Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm

Background

Male-factor infertility is a common condition, and etiology is unknown for a high proportion of cases. Abnormal epigenetic programming of the germline is proposed as a possible mechanism compromising spermatogenesis of some men currently diagnosed with idiopathic infertility. During germ cell maturation and gametogenesis, cells of the germ line undergo extensive epigenetic reprogramming. This process involves widespread erasure of somatic-like patterns of DNA methylation followed by establishment of sex-specific patterns by de novo DNA methylation. Incomplete reprogramming of the male germ line could, in theory, result in both altered sperm DNA methylation and compromised spermatogenesis.

Methodology/Principal Finding

We determined concentration, motility and morphology of sperm in semen samples collected by male members of couples attending an infertility clinic. Using MethyLight and Illumina assays we measured methylation of DNA isolated from purified sperm from the same samples. Methylation at numerous sequences was elevated in DNA from poor quality sperm.

Conclusions

This is the first report of a broad epigenetic defect associated with abnormal semen parameters. Our results suggest that the underlying mechanism for these epigenetic changes may be improper erasure of DNA methylation during epigenetic reprogramming of the male germ line.     

Mode of action of acidocin D20079, a bacteriocin produced by the potential probiotic strain, <Emphasis Type="Italic">Lactobacillus acidophilus</Emphasis> DSM 20079

Lactobacillus acidophilus DSM 20079 is the producer of a novel bacteriocin termed acidocin D20079. In this paper, mode of action using three various concentrations of acidocin D20079 (2,048, 128 and 11.3 AU/ml) was determined against an indicator strain L. delbrueckii subsp. lactis DSM 20076. These concentrations all led to marked decreases in both the number of viable cells and in optical density, indicating that the activity of the acidocin D20079 was bactericidal with concomitant cell lysis. Moreover, the probiotic potential of L. acidophilus DSM 20079 was analyzed for its ability to survive and retain viability at conditions (acid and bile concentrations) mimicking the gastrointestinal (GI) tract, under which it survived exposure to pH 2.0 with a 1.2 log cycle reduction in viability and where 45% of the original population survived in a medium containing 0.3% bile for 3 h.     

A molecular machine biosensor: construction, predictive models and experimental studies

This paper describes the construction, operation and predictive modeling of a molecular machine, functioning as a high sensitivity biosensor. Embedded gramicidin A (gA) ionchannels in a self-assembled tethered lipid bilayer act as biological switches in response to target molecules and provide a signal amplification mechanism that results in high sensitivity molecular detection. The biosensor can be used as a rapid and sensitive point of care diagnostic device in different media such as human serum, plasma and whole blood without the need for pre and post processing steps required in an enzyme-linked immunosorbent assay. The electrical reader of the device provides the added advantage of objective measurement. Novel ideas in the construction of the molecular machine, including fabrication of biochip arrays, and experimental studies of its ability to detect analyte molecules over a wide range of concentrations are presented. Remarkably, despite the complexity of the device, it is shown that the response can be predicted by modeling the analyte fluid flow and surface chemical reactions. The derived predictive models for the sensing dynamics also facilitate determining important variables in the design of a molecular machine such as the ion channel lifetime and diffusion dynamics within the bilayer lipid membrane as well as the bio-molecular interaction rate constants.     

Selection of aptamers for a protein target in cell lysate and their application to protein purification

Functional genomics requires structural and functional studies of a large number of proteins. While the production of proteins through over-expression in cultured cells is a relatively routine procedure, the subsequent protein purification from the cell lysate often represents a significant challenge. The most direct way of protein purification from a cell lysate is affinity purification using an affinity probe to the target protein. It is extremely difficult to develop antibodies, classical affinity probes, for a protein in the cell lysate; their development requires a pure protein. Thus, isolating the protein from the cell lysate requires antibodies, while developing antibodies requires a pure protein. Here we resolve this loop problem. We introduce AptaPIC, Aptamer-facilitated Protein Isolation from Cells, a technology that integrates (i) the development of aptamers for a protein in cell lysate and (ii) the utilization of the developed aptamers for protein isolation from the cell lysate. Using MutS protein as a target, we demonstrate that this technology is applicable to the target protein being at an expression level as low as 0.8% of the total protein in the lysate. AptaPIC has the potential to considerably speed up the purification of proteins and, thus, accelerate their structural and functional studies.     

Discovery of a novel HCV helicase inhibitor by a de novo drug design approach

Herein we report a successful application of a computer-aided design approach to identify a novel HCV helicase inhibitor. A de novo drug design methodology was used to generate an initial set of structures that could potentially bind to a putative binding site. Further structure refinement was carried out through docking a series of focused virtual libraries. The most promising compound was synthesised and it exhibited a submicromolar inhibition of the HCV helicase.     

Human embryonic stem cell-derived neural precursor transplants in collagen scaffolds promote recovery in injured rat spinal cord

Background aimsSeveral studies have reported functional improvement after transplantation of in vivo-derived neural progenitor cells (NPC) into injured spinal cord. However, the potential of human embryonic stem cell-derived NPC (hESC-NPC) as a tool for cell replacement of spinal cord injury (SCI) should be considered.MethodsWe report on the generation of NPC as neural-like tubes in adherent and feeder-free hESC using a defined media supplemented with growth factors, and their transplantation in collagen scaffolds in adult rats subjected to midline lateral hemisection SCI.ResultshESC-NPC were highly expressed molecular features of NPC such as Nestin, Sox1 and Pax6. Furthermore, these cells exhibited the multipotential characteristic of differentiating into neurons and glials in vitro. Implantation of xenografted hESC-NPC into the spinal cord with collagen scaffold improved the recovery of hindlimb locomotor function and sensory responses in an adult rat model of SCI. Analysis of transplanted cells showed migration toward the spinal cord and both neural and glial differentiation in vivo.ConclusionsThese findings show that transplantation of hESC-NPC in collagen scaffolds into an injured spinal cord may provide a new approach to SCI.     

