Divergent downstream biosynthetic pathways are supported by L-cysteine synthases of Mycobacterium tuberculosis.

Mycobacterium tuberculosis's (Mtb) autarkic lifestyle within the host involves rewiring its transcriptional networks to combat host-induced stresses. With the help of RNA sequencing performed under various stress conditions, we identified that genes belonging to Mtb sulfur metabolism pathways are significantly upregulated during oxidative stress. Using an integrated approach of microbial genetics, transcriptomics, metabolomics, animal experiments, chemical inhibition, and rescue studies, we investigated the biological role of non-canonical L-cysteine synthases, CysM and CysK2. While transcriptome signatures of RvΔcysM and RvΔcysK2 appear similar under regular growth conditions, we observed unique transcriptional signatures when subjected to oxidative stress. We followed pool size and labelling (34S) of key downstream metabolites, viz. mycothiol and ergothioneine, to monitor L-cysteine biosynthesis and utilization. This revealed the significant role of distinct L-cysteine biosynthetic routes on redox stress and homeostasis. CysM and CysK2 independently facilitate Mtb survival by alleviating host-induced redox stress, suggesting they are not fully redundant during infection. With the help of genetic mutants and chemical inhibitors, we show that CysM and CysK2 serve as unique, attractive targets for adjunct therapy to combat mycobacterial infection.

Fc-engineered antibodies promote neutrophil-dependent control of Mycobacterium tuberculosis.

Mounting evidence indicates that antibodies can contribute towards control of tuberculosis (TB). However, the underlying mechanisms of humoral immune protection and whether antibodies can be exploited in therapeutic strategies to combat TB are relatively understudied. Here we engineered the receptor-binding Fc (fragment crystallizable) region of an antibody recognizing the Mycobacterium tuberculosis (Mtb) capsule, to define antibody Fc-mediated mechanism(s) of Mtb restriction. We generated 52 Fc variants that either promote or inhibit specific antibody effector functions, rationally building antibodies with enhanced capacity to promote Mtb restriction in a human whole-blood model of infection. While there is likely no singular Fc profile that universally drives control of Mtb, here we found that several Fc-engineered antibodies drove Mtb restriction in a neutrophil-dependent manner. Single-cell RNA sequencing analysis showed that a restrictive Fc-engineered antibody promoted neutrophil survival and expression of cell-intrinsic antimicrobial programs. These data show the potential of Fc-engineered antibodies as therapeutics able to harness the protective functions of neutrophils to promote control of TB.

Modulated synthesis of hcp MOFs for preferential CO2 capture.

We herein show that the µ2-OH bridging groups in the double M12O8(OH)14 clusters of hcp UiO-66 could act as a preferential CO2 sorption site, compared to fcu UiO-66. As such, hcp-UiO-66-0.015 shows a high binary CO2 sorption capacity of 0.31 mmol g-1 and CO2/N2 (15/85) mixture selectivity of 87 at 298 K and 1 bar, which holds great potential for post-combustion CO2 capture.

Baseline single institutional retrospective review of body mass index (BMI) as a prognostic indicator in patients with newly diagnosed glioblastoma (GBM).

