Biogeochemical dynamics in the vadose zone are poorly understood due to the transient nature of chemical and hydrologic conditions, but are nonetheless critical to understanding chemical fate and transport. This study explored the effects of a soil layer on linked geochemical, hydrological, and microbiological processes. Three laboratory soil columns were constructed: a homogenized medium-grained sand, a homogenized organic-rich loam, and a sand-over-loam layered column. Upward and downward infiltration of water was evaluated during experiments to simulate rising water table and rainfall events respectively. In-situ collocated probes measured soil water content, matric potential, and Eh while water samples collected from the same locations were analyzed for Br−, Cl−, NO3−, SO42−, NH4+, Fe2+, and total sulfide. Compared to homogenous columns, the presence of a soil layer altered the biogeochemistry and water flow of the system considerably. Enhanced biogeochemical cycling was observed in the layered column over the texturally homogeneous soil columns. Enumerations of iron and sulfate reducing bacteria showed 1-2 orders of magnitude greater community numbers in the layered column. Mineral and soil aggregate composites were most abundant near the soil-layer interface; the presence of which, likely contributed to an observed order-of-magnitude decrease in hydraulic conductivity. These findings show that quantifying coupled hydrologic-biogeochemical processes occurring at small-scale soil interfaces is critical to accurately describing and predicting chemical changes at the larger system scale. Findings also provide justification for considering soil layering in contaminant fate and transport models because of its potential to increase biodegradation and/or slow the rate of transport of contaminants.
The human neocortex is increased in size and complexity as compared to most other species. Neocortical expansion has recently been attributed to protracted neurogenesis by outer radial glial (oRG) cells in the outer subventricular zone (oSVZ), a region present in humans but not in rodents. The mechanisms of human oRG cell generation are unknown, but are proposed to involve division of ventricular radial glial (vRG) cells; neural stem cells present in all developing mammals. Here we show that human vRG cells produce oRG cells and seed formation of the oSVZ via horizontal divisions, which occur more frequently in humans than in rodents. We further find that oRG cell mitotic behavior is cell intrinsic, and that the basal fiber, inherited by oRG cells after vRG division, determines cleavage angle. Our results suggest that altered regulation of mitotic spindle orientation increased oRG cell numbers, and ultimately neuronal numbers, during human brain evolution.
The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. While many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified over 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising over 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.
Improving academic achievement and reducing the rates of obesity in elementary school students are both of considerable interest. Increased physical activity during academic instruction time during school offers a potential intervention to address both issues. A program titled “Physical Activity Across the Curriculum” (PAAC) was developed in which classroom teachers in 22 elementary schools were trained to deliver academic instruction using physical activity with a primary aim of preventing increased BMI. A secondary analysis of data assessed the impact of PAAC on academic achievement using the Weschler Individual Achievement Test-II and significant improvements were shown for reading, math and spelling in students who participated in PAAC. Based on the results from PAAC, an adequately powered trial will be conducted to assess differences in academic achievement between intervention and control schools called, “Academic Achievement and Physical Activity Across the Curriculum (A + PAAC).”
Seventeen elementary schools were cluster randomized to A + PAAC or control for a 3-year trial. Classroom teachers were trained to deliver academic instruction through moderate-to-vigorous physical activity with a target of 100+ minutes of A + PAAC activities per week. The primary outcome measure is academic achievement measured by the Weschler Individual Achievement Test-III, which was administered at baseline (Fall 2011) and will be repeated in the spring of each year by assessors blinded to condition. Potential mediators of any association between A + PAAC and academic achievement will be examined on the same schedule and include changes in cognitive function, cardiovascular fitness, daily physical activity, BMI, and attention-to-task. An extensive process analysis will be conducted to document the fidelity of the intervention. School and student recruitment/randomization, teacher training, and baseline testing for A + PAAC have been completed. Nine schools were randomized to the intervention and 8 to control. A random sample of students in each school, stratified by gender and grade (A + PAAC = 370, Control = 317), was selected for outcome assessments from those who provided parental consent/child assent. Baseline data by intervention group are presented.
