A perinuclear theca substructure is formed during epididymal guinea pig sperm maturation and disappears in acrosome reacted cells

The perinuclear theca (PT) is a unique cytoskeletal mammalian sperm structure that surrounds the nucleus. Using negatively stained whole-mount preparations, we detected a PT substructure on the apical region of the postacrosomal theca layer of guinea pig spermatozoa. The PT substructure consists of projections resembling eyelashes, circling the sperm head. The PT substructure was absent in caput but appeared in corpus epidydimal spermatozoa. The same finding was observed in sheep and rabbit spermatozoa. The PT substructure persisted in capacitating spermatozoa, but was absent in acrosome reacted gametes. No labeling of the PT substructure was observed by the immunogold technique using antibodies against calmodulin, spectrin, myosin, and vimentin. A 34-kDa band appeared as a possible PT substructure protein. The PT was positive to the antibodies and the presence of the above-mentioned proteins was confirmed by Western blot. F-actin gold label was observed in mature spermatozoa on the PT substructure base zone. Results using cytochalasin D and phalloidin point to a role of F-actin in the PT substructure formation/disassembly processes. Ca(2+), bicarbonate, and proteases might be involved in the mechanism of the substructure disassembly. Novel PT morphological changes occurring during sperm epidydimal maturation and at acrosome reaction, respectively, are discussed in relation to the PT stability and function.     

Communication of stabilizing energy between substructures of a protein

Thermodynamic communication between protein substructures has been investigated by determining the stabilizing effect of mutations at position 52 in the least stable, N-yellow, substructure of cytochrome c on the second least stable, Red, and most stable, Blue, substructures of the protein. A Lys 73 --> His (H73) variant of iso-1-cytochrome c, containing these mutations was used to measure the stability of the Red substructure of cytochrome c through the pH and guanidine hydrochloride (gdnHCl) dependence of the His 73-mediated alkaline conformational transition. The stability of the Blue substructure was measured by global unfolding with gdnHCl and increased by 1 to 3.5 kcal/mol versus the H73 variant. The data demonstrate that the increase in stability of the Red substructure is similar to the increase in global stability, consistent with upward propagation of stabilizing energy from less (N-yellow) to more stable (Red and Blue) protein substructures. The result also supports sequential rather than independent unfolding of the N-yellow and Red substructures of cytochrome c. The data indicate that a leucine at position 52 alters the nature of partial unfolding of the Red substructure, a surprising effect for a single-site mutation. For all variants, the thermodynamics of formation of the Lys 79 alkaline state, which does not unfold the entire Red substructure, shows less stabilization of the portion of the protein unfolded relative to the stabilization of the Blue substructure, indicating that propagation of energy between substructures is somewhat disrupted when unfolding does not correspond to a natural substructure.     

Nanoscale Similarities in the Substructure of the Exines ofFagusPollen Grains andLycopodiumSpores

The exine substructure of an angiosperm,Fagus sylvatica(beech)pollen and a pteridophyte,Lycopodium clavatum(a club moss) sporewas investigated by scanning tunnelling microscopy. These pollenand spores, despite their distinct differences in structureand morphology on a micrometre scale, have very similar substructureon a nanometre scale. The substructure appears to consist ofa multi-helix, i.e. a helical chain in turn wound into a helixwith a self-similarity at smaller and smaller length scales.A simple vectorial form is proposed to describe quantitativelythe multi-helical substructure. Copyright 1998 Annals of BotanyCompany Fagus sylvatica,beech,Lycopodium clavatum, club moss, pollen, spores, exine substructure, scanning tunnelling microscopy.     

Analysis and application of European genetic substructure using 300 K SNP information

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.     

