Construction of novel multi-epitope-based diagnostic biomarker HP16118P and its application in the differential diagnosis of Mycobacterium tuberculosis latent infection.

Tuberculosis (TB) is an infectious disease that significantly threatens human health. However, the differential diagnosis of latent tuberculosis infection (LTBI) and active tuberculosis (ATB) remains a challenge for clinicians in early detection and preventive intervention. In this study, we developed a novel biomarker named HP16118P, utilizing 16 helper T lymphocyte (HTL) epitopes, 11 cytotoxic T lymphocyte (CTL) epitopes, and 8 B cell epitopes identified from 15 antigens associated with LTBI-RD using the IEDB database. We analyzed the physicochemical properties, spatial structure, and immunological characteristics of HP16118P using various tools, which indicated that it is a hydrophilic and relatively stable alkaline protein. Furthermore, HP16118P exhibited good antigenicity and immunogenicity, while being non-toxic and non-allergenic, with the potential to induce immune responses. We observed that HP16118P can stimulate the production of high levels of IFN-γ+ T lymphocytes in individuals with ATB, LTBI, and health controls. IL-5 induced by HP16118P demonstrated potential in distinguishing LTBI individuals and ATB patients (p=0.0372, AUC=0.8214, 95% CI [0.5843 to 1.000]) with a sensitivity of 100% and specificity of 71.43%. Furthermore, we incorporated the GM-CSF, IL-23, IL-5, and MCP-3 induced by HP16118P into 15 machine learning algorithms to construct a model. It was found that the Quadratic discriminant analysis model exhibited the best diagnostic performance for discriminating between LTBI and ATB, with a sensitivity of 1.00, specificity of 0.86, and accuracy of 0.93. In summary, HP16118P has demonstrated strong antigenicity and immunogenicity, with the induction of GM-CSF, IL-23, IL-5, and MCP-3, suggesting their potential for the differential diagnosis of LTBI and ATB.

Mycobacterium tuberculosis: immune response, biomarkers, and therapeutic intervention.

Although tuberculosis (TB) is an infectious disease, the progression of the disease following Mycobacterium tuberculosis (MTB) infection is closely associated with the host's immune response. In this review, a comprehensive analysis of TB prevention, diagnosis, and treatment was conducted from an immunological perspective. First, we delved into the host's immune response mechanisms against MTB infection as well as the immune evasion mechanisms of the bacteria. Addressing the challenges currently faced in TB diagnosis and treatment, we also emphasized the importance of protein, genetic, and immunological biomarkers, aiming to provide new insights for early and personalized diagnosis and treatment of TB. Building upon this foundation, we further discussed intervention strategies involving chemical and immunological treatments for the increasingly critical issue of drug-resistant TB and other forms of TB. Finally, we summarized TB prevention, diagnosis, and treatment challenges and put forward future perspectives. Overall, these findings provide valuable insights into the immunological aspects of TB and offer new directions toward achieving the WHO's goal of eradicating TB by 2035.

From immunology to artificial intelligence: revolutionizing latent tuberculosis infection diagnosis with machine learning.

Latent tuberculosis infection (LTBI) has become a major source of active tuberculosis (ATB). Although the tuberculin skin test and interferon-gamma release assay can be used to diagnose LTBI, these methods can only differentiate infected individuals from healthy ones but cannot discriminate between LTBI and ATB. Thus, the diagnosis of LTBI faces many challenges, such as the lack of effective biomarkers from Mycobacterium tuberculosis (MTB) for distinguishing LTBI, the low diagnostic efficacy of biomarkers derived from the human host, and the absence of a gold standard to differentiate between LTBI and ATB. Sputum culture, as the gold standard for diagnosing tuberculosis, is time-consuming and cannot distinguish between ATB and LTBI. In this article, we review the pathogenesis of MTB and the immune mechanisms of the host in LTBI, including the innate and adaptive immune responses, multiple immune evasion mechanisms of MTB, and epigenetic regulation. Based on this knowledge, we summarize the current status and challenges in diagnosing LTBI and present the application of machine learning (ML) in LTBI diagnosis, as well as the advantages and limitations of ML in this context. Finally, we discuss the future development directions of ML applied to LTBI diagnosis.

