Influenza sequence validation and annotation using VADR.

Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLAN has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions, and has been publicly available as a webserver but not as a standalone tool. VADR is a general sequence validation and annotation software package used by GenBank for Norovirus, Dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool. We have created VADR influenza models based on the FLAN reference sequences and adapted VADR to accurately annotate influenza sequences. VADR and FLAN show consistent results on the vast majority of influenza sequences, and when they disagree VADR is usually correct. VADR can also accurately process influenza D sequences as well as influenza A H17, H18, H19, N10 and N11 subtype sequences, which FLAN cannot. VADR 1.6.3 and the associated influenza models are now freely available for users to download and use.

Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank.

Rapid response to the current coronavirus disease 2019 (COVID-19) pandemic requires fast dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data in order to align diagnostic tests and vaccines with the natural evolution of the virus as it spreads through the world. To facilitate this, the National Library of Medicine's National Center for Biotechnology Information developed an automated pipeline for the deposition and quick processing of SARS-CoV-2 genome assemblies into GenBank for the user community. The pipeline ensures the collection of contextual information about the virus source, assesses sequence quality and annotates descriptive biological features, such as protein-coding regions and mature peptides. The process promotes standardized nomenclature and creates and publishes fully processed GenBank files within minutes of deposition. The software has processed and published 982 454 annotated SARS-CoV-2 sequences, as of 21 October 2021. This development addresses the needs of the scientific community as the sequencing of SARS-CoV-2 genomes increases and will facilitate unrestricted access to and usability of SARS-CoV-2 genomic sequence data, providing important reagents for scientific and public health activities in response to the COVID-19 pandemic. Database URL https://submit.ncbi.nlm.nih.gov/sarscov2/genbank/.

Cortical thickness across the lifespan: Data from 17,075 healthy individuals aged 3-90 years.

Delineating the association of age and cortical thickness in healthy individuals is critical given the association of cortical thickness with cognition and behavior. Previous research has shown that robust estimates of the association between age and brain morphometry require large-scale studies. In response, we used cross-sectional data from 17,075 individuals aged 3-90 years from the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium to infer age-related changes in cortical thickness. We used fractional polynomial (FP) regression to quantify the association between age and cortical thickness, and we computed normalized growth centiles using the parametric Lambda, Mu, and Sigma method. Interindividual variability was estimated using meta-analysis and one-way analysis of variance. For most regions, their highest cortical thickness value was observed in childhood. Age and cortical thickness showed a negative association; the slope was steeper up to the third decade of life and more gradual thereafter; notable exceptions to this general pattern were entorhinal, temporopolar, and anterior cingulate cortices. Interindividual variability was largest in temporal and frontal regions across the lifespan. Age and its FP combinations explained up to 59% variance in cortical thickness. These results may form the basis of further investigation on normative deviation in cortical thickness and its significance for behavioral and cognitive outcomes.

Subcortical volumes across the lifespan: Data from 18,605 healthy individuals aged 3-90 years.

Age has a major effect on brain volume. However, the normative studies available are constrained by small sample sizes, restricted age coverage and significant methodological variability. These limitations introduce inconsistencies and may obscure or distort the lifespan trajectories of brain morphometry. In response, we capitalized on the resources of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium to examine age-related trajectories inferred from cross-sectional measures of the ventricles, the basal ganglia (caudate, putamen, pallidum, and nucleus accumbens), the thalamus, hippocampus and amygdala using magnetic resonance imaging data obtained from 18,605 individuals aged 3-90 years. All subcortical structure volumes were at their maximum value early in life. The volume of the basal ganglia showed a monotonic negative association with age thereafter; there was no significant association between age and the volumes of the thalamus, amygdala and the hippocampus (with some degree of decline in thalamus) until the sixth decade of life after which they also showed a steep negative association with age. The lateral ventricles showed continuous enlargement throughout the lifespan. Age was positively associated with inter-individual variability in the hippocampus and amygdala and the lateral ventricles. These results were robust to potential confounders and could be used to examine the functional significance of deviations from typical age-related morphometric patterns.

Personalized estimates of morphometric similarity in bipolar disorder and schizophrenia.

