Methylation Status of Imprinted Genes and Repetitive Elements in Sperm DNA from Infertile Males

Stochastic, environmentally and/or genetically induced disturbances in the genome-wide epigenetic reprogramming processes during male germ-cell development may contribute to male infertility. To test this hypothesis, we have studied the methylation levels of 2 paternally (H19 and GTL2) and 5 maternally methylated (LIT1, MEST, NESPAS, PEG3, and SNRPN) imprinted genes, as well as of ALU and LINE1 repetitive elements in 141 sperm samples, which were used for assisted reproductive technologies (ART), including 106 couples with strictly male-factor or combined male and female infertility and 28 couples with strictly female-factor infertility. Aberrant methylation imprints showed a significant association with abnormal semen parameters, but did not seem to influence ART outcome. Repeat methylation also differed significantly between sperm samples from infertile and presumably fertile males. However, in contrast to imprinted genes, ALU methylation had a significant impact on pregnancy and live-birth rate in couples with male-factor or combined infertility. ALU methylation was significantly high-er in sperm samples leading to pregnancy and live-birth than in those that did not. Sperm samples leading to abortions showed significantly lower ALU methylation levels than those leading to the birth of a baby. Copyright (C) 2011 S. Karger AG, Base

Green Function Monte Carlo with Stochastic Reconfiguration

A new method for the stabilization of the sign problem in the Green Function Monte Carlo technique is proposed. The method is devised for real lattice Hamiltonians and is based on an iterative ''stochastic reconfiguration'' scheme which introduces some bias but allows a stable simulation with constant sign. The systematic reduction of this bias is in principle possible. The method is applied to the frustrated J1-J2 Heisenberg model, and tested against exact diagonalization data. Evidence of a finite spin gap for J2/J1 >~ 0.4 is found in the thermodynamic limit.Comment: 13 pages, RevTeX + 3 encapsulated postscript figure

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data

Summary: Here we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors. Availability and implementation: BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html. The package is distributed under the GNU Lesser General Public License 3.0. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Direct magneto-optical compression of an effusive atomic beam for high-resolution focused ion beam application

An atomic rubidium beam formed in a 70 mm long two-dimensional magneto-optical trap (2D MOT), directly loaded from a collimated Knudsen source, is analyzed using laser-induced fluorescence. The longitudinal velocity distribution, the transverse temperature and the flux of the atomic beam are reported. The equivalent transverse reduced brightness of an ion beam with similar properties as the atomic beam is calculated because the beam is developed to be photoionized and applied in a focused ion beam. In a single two-dimensional magneto-optical trapping step an equivalent transverse reduced brightness of $(1.0\substack{+0.8-0.4})$ $\times 10^6$ A/(m$^2$ sr eV) was achieved with a beam flux equivalent to $(0.6\substack{+0.3-0.2})$ nA. The temperature of the beam is further reduced with an optical molasses after the 2D MOT. This increased the equivalent brightness to $(6\substack{+5-2})$$\times 10^6$ A/(m$^2$ sr eV). For currents below 10 pA, for which disorder-induced heating can be suppressed, this number is also a good estimate of the ion beam brightness that can be expected. Such an ion beam brightness would be a six times improvement over the liquid metal ion source and could improve the resolution in focused ion beam nanofabrication.Comment: 10 pages, 8 figures, 1 tabl

A High Density of Human Communication-Associated Genes in Chromosome 7q31-q36: Differential Expression in Human and Non-Human Primate Cortices

The human brain is distinguished by its remarkable size, high energy consumption, and cognitive abilities compared to all other mammals and non-human primates. However, little is known about what has accelerated brain evolution in the human lineage. One possible explanation is that the appearance of advanced communication skills and language has been a driving force of human brain development. The phenotypic adaptations in brain structure and function which occurred on the way to modern humans may be associated with specific molecular signatures in today’s human genome and/or transcriptome. Genes that have been linked to language, reading, and/or autism spectrum disorders are prime candidates when searching for genes for human-specific communication abilities. The database and genome-wide expression analyses we present here revealed a clustering of such communication-associated genes (COAG) on human chromosomes X and 7, in particular chromosome 7q31-q36. Compared to the rest of the genome, we found a high number of COAG to be differentially expressed in the cortices of humans and non-human primates (chimpanzee, baboon, and/or marmoset). The role of X-linked genes for the development of human-specific cognitive abilities is well known. We now propose that chromosome 7q31-q36 also represents a hot spot for the evolution of human-specific communication abilities. Selective pressure on the T cell receptor beta locus on chromosome 7q34, which plays a pivotal role in the immune system, could have led to rapid dissemination of positive gene variants in hitchhiking COAG

Unbalanced segregation of a paternal t(9;11)(p24.3;p15.4) translocation causing familial Beckwith-Wiedemann syndrome: a case report.

