Systems immunology of regulatory T cells: can one circuit explain it all?

Regulatory T (Treg) cells play vital roles in immune homeostasis and response, including discrimination between self- and non-self-antigens, containment of immunopathology, and inflammation resolution. These diverse functions are orchestrated by cellular circuits involving Tregs and other cell types across space and time. Despite dramatic progress in our understanding of Treg biology, a quantitative framework capturing how Treg-containing circuits give rise to these diverse functions is lacking. Here, we propose that different facets of Treg function can be interpreted as distinct operating regimes of the same underlying circuit. We discuss how a systems immunology approach, involving quantitative experiments, computational modeling, and machine learning, can advance our understanding of Treg function, and help identify general operating and design principles underlying immune regulation.

Minimal frustration underlies the usefulness of incomplete regulatory network models in biology.

Regulatory networks as large and complex as those implicated in cell-fate choice are expected to exhibit intricate, very high-dimensional dynamics. Cell-fate choice, however, is a macroscopically simple process. Additionally, regulatory network models are almost always incomplete and/or inexact, and do not incorporate all the regulators and interactions that may be involved in cell-fate regulation. In spite of these issues, regulatory network models have proven to be incredibly effective tools for understanding cell-fate choice across contexts and for making useful predictions. Here, we show that minimal frustration-a feature of biological networks across contexts but not of random networks-can compel simple, low-dimensional steady-state behavior even in large and complex networks. Moreover, the steady-state behavior of minimally frustrated networks can be recapitulated by simpler networks such as those lacking many of the nodes and edges and those that treat multiple regulators as one. The present study provides a theoretical explanation for the success of network models in biology and for the challenges in network inference.

Epigenetic factor competition reshapes the EMT landscape.

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene-regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as gene-regulatory networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators, in addition to local transcription factors, and show the counterintuitive consequences of such interactions. We apply our approach to recent experimental findings on the epithelial-mesenchymal transition (EMT). We show that it can explain the puzzling experimental data, as well as provide verifiable predictions.

DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.

Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or 'push' between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.

Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing.

The epithelial-to-mesenchymal transition (EMT) plays a critical role during normal development and in cancer progression. EMT is induced by various signaling pathways, including TGF-ß, BMP, Wnt-ß-catenin, NOTCH, Shh, and receptor tyrosine kinases. In this study, we performed single-cell RNA sequencing on MCF10A cells undergoing EMT by TGF-ß1 stimulation. Our comprehensive analysis revealed that cells progress through EMT at different paces. Using pseudotime clustering reconstruction of gene-expression profiles during EMT, we found sequential and parallel activation of EMT signaling pathways. We also observed various transitional cellular states during EMT. We identified regulatory signaling nodes that drive EMT with the expression of important microRNAs and transcription factors. Using a random circuit perturbation methodology, we demonstrate that the NOTCH signaling pathway acts as a key driver of TGF-ß-induced EMT. Furthermore, we demonstrate that the gene signatures of pseudotime clusters corresponding to the intermediate hybrid EMT state are associated with poor patient outcome. Overall, this study provides insight into context-specific drivers of cancer progression and highlights the complexities of the EMT process.

A mechanistic modeling framework reveals the key principles underlying tumor metabolism.

While aerobic glycolysis, or the Warburg effect, has for a long time been considered a hallmark of tumor metabolism, recent studies have revealed a far more complex picture. Tumor cells exhibit widespread metabolic heterogeneity, not only in their presentation of the Warburg effect but also in the nutrients and the metabolic pathways they are dependent on. Moreover, tumor cells can switch between different metabolic phenotypes in response to environmental cues and therapeutic interventions. A framework to analyze the observed metabolic heterogeneity and plasticity is, however, lacking. Using a mechanistic model that includes the key metabolic pathways active in tumor cells, we show that the inhibition of phosphofructokinase by excess ATP in the cytoplasm can drive a preference for aerobic glycolysis in fast-proliferating tumor cells. The differing rates of ATP utilization by tumor cells can therefore drive heterogeneity with respect to the presentation of the Warburg effect. Building upon this idea, we couple the metabolic phenotype of tumor cells to their migratory phenotype, and show that our model predictions are in agreement with previous experiments. Next, we report that the reliance of proliferating cells on different anaplerotic pathways depends on the relative availability of glucose and glutamine, and can further drive metabolic heterogeneity. Finally, using treatment of melanoma cells with a BRAF inhibitor as an example, we show that our model can be used to predict the metabolic and gene expression changes in cancer cells in response to drug treatment. By making predictions that are far more generalizable and interpretable as compared to previous tumor metabolism modeling approaches, our framework identifies key principles that govern tumor cell metabolism, and the reported heterogeneity and plasticity. These principles could be key to targeting the metabolic vulnerabilities of cancer.

