Lancet Healthy Longev. 2023 Apr;4(4):e166-e175. doi: 10.1016/S2666-7568(23)00021-1.

ABSTRACT

Periodontitis results from dysbiosis of the oral microbiome and affects up to 70% of US adults aged 65 years and older. More than 50 systemic inflammatory disorders and comorbidities are associated with periodontitis, many of which overlap with immunotherapy-associated toxicities. Despite the increasing use of immunotherapy for the treatment of cancer, uncertainty remains as to whether the microbial shift associated with periodontal disease can influence response rates and tolerance to cancer immunotherapy. We herein review the pathophysiology of periodontitis and the local and systemic inflammatory conditions related to oral dysbiosis, and discuss the overlapping adverse profiles of periodontitis and immunotherapy. The effects of the presence of Porphyromonas gingivalis, a key pathogen in periodontitis, highlight how the oral microbiome can affect the hosts' systemic immune responses, and further research into the local and systemic influence of other microorganisms causing periodontal disease is necessary. Addressing periodontitis in an ageing population of people with cancer could have potential implications for the clinical response to (and tolerability of) immunotherapy and warrants further investigation.

PMID:37003275 | DOI:10.1016/S2666-7568(23)00021-1

CPT Pharmacometrics Syst Pharmacol. 2023 Mar 31. doi: 10.1002/psp4.12961. Online ahead of print.

ABSTRACT

Oncology treatments require continuous individual adjustment based on the measurement of multiple clinical parameters. Prediction tools exploiting the patterns present in the clinical data could be used to assist decision making and ease the burden associated to the interpretation of all these parameters. The goal of this study was to predict the evolution of patients with pancreatic cancer at their next visit using information routinely recorded in health records, providing a decision-support system for clinicians. We selected hematological variables as the visit's clinical outcomes, under the assumption that they can be predictive of the evolution of the patient. Multivariate models based on regression trees were generated to predict next-visit values for each of the clinical outcomes selected, based on the longitudinal clinical data as well as on molecular data sets streaming from in silico simulations of individual patient status at each visit. The models predict, with a mean prediction score (balanced accuracy) of 0.79, the evolution trends of eosinophils, leukocytes, monocytes, and platelets. Time span between visits and neutropenia were among the most common factors contributing to the predicted evolution. The inclusion of molecular variables from the systems-biology in silico simulations provided a molecular background for the observed variations in the selected outcome variables, mostly in relation to the regulation of hematopoiesis. In spite of its limitations, this study serves as a proof of concept for the application of next-visit prediction tools in real-world settings, even when available data sets are small.

PMID:37002678 | DOI:10.1002/psp4.12961

Sci Rep. 2023 Mar 31;13(1):5238. doi: 10.1038/s41598-023-32245-9.

ABSTRACT

Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)-proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.

PMID:37002329 | DOI:10.1038/s41598-023-32245-9

Anal Chem. 2023 Mar 31. doi: 10.1021/acs.analchem.3c00426. Online ahead of print.

ABSTRACT

The localized surface plasmon resonance (LSPR) property, depending on the structure (morphology and assembly) of nanoparticles, is very sensitive to the environmental fluctuation. Retaining the colorimetric effect derived from the LSPR property while introducing new optical properties (such as fluorescence) that provide supplementary information is an effective means to improve the controllability in structures and reproducibility in optical properties. DNA as a green and low-cost etching agent has been demonstrated to effectively control the morphology and optical properties (the blue shift of the LSPR peak) of the plasmonic nanoparticles. Herein, taking silver nanotriangles (AgNTs) as a proof of concept, we report a novel strategy to induce precisely tunable LSPR and fluorescence-composited dual-mode signals by using mono-DNA first as an etching agent for etching the morphology of AgNTs and later as a template for synthesizing fluorescent silver nanoclusters (AgNCs). In addition, common templates for synthesizing AgNCs, such as l-glutathione and bovine serum albumin, were demonstrated to have the capability to serve as etching agents. More importantly, these biomolecules as dual-functional capping agents (etching agents and templates) follow the size-dependent rule: as the size of the thiolated biomolecule increases, the blue shift of the LSPR peak increases; at the same time, the fluorescence intensity increases. The enzyme that can change the molecular weight (size) of the biomolecular substrates (DNA, peptides, and proteins) through an enzymatic cleavage reaction was explored to regulate the LSPR and fluorescent properties of the resulting nanoparticles (by etching of AgNTs and synthesis of AgNCs), achieving excellent performance in detection of cancer-related proteases. This study can be expanded to other biopolymers to impact both fundamental nanoscience and applications and provide powerful new tools for bioanalytical biosensors and nanomedicine.

