Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies

SN 2009kf : a UV bright type IIP supernova discovered with Pan-STARRS 1 and GALEX

We present photometric and spectroscopic observations of a luminous type IIP Supernova 2009kf discovered by the Pan-STARRS 1 (PS1) survey and detected also by GALEX. The SN shows a plateau in its optical and bolometric light curves, lasting approximately 70 days in the rest frame, with absolute magnitude of M_V = -18.4 mag. The P-Cygni profiles of hydrogen indicate expansion velocities of 9000km/s at 61 days after discovery which is extremely high for a type IIP SN. SN 2009kf is also remarkably bright in the near-ultraviolet (NUV) and shows a slow evolution 10-20 days after optical discovery. The NUV and optical luminosity at these epochs can be modelled with a black-body with a hot effective temperature (T ~16,000 K) and a large radius (R ~1x10^{15} cm). The bright bolometric and NUV luminosity, the lightcurve peak and plateau duration, the high velocities and temperatures suggest that 2009kf is a type IIP SN powered by a larger than normal explosion energy. Recently discovered high-z SNe (0.7 < z < 2.3) have been assumed to be IIn SNe, with the bright UV luminosities due to the interaction of SN ejecta with a dense circumstellar medium (CSM). UV bright SNe similar to SN 2009kf could also account for these high-z events, and its absolute magnitude M_NUV = -21.5 +/- 0.5 mag suggests such SNe could be discovered out to z ~2.5 in the PS1 survey.Comment: Accepted for publication in APJ

Population Dynamics and Angler Exploitation of the Unique Muskellunge Population in Shoepack Lake, Voyageurs National Park, Minnesota

A unique population of muskellunge Esox masquinongy inhabits Shoepack Lake in Voyageurs National Park, Minnesota. Little is known about its status, dynamics, and angler exploitation, and there is concern for the long-term viability of this population. We used intensive sampling and mark–recapture methods to quantify abundance, survival, growth, condition, age at maturity and fecundity and angler surveys to quantify angler pressure, catch rates, and exploitation. During our study, heavy rain washed out a dam constructed by beavers Castor canadensis which regulates the water level at the lake outlet, resulting in a nearly 50% reduction in surface area. We estimated a population size of 1,120 adult fish at the beginning of the study. No immediate reduction in population size was detected in response to the loss of lake area, although there was a gradual, but significant, decline in population size over the 2-year study. Adults grew less than 50 mm per year, and relative weight (W r) averaged roughly 80. Anglers were successful in catching, on average, two fish during a full day of angling, but harvest was negligible. Shoepack Lake muskellunge exhibit much slower growth rates and lower condition, but much higher densities and angler catch per unit effort (CPUE), than other muskellunge populations. The unique nature, limited distribution, and location of this population in a national park require special consideration for management. The results of this study provide the basis for assessing the long-term viability of the Shoepack Lake muskellunge population through simulations of long-term population dynamics and genetically effective population size

Effects of hatchery broodstock collection on adult Muskellunge populations

Muskellunge Esox masquinongy stocking programs throughout North America rely on the collection of wild adult Muskellunge to acquire gametes for hatchery propagation. The process of collecting, transporting, confining, handling, and spawning broodstock Muskellunge may cause mortality that could alter Muskellunge density, size structure, and population survival rates. We used long‐term Muskellunge capture‐recapture data collected from the Iowa Great Lakes and Clear Lake in northern Iowa, USA to estimate the number and proportion of Muskellunge captured annually and initial mortality rates resulting from broodstock collection. We also evaluated whether Muskellunge apparent survival rates differed between individuals used as broodstock and those that were not captured annually. Finally, we evaluated whether the number of initial mortalities or the number of individuals captured were related to annual population survival estimates. Collectively, 7,010 adult Muskellunge (3,896 males and 3,114 females) captures occurred between 2001‐2017 and population densities within a system ranged from 0.11 to 0.39 fish/ha. An average of 33% (range: 13% ‐76%) of the population was captured during broodstock operations annually. Between 0 and 28 (0.0000 to 0.0191 fish/ha) Muskellunge died at each hatchery annually and more males died than females (total of 150 males and 68 females; 3.9% and 2.2% of captured fish, respectively). However, annual mortalities were generally a low proportion of Muskellunge in the lake (\u3c2%; \u3c0.001 fish/ha). There was some evidence of size selective mortality, particularly for males, where larger individuals (875‐975 mm) were more likely to die, but we found no evidence to suggest that broodstock collection affected annual population survival estimates. Muskellunge broodstock mortality appears to act in a compensatory manner with natural mortality, and other sources of population mortality are more likely to have a greater effect on the population

