Genetic Toolkit for Assessment and Prediction of Population-Level Impacts of Bridge Construction on Birds

Recent studies have highlighted alarming rates of declines in bird populations across the country. The State of California is home to over 650 resident and migrant avian species. Legislation for protecting these species has existed for over a century now, yet tools for identifying populations and understanding seasonal movement remain limited. Recently, genetic and genomic tools have provided a method for understanding population structure, allowing for more informed delineation of management units. The goal of this project was to create a genetic toolkit for identifying breeding populations and assigning individuals to those populations. Ultimately, such tools could be used to assess population-level impacts when there are conflicts with birds at infrastructure construction sites. As a test case, we sequenced entire genomes for 40 individual Anna’s hummingbirds (Calypte anna) from across the state. Based on this initial data, we found low levels of differentiation between sampled locations, suggesting that C. anna in California are not subdivided into different population units. However, there was a weak signal of geography suggesting there may be localized genetic differences in a small proportion of the genome. Follow-up work will focus on a broader sampling across the state of California to clarify any possible population subdivision or geographical patterns of differentiation.View the NCST Project Webpag

Synaptic plasticity in medial vestibular nucleus neurons: comparison with computational requirements of VOR adaptation

Background: Vestibulo-ocular reflex (VOR) gain adaptation, a longstanding experimental model of cerebellar learning, utilizes sites of plasticity in both cerebellar cortex and brainstem. However, the mechanisms by which the activity of cortical Purkinje cells may guide synaptic plasticity in brainstem vestibular neurons are unclear. Theoretical analyses indicate that vestibular plasticity should depend upon the correlation between Purkinje cell and vestibular afferent inputs, so that, in gain-down learning for example, increased cortical activity should induce long-term depression (LTD) at vestibular synapses. Methodology/Principal Findings: Here we expressed this correlational learning rule in its simplest form, as an anti-Hebbian, heterosynaptic spike-timing dependent plasticity interaction between excitatory (vestibular) and inhibitory (floccular) inputs converging on medial vestibular nucleus (MVN) neurons (input-spike-timing dependent plasticity, iSTDP). To test this rule, we stimulated vestibular afferents to evoke EPSCs in rat MVN neurons in vitro. Control EPSC recordings were followed by an induction protocol where membrane hyperpolarizing pulses, mimicking IPSPs evoked by flocculus inputs, were paired with single vestibular nerve stimuli. A robust LTD developed at vestibular synapses when the afferent EPSPs coincided with membrane hyperpolarisation, while EPSPs occurring before or after the simulated IPSPs induced no lasting change. Furthermore, the iSTDP rule also successfully predicted the effects of a complex protocol using EPSP trains designed to mimic classical conditioning. Conclusions: These results, in strong support of theoretical predictions, suggest that the cerebellum alters the strength of vestibular synapses on MVN neurons through hetero-synaptic, anti-Hebbian iSTDP. Since the iSTDP rule does not depend on post-synaptic firing, it suggests a possible mechanism for VOR adaptation without compromising gaze-holding and VOR performance in vivo

Walking Through the Method Zoo: Does Higher Education Really Meet Software Industry Demands?

Software engineering educators are continually challenged by rapidly evolving concepts, technologies, and industry demands. Due to the omnipresence of software in a digitalized society, higher education institutions (HEIs) have to educate the students such that they learn how to learn, and that they are equipped with a profound basic knowledge and with latest knowledge about modern software and system development. Since industry demands change constantly, HEIs are challenged in meeting such current and future demands in a timely manner. This paper analyzes the current state of practice in software engineering education. Specifically, we want to compare contemporary education with industrial practice to understand if frameworks, methods and practices for software and system development taught at HEIs reflect industrial practice. For this, we conducted an online survey and collected information about 67 software engineering courses. Our findings show that development approaches taught at HEIs quite closely reflect industrial practice. We also found that the choice of what process to teach is sometimes driven by the wish to make a course successful. Especially when this happens for project courses, it could be beneficial to put more emphasis on building learning sequences with other courses

The Intracellular Localization of APE 1 /Ref-1: More than a Passive Phenomenon?