PMID:37002208 | DOI:10.1021/acs.analchem.3c00426

Semin Cell Dev Biol. 2023 Mar 29:S1084-9521(23)00070-8. doi: 10.1016/j.semcdb.2023.03.007. Online ahead of print.

ABSTRACT

The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.

PMID:37002131 | DOI:10.1016/j.semcdb.2023.03.007

Cell Syst. 2023 Mar 28:S2405-4712(23)00057-1. doi: 10.1016/j.cels.2023.03.001. Online ahead of print.

ABSTRACT

Antigen-specific T cell receptor (TCR) sequences can have prognostic, predictive, and therapeutic value, but decoding the specificity of TCR recognition remains challenging. Unlike DNA strands that base pair, TCRs bind to their targets with different orientations and different lengths, which complicates comparisons. We present scanning parametrized by normalized TCR length (SPAN-TCR) to analyze antigen-specific TCR CDR3 sequences and identify patterns driving TCR-pMHC specificity. Using entropic analysis, SPAN-TCR identifies 2-mer motifs that decrease the diversity (entropy) of CDR3s. These motifs are the most common patterns that can predict CDR3 composition, and we identify "essential" motifs that decrease entropy in the same CDR3 α or β chain containing the 2-mer, and "super-essential" motifs that decrease entropy in both chains. Molecular dynamics analysis further suggests that these motifs may play important roles in binding. We then employ SPAN-TCR to resolve similarities in TCR repertoires against different antigens using public databases of TCR sequences.

PMID:37001518 | DOI:10.1016/j.cels.2023.03.001

Cell. 2023 Mar 30;186(7):1448-1464.e20. doi: 10.1016/j.cell.2023.02.032.

ABSTRACT

Neutrophils accumulate in solid tumors, and their abundance correlates with poor prognosis. Neutrophils are not homogeneous, however, and could play different roles in cancer therapy. Here, we investigate the role of neutrophils in immunotherapy, leading to tumor control. We show that successful therapies acutely expanded tumor neutrophil numbers. This expansion could be attributed to a Sellhi state rather than to other neutrophils that accelerate tumor progression. Therapy-elicited neutrophils acquired an interferon gene signature, also seen in human patients, and appeared essential for successful therapy, as loss of the interferon-responsive transcription factor IRF1 in neutrophils led to failure of immunotherapy. The neutrophil response depended on key components of anti-tumor immunity, including BATF3-dependent DCs, IL-12, and IFNγ. In addition, we found that a therapy-elicited systemic neutrophil response positively correlated with disease outcome in lung cancer patients. Thus, we establish a crucial role of a neutrophil state in mediating effective cancer therapy.

PMID:37001504 | DOI:10.1016/j.cell.2023.02.032

Talanta. 2023 Mar 23;259:124477. doi: 10.1016/j.talanta.2023.124477. Online ahead of print.