If successful, the A + PAAC approach could be easily and inexpensively scaled and disseminated across elementary schools to improve both educational quality and health. Funding source: R01- DK85317. Trial registration: US NIH Clinical Trials, http://NCT01699295.
Physical activity; Children; Academic achievement; Cluster-randomized trial; Cognitive function; Fitness; Attention to task
The size and surface area of the mammalian brain are thought to be critical determinants of intellectual ability. Recent studies show that development of the gyrated human neocortex involves a lineage of neural stem and transit-amplifying cells that forms the outer subventricular zone (OSVZ), a proliferative region outside the ventricular epithelium. We discuss how proliferation of cells within the OSVZ expands the neocortex by increasing neuron number and modifying the trajectory of migrating neurons. Relating these features to other mammalian species and known molecular regulators of the mouse neocortex suggests how this developmental process could have emerged in evolution.
The human cerebral cortex is an immensely complex structure that subserves critical functions that can be disrupted in developmental and degenerative disorders. Recent innovations in cellular reprogramming and differentiation techniques have provided new ways to study the cellular components of the cerebral cortex. Here we discuss approaches to generate specific subtypes of excitatory cortical neurons from pluripotent stem cells. We review spatial and temporal aspects of cortical neuron specification that can guide efforts to produce excitatory neuron subtypes with increased resolution. Finally, we discuss distinguishing features of human cortical development and their translational ramifications for cortical stem cell technologies.
Ventral tegmental area (VTA) GABA neurons appear to be critical substrates underlying the acute and chronic effects of ethanol on dopamine (DA) neurotransmission in the mesocorticolimbic system implicated in alcohol reward. The aim of this study was to examine the role of midbrain connexin-36 (Cx36) gap junctions (GJs) in ethanol’s rewarding effects. Using behavioral, molecular and electrophysiological methods we compared the effects of ethanol in mature Cx36 knockout (KO) mice and age-matched wild-type (WT) controls. Cx36 KO mice exhibited significantly more ethanol-induced ataxia in the open field test, but less disruption in motor coordination than their WT controls in the rotarod paradigm. Cx36 KO mice and WT mice treated with the Cx36 antagonist mefloquine (MFQ) consumed significantly less ethanol than their vehicle-treated WT controls in the drink-in-the-dark procedure. The firing rate of VTA GABA neurons in WT mice was inhibited by ethanol with an IC50 of 0.25 g/kg, while VTA GABA neurons in KO mice were significantly less sensitive to ethanol. Dopamine neuron sIPSC frequency was reduced by ethanol (30 mM) in WT mice, but not affected in KO mice. Cx36 KO mice evinced a significant up-regulation in DAT and D2 receptors in the VTA, as assessed by quantitative RT-PCR. These findings demonstrate the behavioral relevance of Cx36 GJ-mediated electrical coupling between GABA neurons in mature animals, and suggest that loss of coupling between VTA GABA neurons results in disinhibition of DA neurons, a hyper-DAergic state and lowered hedonic valence for ethanol consumption.
Tissues that generate specialized cell-types in a production line must coordinate developmental mechanisms with physiological demand, although how this occurs is largely unknown. In the C. elegans hermaphrodite, the developmental sex-determination cascade specifies gamete sex in the distal germline, while physiological sperm signaling activates MPK-1/ERK in the proximal germline to control plasma membrane biogenesis/organization during oogenesis. We discovered repeated utilization of a self-contained negative regulatory module, consisting of NOS-3 translational repressor, FEM-CUL-2 (E3 ubiquitin ligase) and TRA-1 (Gli transcriptional repressor), which acts both in sex-determination and in physiological demand control of oogenesis, coordinating these processes. In the distal germline, where MPK-1 is not activated, TRA-1 represses the male fate as NOS-3 functions in translational repression leading to inactivation of the FEM-CUL-2 ubiquitin ligase. In the proximal germline, sperm-dependent physiological MPK-1 activation results in phosphorylation-based inactivation of NOS-3, FEM-CUL-2 mediated degradation of TRA-1 and the promotion of membrane organization during oogenesis.
