Reconstruction of neuronal activity and connectivity patterns in the zebrafish olfactory bulb

In the olfactory bulb (OB), odors evoke distributed patterns of activity across glomeruli that are reorganized by networks of interneurons (INs). This reorganization results in multiple computations including a decorrelation of activity patterns across the output neurons, the mitral cells (MCs). To understand the mechanistic basis of these computations it is essential to analyze the relationship between function and structure of the underlying circuit. I combined in vivo twophoton calcium imaging with dense circuit reconstruction from complete serial block-face electron microscopy (SBEM) stacks of the larval zebrafish OB (4.5 dpf) with a voxel size of 9x9x25nm. To address bottlenecks in the workflow of SBEM, I developed a novel embedding and staining procedure that effectively reduces surface charging in SBEM and enables to acquire SBEM stacks with at least a ten-fold increase in both, signal-to-noise as well as acquisition speed. I set up a high throughput neuron reconstruction pipeline with >30 professional tracers that is available for the scientific community (ariadne-service.com). To assure efficient and accurate circuit reconstruction, I developed PyKNOSSOS, a Python software for skeleton tracing and synapse annotation, and CORE, a skeleton consolidation procedure that combines redundant reconstruction with targeted expert input. Using these procedures I reconstructed all neurons (>1000) in the larval OB. Unlike in the adult OB, INs were rare and appeared to represent specific subtypes, indicating that different sub-circuits develop sequentially. MCs were uniglomerular whereas inter-glomerular projections of INs were complex and biased towards groups of glomeruli that receive input from common types of sensory neurons. Hence, the IN network in the OB exhibits a topological organization that is governed by glomerular identity. Calcium imaging revealed that the larval OB circuitry already decorrelates activity patterns evoked by similar odors. The comparison of inter-glomerular connectivity to the functional interactions between glomeruli indicates that pattern decorrelation depends on specific, non-random inter-glomerular IN projections. Hence, the topology of IN networks in the OB appears to be an important determinant of circuit function

Addressing the needs of traumatic brain injury with clinical proteomics.

BackgroundNeurotrauma or injuries to the central nervous system (CNS) are a serious public health problem worldwide. Approximately 75% of all traumatic brain injuries (TBIs) are concussions or other mild TBI (mTBI) forms. Evaluation of concussion injury today is limited to an assessment of behavioral symptoms, often with delay and subject to motivation. Hence, there is an urgent need for an accurate chemical measure in biofluids to serve as a diagnostic tool for invisible brain wounds, to monitor severe patient trajectories, and to predict survival chances. Although a number of neurotrauma marker candidates have been reported, the broad spectrum of TBI limits the significance of small cohort studies. Specificity and sensitivity issues compound the development of a conclusive diagnostic assay, especially for concussion patients. Thus, the neurotrauma field currently has no diagnostic biofluid test in clinical use.ContentWe discuss the challenges of discovering new and validating identified neurotrauma marker candidates using proteomics-based strategies, including targeting, selection strategies and the application of mass spectrometry (MS) technologies and their potential impact to the neurotrauma field.SummaryMany studies use TBI marker candidates based on literature reports, yet progress in genomics and proteomics have started to provide neurotrauma protein profiles. Choosing meaningful marker candidates from such 'long lists' is still pending, as only few can be taken through the process of preclinical verification and large scale translational validation. Quantitative mass spectrometry targeting specific molecules rather than random sampling of the whole proteome, e.g., multiple reaction monitoring (MRM), offers an efficient and effective means to multiplex the measurement of several candidates in patient samples, thereby omitting the need for antibodies prior to clinical assay design. Sample preparation challenges specific to TBI are addressed. A tailored selection strategy combined with a multiplex screening approach is helping to arrive at diagnostically suitable candidates for clinical assay development. A surrogate marker test will be instrumental for critical decisions of TBI patient care and protection of concussion victims from repeated exposures that could result in lasting neurological deficits