Tailored mesoporous γ-WO3 nanoplates: unraveling their potential for highly sensitive NH3 detection and efficient photocatalysis.

Herein, the monoclinic phase of tungsten oxide (γ-WO3) was successfully obtained after annealing hydrothermally synthesised WO3 powder at 500 °C. As per the result obtained from the N2 adsorption-desorption isotherm, the material has been identified as mesoporous with a specific surface area of 3.71 m2 g-1 from BET (Brunauer-Emmett-Teller) analysis. Moreover, the average pore size (49.52 nm) and volume (0.050 cm3 g-1) were also determined by the BJH (Barrett-Joyner-Halenda) method. FE-SEM (field emission scanning electron microscopy) and HR-TEM (high resolution transmission electron microscopy) have confirmed the formation of nanoplates with an average diameter of approximately 274 nm. Raman spectroscopy has shown peaks at the lower wavenumber region (270 cm-1 and 326 cm-1) and the higher wavenumber region (713 cm-1 and 806 cm-1) for O-W-O bending modes and stretching modes, respectively. The combined effect of relative humidity (RH-11%-RH-95%-RH-11%) and NH3 (150 ppm, 300 ppm, 450 ppm, 600 ppm, 700 ppm, and 800 ppm) was investigated in this reported work. The synthesised γ-WO3 has shown highly responsive behaviour for humidity of 96.5% (RH-11%-95%) and NH3 sensing (under humidity) of 97.4% (RH-11%-95% with 800 ppm NH3). The response and recovery time were calculated as 15 s and 52 s, and 16 s and 54 s for humidity, and NH3 under humidity, respectively. The experimental findings demonstrated that the resistance of the sensor depends on the concentration of NH3 and humidity. Moreover, γ-WO3 has been investigated as a promising catalyst for the dye degradation of methylene blue (MB) with a degradation efficiency of 72.82% and methyl orange (MO) with a degradation efficiency of 53.84% under visible light exposure. This dye degradation occurred within 160 min in the presence of a catalyst under visible light irradiation.

Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer.

Cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. A developmental programme known as epithelial-to-mesenchymal transition (EMT) plays a critical role during metastasis, promoting the loss of polarity and cell-cell adhesion and the acquisition of motile, stem-cell characteristics. Cells undergoing EMT or the reverse mesenchymal-to-epithelial transition (MET) are often associated with metabolic changes, as the change in phenotype often correlates with a different balance of proliferation versus energy-intensive migration. Extensive crosstalk occurs between metabolism and EMT, but how this crosstalk leads to coordinated physiological changes is still uncertain. The elusive connection between metabolism and EMT compromises the efficacy of metabolic therapies targeting metastasis. In this review, we aim to clarify the causation between metabolism and EMT on the basis of experimental studies, and propose integrated theoretical-experimental efforts to better understand the coupled decision-making of metabolism and EMT.

A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells.

