. Clinically and histopathologically, it has the potential to be misdiagnosed as a more common urothelial carcinoma, especially in nonfunctional cases. A high index of suspicion on the part of pathologist can help in identification of characteristic histopathologic feature which coupled with immunohistochemistry can help in establishing the correct diagnosis. We present a case of paraganglioma in a 78-year-old male patient presenting with haematuria. Clinical provisional diagnosis rendered based on cystoscopic findings and radiology was urothelial carcinoma; however, was confirmed to be a case of paraganglioma of bladder on histopathological and immunohistochemical evaluation. A long follow-up is warranted. Herein, we also briefly review the relevant literature.

TbTRF suppresses the TERRA level and regulates the cell cycle-dependent TERRA foci number with a TERRA binding activity in its C-terminal Myb domain.

Telomere repeat-containing RNA (TERRA) has been identified in multiple organisms including Trypanosoma brucei, a protozoan parasite that causes human African trypanosomiasis. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. VSG is expressed exclusively from subtelomeric expression sites, and we have shown that telomere proteins play important roles in the regulation of VSG silencing and switching. In this study, we identify several unique features of TERRA and telomere biology in T. brucei. First, the number of TERRA foci is cell cycle-regulated and influenced by TbTRF, the duplex telomere DNA binding factor in T. brucei. Second, TERRA is transcribed by RNA polymerase I mainly from a single telomere downstream of the active VSG. Third, TbTRF binds TERRA through its C-terminal Myb domain, which also has the duplex DNA binding activity, in a sequence-specific manner and suppresses the TERRA level without affecting its half-life. Finally, levels of the telomeric R-loop and telomere DNA damage were increased upon TbTRF depletion. Overexpression of an ectopic allele of RNase H1 that resolves the R-loop structure in TbTRF RNAi cells can partially suppress these phenotypes, revealing an underlying mechanism of how TbTRF helps maintain telomere integrity.

Di-µ-benzoato-di-µ-ethano-lato-tetra-kis-[µ3-5-(hy-droxy-meth-yl)-2-methyl-4-(oxidometh-yl)pyridin-1-ium-3-olato]tetra-kis-[µ3-5-(hy-droxy-meth-yl)-2-methyl-4-(oxidometh-yl)pyridin-3-olato]di-µ3-oxido-hepta-manganese(II,III) ethanol octa-solvate.

Our work in the area of synthesis of polynuclear manganese complexes and their magnetic properties led to the synthesis and crystallization of the title compound, [Mn7(C8H9NO3)4(C8H10NO3)4(C2H5O)2(C7H5O2)2O2]·8C2H5OH. Herein, we report the molecular and crystal structure of the title compound, which was synthesized by the reaction of Mn(C6H5COO)2 with pyridoxine (PNH2, C8H11NO3) followed by the addition of tetra-methyl-ammonium hydroxide (TMAOH). The core of this centrosymmetric complex is a cage-like structure consisting of six MnIII ions and one MnII ion bound together through Mn-O bonds. The compound crystallizes in hydrogen-bonded layers formed by O-H⋯N hydrogen bonds involving the aromatic amine group of the ligand PN2- with the neighboring O atoms from the PNH- ligand. The crystal structure has large voids present in which highly disordered solvent mol-ecules (ethanol) sit. A solvent mask was calculated and 181 electrons were found in a volume of 843 Å3 in one void per triclinic unit cell. This is consistent with the presence of seven ethanol mol-ecules per formula unit, which accounts for 182 electrons per unit cell. Additionally, one ethanol mol-ecule was found to be ordered in the crystal.

Noncovalently Linked Metallacarboranes on Functionalized Magnetic Nanoparticles as Highly Efficient, Robust, and Reusable Photocatalysts in Aqueous Medium.

A successful homogeneous photoredox catalyst has been fruitfully heterogenized on magnetic nanoparticles (MNPs) coated with a silica layer, keeping intact its homogeneous catalytic properties but gaining others due to the easy magnetic separation and recyclability. The amine-terminated magnetic silica nanoparticles linked noncovalently to H[3,3'-Co(1,2-C2B9H11)2]- (H[1]), termed MSNPs-NH2@H[1], are highly stable and do not produce any leakage of the photoredox catalyst H[1] in water. The magnetite MNPs were coated with SiO2 to provide colloidal stability and silanol groups to be tethered to amine-containing units. These were the MSNPs-NH2 on which was anchored, in water, the cobaltabis(dicarbollide) complex H[1] to obtain MSNPs-NH2@H[1]. Both MSNPs-NH2 and MSNPs-NH2@H[1] were evaluated to study the morphology, characterization, and colloidal stability of the MNPs produced. The heterogeneous MSNP-NH2@H[1] system was studied for the photooxidation of alcohols, such as 1-phenylethanol, 1-hexanol, 1,6-hexanediol, or cyclohexanol among others, using catalyst loads of 0.1 and 0.01 mol %. Surfactants were introduced to prevent the aggregation of MNPs, and cetyl trimethyl ammonium chloride was chosen as a surfactant. This provided adequate stability, without hampering quick magnetic separation. The results proved that the catalysis could be speeded up if aggregation was prevented. The recyclability of the catalytic system was demonstrated by performing 12 runs of the MSNPs-NH2@H[1] system, each one without loss of selectivity and yield. The cobaltabis(dicarbollide) catalyst supported on silica-coated magnetite nanoparticles has proven to be a robust, efficient, and easily reusable system for the photooxidation of alcohols in water, resulting in a green and sustainable heterogeneous catalytic system.