Human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/Ref-1) is a perfect paradigm of the functional complexity of a biological macromolecule. First, it plays a crucial role, by both redox-dependent and –independent mechanisms, as a transcriptional coactivator for different transcription factors, either ubiquitous (i.e., AP-1, Egr-1, NF-κB, p53, HIF) or tissue-specific (i.e., PEBP-2, Pax-5 and -8, TTF-1), in controlling different cellular processes such as apoptosis, proliferation, and differentiation. Second, it acts, as an apurinic/apyrimidinic endonuclease, during the second step of the DNA base excision repair pathway, which is responsible for the repair of cellular alkylation and oxidative DNA damages. Third, it controls the intracellular reactive oxygen species production by negatively regulating the activity of the Ras-related GTPase Rac1. Despite these known functions of APE1/Ref-1, information is still scanty about the molecular mechanisms responsible for the coordinated control of its several activities. Some evidence suggests that the expression and subcellular localization of APE1/Ref-1 are finely tuned. APE1/Ref-1 is a ubiquitous protein, but its expression pattern differs according to the different cell types. APE1/Ref-1 subcellular localization is mainly nuclear, but cytoplasmic staining has also been reported, the latter being associated with mitochondria and/or presence within the endoplasmic reticulum. It is not by chance that both expression and subcellular localization are altered in several metabolic and proliferative disorders, such as in tumors and aging. Moreover, a fundamental role played by different posttranslational modifications in modulating APE1/Ref-1 functional activity is becoming evident. In the present review, we tried to put together a growing body of information concerning APE1/Ref-1's different functions, shedding new light on present and future directions to understand fully this unique molecule

In-situ monitoring for CVD processes

Aiming towards process control of industrial high yield/high volume CVD reactors, the potential of optical sensors as a monitoring tool has been explored. The sensors selected are based on both Fourier transform infrared spectroscopy (FTIR) and tunable diode laser spectroscopy (NIR-DLS). The former has the advantage of wide spectral capability, and well established databases. NIR-DLS spectroscopy has potentially high sensitivity, laser spatial resolution, and the benefits of comparatively easier integration capabilities-including optical fibre compatibility. The proposed technical approach for process control is characterised by a 'chemistry based' feedback system with in-situ optical data as input information. The selected optical sensors continuously analyze the gas phase near the surface of the growing layer. The spectroscopic data has been correlated with process performance and layer properties which, in turn establish data basis for process control. The new process control approach is currently being verified on different industrialised CVD coaters. One of the selected applications deals with the deposition of SnO2 layers on glass based on the oxidation of (CH3)2SnCl2, which is used in high volume production for low-E glazing

Hybrid Software Development Approaches in Practice: A European Perspective

Agile and traditional development approaches are used in combination in todays software development. To improve the understanding and to provide better guidance for selecting appropriate development approaches, it is important to analyze such combinations in practice. Results obtained from an online survey strongly confirm that hybrid development approaches are widely used in industry. Our results show that hybrid development approaches: (i) have become reality for nearly all companies; (ii) are applied to specific projects even in the presence of company-wide policies for process usage; (iii) are neither planned nor designed but emerge from the evolution of different work practices; and, (iv) are consistently used regardless of company size or industry secto

C-C bond-forming reactions of ground-state aryl halides under reductive activation

Under basic conditions aryl halides can undergo SRN1 reactions, BHAS reactions and benzyne formations. Appropriate complex substrates afford an opportunity to study inherent selectivities. SRN1 reactions are usually favoured under photoactivated conditions, but this paper reports their success using ground-state and transition metal-free conditions. In benzene, the enolate salt 12, derived by deprotonation of diketopiperazine 11, behaves as an electron donor, and assists the initiation of the reactions, but in DMSO, it is not required. The outcomes are compared and contrasted with a recent photochemical study on similar substrates. A particular difference is the prevalence of hydride shuttle reactions under relatively mild thermal conditions