Characterization of SchTPSs Enables Construction of Yeast for the Bioproduction of α-Cadinol and the Related Sesquiterpenes.

Plant volatile sesquiterpenes (PVSs) play important roles in chemical plant defense. However, it is difficult to isolate sufficient PVSs for deep investigations due to their low contents and chemical and physical properties close to those of other lipids. The extracts of Stellera chamaejasme L. exhibit insecticidal, fungicidal, and allelopathic activities. In this study, we identified three sesquiterpene synthase genes (SchTPS5, SchTPS6, and SchTPS7) from S. chamaejasme L. SchTPS7 is an α-farnesene synthase. SchTPS5 and SchTPS6 are two catalytically promiscuous sesquiterpene synthases, and α-cadinol and τ-muurolol are the predominant products for both of them in Saccharomyces cerevisiae. This study, for the first time, reports plant sesquiterpene synthases capable of producing α-cadinol and/or τ-muurolol in a heterologous host. More intriguingly, seven out of eight products of SchTPS6 in S. cerevisiae possess various insecticidal, fungicidal, and herbicidal activities. Building on this finding, we used SchTPS6 to construct an engineered S. cerevisiae for the production of these sesquiterpenes. The titers of two major products α-cadinol and τ-muurolol, respectively, reached 46.2 ± 4.0 and 11.2 ± 1.4 mg/L in a flask. This study lays a foundation for the development of new agrochemical mixtures.

Immunotherapy and biomarkers in patients with lung cancer with tuberculosis: Recent advances and future Directions.

Lung cancer (LC) and tuberculosis (TB) are two major global public health problems, and the incidence of LC-TB is currently on the rise. Therefore effective clinical interventions are crucial for LC-TB. The aim of this review is to provide up-to-date information on the immunological profile and therapeutic biomarkers in patients with LC-TB. We discuss the immune mechanisms involved, including the immune checkpoints that play an important role in the treatment of patients with LC-TB. In addition, we explore the susceptibility of patients with LC to TB and summarise the latest research on LC-TB. Finally, we discuss future prospects in this field, including the identification of potential targets for immune intervention. In conclusion, this review provides important insights into the complex relationship between LC and TB and highlights new advances in the detection and treatment of both diseases.

Next-Generation TB Vaccines: Progress, Challenges, and Prospects.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is a prevalent global infectious disease and a leading cause of mortality worldwide. Currently, the only available vaccine for TB prevention is Bacillus Calmette-Guérin (BCG). However, BCG demonstrates limited efficacy, particularly in adults. Efforts to develop effective TB vaccines have been ongoing for nearly a century. In this review, we have examined the current obstacles in TB vaccine research and emphasized the significance of understanding the interaction mechanism between MTB and hosts in order to provide new avenues for research and establish a solid foundation for the development of novel vaccines. We have also assessed various TB vaccine candidates, including inactivated vaccines, attenuated live vaccines, subunit vaccines, viral vector vaccines, DNA vaccines, and the emerging mRNA vaccines as well as virus-like particle (VLP)-based vaccines, which are currently in preclinical stages or clinical trials. Furthermore, we have discussed the challenges and opportunities associated with developing different types of TB vaccines and outlined future directions for TB vaccine research, aiming to expedite the development of effective vaccines. This comprehensive review offers a summary of the progress made in the field of novel TB vaccines.

Characterization of Guaiene Synthases from Stellera chamaejasme L. Flowers and Their Application in De novo Production of (-)-Rotundone in Yeast.

