Complex organization of CTF/NF-I, C/EBP, and HNF3 binding sites within the promoter of the liver-specific vitellogenin gene.

Vitellogenin genes are expressed specifically in the liver of female oviparous vertebrates under the strict control of estrogen. To explain this tissue-specific expression, we performed a detailed analysis of the Xenopus laevis vitellogenin gene B1 promoter by DNase I footprinting and gel mobility-shift assays. We characterized five binding sites for the ubiquitous factor CTF/NF-I. Two of these sites are close to the TATA-box, whereas the others are located on both sides of the estrogen responsive unit formed by two imperfect estrogen response elements. Moreover two liver-enriched factors, C/EBP and HNF3, were found to interact with multiple closely spaced proximal promoter elements in the first 100 base pairs upstream of the TATA-box. To confirm the physiological significance of this in vitro analysis, in vivo DNase I footprinting experiments were carried out using the ligation-mediated polymerase chain reaction technique. The various cis-elements characterized in vitro as binding sites for known transcription factors and more particularly for liver-enriched transcription factors are efficiently recognized in vivo as well, suggesting that they play an important role in the control of the liver-specific vitellogenin gene B1 expression.

SOURCE, FATE AND FUNCTION OF EARLY GLIAL CELLS EXPRESSING NKX2.1 IN MOUSE EMBRYONIC BRAINS

The brain tissue is made of neuronal and glial cells generated in the germinal layer bordering the ventricles. These cells divide, differentiate and migrate following specific pathways. The specification of GABAergic interneurons and glutamatergic neurons has been broadly studied but little is known about the origin, the fate and the function of early glial cells in the embryonic telencephalon. It has been commonly accepted since long that the glial cells and more particularly the astrocytes were generated after neurogenesis from the dorsal telencephalon. However, our work shows that, unlike what was previously thought, numerous glial cells (astroglia and polydendrocytes) are generated during neurogenesis in the early embryonic stages from E14.5 to E16.5, and originate from the ventral Nkx2.1-expressing precursors instead. NK2 homeobox 1 (Nkx2.1) is a member of the NK2 family of homeodomaincontaining transcription factors. The specification of the MGE precursors requires the expression of the Nkx2.1 homeobox gene. Moreover, Nkx2.1 is previously known to regulate the specification of GABAergic interneurons and early oligodendrocytes in the ventral telencephalon. Here, in my thesis work, I have discovered that, in addition, Nkx2.1 also regulates astroglia and polydendrocytes differentiation. The use of Nkx2.1 antibody and Nkx2.1 riboprobe have revealed the presence of numerous Nkx2.1-positive cells that express astroglial markers (like GLAST and GFAP) in the entire embryonic brain. Thus, to selectively fate map MGE-derived GABAergic interneurons and glia, we crossed Nkx2.1-Cre mice, Glast-Cre ERT+/- inducible mice and NG2-Cre mice with the Cre reporter Rosa26-lox-STOP-lox-YFP (Rosa26-YFP) mice. The precise origin of Nkx2.1-positive astroglia has been directly ascertained by combining glial immunostaining and focal electroporation of the pCAG-GS-EGFP plasmids into the subpallial domains of organotypic slices, as well as, by using in vitro neurosphere experiments and in utero electroporation of the pCAG-GS-tomato plasmid into the ventral pallium of E14.5 Nkx2.1-Cre+/Rosa-YFP+/- embryos. We have, thus, confirmed that the three germinal regions of the ventral telencephalon i.e. the MGE, the AEP/POA and the triangular septal nucleus are able to generate early astroglial cells. Moreover, immunohistochemistry for several astroglial cells and polydendrocyte markers, both in the Nkx2.1-/- and control embryos and in the neurospheres, has revealed a severe loss of both glial cell types in the Nkx2.1 mutants. We found that the loss of glia corresponded to a decrease of Nkx2.1-derived precursor division capacity and glial differentiation. There was a drastic decrease of BrdU+ dividing cells labeled for Nkx2.1 in the MGE*, the POA* and the septal nucleus* of Nkx2.1 mutants. In addition, we noticed that while some remaining Nkx2.1+ precursors still succeeded to give rise to post-mitotic neurons in vitro and in vivo in the Nkx2.1-/-, they completely lost the capacity to differentiate in astrocytes. Altogether, these observations indicate for the first time