ABSTRACT

Direct-infusion tandem mass spectrometry (DI-MS/MS) is an excellent tool for large cohort high-throughput quantitative metabolomics, MS imaging and single cell studies but incapable of discriminating isomers/isobars with similar MS spectral features. With experimental and density-functional theory (DFT) approaches, here, we comprehensively investigated the fragmentation pathways and characteristics of differential ion-mobility spectrometry (DMS) for three citrate isomers (citrate, isocitrate, glucaro-1,4-lactone) and an isobar (quinate) co-existing in biological sample such as urine. Results showed that all these compounds gave better MS spectra in negative-ion mode than positive-ion one and had numerous fragment ions under collision-induced dissociation (CID) with sequential losses of H2O and CO2. All observed fragment ions were assignable by combining experimental with DFT calculation results. A DI-DMS-MS/MS method was then developed to simultaneously quantify these four isomers/isobars with m/z 191-87 (CoV, -5.5 V), 191-73 (CoV, -3.5 V), 191-85 (CoV, -29.5 V) and m/z 191-93 (CoV, -41.5 V) for citrate, isocitrate, glucaro-1,4-lactone and quinate, respectively. The low limit-of-quantification was below 5.5 nM whilst accuracy was above 94% for all above compounds. The urinary concentrations of them in human and C57BL/6 mouse samples were further quantified showing clear inter-individual and inter-species level differences with significantly higher levels of isocitrate, glucaro-1,4-lactone and quinate in human urine samples than mouse ones. This provides an approach to understand the detailed fragmentation pathways for organic isomers/isobars and a high-throughput MS strategy to quantify them in complex mixtures for metabolomics, lipidomics, foodomics and exposomics especially when chromatographic separations are not useable.

PMID:37001399 | DOI:10.1016/j.talanta.2023.124477

Curr Opin Virol. 2023 Mar 29;60:101316. doi: 10.1016/j.coviro.2023.101316. Online ahead of print.

ABSTRACT

Inspite of the available antiviral therapy, hepatitis C virus (HCV) remains a global health burden and a prophylactic vaccine would help to eliminate the risk to develop chronic liver diseases. Structural insights into the function of the glycoproteins E1 and E2 in virus entry and the interplay with the host's humoral immune response are key for informed vaccine development. We review recently reported structural insights into receptor binding of HCV glycoproteins and the assembly of an intact membrane-bound E1-E2 heterodimer. These data are used together with available functional data to draw a simplified model of virus entry, which highlights gaps in our current knowledge that warrant further research to fully understand this process at the atomic level.

PMID:37001334 | DOI:10.1016/j.coviro.2023.101316

Diagn Microbiol Infect Dis. 2023 Mar 6;106(2):115930. doi: 10.1016/j.diagmicrobio.2023.115930. Online ahead of print.

ABSTRACT

BACKGROUND: The dissemination of NDM-1 carbapenemases (New Delhi Metallo-β-lactamase) is a global public health problem, mainly in developing countries. The aim of this study was to characterize the spread of NDM-producing bacteria in the Southern Brazilian states analyzing epidemiological, molecular, and antimicrobial susceptibility aspects.

METHODS: A total of 10,684 carbapenem-resistant isolates of Enterobacterales, Pseudomonas spp. and Acinetobacter spp. obtained from several hospitals in eight cities in Southern Brazil were screened, and 486 NDM-producing bacteria were selected.

RESULTS: The incidence varied from 0.5 to 77 cases/100.000 habitants. ST11, ST15, ST340 and ST674 were the most common in K. pneumoniae. A total of 5 plasmids were identified in one K. pneumoniae strain: Col440I, Col440II, IncFIA(HI1), IncFIB(K), IncFIB(pQil)/ IncFII(K), and IncR.

CONCLUSIONS: The number of patients with NDM-producing bacteria has increased in Southern Brazil, whose gene is present in different plasmids, explaining the expansion of this enzyme.

PMID:37001228 | DOI:10.1016/j.diagmicrobio.2023.115930

J Phys Chem B. 2023 Mar 31. doi: 10.1021/acs.jpcb.3c00429. Online ahead of print.

