TREC 2006 Genomics Track Sample Passages and Aspects

Created by Phoebe Johnson, PhD, Biogen Idec, and formatted by William Hersh, Track Chair

This page contains some sample passages and aspects for two topics for the TREC 2006 Genomics Track.  This data is presented with the following caveats:
Each passage is copied verbatim from the document (as will be done for gold standard passages in the track).  Each group of passages with the same unique set of one or more MeSH terms should be considered an aspect.  This data is also available in an Excel spreadsheet for easier manipulation.

Sample Question 1

This question was derived from topic 128 of the TREC 2005 Genomics Track.  The question for this topic is, How do gamma-aminobutyric acid receptors (GABABRs) inhibit synaptic transmission?

PMID Passage MeSH
9453541 GABA induced an increase in intracellular calcium concentration, indicating the presence of functional receptors for this transmitter. Characterization of the GABA-evoked calcium response and whole-cell currents indicated that these responses were mediated by GABA(A) receptors. Reverse transcription-polymerase chain reaction revealed differential expression of mRNAs for specific GABA(A) receptor subunits. Messages for the alpha2, alpha4, beta1, and delta subunits were readily detected by reverse transcription-polymerase chain reaction, Calcium Signaling; Gene Expression; Neural Conduction
9622011 It is possible that the three GABA(A) receptor subunits (alpha4, beta1, and gamma1) found in precursor cells form the Cl- channels detected electrophysiologically. The functional GABA(A) receptor/Cl- channels and associated regulation of their cytoplasmic Ca2+ levels via bicuculline-sensitive mechanisms may play significant roles in the regulation of neural cell proliferation in this model neuroepithelium. Calcium Signaling; Chloride Channels; Ion Channel Gating
10366626 Biophysical analyses of GABA-activated Cl currents in ZI cells revealed two types of receptor-coupled channel properties: one comprising short-lasting openings, high affinity for GABA, and low sensitivity to diazepam, and the other with long-lasting openings, low affinity for GABA, and high sensitivity to diazepam. Both types of channel activity were found in the same cell. Channel kinetics were well modeled by fitting dwell time distributions to biliganded activation and included two open and five closed states. We propose that short- and long-lasting openings correspond to GABAA receptor/Cl channels containing 412 and 512 subunits, respectively. Chloride Channels; Ion Channel Gating
10493732 Clonazepam augmentation correlated positively with the relative expression of 1- and 2-mRNAs and negatively with 4- and -mRNAs. These data demonstrate that specific GABAR subunit mRNAs exhibit coordinated control of expression in individual DGCs, which has significant impact on inhibitory function. Gene Expression; Dentate Gyrus
11050117 Constitutive Endocytosis of GABAA Receptors by an Association with the Adaptin AP2 Complex Modulates Inhibitory Synaptic Currents in Hippocampal Neurons Hippocampus; Endocytosis
11264309 During migration from the VZ/SVZ to the CP/SP, differentiating cortical neurons became predominantly GABAergic, and their dominant GABAA receptor subunit expression pattern changed from 411 to 3323 coincident with an increasing potency of GABA on GABAA receptor-mediated depolarization. Cell Movement
11489254 alpha4 upregulation was inversely correlated with BDZ potentiation of GABA-gated current, assessed using whole cell patch clamp techniques on acutely isolated hippocampal pyramidal cells. A near total BDZ insensitivity was observed by 2-3 days of hormone exposure in association with the maximal increase in alpha4 levels Hippocampus/drug effects; Gene Expression