PURPOSE: Glioblastoma (GBM) is the most common primary brain cancer in adults with a very poor prognosis. Metabolic drivers of tumorigenesis are highly relevant within the central nervous system, where glucose is the critical source of energy. The impact of obesity on survival outcomes in patients with GBM is not well established. This study investigates the prognostic value of body mass index (BMI) in patients diagnosed with GBM. METHODS: Adult patients with newly diagnosed GBM treated at Thomas Jefferson University Hospital between January 1, 2008, and December 31, 2022, were included in the study. BMI was calculated using the formula BMI = kg/m2. Patients BMI groups were underweight (BMI < 19.00), normal weight (BMI 19.00-24.99), overweight (BMI 25-29.99), and obese (BMI > 30.00). All patients received 60 Gy of radiation therapy with concurrent and adjuvant temozolomide following maximal safe resection. A difference in clinical outcomes of overall survival (OS) and progression-free survival (PFS) were evaluated between the groups using Kaplan-Meier and log-rank tests. RESULTS: A total of 392 patients met inclusion criteria. The median age was 60.3 (range 18.9-86.7), with 144 females and 248 males. Median BMI was 27.0 (Range; 17.7-52.9). Non-overweight GBM patients (BMI < 25.00, OS 2.1 years, CI 1.7-2.4 years) had increased overall survival compared to overweight patients (BMI ≥ 25.00, OS 1.5 years, CI 1.4-1.6 years) (p < 0.001). Patients with MGMT-methylated GBM also had significantly greater OS and PFS compared to MGMT-unmethylated patients (p < 0.001). Non-overweight GBM patients (BMI < 25.00, median PFS 1.5 years, CI 1.3-2.0 years) also had increased progression-free survival compared to overweight patients (BMI ≥ 25.00, median PFS 1.1 years, CI 0.9-1.2 years) (p < 0.001). CONCLUSIONS: Our study indicates normal BMI (19.00-24.99) at the time of GBM diagnosis is a favorable prognostic indicator for overall and progression-free survival. Additional studies are warranted for further analysis of BMI and survival outcomes in GBM patients.

Transformer-based land use and land cover classification with explainability using satellite imagery.

Transformer-based models have greatly improved Land Use and Land Cover (LULC) applications. Their revolutionary ability to analyze and extract key information has greatly advanced the field. However, the high computational cost of these models presents a considerable obstacle to their practical implementation. Therefore, this study aims to strike a balance between computational cost and accuracy when employing transformer-based models for LULC analysis. We exploit transfer learning and fine-tuning strategies to optimize the resource utilization of transformer-based models. Furthermore, transparency is the core principle of our methodology to promote fairness and trust in applying LULC models across various domains, including forestry, environmental studies, and urban or rural planning. To ensure transparency, we have employed Captum, which enables us to uncover and mitigate potential biases and interpret AI-driven decisions. Our results indicate that transfer learning can potentially improve transformer-based models in satellite image classification, and strategic fine-tuning can maintain efficiency with minimal accuracy trade-offs. This research highlights the potential of Explainable AI (XAI) in Transformer-based models for achieving more efficient and transparent LULC analysis, thereby encouraging continued innovation in the field.

Novel frameless LINAC radiosurgery solution for uveal melanoma.

Introduction: Radiation treatment has replaced enucleation as an organ-preservation treatment for patients with uveal melanoma (UM). We developed a novel non-invasive, frameless LINAC based solution for fractionated stereotactic radiosurgery (fSRS) treatment. Methods: We designed and constructed the a stereotactic ocular localization box that can be attached and indexed to a stereotactic LINAC tabletop. It contains adjustable LED lights as a gaze focus point and CCD camera for monitoring of the patient's eye position. The device also has 6 infrared spheres compatible with the ExacTRAC IGRT system. Treatment plans were developed using iPLAN Dose version 4.5, with conformal dynamic arcs and 6MV photon beam in flattening filter free mode, dosed to 50Gy in 5 fractions. During treatment, patients were instructed to stare at the light when a radiation beam is prepared and ready for delivery. Eye movement was tracked throughout treatment. Residual setup errors were recorded for evaluation. Results: The stereotactic ocular localization box was 3D-printed with polylactic acid material and attached to the stereotactic LINAC tabletop. 10 patients were treated to evaluate the feasibility, tolerability and setup accuracy. Median treatment time for each arc is 17.3 ± 2.4 seconds (range: 13.8-23.4). After ExacTRAC setup, the residual setup errors are -0.1 ± 0.3 mm laterally, -0.1 ± 0.3 mm longitudinally, and 0 ± 0.2 mm vertically. The residue rotational errors are -0.1 ± 0.3 degree pitch, 0.1 ± 0.2 degree roll, and 0 ± 0.2 degree couch rotation. All patients received treatment successfully. Conclusion: We successfully developed a novel non-invasive frameless mask-based LINAC solution for SRS for uveal melanoma, or other ocular tumors. It is well tolerated with high set up accuracy. Future directions for this localization box would include a multi-center trial to assess the efficacy and reproducibility in the fabrication and execution of such a solution for UM therapy.

