A cellular stress-directed bistable switch controls the crosstalk between autophagy and apoptosis

Decision-making between life and death is one of the most important tasks of cells to maintain their genetic integrity. While the surviving mechanism is driven by Beclin1-dependent autophagy, the suicide processes are controlled by caspases-mediated apoptosis. Interestingly, both these processes share regulators such as Bcl2 and influence each other through feedback loops. The physiological relevance of the crosstalk between autophagy and apoptosis is still unclear. To gain system level insights, we have developed a mathematical model of the autophagy-apoptosis crosstalk. Our analysis reveals that a combination of Bcl2-dependent regulation and feedback loops between Beclin1 and caspases robustly enforces a sequential activation of cellular responses depending upon the intensity and duration of stress levels. The amplifying loops for caspases activation involving Beclin1-dependent inhibition of caspases and cleavage of Beclin1 by caspases (Beclin1 caspases Beclin1; caspases → cleaved Beclin1 → caspases) not only make the system bistable but also help to switch off autophagy at high stress levels. The presence of an additional positive feedback loop between Bcl2 and caspases helps to maintain the caspases activation by making the switch irreversible. Our results provide a framework for further experiments and modelling. © 2013 The Royal Society of Chemistry

Multiple system-level feedback loops control life-and-death decisions in endoplasmic reticulum stress

Scientific results have revealed that autophagy is able to promote cell survival in response to endoplasmic reticulum (ER) stress while drastic events result in apoptotic cell death. Here, we analyse the important crosstalk of life-and-death decisions from a systems biological perspective by studying the regulatory modules of the unfolded protein response (UPR). While a double negative loop between autophagy and apoptosis inducers is crucial for the switch-like characteristic of the stress response mechanism, a positive feedback loop between ER stress sensors is also essential. Corresponding to experimental data, here, we show the dynamical significance of Gadd34-CHOP connections inside the PERK branch of the UPR. The multiple system-level feedback loops seem to be crucial for managing a robust life-and-death decision depending on the level and durability of cellular stress

Passive Transdermal Systems Whitepaper Incorporating Current Chemistry, Manufacturing and Controls (CMC) Development Principles

In this whitepaper, the Manufacturing Technical Committee (MTC) of the Product Quality Research Institute has updated the 1997 Transdermal Drug Delivery Systems Scale-Up and Post Approval Change workshop report findings to add important new product development and control principles. Important topics reviewed include ICH harmonization, quality by design, process analytical technologies, product and process validation, improvements to control of critical excipients, and discussion of Food and Drug Administration’s Guidance on Residual Drug in Transdermal and Related Drug Delivery Systems as well as current thinking and trends on in vitro–in vivo correlation considerations for transdermal systems

Mapping private pharmacies and their characteristics in Ujjain district, Central India

<p>Abstract</p> <p>Background</p> <p>In India, private pharmacies are ubiquitous yet critical establishments that facilitate community access to medicines. These are often the first points of treatment seeking in parts of India and other low income settings around the world. The characteristics of these pharmacies including their location, drug availability, human resources and infrastructure have not been studied before. Given the ubiquity and popularity of private pharmacies in India, such information would be useful to harness the potential of these pharmacies to deliver desirable public health outcomes, to facilitate regulation and to involve in initiatives pertaining to rational drug use. This study was a cross sectional survey that mapped private pharmacies in one district on a geographic information system and described relevant characteristics of these units.</p> <p>Methods</p> <p>This study of pharmacies was a part of larger cross sectional survey carried out to map all the health care providers in Ujjain district (population 1.9 million), Central India, on a geographic information system. Their location vis-à-vis formal providers of health services were studied. Other characteristics like human resources, infrastructure, clients and availability of tracer drugs were also surveyed.</p> <p>Results</p> <p>A total 475 private pharmacies were identified in the district. Three-quarter were in urban areas, where they were concentrated around physician practices. In rural areas, pharmacies were located along the main roads. A majority of pharmacies simultaneously retailed medicines from multiple systems of medicine. Tracer parenteral antibiotics and injectable steroids were available in 83.7% and 88.7% pharmacies respectively. The proportion of clients without prescription was 39.04%. Only 11.58% of staff had formal pharmacist qualifications. Power outages were a significant challenge.</p> <p>Conclusion</p> <p>This is the first mapping of pharmacies & their characteristics in India. It provides evidence of the urban dominance and close relationship between healthcare provider location and pharmacy location. The implications of this relationship are discussed. The study reports a lack of qualified staff in the presence of a high proportion of clients attending without a prescription. The study highlights the need for the better implementation of regulation. Besides facilitating regulation & partnerships, the data also provides a sampling frame for future interventional studies on these pharmacies.</p