Asian Carp in the Missouri River: Analysis from Multiple Missouri River Habitat and Fisheries Programs

Bighead carp Hypophthalmichthys nobilis, silver carp H. molitrix, black carp Mylopharyngodon piceus, and grass carp Ctenopharyngodon idella, collectively referred to as Asian carps, are invasive species that were either accidentally or intentionally introduced into the Mississippi River basin. The expansion of Asian carp into the Missouri River is not well understood and knowledge of population characteristics within this river were lacking. The objectives of this study were to describe the relative abundance, size structure, and spatial and temporal trends of Asian carp using multiple gears from three long-term fish community monitoring programs in the Missouri River downstream of Gavins Point Dam, South Dakota and Nebraska from 2003 to 2007. A total of 1,307 bighead, 1,280 silver, 624 grass, and 0 black carp were captured. The majority of adult bighead carp were captured in overnight hoop nets (38%) and adult silver (14%) and grass carp (23%) were most commonly caught in overnight experimental gill nets. Mini-fyke nets captured almost exclusively, young of the year Asian carp (≤ 80 mm), while gill, trammel, and hoop nets collected a wide length range of fish (81 – 1,200 mm). The relative abundance of all three Asian carp species did not significantly differ among years; however, spatial trends were found as relative abundance was highest in the Missouri River downstream of the Platte River. Short Asian carp weighed less in the Gavins Point reach compared to downstream of the Grand River in Missouri. Conversely, long Asian carp in the Gavins Point reach attained greater weights than fish of similar length downstream. We found that multiple sampling gears are necessary to monitor Asian carp population characteristics in the Missouri River. Asian carp populations appear to be well established in the Missouri River and it is increasingly important to understand the affects these invasive species have on the native fish community

Asian Carp in the Missouri River: Analysis from Multiple Missouri River Habitat and Fisheries Programs

Bighead carp Hypophthalmichthys nobilis, silver carp H. molitrix, black carp Mylopharyngodon piceus, and grass carp Ctenopharyngodon idella, collectively referred to as Asian carps, are invasive species that were either accidentally or intentionally introduced into the Mississippi River basin. The expansion of Asian carp into the Missouri River is not well understood and knowledge of population characteristics within this river were lacking. The objectives of this study were to describe the relative abundance, size structure, and spatial and temporal trends of Asian carp using multiple gears from three long-term fish community monitoring programs in the Missouri River downstream of Gavins Point Dam, South Dakota and Nebraska from 2003 to 2007. A total of 1,307 bighead, 1,280 silver, 624 grass, and 0 black carp were captured. The majority of adult bighead carp were captured in overnight hoop nets (38%) and adult silver (14%) and grass carp (23%) were most commonly caught in overnight experimental gill nets. Mini-fyke nets captured almost exclusively, young of the year Asian carp (≤ 80 mm), while gill, trammel, and hoop nets collected a wide length range of fish (81 – 1,200 mm). The relative abundance of all three Asian carp species did not significantly differ among years; however, spatial trends were found as relative abundance was highest in the Missouri River downstream of the Platte River. Short Asian carp weighed less in the Gavins Point reach compared to downstream of the Grand River in Missouri. Conversely, long Asian carp in the Gavins Point reach attained greater weights than fish of similar length downstream. We found that multiple sampling gears are necessary to monitor Asian carp population characteristics in the Missouri River. Asian carp populations appear to be well established in the Missouri River and it is increasingly important to understand the affects these invasive species have on the native fish community

Lexical co-occurrence and lexical inheritance. emotion lexemes in German: a lexicographic case study

