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Egg envelopes in vertebrates.

As the material presented in this chapter was being collated, our existing perceptions about the basic similarities of vertebrate (and indeed most, if not all, invertebrate) egg envelopes became increasingly strengthened. Perhaps without exception, all vertebrate and invertebrate eggs acquire a "vitelline" envelope. Interestingly, its filamentous ultrastructure and chemical composition--basically protein and carbohydrate--is similar in all species as is its permeability to large molecules. Furthermore, many (if not all) of its functions are shared among the animal phyla as is its potential to become altered at the time of fertilization and, in its altered state, to provide a new set of modi operandi. It provides sperm receptors that are generally species specific and helps prevent polyspermy; it protects the developing embryo yet yields at the time of hatching. In most vertebrate eggs (including some mammals), a jelly or albumen coat is added to the vitelline envelope. These components may vary immensely in thickness, but again their basic chemical composition is common to all. The functions of these envelopes, while perhaps somewhat less clear than those of the vitelline envelope, are related to species-specific fertilization and to embryonic protection. Albumen serves a nutritional role--most clearly shown in the birds. Finally, the shell membrane and shell present in diverse groups contribute additional adaptations for embryo protection. Vertebrate egg envelopes, then, are basically similar; the modifications, including the addition of shell membranes and shells in some groups, reflect adaptations to differing reproductive strategies and to the environmental exigencies with which the egg must cope. With the growth of our understanding about the structure, chemistry, function, and evolution of egg envelopes new questions will continually be formulated. Many will be the same as those asked years ago but they will be answered with newer techniques and with greater insight.

Animals↗

Assessing genetic diversity of wheat ( Triticum aestivum L.) germplasm using microsatellite markers.

A set of 24 wheat microsatellite markers, representing at least one marker from each chromosome, was used for the assessment of genetic diversity in 998 accessions of hexaploid bread wheat ( Triticum aestivum L.) which originated from 68 countries of five continents. A total of 470 alleles were detected with an average allele number of 18.1 per locus. The highest number of alleles per locus was detected in the B genome with 19.9, compared to 17.4 and 16.5 for genomes A and D, respectively. The lowest allele number per locus among the seven homoeologous groups was observed in group 4. Greater genetic variation exists in the non-centromeric regions than in the centromeric regions of chromosomes. Allele numbers increased with the repeat number of the microsatellites used and their relative distance from the centromere, and was not dependent on the motif of microsatellites. Gene diversity was correlated with the number of alleles. Gene diversity according to Nei for the 26 microsatellite loci varied from 0.43 to 0.94 with an average of 0.77, and was 0.78, 0.81 and 0.73 for three genomes A, B and D, respectively. Alleles for each locus were present in regular two or three base-pair steps, indicating that the genetic variation during the wheat evolution occurred step by step in a continuous manner. In most cases, allele frequencies showed a normal distribution. Comparative analysis of microsatellite diversity among the eight geographical regions revealed that the accessions from the Near East and the Middle East exhibited more genetic diversity than those from the other regions. Greater diversity was found in Southeast Europe than in North and Southwest Europe. The present study also indicates that microsatellite markers permit the fast and high throughput fingerprinting of large numbers of accessions from a germplasm collection in order to assess genetic diversity.

Journal Article↗

Cytogenetic studies of human brain tumors and their clinical significance. II. Meningioma.

Cytogenetic study of 45 meningiomas from 31 female and 14 male patients are reported. No chromosomal abnormalities were found in nine (20%). These were predominantly meningotheliomatous, and were from younger patients (average age, 46 years). Monosomy 22 was noted in only 20% and in 12 patients (27%) with other losses and rearrangements. Among the latter, 50% were either recurrent or recurrent and invasive, the majority were fibromatous and occurred in older patients. Nonrandom loss was observed of the Y and abnormalities of chromosomes #1, #7, and #14 and, to a lesser extent, chromosomes #18, #19, and #20. Meningiomas may begin with no chromosomal abnormalities, having meningotheliomatous histopathologic appearance, occur in younger patients, and are less aggressive. Karyotypic evolution following loss of a chromosome #22 continues with losses and rearrangements of other chromosomes with apparent nonrandom involvement of chromosomes #1, #7, #14 and Y. This karyotypic change is associated with aggressive tumor behavior and fibromatous morphology.

Adult↗

Clinical and lesion morphologic determinants of coronary angioplasty success and complications: current experience.