Implications of variable synaptic weights for rate and temporal coding of cerebellar outputs.

Purkinje cell (PC) synapses onto cerebellar nuclei (CbN) neurons allow signals from the cerebellar cortex to influence the rest of the brain. PCs are inhibitory neurons that spontaneously fire at high rates, and many PC inputs are thought to converge onto each CbN neuron to suppress its firing. It has been proposed that PCs convey information using a rate code, a synchrony and timing code, or both. The influence of PCs on CbN neuron firing was primarily examined for the combined effects of many PC inputs with comparable strengths, and the influence of individual PC inputs has not been extensively studied. Here, we find that single PC to CbN synapses are highly variable in size, and using dynamic clamp and modeling we reveal that this has important implications for PC-CbN transmission. Individual PC inputs regulate both the rate and timing of CbN firing. Large PC inputs strongly influence CbN firing rates and transiently eliminate CbN firing for several milliseconds. Remarkably, the refractory period of PCs leads to a brief elevation of CbN firing prior to suppression. Thus, individual PC-CbN synapses are suited to concurrently convey rate codes and generate precisely timed responses in CbN neurons. Either synchronous firing or synchronous pauses of PCs promote CbN neuron firing on rapid time scales for nonuniform inputs, but less effectively than for uniform inputs. This is a secondary consequence of variable input sizes elevating the baseline firing rates of CbN neurons by increasing the variability of the inhibitory conductance. These findings may generalize to other brain regions with highly variable inhibitory synapse sizes.

A mitochondrial quality control mechanism reverses the phagosome maturation arrest caused by Mycobacterium tuberculosis.

Phagosome maturation arrest (PMA) imposed by Mycobacterium tuberculosis ( Mtb ) is a classic tool that helps Mtb evade macrophage anti-bacterial responses. The exclusion of RAB7, a small GTPase, from Mtb -phagosomes underscores PMA. Here we report an unexpected mechanism that triggers crosstalk between the mitochondrial quality control (MQC) and the phagosome maturation pathways that reverses the PMA. CRISPR-mediated p62/SQSTM1 depletion ( p62 KD ) blocks mitophagy flux without impacting mitochondrial quality. In p62 KD cells, Mtb growth and survival are diminished, mainly through witnessing an increasingly oxidative environment and increased lysosomal targeting. The lysosomal targeting of Mtb is facilitated by enhanced TOM20 + mitochondria-derived vesicles (MDVs) biogenesis, a key MQC mechanism. In p62 KD cells, TOM20 + -MDVs biogenesis is MIRO1/MIRO2-dependent and delivered to lysosomes for degradation in a RAB7-dependent manner. Upon infection in p62 KD cells, TOM20 + -MDVs get extensively targeted to Mtb -phagosomes, inadvertently facilitating RAB7 recruitment, PMA reversal and lysosomal targeting of Mtb . Triggering MQC collapse in p62 KD cells further diminishes Mtb survival signifying cooperation between redox- and lysosome-mediated mechanisms. The MQC-anti-bacterial pathway crosstalk could be exploited for host-directed anti-tuberculosis therapies.

Statistical Analysis and Health Risk Assessment: Vegetables Irrigated with Wastewater in Kirri Shamozai, Pakistan.

One of the primary environmental routes through which humans are exposed to metals and may be exposed to health risks is the food chain's contamination with heavy metals. The study observed the risks posed by contaminants in vegetables produced in soil that received wastewater irrigation, as well as their origins and the human health impacts. Eight harmful metals (Cu, Fe, Zn, Mn, Pb, Cd, Ni, and Cr) were tested for concentration levels in water, soil, and vegetable samples using analytical techniques and an atomic absorption spectrophotometer. The present study investigated the potential health implications associated with the consumption of vegetables irrigated using wastewater containing heavy metals. The results indicated a notable accumulation of heavy metals in plant and soil samples obtained from Kirri Shamozai, Pakistan. In comparison to vegetables cultivated in soil irrigated with fresh water, the concentration levels of heavy metals in vegetables grown on soil irrigated with untreated wastewater were considerably higher at (P ≤ 0.001) and above the World Health Organization (WHO) recommended limits. The results showed that heavy metals had significantly accumulated in the soil and had permeated into the crops. Heavy metal concentrations in vegetables cultivated on land irrigated with wastewater were more significant than those grown on land irrigated with freshwater. They exceeded US EPA and World Health Organization (WHO) limits. PCA results for Pb, Cu, and Cr are the main issues impacting water quality and health hazards. The PCA results show that the soil has an extensive loading of heavy metals Cd, Ni, and Mn.