ABSTRACT

Although Venezuelan equine encephalitis virus (VEEV) is a life-threatening pathogen with a capacity for epidemic outbreaks, there are no FDA-approved VEEV antivirals for humans. VEEV cytotoxicity is partially attributed to the formation of a tetrameric complex between the VEEV capsid protein, the nuclear import proteins importin-α and importin-β, and the nuclear export protein CRM1, which together block trafficking through the nuclear pore complex. Experimental studies have identified small molecules from the CL6662 scaffold as potential inhibitors of the viral nuclear localization signal (NLS) sequence binding to importin-α. However, little is known about the molecular mechanism of CL6662 inhibition. To address this issue, we employed all-atom replica exchange molecular dynamics simulations to probe, in atomistic detail, the binding mechanism of CL6662 ligands to importin-α. Three ligands, including G281-1485 and two congeners with varying hydrophobicities, were considered. We investigated the distribution of ligand binding poses, their locations, and ligand specificities measured by the strength of binding interactions. We found that G281-1485 binds nonspecifically without forming well-defined binding poses throughout the NLS binding site. Binding of the less hydrophobic congener becomes strongly on-target with respect to the NLS binding site but remains nonspecific. However, a more hydrophobic congener is a strongly specific binder and the only ligand out of three to form a well-defined binding pose, while partially overlapping with the NLS binding site. On the basis of free energy estimates, we argue that all three ligands weakly compete with the viral NLS sequence for binding to importin-α in an apparent compromise to preserve host NLS binding. We further show that all-atom replica exchange binding simulations are a viable tool for studying ligands binding nonspecifically without forming well-defined binding poses.

PMID:37001021 | DOI:10.1021/acs.jpcb.3c00429

J Nat Prod. 2023 Mar 31. doi: 10.1021/acs.jnatprod.2c01145. Online ahead of print.

ABSTRACT

The first total synthesis of the natural product (13R,14S,15R)-13-hydroxy-14-deoxyoxacyclododecindione, which was isolated in 2018 as a member of the oxacyclododecindione family, is reported. A synthetic strategy through intramolecular Friedel-Crafts acylation combined with the stereoselective synthesis of a new triol key fragment allowed the preparation of the macrolactone. Due to mismatching physical data of the synthetic product, a revision of the configuration of the natural product isolated in 2018 is required. Light-induced E/Z-isomerism of the macrolactone backbone is described for the first time in the class of oxacyclododecindione-type macrolactones. The hydroxylated macrolactone prepared herein was found to show highly promising IC50 values in biological assays addressing the inhibition of inflammatory responses.

PMID:37001011 | DOI:10.1021/acs.jnatprod.2c01145

STAR Protoc. 2023 Mar 29;4(2):102203. doi: 10.1016/j.xpro.2023.102203. Online ahead of print.

ABSTRACT

Characterizing transcription factor (TF) genomic colocalization is essential for identifying cooperative binding of TFs in controlling gene expression. Here, we introduce a protocol for using PAD2, an interactive web application that enables the investigation of colocalization of various TFs and chromatin-regulating proteins from mouse embryonic stem cells at various functional genomic regions. We describe steps for accessing and searching the PAD2 database and selecting and submitting genomic regions. We then detail protein colocalization analysis using heatmap and ranked correlation plot. For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).1.

PMID:37000617 | DOI:10.1016/j.xpro.2023.102203

Funct Integr Genomics. 2023 Mar 31;23(2):112. doi: 10.1007/s10142-023-01023-1.

ABSTRACT

Reproduction-manipulating bacteria like Wolbachia can shift sex ratios in insects towards females, but skewed sex ratios may also arise from genetic conflicts. The flea beetle Altica lythri harbors three main mtDNA strains that are coupled to three different Wolbachia infections. Depending on the mtDNA types, the females produce either offspring with a balanced sex ratio or exclusively daughters. To obtain markers that can monitor when sex bias arises in the beetle's ontogeny, we elucidated the sex determination cascade of A. lythri. We established a RT-PCR method based on length variants of dsx (doublesex) transcripts to determine the sex of morphologically indistinguishable eggs and larvae. In females of one mtDNA type (HT1/HT1*) known to produce only daughters, male offspring were already missing at the egg stage while for females of another type (HT2), the dsx splice variants revealed a balanced sex ratio among eggs and larvae. Our data suggest that the sex determination cascade in A. lythri is initiated by maternally transmitted female-specific tra (transformer) mRNA as primary signal. This tra mRNA seems to be involved in a positive feedback loop that maintains the production of the female splice variant, as known for female offspring in Tribolium castaneum. The translation of the maternally transmitted female tra mRNA must be inhibited in male offspring, but the underlying primary genetic signal remains to be identified. We discuss which differences between the mtDNA types can influence sex determination and lead to the skewed sex ratio of HT1.

