Computational discovery and analysis of metabolic pathways

Finding novel or non-standard metabolic pathways, possibly spanning multiple species, has important applications in fields such as metabolic engineering, metabolic network analysis, and metabolic network reconstruction. Traditionally, this has been a manual process, but the large volume of metabolic data now available has created a need for computational tools to automatically identify biologically relevant pathways. This thesis presents new algorithms for automatically finding biologically meaningful linear and branched metabolic pathways in multi-genome scale metabolic networks. These algorithms utilize atom mapping data, which provides the correspondence between atoms in the substrates to atoms in the products of a chemical reaction, to find pathways which conserve a given number of atoms between desired start and target compounds. The first algorithm presented identifies atom conserving linear pathways by explicitly tracking atoms during an exploration of a graph structure constructed from the atom mapping data. The explicit tracking of atoms enables finding branched pathways because it provides automatic identification of the reactions and compounds through which atoms are lost or gained. The thesis then describes two algorithmic approaches for identifying branched metabolic pathways based upon atom conserving linear pathways. One approach takes one linear pathway at a time and attempts to add branches that connect loss and gain compounds. The other approach takes a group of linear pathways and attempts to merge pathways that move mutually exclusive sets of atoms from the start to the target compounds. Comparisons to known metabolic pathways demonstrate that atom tracking causes the algorithms to avoid many unrealistic connections, often found in previous approaches, and return biologically meaningful pathways. While the theoretical complexity of finding even linear atom conserving pathways is high, by choosing the appropriate representations and heuristics, and perhaps due to the structure of the underlying data, the algorithms in this thesis have practical running times on real data. The results also demonstrate the potential of the algorithms to find novel or non-standard pathways that may span multiple organisms

Parrondo's games as a discrete ratchet

We write the master equation describing the Parrondo's games as a consistent discretization of the Fokker--Planck equation for an overdamped Brownian particle describing a ratchet. Our expressions, besides giving further insight on the relation between ratchets and Parrondo's games, allow us to precisely relate the games probabilities and the ratchet potential such that periodic potentials correspond to fair games and winning games produce a tilted potential.Comment: 4 pages, 3 figure

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest

The virulence of Mycobacterium tuberculosis depends on the ability of the bacilli to switch between replicative (growth) and non-replicative (dormancy) states in response to host immunity. However, the gene regulatory events associated with transition to dormancy are largely unknown. To address this question, we have assembled the largest M. tuberculosis transcriptional-regulatory network to date, and characterized the temporal response of this network during adaptation to stationary phase and hypoxia, using published microarray data. Distinct sets of transcriptional subnetworks (origons) were responsive at various stages of adaptation, showing a gradual progression of network response under both conditions. Most of the responsive origons were in common between the two conditions and may help define a general transcriptional signature of M. tuberculosis growth arrest. These results open the door for a systems-level understanding of transition to non-replicative persistence, a phenotypic state that prevents sterilization of infection by the host immune response and promotes the establishment of latent M. tuberculosis infection, a condition found in two billion people worldwide

CD4+ T Cell Help Impairs CD8+ T Cell Deletion Induced by Cross-presentation of Self-Antigens and Favors Autoimmunity

Self-antigens expressed in extrathymic tissues such as the pancreas can be transported to draining lymph nodes and presented in a class I–restricted manner by bone marrow-derived antigen-presenting cells. Such cross-presentation of self-antigens leads to CD8+ T cell tolerance induction via deletion. In this report, we investigate the influence of CD4+ T cell help on this process. Small numbers of autoreactive OVA-specific CD8+ T cells were unable to cause diabetes when adoptively transferred into mice expressing ovalbumin in the pancreatic β cells. Coinjection of OVA-specific CD4+ helper T cells, however, led to diabetes in a large proportion of mice (68%), suggesting that provision of help favored induction of autoimmunity. Analysis of the fate of CD8+ T cells indicated that CD4+ T cell help impaired their deletion. These data indicate that control of such help is critical for the maintenance of CD8+ T cell tolerance induced by cross-presentation

Minimal Brownian Ratchet: An Exactly Solvable Model

We develop an exactly-solvable three-state discrete-time minimal Brownian ratchet (MBR), where the transition probabilities between states are asymmetric. By solving the master equations we obtain the steady-state probabilities. Generally the steady-state solution does not display detailed balance, giving rise to an induced directional motion in the MBR. For a reduced two-dimensional parameter space we find the null-curve on which the net current vanishes and detailed balance holds. A system on this curve is said to be balanced. On the null-curve, an additional source of external random noise is introduced to show that a directional motion can be induced under the zero overall driving force. We also indicate the off-balance behavior with biased random noise.Comment: 4 pages, 4 figures, RevTex source, General solution added. To be appeared in Phys. Rev. Let