12522171 following neuroactive steroid exposure, a subpopulation of synaptic GABARs pharmacologically characterized as 4-containing decay more quickly than BDZ-responsive synaptic currents. Conversely, states that decrease expression of the 4 subunit are characterized by increases in GABAR-mediated Cl flux (Papadeas et al. 2001). Ion Channel Gating
14684873 flumazenil, a partial inverse agonist and antagonist, respectively, in control cells, both acted as positive modulators of GABA responses after discontinuation of prolonged ethanol treatment, consistent with the notion that ethanol withdrawal increases the abundance of GABAA receptors containing the 4 subunit. Ion Channel Gating
14966300 In conclusion, the results presented in this manuscript demonstrate that 4ß22 and 4ß2 receptors are activated by GABA and PB. The strong responses seen in the presence of PB suggest a role for 4 subunit-containing receptors in PB-mediated effects in the mammalian nervous system. The presumed extrasynaptic location of the 4ß2 receptors makes these receptors an attractive target of barbiturates in controlling tonic inhibitory conductance. Phenobarbital; Neural Conduction
15199051 Here we describe the identification and functional characterization of four-amino acid motifs specific for individual subunits of the GABAA receptor, which control the sensitivity to GABA of the resulting receptor. Exchange between subunits of the whole motif but not of single amino acids resulted in transfer of the respective GABA sensitivities for most receptors of the general composition i32, where i ranges from 1 to 6. Thus, our findings may provide insight into the mechanistic features responsible for the molecular diversity of GABAergic neurotransmission and deliver tools to further dissect the biological significance of GABAA receptor heterogeneity. Neural Conduction
8578436 Increasing evidence points to an important role for GABA in epilepsy and various neuropsychiatric disorders. Recent advances in molecular biology and complementary information derived from pharmacology, biochemistry, electrophysiology, anatomy and cell biology, and behavior have led to a phenomenal growth in our understanding of the structure, function, regulation, and evolution of the GABAA receptor. Benzodiazepines, barbiturates, steroids, polyvalent cations, and ethanol act as positive or negative modulators of receptor function. The description of a receptor gene superfamily comprising the subunits of the GABAA, nicotinic acetylcholine, and glycine receptors has led to a new way of thinking about gene expression and receptor assembly in the nervous system. Seventeen genetically distinct subunit subtypes (alpha 1-alpha 6, beta 1-beta 4, gamma 1-gamma 4, delta, p1-p2) and alternatively spliced variants contribute to the molecular architecture of the GABAA receptor. Neuropsychology
9582073 Here we report a progesterone-withdrawal paradigm, designed to mimic PMS and post-partum syndrome in a rat model. In this model, withdrawal of progesterone leads to increased seizure susceptibility and insensitivity to benzodiazepine sedatives through an effect on gene transcription. Specifically, this effect was due to reduced levels of 3alpha,5alpha-THP which enhance transcription of the gene encoding the alpha4 subunit of the GABA(A) receptor. We also find that increased susceptibility to seizure after progesferone withdrawal is due to a sixfold decrease in the decay time for GABA currents and consequent decreased inhibitory function. Blockade of the alpha4 gene transcript prevents these withdrawal properties. PMS symptoms may therefore be attributable, in part, to alterations in expression of GABA(A) receptor subunits as a result of progesterone withdrawal. Premenstrual Syndrome; Seizures; Gene Expression; Progesterone; Neural Conduction