Disruption of T-even Bacteriophages by Dimethyl Sulfoxide

Dimethyl sulfoxide (DMSO) disrupted T-even bacteriophages as well as lambda bacteriophage. The component substructures of T2L, T4B01, or T6, in particular heads, were readily isolated after treatment with 67% DMSO (v/v). In contrast, concentrations of DMSO above 50% not only separated heads from tails of bacteriophage lambda but led to degradation of the lambda heads. Examination of the isolated free heads of T-even bacteriophage indicated that a distinct neck substructure was attached to one apex of the head. On some free tails a similar neck substructure was also found at the proximal end of the sheath. The dimensions of this neck substructure were found to be about 130 by 180 A; by virtue of its size and morphological attachment to the free heads, it was concluded that this was a distinct substructure and not an extension of the tail tube.     

A UV-induced, Mg(2+)-dependent crosslink traps an active form of domain 3 of a self-splicing group II intron.

In vitro irradiation of a15 gamma group II intron RNA with low doses of 254 nm UV light induces a single major crosslink. This crosslink was mapped within the domain 3 substructure of this RNA and one of the participating nucleotides was identified. When an RNA containing only the domain 3 substructure is irradiated under the same conditions, an intramolecular crosslink forms between two specific pyrimidines, one of them identical to the nucleotide crosslinked in the full-length intron RNA. In both RNAs, the crosslink is magnesium ion-dependent and photoreversible. A trans assay for domain 3 function was developed and used to find that the crosslinked domain 3 RNA remains highly reactive. This suggests that crosslinking has trapped a functional, Mg(2+)-induced folded state of this group II intron substructure and that this folding is probably independent of the other domains of the intron.     

Impact of Population Substructure on Trend Tests for Genetic Case–Control Association Studies

Summary .  Hidden population substructure in case–control data has the potential to distort the performance of Cochran–Armitage trend tests (CATTs) for genetic associations. Three possible scenarios that may arise are investigated here: (i) heterogeneity of genotype frequencies across unidentified subpopulations (PSI), (ii) heterogeneity of genotype frequencies and disease risk across unidentified subpopulations (PSII), and (iii) cryptic correlations within unidentified subpopulations. A unified approach is presented for deriving the bias and variance distortion under the three scenarios for any CATT in a general family. Using these analytical formulas, we evaluate the excess type I errors of the CATTs numerically in the presence of population substructure. Our results provide insight into the properties of some proposed corrections for bias and variance distortion and show why they may not fully correct for the effects of population substructure.     

Bayesian analysis of genetic differentiation between populations

We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.     

Rare-Variant Extensions of the Transmission Disequilibrium Test: Application to Autism Exome Sequence Data

Many population-based rare-variant (RV) association tests, which aggregate variants across a region, have been developed to analyze sequence data. A drawback of analyzing population-based data is that it is difficult to adequately control for population substructure and admixture, and spurious associations can occur. For RVs, this problem can be substantial, because the spectrum of rare variation can differ greatly between populations. A solution is to analyze parent-child trio data, by using the transmission disequilibrium test (TDT), which is robust to population substructure and admixture. We extended the TDT to test for RV associations using four commonly used methods. We demonstrate that for all RV-TDT methods, using proper analysis strategies, type I error is well-controlled even when there are high levels of population substructure or admixture. For trio data, unlike for population-based data, RV allele-counting association methods will lead to inflated type I errors. However type I errors can be properly controlled by obtaining p values empirically through haplotype permutation. The power of the RV-TDT methods was evaluated and compared to the analysis of case-control data with a number of genetic and disease models. The RV-TDT was also used to analyze exome data from 199 Simons Simplex Collection autism trios and an association was observed with variants in ABCA7. Given the problem of adequately controlling for population substructure and admixture in RV association studies and the growing number of sequence-based trio studies, the RV-TDT is extremely beneficial to elucidate the involvement of RVs in the etiology of complex traits.     