Withdrawal from chronic ethanol enhances ventral tegmental area (VTA) GABA neuron excitability and reduces mesolimbic dopamine (DA) neurotransmission, which is suppressed by acupuncture at Shenmen (HT7) points (Zhao et al., 2006). The aim of this study was to evaluate the effects of HT7 acupuncture on VTA GABA neuron excitability, ethanol inhibition of VTA GABA neuron firing rate, and ethanol self-administration. A role for opioid receptors (ORs) in ethanol and acupuncture effects is also explored.
Using electrophysiological methods in mature rats, we evaluated the effects of HT7 stimulation and opioid antagonists on VTA GABA neuron firing rate. Using behavioral paradigms in rats, we evaluated the effects of HT7 stimulation and opioid antagonists on ethanol self-administration using a modification of the sucrose fading procedure.
HT7 stimulation produced a biphasic modulation of VTA GABA neuron firing rate characterized by transient enhancement followed by inhibition and subsequent recovery in 5 min. HT7 inhibition of VTA GABA neuron firing rate was blocked by systemic administration of the non-selective μ-opioid receptor (MOR) antagonist naloxone. HT7 stimulation significantly reduced ethanol suppression of VTA GABA neuron firing rate, which was also blocked by naloxone. HT7 acupuncture reduced ethanol self-administration without affecting sucrose consumption. Systemic administration of the δ-opioid receptor (DOR) antagonist naltrindole blocked ethanol suppression of VTA GABA neuron firing rate and significantly reduced ethanol self-administration without affecting sucrose consumption.
These findings suggest that DOR-mediated opioid modulation of VTA GABA neurons may mediate acupuncture’s role in modulating mesolimbic DA release and suppressing the reinforcing effects of ethanol.
GABA; opioid; VTA; ethanol; acupuncture; dopamine
To classify automatically lung tumor–node–metastases (TNM) cancer stages from free-text pathology reports using symbolic rule-based classification.
By exploiting report substructure and the symbolic manipulation of systematized nomenclature of medicine–clinical terms (SNOMED CT) concepts in reports, statements in free text can be evaluated for relevance against factors relating to the staging guidelines. Post-coordinated SNOMED CT expressions based on templates were defined and populated by concepts in reports, and tested for subsumption by staging factors. The subsumption results were used to build logic according to the staging guidelines to calculate the TNM stage.
The accuracy measure and confusion matrices were used to evaluate the TNM stages classified by the symbolic rule-based system. The system was evaluated against a database of multidisciplinary team staging decisions and a machine learning-based text classification system using support vector machines.
Overall accuracy on a corpus of pathology reports for 718 lung cancer patients against a database of pathological TNM staging decisions were 72%, 78%, and 94% for T, N, and M staging, respectively. The system's performance was also comparable to support vector machine classification approaches.
A system to classify lung TNM stages from free-text pathology reports was developed, and it was verified that the symbolic rule-based approach using SNOMED CT can be used for the extraction of key lung cancer characteristics from free-text reports. Future work will investigate the applicability of using the proposed methodology for extracting other cancer characteristics and types.
Patients presenting to Emergency Departments may be categorised into different symptom groups for the purpose of research and quality improvement. The grouping is challenging due to the variability in the way presenting complaints are recorded by clinical staff. This work proposes analysis of the presenting complaint free-text using the semantics encoded in the SNOMED CT ontology. This work demonstrates a validated prototype system that can classify unstructured free-text narratives into patient’s symptom group. A rule-based mechanism was developed using variety of keywords to identify the patient’s symptom group. The system was validated against the manual identification of the symptom groups by two expert clinical research nurses on 794 patient presentations from six participating hospitals. The comparison of system results with one clinical research nurse showed 99.3% sensitivity; 80.0% specificity and 0.9 F-score for identifying “chest pain” symptom group.
Ventral tegmental area (VTA) γ-aminobutyric acid (GABA) neurons appear to be critical substrates underlying the acute and chronic effects of ethanol on dopamine (DA) neurotransmission in the mesocorticolimbic system implicated in drug reward. VTA GABA neuron firing rate is reduced by acute ethanol and enhanced by DA via D2 receptor activation. The objective of this study was to evaluate the role of D2 receptors in acute ethanol inhibition of VTA GABA neuron activity, as well as the adaptation of D2 receptors by chronic ethanol consumption.
