Constraining the complexity of promoter dynamics using fluctuations in gene expression.

Gene expression is an inherently stochastic process with transcription of mRNAs often occurring in bursts: short periods of activity followed by typically longer periods of inactivity. While a simple model involving switching between two promoter states has been widely used to analyze transcription dynamics, recent experimental observations have provided evidence for more complex kinetic schemes underlying bursting. Specifically, experiments provide evidence for complexity in promoter dynamics during the switch from the transcriptionally inactive to the transcriptionally active state. An open question in the field is: what is the minimal complexity needed to model promoter dynamics and how can we determine this? Here, we show that measurements of mRNA fluctuations can be used to set fundamental bounds on the complexity of promoter dynamics. We study models wherein the switching time distribution from transcriptionally inactive to active states is described by a general waiting-time distribution. Using approaches from renewal theory and queueing theory, we derive analytical expressions which connect the Fano factor of mRNA distributions to the waiting-time distribution for promoter switching between inactive and active states. The results derived lead to bounds on the minimal number of promoter states and thus allow us to derive bounds on the minimal complexity of promoter dynamics based on single-cell measurements of mRNA levels.

A stochastic model for post-transcriptional regulation of rare events in gene expression.

Post-transcriptional regulation of gene expression is often a critical component of cellular processes involved in cell-fate decisions. Correspondingly, considerable efforts have focused on modeling post-transcriptional regulation of stochastic gene expression and on quantifying its impact on the mean and variance of protein levels. However, the impact of post-transcriptional regulation on rare events corresponding to large deviations in gene expression is less well understood. Here, we study a simple model involving post-transcriptional control of gene expression and characterize the impact of regulation on large deviations in activity fluctuations. We derive analytical results for the large deviation function for protein production rate and for the corresponding driven process which characterizes system fluctuations conditional on the rare event. Our results suggest that fluctuations in burst size rather than frequency play a dominant role in controlling rare events. The results derived also provide insight into how post-transcriptional regulation can be used to fine-tune the probability of rare fluctuations and to thereby control phenotypic variation in a population of cells.

Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit.

Noncoding small RNAs (sRNAs) are known to play a key role in regulating diverse cellular processes, and their dysregulation is linked to various diseases such as cancer. Such diseases are also marked by phenotypic heterogeneity, which is often driven by the intrinsic stochasticity of gene expression. Correspondingly, there is significant interest in developing quantitative models focusing on the interplay between stochastic gene expression and regulation by sRNAs. We consider the canonical model of regulation of stochastic gene expression by sRNAs, wherein interaction between constitutively expressed sRNAs and mRNAs leads to stoichiometric mutual degradation. The exact solution of this model is analytically intractable given the nonlinear interaction term between sRNAs and mRNAs, and theoretical approaches typically invoke the mean-field approximation. However, mean-field results are inaccurate in the limit of strong interactions and low abundances; thus, alternative theoretical approaches are needed. In this work, we obtain analytical results for the canonical model of regulation of stochastic gene expression by sRNAs in the strong interaction limit. We derive analytical results for the steady-state generating function of the joint distribution of mRNAs and sRNAs in the limit of strong interactions and use the results derived to obtain analytical expressions characterizing the corresponding protein steady-state distribution. The results obtained can serve as building blocks for the analysis of genetic circuits involving sRNAs and provide new insights into the role of sRNAs in regulating stochastic gene expression in the limit of strong interactions.

Stochastic gene expression conditioned on large deviations.

The intrinsic stochasticity of gene expression can give rise to large fluctuations and rare events that drive phenotypic variation in a population of genetically identical cells. Characterizing the fluctuations that give rise to such rare events motivates the analysis of large deviations in stochastic models of gene expression. Recent developments in non-equilibrium statistical mechanics have led to a framework for analyzing Markovian processes conditioned on rare events and for representing such processes by conditioning-free driven Markovian processes. We use this framework, in combination with approaches based on queueing theory, to analyze a general class of stochastic models of gene expression. Modeling gene expression as a Batch Markovian Arrival Process (BMAP), we derive exact analytical results quantifying large deviations of time-integrated random variables such as promoter activity fluctuations. We find that the conditioning-free driven process can also be represented by a BMAP that has the same form as the original process, but with renormalized parameters. The results obtained can be used to quantify the likelihood of large deviations, to characterize system fluctuations conditional on rare events and to identify combinations of model parameters that can give rise to dynamical phase transitions in system dynamics.

Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models.

Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Such bursting has important consequences for cell-fate decisions in diverse processes ranging from HIV-1 viral infections to stem-cell differentiation. It is generally assumed that bursts are geometrically distributed and that they arrive according to a Poisson process. On the other hand, recent single-cell experiments provide evidence for complex burst arrival processes, highlighting the need for analysis of more general stochastic models. To address this issue, we invoke a mapping between general stochastic models of gene expression and systems studied in queueing theory to derive exact analytical expressions for the moments associated with mRNA/protein steady-state distributions. These results are then used to derive noise signatures, i.e. explicit conditions based entirely on experimentally measurable quantities, that determine if the burst distributions deviate from the geometric distribution or if burst arrival deviates from a Poisson process. For non-Poisson arrivals, we develop approaches for accurate estimation of burst parameters. The proposed approaches can lead to new insights into transcriptional bursting based on measurements of steady-state mRNA/protein distributions.

A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa.

CsrA/RsmA homologs are an extensive family of ribonucleic acid (RNA)-binding proteins that function as global post-transcriptional regulators controlling important cellular processes such as secondary metabolism, motility, biofilm formation and the production and secretion of virulence factors in diverse bacterial species. While direct messenger RNA binding by CsrA/RsmA has been studied in detail for some genes, it is anticipated that there are numerous additional, as yet undiscovered, direct targets that mediate its global regulation. To assist in the discovery of these targets, we propose a sequence-based approach to predict genes directly regulated by these regulators. In this work, we develop a computer code (CSRA_TARGET) implementing this approach, which leads to predictions for several novel targets in Escherichia coli and Pseudomonas aeruginosa. The predicted targets in other bacteria, specifically Salmonella enterica serovar Typhimurium, Pectobacterium carotovorum and Legionella pneumophila, also include global regulators that control virulence in these pathogens, unraveling intricate indirect regulatory roles for CsrA/RsmA. We have experimentally validated four predicted RsmA targets in P. aeruginosa. The sequence-based approach developed in this work can thus lead to several testable predictions for direct targets of CsrA homologs, thereby complementing and accelerating efforts to unravel global regulation by this important family of proteins.

Exact distributions for stochastic gene expression models with bursting and feedback.

Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to phenotypic variation across a population of genetically identical cells. Recent experiments indicate that bursting and feedback mechanisms play important roles in controlling noise in gene expression and phenotypic variation. A quantitative understanding of the impact of these factors requires analysis of the corresponding stochastic models. However, for stochastic models of gene expression with feedback and bursting, exact analytical results for protein distributions have not been obtained so far. Here, we analyze a model of gene expression with bursting and feedback regulation and obtain exact results for the corresponding protein steady-state distribution. The results obtained provide new insights into the role of bursting and feedback in noise regulation and optimization. Furthermore, for a specific choice of parameters, the system studied maps on to a two-state biochemical switch driven by a bursty input noise source. The analytical results derived provide quantitative insights into diverse cellular processes involving noise in gene expression and biochemical switching.

Cancer: tilting at windmills?

One of the striking characteristics of cancer cells is their phenotypic diversity and ability to switch phenotypes in response to environmental fluctuations. Such phenotypic changes (e.g. from drug-sensitive to drug-resistant), which are critical for survival and proliferation, are widely believed to arise due to mutations in the cancer cell's genome. However, there is growing concern that such a deterministic view is not entirely consistent with multiple lines of evidence which indicate that cancer can arise in the absence of mutations and can even be reversed to normalcy despite the mutations. In this Commentary, we wish to present an alternate view that highlights how stochasticity in protein interaction networks (PINs) may play a key role in cancer initiation and progression. We highlight the potential role of intrinsically disordered proteins (IDPs) and submit that targeting IDPs can lead to new insights and treatment protocols for cancer.

Intrinsic noise in stochastic models of gene expression with molecular memory and bursting.

Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein levels across a population of cells. In this work, we analyze a stochastic model of bursty gene expression which considers general waiting-time distributions governing arrival and decay of proteins. By mapping the system to models analyzed in queueing theory, we derive analytical expressions for the noise in steady-state protein distributions. The derived results extend previous work by including the effects of arbitrary probability distributions representing the effects of molecular memory and bursting. The analytical expressions obtained provide insight into the role of transcriptional, post-transcriptional, and post-translational mechanisms in controlling the noise in gene expression.

Computational modeling of differences in the quorum sensing induced luminescence phenotypes of Vibrio harveyi and Vibrio cholerae.

