Genetics

To examine transcription factor (TF) network(s), we created mouse ES cell lines, in each of which one of 50 TFs tagged with a FLAG moiety is inserted into a ubiquitously controllable tetracyclinerepressible locus. Of the 50 TFs, Cdx2 provoked the most extensive transcriptome perturbation in ES cells, followed by Esx1, Sox9, Tcf3, Klf4, and Gata3. ChIP-Seq revealed that CDX2 binds to promoters of up-regulated target genes. By contrast, genes down-regulated by CDX2 did not show CDX2 binding, but were enriched with binding sites for POU5F1, SOX2, and NANOG. Genes with binding sites for these core TFs were also down-regulated by the induction of at least 15 other TFs, suggesting a common initial step for ES cell differentiation mediated by interference with the binding of core TFs to their target genes. These ES cell lines provide a fundamental resource to study biological networks in ES cells and mice.

Exceptional genomic stability is one of the hallmarks of mouse embryonic stem (ES) cells. However, the genes contributing to this stability remain obscure. We previously identified Zscan4 as a specific marker for 2-cell embryo and ES cells. Here we show that Zscan4 is involved in telomere maintenance and long-term-genomic stability in ES cells. Only 5% of ES cells express Zscan4 at a given time, but nearly all ES cells activate Zscan4 at least once within nine passages. The transient Zscan4-positive state is associated with rapid telomere extension by telomere recombination and upregulation of meiosis-specific homologous recombination genes, which encode proteins that are colocalized with ZSCAN4 on telomeres. Furthermore, Zscan4 knockdown shortens telomeres, increases karyotype abnormalities and spontaneous sister chromatid exchange, and slows down cell proliferation until reaching crisis by eight passages. Together, our data reveal a unique mode of genome maintenance in ES cells.

Here we report the generation and characterization of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7-10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phenotypes. These cell lines and microarray data provide building blocks for a variety of future biomedical research applications as a community resource.

In this paper, we consider shifted tridiagonal matrices. We prove that the standard algorithm to compute the LU factorization in this situation is mixed forward-backward stable and, therefore, componentwise forward stable. Moreover, we give a formula to compute the corresponding condition number in O(n) flops. . 65F35, 65F50, 15A12, 15A23, 65G50.

In this paper, we consider shifted tridiagonal matrices. We prove that the standard algorithm to compute the LU factorization in this situation is mixed forward-backward stable and, therefore, componentwise forward stable. Moreover, we give a formula to compute the corresponding condition number in O(n) flops. . 65F35, 65F50, 15A12, 15A23, 65G50.

Detailed knowledge of both synaptic connectivity and the spatial proximity of neurons is crucial for understanding wiring specificity in the nervous system. Here, we volumetrically reconstructed the C. Elegans nerve ring from legacy serial-sectioned electron micrographs at two distinct time points: the L4 and young adult. The new volumetric reconstructions provide detailed spatial and morphological information of neural processes in the nerve ring. Our analysis suggests that the nerve ring exhibits three levels of wiring specificity: spatial, synaptic and subcellular. Neuron classes innervate well defined neighborhoods and aggregate functionally similar synapses to support distinct computational pathways. Connectivity fractions vary based on neuron class and synapse type. We find that the variability in process placement accounts for less than 20% of the variability in synaptic connectivity and models based only on spatial information cannot account for the reproducibility of synapt...

The nematode Caenorhabditis elegans is a leading model system in genetics, development and neurobiology; its transparent body and small size make it particularly suitable for fluorescent imaging of cells and neurons within microfluidic setups. Simultaneously recording activity in bilaterally symmetric cells has proved difficult in C. elegans because the worm enters the chip and is then immobilised when it is lying on one side of the body. We developed a side-view rotatable microfluidic device that allows us to image a pair of bilateral neurons in a single focal plane of an epi-fluorescence microscope. We demonstrated the utility of the device by recording the responses of immobilised worms to controlled stimuli, focusing on the responses of two classes of head sensory neurons to changes in NaCl concentration. The results indicate that responses of ASE left and right and ASH left and right sensory neurons are stochastic. Simultaneous recordings of ASH left and right neurons tend to synchronise, pointing to a role of gap junctional connectivity. The anatomy of the C. elegans nerve ring makes this microfluidic approach ideally suited for the study of spatially extended pairs of neurons or larger neuronal circuits that lie within a limited depth of field.

