MBAT: A scalable informatics system for unifying digital atlasing workflows

Background  

Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data.     

Cross-connections coordinate postural motoneuron activity in the crayfish abdomen

Intracellular recordings and dye injections were used to examine mutual coupling among slow abdominal postural motoneurons in the 4th abdominal ganglion in crayfish (Procambarus clarkii). Intracellular current injection into one motoneuron altered the spike firing rate of some of its synergists. Depending on the polarity of the injected current, the premotor effect on the synergists was excitatory or inhibitory. The magnitude of the effect was intensity dependent. No dye coupling was found among the motoneurons following injection of Lucifer yellow. The morphological basis of the coupling was examined by differential filling of motoneuron pairs, one with horseradish peroxidase and the other with Lucifer yellow. The stained motoneurons were simultaneously visualized under light microscopy to determine the proximity of their differently colored dendrites. It was thus possible to locate the site of the presumed monosynaptic contacts between them. Combined physiological and morphological evidence suggests that these neurons are mutually coupled, forming part of an integrative system for abdominal posture control in crayfish.     

Physiological and developmental implications of motor unit anatomy

There is increasing evidence that the architectural design and arrangement of the fibers within a motor unit have important physiological and developmental ramifications. Limited data, however, are available to directly address this issue. In the present study the physiological properties of one motor unit in each of seven cat tibialis anterior (TA) muscles were determined. Each of these units then was repetitively stimulated to deplete the glycogen in all muscle fibers within the unit. Subsequently, the length, type of ending, and spatial distribution of fibers sampled from these physiologically and histochemically typed motor units were determined. Four fast fatigable (FF), one fast, fatigue resistant (FR), and two slow (S) motor units (MU) were studied. The samples consisted of all those glycogen-depleted fibers (9-27) contained within a single fascicle or a circumscribed area of each of the motor unit territories. The mean fiber lengths for the two slow motor units were 35.9 and 45.5 mm. The mean fiber lengths for the fast motor unit samples ranged from 8.8 to 48.5 mm. Some fibers of both the fast and slow units reached lengths of 58 mm. Most of the fibers in the slow units extended the entire distance between the proximal and distal musculotendinous planes, had relatively constant cross-sectional areas, and terminated at the tendon as blunt endings. In contrast, the majority of the fibers in the fast units terminated intrafascicularly at one end, and the cross-sectional area decreased progressively along their lengths, that is, showed a tapering pattern for a significant proportion of their lengths. Therefore, the force generated by units that end midfascicularly would appear to be transmitted to connective tissue elements and/or adjacent fibers. All fibers of a fast unit within a fascicle were located at approximately the same proximo-distal location. Thus, developmentally the selection of muscle fibers by a motoneuron would seem to be influenced by their spatial distribution. The architectural complexities of motor units also have clear implications for the mechanical interactions of active and inactive motor units. For example, the tension capabilities of a motor unit may be influenced not only by the spatial arrangement of its own fibers, but also by the level of activation of neighboring motor units.     

Linear and nonlinear relationships between neuronal activity, oxygen metabolism, and hemodynamic responses

We investigated the relationship between neuronal activity, oxygen metabolism, and hemodynamic responses in rat somatosensory cortex with simultaneous optical intrinsic signal imaging and spectroscopy, laser Doppler flowmetry, and local field potential recordings. Changes in cerebral oxygen consumption increased linearly with synaptic activity but with a threshold effect consistent with the existence of a tissue oxygen buffer. Modeling analysis demonstrated that the coupling between neuronal activity and hemodynamic response magnitude may appear linear over a narrow range but incorporates nonlinear effects that are better described by a threshold or power law relationship. These results indicate that caution is required in the interpretation of perfusion-based indicators of brain activity, such as functional magnetic resonance imaging (fMRI), and may help to refine quantitative models of neurovascular coupling.     