Bipolar disorder and schizophrenia are associated with brain morphometry alterations. This study investigates inter-individual variability in brain structural profiles, both within diagnostic groups and between patients and healthy individuals. Brain morphometric measures from three independent samples of patients with schizophrenia (n = 168), bipolar disorder (n = 122), and healthy individuals (n = 180) were modeled as single vectors to generated individualized profiles of subcortical volumes and regional cortical thickness. These profiles were then used to compute a person-based similarity index (PBSI) for subcortical volumes and for regional cortical thickness, to quantify the within-group similarity of the morphometric profile of each individual to that of the other participants in the same diagnostic group. There was no effect of diagnosis on the PBSI for subcortical volumes. In contrast, compared to healthy individuals, the PBSI for cortical thickness was lower in patients with schizophrenia (effect size = 0.4, p ≤ 0.0002), but not in patients with bipolar disorder. The results were robust and reproducible across samples. We conclude that disease mechanisms for these disorders produce modest inter-individual variations in brain morphometry that should be considered in future studies attempting to cluster patients in subgroups.

Data-driven approaches for identifying links between brain structure and function in health and disease.

Brain imaging technology provides a powerful tool to visualize the living human brain, provide insights into disease mechanisms, and potentially provide a tool to assist clinical decision-making. The brain has a very specific structural substrate providing a foundation for functional information; however, most studies ignore the very interesting and complex relationships between brain structure and brain function. While a variety of approaches have been used to study how brain structure informs function, the study of such relationships in living humans in most cases is limited to noninvasive approaches at the macroscopic scale. The use of data-driven approaches to link structure and function provides a tool which is especially important at the macroscopic scale at which we can study the human brain. This paper reviews data-driven approaches, with a focus on independent component analysis approaches, which leverage higher order statistics to link together macroscopic structural and functional MRI data. Such approaches provide the benefit of allowing us to identify links which do not necessarily correspond spatially (eg, structural changes in one region related to functional changes in other regions). They also provide a "network level" perspective on the data, by enabling us to identify sets of brain regions that covary together. This also opens up the ability to evaluate both within and between network relationships. A variety of examples are presented, including several showing the potential of such approaches to inform us about mental illness, particularly about schizophrenia.

La tecnología de las imágenes cerebrales provee una herramienta poderosa para visualizar el cerebro humano en vivo, aporta información sobre los mecanismos de la enfermedad y potencialmente entrega una herramienta para apoyar la toma de decisiones clínicas. El cerebro tiene un sustrato estructural muy específico que sirve de base para la información funcional; sin embargo, la mayoría de los estudios ignora las relaciones muy complejas e interesantes entre la estructura y la función del cerebro. Si bien se ha empleado una variedad de enfoques para estudiar cómo la estructura cerebral da cuenta de su función, el estudio de estas relaciones en humanos vivos en la mayoría de los casos se limita a enfoques no invasivos a escala macroscópica. El empleo de propuestas en base a datos para relacionar estructura y función entrega una herramienta que es especialmente importante a escala macroscópica, con la cual podemos estudiar el cerebro humano. Este artículo revisa las propuestas en base a datos, focalizándose en las propuestas de análisis de componente independiente, que aprovechan las estadísticas de orden superior para relacionar los datos macroscópicos estructurales y la información de la RNM funcional. Dichas propuestas nos permiten identificar vinculationes que no necesariamente tienen una correspondencia espacial (por ej. cambios estructurales en una región relacionados con cambios funcionales en otras regiones). Además aportan una perspectiva de "nivel de red" de los datos, lo que permite identificar grupos de regiones cerebrales correlationados entre ellos. Esto también abre la capacidad de evaluar tanto dentro como entre las relaciones de la red. Se presenta una variedad de ejemplos, incluyendo algunos que muestran el potencial de tales propuestas para conocer acerca de la enfermedad mental, especialmente sobre la esquizofrenia.

L'imagerie cérébrale est un outil puissant de visualisation du cerveau humain vivant, elle offre un aperçu des mécanismes pathologiques et apporte potentiellement un moyen d'assistance à la prise de décision clinique. Le cerveau présente un substrat structurel très spécifique permettant de fonder les informations fonctionnelles ; cependant, la plupart des études ignorent les relations très intéressantes et complexes existant entre la structure et la fonction cérébrales. Bien qu'une multitude d'approches ont été utilisées pour étudier comment la structure cérébrale informe la fonction, l'étude de ces relations chez les humains vivants est dans la plupart des cas limitée aux approches non invasives à l'échelle macroscopique. L'approche guidée par les données pour lier la structure et la fonction fournit un outil particulièrement important à l'échelle macroscopique, qui permet d'étudier le cerveau humain. Cet article présente les approches guidées par les données, et insiste sur l'analyse en composantes indépendantes, qui exploite des statistiques d'ordre plus élevé pour lier entre elles des données d'IRM structurelles et fonctionnelles macroscopiques. Ces approches ont l'avantage de permettre d'identifier des liens qui ne correspondent pas nécessairement spatialement (par ex. des changements structuraux d'une région liés à des changements fonctionnels d'autres régions). Elles apportent aussi une perspective de « niveau de réseau ¼ sur les données, et permettent d'identifier des groupes de régions cérébrales corrélés entre eux. Ceci ouvre aussi la possibilité d'évaluer les relations à la fois intra- et inter-réseau. Plusieurs exemples sont présentés, dont certains montrent le potentiel d'information de telles approches sur les maladies mentales, en particulier sur la schizophrénie.

