An axon initial segment is required for temporal precision in action potential encoding by neuronal populations

Central neurons initiate action potentials (APs) in the axon initial segment (AIS), a compartment characterized by a high concentration of voltage-dependent ion channels and specialized cytoskeletal anchoring proteins arranged in a regular nanoscale pattern. Although the AIS was a key evolutionary innovation in neurons, the functional benefits it confers are not clear. Using a mutation of the AIS cytoskeletal protein \beta IV-spectrin, we here establish an in vitro model of neurons with a perturbed AIS architecture that retains nanoscale order but loses the ability to maintain a high NaV density. Combining experiments and simulations we show that a high NaV density in the AIS is not required for axonal AP initiation; it is however crucial for a high bandwidth of information encoding and AP timing precision. Our results provide the first experimental demonstration of axonal AP initiation without high axonal channel density and suggest that increasing the bandwidth of the neuronal code and hence the computational efficiency of network function was a major benefit of the evolution of the AIS.Comment: Title adjusted, no other change

Evaluating the Impact of Nitrogen Fertilization Treatments and Irrigation on Soil Health Indicators in a Long-Term Crop Rotation Research Plot

Abstract Many agriculturalists have been focusing on the most efficient farming method that would produce the maximum yield while still sustaining the soil ecosystem. Soil samples were collected from the “Old Rotation” area (Auburn University, Auburn, AL), and were assessed for soil biochemical, chemical and biological characteristics related to soil quality. Treatments of the experimental site were a control with no legumes or N fertilizer; cotton every year with winter legumes; a 3-yr cotton-corn-soybean rotation with wheat and winter legumes; and cotton every year with N fertilizer. Impacts of irrigation were also tested between the sites. Assays were performed measuring phosphomonoesterase and phosphodiesterase activity, soil organic carbon, soil pH, and microbial diversity. The 3-year and winter legume rotations showed significant differences in the structure and membership of microbial communities and differences in biochemical activity. These results further demonstrate the ability of crop rotation to enhance the soil health of agricultural ecosystems. Keywords: Nitrogen Fertilization, Irrigation, Crop Rotation, Soil Ecology, Enzymatic Activit

The evolutionary dynamics of genomic regulatory blocks in metazoan genomes

Developmental genes require intricate control of the timing, location and magnitude of their expression. This is provided by multiple evolutionarily conserved enhancers, known as conserved non-coding elements (CNEs). CNEs cluster around their target genes, forming long syntenic arrays known as genomic regulatory blocks (GRBs). Current methods for GRB identification rely on the selection of arbitrary minimum conservation thresholds, impeding their performance in many contexts. In this thesis, I propose a novel measure of pairwise genome conservation that eliminates the need for conservation thresholds, and use this measure to study the evolutionary dynamics of GRBs in metazoa. I define sets of GRBs based on their rate of regulatory turnover – high turnover GRBs (htGRBs) and low turnover GRBs (ltGRBs) – in three independent metazoan lineages. I show that ht- and ltGRBs target functionally distinct classes of genes, and that these genes tend to be expressed during late and early development respectively, potentially contributing to their differing tolerance of regulatory turnover. Moreover, the differences between ht- and ltGRBs are consistent across all three lineages, suggesting that similar evolutionary pressures have defined the rate of turnover in these GRBs since their emergence in the metazoan ancestor. Next I identify GRBs in the extremely compact Caenorhabditis elegans and Oikopleura dioica genomes for the first time, and use these GRBs to investigate the effects of genome compaction on GRB size and composition. I show that GRB size scales proportionally with genome size and that GRBs exhibit similar enrichment and depletion of specific genomic features. This suggests that regardless of background genome content, GRBs are under similar pressure to maintain a permissive environment for long-range gene regulation. The development of a threshold-free GRB identification method has facilitated the analysis of GRBs in both closely related species and compact genomes, providing further insights into their origin and evolution.Open Acces