Epithelial-mesenchymal heterogeneity implies that cells within the same tumor can exhibit different phenotypes-epithelial, mesenchymal, or one or more hybrid epithelial-mesenchymal phenotypes. This behavior has been reported across cancer types, both in vitro and in vivo, and implicated in multiple processes associated with metastatic aggressiveness including immune evasion, collective dissemination of tumor cells, and emergence of cancer cell subpopulations with stem cell-like properties. However, the ability of a population of cancer cells to generate, maintain, and propagate this heterogeneity has remained a mystifying feature. Here, we used a computational modeling approach to show that epithelial-mesenchymal heterogeneity can emerge from the noise in the partitioning of biomolecules (such as RNAs and proteins) among daughter cells during the division of a cancer cell. Our model captures the experimentally observed temporal changes in the fractions of different phenotypes in a population of murine prostate cancer cells, and describes the hysteresis in the population-level dynamics of epithelial-mesenchymal plasticity. The model is further able to predict how factors known to promote a hybrid epithelial-mesenchymal phenotype can alter the phenotypic composition of a population. Finally, we used the model to probe the implications of phenotypic heterogeneity and plasticity for different therapeutic regimens and found that co-targeting of epithelial and mesenchymal cells is likely to be the most effective strategy for restricting tumor growth. By connecting the dynamics of an intracellular circuit to the phenotypic composition of a population, our study serves as a first step towards understanding the generation and maintenance of non-genetic heterogeneity in a population of cancer cells, and towards the therapeutic targeting of phenotypic heterogeneity and plasticity in cancer cell populations.

Biological Networks Regulating Cell Fate Choice Are Minimally Frustrated.

Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous studies, focusing on identifying topological features that are present in biological networks but not in random networks, have, however, provided few functional insights. We use a Boolean modeling framework and ideas from the spin glass literature to identify functional differences between five real biological networks and random networks with similar topological features. We show that minimal frustration is a fundamental property that allows biological networks to robustly establish cell types and regulate cell fate choice, and that this property can emerge in complex networks via Darwinian evolution. The study also provides clues regarding how the regulation of cell fate choice can go awry in a disease like cancer and lead to the emergence of aberrant cell types.

The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences.

The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single-nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic environment, it is possible that selection to explore a large fraction of the space of functional proteins also occurred. To determine whether selection for such a property played a role during the emergence of the nearly universal standard genetic code, we investigated the number of functional variants of the Escherichia coli PhoQ protein explored at different time scales under translation using different genetic codes. We found that the standard genetic code is highly optimal for exploring a large fraction of the space of functional PhoQ variants at intermediate time scales as compared to random codes. Environmental changes, in response to which genetic diversity in a population provides a fitness advantage, are likely to have occurred at these intermediate time scales. Our results indicate that the ability of the standard code to explore a large fraction of the space of functional sequence variants arises from a balance between robustness and flexibility and is largely independent of the property of the standard code to minimize the phenotypic effects of mutations. We propose that selection to explore a large fraction of the functional sequence space while minimizing the phenotypic effects of mutations contributed toward the emergence of the standard code as the universal genetic code.

Hierarchy in gene expression is predictive of risk, progression, and outcome in adult acute myeloid leukemia.

Cancer progresses with a change in the structure of the gene network in normal cells. We define a measure of organizational hierarchy in gene networks of affected cells in adult acute myeloid leukemia (AML) patients. With a retrospective cohort analysis based on the gene expression profiles of 116 AML patients, we find that the likelihood of future cancer relapse and the level of clinical risk are directly correlated with the level of organization in the cancer related gene network. We also explore the variation of the level of organization in the gene network with cancer progression. We find that this variation is non-monotonic, which implies the fitness landscape in the evolution of AML cancer cells is non-trivial. We further find that the hierarchy in gene expression at the time of diagnosis may be a useful biomarker in AML prognosis.

A correlation study of sustainable development goal (SDG) interactions.