OBJECTIVES: This study evaluated the validity of the American College of Cardiology/American Heart Association ABC lesion classification scheme and its modifications. BACKGROUND: With the continued refinement in angioplasty technique and equipment evolution, the lesion morphologic determinants of immediate angioplasty outcome have changed significantly. Hence, the validity of the classification scheme has been questioned. METHODS: We assessed the lesion morphologic determinants of immediate angioplasty outcome in 729 consecutive patients who underwent coronary angioplasty of 994 vessels and 1,248 lesions. RESULTS: Angioplasty success was achieved in 91% of lesions, and abrupt closure occurred in 3%. Success was achieved in 96%, 93% and 80% of type A, B and C lesions, respectively (A vs. B, p = NS; B vs. C, p < 0.001; A vs. C, p < 0.001; A vs. B1, p = NS; A vs. B2, p = 0.03; B1 vs. B2, p = 0.02; B2 vs. C, p < 0.001; C1 vs. C2, p = NS). Abrupt closure occurred in 2.1%, 2.6% and 5% of type A, B and C lesions, respectively (A vs. B, B vs. C, A vs. C and A vs. B1, all p = NS; B1 vs. B2, p = 0.01; B2 vs. C1, p = NS; C1 vs. C2, p = 0.04). Type B characteristics had a success rate ranging from 74% to 95% and an abrupt closure rate ranging from 2.2% to 14%. Type C characteristics had a success rate ranging from 57% to 88% and an abrupt closure rate ranging from 0% to 16%. Longer lesions, calcified lesions, diameter stenosis of 80% to 99% and presence of thrombus were predictive of a lower success rate. Longer lesions, angulated lesions, diameter stenosis of 80% to 99% and calcified lesions were predictive of an abrupt closure. CONCLUSIONS: The previously proposed classification schemes are outdated and need to be changed for application in current angioplasty practice. Analyzing specific lesion morphologic characteristics rather than applying a simple lesion classification score when evaluating angioplasty outcome may be more useful because it provides a more precise profile of the lesion and allows better patient stratification and selection.

Adult↗

Three-dimensional structures of fibrillar Sm proteins: Hfq and other Sm-like proteins.

Hfq is a nucleic acid-binding protein that functions as a global regulator of gene expression by virtue of its interactions with several small, non-coding RNA species. Originally identified as an Escherichia coli host factor required for RNA phage Qbeta replication, Hfq is now known to post-transcriptionally regulate bacterial gene expression by modulating both mRNA stability and translational activity. Recently shown to be a member of the diverse Sm protein family, Hfq adopts the OB-like fold typical of other Sm and Sm-like (Lsm) proteins, and also assembles into toroidal homo-oligomers that bind single-stranded RNA. Similarities between the structures, functions, and evolution of Sm/Lsm proteins and Hfq are continually being discovered, and we now report an additional, unexpected biophysical property that is shared by Hfq and other Sm proteins: E.coli Hfq polymerizes into well-ordered fibres whose morphologies closely resemble those found for Sm-like archaeal proteins (SmAPs). However, the hierarchical assembly of these fibres is dissimilar: whereas SmAPs polymerize into polar tubes (and striated bundles of such tubes) by head-to-tail stacking of individual homo-heptamers, helical Hfq fibres are formed by cylindrical slab-like layers that consist of 36 subunits arranged as a hexamer of Hfq homo-hexamers (i.e. protofilaments in a 6 x 6 arrangement). The different fibrillar ultrastructures formed by Hfq and SmAP are presented and examined herein, with the overall goal of elucidating another similarity amongst the diverse members of the Sm protein family.

Archaeal Proteins↗

Ploidy status rarely changes in myeloma patients at disease progression.

Hyperdiploid and non-hyperdiploid multiple myeloma represents distinct biological entities characterized by different patterns of genetic changes. We sought to determine whether ploidy category (non-hyperdiploid versus hyperdiploid) remains stable over time from diagnosis to progression. Of the 43 patients studied (39 by flow cytometry DNA index and 4 by a FISH-based index), only five (12%) altered their ploidy status at progression. In three of these patients, the change may possibly be attributable to technical artifacts because of the low absolute change in DNA index. For those who retain their ploidy subtypes, the DNA index change minimally (3.75+/-4.87%). It would appear that the initiating genetic events underlying hyperdiploid and non-hyperdiploid MM that marks them out as distinct entities continue to dominate and persist during disease evolution and progression.

DNA, Neoplasm↗

Cyanophage infection and photoinhibition in marine cyanobacteria.