Spermiogenesis in the spider,Pisaurina Sp.: A fine structure study

A fine structure study of spermatids and spermatozoa of the spider, Pisaurina sp. demonstrates that early spermiogenesis is similar to other flagellate spermatozoa. An acrosome forms from a Golgi-derived, acrosomal vesicle, a perforatorium indents acromosome and nucleus, a flagellum with a three-plus-nine tubule substructure is formed and nuclear chromatin condenses during spermiogenesis. Divergence from typical spermatozoa includes the presence of a three-tubule substructure of the central flagellar shaft, progressive rounding-up of late spermatids with concomitant incorporation of previously formed flagellum. This evidence is presented in terms of its possible functional significance in fertilization and gamete fusion in spiders.     

Ultrastructure of crossbands in prosthecae of Asticcacaulis species.

Triton X-treated prosthecae from Asticcacaulis excentricus and A. biprosthecum were sonicated and examined with a electron microscope. Crossbands had a substructure of concentric rings and were digested by lysozyme.     

The power of genomic control

Although association analysis is a useful tool for uncovering the genetic underpinnings of complex traits, its utility is diminished by population substructure, which can produce spurious association between phenotype and genotype within population-based samples. Because family-based designs are robust against substructure, they have risen to the fore of association analysis. Yet, if population substructure could be ignored, this robustness can come at the price of power. Unfortunately it is rarely evident when population substructure can be ignored. Devlin and Roeder recently have proposed a method, termed "genomic control" (GC), which has the robustness of family-based designs even though it uses population-based data. GC uses the genome itself to determine appropriate corrections for population-based association tests. Using the GC method, we contrast the power of two study designs, family trios (i.e., father, mother, and affected progeny) versus case-control. For analysis of trios, we use the TDT test. When population substructure is absent, we find GC is always more powerful than TDT; furthermore, contrary to previous results, we show that as a disease becomes more prevalent the discrepancy in power becomes more extreme. When population substructure is present, however, the results are more complex: TDT is more powerful when population substructure is substantial, and GC is more powerful otherwise. We also explore general issues of power and implementation of GC within the case-control setting and find that, economically, GC is at least comparable to and often less expensive than family-based methods. Therefore, GC methods should prove a useful complement to family-based methods for the genetic analysis of complex traits.     

Polarization sensitive coherent anti-Stokes Raman scattering spectroscopy of the amide I band of proteins in solutions.

Polarization sensitive coherent anti-Stokes Raman scattering (PCARS) spectroscopy is a fruitful technique to study Raman vibrations of diluted molecules under off-electron resonant conditions. We apply PCARS as a direct spectroscopic method to investigate the broad amide I band of proteins in heavy water. In spontaneous Raman spectroscopy, this band is not well resolved. We fit a number of spectra taken of each protein under different polarization conditions, with a single set of parameters. It then appears that some substructure is observed in the amide I band. From this substructure, we determine the percentage of alpha-helix, beta-sheet, and random coil for the proteins lysozyme, albumin, ribonuclease A, and alpha-chymotrypsin.     

Privileged structure-based quinazolinone natural product-templated libraries: identification of novel tubulin polymerization inhibitors

A focused quinazolinone natural product-templated library was designed and synthesized. Compounds from this privileged structure-based library were identified as antimitotic agents acting through destabilization of tubulin polymerization. The results suggested that 2 could be a privileged substructure.     

Semisynthesis of triptolide analogues: effect of γ-lactone and C-14 substituents on cytotoxic activities

Triptolide γ-lactone and C-14 analogues were prepared and evaluated cytotoxity against human lung adenocarcinoma epithelial A549 cells and human colon adenocarcinoma HT-29 cells. γ-Lactone substructure and C-14 substituents affected the biological activities significantly.     

Identification of non-furan containing A2A antagonists using database mining and molecular similarity approaches

Database searching led to the identification of potent A(2A) antagonists which do not contain the privileged furan moiety and which show selectivity over A(1) receptors. Simple substructure searching on a proprietary database identified compounds with activities in the low nM range. A targeted approach to the identification of non-furan containing compounds resulted in the identification of two novel series, with potency, selectivity and directional SAR from screening 113 compounds.