that the transcription factor Nkx2.1 regulates the proliferation and differentiation of precursors in three subpallial domains that generate early embryonic astroglia and polydendrocytes. Furthermore, in order to investigate the potential function of these early Nkx2.1- derived glia, we have performed multiple immunohistochemical stainings on Nkx2.1-/- and wild-type animals, and Nkx2.1-Cre mice that were crossed to Rosa-DTA+/- mice in which the highly toxic diphtheria toxin aided to selectively deplete a majority of the Nkx2.1-derived cells. Interestingly, in these two mutants, we observed a drastic and significant loss of GFAP+, GLAST+, NG2+ and S100ß+ astroglial cells at the telencephalic midline and in the medial cortical areas. This cells loss could be directly correlated with severe axonal guidance defects observed in the corpus callosum (CC), the hippocampal commissure (HIC), the fornix (F) and the anterior commissure (AC). Axonal guidance is a key step allowing neurons to form specific connections and to become organized in a functional network. The contribution of guidepost cells inside the CC and the AC in mediating the growth of commissural axons have until now been attributed to specialized midline guidepost astroglia. Previous published results in our group have unravelled that, during embryonic development, the CC is populated in addition to astroglia by numerous glutamatergic and GABAergic guidepost neurons that are essential for the correct midline crossing of callosal axons. Therefore, the relative contribution of individual neuronal or glial populations towards the guidance of commissural axons remains largely to be investigated to understand guidance mechanisms further. Thus, we crossed Nkx2.1-Cre mice with NSE-DTA+/- mice that express the diphtheria toxin only in neurons and allowed us to selectively deplete Nkx2.1-derived GABAergic neurons. Interestingly, in the Nkx2.1-/- mice, the CC midline was totally disorganized and the callosal axons partly lost their orientation, whereas in the Nkx2.1Cre+/Rosa-DTA+/- and the Nkx2.1Cre+/NSE-DTA+/- mice, the axonal organization of the CC was not affected. In the three types of mice, hippocampal axons of the fornix were not properly fasciculated and formed disoriented bundles through the septum. Additionally, the AC formation was completely absent in Nkx2.1-/- mice and the AC was divided into two/three separate paths in the Nkx2.1Cre+/Rosa-DTA+/- mice that project in wrong territories. On the other hand, the AC didn't form or was reduced to a relatively narrower tract in the Nkx2.1Cre+/NSE-DTA+/- mice as compared to wild-type AC. These results clearly indicate that midline Nkx2.1-derived cells play a major role in commissural axons pathfinding and that both Nkx2.1-derived guidepost neurons and glia are necessary elements for the correct development of these commissures. Furthermore, during our investigations on Nkx2.1-/- and Nkx2.1Cre+/Rosa-DTA+/- mice, we noticed similar and severe defects in the erythrocytes distribution and the blood vessels network morphology in the embryonic brain of both mutants. As the Cre-mediated recombination was never observed to occur in the blood vessels of Nkx2.1-Cre mice, we inferred that the vessels defects observed were due to the loss of Nkx2.1-derived cells and not to the cells autonomous effects of Nkx2.1 in regulating endothelial cell precursors. Thereafter, the respective contribution of individual Nkx2.1-regulated neuronal or glial populations in the blood vessels network building were studied with the use of transgenic mice strains. Indeed, the use of Nkx2.1Cre+/NSE-DTA+/- mice indicated that the Nkx2.1-derived neurons were not implicated in this process. Finally, to discriminate between the two Nkx2.1-derived glial cell populations, the GLAST+ astroglia and the NG2+ polydendrocytes, an NG2-Cre mouse strain crossed to the Rosa-DTA+/- mice was used. In that mutant, the blood vessel network and the erythrocytes distribution were similarly affected as observed in Nkx2.1Cre+/Rosa-DTA+/- animals. Therefore, this result indicates that most probably, the NG2+ polydendrocytes are involved in helping to build the vessels network in the brain. Taken altogether, these observations show that during brain development, Nkx2.1- derived embryonic glial cells act as guidepost cells on the guidance of axons as well as forming vessels. Both Nkx2.1-regulated guidepost GABAergic neurons and glia collaborate to guide growing commissural axons, while polydendrocytes are implicated in regulating brain