ABSTRACTAnimal nervous system organization is crucial for all body functions and its disruption can manifest in severe cognitive and behavioral impairment. This organization relies on features across scales, from nano-level localization of synapses, through multiplicities of neuronal morphologies and their contribution to circuit organization, to the high level stereotyped connections between different regions of the brain. The sheer complexity of this organ means that to date, we have yet to reconstruct and model the structure of a complete nervous system that is integrated across all these scales. Here, we present a complete structure-function model of the nematode C. elegans main neuropil, the nerve ring, which we derive by integrating the volumetric reconstruction from two animals with corresponding synaptic and gap junctional connectomes. Whereas previously the nerve ring was considered a densely packed tract of axons, we uncover internal organization into 5 functional bundles ...

Matrix-enhanced secondary ionization mass spectrometry (ME-SIMS) is a technique used for the molecular analysis of biomaterials. It combines the analysis techniques of time-of-flight secondary ionization mass spectrometry (ToF-SIMS) with sample preparations similar to those used in matrix assisted laser desorption ionization (MALDI). This report addresses two issues: the sample morphology of the solid “crystalline” matrix 2,5 dihydroxybenzoic acid (2,5 DHB) caused by ToF-SIMS, and the potential use of room temperature ionic liquids (RTILs) as a matrix for ME-SIMS. Concerning the former, it was observed that surface degradation of the 2,5 DHB is caused by the vacuum and high voltage which are used in ToF-SIMS. Furthermore, this degradation is difficult to characterize. Concerning the latter, this report will present methodologies which were initially developed to implement RTILs in ToF-SIMS analysis, and some interesting problems which arise from SIMS analysis on RTILs will also be d...

Part I considers the stereotypic patterns of synaptic connectivity in neural circuits, referred to as wiring specificity. Two aspects of wiring specificity are lamina specificity - placing synaptic partners in close spatial proximity - and synaptic specificity - making the appropriate synaptic connections among many physically adjacent neurons. Combinatorial expression patterns of surface proteins could be used to uniquely label neurons for the purposes of synaptic specificity. To test this model in the worm, the C. elegans nerve ring was volumetrically reconstructed from serial sectioned legacy electron micrographs, which provides detailed spatial and morphological information of neural processes in the nerve ring. Comparing the spatial data with the synaptic wiring diagram shows that the C. elegans nerve ring exhibits both lamina-like specificity and synaptic specificity. Combinatorial expression patterns of CAM genes in nerve ring neurons were analyzed. If a few key conditions re...

Idiopathic generalized epilepsy (IGE) syndromes represent about 30% of all epilepsies. They have strong, but elusive, genetic components and sex-specific seizure expression. Multiple linkage and population association studies have connected the bromodomain-containing gene BRD2 to forms of IGE. In mice, a null mutation at the homologous Brd2 locus results in embryonic lethality while heterozygous Brd2+/2 mice are viable and overtly normal. However, using the flurothyl model, we now show, that compared to the Brd2+/+ littermates, Brd2+/2 males have a decreased clonic, and females a decreased tonic-clonic, seizure threshold. Additionally, long-term EEG/video recordings captured spontaneous seizures in three out of five recorded Brd2+/2 female mice. Anatomical analysis of specific regions of the brain further revealed significant differences in Brd2+/2 vs +/+ mice. Specifically, there were decreases in the numbers of GABAergic (parvalbuminor GAD67-immunopositive) neurons along the basal ganglia pathway, i.e., in the neocortex and striatum of Brd2+/2 mice, compared to Brd2+/+ mice. There were also fewer GABAergic neurons in the substantia nigra reticulata (SNR), yet there was a minor, possibly compensatory increase in the GABA producing enzyme GAD67 in these SNR cells. Further, GAD67 expression in the superior colliculus and ventral medial thalamic nucleus, the main SNR outputs, was significantly decreased in Brd2+/2 mice, further supporting GABA downregulation. Our data show that the non-channel-encoding, developmentally critical Brd2 gene is associated with i) sex-specific increases in seizure susceptibility, ii) the development of spontaneous seizures, and iii) seizure-related anatomical changes in the GABA system, supporting BRD2's involvement in human IGE.

