A First Exposure to Statistical Mechanics for Life Scientists

Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a clue that it might have some bearing on the analysis of the molecules of living matter. As a result of data on biological systems becoming increasingly quantitative, there is a concomitant demand that the models set forth to describe biological systems be themselves quantitative. We describe how statistical mechanics is part of the quantitative toolkit that is needed to respond to such data. The power of statistical mechanics is not limited to traditional physical and chemical problems and there are a host of interesting ways in which these ideas can be applied in biology. This article reports on our efforts to teach statistical mechanics to life science students and provides a framework for others interested in bringing these tools to a nontraditional audience in the life sciences.Comment: 27 pages, 16 figures. Submitted to American Journal of Physic

Scavenging vs hunting affects behavioral traits of an opportunistic carnivore

Background. Human-induced changes to ecosystems transform the availability of resources to predators, including altering prey populations and increasing access to anthropogenic foods. Opportunistic predators are likely to respond to altered food resources by changing the proportion of food they hunt versus scavenge. These shifts in foraging behavior will affect species interactions through multiple pathways, including by changing other aspects of predator behavior such as boldness, innovation, and social structure. Methods. To understand how foraging behavior impacts predator behavior, we conducted a controlled experiment to simulate hunting by introducing a prey model to captive coyotes (Canis latrans) and compared their behavior to coyotes that continued to scavenge over one year. We used focal observations to construct behavioral budgets, and conducted novel object, puzzle box, and conspecific tests to evaluate boldness, innovation, and response to conspecifics. Results. We documented increased time spent resting by hunting coyotes paired with decreased time spent active. Hunting coyotes increased boldness and persistence but there were no changes in innovation. Our results illustrate how foraging behavior can impact other aspects of behavior, with potential ecological consequences to predator ecology, predator-prey dynamics, and human-wildlife conflict; however, the captive nature of our study limits specific conclusions related to wild predators. We conclude that human-induced behavioral changes could have cascading ecological implications that are not fully understood

Effects of early‑life experience on innovation and problem‑solving in captive coyotes

Early-life experience often shapes behaviors like innovation and exploration. These behaviors are important to animals encountering novel food resources in diverse habitats, such as mesocarnivores in urban areas. To understand if early-life experiences impact later-life behavior, we examined how coyotes (Canis latrans) responded to a multi-access puzzle box at two life stages: pup (~ 7 weeks) and dispersal (~ 10 months). We first exposed pups, still living with their parents and littermates, to a baited puzzle box. At dispersal age, we again tested both these pups and an age-matched control group that was not exposed to the puzzle box as pups, both as individuals and with their pair-mate. We quantified problem-solving capability, latency to approach, and time spent in proximity to the puzzle box. Most pup litters solved two of the three access points, but no dispersal-age coyotes solved any access point. The amount of time dispersal-age coyotes spent near the box during pair-testing increased with (1) more time spent near the box during single-testing, (2) more time their pair-mate spent near the box during pair-testing, and (3) if their pair-mate came from a litter that previously solved the box. These results suggest that early-life experience and social interactions influence exploratory behavior at dispersal age, but coyotes exhibit increased avoidance behavior at this life stage, which corresponds with the life stage that overall survivorship decreases. Our study provides insight into how early-life experiences shape adult behavior in mesocarnivores

Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro

Shigella flexneri is an enteropathogen responsible for severe dysentery in humans. VirF is a key transcriptional regulator that activates the expression of the downstream virulence factors required for cellular invasion and cell-to-cell spread of this pathogen. There are several environmental factors that induce the translation of VirF including temperature, pH, osmolarity and post-transcriptional RNA modification. Durand and colleagues (vacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase of Escherichia coli K-12. J. Bacteriol., 176, 4627–4634) have demonstrated a correlation between VirF and tRNA-guanine transglycosylase (TGT), which catalyzes the exchange of the hypermodified base queuine for the guanine in the wobble position of certain tRNAs. They characterized tgt- mutant S. flexneri strains in which the translation of VirF is markedly reduced and the bacteria are unable to invade host cells. Although the function of TGT is to modify tRNA, we report that the virF mRNA is recognized by the Escherichia coli TGT (99% identity to the S. flexneri TGT) in vitro. Further, we show that this recognition results in the site-specific modification of a single base in the virF mRNA. In the context of previous reports that small molecule binding motifs (‘riboswitches’) in mRNAs modulate mRNA conformation and translation, our observations suggest that TGT may modulate the translation of VirF by base modification of the VirF encoding mRNA

A First Exposure to Statistical Mechanics for Life Scientists: Applications to Binding

Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a clue that it might have some bearing on the analysis of the molecules of living matter. As a result of data on biological systems becoming increasingly quantitative, there is a concomitant demand that the models set forth to describe biological systems be themselves quantitative. We describe how statistical mechanics is part of the quantitative toolkit that is needed to respond to such data. The power of statistical mechanics is not limited to traditional physical and chemical problems and there are a host of interesting ways in which these ideas can be applied in biology. This article reports on our efforts to teach statistical mechanics to life science students with special reference to binding problems in biology and provides a framework for others interested in bringing these tools to a nontraditional audience in the life sciences. 1 1 Does Statistical Mechanics Matter in Biology

Developing an Indigenous, Entry-Level Master’s Degree Program in a Country with an Emerging OT Profession

In the Republic of Trinidad and Tobago the full range of physical, mental, psychological, and socially derived problems of occupational engagement exist. Occupational therapy is often a part of the health care team to address these challenges; however, the profession is at an emergent stage in the country. This paper describes a process used for the development of an indigenous entry-level master’s degree program in occupational therapy. The process was also supported and enhanced by the collaborative relationships among key stakeholders, including global partners. A qualitative design process was used to analyze the health care needs, barriers, and strategies that impact the sustainability of the proposed program. This included 47 survey respondents, 10 semi-structured interviews, and a focus group. The findings led to the development of curricular threads that informed the curricular framework of the program. The curricular framework will safeguard the sustainability of the program and the clinical relevance of its content and methods relative to the community the graduates will serve. Systematic review of curricular design and program outcomes is needed to enhance the intended learning experience of the occupational therapy students

FACS-sorted putative oogonial stem cells from the ovary are neither DDX4-positive nor germ cells

Whether the adult mammalian ovary contains oogonial stem cells (OSCs) is controversial. They have been isolated by a live-cell sorting method using the germ cell marker DDX4, which has previously been assumed to be cytoplasmic, not surfacebound. Furthermore their stem cell and germ cell characteristics remain disputed. Here we show that although OSC-like cells can be isolated from the ovary using an antibody to DDX4, there is no good in silico modelling to support the existence of a surfacebound DDX4. Furthermore these cells when isolated were not expressing DDX4, and did not initially possess germline identity. Despite these unremarkable beginnings, they acquired some pre-meiotic markers in culture, including DDX4, but critically never expressed oocyte-specific markers, and furthermore were not immortal but died after a few months. Our results suggest that freshly isolated OSCs are not germ stem cells, and are not being isolated by their DDX4 expression. However it may be that culture induces some pre-meiotic markers. In summary the present study offers weight to the dogma that the adult ovary is populated by a fixed number of oocytes and that adult de novo production is a rare or insignificant event