angiogenesis. - Le tissu cérébral est composé de cellules neuronales et gliales générées dans les couches germinales qui bordent les ventricules. Ces cellules se divisent, se différencient et migrent selon des voies particulières. La spécification des interneurones GABAergiques et des neurones glutamatergiques a été largement étudiée, par contre, l'origine, le destin et la fonction des cellules gliales précoces du télencéphale embryonnaire restent peu élucidées. Depuis longtemps, il était communément accepté que les cellules gliales, et plus particulièrement les astrocytes, sont générés après la neurogénèse à partir du télencéphale dorsal. Toutefois, notre travail montre que de nombreuses cellules gliales sont générées à partir de précurseurs ventraux qui expriment le gène Nkx2.1, entre E14.5 et E16.5, c'est-à dire,à des stades embryonnaires très précoces. Le gène NK2 homéobox 1 (Nkx2.1) appartient à une famille de facteurs de transcription appelée NK2. Il s'agit de protéines qui contiennent un homéo-domaine. La spécification des précurseurs de la MGE requiert l'expression du gène homéobox Nkx2.1. De plus, la fonction du gène Nkx2.1 dans la régulation de la spécification des interneurones GABAergiques et des oligodendrocytes dans le télencéphale ventral était déjà connue. Au cours de mon travail de thèse, j'ai également mis en évidence que, Nkx2.1 régule aussi les étapes de prolifération et de différenciation de divers sous-types de cellules gliales soit de type astrocytes ou bien polydendrocytes. L'utilisation d'un anticorps contre la protéine Nkx2.1 ainsi qu'une sonde à ribonucléotides contre l'ARN messager du gène Nkx2.1 ont révélé la présence de nombreuses cellules positives pour Nkx2.1 qui exprimaient des marqueurs astrocytaires (comme GLAST et GFAP) dans le télencéphale embryonnaire. Afin de déterminer de manière sélective le sort des interneurones GABAergiques, des polydendrocytes et des astrocytes dérivés de la MGE, nous avons croisé soit des souris Nkx2.1-Cre, des souris Glast-Cre ERT+/- inductibles ou bien des souris NG2-Cre avec des souris Rosa26-lox-STOP-lox-YFP (Rosa26-YFP) Cre rapportrices. L'origine précise des astroglies positives pour Nkx2.1 a été directement établie en combinant une coloration immunologique pour les glies et une électroporation focale d'un plasmide pCAG-GS-EGFP dans les domaines subpalliaux de tranches organotypiques, puis également, par des cultures de neurosphères in vitro et des expériences d'électroporation in utero d'un plasmide pCAG-GS-tomato dans le pallium ventral d'embryons Nkx2.1-Cre+/Rosa- YFP+/- au stade E14.5. Nous avons donc confirmé que les trois régions germinales du télencéphale ventral, c'est-à-dire, la MGE, l'AEP/POA et le noyau triangulaire septal sont capables de générer des cellules astrogliales. D'autre part, l'immunohistochimie pour plusieurs marqueurs d'astrocytes ou de polydendrocytes, dans les embryons Nkx2.1-/- et contrôles ainsi que dans les neurosphères, a révélé une sévère perte de ces deux types gliaux chez les mutants. Nous avons trouvé que la perte de glies correspondait à une diminution de la capacité de division des précurseurs dérivés de Nkx2.1, ainsi que l'incapacité de ces précurseurs de se différencier en cellules gliales. Nous avons en effet observé une diminution importante des cellules BrdU+ en division exprimant Nkx2.1dans la MGE*, la POA* et le noyau septal* des mutants pour Nkx2.1. D'autre part, nous avons pu mettre en évidence aussi bien in vitro, qu'in vivo, que certains précurseurs Nkx2.1+ chez le mutant gardent la capacité à se différencier en neurones tandis qu'ils perdent celle de se différencier en cellules gliales. Prises dans leur ensemble, ces observations indiquent pour la première fois que le facteur de transcription Nkx2.1 régule les étapes de prolifération et de différentiation des précurseurs des trois domaines subpalliaux qui génèrent les astroglies et polydendrocytes embryonnaires précoces. Par la suite, dans le but de comprendre la fonction potentielle de ces glies précoces, nous avons procédé à de multiples colorations immunohistochimiques sur des animaux Nkx2.1-/- et sauvages, ainsi que sur des souris Nkx2.1-Cre croisées à des souris Rosa-DTA+/- dans lesquelles la toxine diphthérique hautement toxique a permis de supprimer sélectivement la majorité des cellules dérivées de Nkx2.1. De manière intéressante, nous avons observé dans ces deux mutants, une perte drastique et significative de cellules astrogliales GFAP+, GLAST+ et polydendrocytaires NG2+ et S100ß+ dans le télencéphale, à la midline