Vibrio harveyi and Vibrio cholerae have quorum sensing pathways with similar design and highly homologous components including multiple small RNAs (sRNAs). However, the associated luminescence phenotypes of strains with sRNA deletions differ dramatically: in V. harveyi, the sRNAs act additively; however, in V. cholerae, the sRNAs act redundantly. Furthermore, there are striking differences in the luminescence phenotypes for different pathway mutants in V. harveyi and V. cholerae. However, these differences have not been connected with the observed differences for the sRNA deletion strains in these bacteria. In this work, we present a model for quorum sensing induced luminescence phenotypes focusing on the interactions of multiple sRNAs with target mRNA. Within our model, we find that one key parameter - the fold-change in protein concentration necessary for luminescence activation - can control whether the sRNAs appear to act additively or redundantly. For specific parameter choices, we find that differences in this key parameter can also explain hitherto unconnected luminescence phenotypes differences for various pathway mutants in V. harveyi and V. cholerae. The model can thus provide a unifying explanation for observed differences in luminescence phenotypes and can also be used to make testable predictions for future experiments.

Regulatory targets of quorum sensing in Vibrio cholerae: evidence for two distinct HapR-binding motifs.

The quorum-sensing pathway in Vibrio cholerae controls the expression of the master regulator HapR, which in turn regulates several important processes such as virulence factor production and biofilm formation. While HapR is known to control several important phenotypes, there are only a few target genes known to be transcriptionally regulated by HapR. In this work, we combine bioinformatic analysis with experimental validation to discover a set of novel direct targets of HapR. Our results provide evidence for two distinct binding motifs for HapR-regulated genes in V. cholerae. The first binding motif is similar to the motifs recently discovered for orthologs of HapR in V. harveyi and V. vulnificus. However, our results demonstrate that this binding motif can be of variable length in V. cholerae. The second binding motif shares common elements with the first motif, but is of fixed length and lacks dyad symmetry at the ends. The contributions of different bases to HapR binding for this second motif were demonstrated using systematic mutagenesis experiments. The current analysis presents an approach for systematically expanding our knowledge of the quorum-sensing regulon in V. cholerae and other related bacteria.

Neurosyphilis, A True Chameleon of Neurology.

BACKGROUND: Neurosyphilis (NS) is a rarely encountered scenario today. Manifestations are heterogeneous, and their characteristics have changed in the antibiotic era. A differential diagnosis of NS is not commonly thought of even with relevant clinical-radiological features, as it mimics many common neurological syndromes. OBJECTIVES: To study the manifestations of NS in the present era and the process of diagnosis. METHOD: The data of ten patients with NS was collected and analyzed. Their background data, clinical features, investigations, the process of reaching the diagnosis, management and outcomes were recorded. OBSERVATIONS AND RESULTS: The manifestations of NS in our cohort included six patients with cognitive decline/encephalopathy and one each with meningitis with cranial nerve palsies, cerebellar ataxia, myelitis and asymptomatic NS. The presence of Argyll Robertson pupil helped to clinch diagnosis in one patient. Treponemal tests were ordered in two patients only after alternative etiologies were looked at, to begin with, whereas in six patients treponemal test was requested as a part of standard workup for dementia/ataxia. CONCLUSIONS: NS dementia and behavior changes are mistaken for degenerative, vascular, nutritional causes, autoimmune encephalitis or prion disease. Meningitis has similarities with infective (tubercular), granulomatous (sarcoidosis, Wegener's), collagen vascular disease and neoplastic meningitis, and myelitis simulates demyelination or nutritional myelopathy (B12 deficiency). Rarely, NS can also present with cerebellar ataxia. Contemplate NS as one of the rare causes for such syndromes, and its early treatment produces good outcomes.

Myelin Oligodendrocyte Glycoprotein (MOG)-IgG Associated Demyelinating Disease: Our Experience with this Distinct Syndrome.