Diminished neural network dynamics after moderate and severe traumatic brain injury.

Over the past decade there has been increasing enthusiasm in the cognitive neurosciences around using network science to understand the system-level changes associated with brain disorders. A growing literature has used whole-brain fMRI analysis to examine changes in the brain's subnetworks following traumatic brain injury (TBI). Much of network modeling in this literature has focused on static network mapping, which provides a window into gross inter-nodal relationships, but is insensitive to more subtle fluctuations in network dynamics, which may be an important predictor of neural network plasticity. In this study, we examine the dynamic connectivity with focus on state-level connectivity (state) and evaluate the reliability of dynamic network states over the course of two runs of intermittent task and resting data. The goal was to examine the dynamic properties of neural networks engaged periodically with task stimulation in order to determine: 1) the reliability of inter-nodal and network-level characteristics over time and 2) the transitions between distinct network states after traumatic brain injury. To do so, we enrolled 23 individuals with moderate and severe TBI at least 1-year post injury and 19 age- and education-matched healthy adults using functional MRI methods, dynamic connectivity modeling, and graph theory. The results reveal several distinct network "states" that were reliably evident when comparing runs; the overall frequency of dynamic network states are highly reproducible (r-values>0.8) for both samples. Analysis of movement between states resulted in fewer state transitions in the TBI sample and, in a few cases, brain injury resulted in the appearance of states not exhibited by the healthy control (HC) sample. Overall, the findings presented here demonstrate the reliability of observable dynamic mental states during periods of on-task performance and support emerging evidence that brain injury may result in diminished network dynamics.

Frequency-Specific Neural Signatures of Spontaneous Low-Frequency Resting State Fluctuations in Psychosis: Evidence From Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) Consortium.

BACKGROUND: We quantified frequency-specific, absolute, and fractional amplitude of low-frequency fluctuations (ALFF/fALFF) across the schizophrenia (SZ)-psychotic bipolar disorder (PBP) psychosis spectrum using resting functional magnetic resonance imaging data from the large BSNIP family study. METHODS: We assessed 242 healthy controls (HC), 547 probands (180 PBP, 220 SZ, and 147 schizoaffective disorder-SAD), and 410 of their first-degree relatives (134 PBPR, 150SZR, and 126 SADR). Following standard preprocessing in statistical parametric mapping (SPM8), we computed absolute and fractional power (ALFF/fALFF) in 2 low-frequency bands: slow-5 (0.01-0.027 Hz) and slow-4 (0.027-0.073 Hz). We evaluated voxelwise post hoc differences across traditional Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition diagnostic categories. RESULTS: Across ALFF/fALFF, in contrast to HC, BP/SAD showed hypoactivation in frontal/anterior brain regions in the slow-5 band and hypoactivation in posterior brain regions in the slow-4 band. SZ showed consistent hypoactivation in precuneus/cuneus and posterior cingulate across both bands and indices. Increased ALFF/fALFF was noted predominantly in deep subcortical and temporal structures across probands in both bands and indices. Across probands, spatial ALFF/fALFF differences in SAD resembled PBP more than SZ. None of these ALFF/fALFF differences were detected in relatives. CONCLUSIONS: Results suggest ALFF/fALFF is a putative biomarker rather than a familial endophenotype. Overall sensitivity to discriminate proband brain alteration was stronger for fALFF than ALFF. Patterns of differences noted in SAD were more similar to those observed in PBP. Differential effects were noted across the 2 frequency bands, more prominently for BP/SAD compared with SZ, suggesting frequency-sensitive physiologic mechanisms for the former.

Visual hallucinations are associated with hyperconnectivity between the amygdala and visual cortex in people with a diagnosis of schizophrenia.