et dans les aires corticales médianes. Ces pertes ont pu être directement corrélées avec des défauts de guidage axonal observés dans le corps calleux (CC), la commissure hippocampique (HIC), le fornix (F) et la commissure antérieure (AC). Le guidage axonal est une étape clé permettant aux neurones de former des connections spécifiques et de s'organiser dans un réseau fonctionnel. La contribution des cellules « guidepost » dans le CC et dans la AC comme médiateurs de la croissance des axones commissuraux à jusqu'à aujourd'hui été attribuée spécifiquement à des astroglies « guidepost » de la midline. Des résultats publiés précédemment dans notre groupe, ont permis de montrer que, pendant le développement embryonnaire, le CC est peuplé en plus de la glie par de nombreux neurones « guidepost » glutamatergiques et GABAergiques qui sont essentiels pour le croisement correct des axones callosaux à la midline. Ainsi, la contribution relative des populations individuelles neuronales ou gliales pour le guidage des axones commissuraux demande à être approfondie afin de mieux comprendre les mécanismes de guidage. A ces fins, nous avons croisé des souris Nkx2.1-Cre avec des souris NSE-DTA+/- qui expriment la toxine diphthérique uniquement dans les neurones et ainsi, nous avons pu sélectivement supprimer les neurones dérivés de domaines Nkx2.1+. Dans les souris Nkx2.1-/-,nous avons découvert que le CC était désorganisé avec des axones callosaux perdant partiellement leur orientation, alors que dans les souris Nkx2.1Cre+/Rosa-DTA+/- et Nkx2.1Cre+/NSE-DTA+/-, l'organisation axonale n'était pas affectée. De plus, les faisceaux hippocampiques du fornix étaient défasciculés dans les trois types de mutants. Par ailleurs, la formation de la commissure antérieure (AC) était complètement absente dans les souris Nkx2.1-/- d'une part, et d'autre part, celle-ci était divisée en deux à trois voies séparées dans les souris Nkx2.1Cre+/Rosa-DTA+/-. Finalement, la AC était soit absente, soit réduite de manière ne former plus qu'un faisceau relativement plus étroit dans les souris Nkx2.1Cre+/NSE-DTA+/- en comparaison avec la AC sauvage. Ces derniers résultats indiquent clairement que les cellules dérivées de Nkx2.1 à la midline, jouent un rôle majeur dans le guidage des axones commissuraux et que, autant les neurones, que les astrocytes « guidepost » dérivés de Nkx2.1, sont des éléments nécessaires au développement correct de ces commissures. En outre, lors de nos investigations sur les souris Nkx2.1-/- et Nkx2.1Cre+/Rosa-DTA+/-, nous avons remarqués des défauts sévères et similaires dans la distribution des erythrocytes et dans la morphologie du réseau de vaisseaux sanguins dans le cerveau embryonnaire des deux mutants précités. Puisque nous n'avons jamais observé de recombinaison de la Cre recombinase dans les vaisseaux sanguins des souris Nkx2.1Cre, nous en avons déduit que les défauts de vaisseaux observés étaient dus à la perte de cellules dérivées de Nkx2.1. Il existerait donc en plus de la fonction cellulaire autonome de Nkx2.1 reconnue pour régulée directement la spécification des cellules endothéliales, une fonction indirecte de Nkx2.1. Afin de déterminer la contribution respective des populations individuelles neuronales ou gliales régulées par Nkx2.1 dans la construction du réseau de vaisseaux sanguins, nous avons utilisé diverses lignées de souris transgéniques. L'utilisation de souris Nkx2.1Cre+/NSE-DTA+/- a indiqué que les neurones dérivés de Nkx2.1 n'étaient pas impliqués dans ce processus. Finalement, afin de discriminer entre les deux populations de cellules gliales dérivées de Nkx2.1, les astroglies et les polydendrocytes, nous avons croisé une lignée de souris NG2-Cre avec des souris Rosa-DTA+/-. Dans ce dernier mutant, le réseau de vaisseaux sanguins du cortex ainsi que la distribution des erythrocytes étaient affectés de la même manière que dans le cortex des souris Nkx2.1Cre+/Rosa-DTA+/-. Par conséquent, ce résultat indique que très probablement, les polydendrocytes NG2+ sont impliqués dans la mise en place du réseau de vaisseaux dans le cerveau. Prises dans leur ensemble, ces observations montrent que durant le développement embryonnaire du cerveau, des sous-populations de glies régulées par Nkx2.1 jouent un rôle de cellules « guidepost » dans le guidage des axones, ainsi que des vaisseaux. Les polydendrocytes sont impliquées dans la régulation de l'angiogenèse tandis que, autant les neurones GABAergiques que les astrocytes collaborent dans le guidage des axones commissuraux en croissance.