Members of two cyanobacterial genera, Synechococcus and Prochlorococcus, are dominant within the prokaryotic component of the picophytoplankton and contribute significantly to global photosynthetic productivity. These organisms are known to be susceptible to infection by bacteriophages (viruses that infect bacteria) and it is believed that phage infection in the oceans has exerted selective pressures on the evolution of both phage and host and continues to influence community structure. Understanding of the processes of host-phage interaction within the marine environment is limited; however, new insights have arisen from sequence analysis of the genome of the bacteriophage S-PM2, which infects Synechococcus strains. The phage was found to encode homologs of the key photosystem II reaction center core polypeptides, D1 and D2. These reaction center polypeptides are known to be rapidly turned over in uninfected cells in a repair cycle that helps to protect oxygenic phototrophs against photoinhibition. This finding suggests that bacteriophages infecting marine cyanobacteria may play an active role in protecting their hosts against photoinhibition, thereby ensuring an energy supply for replication by preventing the deleterious effects on host cell integrity seen during acute photoinhibition.

Amino Acid Sequence↗

Recombination in the alphaherpesvirus bovine herpesvirus 1.

Herpesviruses are DNA viruses characterized by a low rate of nucleotide substitution. Therefore, other mechanisms must be involved to their evolution, like recombination that can be seen as an essential evolutionary driving force of these viruses. Recombination contributes to the long-term evolution of alphaherpesviruses. It acts also to continuously create new alphaherpesvirus strains. We have used bovine herpesvirus 1 to investigate recombination both within DNA concatemers in infected cells and in vitro and in vivo at the end of the lytic cycle. The following results have been obtained: (i) intramolecular recombination occurs at the level of concatemers and gives rise to genomic segment inversions; (ii) intraspecific recombination occurs frequently both in vitro and in vivo; (iii) interspecific recombination is possible and requires two highly genetically related viruses; (iv) only simultaneous or closely separated infections lead to the production of recombinant viruses; (v) recombination between wild-type and glycoprotein defective vaccine virus can produce a glycoprotein defective virus keeping part of the virulence of parental wild-type virus. Recombination, by exchanging genomic segments, may modify the virulence of alphaherpesviruses. It must be carefully assessed for the biosafety of antiviral therapy, alphaherpesvirus-based vectors and live attenuated vaccines.

Alphaherpesvirinae↗

Gestational evolution of small intestine motility in preterm and term infants.

Continuous perfusion manometry was performed in 31 preterm and term infants to assess the influence of gestational age on small intestinal motility. Gestational ages ranged from 27 to 42 weeks. All 8 term infants had interdigestive cycles that included all three phases. Only 4 of 23 preterm infants had complete interdigestive cycles. The remaining 19 preterm infants had only periods of motor quiescence and nonpropagating contractions. In term infants the interdigestive cycle was significantly shorter and the amplitude of phase 3 activity was significantly greater (p less than 0.01); velocity and duration of phase 3 activity were similar in both groups of infants. Rhythmic nonpropagating activity, or clusters, made up more than 60% of the phase 2 activity in both term and preterm infants. Although clusters did not propagate across three or more leads, approximately 25% of cluster activity was propagated across two leads. The duration of total cluster activity was similar for all gestational ages, but the frequency of clusters decreased and the mean duration of individual clusters increased with gestational age (both p less than 0.01). The amplitude of individual pressure peaks in clusters and phase 3 increased significantly with gestational age (p less than 0.03 and p less than 0.01, respectively). The motility index also increased with gestational age (p less than 0.02). We conclude that small intestinal motility is more immature in preterm infants than in term infants. Furthermore, cluster activity, which increases in duration and amplitude with gestational age, may be an immature form of phase 3 activity. These data and techniques will provide neonatologists with a direct way of tracking preterm intestinal motor function to provide more appropriate enteral nutrition.

Enteral Nutrition↗

Current status of carotid imaging by MRA.

Magnetic resonance imaging of the lumen of the carotid artery, or magnetic resonance angiography (MRA) of the carotid, has gone through a long evolutionary period to become a routine imaging modality in many centers. Further improvements are becoming available. There are better gradients available for scanners, high resolution neck surface coils allow improved signal to noise ratios, and contrast agents which have a longer intravascular dwell time are about to be introduced. Thus, further evolution of this modality will result in continued improvement in our ability to define the vascular lumenal edge and give the added advantage of in vivo plaque imaging. At present, these newer developments are available only in research centers.