Rural Land Management Impacts on Catchment Scale Flood Risk

This thesis examines the relationship between rural land management and downstream flood risk. The recent increase in flood frequency and magnitude has been hypothesised to have been caused by either climate change or land management. The theoretical basis for why these factors might increase flood risk is well known, but showing their impact on downstream flood risk remains a challenge. Field scale studies have found that changing land management practices does affect local runoff and streamflow. Upscaling these effects to the catchment scale continues to be problematic,both conceptually and, more importantly, methodologically. Conceptually, upscaling is critical. As land management may impact upon the relative timing as well as the magnitude of runoff, any changes in land management practice may lead to changes in the synchronisation of tributaries flows, either reducing or increasing downstream flood risk. Methodologically, understanding this effect requires capturing the spatial resolution associated with field-scale hydrological processes simultaneously with the upscaling of these processes to the downstream locations where flood risk is of concern. Most approaches to this problem aim to upscale from individual grid cells to whole catchments, something that restricts the complexity of possible process representation,produces models that may not be parsimonious with the data needed to calibrate them and, faced with data uncertainties, provides computational limitations on the extent to which model uncertainty can be fully explored. Rather than upscaling to problems of concern, this thesis seeks to downscale from locations of known flood risk, as a means of identifying where land use management changes might be beneficial and then uses numerical modelling to identify the kinds of management changes required in those downscaled locations. Thus, the aim of this thesis is to test an approach to understanding the impacts of rural land management upon flood risk based upon catchment-to-source downscaling. This thesis uses the case study of the River Eden catchment (2400 km2) as a test case. Firstly the downstream flood risk problem was assessed using both gauged data and documentary evidence to investigate the historical flood record. This found the last decade does not differ significantly from previous flood rich periods, which were defined as 1) 1873-1904; 2) 1923-1933; and 3) 1994-present. Second, the potential causes of floods within the catchment were investigated; firstly climate variability was assessed using Lamb weather types, which found that five weather types were responsible for causing 90% of the floods in the last 30 years. Third, spatial downscaling of catchment-scale flood risk was undertaken using two methods; databased statistical analysis; and hydraulic modelling. Both approaches consider the magnitudes and the timing of the flows from each major sub-catchment. The statistical approach involved a principal components analysis to simplify the complex subcatchment interactions and a stepwise regression to predict downstream flood risk. The hydraulic modelling approach used iSIS-Flow to undertake a series of numerical experiments, where the input hydrographs from each tributary were shifted individually and the effect on downstream peak stage assessed. Both these approaches found that the Upper Eden and Eamont sub-catchments were the most important in explaining downstream flood risk. The Eamont sub-catchment was chosen for future analysis as:(1) it was shown to have a significant impact on downstream flood risk; and (2) it had range of data and information needed for modelling land use changes. The second part of this thesis explored the land management scenarios that could be used to reduce flood risk at the catchment scale. The scenarios to be tested were determined through a stakeholder participation approach, whereby workshops were held to brainstorm and prioritise land management options, and then to identify specific locations within the Eamont sub-catchment where they could tested. There were two main types of land management scenarios chosen: (1) landscape-scale changes,including afforestation and compaction; and (2) channel modification and floodplain storage scenarios, including flood bank removal and wet woodland creation. The hydrological model CRUM3 was used to test the catchment scale land use changes,while the hydraulic model iSIS-Flow was used to test the channel and floodplain scenarios. It was found that through changing the whole of a small sub-catchment(Dacre Beck), the scenarios of reducing compaction and arabilisation could reduce catchment scale (2400 km2) flood risk by up to 3.5% for a 1 in 175 year flood event(January 2005). Changing localised floodplain roughness reduced sub-catchment (Lowther) peak stage by up to 0.134 m. This impact diminished to hardly any effect on peak flow magnitudes at the sub-catchment scale (Eamont). However, these scenarios caused a delay of the flood peak by up to 5 hours at the sub-catchment scale, which has been found to reduce peak stage at Carlisle by between 0.167 m to 0.232 m, corresponding to a 5.8% decrease in peak discharge. A key conclusion is that land management practices have been shown to have an effect on catchment scale flooding, even for extreme flood events. However, the effect of land management scenarios are both spatially and temporally dependent i.e. the same land management practice has different effects depending on where it is implemented, and when implemented in the same location has different effects on different flood events

Space applications of Automation, Robotics and Machine Intelligence Systems (ARAMIS). Volume 3: ARAMIS overview

An overview of automation, robotics, and machine intelligence systems (ARAMIS) is provided. Man machine interfaces, classification, and capabilities are considered

Higher order chromosome organization and recombination dynamics of meiotic prophase I in mouse spermatocytes