As universities are the change agent of society, institutions from all nations set their goals to transform the world by exploring various societal challenges that humans are facing. Together, the higher education systems across the world developing strategies based on the United Nations' Sustainable Development Goals (SDGs). The current study aimed to provide policymakers, academics, and researchers an insight on the influence of 16 SDGs on each other paving the way for the universities to set a clear goal in attaining Sustainable Development goals by 2030. To analyze the SDGs' interactions towards each other, 201,844 research publications from India during five years on 16 SDGs are retrieved from the Scopus database. Spearman Rank Correlation is applied to understand the correlation of each SDG towards one another. We could observe converging results out of the interactions among the SDGs. A significant positive and moderately positive correlation between pairs of SDGs are identified. While a significant number of negative correlations is also classified which need deep thinking among researchers to develop healthy relationships. The most frequent interactions between SDGs is a positive sign for any university in strategizing the goal towards SDGs. The association of all university stakeholders and some constitutional and cultural changes are necessary to put SDGs at the core of the management of the university. Embracing this task by researchers will improve the overall performance of universities. The analysis presented in the present study is useful for academics, governments, funding agencies, researchers, and policy-makers.

Fracture resistance of post and core in immediate and delayed post space in trauma simulated teeth.

INTRODUCTION: This research aims to assess and analyze the fracture resistance of GC Everstick post with separate composite core buildup and Edelweiss prefabricated resin composite post and core single unit into immediate and delayed post space prepared teeth. METHODS: A total of 120 extracted human mandibular premolars have been subjected to a standardized protocol of mechanical trauma to simulate tooth fracture. Teeth samples were randomly divided into four groups (n = 30) on the basis of time taken for the preparation of post space (approximately following root canal obturation and 24 h after root canal obturation) for the single unit Edelweiss post and core system and GC post with separate core buildup. Compressive load has been utilized to do the analysis necessary to establish the fracture resistance using a universal testing machine. The fracture force calculated was in Newtons (N), and a stereomicroscope was utilized for investigating the common causes of failure. RESULTS: In an immediate post space prepared tooth, the GC post exhibited a mean failure load of 970.584 N. In contrast, the Edelweiss post, and core system showed a significantly higher mean failure load of 1250.349 N. In delayed post space prepared tooth, the GC Everstick post exhibited a mean failure load of 950.287 N. In contrast, the Edelweiss post, and core system showed a significantly higher mean failure load of 1229.348 N. CONCLUSION: This study aims to assess and analyze the fracture resistance of the GC Everstick post with separate composite core buildup and the Edelweiss prefabricated resin composite post and core single unit in immediate and delayed post space prepared teeth. The study results showed that the failure modes in both groups were non-catastrophic in nature. These findings suggest that the Edelweiss post and core system may be a more suitable option for restoring teeth that have been subjected to traumatic conditions. The study provides valuable information for dental professionals in their decision-making process for post and core restoration techniques in teeth that have been subjected to trauma.

Comparison of Dentinal Tubular Penetration of Intracanal Heated and Preheated Sodium Hypochlorite Through Different Agitation Techniques.

INTRODUCTION: The efficacy of sodium hypochlorite (NaOCl) as an intracanal irrigant is widely debated in endodontic therapy. This study aimed to analyze and compare the penetration abilities of different modes of NaOCl application and assess the impact of various agitation strategies on promoting root canal cleanliness. MATERIALS AND METHODS: This study included 168 single-rooted mandibular premolars that were randomly divided into 8 groups. The 2 modes of application of 5% NaOCl evaluated were intracanal heating and preheating, and the agitation strategies included ultrasonic, sonic, and manual dynamic agitations. The samples were sectioned and observed at a magnification of 1000 × under a scanning electron microscope. RESULTS: The analysis of variance test showed a statistically significant difference among the various groups of agitation (P < .05). The post hoc Tukey test confirmed that preheated NaOCl with ultrasonic agitation, intracanal-heated NaOCl with sonic agitation, and manual dynamic agitation had significantly higher debris scores of 1, 4, and 5, respectively, in the apical third of the canal. CONCLUSION: The results indicated that the combination of intracanal-heated NaOCl and ultrasonic agitation is an effective method for reducing debris in the root canal system. These findings highlight the importance of considering both the mode of application and the agitation strategies when optimizing the use of NaOCl as an intracanal irrigant in endodontic therapy.

Antiphased dust deposition and productivity in the Antarctic Zone over 1.5 million years.

The Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report a high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.5 Ma, thus doubling that from Antarctic ice-cores. We find a 5 to 15-fold increase in dust deposition during glacials and a 2 to 5-fold increase in biogenic silica deposition, reflecting higher ocean productivity during interglacials. This antiphasing persisted throughout the last 25 glacial cycles. Dust deposition became more pronounced across the Mid-Pleistocene Transition (MPT) in the Southern Hemisphere, with an abrupt shift suggesting more severe glaciations since ~0.9 Ma. Productivity was intermediate pre-MPT, lowest during the MPT and highest since 0.4 Ma. Generally, glacials experienced extended sea-ice cover, reduced bottom-water export and Weddell Gyre dynamics, which helped lower atmospheric CO2 levels.

Ancient marine sediment DNA reveals diatom transition in Antarctica.

Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.

Episodes of Early Pleistocene West Antarctic Ice Sheet Retreat Recorded by Iceberg Alley Sediments.

Ice loss in the Southern Hemisphere has been greatest over the past 30 years in West Antarctica. The high sensitivity of this region to climate change has motivated geologists to examine marine sedimentary records for evidence of past episodes of West Antarctic Ice Sheet (WAIS) instability. Sediments accumulating in the Scotia Sea are useful to examine for this purpose because they receive iceberg-rafted debris (IBRD) sourced from the Pacific- and Atlantic-facing sectors of West Antarctica. Here we report on the sedimentology and provenance of the oldest of three cm-scale coarse-grained layers recovered from this sea at International Ocean Discovery Program Site U1538. These layers are preserved in opal-rich sediments deposited ∼1.2 Ma during a relatively warm regional climate. Our microCT-based analysis of the layer's in-situ fabric confirms its ice-rafted origin. We further infer that it is the product of an intense but short-lived episode of IBRD deposition. Based on the petrography of its sand fraction and the Phanerozoic 40Ar/39Ar ages of hornblende and mica it contains, we conclude that the IBRD it contains was likely sourced from the Weddell Sea and/or Amundsen Sea embayment(s) of West Antarctica. We attribute the high concentrations of IBRD in these layers to "dirty" icebergs calved from the WAIS following its retreat inland from its modern grounding line. These layers also sit at the top of a ∼366-m thick Pliocene and early Pleistocene sequence that is much more dropstone-rich than its overlying sediments. We speculate this fact may reflect that WAIS mass-balance was highly dynamic during the ∼41-kyr (inter)glacial world.

Plantar Lichen Planus: An Atypical Presentation at a Young Age.

Lichen planus is a chronic lichenoid dermatosis commonly encountered by dermatologists worldwide, affecting skin, mucosa, and scalp. The current case describes a rare variant of lichen planus, plantar lichen planus, in a 17-year-old male who presented with erythematous scaly plaques on the sole for two years associated with walking discomfort. The lesion was subjected to skin biopsy and a diagnosis of lichen planus was made considering the histopathological and clinical findings. Plantar lichen planus can often be misdiagnosed. Treating plantar lichen planus can be a therapeutic challenge and, thus, more insight is needed regarding treatment protocol or outcome of such cases.

Mathematical Modeling of Plasticity and Heterogeneity in EMT.

The epithelial-mesenchymal transition (EMT) and the corresponding reverse process, mesenchymal-epithelial transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at both biochemical and morphological levels. A recent surge in identifying the molecular mechanisms underlying EMT/MET has led to the development of various mathematical models that have contributed to our improved understanding of dynamics at single-cell and population levels: (a) multi-stability-how many phenotypes can cells attain during an EMT/MET?, (b) reversibility/irreversibility-what time and/or concentration of an EMT inducer marks the "tipping point" when cells induced to undergo EMT cannot revert?, (c) symmetry in EMT/MET-do cells take the same path when reverting as they took during the induction of EMT?, and (d) non-cell autonomous mechanisms-how does a cell undergoing EMT alter the tendency of its neighbors to undergo EMT? These dynamical traits may facilitate a heterogenous response within a cell population undergoing EMT/MET. Here, we present a few examples of designing different mathematical models that can contribute to decoding EMT/MET dynamics.