Using electrophysiological methods, we evaluated the effects of intraperitoneal ethanol on DA activation of VTA GABA neurons, the effects of DA antagonists on ethanol inhibition of their firing rate, as well as adaptations in firing rate following chronic ethanol consumption. Using single cell quantitative RT-polymerase chain reaction (PCR), we evaluated the expression of VTA GABA neuron D2 receptors in rats consuming ethanol versus pair-fed controls.
In acute ethanol studies, microelectrophoretic activation of VTA GABA neurons by DA was inhibited by acute intraperitoneal ethanol, and intravenous administration of the D2 antagonist eticlopride blocked ethanol suppression of VTA GABA neuron firing rate. In chronic ethanol studies, while there were no signs of withdrawal at 24 hours, or significant adaptation in firing rate or response to acute ethanol, there was a significant down-regulation in the expression of D2 receptors in ethanol-consuming rats versus pair-fed controls.
Inhibition of DA activation of VTA GABA neuron firing rate by ethanol, as well as eticlopride block of ethanol inhibition of VTA GABA neuron firing rate, suggests an interaction between ethanol and DA neurotransmission via D2 receptors, perhaps via enhanced DA release in the VTA subsequent to ethanol inhibition of GABA neurons. Down-regulation of VTA GABA neuron D2 receptors by chronic ethanol might result from persistent DA release onto GABA neurons.
GABA; VTA; Ethanol; D2 Receptors; Adaptation; Dopamine
Ventral tegmental area (VTA) GABA neurons appear to be critical regulators of mesocorticolimbic dopamine (DA) neurotransmission, which has been implicated in alcohol reward. The aim of this study was to evaluate the effects of low-dose “non-contingent” intravenous (IV) ethanol (0.01–0.1 g/kg) on VTA GABA neuron firing rate and synaptic responses, as well as VTA GABA neuron firing rate during low-dose “contingent” IV ethanol self-administration. Intravenous administration of 0.01–0.03 g/kg ethanol significantly increased VTA GABA neuron firing rate and afferent-evoked synaptic responses. In the runway self-administration paradigm, presentation of an olfactory cue (S+; almond extract) or no-cue (S−; no odor) in the Start box was paired with IV administration of low-dose ethanol (0.01 g/kg) or saline in the Target box. Runway excursion times decreased significantly in association during S+, and increased significantly during S− conditions. The firing rate of VTA GABA neurons markedly increased when rats received 0.01 g/kg IV ethanol in the Target box. VTA GABA neuron firing increased in the Start box of the runway in association with S+, but not S−. These findings demonstrate that VTA GABA neurons are activated by low-dose IV ethanol and that their firing rate increases in anticipation of ethanol reward.
self-administration; GABA; ventral tegmental area; runway; reward; ethanol
The transition of oocytes from meiosis I (MI) to meiosis II (MII) requires partial cyclin B degradation to allow MI exit without S phase entry. Rapid reaccumulation of cyclin B allows direct progression into MII, producing a cytostatic factor (CSF)-arrested egg. It has been reported that dampened translation of the anaphase-promoting complex (APC) inhibitor Emi2 at MI allows partial APC activation and MI exit. We have detected active Emi2 translation at MI and show that Emi2 levels in MI are mainly controlled by regulated degradation. Emi2 degradation in MI depends not on Ca2+/calmodulin-dependent protein kinase II (CaMKII), but on Cdc2-mediated phosphorylation of multiple sites within Emi2. As in MII, this phosphorylation is antagonized by Mos-mediated recruitment of PP2A to Emi2. Higher Cdc2 kinase activity in MI than MII allows sufficient Emi2 phosphorylation to destabilize Emi2 in MI. At MI anaphase, APC-mediated degradation of cyclin B decreases Cdc2 activity, enabling Cdc2-mediated Emi2 phosphorylation to be successfully antagonized by Mos-mediated PP2A recruitment. These data suggest a model of APC autoinhibition mediated by stabilization of Emi2; Emi2 proteins accumulate at MI exit and inhibit APC activity sufficiently to prevent complete degradation of cyclin B, allowing MI exit while preventing interphase before MII entry.