The neuronal adhesion protein D2 in differentiating aggregates of brain cells.

The D2-protein is a high molecular weight protein involved in interneuronal adhesion. The concentration of D2-protein was measured both in aggregates of fetal rat telencephalic cells cultured in a chemically defined medium and in developing forebrain. Both the concentration of the D2-protein and the degree of sialylation were changed in the cultures in parallel with the corresponding values obtained from postnatal forebrain. In the cultures the highest specific concentration of D2-protein was observed after 12 days in culture. This value was 2.7 times higher than the average value of adult rat forebrain. Antibodies to D2-protein have previously been shown to inhibit fasciculation of neuritic fibers extending from cultured explants of sympathetic ganglia. We investigated the effect of such antibodies on the differentiation of aggregating telencephalic cells. By adding surplus antibodies to the cultures from day 11 to day 16 we were able to decrease the specific concentration of D2-protein on the neurons by 53% measured at day 19. The decrease was not compensated fully even after further 10 days in the culture. Although the concentration of D2-protein was decreased during the period of synaptogenesis no change was found in the specific concentration of a marker of mature synapses, the D3-protein. Thus, in this culture system synaptogenesis could proceed to an unimpaired extent in the presence of a decreased concentration of a putatively involved adhesion molecule. However, the specific concentration of two markers of myelination, 2',3'-cyclic nucleotide 3'-phosphodiesterase and myelin basic protein, were both increased, suggesting an antibody-induced stimulation of myelination in the cultured aggregates.

Several neuronal and axonal types form long intrinsic connections in the cat primary auditory cortical field (AI).

Intrinsic connections in the cat primary auditory field (AI) as revealed by injections of Phaseolus vulgaris leucoagglutinin (PHA-L) or biocytin, had an anisotropic and patchy distribution. Neurons, labelled retrogradely with PHA-L were concentrated along a dorsoventral stripe through the injection site and rostral to it; the spread of rostrally located neurons was greater after injections into regions of low rather than high characteristic frequencies. The intensity of retrograde labelling varied from weak and granular to very strong and Golgi-like. Out of 313 Golgi like retrogradely labelled neurons 79.6% were pyramidal, 17.2% multipolar, 2.6% bipolar, and 0.6% bitufted; 13.4% were putatively inhibitory, i.e. aspiny or sparsely spiny multipolar, or bitufted. Individual anterogradely labelled intrinsic axons were reconstructed for distances of 2 to 7 mm. Five main types were distinguished on the basis of the branching pattern and the location of synaptic specialisations. Type 1 axons travelled horizontally within layers II to VI and sent collaterals at regular intervals; boutons were only present in the terminal arborizations of these collaterals. Type 2 axons also travelled horizontally within layers II to VI and had rather short and thin collateral branches; boutons or spine-like protrusions occurred in most parts of the axon. Type 3 axons travelled obliquely through the cortex and formed a single terminal arborization, the only site where boutons were found. Type 4 axons travelled for some distance in layer I; they formed a heterogeneous group as to their collaterals and synaptic specializations. Type 5 axons travelled at the interface between layer VI and the white matter; boutons en passant, spine-like protrusions, and thin short branches with boutons en passant were frequent all along their trajectory. Thus, only some axonal types sustain the patchy pattern of intrinsic connectivity, whereas others are involved in a more diffuse connectivity.

Defining responses to therapy and study outcomes in clinical trials of invasive fungal diseases: Mycoses Study Group and European Organization for Research and Treatment of Cancer consensus criteria.