Meiotic recombination is required for parental chromosomes to find each other (pairing/synapsis) and to exchange genetic information thus allowing faithful segregation of chromosomes and the production of haploid gametes. At the start of meiotic prophase I, meiotic chromosomes organize into loop arrays that extrude out of the chromosome axis. Then, a large number of programmed double-strand breaks (DSBs) are formed at specific chromosomal locations or “hotspots” on parental chromosomes, which are repaired by homologous recombination (HR). HR produces either crossovers, which result in the exchange of flanking markers between homologs, or noncrossovers, which are short regions ofgene conversion to the donor genotype. Crossover formation is critical for proper chromosome segregation and crossovers arise from crossover precursors that form at a subset of DSBs that are designated to become future crossovers. Our current understanding of meiotic progression in mammals is largely derived from cytological observation.Many semi-redundant HR pathways can repair meiotic DSBs; however, the time at which different pathways are active, how the pathways interact, and the relative contribution of each pathway towards maintaining germline genomic integrity are poorly understood in vivoat endogenous sites, especially in a mammalian system. More importantly, how germline genome integrity is ensured at both the DNA level by recombination activity and by higher order chromosome structural changes has not been defined. Failure to maintain germline genome integrity can lead to aneuploidy, genetic disorders, birth defects and miscarriages. To define and dissect the temporal dynamics of different HR pathways and chromosome organization in vivo, I have established a novel and robust system to synchronize mouse spermatogenesis in F1 hybrid mice using the inhibitor WIN 18,446. My synchronizationprotocol allows the isolation of cells at specific stages of meiotic prophase I by flow cytometry, allowing me to analyze recombination outcomes at two meiotic hotspots and perform genome-wide Hi-C, a chromosome conformation capture method combined with high-throughput sequencing to investigate changes in higher order chromosome architecture during prophase I. Here, I provide the first direct molecular evidence that HR pathways that lead to to distinct meiotic outcomes aretemporally regulated. I have identified two novel classes of noncrossover pathways: 1) one that likely regulates the pairing/synapsis of parental chromosomes during early prophase I; and 2) one that derives from the crossover/noncrossover decision during mid-prophase I. My data show that crossover formation is suppressed until full synapsis is achieved at mid-prophase I, suggesting a previously unknown mechanism that prevents deleterious premature recombination. In addition, I show that alternative repair pathways are not activated until late prophase I, thus preventing designated crossover precursors from inappropriately forming noncrossovers. Furthermore, the Hi-C data I present provides evidence for dynamic genome reorganization during meiotic prophase I. There is evidence for loop array formation and loop extrusion as chromosomes condense. While topologically associating domains disappear at the onset of meiotic prophase I, chromosome compartments are well maintained. Most meiotic DSBs occur within a gene-dense open compartment A, suggesting that higher order chromosome structure plays an important role in meiotic recombination. Finally, interhomolog interactions and specialized chromosomal architecture in regions of pairing and synapsis could be inferred. Taken together, my data reveals that both chromosome recombination and chromosome structure are highly regulated to ensure chromosome pairing and segregation. These results provide important, novel insights to the field of meiosis and our understanding of germline genomic integrity and mammalian reproductive health

Free-living nematodes detection using next-generation sequencing technology

The role of nematodes as biological indicators and as key players in nutrient cycling is well recognized. Others have been shown to cause immense losses in food production. Despite their importance, identification of nematodes has been hindered by difficulties in species identification using classical morphology. Alternative molecular-based methods including AFLP, PCR-RFLP and DNA barcoding used alone or in combination with the traditional methods can be time consuming when analysing multiple specimens in a sample. Metabarcoding provides the possibility to identify an array of individuals from many samples simultaneously. The challenge of this approach has been how to identify the most suitable DNA marker(s) as well as the lack of robust analysis pipeline for the sequence data. An evaluation of the performance of four candidate DNA markers (NF1-18Sr2b, SSUFO4- SSUR22, D3Af-D3Br and JB3-JB5) on a mock community of nematodes showed NF1- 18Sr2b is most suitable in terms of coverage and availability of reference sequences. Assessment of the most common bioinformatic tools (QIIME, MOTHUR and USEARCH) showed USEARCH had the best clustering algorithm, was the fastest, had best operational taxonomic units (otus) to actual diversity ratio and ranked the best in userfriendliness. In another mock community experiment, read numbers of taxa showed no correlation with their actual abundance in the community largely due to bias in amplification and copy numbers of the marker region. Analysis of samples collected from a tillage and traffic experiment using morphological approach showed strong inhibition of herbivores by deep tillage and zero traffic. Bacterivores in general were inhibited by traffic and not affected by tillage. Appraisal of the metabarcoding approach using samples from the same experiment showed at broader classification levels (trophic groups and functional guild), abundance biases associated with the mock community experiment were minimal, the broad implication being metabarcoding data may be useful for assessing quality soil based on the structure of its nematode community