Velo-cardio-facial/DiGeorge syndrome, also known as 22q11.2 deletion syndrome, is a congenital anomaly disorder characterized by craniofacial anomalies including velo-pharyngeal insufficiency, facial muscle hypotonia and feeding difficulties, in part due to hypoplasia of the branchiomeric muscles. Inactivation of both alleles of mouse Tbx1, encoding a T-box transcription factor, deleted on chromosome 22q11.2, results in reduction or loss of branchiomeric muscles. To identify downstream pathways, we performed gene profiling of microdissected pharyngeal arch one (PA1) from Tbx1 1/1 and Tbx1 2/2 embryos at stages E9.5 (somites 20 -25) and E10.5 (somites 30 -35). Basic helix -loop -helix (bHLH) transcription factors were reduced, while secondary heart field genes were increased in expression early and were replaced by an increase in expression of cellular stress response genes later, suggesting a change in gene expression patterns or cell populations. Lineage tracing studies using Mesp1 Cre and T-Cre drivers showed that core mesoderm cells within PA1 were present at E9.5 but were greatly reduced by E10.5 in Tbx1 2/2 embryos. Using Tbx1 Cre knock-in mice, we found that cells are lost due to apoptosis, consistent with increase in expression of cellular stress response genes at E10.5. To determine whether Tbx1 is required autonomously in the core mesoderm, we used Mesp1 Cre and T-Cre mesodermal drivers in combination with inactivate Tbx1 and found reduction or loss of branchiomeric muscles from PA1. These mechanistic studies inform us that Tbx1 is required upstream of key myogenic genes needed for core mesoderm cell survival and fate, between E9.5 and E10.5, resulting in formation of the branchiomeric muscles.

How do animals integrate internal drives and external environmental cues to coordinate behaviors? We address this question by studying mate-searching behavior in C. elegans. C. elegans males explore their environment in search of mates (hermaphrodites) and will leave food if mating partners are absent . However, when mates and food coincide, male exploratory behavior is suppressed and males are retained on the food source . We show that the drive to explore is stimulated by male-specific neurons in the tail, the ray neurons. Periodic contact with the hermaphrodite detected through ray neurons changes the male's behavior during periods of no contact and prevents the male from leaving the food source. The hermaphrodite signal is conveyed by male-specific interneurons that are postsynaptic to the rays and that send processes to the major integrative center in the head. This study identifies key parts of the neural circuit that regulates a sexual appetitive behavior in C. elegans.

The Caenorhabditis elegans body axis, like that of other animals, is patterned by the action of Hox genes. In order to examine the function of one C. elegans Hox gene in depth, we determined the postembryonic expression pattern of egl-5, the C. elegans member of the Abdominal-B Hox gene paralog group, by means of whole-mount staining with a polyclonal antibody. A major site of egl-5 expression and function is in the epithelium joining the posterior digestive tract with the external epidermis. Patterning this region and its derived structures is a conserved function of Abd-B paralog group genes in other animals. Cells that initiate egl-5 expression during embryogenesis are clustered around the presumptive anus.

Hox genes are highly conserved segmental identity genes well known for their complex expression patterns and divergent targets. Here we present an analysis of cis-regulatory elements in the Caenorhabditis elegans Hox gene egl-5, which is expressed in multiple tissues in the posterior region of the nematode. We have utilized phylogenetic footprinting to efficiently identify cis-regulatory elements and have characterized these with gfp reporters and tissue-specific rescue experiments. We have found that the complex expression pattern of egl-5 is the cumulative result of the activities of multiple tissue or local region-specific activator sequences that are conserved both in sequence and near-perfect order in the related nematode Caenorhabditis briggsae. Two conserved regulatory blocks analyzed in detail contain multiple sites for both positively and negatively acting factors. One of these regions may promote activation of egl-5 in certain cells via the Wnt pathway. Positively acting regions are repressed in inappropriate tissues by additional negative pathways acting at other sites within the promoter. Our analysis has allowed us to implicate several new regulatory factors significant to the control of egl-5 expression.

Ephrins and semaphorins regulate a wide variety of developmental processes, including axon guidance and cell migration. We have studied the roles of the ephrin EFN-4 and the semaphorin MAB-20 in patterning cell-cell contacts among the cells that give rise to the ray sensory organs of Caenorhabditis elegans. In wild-type, contacts at adherens junctions form only between cells belonging to the same ray. In efn-4 and mab-20 mutants, ectopic contacts form between cells belonging to different rays. Ectopic contacts also occur in mutants in regulatory genes that specify ray morphological identity. We used efn-4 and mab-20 reporters to investigate whether these ray identity genes function through activating expression of efn-4 or mab-20 in ray cells. mab-20 reporter expression in ray cells was unaffected by mutants in the Pax6 homolog mab-18 and the Hox genes egl-5 and mab-5, suggesting that these genes do not regulate mab-20 expression. We find that mab-18 is necessary for activating efn-4 reporter expression, but this activity alone is not sufficient to account for mab-18 function in controlling cell-cell contact formation. In egl-5 mutants, efn-4 reporter expression in certain ray cells was increased, inconsistent with a simple repulsion model for efn-4 action. The evidence indicates that ray identity genes primarily regulate ray morphogenesis by pathways other than through regulation of expression of semaphorin and ephrin.