Invasive fungal diseases (IFDs) have become major causes of morbidity and mortality among highly immunocompromised patients. Authoritative consensus criteria to diagnose IFD have been useful in establishing eligibility criteria for antifungal trials. There is an important need for generation of consensus definitions of outcomes of IFD that will form a standard for evaluating treatment success and failure in clinical trials. Therefore, an expert international panel consisting of the Mycoses Study Group and the European Organization for Research and Treatment of Cancer was convened to propose guidelines for assessing treatment responses in clinical trials of IFDs and for defining study outcomes. Major fungal diseases that are discussed include invasive disease due to Candida species, Aspergillus species and other molds, Cryptococcus neoformans, Histoplasma capsulatum, and Coccidioides immitis. We also discuss potential pitfalls in assessing outcome, such as conflicting clinical, radiological, and/or mycological data and gaps in knowledge.

Some aspects of the neuronal cytoskeleton in development.

The review is focused on developmental aspects of the neuronal cytoskeleton, its molecular composition and the intracellular distribution of its elements. It includes a survey of the molecular properties of several cytoskeletal proteins such as tubulins, microtubule-associated proteins, neurofilament subunits, actins and brain spectrins. Furthermore it is addressed how microtubules, neurofilaments, microfilaments and the spectrin-based membrane cytoskeleton are involved in the generation of the neuronal cytoarchitecture, and how changes in the molecular composition of the cytoskeleton during the differentiation process of a neuron may correlate with cell function.

Genomic organization and gene expression in a chromosomal region of Leishmania major.

Little is known about the relation between the genome organization and gene expression in Leishmania. Bioinformatic analysis can be used to predict genes and find homologies with known proteins. A model was proposed, in which genes are organized into large clusters and transcribed from only one strand, in the form of large polycistronic primary transcripts. To verify the validity of this model, we studied gene expression at the transcriptional, post-transcriptional and translational levels in a unique locus of 34kb located on chr27 and represented by cosmid L979. Sequence analysis revealed 115 ORFs on either DNA strand. Using computer programs developed for Leishmania genes, only nine of these ORFs, localized on the same strand, were predicted to code for proteins, some of which show homologies with known proteins. Additionally, one pseudogene, was identified. We verified the biological relevance of these predictions. mRNAs from nine predicted genes and proteins from seven were detected. Nuclear run-on analyses confirmed that the top strand is transcribed by RNA polymerase II and suggested that there is no polymerase entry site. Low levels of transcription were detected in regions of the bottom strand and stable transcripts were identified for four ORFs on this strand not predicted to be protein-coding. In conclusion, the transcriptional organization of the Leishmania genome is complex, raising the possibility that computer predictions may not be comprehensive.

Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication.

Selective pressures related to gene function and chromosomal architecture are acting on genome sequences and can be revealed, for instance, by appropriate genometric methods. Cumulative nucleotide skew analyses, i.e., GC, TA, and ORF orientation skews, predict the location of the origin of DNA replication for 88 out of 100 completely sequenced bacterial chromosomes. These methods appear fully reliable for proteobacteria, Gram-positives, and spirochetes as well as for euryarchaeotes. Based on this genome architecture information, coorientation analyses reveal that in prokaryotes, ribosomal RNA (rRNA) genes encoding the small and large ribosomal subunits are all transcribed in the same direction as DNA replication; that is, they are located along the leading strand. This result offers a simple and reliable method for circumscribing the region containing the origin of the DNA replication and reveals a strong selective pressure acting on the orientation of rRNA genes similar to the weaker one acting on the orientation of ORFs. Rate of coorientation of transfer RNA (tRNA) genes with DNA replication appears to be taxon-specific. Analyzing nucleotide biases such as GC and TA skews of genes and plotting one against the other reveals a taxonomic clusterization of species. All ribosomal RNA genes are enriched in Gs and depleted in Cs, the only so far known exception being the rRNA genes of deuterostomian mitochondria. However, this exception can be explained by the fact that in the chromosome of the human mitochondrion, the model of the deuterostomian organelle genome, DNA replication, and rRNA transcription proceed in opposite directions. A general rule is deduced from prokaryotic and mitochondrial genomes: ribosomal RNA genes that are transcribed in the same direction as the DNA replication are enriched in Gs, and those transcribed in the opposite direction are depleted in Gs.

The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture.

Using numerical simulations, we investigate the underlying physical effects responsible for the overall organization of chromosomal territories in interphase nuclei. In particular, we address the following three questions: (i) why are chromosomal territories with relatively high transcriptional activity on average, closer to the centre of cell's nucleus than those with the lower activity? (ii) Why are actively transcribed genes usually located at the periphery of their chromosomal territories? (iii) Why are pair-wise contacts between active and inactive genes less frequent than those involving only active or only inactive genes? We show that transcription factories-mediated contacts between active genes belonging to different chromosomal territories are instrumental for all these features of nuclear organization to emerge spontaneously due to entropic effects arising when chromatin fibres are highly crowded.