INTRODUCTION: While auditory verbal hallucinations (AH) are a cardinal symptom of schizophrenia, people with a diagnosis of schizophrenia (SZ) may also experience visual hallucinations (VH). In a retrospective analysis of a large sample of SZ and healthy controls (HC) studied as part of the functional magnetic resonance imaging (fMRI) Biomedical Informatics Research Network (FBIRN), we asked if SZ who endorsed experiencing VH during clinical interviews had greater connectivity between visual cortex and limbic structures than SZ who did not endorse experiencing VH. METHODS: We analyzed resting state fMRI data from 162 SZ and 178 age- and gender-matched HC. SZ were sorted into groups according to clinical ratings on AH and VH: SZ with VH (VH-SZ; n = 45), SZ with AH but no VH (AH-SZ; n = 50), and SZ with neither AH nor VH (NoH-SZ; n = 67). Our primary analysis was seed based, extracting connectivity between visual cortex and the amygdala (because of its role in fear and negative emotion) and visual cortex and the hippocampus (because of its role in memory). RESULTS: Compared with the other groups, VH-SZ showed hyperconnectivity between the amygdala and visual cortex, specifically BA18, with no differences in connectivity among the other groups. In a voxel-wise, whole brain analysis comparing VH-SZ with AH-SZ, the amygdala was hyperconnected to left temporal pole and inferior frontal gyrus in VH-SZ, likely due to their more severe thought broadcasting. CONCLUSIONS: VH-SZ have hyperconnectivity between subcortical areas subserving emotion and cortical areas subserving higher order visual processing, providing biological support for distressing VH in schizophrenia.

The rich get richer: brain injury elicits hyperconnectivity in core subnetworks.

There remains much unknown about how large-scale neural networks accommodate neurological disruption, such as moderate and severe traumatic brain injury (TBI). A primary goal in this study was to examine the alterations in network topology occurring during the first year of recovery following TBI. To do so we examined 21 individuals with moderate and severe TBI at 3 and 6 months after resolution of posttraumatic amnesia and 15 age- and education-matched healthy adults using functional MRI and graph theoretical analyses. There were two central hypotheses in this study: 1) physical disruption results in increased functional connectivity, or hyperconnectivity, and 2) hyperconnectivity occurs in regions typically observed to be the most highly connected cortical hubs, or the "rich club". The current findings generally support the hyperconnectivity hypothesis showing that during the first year of recovery after TBI, neural networks show increased connectivity, and this change is disproportionately represented in brain regions belonging to the brain's core subnetworks. The selective increases in connectivity observed here are consistent with the preferential attachment model underlying scale-free network development. This study is the largest of its kind and provides the unique opportunity to examine how neural systems adapt to significant neurological disruption during the first year after injury.

The impact of NMDA receptor blockade on human working memory-related prefrontal function and connectivity.

Preclinical research suggests that N-methyl-D-aspartate glutamate receptors (NMDA-Rs) have a crucial role in working memory (WM). In this study, we investigated the role of NMDA-Rs in the brain activation and connectivity that subserve WM. Because of its importance in WM, the lateral prefrontal cortex, particularly the dorsolateral prefrontal cortex and its connections, were the focus of analyses. Healthy participants (n=22) participated in a single functional magnetic resonance imaging session. They received saline and then the NMDA-R antagonist ketamine while performing a spatial WM task. Time-course analysis was used to compare lateral prefrontal activation during saline and ketamine administration. Seed-based functional connectivity analysis was used to compare dorsolateral prefrontal connectivity during the two conditions and global-based connectivity was used to test for laterality in these effects. Ketamine reduced accuracy on the spatial WM task and brain activation during the encoding and early maintenance (EEM) period of task trials. Decrements in task-related activation during EEM were related to performance deficits. Ketamine reduced connectivity in the DPFC network bilaterally, and region-specific reductions in connectivity were related to performance. These results support the hypothesis that NMDA-Rs are critical for WM. The knowledge gained may be helpful in understanding disorders that might involve glutamatergic deficits such as schizophrenia and developing better treatments.

The NKI-Rockland Sample: A Model for Accelerating the Pace of Discovery Science in Psychiatry.