Missouri mothers and their children: A family study of the effects of genetics and the prenatal environment

The Missouri Mothers and Their Children Study was specifically designed to critically investigate prenatal environmental influences on child attention problems and associated learning and cognitive deficits. The project began as a pilot study in 2004 and was formally launched in 2008. Participants in the study were initially identified via the Department of Vital Statistics birth record database. Interview and lab-based data were obtained from (1) mothers of Missouri-born children (born 1998–2005), who smoked during one pregnancy but not during another pregnancy, (2) biological fathers when available, and (3) the children [i.e., full sibling pairs discordant for exposure to maternal smoking during pregnancy (SDP)]. This within-mother, between-pregnancy contrast provides the best possible methodological control for many stable maternal and familial confounding factors (e.g., heritable and socio-demographic characteristics of the mother that predict increased probability of SDP). It also controls for differences between mothers who do and do not smoke during pregnancy, and their partners, that might otherwise artifactually create, or alternatively mask, associations between SDP and child outcomes. Such a design will therefore provide opportunities to determine less biased effect sizes while also allowing us to investigate (on a preliminary basis) the possible contribution of paternal or other second-hand smoke exposure during the pre-, peri- and postnatal periods to offspring outcome. This protocol has developed a cohort that can be followed longitudinally through periods typically associated with increased externalizing symptoms and substance use initiation

The State of AI Ethics Report (June 2020)

These past few months have been especially challenging, and the deployment of technology in ways hitherto untested at an unrivalled pace has left the internet and technology watchers aghast. Artificial intelligence has become the byword for technological progress and is being used in everything from helping us combat the COVID-19 pandemic to nudging our attention in different directions as we all spend increasingly larger amounts of time online. It has never been more important that we keep a sharp eye out on the development of this field and how it is shaping our society and interactions with each other. With this inaugural edition of the State of AI Ethics we hope to bring forward the most important developments that caught our attention at the Montreal AI Ethics Institute this past quarter. Our goal is to help you navigate this ever-evolving field swiftly and allow you and your organization to make informed decisions. This pulse-check for the state of discourse, research, and development is geared towards researchers and practitioners alike who are making decisions on behalf of their organizations in considering the societal impacts of AI-enabled solutions. We cover a wide set of areas in this report spanning Agency and Responsibility, Security and Risk, Disinformation, Jobs and Labor, the Future of AI Ethics, and more. Our staff has worked tirelessly over the past quarter surfacing signal from the noise so that you are equipped with the right tools and knowledge to confidently tread this complex yet consequential domain

Circulating 25-Hydroxyvitamin D Concentration and Risk of Breast, Prostate, and Colorectal Cancers: The Melbourne Collaborative Cohort Study.

BACKGROUND: The role of vitamin D in cancer risk remains controversial, and limited data exist on associations between vitamin D and subtypes of specific cancers. We investigated associations between circulating 25-hydroxyvitamin D (25(OH)D) and risk of colorectal, breast, and prostate cancers, including subtypes. METHODS: A case-cohort study within the Melbourne Collaborative Cohort Study included 547 colorectal, 634 breast, and 824 prostate cancers, and a sex-stratified random sample of participants (n = 2,996). Concentration of 25(OH)D in baseline-dried blood spots was measured using LC-MS/MS. Cox regression yielded adjusted HRs and 95% confidence intervals (CI) for each cancer in relation to plasma-equivalent 25(OH)D concentration. Associations by stage and BRAF/KRAS status for colorectal cancer, estrogen receptor status for breast cancer, and aggressiveness for prostate cancer were examined in competing risks models. RESULTS: 25(OH)D concentrations were inversely associated with risk of colorectal cancer [highest vs. lowest 25(OH)D quintile: HR, 0.71; 95% confidence interval (CI), 0.51-0.98], which was limited to women (HR, 0.52; 95% CI, 0.33-0.82). Circulating 25(OH)D was also inversely associated with BRAF V600E-positive colorectal cancer (per 25 nmol/L increment: HR, 0.71; 95% CI, 0.50-1.01). There were no inverse associations with breast cancer (HR, 0.98; 95% CI, 0.70-1.36) or prostate cancer (HR, 1.11; 95% CI, 0.82-1.48). CONCLUSIONS: Circulating 25(OH)D concentration was inversely associated with colorectal cancer risk for women, but not with risk of breast cancer or prostate cancer. IMPACT: Vitamin D might play a role in preventing colorectal cancer. Further studies are required to confirm whether vitamin D is associated with specific tumor subtypes