9651210 This withdrawal profile is similar to that reported for other GABAA-modulatory drugs such as the benzodiazepines (BDZs), barbiturates, and ethanol. These changes were also associated with significant two and threefold increases in both the mRNA and protein for the 4 subunit of the GABAA receptor, respectively, in hippocampus. The pseudopregnancy paradigm may be a useful model for periods of endogenous 3,5-THP withdrawal such as premenstrual syndrome and postpartum or postmenopausal dysphoria, when increased emotional lability and BDZ insensitivity have been reported. Gene Expression; Hippocampus; Premenstrual Syndrome; Pseudopregnancy
9685573 Further, no significant differences were found between groups in the mRNA levels for the alpha3 subunit, alpha4 subunit, GAD65, and GAD67. These results suggest that the behaviors related to conflict and uncontrollable aversive stimuli (yoked control group) are accompanied and perhaps mediated by selective changes in the GABAA alpha1 or alpha2 subunits, respectively. Punishment; Conflict (Psychology); Gene Expression
10461213 Disorders of inappropriate or excessive anxiety can be treated with benzodiazepine agonists, such as Valium, which bind to the subunit of the GABAA receptor and increase inhibition. There is considerable evidence for abnormal GABA receptor function in panic disorder9. Anxiety
11489254 Up-regulation of the alpha4 GABAR subunit was also reflected by an increase in anxiety in the elevated plus maze. Anxiety; Gene Expression
11495904 For GABAA receptors containing 4 subunits, our experiments reveal that inclusion of instead of 2 subunits can increase the affinity and in some cases the efficacy of agonists and can increase the efficacy of allosteric modulators. Pregnanolone was a particularly efficacious modulator of 43 receptors, consistent with a central role for this subunit combination in premenstrual syndrome. Premenstrual Syndrome; Gene Expression; Allosteric Regulation
12581182 The sex differences in the ASR were paralleled by sex differences in the expression of the GABAA-R alpha4 subunit in the amygdala such that alpha4 subunit expression was up-regulated in females during PWD whereas alpha4 levels in males undergoing PWD were not altered relative to controls. These findings might have implications regarding gender differences in human mood disorders and the aetiology of premenstrual anxiety. Anxiety; Progesterone; Amygdala
12606703 However, continuous exposure to progesterone increases anxiety in association with increased expression of the Anxiety; Progesterone
12702713 Previous studies in mice with a targeted disruption of the subunit revealed a considerable attenuation of behavioral responses to neuroactive steroids but not to other neuromodulatory drugs. Here we show that subunit loss leads to a concomitant reduction in hippocampal 4 subunit levels. Hippocampus
14960621 In addition, mRNA of the 1, 3, 4, and receptor subunits was reduced in the frontopolar region of suicide victims. Interestingly, a partial analysis of the GABAA receptor functional genome revealed high cross-correlations between subunit expression in cortical regions of nondepressed individuals, suggesting a high degree of coordinated gene regulation. However, in suicide brains, this regulation was perturbed, independent of overall subunit abundance. These findings raise the possibility that the CRH and GABAA receptor subunit changes, or the disturbed coordination between these GABAA receptor subunits, contribute to depression and/or suicidality or are secondary to the illness/distress associated with it. Suicide; Gene Expression
15280440 There were no changes in 4 mRNA levels. Gene Expression
15708482 Increased expression of alpha4beta1delta GABA(A) receptors in the interneurones of the PAG could render the panic circuitry abnormally excitable by disinhibiting the ongoing GABAergic inhibition. Similar changes in neuronal excitability within the PAG in women consequent to falling steroid levels in the late luteal phase of the menstrual cycle could contribute to the development of pre-menstrual dysphoria. Periaqueductal Gray; Gene Expression; Premenstrual Syndrome; Panic