Computational modelling of meiotic entry and commitment

In response to developmental and environmental conditions, cells exit the mitotic cell cycle and enter the meiosis program to generate haploid gametes from diploid germ cells. Once cells decide to enter the meiosis program they become irreversibly committed to the completion of meiosis irrespective of the presence of cue signals. How meiotic entry and commitment occur due to the dynamics of the regulatory network is not well understood. Therefore, we constructed a mathematical model of the regulatory network that controls the transition from mitosis to meiosis in Schizosaccharomyces pombe. Upon nitrogen starvation, yeast cells exit mitosis and undergo conjugation and meiotic entry. The model includes the regulation of Mei2, an RNA binding protein required for conjugation and meiotic entry, by multiple feedback loops involving Pat1, a kinase that keeps cells in mitosis, and Ste11, a transcription activator required for the sexual differentiation. The model accounts for various experimental observations and demonstrates that the activation of Mei2 is bistable, which ensures the irreversible commitment to meiosis. Further, we show by integrating the meiosis-specific regulation with a cell cycle model, the dynamics of cell cycle exit, G1 arrest and entry into meiosis under nitrogen starvation. © 2017 The Author(s)

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region

DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability

A Mathematical Model of Mitotic Exit in Budding Yeast: The Role of Polo Kinase

Cell cycle progression in eukaryotes is regulated by periodic activation and inactivation of a family of cyclin–dependent kinases (Cdk's). Entry into mitosis requires phosphorylation of many proteins targeted by mitotic Cdk, and exit from mitosis requires proteolysis of mitotic cyclins and dephosphorylation of their targeted proteins. Mitotic exit in budding yeast is known to involve the interplay of mitotic kinases (Cdk and Polo kinases) and phosphatases (Cdc55/PP2A and Cdc14), as well as the action of the anaphase promoting complex (APC) in degrading specific proteins in anaphase and telophase. To understand the intricacies of this mechanism, we propose a mathematical model for the molecular events during mitotic exit in budding yeast. The model captures the dynamics of this network in wild-type yeast cells and 110 mutant strains. The model clarifies the roles of Polo-like kinase (Cdc5) in the Cdc14 early anaphase release pathway and in the G-protein regulated mitotic exit network

Multiple Signals Converge on a Differentiation MAPK Pathway

An important emerging question in the area of signal transduction is how information from different pathways becomes integrated into a highly coordinated response. In budding yeast, multiple pathways regulate filamentous growth, a complex differentiation response that occurs under specific environmental conditions. To identify new aspects of filamentous growth regulation, we used a novel screening approach (called secretion profiling) that measures release of the extracellular domain of Msb2p, the signaling mucin which functions at the head of the filamentous growth (FG) MAPK pathway. Secretion profiling of complementary genomic collections showed that many of the pathways that regulate filamentous growth (RAS, RIM101, OPI1, and RTG) were also required for FG pathway activation. This regulation sensitized the FG pathway to multiple stimuli and synchronized it to the global signaling network. Several of the regulators were required for MSB2 expression, which identifies the MSB2 promoter as a target “hub” where multiple signals converge. Accessibility to the MSB2 promoter was further regulated by the histone deacetylase (HDAC) Rpd3p(L), which positively regulated FG pathway activity and filamentous growth. Our findings provide the first glimpse of a global regulatory hierarchy among the pathways that control filamentous growth. Systems-level integration of signaling circuitry is likely to coordinate other regulatory networks that control complex behaviors