The Demoiselle of X-Inactivation: 50 Years Old and As Trendy and Mesmerising As Ever

In humans, sexual dimorphism is associated with the presence of two X chromosomes in the female, whereas males possess only one X and a small and largely degenerate Y chromosome. How do men cope with having only a single X chromosome given that virtually all other chromosomal monosomies are lethal? Ironically, or even typically many might say, women and more generally female mammals contribute most to the job by shutting down one of their two X chromosomes at random. This phenomenon, called X-inactivation, was originally described some 50 years ago by Mary Lyon and has captivated an increasing number of scientists ever since. The fascination arose in part from the realisation that the inactive X corresponded to a dense heterochromatin mass called the “Barr body” whose number varied with the number of Xs within the nucleus and from the many intellectual questions that this raised: How does the cell count the X chromosomes in the nucleus and inactivate all Xs except one? What kind of molecular mechanisms are able to trigger such a profound, chromosome-wide metamorphosis? When is X-inactivation initiated? How is it transmitted to daughter cells and how is it reset during gametogenesis? This review retraces some of the crucial findings, which have led to our current understanding of a biological process that was initially considered as an exception completely distinct from conventional regulatory systems but is now viewed as a paradigm “par excellence” for epigenetic regulation

Computations of cuspidal cohomology of congruence subgroups of SL(3, Z)

Algorithms are presented which find a basis of the vector space of cuspidal cohomology of certain congruence subgroups of SL(3, ) and which determine the action of the Hecke operators on this space. These algorithms were implemented on a computer. Four pairs of cuspidal classes were found with prime level less than 100. Tables are given of the eigenvalues of the first few Hecke operators on these classes

Natively Unstructured Loops Differ from Other Loops

Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%–70% of all worm proteins observed to have more than seven protein–protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested that long unstructured loops are a major part of unstructured regions in molecular networks

Oligomycin resistant mutants of Saccharomyces Cerevisiae : the class structure

A series of oligomycin resistant mutants has been isolated following u.v. irradiation. The phenotypic and genotypic properties of these mutants, which show high levels of resistance to oligomycin and rutamycin, have been investigated and, on the basis of these results, it has been possible to divide the mutants into two main classes, class I and class II. Class I Mutants of this class show low levels of cross resistance (increases of two-to-four-fold) to various uncouplers such as TTFB, 1799 and chloro CCP, to inhibitors of oxidative phosphorylation like aurovertin and triethyltin, to the inhibitor of electron transport, antimycin A, and protein synthesis inhibitors such as cycloheximide, mikamycin, chloramphenicol and erythromycin. The mutants are apparently, however, resistant to neither DNP nor octylDNP. In a high percentage of the mutants, exposure to low temperatures (20ºC) resulted in the loss of the primary resistance to oligomycin and rutamycin, though the secondary cross resistances were apparently unaffected. No effect of either high or low temperatures on either the fermentable or non-fermentable growth of these mutants were apparent. No alteration in the growth rate of the majority of the strains or in their appearance on electron microscopic examination was detected, though their growth yield is 15 – 20% lower than the wild type strain. Genetic analysis has revealed that this class of mutant clearly differs genotypically as well as phenotypically from the class II mutants and moreover, had indicated that the determinant controlling oligomycin resistance is a nuclear gene. The genetics of the mutants exhibited many anomalous features, which remain to be explained, many of the experiments in this thesis describing, rather than explaining the phenomena observed. Class II The mutants in this class show resistance only to oligomycin and rutamycin. No cold or heat sensitivity of growth was observed and only one mutant in this class shoed any temperature sensitivity with regard to its oligomycin resistance. No alteration in the growth rate, growth yield or mitochondrial morphology of any of the mutants in this class was found. Genetic analysis of these mutants revealed that all the mutants tested showed cytoplasmic inheritance, the genetic determinant being located on the mitochondrial DNA. Allelism tests have demonstrated that genotypically the class is not homogeneous and the mutants were sub-divided into two non-allelic recombination groups. The genetic determinants concerned in each sub-group were confirmed to lie on mDNA

The MouseTsxGene Is Expressed in Sertoli Cells of the Adult Testis and Transiently in Premeiotic Germ Cells during Puberty

AbstractTsxis a gene of unknown function that was previously shown to be expressed specifically in the testis. In order to gain insight into the function ofTsxits pattern of expression was characterized with regard to both timing and cell type in the testis. Northern blot analysis of early postnatal testes showed not only thatTsxmessage was detectable shortly after birth, but that it increased substantially between 7 and 12 days postpartum (dpp), roughly coincident with the onset of meiosis in the mouse. AlternativeTsxtranscripts, detected by RT-PCR, included a spliced form that first appeared at around 12 dpp.In situhybridization revealedTsxsignal in the somatic Sertoli cells of the adult testis. Consistent with the data from Northern blots,in situhybridization signal was first detectable in normal pubertal testes at 12 dpp. An anti-Tsx polyclonal antiserum specifically stained premeiotic germ cells in addition to Sertoli cells of pubertal testes at 16, 19, and 27 dpp. Tsx immunostaining in germ cells was nuclear, while Sertoli cells displayed signal throughout the cytoplasm and nucleus. In the adult, Tsx was detected exclusively in Sertoli cells. In contrast, in the adult testis of the oligotriche (olt) mutant, where spermatogenesis is blocked after meiosis, Tsx protein was still present in the spermatogonial nuclei of a subset of tubules. Taken together, these results demonstrate thatTsxexpression is induced in both premeiotic germ cells and Sertoli cells during the first wave of spermatogenesis, but that expression is maintained at a detectable level only in Sertoli cells of the normal adult. The persistence ofTsxexpression seen in spermatogonia of the adultoltmutant supports the hypothesis that during the first wave of normal spermatogenesis, the advent of a late-stage cell type, either elongating spermatid or spermatozoan, is responsible for extinguishing expression in spermatogonia in normal adult testis. To our knowledge,Tsxis the first gene to show a pattern of germ cell expression that is apparently specific to the pubertal testis