Four terpene synthases for the biosynthesis of volatile terpenoids were identified from the transcriptome of Stellera chamaejasme L. flowers, including SchTPS1, SchTPS2, SchTPS3, and SchTPS4. Their functions were characterized by synthetic biology approaches in Escherichia coli and in vitro enzymatic assays. SchTPS1, SchTPS2, and SchTPS3 are guaiene synthases, while SchTPS4 is an (E,E)-geranyl linalool synthase. Next, SchTPS1 and α-guaiene 2-oxidase VvSTO2 were co-expressed in Saccharomyces cerevisiae to reconstruct the biosynthetic pathway of (-)-rotundone, which is a unique aroma compound in fruits, vegetables, and wines. This is the first report for the construction of a (-)-rotundone-producing microbial platform.

Identification of prolyl hydroxylation modifications in mammalian cell proteins.

Prolyl hydroxylation is a PTM that plays an important role in the formation of collagen fibrils and in the oxygen-dependent regulation of hypoxia inducible factor-α (HIF-α). While this modification has been well characterized in the context of these proteins, it remains unclear to what extent it occurs in the remaining mammalian proteome. We explored this question using MS to analyze cellular extracts subjected to various fractionation strategies. In one strategy, we employed the von Hippel Lindau tumor suppressor protein, which recognizes prolyl hydroxylated HIF-α, as a scaffold for generating hydroxyproline capture reagents. We report novel sites of prolyl hydroxylation within five proteins: FK506-binding protein 10, myosin heavy chain 10, hexokinase 2, pyruvate kinase, and C-1 Tetrahydrofolate synthase. Furthermore, we show that identification of prolyl hydroxylation presents a significant technical challenge owing to widespread isobaric methionine oxidation, and that manual inspection of spectra of modified peptides in this context is critical for validation.

Defective Tibetan PHD2 binding to p23 links high altitude adaption to altered oxygen sensing.

The Tibetan population has adapted to the chronic hypoxia of high altitude. Tibetans bear a genetic signature in the prolyl hydroxylase domain protein 2 (PHD2/EGLN1) gene, which encodes for the central oxygen sensor of the hypoxia-inducible factor (HIF) pathway. Recent studies have focused attention on two nonsynonymous coding region substitutions, D4E and C127S, both of which are markedly enriched in the Tibetan population. These amino acids reside in a region of PHD2 that harbors a zinc finger, which we have previously discovered binds to a Pro-Xaa-Leu-Glu (PXLE) motif in the HSP90 cochaperone p23, thereby recruiting PHD2 to the HSP90 pathway to facilitate HIF-α hydroxylation. We herein report that the Tibetan PHD2 haplotype (D4E/C127S) strikingly diminishes the interaction of PHD2 with p23, resulting in impaired PHD2 down-regulation of the HIF pathway. The defective binding to p23 depends on both the D4E and C127S substitutions. We also identify a PXLE motif in HSP90 itself that can mediate binding to PHD2 but find that this interaction is maintained with the D4E/C127S PHD2 haplotype. We propose that the Tibetan PHD2 variant is a loss of function (hypomorphic) allele, leading to augmented HIF activation to facilitate adaptation to high altitude.

Prolyl hydroxylase domain protein 2 (PHD2) binds a Pro-Xaa-Leu-Glu motif, linking it to the heat shock protein 90 pathway.

Prolyl hydroxylase domain protein 2 (PHD2, also known as Egg Laying Defective Nine homolog 1) is a key oxygen-sensing protein in metazoans. In an oxygen-dependent manner, PHD2 site-specifically prolyl hydroxylates the master transcription factor of the hypoxic response, hypoxia-inducible factor-α (HIF-α), thereby targeting HIF-α for degradation. In this report we show that the heat shock protein 90 (HSP90) co-chaperones p23 and FKBP38 interact via a conserved Pro-Xaa-Leu-Glu motif (where Xaa = any amino acid) in these proteins with the N-terminal Myeloid Nervy and DEAF-1 (MYND)-type zinc finger of PHD2. Knockdown of p23 augments hypoxia-induced HIF-1α protein levels and HIF target genes. We propose that p23 recruits PHD2 to the HSP90 machinery to facilitate HIF-1α hydroxylation. These findings identify a link between two ancient pathways, the PHD:HIF and the HSP90 pathways, and suggest that this link was established concurrent with the emergence of the PHD:HIF pathway in evolution.