The National Institute of Mental Health strategic plan for advancing psychiatric neuroscience calls for an acceleration of discovery and the delineation of developmental trajectories for risk and resilience across the lifespan. To attain these objectives, sufficiently powered datasets with broad and deep phenotypic characterization, state-of-the-art neuroimaging, and genetic samples must be generated and made openly available to the scientific community. The enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) is a response to this need. NKI-RS is an ongoing, institutionally centered endeavor aimed at creating a large-scale (N > 1000), deeply phenotyped, community-ascertained, lifespan sample (ages 6-85 years old) with advanced neuroimaging and genetics. These data will be publically shared, openly, and prospectively (i.e., on a weekly basis). Herein, we describe the conceptual basis of the NKI-RS, including study design, sampling considerations, and steps to synchronize phenotypic and neuroimaging assessment. Additionally, we describe our process for sharing the data with the scientific community while protecting participant confidentiality, maintaining an adequate database, and certifying data integrity. The pilot phase of the NKI-RS, including challenges in recruiting, characterizing, imaging, and sharing data, is discussed while also explaining how this experience informed the final design of the enhanced NKI-RS. It is our hope that familiarity with the conceptual underpinnings of the enhanced NKI-RS will facilitate harmonization with future data collection efforts aimed at advancing psychiatric neuroscience and nosology.

Tuning in to the voices: a multisite FMRI study of auditory hallucinations.

INTRODUCTION: Auditory hallucinations or voices are experienced by 75% of people diagnosed with schizophrenia. We presumed that auditory cortex of schizophrenia patients who experience hallucinations is tonically "tuned" to internal auditory channels, at the cost of processing external sounds, both speech and nonspeech. Accordingly, we predicted that patients who hallucinate would show less auditory cortical activation to external acoustic stimuli than patients who did not. METHODS: At 9 Functional Imaging Biomedical Informatics Research Network (FBIRN) sites, whole-brain images from 106 patients and 111 healthy comparison subjects were collected while subjects performed an auditory target detection task. Data were processed with the FBIRN processing stream. A region of interest analysis extracted activation values from primary (BA41) and secondary auditory cortex (BA42), auditory association cortex (BA22), and middle temporal gyrus (BA21). Patients were sorted into hallucinators (n = 66) and nonhallucinators (n = 40) based on symptom ratings done during the previous week. RESULTS: Hallucinators had less activation to probe tones in left primary auditory cortex (BA41) than nonhallucinators. This effect was not seen on the right. DISCUSSION: Although "voices" are the anticipated sensory experience, it appears that even primary auditory cortex is "turned on" and "tuned in" to process internal acoustic information at the cost of processing external sounds. Although this study was not designed to probe cortical competition for auditory resources, we were able to take advantage of the data and find significant effects, perhaps because of the power afforded by such a large sample.

Impairment of working memory maintenance and response in schizophrenia: functional magnetic resonance imaging evidence.

BACKGROUND: Comparing prefrontal cortical activity during particular phases of working memory in healthy subjects and individuals diagnosed with schizophrenia might help to define the phase-specific deficits in cortical function that contribute to cognitive impairments associated with schizophrenia. This study featured a spatial working memory task, similar to that used in nonhuman primates, that was designed to facilitate separating brain activation into encoding, maintenance, and response phases. METHODS: Fourteen patients with schizophrenia (4 medication-free) and 12 healthy comparison participants completed functional magnetic resonance imaging while performing a spatial working memory task with two levels of memory load. RESULTS: Task accuracy was similar in patients and healthy participants. However, patients showed reductions in brain activation during maintenance and response phases but not during the encoding phase. The reduced prefrontal activity during the maintenance phase of working memory was attributed to a greater rate of decay of prefrontal activity over time in patients. Cortical deficits in patients did not appear to be related to antipsychotic treatment. In patients and in healthy subjects, the time-dependent reduction in prefrontal activity during working memory maintenance correlated with poorer performance on the memory task. CONCLUSIONS: Overall, these data highlight that basic research insights into the distinct neurobiologies of the maintenance and response phases of working memory are of potential importance for understanding the neurobiology of cognitive impairment in schizophrenia and advancing its treatment.

Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex.

Long-range enhancer-promoter interactions are commonly seen in complex genetic loci such as Hox genes and globin genes. In the case of the Drosophila Antennapedia complex, the T1 enhancer bypasses the neighboring ftz gene and interacts with the distant Scr promoter to activate expression in posterior head segments. Previous studies identified a 450-bp promoter-proximal sequence, the tethering element, which is essential for T1-Scr interactions. To obtain a more comprehensive view of how individual enhancers selectively interact with appropriate target genes, we used bioinformatic methods to identify new cis-regulatory DNAs in the approximately 50-kb Scr-Antp interval. Three previously uncharacterized regulatory elements were identified: a distal T1 tethering sequence mapping >40 kb from the proximal tethering sequence, a repressor element that excludes activation of Scr by inappropriate enhancers, and a new ftz enhancer that directs expression within the limits of stripes 1 and 5. Many of the regulatory DNAs in the Scr-Antp interval are transcribed, including the proximal and distal tethering elements. We suggest that homotypic interactions between the tethering elements stabilize long-range T1-Scr interactions during development.

