NEXUS/Physics: An interdisciplinary repurposing of physics for biologists

In response to increasing calls for the reform of the undergraduate science curriculum for life science majors and pre-medical students (Bio2010, Scientific Foundations for Future Physicians, Vision & Change), an interdisciplinary team has created NEXUS/Physics: a repurposing of an introductory physics curriculum for the life sciences. The curriculum interacts strongly and supportively with introductory biology and chemistry courses taken by life sciences students, with the goal of helping students build general, multi-discipline scientific competencies. In order to do this, our two-semester NEXUS/Physics course sequence is positioned as a second year course so students will have had some exposure to basic concepts in biology and chemistry. NEXUS/Physics stresses interdisciplinary examples and the content differs markedly from traditional introductory physics to facilitate this. It extends the discussion of energy to include interatomic potentials and chemical reactions, the discussion of thermodynamics to include enthalpy and Gibbs free energy, and includes a serious discussion of random vs. coherent motion including diffusion. The development of instructional materials is coordinated with careful education research. Both the new content and the results of the research are described in a series of papers for which this paper serves as an overview and context.Comment: 12 page

Altering the trajectory of early postnatal cortical development can lead to structural and behavioural features of autism

<p>Abstract</p> <p>Background</p> <p>Autism is a behaviourally defined neurodevelopmental disorder with unknown etiology. Recent studies in autistic children consistently point to neuropathological and functional abnormalities in the temporal association cortex (TeA) and its associated structures. It has been proposed that the trajectory of postnatal development in these regions may undergo accelerated maturational alterations that predominantly affect sensory recognition and social interaction. Indeed, the temporal association regions that are important for sensory recognition and social interaction are one of the last regions to mature suggesting a potential vulnerability to early maturation. However, direct evaluation of the emerging hypothesis that an altered time course of early postnatal development can lead to an ASD phenotype remains lacking.</p> <p>Results</p> <p>We used electrophysiological, histological, and behavioural techniques to investigate if the known neuronal maturational promoter valproate, similar to that in culture systems, can influence the normal developmental trajectory of TeA <it>in vivo</it>. Brain sections obtained from postnatal rat pups treated with VPA <it>in vivo </it>revealed that almost 40% of cortical cells in TeA prematurely exhibited adult-like intrinsic electrophysiological properties and that this was often associated with gross cortical hypertrophy and a reduced predisposition for social play behaviour.</p> <p>Conclusions</p> <p>The co-manifestation of these functional, structural and behavioural features suggests that alteration of the developmental time course in certain high-order cortical networks may play an important role in the neurophysiological basis of autism.</p

Habitat Specialization in Tropical Continental Shelf Demersal Fish Assemblages

The implications of shallow water impacts such as fishing and climate change on fish assemblages are generally considered in isolation from the distribution and abundance of these fish assemblages in adjacent deeper waters. We investigate the abundance and length of demersal fish assemblages across a section of tropical continental shelf at Ningaloo Reef, Western Australia, to identify fish and fish habitat relationships across steep gradients in depth and in different benthic habitat types. The assemblage composition of demersal fish were assessed from baited remote underwater stereo-video samples (n = 304) collected from 16 depth and habitat combinations. Samples were collected across a depth range poorly represented in the literature from the fringing reef lagoon (1–10 m depth), down the fore reef slope to the reef base (10–30 m depth) then across the adjacent continental shelf (30–110 m depth). Multivariate analyses showed that there were distinctive fish assemblages and different sized fish were associated with each habitat/depth category. Species richness, MaxN and diversity declined with depth, while average length and trophic level increased. The assemblage structure, diversity, size and trophic structure of demersal fishes changes from shallow inshore habitats to deeper water habitats. More habitat specialists (unique species per habitat/depth category) were associated with the reef slope and reef base than other habitats, but offshore sponge-dominated habitats and inshore coral-dominated reef also supported unique species. This suggests that marine protected areas in shallow coral-dominated reef habitats may not adequately protect those species whose depth distribution extends beyond shallow habitats, or other significant elements of demersal fish biodiversity. The ontogenetic habitat partitioning which is characteristic of many species, suggests that to maintain entire species life histories it is necessary to protect corridors of connected habitats through which fish can migrate

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

I. The kinetics of the reactions of silver, lead, and thallium with thioacetamide. II. The distribution of barium, titanium, manganese, chromium, iron, nickel and cobalt in stony meteorites

NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. The precipitation of silver from acid solutions by thioacetamide at 60°C was investigated. Below pH 2 the reaction takes place predominantly by the hydrolysis of thioacetamide to form hydrogen sulfide. Above pH 2 a direct reaction between the silver and thioacetamide has a significant effect. The direct reaction rate equation was found to be [...]. At 60°C in a malonic acid - 0.1 VF sodium hydrogen malonate buffer k" is 8.6 x 10(-7) mole 7/2 liter 7/2 minute(-1). The presence of chloride ion inhibits the rate of direct reaction between lead and thioacetamide. The reaction is first order with respect to PbCl+ and about 50% slower than with Pb++ at 90°. Thallous sulfide is precipitated by thioacetamide by both hydrolysis and direct reactions. The direct reaction is second order with respect to thallium, first order with respect to thioacetamide and probably inverse half order with respect to hydrogen ion. The concentrations of barium, manganese and titanium have been determined spectrographically in 94 stony meteorites. There appear to be four barium concentration groups with median barium concentrations of 5, 10, 25 and 150 ppm. For the falls the average concentrations of manganese and titanium are 0.260 ± 0.028% and 0.064 ± 0.008%. For the finds the manganese content is 0.235 ± 0.023% and the titanium content is 0.059 ± 0.007%. The presence of grouping in chondrites has been confirmed by X-ray fluorescence spectroscopic analysis

Adsorption of arsenite and arsenate on amorphous iron hydroxide

Adsorption isotherms in solutions with ionic strengths of 0.01 at 25°C were measured over the arsenite and arsenate concentration range 10−7−10−3 M and the pH range 4–10. At low concentrations, these isotherms obeyed equations of the Langmuir type. At higher concentrations the adsorption isotherms were linear, indicating the existence of more than one type of surface site on the amorphous iron hydroxide adsorbent. Removal of arsenite and arsenate by amorphous iron hydroxide throughout the concentration range were determined as a function of pH. By careful selection of the relative concentration of arsenic and amorphous iron hydroxide and pH, removals on the order of 92% can be achieved