Magnetic Nanoparticles Fishing for Biomarkers in Artificial Saliva.

Magnetic nanoparticles (MNPs) were synthesized using the colloidal co-precipitation method and further coated with silica using the Stöber process. These were functionalized with carboxylic and amine functionalities for further covalent immobilization of antibodies on these MNPs. The procedure for covalent immobilization of antibodies on MNPs was developed using 1-ethyl-3-(dimethylaminopropyl)carbodiimide (EDC) and N-hydroxysuccinimide (NHS). The evaluation of the efficiency of the coupling reaction was carried out by UV-vis spectrophotometry. The developed antibodies coupled to MNPs were tested for the pre-concentration of two biomarkers tumor necrosis factor alpha (TNF-α) and Interleukin-10 (IL-10). Both biomarkers were assessed in the matrix based on phosphate-buffered saline solution (PBS) and artificial saliva (AS) to carry out the demonstration of the format assay. Supernatants were used to determine the number of free biomarkers for both studies. Reduction of the nonspecific saliva protein adsorption on the surface of the complex antibodies-MNPs to levels low enough to allow the detection of biomarkers in complex media has been achieved.

Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes.

Trypanosoma brucei is a kinetoplastid parasite that causes African trypanosomiasis, which is fatal if left untreated. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune responses. VSGs are exclusively expressed from subtelomeric expression sites (ESs) where VSG genes are flanked by upstream 70 bp repeats and downstream telomeric repeats. The telomere downstream of the active VSG is transcribed into a long-noncoding RNA (TERRA), which forms RNA:DNA hybrids (R-loops) with the telomeric DNA. At an elevated level, telomere R-loops cause more telomeric and subtelomeric double-strand breaks (DSBs) and increase VSG switching rate. In addition, stabilized R-loops are observed at the 70 bp repeats and immediately downstream of ES-linked VSGs in RNase H defective cells, which also have an increased amount of subtelomeric DSBs and more frequent VSG switching. Although subtelomere plasticity is expected to be beneficial to antigenic variation, severe defects in subtelomere integrity and stability increase cell lethality. Therefore, regulation of the telomere and 70 bp repeat R-loop levels is important for the balance between antigenic variation and cell fitness in T. brucei. In addition, the high level of the active ES transcription favors accumulation of R-loops at the telomere and 70 bp repeats, providing an intrinsic mechanism for local DSB formation, which is a strong inducer of VSG switching.

The key to controlling the morphologies of quantum nanocrystals: spherical carborane ligands.

By minor structure modification of spherical carborane ligands, in a similar synthetic procedure, large morphological changes are produced in Quantum Nanocrystals (QNCs). The spheres are icosahedral C2B10H12 molecules with binding sites on the carbon, and the QNCs produced are Quantum Dots, Rods, Rings and Tetrapods. These QNCs demonstrated high stability and impeccable emissive properties for more than a year.

Combining magnetic nanoparticles and icosahedral boron clusters in biocompatible inorganic nanohybrids for cancer therapy.

The potential biomedical applications of the MNPs nanohybrids coated with m-carboranylphosphinate (1-MNPs) as a theranostic biomaterial for cancer therapy were tested. The cellular uptake and toxicity profile of 1-MNPs from culture media by human brain endothelial cells (hCMEC/D3) and glioblastoma multiform A172 cell line were demonstrated. Prior to testing 1-MNPs' in vitro toxicity, studies of colloidal stability of the 1-MNPs' suspension in different culture media and temperatures were carried out. TEM images and chemical titration confirmed that 1-MNPs penetrate into cells. Additionally, to explore 1-MNPs' potential use in Boron Neutron Capture Therapy (BNCT) for treating cancer locally, the presence of the m-carboranyl coordinated with the MNPs core after uptake was proven by XPS and EELS. Importantly, thermal neutrons irradiation in BNCT reduced by 2.5 the number of cultured glioblastoma cells after 1-MNP treatment, and the systemic administration of 1-MNPs in mice was well tolerated with no major signs of toxicity.