Segmentation of computer tomography image using local robust statistics and region-scalable fitting.

Intensity inhomogeneity may cause considerable difficulties in segmentation of CT image. In order to overcome the difficulties caused by intensity inhomogeneity, the region-scalable fitting (RSF) model was put forward. RSF model draws upon intensity information in local regions with a controllable scale. But only using intensity information may lead to slow convergence rate and poor denoise ability. Combining the method of robust statistics, RSF model is improved in this paper. In the improved model, the intensity in RSF model is replaced with local robust statistics which is the weighted combination of inter-quartile range, mean absolute deviation and intensity median in local region. Inter-quartile range and mean absolute deviation in local region are introduced to sharpen object boundaries, and intensity median in local region is introduced to reduce image noise. The contrast experiments between RSF model and the improved model are provided, which demonstrate the fast convergence rate and robustness to noise of the improved model.

A study of the 15N NMR chemical shifts in substituted anilines and phenylhydrazines, and their derivatives.

The analysis of (15)N chemical shift data from over a hundred anilines, N-methyl anilines, N,N-dimethyl anilines and phenylhydrazines with substituents in the phenyl ring leads to an empirical equation, delta(cal) = deltaon + Deltao + Deltam + Deltap, for calculating (15)N NMR chemical shifts of the amino group. This equation is based on a linear regression analysis using eighteen substituent parameters and leads to good conformity with the expected data.

Steady-state kinetics and inhibitory action of antitubercular phenothiazines on mycobacterium tuberculosis type-II NADH-menaquinone oxidoreductase (NDH-2).

Type-II NADH-menaquinone oxidoreductase (NDH-2) is an essential respiratory enzyme of the pathogenic bacterium Mycobacterium tuberculosis (Mtb) that plays a pivotal role in its growth. In the present study, we expressed and purified highly active Mtb NDH-2 using a Mycobacterium smegmatis expression system, and the steady-state kinetics and inhibitory actions of phenothiazines were characterized. Purified NDH-2 contains a non-covalently bound flavin adenine dinucleotide cofactor and oxidizes NADH with quinones but does not react with either NADPH or oxygen. Ubiquinone-2 (Q2) and decylubiquinone showed high electron-accepting activity, and the steady-state kinetics and the NADH-Q2 oxidoreductase reaction were found to operate by a ping-pong reaction mechanism. Phenothiazine analogues, trifluoperazine, Compound 1, and Compound 2 inhibit the NADH-Q2 reductase activity with IC50 = 12, 11, and 13 microm, respectively. Trifluoperazine inhibition is non-competitive for NADH, whereas the inhibition kinetics is found to be uncompetitive in terms of Q2.

Inhibitors of type II NADH:menaquinone oxidoreductase represent a class of antitubercular drugs.

Mycobacterium tuberculosis (Mtb) is an obligate aerobe that is capable of long-term persistence under conditions of low oxygen tension. Analysis of the Mtb genome predicts the existence of a branched aerobic respiratory chain terminating in a cytochrome bd system and a cytochrome aa(3) system. Both chains can be initiated with type II NADH:menaquinone oxidoreductase. We present a detailed biochemical characterization of the aerobic respiratory chains from Mtb and show that phenothiazine analogs specifically inhibit NADH:menaquinone oxidoreductase activity. The emergence of drug-resistant strains of Mtb has prompted a search for antimycobacterial agents. Several phenothiazines analogs are highly tuberculocidal in vitro, suppress Mtb growth in a mouse model of acute infection, and represent lead compounds that may give rise to a class of selective antibiotics.

A study of the 17O carbonyl chemical shifts in substituted benzaldehydes.

An analysis of 17O carbonyl chemical shifts of 50 substituted benzaldehydes leads to an empirical equation, delta(cal)(17O) = 564.0 + (sigma)(delta)o + (sigma)(delta)m + (sigma)(delta)p + C, for calculating 17O chemical shifts. This equation is based on a linear regression analysis using 11 substituent parameters and leads to good conformity with the expected data.