Simulated Effects of Recruitment Variability, Exploitation, and Reduced Habitat Area on the Muskellunge Population in Shoepack Lake, Voyageurs National Park, Minnesota

The genetically unique population of muskellunge Esox masquinongy inhabiting Shoepack Lake in Voyageurs National Park, Minnesota, is potentially at risk for loss of genetic variability and long-term viability. Shoepack Lake has been subject to dramatic surface area changes from the construction of an outlet dam by beavers Castor canadensis and its subsequent failure. We simulated the long-term dynamics of this population in response to recruitment variation, increased exploitation, and reduced habitat area. We then estimated the effective population size of the simulated population and evaluated potential threats to long-term viability, based on which we recommend management actions to help preserve the long-term viability of the population. Simulations based on the population size and habitat area at the beginning of a companion study resulted in an effective population size that was generally above the threshold level for risk of loss of genetic variability, except when fishing mortality was increased. Simulations based on the reduced habitat area after the beaver dam failure and our assumption of a proportional reduction in population size resulted in an effective population size that was generally below the threshold level for risk of loss of genetic variability. Our results identified two potential threats to the long-term viability of the Shoepack Lake muskellunge population, reduction in habitat area and exploitation. Increased exploitation can be prevented through traditional fishery management approaches such as the adoption of no-kill, barbless hook, and limited entry regulations. Maintenance of the greatest possible habitat area and prevention of future habitat area reductions will require maintenance of the outlet dam built by beavers. Our study should enhance the long-term viability of the Shoepack Lake muskellunge population and illustrates a useful approach for other unique populations

Post hoc immunostaining of GABAergic neuronal subtypes following in vivo two-photon calcium imaging in mouse neocortex

GABAergic neurons in the neocortex are diverse with regard to morphology, physiology, and axonal targeting pattern, indicating functional specializations within the cortical microcircuitry. Little information is available, however, about functional properties of distinct subtypes of GABAergic neurons in the intact brain. Here, we combined in vivo two-photon calcium imaging in supragranular layers of the mouse neocortex with post hoc immunohistochemistry against the three calcium-binding proteins parvalbumin, calretinin, and calbindin in order to assign subtype marker profiles to neuronal activity. Following coronal sectioning of fixed brains, we matched cells in corresponding volumes of image stacks acquired in vivo and in fixed brain slices. In GAD67-GFP mice, more than 95% of the GABAergic cells could be unambiguously matched, even in large volumes comprising more than a thousand interneurons. Triple immunostaining revealed a depth-dependent distribution of interneuron subtypes with increasing abundance of PV-positive neurons with depth. Most importantly, the triple-labeling approach was compatible with previous in vivo calcium imaging following bulk loading of Oregon Green 488 BAPTA-1, which allowed us to classify spontaneous calcium transients recorded in vivo according to the neurochemically defined GABAergic subtypes. Moreover, we demonstrate that post hoc immunostaining can also be applied to wild-type mice expressing the genetically encoded calcium indicator Yellow Cameleon 3.60 in cortical neurons. Our approach is a general and flexible method to distinguish GABAergic subtypes in cell populations previously imaged in the living animal. It should thus facilitate dissecting the functional roles of these subtypes in neural circuitry

Development of the NIH PROMIS® Sexual Function and Satisfaction Measures in Patients with Cancer

We describe the development and validation of the PROMIS Sexual Function and Satisfaction (PROMIS SexFS) measures version 1.0 for cancer populations

A Compact Multiphoton 3D Imaging System for Recording Fast Neuronal Activity

We constructed a simple and compact imaging system designed specifically for the recording of fast neuronal activity in a 3D volume. The system uses an Yb:KYW femtosecond laser we designed for use with acousto-optic deflection. An integrated two-axis acousto-optic deflector, driven by digitally synthesized signals, can target locations in three dimensions. Data acquisition and the control of scanning are performed by a LeCroy digital oscilloscope. The total cost of construction was one order of magnitude lower than that of a typical Ti:sapphire system. The entire imaging apparatus, including the laser, fits comfortably onto a small rig for electrophysiology. Despite the low cost and simplicity, the convergence of several new technologies allowed us to achieve the following capabilities: i) full-frame acquisition at video rates suitable for patch clamping; ii) random access in under ten microseconds with dwelling ability in the nominal focal plane; iii) three-dimensional random access with the ability to perform fast volume sweeps at kilohertz rates; and iv) fluorescence lifetime imaging. We demonstrate the ability to record action potentials with high temporal resolution using intracellularly loaded potentiometric dye di-2-ANEPEQ. Our design proffers easy integration with electrophysiology and promises a more widespread adoption of functional two-photon imaging as a tool for the study of neuronal activity. The software and firmware we developed is available for download at http://neurospy.org/ under an open source license