Malnutrition impairs alveolar fluid clearance in rat lungs

Inadequate nutrition complicates the clinical course of critically ill patients, and many of these patients develop pulmonary edema. However, little is known about the effect of malnutrition on the mechanisms that resolve alveolar edema. Therefore, we studied the mechanisms responsible for the decrease in alveolar fluid clearance in rats exposed to malnutrition. Rats were allowed access to water, but not to food, for 120 h. Then, the left and right lungs were isolated for the measurement of lung water volume and alveolar fluid clearance, respectively. The rate of alveolar fluid clearance was measured by the progressive increase in the concentration of Evans blue dye that was instilled into the distal air spaces with an isosmolar 5% albumin solution over 1 h. Malnutrition decreased alveolar fluid clearance by 38% compared with controls. Amiloride (10(-3) M) abolished alveolar fluid clearance in malnourished rats. Either refeeding for 120 h following nutritional deprivation for 120 h or an oral supply of sodium glutamate during nutritional deprivation for 120 h restored alveolar fluid clearance to 91 and 86% of normal, respectively. Dibutyryl-cGMP, a cyclic nucleotide-gated cation channel agonist, increased alveolar fluid clearance in malnourished rats supplied with sodium glutamate. Terbutaline, a beta(2)-adrenergic agonist, increased alveolar fluid clearance in rats under all conditions (control, malnutrition, refeeding, and glutamate-treated). These results indicate that malnutrition impairs primarily amiloride-insensitive and dibutyryl-cGMP-sensitive alveolar fluid clearance, but this effect is partially reversible by refeeding, treatment with sodium glutamate, or beta-adrenergic agonist therapy.     

Expression and characterization of Rab38, a new member of the Rab small G protein family

Rab38 is a new member of the Rab small G protein family that regulates intracellular vesicle trafficking. Rab38 is expressed in melanocytes and it has been clarified that a point mutation in the postulated GTP-binding domain of Rab38 is the gene responsible for oculocutaneous albinism in chocolate mice. However, basic information regarding recombinant protein production, intracellular location, and tissue-specific expression pattern has not yet been reported. We produced recombinant Rab38 using a baculovirus/insect cell-protein expression system. A combination of Triton X-114 phase separation and nickel-affinity chromatography yielded exclusively prenylated Rab38 that bound [alpha-32P]-GTP. The mRNA and the native protein were expressed in a tissue-specific manner, e.g., in the lung, skin, stomach, liver, and kidney. Freshly isolated rat alveolar type II cells were highly positive for the mRNA signal, but the signal was rapidly lost over time. Immunofluorescence staining demonstrated that expressed GST-tagged Rab38 was mainly co-localized with endoplasmic reticulum-resident protein and also partly with intermittent vesicles between the endoplasmic reticulum and the Golgi complex. These results indicate that Rab38 is expressed non-ubiquitously in specific tissues and regulates early vesicle transport relating to the endoplasmic reticulum, and hence suggest that Rab38 abnormality may cause multiple organ diseases as well as oculocutaneous albinism.     

Expression and function of a limb‐patterning gene Distal‐less in the soldier‐specific morphogenesis in the nasute termite Nasutitermes takasagoensis

One of the major foci in evolutionary developmental biology is to understand developmental mechanisms that underlie the acquisition of morphological novelties. Termite soldiers, the highly specialized defensive caste, show exaggerated species‐specific morphologies, mostly enlarged mandibles. Soldiers of the subfamily Nasutitermitinae (Termitidae), however, possess a novel structure for defense in their heads, that is a horn‐like frontal projection (nasus) from which defensive chemicals are discharged. Just prior to the molt into presoldiers (the preceding stage to soldiers) from workers, a nasus disc, or a nasus primordium, is observed under the worker head cuticle. In order to understand the developmental underpinnings of this evolutionarily novel structure, the role of a homeobox gene Distal‐less (Dll) during nasus development was examined in this study, using a nasute termite Nasutitermes takasagoensis. Histological observations showed that complex developmental processes comprising epidermal evagination and invagination through changes in cell shape and cell proliferation formed the projection and the gland. Immunohistochemistry showed that Dll was localized in the developing nasus disc, but not in the frontal‐gland primordium. Consistent with this finding, Dll RNA interference only repressed nasus growth not the frontal‐gland formation. Taken together, the co‐option of Dll is suggested to contribute to the acquisition of a novel defensive structure in a termite lineage, coupled with the acquisition of adaptive defensive behaviors.     

Mouth pressure curve on abrupt interruption of airflow during forced expiration

An attempt was made to investigate how the mouth pressure curve represents the process of air flowing into the collapsed segment downstream to the choke point when the airflow is abruptly interrupted at the mouth during forced expiration. Immediately after the interruption of airflow, the mouth pressure suddenly increased (phase 1), followed by a slower rise in pressure (phase 2) within approximately 100 ms until the pressure reached the alveolar pressure. The pleural and alveolar pressures remained constant during this process. The first phase of the abrupt rise represented the pressure induced by the instantaneous interruption of the airflow itself. Analysis of the supramaximal flow (Vsupramax) observed after resumption of the airflow suggested that the choke point remained constant during the second phase of the mouth pressure after interruption of maximal flow (Vmax). From these results, examination of the second phase of the mouth pressure curve may provide useful information about the downstream segment of the airway.