Differences in clinical outcomes based on molecular markers in glioblastoma patients treated with concurrent tumor-treating fields and chemoradiation: exploratory analysis of the SPARE trial.

BACKGROUND: Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Despite enormous research efforts, GBM remains a deadly disease. The standard-of-care treatment for patients with newly diagnosed with GBM as per the National Cancer Comprehensive Cancer Network (NCCN) is maximal safe surgical resection followed by concurrent chemoradiation and maintenance temozolomide (TMZ) with adjuvant tumor treating fields (TTF). TTF is a non-pharmacological intervention that delivers low-intensity, intermediate frequency alternating electric fields that arrests cell proliferation by disrupting the mitotic spindle. TTF have been shown in a large clinical trial to improve patient outcomes when added to radiation and chemotherapy. The SPARE trail (Scalp-sparing radiation with concurrent temozolomide and tumor treating fields) evaluated adding TTF concomitantly to radiation and chemotherapy. METHODS: This study is an exploratory analysis of the SPARE trial looking at the prognostic significance of common GBM molecular alterations, namely MGMT, EGFR, TP53, PTEN and telomerase reverse transcriptase (TERT), in this cohort of patients treated with concomitant TTF with radiation and chemotherapy. RESULTS: As expected, MGMT promoter methylation was associated with improved overall survival (OS) and progression-free survival (PFS) in this cohort. In addition, TERT promoter mutation was associated with improved OS and PFS in this cohort as well. CONCLUSIONS: Leveraging the molecular characterization of GBM alongside advancing treatments such as chemoradiation with TTF presents a new opportunity to improve precision oncology and outcomes for GBM patients.

Data quality model for assessing public COVID-19 big datasets.

For decision-making support and evidence based on healthcare, high quality data are crucial, particularly if the emphasized knowledge is lacking. For public health practitioners and researchers, the reporting of COVID-19 data need to be accurate and easily available. Each nation has a system in place for reporting COVID-19 data, albeit these systems' efficacy has not been thoroughly evaluated. However, the current COVID-19 pandemic has shown widespread flaws in data quality. We propose a data quality model (canonical data model, four adequacy levels, and Benford's law) to assess the quality issue of COVID-19 data reporting carried out by the World Health Organization (WHO) in the six Central African Economic and Monitory Community (CEMAC) region countries between March 6,2020, and June 22, 2022, and suggest potential solutions. These levels of data quality sufficiency can be interpreted as dependability indicators and sufficiency of Big Dataset inspection. This model effectively identified the quality of the entry data for big dataset analytics. The future development of this model requires scholars and institutions from all sectors to deepen their understanding of its core concepts, improve integration with other data processing technologies, and broaden the scope of its applications.

Implications of variable synaptic weights for rate and temporal coding of cerebellar outputs.

Purkinje cell (PC) synapses onto cerebellar nuclei (CbN) neurons convey signals from the cerebellar cortex to the rest of the brain. PCs are inhibitory neurons that spontaneously fire at high rates, and many uniform sized PC inputs are thought to converge onto each CbN neuron to suppress or eliminate firing. Leading theories maintain that PCs encode information using either a rate code, or by synchrony and precise timing. Individual PCs are thought to have limited influence on CbN neuron firing. Here, we find that single PC to CbN synapses are highly variable in size, and using dynamic clamp and modelling we reveal that this has important implications for PC-CbN transmission. Individual PC inputs regulate both the rate and timing of CbN firing. Large PC inputs strongly influence CbN firing rates and transiently eliminate CbN firing for several milliseconds. Remarkably, the refractory period of PCs leads to a brief elevation of CbN firing prior to suppression. Thus, PC-CbN synapses are suited to concurrently convey rate codes, and generate precisely-timed responses in CbN neurons. Variable input sizes also elevate the baseline firing rates of CbN neurons by increasing the variability of the inhibitory conductance. Although this reduces the relative influence of PC synchrony on the firing rate of CbN neurons, synchrony can still have important consequences, because synchronizing even two large inputs can significantly increase CbN neuron firing. These findings may be generalized to other brain regions with highly variable sized synapses.