Advances in Data Mining Knowledge Discovery and Applications

Advances in Data Mining Knowledge Discovery and Applications aims to help data miners, researchers, scholars, and PhD students who wish to apply data mining techniques. The primary contribution of this book is highlighting frontier fields and implementations of the knowledge discovery and data mining. It seems to be same things are repeated again. But in general, same approach and techniques may help us in different fields and expertise areas. This book presents knowledge discovery and data mining applications in two different sections. As known that, data mining covers areas of statistics, machine learning, data management and databases, pattern recognition, artificial intelligence, and other areas. In this book, most of the areas are covered with different data mining applications. The eighteen chapters have been classified in two parts: Knowledge Discovery and Data Mining Applications

Caveolin-1 recruitment to the trailing edge of motile cells results in focal adhesion disassembly and nascent interaction with actin stress fibers

The protein caveolin-1 has been shown to positively affect angiogenesis and vascular remodeling in vivo via studies using knockout mice. In fact, defects in these two processes are among the major hallmarks of an otherwise benign caveolin-null phenotype. Current dogma on the function of caveolin-1 does not predict or account for these deficits. The overall objective of the following studies was to uncover the role of caveolin-1 in angiogenesis and vascular remodeling through study of the protein in cell-substratum remodeling during cell motility in vitro.;In the first study, caveolin-1 and its parent organelle, caveolae, conspicuously polarize to the rear of migrating human umbilical vein endothelial cells. Moreover, caveolin-1 localizated at the cell rear is mutually exclusive with focal adhesion staining and lamellipodial protrusion. Acute caveolin-1 knockdown by small, interfering RNA diminished the ability of endothelial cells to polarize and migrate toward a chemotactic stimulus.;In the second study, live cell imaging was used to study the dynamics between caveolin-1, focal adhesions, and the actin cytoskeleton. Caveolin-1 recruitment and transient association with focal adhesions at the trailing edge resulted in adhesion sliding and disassembly, concomitant with recoil of the trailing edge into the cell body proper. Moreover, association of caveolin-1 with actin stress fibers previously associated with adhesions in the collapsing trailing edge was observed. Mouse embryonic fibroblasts from caveolin-1 null mice demonstrated defects in trailing edge recoil compared to control cells with no decrease in cell contractility, suggesting a specific deficit in adhesion disassembly. Furthermore, caveolin-null cells displayed a decrease in overall chemokinetic motility and an increase in directional persistence, an indication that caveolin-1 contributes to movement plasticity via trailing edge focal adhesion disassembly.;In the final study, the interaction of polarized caveolin-1 with actin stress fibers at the cell rear was characterized. Caveolin-1 predictably associated with the cell perimeter depending on the direction of cell migration. Importantly, inhibition on non-muscle myosin by blebbistatin treatment abrogated initial polarization of caveolin-1, but did not affect caveolin-1 that had already polarized. Using live cell imaging in conjunction with photobleaching, actin-associated caveolin-1 was found to be extremely static upon polarization to the cell rear. In contrast, the initial polarization of caveolin-1 to retracting areas was highly dynamic. Furthermore, GM1 internalization at the cell rear was negligible, confirming that polarized caveolae are highly static. Forced disruption of the actin cytoskeleton by cytochalasin D treatment resulted in caveolin-1 depolarization and disaggregation into small puncta displaying frenetic, kiss-and-run movement. Furthermore, cytoskeletal remodeling in response to change in direction of a cell resulted in similar caveolin depolarization.;In summary, stress fibers associate with and exert traction on trailing edge focal adhesions during cell motility. This traction force is prerequisite for caveolin-1 recruitment. Arrival and transient association of caveolin-1 with focal adhesions results in adhesion disassembly and stable interaction of caveolin with actin stress fibers. Thus, a novel mechanism in cellular mechanotransduction can be described, whereby cells utilize caveolin-1 recruitment to relieve strain generated at the cell perimeter by the actin cytoskeleton during movement. This novel function of caveolin-1 may analogously occur in vivo, beyond the context of endothelial cell migration. The deficits in angiogenesis and vascular remodeling seen in caveolin-1 null mice might thus be explained by the role of caveolin-1 in cell-substratum remodeling in response to strain