Sample Question 2

This question was derived from topic 149 of the TREC 2005 Genomics Track.  The question for this topic is, How do mutations in the alpha 4-GABAA receptor gene affect behavior?

PMID Passage MeSH
8578436 Increasing evidence points to an important role for GABA in epilepsy and various neuropsychiatric disorders. Recent advances in molecular biology and complementary information derived from pharmacology, biochemistry, electrophysiology, anatomy and cell biology, and behavior have led to a phenomenal growth in our understanding of the structure, function, regulation, and evolution of the GABAA receptor. Benzodiazepines, barbiturates, steroids, polyvalent cations, and ethanol act as positive or negative modulators of receptor function. The description of a receptor gene superfamily comprising the subunits of the GABAA, nicotinic acetylcholine, and glycine receptors has led to a new way of thinking about gene expression and receptor assembly in the nervous system. Seventeen genetically distinct subunit subtypes (alpha 1-alpha 6, beta 1-beta 4, gamma 1-gamma 4, delta, p1-p2) and alternatively spliced variants contribute to the molecular architecture of the GABAA receptor. Neuropsychology
9582073 Here we report a progesterone-withdrawal paradigm, designed to mimic PMS and post-partum syndrome in a rat model. In this model, withdrawal of progesterone leads to increased seizure susceptibility and insensitivity to benzodiazepine sedatives through an effect on gene transcription. Specifically, this effect was due to reduced levels of 3alpha,5alpha-THP which enhance transcription of the gene encoding the alpha4 subunit of the GABA(A) receptor. We also find that increased susceptibility to seizure after progesferone withdrawal is due to a sixfold decrease in the decay time for GABA currents and consequent decreased inhibitory function. Blockade of the alpha4 gene transcript prevents these withdrawal properties. PMS symptoms may therefore be attributable, in part, to alterations in expression of GABA(A) receptor subunits as a result of progesterone withdrawal. Premenstrual Syndrome; Seizures; Gene Expression; Progesterone; Neural Conduction
9651210 This withdrawal profile is similar to that reported for other GABAA-modulatory drugs such as the benzodiazepines (BDZs), barbiturates, and ethanol. These changes were also associated with significant two and threefold increases in both the mRNA and protein for the 4 subunit of the GABAA receptor, respectively, in hippocampus. The pseudopregnancy paradigm may be a useful model for periods of endogenous 3,5-THP withdrawal such as premenstrual syndrome and postpartum or postmenopausal dysphoria, when increased emotional lability and BDZ insensitivity have been reported. Gene Expression; Hippocampus; Premenstrual Syndrome; Pseudopregnancy
9685573 Further, no significant differences were found between groups in the mRNA levels for the alpha3 subunit, alpha4 subunit, GAD65, and GAD67. These results suggest that the behaviors related to conflict and uncontrollable aversive stimuli (yoked control group) are accompanied and perhaps mediated by selective changes in the GABAA alpha1 or alpha2 subunits, respectively. Punishment; Conflict (Psychology); Gene Expression
10461213 Disorders of inappropriate or excessive anxiety can be treated with benzodiazepine agonists, such as Valium, which bind to the subunit of the GABAA receptor and increase inhibition. There is considerable evidence for abnormal GABA receptor function in panic disorder9. Anxiety
11489254 Up-regulation of the alpha4 GABAR subunit was also reflected by an increase in anxiety in the elevated plus maze. Anxiety; Gene Expression
11495904 For GABAA receptors containing 4 subunits, our experiments reveal that inclusion of instead of 2 subunits can increase the affinity and in some cases the efficacy of agonists and can increase the efficacy of allosteric modulators. Pregnanolone was a particularly efficacious modulator of 43 receptors, consistent with a central role for this subunit combination in premenstrual syndrome. Premenstrual Syndrome; Gene Expression; Allosteric Regulation
12581182 The sex differences in the ASR were paralleled by sex differences in the expression of the GABAA-R alpha4 subunit in the amygdala such that alpha4 subunit expression was up-regulated in females during PWD whereas alpha4 levels in males undergoing PWD were not altered relative to controls. These findings might have implications regarding gender differences in human mood disorders and the aetiology of premenstrual anxiety. Anxiety; Progesterone; Amygdala
12606703 However, continuous exposure to progesterone increases anxiety in association with increased expression of the Anxiety; Progesterone
12702713 Previous studies in mice with a targeted disruption of the subunit revealed a considerable attenuation of behavioral responses to neuroactive steroids but not to other neuromodulatory drugs. Here we show that subunit loss leads to a concomitant reduction in hippocampal 4 subunit levels. Hippocampus
14960621 In addition, mRNA of the 1, 3, 4, and receptor subunits was reduced in the frontopolar region of suicide victims. Interestingly, a partial analysis of the GABAA receptor functional genome revealed high cross-correlations between subunit expression in cortical regions of nondepressed individuals, suggesting a high degree of coordinated gene regulation. However, in suicide brains, this regulation was perturbed, independent of overall subunit abundance. These findings raise the possibility that the CRH and GABAA receptor subunit changes, or the disturbed coordination between these GABAA receptor subunits, contribute to depression and/or suicidality or are secondary to the illness/distress associated with it. Suicide; Gene Expression
15280440 There were no changes in 4 mRNA levels. Gene Expression
15708482 Increased expression of alpha4beta1delta GABA(A) receptors in the interneurones of the PAG could render the panic circuitry abnormally excitable by disinhibiting the ongoing GABAergic inhibition. Similar changes in neuronal excitability within the PAG in women consequent to falling steroid levels in the late luteal phase of the menstrual cycle could contribute to the development of pre-menstrual dysphoria. Periaqueductal Gray; Gene Expression; Premenstrual Syndrome; Panic

Last updated May 29, 2006 by William Hersh.