Arteriosclerosis↗

Molybdenum and tungsten in biology.

Molybdenum is the only second-row transition metal that is required by most living organisms, and the few species that do not require molybdenum use tungsten, which lies immediately below molybdenum in the periodic table. Because of their unique chemical versatility and unusually high bioavailability these two transition metals have been incorporated into the active sites of enzymes over the course of evolution. Enzymes that contain molybdenum or tungsten continue to be discovered and several crystal structures have become available recently. This new structural information has been complemented by spectroscopic and kinetic methods, as well as computational approaches. Together, these studies provide an increasingly detailed view of the reaction mechanisms and the correlation between the electronic structure of the active site and catalytic function, one of the fundamental goals in metallobiochemistry.

Aldehyde Oxidoreductases↗

ICH-harmonised guidances on genotoxicity testing of pharmaceuticals: evolution, reasoning and impact.

The International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) has convened an expert working group which consisted of the authors of this paper and their respective committees, consulting groups and task forces. Two ICH guidances regarding genotoxicity testing have been issued: S2A, 'Guidance on Specific Aspects of Regulatory Genotoxicity Tests' and S2B, 'Genotoxicity: A Standard Battery for Genotoxicity Testing of Pharmaceuticals.' Together, these guidance documents now form the regulatory backbone for genotoxicity testing and assessment of pharmaceuticals in the European Union, Japan, and the USA. These guidances do not constitute a revolutionary new approach to genotoxicity testing and assessment, instead they are an evolution from preexisting regional guidelines, guidances and technical approaches. Both guidances describe a number of specific criteria as well as a general test philosophy in genotoxicity testing. Although these guidances were previously released within the participating regions in their respective regulatory communiqués, to ensure their wider distribution and better understanding, the texts of the guidances are reproduced here in their entirety (see Appendix A) and the background for the recommendations are described. The establishment of a standard battery for genotoxicity testing of pharmaceuticals was one of the most important issues of the harmonisation effort. This battery currently consists of: (i) a test for gene mutation in bacteria, (ii) an in vitro test with cytogenetic evaluation of chromosomal damage with mammalian cells or an in vitro mouse lymphoma tk assay, (iii) an in vivo test for chromosomal damage using rodent hematopoietic cells. A major change in testing philosophy is the acceptance of the interchangeability of testing for chromosomal aberrations in mammalian cells and the mouse lymphoma tk assay. This agreement was reached on the basis of the extensive review of databases and newly generated experimental data which are in part described in this publication. The authors are fully aware of the fact that some of the recommendations given in these ICH guidances are transient in nature and that the dynamic qualities and ongoing evolution of genetic toxicology makes necessary a continuous maintenance process that would serve to update the guidance as necessary.

Animals↗

Preserving genes, species, or ecosystems? Healing the fractured foundations of conservation policy.

The scientific foundations of conservation policy are the subject of a recent tripolar debate, with systematists arguing for the primacy of phylogenetic rankings, ecologists arguing for protection at the level of populations or ecosystems, and evolutionary biologists urging more attention for the factors that enhance adaptation and biodiversity. In the field of conservation genetics, this controversy is manifested in the diverse viewpoints of molecular systematists, population biologists, and evolutionary (and quantitative) geneticists. A resolution of these viewpoints is proposed here, based on the premise that preserving particular objects (genes, species, or ecosystems) is not the ultimate goal of conservation. In order to be successful, conservation efforts must preserve the processes of life. This task requires the identification and protection of diverse branches in the tree of life (phylogenetics), the maintenance of life-support systems for organisms (ecology), and the continued adaptation of organisms to changing environments (evolution). None of these objectives alone is sufficient to preserve the threads of life across time. Under this temporal perspective, molecular genetic technologies have applications in all three conservation agendas; DNA sequence comparisons serve the phylogenetic goals, population genetic markers serve the ecological goals, quantitative genetics and genome explorations serve the evolutionary goals.

Animals↗

Modeling gene and genome duplications in eukaryotes.

Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.

Arabidopsis↗

Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.