Coordinate regulation of an extended chromosome domain.

Spitz et al (2003[this issue of Cell]) describe the properties of a novel cis-regulatory DNA element, the global control region (GCR), which regulates gene expression over distances of several hundred kilobases at the mouse HoxD complex. The GCR provides an explanation for the colinear genetic linkage and expression of individual Hox genes within developing limbs.

Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex.

The correct spatial expression of two Drosophila bithorax complex (BX-C) genes, abdominal-A (abdA) and Abdominal-B (AbdB), is dependent on the 100-kb intergenic infraabdominal (iab) region. The iab region is known to contain a number of different domains (iab2 through iab8) that harbor cis-regulatory elements responsible for directing expression of abdA and AbdB in the second through eighth abdominal segments. Here, we use in situ hybridization to perform high-resolution mapping of the transcriptional activity in the iab control regions. We show that transcription of the control regions themselves is abundant and precedes activation of the abdA and AbdB genes. As with the homeotic genes of the BX-C, the transcription patterns of the RNAs from the iab control regions demonstrate colinearity with the sequence of the iab regions along the chromosome and the domains in the embryo under the control of the specific iab regions. These observations suggest that the intergenic RNAs may play a role in initiating cis regulation at the BX-C early in development.

Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex.

Insulator DNAs and promoter competition regulate enhancer-promoter interactions within complex genetic loci. Here we provide evidence for a third mechanism: promoter-proximal tethering elements. The Scr-ftz region of the Antennapedia gene complex includes two known enhancers, AE1 and T1. AE1 selectively interacts with the ftz promoter to maintain pair-rule stripes of ftz expression during gastrulation and germ-band elongation. The T1 enhancer, located 3' of the ftz gene and approximately 25 kb 5' of the Scr promoter, selectively activates Scr expression in the prothorax and posterior head segments. A variety of P element minigenes were examined in transgenic embryos to determine the basis for specific AE1-ftz and T1-Scr interactions. A 450-bp DNA fragment located approximately 100 bp 5' of the Scr transcription start site is essential for T1-Scr interactions and can mediate long-range activation of a ftz/lacZ reporter gene when placed 5' of the ftz promoter. We suggest that the Scr450 fragment contains tethering elements that selectively recruit T1 to the Scr promoter. Tethering elements might regulate enhancer-promoter interactions at other complex genetic loci.

Object activation from features in the semantic system.

The human brain is thought to elicit an object representation via co-activation of neural regions that encode various object features. The cortical regions and mechanisms involved in this process have never been elucidated for the semantic system. We used functional magnetic resonance imaging (fMRI) to evaluate regions activated during a task designed to elicit object activation within the semantic system (e.g., presenting the words "desert" and "humps" with the task to determine if they combine to form an object, in this case a "camel"). There were signal changes in the thalamus for word pairs that activated an object, but not for pairs that (a) failed to activate an object, (b) were simply semantically associated, or (c) were members of the same category. These results suggest that the thalamus has a critical role in coordinating the cortical activity required for activating an object concept in the semantic system.

Object activation in semantic memory from visual multimodal feature input.

The human brain's representation of objects has been proposed to exist as a network of coactivated neural regions present in multiple cognitive systems. However, it is not known if there is a region specific to the process of activating an integrated object representation in semantic memory from multimodal feature stimuli (e.g., picture-word). A previous study using word-word feature pairs as stimulus input showed that the left thalamus is integrally involved in object activation (Kraut, Kremen, Segal, et al., this issue). In the present study, participants were presented picture-word pairs that are features of objects, with the task being to decide if together they "activated" an object not explicitly presented (e.g., picture of a candle and the word "icing" activate the internal representation of a "cake"). For picture-word pairs that combine to elicit an object, signal change was detected in the ventral temporo-occipital regions, pre-SMA, left primary somatomotor cortex, both caudate nuclei, and the dorsal thalami bilaterally. These findings suggest that the left thalamus is engaged for either picture or word stimuli, but the right thalamus appears to be involved when picture stimuli are also presented with words in semantic object activation tasks. The somatomotor signal changes are likely secondary to activation of the semantic object representations from multimodal visual stimuli.