A role for non-coding Tsix transcription in partitioning chromatin domains within the mouse X-inactivation centre

<p>Abstract</p> <p>Background</p> <p>Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region (<it>Xic</it>), the <it>Xist </it>locus, which triggers X-inactivation, is juxtaposed to a large domain of H3K27 trimethylation (H3K27me3).</p> <p>Results</p> <p>We describe here that developmentally regulated transcription of <it>Tsix</it>, a crucial non-coding antisense to <it>Xist</it>, is required to block the spreading of the H3K27me3 domain to the adjacent H3K4me2-rich <it>Xist </it>region. Analyses of a series of distinct <it>Tsix </it>mutations suggest that the underlying mechanism involves the RNA Polymerase II accumulating at the <it>Tsix </it>3'-end. Furthermore, we report additional unexpected long-range effects of <it>Tsix </it>on the distal sub-region of the <it>Xic</it>, involved in <it>Xic</it>-<it>Xic </it>trans-interactions.</p> <p>Conclusion</p> <p>These data point toward a role for transcription of non-coding RNAs as a developmental strategy for the establishment of functionally distinct domains within the mammalian genome.</p

Epidermal growth factor receptor tyrosine kinase inhibition is not protective in PCK rats

Epidermal growth factor receptor tyrosine kinase inhibition is not protective in PCK rats.BackgroundAdvances in the understanding of cystogenesis, identification of the PKHD1 gene and availability of a rat model (the PCK rat) caused by a Pkhd1 mutation facilitate testing of therapies for autosomal-recessive polycystic kidney disease (ARPKD). Considerable support exists for the importance of the epidermal growth factor (EGF)/transforming growth factor-alpha (TGF-α)/EGF receptor (EGFR) axis and of the adenylyl cyclase-adenosine 3′,5′-cyclic monophosphate (cAMP) pathway in the pathogenesis of cyst formation and progressive enlargement.MethodsTo determine whether EGFR tyrosine kinase inhibition is protective in the PCK rat, male and female animals were treated with EKI-785 or EKB-569 or with vehicle alone between 3 and 10 weeks of age. Biochemical and histomorphometric analysis, immunohistochemistry, immunoblotting, enzyme immunoassay, and quantitative reverse transcription-polymerase chain reaction (RT-PCR) were used to ascertain the effects of treatment.ResultsContrary to other murine models of ARPKD, overexpression and apical mislocalization of EGFR were not detected in the PCK rats. Consistent with these expression results, EKI-785 or EKB-569 administration had no effect or worsened PKD, and had no effect on the development of fibrocystic liver disease. Increased renal cAMP and vasopressin V2 receptor expression were observed in the EKI-785–treated animals.ConclusionEGFR tyrosine kinase inhibition did not protect PCK rats from the development of PKD. This may be due to effects on collecting duct cAMP that counteract possible beneficial effects on the extracellular-regulated protein kinase (ERK)/mitogen-activated protein kinase (MAPK) pathway, particularly in the absence of EGFR overexpression or mislocalization. The relevance of these observations to the treatment of human cystic kidney diseases deserves further study

Network Representation of T-Cell Repertoire— A Novel Tool to Analyze Immune Response to Cancer Formation

The T cell repertoire potentially presents complexity compatible, or greater than, that of the human brain. T cell based immune response is involved with practically every part of human physiology, and high-throughput biology needed to follow the T-cell repertoire has made great leaps with the advent of massive parallel sequencing [1]. Nevertheless, tools to handle and observe the dynamics of this complexity have only recently started to emerge [e.g., 2, 3, 4] in parallel with sequencing technologies. Here, we present a network-based view of the dynamics of the T cell repertoire, during the course of mammary tumors development in a mouse model. The transition from the T cell receptor as a feature, to network-based clustering, followed by network-based temporal analyses, provides novel insights to the workings of the system and provides novel tools to observe cancer progression via the perspective of the immune system. The crux of the approach here is at the network-motivated clustering. The purpose of the clustering step is not merely data reduction and exposing structures, but rather to detect hubs, or attractors, within the T cell receptor repertoire that might shed light on the behavior of the immune system as a dynamic network. The Clone-Attractor is in fact an extension of the clone concept, i.e., instead of looking at particular clones we observe the extended clonal network by assigning clusters to graph nodes and edges to adjacent clusters (editing distance metric). Viewing the system as dynamical brings to the fore the notion of an attractors landscape, hence the possibility to chart this space and map the sample state at a given time to a vector in this large space. Based on this representation we applied two different methods to demonstrate its effectiveness in identifying changes in the repertoire that correlate with changes in the phenotype: (1) network analysis of the TCR repertoire in which two measures were calculated and demonstrated the ability to differentiate control from transgenic samples, and, (2) machine learning classifier capable of both stratifying control and trangenic samples, as well as to stratify pre-cancer and cancer samples

Phase separation drives X-chromosome inactivation: a hypothesis

The long non-coding RNA Xist induces heterochromatinization of the X chromosome by recruiting repressive protein complexes to chromatin. Here we gather evidence, from the literature and from computational analyses, showing that Xist assemblies are similar in size, shape and composition to phase-separated condensates, such as paraspeckles and stress granules. Given the progressive sequestration of Xist’s binding partners during X-chromosome inactivation, we formulate the hypothesis that Xist uses phase separation to perform its function