Phylogenetic analyses are increasingly used in attempts to clarify transmission patterns of human immunodeficiency virus type 1 (HIV-1), but there is a continuing discussion about their validity because convergent evolution and transmission of minor HIV variants may obscure epidemiological patterns. Here we have studied a unique HIV-1 transmission cluster consisting of nine infected individuals, for whom the time and direction of each virus transmission was exactly known. Most of the transmissions occurred between 1981 and 1983, and a total of 13 blood samples were obtained approximately 2-12 years later. The p17 gag and env V3 regions of the HIV-1 genome were directly sequenced from uncultured lymphocytes. A true phylogenetic tree was constructed based on the knowledge about when the transmissions had occurred and when the samples were obtained. This complex, known HIV-1 transmission history was compared with reconstructed molecular trees, which were calculated from the DNA sequences by several commonly used phylogenetic inference methods [Fitch-Margoliash, neighbor-joining, minimum-evolution, maximum-likelihood, maximum-parsimony, unweighted pair group method using arithmetic averages (UPGMA), and a Fitch-Margoliash method assuming a molecular clock (KITSCH)]. A majority of the reconstructed trees were good estimates of the true phylogeny; 12 of 13 taxa were correctly positioned in the most accurate trees. The choice of gene fragment was found to be more important than the choice of phylogenetic method and substitution model. However, methods that are sensitive to unequal rates of change performed more poorly (such as UPGMA and KITSCH, which assume a constant molecular clock). The rapidly evolving V3 fragment gave better reconstructions than p17, but a combined data set of both p17 and V3 performed best. The accuracy of the phylogenetic methods justifies their use in HIV-1 research and argues against convergent evolution and selective transmission of certain virus variants.

Amino Acid Sequence↗

Asynchronous nuclear division cycles in multinucleated cells.

Synchronous mitosis is common in multinucleated cells. We analyzed a unique asynchronous nuclear division cycle in a multinucleated filamentous fungus, Ashbya gossypii. Nuclear pedigree analysis and observation of GFP-labeled spindle pole bodies demonstrated that neighboring nuclei in A. gossypii cells are in different cell cycle stages despite close physical proximity. Neighboring nuclei did not differ significantly in their patterns of cyclin protein localization such that both G1 and mitotic cyclins were present regardless of cell cycle stage, suggesting that the complete destruction of cyclins is not occurring in this system. Indeed, the expression of mitotic cyclin lacking NH(2)-terminal destruction box sequences did not block cell cycle progression. Cells lacking AgSic1p, a predicted cyclin-dependent kinase (CDK) inhibitor, however, showed aberrant multipolar spindles and fragmented nuclei that are indicative of flawed mitoses. We hypothesize that the continuous cytoplasm in these cells promoted the evolution of a nuclear division cycle in which CDK inhibitors primarily control CDK activity rather than oscillating mitotic cyclin proteins.

Active Transport, Cell Nucleus↗

Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy.

A molecular and phylogenetic characterization on env and gag subgenomic regions has been performed in our laboratory on HIV-1 variants identified in seropositive individuals residing in Italy, infected in the 1999-2001 period, and five non-B-subtype HIV-1 isolates have been described. To confirm the phylogenetic characterization and to determine the genomic organization of three non-B HIV-1 isolates (A, G, and CRF02- AG), the complete gag, pol, and gp120 ORFs (approx. 6900 bp) have been sequenced for each of them. The phylogenetic tree analyses performed on the whole sequence or on individual genes suggested, for the A and G isolates, the identification of divergent strains that do not cluster into any of the known subsubtypes. This has been further validated by pairwise distance analysis. On the contrary, the phylogenetic classification of the CRF02-AG isolate has been confirmed and an overall typical pattern of intragenomic breakpoints has been observed by a Simplot analysis. These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates.

Genes, env↗

The medical content of English almanacs 1640-1700.

There has been a great deal of recent interest in popular health care in early modern England, resulting in studies on a range of topics from practitioners through remedial treatment. Over the past decade, the history of books has also attracted growing interest. This is particularly true for the seventeenth century, a period marked by a dramatic rise in all types of printed works. The 1640s are especially significant in the evolution of printed vernacular medical publications, which continued to flourish during the rest of the century. While recent studies on popular medical books have contributed greatly to our understanding of contemporary medical beliefs and practices, they have failed to properly recognize the effect that almanacs had on early modern medicine. Although their primary function was not to disseminate medical information, most provided a great deal of medical information. Furthermore, these cheap, annual publications targeted and were read by a wide cross-section of the public, making them the first true form of British mass media. This article is based on the content of 1,392 almanacs printed between 1640 and 1700, which may make it the largest comparative study of the medical content of any early modern printed works. The project has resulted in two major findings. First of all, almanacs played a major part in the dissemination, continuing popularity, and longevity of traditional astrological and Galenic beliefs and practices. Secondly, at the same time, almanacs played an important early role in the growth of medical materialism in Britain.

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