In the present paper, we tackle the problem of the compact and efficient representation of restricted lexical co-occurrence information in the lexicon along semantic lines. The theoretical framework for this study is the Meaning Text Theory (MTT) and, more specifically, the lexicographic part of MIT --- the Explanatory Combinatorial Dictionary (ECD), which contains for each lexeme (i) its semantic definition, (ii) a systematic description of its restricted lexical co-occurrence in terms of Lexical Functions(LF), and (iii) its Government Pattern. The data domain is the semantic field of emotion lexemes in German. In order to represent the restricted lexical co-occurrence (or collocations) of the lexemes in this field, we suggest the following procedure:1.    Construct approximate descriptions of their meaning, i.e. what we call the abridged lexicographic definitions. Formulated in terms of semantic features, these definitions are supposed to provide as much semantic information as necessary for establishing correlations between the semantic features of a lexeme and its collocates.2.    Specify their syntactic Government Patterns, which are needed for a clearer picture of their co-occurrence --- syntactic as well as lexical.3.    Specify their restricted lexical co-occurrence with the verbs chosen.4.    Establish correlations between the values of LFs and the semantic features in the abridged definitions of the emotion lexemes.5.    Based on these correlations, extract recurrent values of LFs (and recurrent Government Patterns) from individual lexical entries and list them under what we call the generic lexeme of the semantic field under study --- in this case, GEFÜHL 'emotion'. This leads on the one hand, to "compressed" lexical entries for emotion lexemes, and on the other hand, to the creation of a lexical entry of a new type: the "public" entry of a generic lexeme.Keywords: lexicography, lexicon, german emotion lexemes, lexical co-occurrence, collocations, meaning text theory, lexical functions, semantic features, semantico-lexical correlations, information extraction, inheritance, individual lexical subentry, public lexical subentr

DIRK Schemes with High Weak Stage Order

Runge-Kutta time-stepping methods in general suffer from order reduction: the observed order of convergence may be less than the formal order when applied to certain stiff problems. Order reduction can be avoided by using methods with high stage order. However, diagonally-implicit Runge-Kutta (DIRK) schemes are limited to low stage order. In this paper we explore a weak stage order criterion, which for initial boundary value problems also serves to avoid order reduction, and which is compatible with a DIRK structure. We provide specific DIRK schemes of weak stage order up to 3, and demonstrate their performance in various examples.Comment: 10 pages, 5 figure

Studies on processing, particle formation, and immunogenicity of the HIV-1 gag gene product: a possible component of a HIV vaccine

Antigens in a particulate conformation were shown to be highly immunogenic in mammals. For this reason, the particle forming capacity of derivatives of the HIV-1 group specific core antigen p55 gag was assayed and compared dependent on various expression systems: recombinant bacteria, vaccinia- and baculoviruses were established encoding the entire core protein p55 either in its authentic sequence or lacking the myristylation consensus signal. Moreover, p55 gag was expressed in combination with the protease (p55-PR) or with the entire polymerase (p55-pol), respectively. Budding of 100-160 nm p55 core particles, resembling immature HIV-virions, was observed in the eucaryotic expression systems only. In comparison to the vaccinia virus driven expression of p55 in mammalian cells, considerably higher yields of particulate core antigen were obtained by infection of Spodoptera frugiperda (Sf9) insect cells with the recombinant Autographa californica nuclear polyhedrosis (AcMNPV) baculovirus. Mutation of the NH2-terminal myristylation signal sequence prevented budding of the immature core particles. Expression of the HIV p55-PR gene construct by recombinant baculovirus resulted in complete processing of the p55 gag precursor molecule in this system. The introduction of an artificial frameshift near the natural frameshift site resulted in constitutive expression of the viral protease and complete processing of p55, both in Escherichia coli and in vaccinia virus infected cells. Interestingly, significant processing of p55 resembling that of HIV infected H9 cells could also be achieved in the vaccinia system by fusing the entire pol gene to the gag gene. Moreover, processing was not found to be dependent on amino-terminal myristylation of the gag procursor molecule, which is in contrast to observations with type C and type D retrovirus. However, complete processing of p55 into p24, p17, p9 and p6 abolished particle formation. Purified immature HIV-virus like particles were highly immunogenic in rabbits, leading to a strong humoral immune response after immunization. Empty immature p55 gag particles represent a noninfectious and attractive candidate for a basic vaccine component