BACKGROUND: Discovery of serum myelin oligodendrocyte glycoprotein (MOG) antibody testing in demyelination segregated MOG-IgG disease from AQ-4-IgG positive NMOSD. AIMS: To study clinico-radiological manifestations, pattern of laboratory and electrophysiological investigations and response to treatment through follow up in MOG-IgG positive patients. METHOD: Retrospective data of MOG-IgG positive patients was collected. Demographics, clinical manifestations at onset and at follow up and relapses, anti AQ-4-IgG status, imaging and all investigations were performed, treatment of relapses and further immunomodulatory therapy were captured. RESULTS: In our 30 patients, F: M ratio was 2.75:1 and adult: child ratio 4:1. Relapses at presentation were optic neuritis {ON}(60%), longitudinally extensive transverse myelitis {LETM}(20%), acute disseminated encephalomyelitis {ADEM}(13.4%), simultaneous ON with myelitis (3.3%) and diencephalic Syndrome (3.3%). Salient MRI features were ADEM-like lesions, middle cerebellar peduncle fluffy infiltrates, thalamic and pontine lesions and longitudinally extensive ON {LEON} as well as non-LEON. Totally, 50% patients had a relapsing course. Plasma exchange and intravenous immunoglobulin worked in patients who showed a poor response to intravenous methylprednisolone. Prednisolone, Azathioprine, Mycophenolate and Rituximab were effective attack preventing agents. CONCLUSIONS: MOG-IgG related manifestations in our cohort were monophasic/recurrent/simultaneous ON, myelitis, recurrent ADEM, brainstem encephalitis and diencephalic Syndrome. MRI features suggestive of MOG-IgG disease were confluent ADEM-like lesions, middle cerebellar peduncle fluffy lesions, LETM, LEON and non-LEON. Where indicated, patients need to go on immunomodulation as it has a relapsing course and can accumulate significant disability. Because of its unique manifestations, it needs to be considered as a distinct entity. To the best of our knowledge, this is the largest series of MOG-IgG disease reported from India.

Acute haemorrhagic leukoencephalitis (AHLE) - our experience and a short review.

BACKGROUND: Acute haemorrhagic leukoencephalitis (AHLE), a rare variant of acute disseminated encephalomyelitis (ADEM), often presents differently from classical ADEM, thereby posing a diagnostic challenge to the clinician. AIM: To report AHLE, its clinic-radiological manifestations, process of diagnosis and prognosis. METHOD AND RESULTS: Eight patients presented with altered sensorium, acute focal deficits with or without seizures. Initial workup showed evidence of haemorrhagic lobar or thalamic lesions in seven patients. All patients underwent extensive evaluation for collagen vascular disease and vasculitis profile, autoimmune encephalitis panel and aquaporin-4 antibody, which were found to be normal. Cerebrospinal fluid (CSF) biochemistry and microscopy was non-contributory and CSF viral PCRs, toxoplasma antibodies, cryptococcal antigen were also negative. All patients had progressively worsening sensorium and neurological deficits. Repeat MRIs showed increase in oedema in the lesions and appearance/expansion of haemorrhage in the thalamic/hemispherical lesions. All patients received intravenous methylprednisolone (IVMP) without any benefit. Four patients underwent plasmapheresis (PLEX), one received intravenous immunoglobulin (IVIG) and one received both second line immunotherapies, without significant improvement. Brain biopsy (performed in three patients) showed inflammatory demyelination and areas of haemorrhage, thus confirming the diagnosis. Six patients succumbed in 7-30 days of the illness, despite aggressive treatment and only two survived, albeit with a significant disability. CONCLUSION: AHLE is a rare, yet very severe variant of ADEM. MRI shows lesions with haemorrhages, oedema and mass effect and histology findings reveal inflammatory infiltrates, haemorrhagic foci and fibrinoid necrosis of vessel walls. Prognosis is worse as compared to the classic ADEM, with a high mortality rate. To the best of our knowledge, this is one of the largest series of AHLE to have been reported anywhere in the world. KEYMESSAGE: Acute encephalopathy, multifocal deficits accompanied by haemorrhagic CNS demyelinating lesions with oedema and mass effect are the key features of AHLE. It is a rare, yet very severe form of ADEM with very high morbidity and mortality.

Post-transcriptional regulation of noise in protein distributions during gene expression.

The intrinsic stochasticity of gene expression can lead to a large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in particular, there is considerable interest in understanding the role of post-transcriptional regulation. To address this issue, we propose and analyze a stochastic model for post-transcriptional regulation of gene expression. The analytical solution of the model provides insight into the effects of different mechanisms of post-transcriptional regulation on the noise in protein distributions. The results obtained also demonstrate how different sources of intrinsic noise in gene expression can be discriminated based on observations of regulated protein distributions.

Skeletal muscle involvement in human immunodeficiency virus infection: a report of four cases.

Human immunodeficiency virus (HIV) may affect any part of the neuraxis and may affect skeletal muscle in many ways, ranging from myofiber atrophy in the wasting syndrome to inflammatory muscle disease and a host of opportunistic infections involving muscle. We report here a case series of 4 zidovudine-naοve patients with proven HIV infection with myopathy. One was a case of HIV wasting syndrome, and the three others were diagnosed as HIV polymyositis. Muscle biopsy proved invaluable in the characterization of these cases.