Short-Term Forecasting of Monkeypox Cases Using a Novel Filtering and Combining Technique.

In the modern world, new technologies such as artificial intelligence, machine learning, and big data are essential to support healthcare surveillance systems, especially for monitoring confirmed cases of monkeypox. The statistics of infected and uninfected people worldwide contribute to the growing number of publicly available datasets that can be used to predict early-stage confirmed cases of monkeypox through machine-learning models. Thus, this paper proposes a novel filtering and combination technique for accurate short-term forecasts of infected monkeypox cases. To this end, we first filter the original time series of the cumulative confirmed cases into two new subseries: the long-term trend series and residual series, using the two proposed and one benchmark filter. Then, we predict the filtered subseries using five standard machine learning models and all their possible combination models. Hence, we combine individual forecasting models directly to obtain a final forecast for newly infected cases one day ahead. Four mean errors and a statistical test are performed to verify the proposed methodology's performance. The experimental results show the efficiency and accuracy of the proposed forecasting methodology. To prove the superiority of the proposed approach, four different time series and five different machine learning models were included as benchmarks. The results of this comparison confirmed the dominance of the proposed method. Finally, based on the best combination model, we achieved a forecast of fourteen days (two weeks). This can help to understand the spread and lead to an understanding of the risk, which can be utilized to prevent further spread and enable timely and effective treatment.

Heavy Metals in Vegetables: Screening Health Risks of Irrigation with Wastewater in Peri-Urban Areas of Bhakkar, Pakistan.

One of the key concerns in public health is food security in the food sector. Due to the large amounts of potentially hazardous metals in wastewater, this practice may pose serious environmental and health risks to neighboring residents. In this study, the health effects of heavy metals in vegetables irrigated with wastewater were studied. The findings indicated a massive accumulation of heavy metals in wastewater-irrigated soil and vegetables collected from Bhakkar, Pakistan. The current study looked at the effects of wastewater irrigation on metal buildup in the soil-plant continuum and the health hazards that come with it (Cd, Co, Ni, Mn, Pb, and Fe). Heavy metal concentrations in vegetables cultivated on soil irrigated with untreated wastewater were not significantly lower (p ≥ 0.05) than in vegetables grown on wastewater-irrigated soil and were below the World Health Organization's recommended limits. A considerable amount of the selected hazardous metals was also swallowed by adults and children who consumed these vegetables, according to the research. On soil that had received wastewater irrigation, Ni and Mn were substantially different at p ≥ 0.001 levels. Pb, Ni, and Cd had health risk scores higher than the ones in all ingested vegetables, while Mn had a health risk score greater than the ones in turnips, carrots, and lettuce. The results also showed that both adults and children who consumed these vegetables absorbed a significant amount of the chosen toxic metals. Pb and Cd were shown to be the most dangerous chemical compounds to human health, and everyday consumption of agricultural plants irrigated with wastewater may pose a health risk, according to the health risk criteria.

Cerebellar granule cell signaling is indispensable for normal motor performance.

Within the cerebellar cortex, mossy fibers (MFs) excite granule cells (GCs) that excite Purkinje cells (PCs), which provide outputs to the deep cerebellar nuclei (DCNs). It is well established that PC disruption produces motor deficits such as ataxia. This could arise from either decreases in ongoing PC-DCN inhibition, increases in the variability of PC firing, or disruption of the flow of MF-evoked signals. Remarkably, it is not known whether GCs are essential for normal motor function. Here we address this issue by selectively eliminating calcium channels that mediate transmission (CaV2.1, CaV2.2, and CaV2.3) in a combinatorial manner. We observe profound motor deficits but only when all CaV2 channels are eliminated. In these mice, the baseline rate and variability of PC firing are unaltered, and locomotion-dependent increases in PC firing are eliminated. We conclude that GCs are indispensable for normal motor performance and that disruption of MF-induced signals impairs motor performance.