BACKGROUND: The vast majority of cases with Beckwith-Wiedemann syndrome (BWS) are caused by a molecular defect in the imprinted chromosome region 11p15.5. The underlying mechanisms include epimutations, uniparental disomy, copy number variations, and structural rearrangements. In addition, maternal loss-of-function mutations in CDKN1C are found. Despite growing knowledge on BWS pathogenesis, up to 20% of patients with BWS phenotype remain without molecular diagnosis. CASE PRESENTATION: Herein, we report an Iranian family with two females affected with BWS in different generations. Bisulfite pyrosequencing revealed hypermethylation of the H19/IGF2: intergenic differentially methylated region (IG DMR), also known as imprinting center 1 (IC1) and hypomethylation of the KCNQ1OT1: transcriptional start site (TSS) DMR (IC2). Array CGH demonstrated an 8 Mb duplication on chromosome 11p15.5p15.4 (205,827-8,150,933) and a 1 Mb deletion on chromosome 9p24.3 (209,020-1,288,114). Chromosome painting revealed that this duplication-deficiency in both patients is due to unbalanced segregation of a paternal reciprocal t(9;11)(p24.3;p15.4) translocation. CONCLUSIONS: This is the first report of a paternally inherited unbalanced translocation between the chromosome 9 and 11 short arms underlying familial BWS. Copy number variations involving the 11p15.5 region are detected by the consensus diagnostic algorithm. However, in complex cases which do not only affect the BWS region itself, characterization of submicroscopic chromosome rearrangements can assist to estimate the recurrence risk and possible phenotypic outcomes

A family case of fertile human 45,X,psu dic(15;Y) males

We report on a familial case including four male probands from three generations with a 45,X,psu dic(15;Y)(p11.2;q12) karyotype. 45,X is usually associated with a female phenotype and only rarely with maleness, due to translocation of small Y chromosomal fragments to autosomes. These male patients are commonly infertile because of missing azoospermia factor regions from the Y long arm. In our familial case we found a pseudodicentric translocation chromosome, that contains almost the entire chromosomes 15 and Y. The translocation took place in an unknown male ancestor of our probands and has no apparent effect on fertility and phenotype of the carrier. FISH analysis demonstrated the deletion of the pseudoautosomal region 2 (PAR2) from the Y chromosome and the loss of the nucleolus organizing region (NOR) from chromosome 15. The formation of the psu dic(15;Y) chromosome is a reciprocal event to the formation of the satellited Y chromosome (Yqs). Statistically, the formation of 45,X,psu dic(15;Y) (p11.2;q12) is as likely as the formation of Yqs. Nevertheless, it has not been described yet. This can be explained by the dicentricity of this translocation chromosome that usually leads to mitotic instability and meiotic imbalances. A second event, a stable inactivation of one of the two centromeres is obligatory to enable the transmission of the translocation chromosome and thus a stably reduced chromosome number from father to every son in this family

Charge fluctuations close to phase separation in the two dimensional t-J model

We have studied the t-J model using the Green Function Monte Carlo technique. We have obtained accurate energies well converged in the thermodynamic limit, by performing simulations up to 242 lattice sites. By studying the energy as a function of hole doping we conclude that there is no phase separation in the physical region, relevant for HTc superconductors. This finding is further supported by the hole-hole correlation function calculation. Remarkably, by approaching the phase separation instability, for $J_c/t\sim 0.5$,this function displays enhanced fluctuations at incommensurate wavevectors, scaling linearly with the doping, in agreement with experimental findings.Comment: To appear on Phys. Rev. Let

Green Function Monte Carlo with Stochastic Reconfiguration: an effective remedy for the sign problem disease

A recent technique, proposed to alleviate the ``sign problem disease'', is discussed in details. As well known the ground state of a given Hamiltonian $H$ can be obtained by applying the imaginary time propagator $e^{-H \tau}$ to a given trial state $\psi_T$ for large imaginary time $\tau$ and sampling statistically the propagated state $\psi_{\tau} = e^{-H \tau} \psi_T$. However the so called ``sign problem'' may appear in the simulation and such statistical propagation would be practically impossible without employing some approximation such as the well known ``fixed node'' approximation (FN). This method allows to improve the FN dynamic with a systematic correction scheme. This is possible by the simple requirement that, after a short imaginary time propagation via the FN dynamic, a number $p$ of correlation functions can be further constrained to be {\em exact} by small perturbation of the FN propagated state, which is free of the sign problem. By iterating this scheme the Monte Carlo average sign, which is almost zero when there is sign problem, remains stable and finite even for large $\tau$. The proposed algorithm is tested against the exact diagonalization results available on finite lattice. It is also shown in few test cases that the dependence of the results upon the few parameters entering the stochastic technique can be very easily controlled, unless for exceptional cases.Comment: 44 pages, RevTeX + 5 encaplulated postscript figure