Direct regulation by the Vibrio cholerae regulator ToxT to modulate colonization and anticolonization pilus expression.

The pathogen Vibrio cholerae uses a large number of coordinated transcriptional regulatory events to transition from its environmental reservoir to the host and establish itself at its preferred colonization site at the host intestinal mucosa. The key regulator in this process is the AraC/XylS family transcription factor, ToxT, which plays critical roles in pathogenesis, including the regulation of two type IV pili, the anticolonization factor mannose-sensitive hemagglutinin and the toxin-coregulated pilus. Previously, it was thought ToxT required dimerization in order to effect transcriptional regulation at its cognate promoters. Here, we present evidence that ToxT directly represses transcription of the msh operon by binding to three promoters within this operon and that dimerization may not be required for transcriptional repression of target promoters by ToxT, suggesting that this regulator uses different mechanisms to modulate the transcriptional repertoire of V. cholerae.

A model for signal transduction during quorum sensing in Vibrio harveyi.

We present a framework for analyzing luminescence regulation during quorum sensing in the bioluminescent bacterium Vibrio harveyi. Using a simplified model for signal transduction in the quorum sensing pathway, we identify key dimensionless parameters that control the system's response. These parameters are estimated using experimental data on luminescence phenotypes for different mutant strains. The corresponding model predictions are consistent with results from other experiments which did not serve as input for determining model parameters. Furthermore, the proposed framework leads to novel testable predictions for luminescence phenotypes and for responses of the network to different perturbations.

Once daily baclofen sustained release or gastro-retentive system are acceptable alternatives to thrice daily baclofen immediate release at same daily dosage in patients.

BACKGROUND: Baclofen, a GABA-agonist, is currently available as an immediate release (IR) formulation for relieving neurogenic spasticity in a variety of disorders. Baclofen IR requires to be administered three times a day which inadvertently increases the chances of medication noncompliance among patients and is also associated with side effects such as drowsiness and muscle weakness. AIM: To overcome the shortcomings of baclofen IR, two modified formulations, baclofen sustained release (SR) and gastric retentive system (GRS), have been proposed to be equivalent in efficacy to baclofen IR with the administration of a single daily dose. MATERIALS AND METHODS: Ninety patients with chronic neurogenic muscular spasticity were enrolled requiring 10-20 mg of baclofen IR every eight hours. The patients were randomized to two treatment arms: SR (n = 46) or GRS (n = 44) at the same once-daily dose for four weeks. Efficacy was measured by Ashworth score for muscle tone, spasm score, reflex score, 30-item functional independence score, and patient's diary score for three most affected activities of daily life. RESULTS: The mean Ashworth score changed significantly (P = 0.00) for patients in the SR group from 3.03-2.69 (-0.35) and 3.07-2.70 (-0.37) for patients in the GRS group. There was no significant difference (P = 0.87) between baseline-adjusted Ashworth score reductions on SR (-0.35) and GRS (-0.37). Similar results were obtained for spasm, reflex, and functional independence scores. The mean baseline-adjusted patient-diary scores did not differ significantly between 8 am, 12 pm, 4 pm, and 8 pm (P = 0.96), either on SR (-5.3 to -6.1) or GRS (-7.3 to -8.1), indicating a uniform effect round-the-day on both. Further, sedation scores (mean +/- SEM) decreased significantly (P < 0.05) on both SR (10.36 +/- 1.37 to 6.18 +/- 0.92) and GRS (8.14 +/- 1.57 to 5.33 +/- 1.11), suggesting better toleration. CONCLUSION: Once-daily baclofen SR and GRS are efficacious, convenient, and better-tolerated alternatives to baclofen IR in patients with neurogenic spasticity.

A Free Energy Based Approach for Distance Metric Learning.

We present a reformulation of the distance metric learning problem as a penalized optimization problem, with a penalty term corresponding to the von Neumann entropy of the distance metric. This formulation leads to a mapping to statistical mechanics such that the metric learning optimization problem becomes equivalent to free energy minimization. Correspondingly, our approach leads to an analytical solution of the optimization problem based on the Boltzmann distribution. The mapping established in this work suggests new approaches for dimensionality reduction and provides insights into determination of optimal parameters for the penalty term. Furthermore, we demonstrate that the metric projects the data onto direction of maximum dissimilarity with optimal and tunable separation between classes and thus the transformation can be used for high dimensional data visualization, classification, and clustering tasks. We benchmark our method against previous distance learning methods and provide an efficient implementation in an R package available to download at: https://github.com/kouroshz/fenn.