Linkage and sequence analysis indicate that CCBE1 is mutated in recessively inherited generalised lymphatic dysplasia

Generalised lymphatic dysplasia (GLD) is characterised by extensive peripheral lymphoedema with visceral involvement. In some cases, it presents in utero with hydrops fetalis. Autosomal dominant and recessive inheritance has been reported. A large, non-consanguineous family with three affected siblings with generalised lymphatic dysplasia is presented. One child died aged 5 months, one spontaneously miscarried at 17 weeks gestation, and the third has survived with extensive lymphoedema. All three presented with hydrops fetalis. There are seven other siblings who are clinically unaffected. Linkage analysis produced two loci on chromosome 18, covering 22 Mb and containing 150 genes, one of which is CCBE1. A homozygous cysteine to serine change in CCBE1 has been identified in the proband, in a residue that is conserved across species. High density SNP analysis revealed homozygosity (a region of 900 kb) around the locus for CCBE1 in all three affected cases. This indicates a likely ancestral mutation that is common to both parents; an example of a homozygous mutation representing Identity by Descent (IBD) in this pedigree. Recent studies in zebrafish have shown this gene to be required for lymphangiogenesis and venous sprouting and are therefore supportive of our findings. In view of the conserved nature of the cysteine, the nature of the amino acid change, the occurrence of a homozygous region around the locus, the segregation within the family, and the evidence from zebrafish, we propose that this mutation is causative for the generalised lymphatic dysplasia in this family, and may be of relevance in cases of non-immune hydrops fetalis.     

Integrating the costs of plant toxins and predation risk in foraging decisions of a mammalian herbivore

Foraging herbivores must satisfy their nutrient requirements in a world of toxic plants while also avoiding predators. Plant toxins and perceived predation risk at food patches should both reduce patch residency time, but the relative strengths of these factors on feeding decisions has rarely been quantified. Using an arboreal generalist herbivore, the common brushtail possum Trichosurus vulpecula, we tested the effects on food intake of the plant toxin, cineole, and regurgitated pellets from one of its predators, the powerful owl Ninox strenua at the small spatial scale of the food patch. We used the giving-up density (GUD) framework, with animals harvesting food items (sultanas) in an inedible matrix (small pebbles). We ran two consecutive field experiments in a eucalypt woodland in eastern Australia, 1 month apart in the same location. In experiment 1, there was a significant interaction between cineole [at 17% of dry matter (DM)] and owl pellets. The GUD was lowest in the absence of both cineole and owl pellet, intermediate in the presence of owl pellet; and highest with cineole ± owl pellet. The effect of owl pellet diminished over time. In experiment 2, only cineole (at 10% DM) increased the GUD significantly. The difference in effect of owl pellet was probably due to both habituation and freshness of the cue. Our study demonstrates the importance of synthesising predator–prey and plant–herbivore ecology to better understand the complex set of constraints influencing foraging herbivores. The greater effect of toxin than fear on possums is likely to be due to its high, but ecologically relevant concentration. This highlights the need to explore the relative and net impacts of a range of concentrations of plant toxins and predation risks.     

Cucurbitacins from Bryonia cretica

From the roots of Bryonia cretica L. two new cucurbitacins, isocucurbitacins G (1) and H (2), along with three known cucrbitacins, cucurbitacins G (3), H (4), and J (5) were isolated. The structures of 1 and 2 were determined on the basis of 1D and 2D NMR spectroscopic analysis and X-ray crystallography. The relative stereochemistries of the side chains of 3–5 were also established by comparison of their NMR data and X-ray crystallography.     

Retinal patterning by Pax6‐dependent cell adhesion molecules

Long‐standing evidence gained from Pax6 mutant embryos pointed to an involvement of Pax6‐dependent cell adhesion molecules in patterning the central nervous system and, in particular, the retina. However, direct evidence for such pathways remained elusive. We here present direct evidence that knockdown of Pax6 expression by morpholino antisense molecules in Xenopus embryos and knockdown of maternal N‐cadherin (mNcad), N‐cadherin (Ncad) and neural cell adhesion molecule (NCAM) produce similar phenotypes. Eye formation is reduced and retinal lamination is heavily disorganized. In Pax6 knockdown embryos, the levels of mRNAs coding for these cell adhesion molecules are markedly reduced. Overexpression of Pax6 efficiently rescues the phenotype of Pax6 knockdown embryos and restores expression of these putative target genes. Rescue of Pax6‐deficiency by the putative target gene mNcad moderately rescues eye formation. The promoters of the genes coding for cell adhesion molecules contain several putative Pax6 binding sites, as determined by computer analysis. Chromatin immunoprecipitation shows that, in embryonic heads, Pax6 binds to promoter regions containing such predicted binding sites. Thus, several cell adhesion molecules are direct target genes of Pax6 and cooperate in retinal patterning. © 2010 Wiley Periodicals, Inc. Develop Neurobiol 70: 764–780, 2010