Gene organization of the mating type regions in the ectomycorrhizal fungus Laccaria bicolor reveals distinct evolution between the two mating type loci

In natural conditions, basidiomycete ectomycorrhizal fungi such as Laccaria bicolor are typically in the dikaryotic state when forming symbioses with trees, meaning that two genetically different individuals have to fuse or 'mate'. Nevertheless, nothing is known about the molecular mechanisms of mating in these ecologically important fungi. Here, advantage was taken of the first sequenced genome of the ectomycorrhizal fungus, Laccaria bicolor, to determine the genes that govern the establishment of cell-type identity and orchestrate mating. The L. bicolor mating type loci were identified through genomic screening. The evolutionary history of the genomic regions that contained them was determined by genome-wide comparison of L. bicolor sequences with those of known tetrapolar and bipolar basidiomycete species, and by phylogenetic reconstruction of gene family history. It is shown that the genes of the two mating type loci, A and B, are conserved across the Agaricales, but they are contained in regions of the genome with different evolutionary histories. The A locus is in a region where the gene order is under strong selection across the Agaricales. By contrast, the B locus is in a region where the gene order is likely under a low selection pressure but where gene duplication, translocation and transposon insertion are frequent.

Concise reviews: in vitro-produced pancreas organogenesis models in three dimensions: self-organization from few stem cells or progenitors.

Three-dimensional models of organ biogenesis have recently flourished. They promote a balance between stem/progenitor cell expansion and differentiation without the constraints of flat tissue culture vessels, allowing for autonomous self-organization of cells. Such models allow the formation of miniature organs in a dish and are emerging for the pancreas, starting from embryonic progenitors and adult cells. This review focuses on the currently available systems and how these allow new types of questions to be addressed. We discuss the expected advancements including their potential to study human pancreas development and function as well as to develop diabetes models and therapeutic cells.

Neuronal adaptation effects in decision making

Recently, there has been an increased interest on the neural mechanisms underlying perceptual decision making. However, the effect of neuronal adaptation in this context has not yet been studied. We begin our study by investigating how adaptation can bias perceptual decisions. We considered behavioral data from an experiment on high-level adaptation-related aftereffects in a perceptual decision task with ambiguous stimuli on humans. To understand the driving force behind the perceptual decision process, a biologically inspired cortical network model was used. Two theoretical scenarios arose for explaining the perceptual switch from the category of the adaptor stimulus to the opposite, nonadapted one. One is noise-driven transition due to the probabilistic spike times of neurons and the other is adaptation-driven transition due to afterhyperpolarization currents. With increasing levels of neural adaptation, the system shifts from a noise-driven to an adaptation-driven modus. The behavioral results show that the underlying model is not just a bistable model, as usual in the decision-making modeling literature, but that neuronal adaptation is high and therefore the working point of the model is in the oscillatory regime. Using the same model parameters, we studied the effect of neural adaptation in a perceptual decision-making task where the same ambiguous stimulus was presented with and without a preceding adaptor stimulus. We find that for different levels of sensory evidence favoring one of the two interpretations of the ambiguous stimulus, higher levels of neural adaptation lead to quicker decisions contributing to a speed–accuracy trade off.

The neuronal basis of attention: rate versus synchronization modulation

Extensive theoretical and experimental work on the neuronal correlates of visual attention raises two hypotheses about the underlying mechanisms. The first hypothesis, named biased competition, originates from experimental single-cell recordings that have shown that attention upmodulates the firing rates of the neurons encoding the attended features and downregulates the firing rates of the neurons encoding the unattended features. Furthermore, attentional modulation of firing rates increases along the visual pathway. The other, newer hypothesis assigns synchronization a crucial role in the attentional process. It stems from experiments that have shown that attention modulates gamma-frequency synchronization. In this paper, we study the coexistence of the two phenomena using a theoretical framework. We find that the two effects can vary independently of each other and across layers. Therefore, the two phenomena are not concomitant. However, we show that there is an advantage in the processing of information if rate modulation is accompanied by gamma modulation, namely that reaction times are shorter, implying behavioral relevance for gamma synchronization.