PMID:37000335 | DOI:10.1007/s10142-023-01023-1

Bull Math Biol. 2023 Mar 31;85(5):39. doi: 10.1007/s11538-023-01136-5.

ABSTRACT

Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to understand the dependence of the stochastic behavior of these systems on the chemical reaction rate parameters. Towards solving this problem, in this paper we develop theoretical tools called comparison theorems that provide stochastic ordering results for SCRNs. These theorems give sufficient conditions for monotonic dependence on parameters in these network models, which allow us to obtain, under suitable conditions, information about transient and steady-state behavior. These theorems exploit structural properties of SCRNs, beyond those of general continuous-time Markov chains. Furthermore, we derive two theorems to compare stationary distributions and mean first passage times for SCRNs with different parameter values, or with the same parameters and different initial conditions. These tools are developed for SCRNs taking values in a generic (finite or countably infinite) state space and can also be applied for non-mass-action kinetics models. When propensity functions are bounded, our method of proof gives an explicit method for coupling two comparable SCRNs, which can be used to simultaneously simulate their sample paths in a comparable manner. We illustrate our results with applications to models of enzymatic kinetics and epigenetic regulation by chromatin modifications.

PMID:37000280 | DOI:10.1007/s11538-023-01136-5

Elife. 2023 Mar 31;12:e86139. doi: 10.7554/eLife.86139.

ABSTRACT

Cardiometabolic diseases encompass a range of interrelated conditions that arise from underlying metabolic perturbations precipitated by genetic, environmental, and lifestyle factors. While obesity, dyslipidaemia, smoking, and insulin resistance are major risk factors for cardiometabolic diseases, individuals still present in the absence of such traditional risk factors, making it difficult to determine those at greatest risk of disease. Thus, it is crucial to elucidate the genetic, environmental, and molecular underpinnings to better understand, diagnose, and treat cardiometabolic diseases. Much of this information can be garnered using systems genetics, which takes population-based approaches to investigate how genetic variance contributes to complex traits. Despite the important advances made by human genome-wide association studies (GWAS) in this space, corroboration of these findings has been hampered by limitations including the inability to control environmental influence, limited access to pertinent metabolic tissues, and often, poor classification of diseases or phenotypes. A complementary approach to human GWAS is the utilisation of model systems such as genetically diverse mouse panels to study natural genetic and phenotypic variation in a controlled environment. Here, we review mouse genetic reference panels and the opportunities they provide for the study of cardiometabolic diseases and related traits. We discuss how the post-GWAS era has prompted a shift in focus from discovery of novel genetic variants to understanding gene function. Finally, we highlight key advantages and challenges of integrating complementary genetic and multi-omics data from human and mouse populations to advance biological discovery.

PMID:37000167 | DOI:10.7554/eLife.86139

Medicine (Baltimore). 2023 Mar 31;102(13):e33420. doi: 10.1097/MD.0000000000033420.