The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein.

SigA (σA) is an essential protein and the primary sigma factor in Mycobacterium tuberculosis (Mtb). However, due to the absence of genetic tools, our understanding of the role and regulation of σA activity and its molecular attributes that help modulate Mtb survival is scant. Here, we generated a conditional gene replacement of σA in Mtb and showed that its depletion results in a severe survival defect in vitro, ex vivo, and in vivo in a murine infection model. Our RNA-seq analysis suggests that σA either directly or indirectly regulates ∼57% of the Mtb transcriptome, including ∼28% of essential genes. Surprisingly, we note that despite having ∼64% similarity with σA, overexpression of the primary-like σ factor SigB (σB) fails to compensate for the absence of σA, suggesting minimal functional redundancy. RNA-seq analysis of the Mtb σB deletion mutant revealed that 433 genes are regulated by σB, of which 283 overlap with the σA transcriptome. Additionally, surface plasmon resonance, in vitro transcription, and functional complementation experiments reveal that σA residues between 132-179 that are disordered and missing from all experimentally determined σA-RNAP structural models are imperative for σA function. Moreover, phosphorylation of σA in the intrinsically disordered N-terminal region plays a regulatory role in modulating its activity. Collectively, these observations and analysis provide a rationale for the centrality of σA for the survival and pathogenicity of this bacillus.

Hydrophobicity of Cholic Acid-Derived Amphiphiles Dictates the Antimicrobial Specificity.

The unique structural components of cell membranes of Gram-positive bacteria, Gram-negative bacteria, and mycobacteria provide an excellent therapeutic target for developing highly specific antimicrobials. Here, we report the synthesis of nine cholic acid (CA)-derived amphiphiles, where three hydroxyl groups of CA were tethered to dimethylamino pyridine and the C24-carboxyl group was conjugated with different alkyl chains. Structure-activity investigations revealed that amphiphile 1 harboring a methyl group has antimicrobial activity against mycobacterial species. On the other hand, amphiphile 7 containing an octyl chain was selective against Gram-positive and Gram-negative bacilli. Biochemical assays confirmed the selective membrane permeabilization abilities of amphiphiles 1 and 7. Importantly, we demonstrate the selective actions of amphiphiles in clearing biofilms, intracellular bacteria, and wound infections. Therefore, for the first time, we show that the unique structural features of CA-derived amphiphiles dictate selective activity against specific bacterial species.

Unusually Slow Spike Frequency Adaptation in Deep Cerebellar Nuclei Neurons Preserves Linear Transformations on the Subsecond Timescale.

Purkinje cells (PCs) are spontaneously active neurons of the cerebellar cortex that inhibit glutamatergic projection neurons within the deep cerebellar nuclei (DCN) that provide the primary cerebellar output. Brief reductions of PC firing rapidly increase DCN neuron firing. However, prolonged reductions of PC inhibition, as seen in some disease states, certain types of transgenic mice, during optogenetic suppression of PC firing, and in acute slices of the cerebellum, do not lead to large, sustained increases in DCN firing. Here we test whether DCN neurons undergo spike frequency adaptation that could account for these properties. We perform current-clamp recordings at near physiological temperature in acute brain slices from mice of both sexes to examine how DCN neurons respond to prolonged depolarizations. DCN neuron adaptation is exceptionally slow and bidirectional. A depolarizing current step evokes large initial increases in firing that decay to ∼20% of the initial increase within ∼10 s. We find that spike frequency adaptation in DCN neurons is mediated by a novel mechanism that is independent of the most promising candidates, including calcium entry and Na+-activated potassium channels mediated by Slo2.1 and Slo2.2 Slow adaptation allows DCN neurons to gradually and bidirectionally adapt to prolonged currents but to respond linearly to current injection on rapid timescales. This suggests that an important consequence of slow adaptation is that DCN neurons respond linearly to the rate of PC firing on rapid timescales but adapt to slow firing rate changes of PCs on long timescales.SIGNIFICANCE STATEMENT Excitatory neurons in the cerebellar nuclei provide the primary output from the cerebellum. This study finds that these neurons exhibit very slow bidirectional spike frequency adaptation that has important implications for cerebellar function. This mechanism allows neurons in the cerebellar nuclei to adapt to long-lasting changes in synaptic drive while also remaining responsive to short-term changes in excitatory or inhibitory drive.

Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival.

Mycobacterium tuberculosis encodes ~200 transcription factors that modulate gene expression under different microenvironments in the host. Even though high-throughput chromatin immunoprecipitation sequencing and transcriptome sequencing (RNA-seq) studies have identified the regulatory network for ~80% of transcription factors, many transcription factors remain uncharacterized. EmbR is one such transcription factor whose in vivo regulon and biological function are yet to be elucidated. Previous in vitro studies suggested that phosphorylation of EmbR by PknH upregulates the embCAB operon. Using a gene replacement mutant of embR, we investigated its role in modulating cellular morphology, antibiotic resistance, and survival in the host. Contrary to the prevailing hypothesis, under normal growth conditions, EmbR is neither phosphorylated nor impacted by ethambutol resistance through the regulation of the embCAB operon. The embR deletion mutant displayed attenuated M. tuberculosis survival in vivo. RNA-seq analysis suggested that EmbR regulates operons involved in the secretion pathway, lipid metabolism, virulence, and hypoxia, including well-known hypoxia-inducible genes devS and hspX. Lipidome analysis revealed that EmbR modulates levels of all lysophospholipids, several phospholipids, and M. tuberculosis-specific lipids, which is more pronounced under hypoxic conditions. We found that the EmbR mutant is hypersusceptible to hypoxic stress, and RNA sequencing performed under hypoxic conditions indicated that EmbR majorly regulates genes involved in response to acidic pH, hypoxia, and fatty acid metabolism. We observed condition-specific phosphorylation of EmbR, which contributes to EmbR-mediated transcription of several essential genes, ensuring enhanced survival. Collectively, the study establishes EmbR as a key modulator of hypoxic response that facilitates mycobacterial survival in the host. IMPORTANCE Mycobacterium tuberculosis modulates its transcriptional machinery in response to dynamic microenvironments encountered within the host. In this study, we identified that EmbR, a transcription factor, plays important roles in modulating cellular morphology, antibiotic resistance, and survival in the host. We found that EmbR undergoes condition-specific phosphorylation for its activation. Together, the study establishes a key role of EmbR as a transcriptional activator of genes belonging to multiple pathways, viz., virulence, secretion, or polyketide synthesis, that aid in mycobacterial survival during hypoxia and within the host.

Development of a Highly Specific, Selective, and Sensitive Fluorescent Probe for Detection of Mycobacteria in Human Tissues.

Tuberculosis (TB), including extrapulmonary TB, is responsible for more than one million deaths in a year worldwide. Existing methods of mycobacteria detection have poor sensitivity, selectivity, and specificity, especially in human tissues. Herein, the synthesis of a cholic acid-derived fluorescent probe (P4) that can specifically stain the mycobacterium species is presented. It is shown that P4 probe specifically binds with mycobacterial lipids, trehalose monomycolate, and phosphatidylinositol mannoside 6. P4 probe can detect mycobacteria in polymicrobial planktonic cultures and biofilms with high specificity, selectivity, and sensitivity. Moreover, it can detect a single mycobacterium in the presence of 10 000 other bacilli. Unlike the probes that depend on active mycobacterial enzymes, the membrane-specific P4 probe can detect mycobacteria even in formalin-fixed paraffin-embedded mice and human tissue sections. Therefore, the ability of the P4 probe to detect mycobacteria in different biological milieu makes it a potential candidate for diagnostic and prognostic applications in clinical settings.