To independently assess the contribution of ground-state pseudoallylic strain to the enormous rates of amide bond cleavage in tertiary amide derivatives of Kemp’s triacid, we have studied four amide derivatives of (1α-3α-5β)-5-t-butyl-1,3-cyclohexanedicarboxylic acid. Our results confirm that absent pseudoallylic strain, a 1,3-diaxial interaction of an amide with a carboxylic acid leads to only a 2,400-fold increase in the rate of amide bond cleavage as compared with the rate of hydrolysis of an unactivated peptide bond.
Polymer hydrogels synthesized by crosslinking poly(allylamine hydrochloride) with (±)-epichlorohydrin in the presence of D-glucose-6-phosphate monobarium salt do not show imprinting on the molecular level. A series of hydrogels were prepared using the following five templates: D-glucose-6-phosphate monobarium salt, D-glucose, L-glucose, barium hydrogen phosphate (BaHPO4), and D-gluconamide; a hydrogel was also prepared in the absence of a template. For all six hydrogels, batch binding studies were conducted with D-glucose, L-glucose, D-fructose and D-gluconamide. The extent of analyte sugar binding was determined using 1H-NMR. Each hydrogel shows approximately the same relative binding affinity for the different sugar derivatives, and none displays selectivity for either glucose enantiomer. The results of the binding studies correlate with the octanol-water partition coefficients of the sugars, indicative that differential solubilities in the bulk polymer account for the binding affinities observed. Thus, in contrast to templated hydrogels prepared using methacrylate- or acrylamide-based reagents, true imprinting does not occur in this novel, crosslinked-poly(allylamine hydrochloride) system.
During interkinesis, a metaphase II (MetII) spindle is built immediately after the completion of meiosis I. Oocytes then remain MetII arrested until fertilization. In mouse, we find that early mitotic inhibitor 2 (Emi2), which is an anaphase-promoting complex inhibitor, is involved in both the establishment and the maintenance of MetII arrest. In MetII oocytes, Emi2 needs to be degraded for oocytes to exit meiosis, and such degradation, as visualized by fluorescent protein tagging, occurred tens of minutes ahead of cyclin B1.
Emi2 antisense morpholino knockdown during oocyte maturation did not affect polar body (PB) extrusion. However, in interkinesis the central spindle microtubules from meiosis I persisted for a short time, and a MetII spindle failed to assemble. The chromatin in the oocyte quickly decondensed and a nucleus formed. All of these effects were caused by the essential role of Emi2 in stabilizing cyclin B1 after the first PB extrusion because in Emi2 knockdown oocytes a MetII spindle was recovered by Emi2 rescue or by expression of nondegradable cyclin B1 after meiosis I.
Progression through mitosis requires activation of cyclin B/Cdk1 and its downstream targets, including Polo-like kinase and the anaphase-promoting complex (APC), the ubiquitin ligase directing degradation of cyclins A and B. Recent evidence shows that APC activation requires destruction of the APC inhibitor Emi1. In prophase, phosphorylation of Emi1 generates a D-pS-G-X-X-pS degron to recruit the SCFβTrCP ubiquitin ligase, causing Emi1 destruction and allowing progression beyond prometaphase, but the kinases directing this phosphorylation remain undefined. We show here that the polo-like kinase Plk1 is strictly required for Emi1 destruction and that overexpression of Plk1 is sufficient to trigger Emi1 destruction. Plk1 stimulates Emi1 phosphorylation, βTrCP binding, and ubiquitination in vitro and cyclin B/Cdk1 enhances these effects. Plk1 binds to Emi1 in mitosis and the two proteins colocalize on the mitotic spindle poles, suggesting that Plk1 may spatially control Emi1 destruction. These data support the hypothesis that Plk1 activates the APC by directing the SCF-dependent destruction of Emi1 in prophase.