ABSTRACT

Melanin deposition is the main cause of skin darkening, which can lead to severe physical and psychological distress, necessitating the development of approaches for preserving skin health and fairness. Tyrosinase (TYR) is the rate-limiting enzyme in melanin synthesis, and its activity directly determines the degree of melanin accumulation in the skin, which in turn affects skin color. Currently, TYR inhibitors derived from natural products are widely used for skin whitening. San-Bai decoction (SBD) is effective for skin whitening and softening, but its mechanism of action, efficacy and high efficiency TYR inhibitors for skin whitening remain poorly understood. Here, we employed systems biology and network pharmacology to analyze the active compounds and targets of SBD, using the follow databases: TCMIP, TCMID, and BATMAN-TCM. Construct a molecular network centered on the regulation of TYR by SBD in skin whitening, using STRING database and cytoscape. Enrichment analysis using KOBAS database and ClusterProfiler. Virtual screening of candidate TYR inhibitors using Molecular Operating Environment software and Amber 18 software. SBD may act through tyrosine metabolism, melanogenesis, and other signaling pathways to regulate TYR activity and inhibit melanogenesis. We identified TYR and ESR1 as possible key targets for the whitening effect of SBD and screened out pentagalloylglucose, 1,3,6-tri-O-galloyl-beta-D-glucose, 1,2,4,6-tetragalloylglucose, and liquiritigenin 4',7-diglucoside as inhibitors of TYR, in addition to glycyrrhizic acid, pachymic acid methyl ester, nicotiflorin, gamma-sitosterol, and isoliensinine as inhibitors of ESR1. We also performed virtual drug screening of a library of natural small-molecule compounds (19,505 in total) and screened out lycopsamine, 2-phenylethyl b-D-glucopyranoside, and 6-beta-hydroxyhyoscyamine as inhibitors of TYR. We identified natural compounds with the potential for skin whitening through inhibition of TYR, thus advancing research on SBD and its applications.

PMID:37000099 | DOI:10.1097/MD.0000000000033420

Curr Med Chem. 2023 Mar 31. doi: 10.2174/0929867330666230331101458. Online ahead of print.

ABSTRACT

INTRODUCTION: Angiogenesis involves the development of new blood vessels. Biochemical signals start this process in the body, which is followed by migration, growth, and differentiation of endothelial cells that line the inside wall of blood vessels. This process is vital for the growth of cancer cells and tumors.

MATERIALS AND METHODS: We started our analysis by composing a list of genes that have a validated impact in humans with respect to angiogenesis-related phenotypes. Here, we have investigated the expression patterns of angiogenesis-related genes in the context of previously published single-cell RNA-Seq data from prostate and breast cancer samples.

RESULTS: Using a protein-protein interaction network, we showed how different modules of angiogenesis-related genes are overexpressed in different cell types. In our results, genes, such as ACKR1, AQP1, and EGR1, showed a strong cell type-dependent overexpression pattern in the two investigated cancer types, which can potentially be helpful in the diagnosis and follow-up of patients with prostate and breast cancer.

CONCLUSION: Our work demonstrates how different biological processes in distinct cell types contribute to the angiogenesis process, which can provide clues regarding the potential application of targeted inhibition of the angiogenesis process.

PMID:36999716 | DOI:10.2174/0929867330666230331101458

Front Genet. 2023 Mar 13;14:997383. doi: 10.3389/fgene.2023.997383. eCollection 2023.

ABSTRACT

RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and clinical science. Its immense popularity is due in large part to the continuous efforts of the bioinformatics community to develop accurate and scalable computational tools to analyze the enormous amounts of transcriptomic data that it produces. RNA-seq analysis enables genes and their corresponding transcripts to be probed for a variety of purposes, such as detecting novel exons or whole transcripts, assessing expression of genes and alternative transcripts, and studying alternative splicing structure. It can be a challenge, however, to obtain meaningful biological signals from raw RNA-seq data because of the enormous scale of the data as well as the inherent limitations of different sequencing technologies, such as amplification bias or biases of library preparation. The need to overcome these technical challenges has pushed the rapid development of novel computational tools, which have evolved and diversified in accordance with technological advancements, leading to the current myriad of RNA-seq tools. These tools, combined with the diverse computational skill sets of biomedical researchers, help to unlock the full potential of RNA-seq. The purpose of this review is to explain basic concepts in the computational analysis of RNA-seq data and define discipline-specific jargon.

PMID:36999049 | PMC:PMC10043755 | DOI:10.3389/fgene.2023.997383

Front Microbiol. 2023 Mar 14;14:1126030. doi: 10.3389/fmicb.2023.1126030. eCollection 2023.

ABSTRACT

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.

PMID:36998399 | PMC:PMC10043229 | DOI:10.3389/fmicb.2023.1126030