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PubMed2005

Evaluation of a neural networks QSAR method based on ligand representation using substituent descriptors. Application to HIV-1 protease inhibitors.

We present here a neural networks method designed to predict biological activity based on a local representation of the ligand. The compounds of the series are represented by a vector mapping for each of four substituent properties: volume, log P, dipole moment and a simple 'steric' parameter relating to its shape. This ligand representation was tested using neural networks on a set of 42 cyclic-urea derivatives, inhibiting HIV-1 protease. The leave-one-out cross-validation using all descriptors in the input gave a correlation factor between prediction and experiment of 0.76 for the overall set and 0.88 when three outliers were left out. To rank the significance of the four descriptors, we further tested all combinations of two and three parameters for each substituent, using two disjunctive testing sets of five inhibitors. In these sets, vectors with extreme descriptor values were used either in the training or the testing set (sets A and B, respectively). The method is a very good interpolator (set A, 95+/-2% accuracy) but a less effective extrapolator (set B, 85+/-2% accuracy). Generally, the combinations including the 'steric' parameter predict better than average, while those containing the volume are less effective. The best prediction, 98.8+/-1.2%, was obtained when log P, the dipole and the steric parameter were used on set A. At the opposite end, the lowest ranked descriptor set was obtained when replacing log P with the volume, giving 92.3+/-6.7% accuracy over the set A.

Combinatorial Chemistry Techniques↗

PubMed2004

Structure and stability of cohesin's Smc1-kleisin interaction.

A multisubunit complex called cohesin forms a huge ring structure that mediates sister chromatid cohesion, possibly by entrapping sister DNAs following replication. Cohesin's kleisin subunit Scc1 completes the ring, connecting the ABC-like ATPase heads of a V-shaped Smc1/3 heterodimer. Proteolytic cleavage of Scc1 by separase triggers sister chromatid disjunction, presumably by breaking the Scc1 bridge. One half of the SMC-kleisin bridge is revealed here by a crystal structure of Smc1's ATPase complexed with Scc1's C-terminal domain. The latter forms a winged helix that binds a pair of beta strands in Smc1's ATPase head. Mutation of conserved residues within the contact interface destroys Scc1's interaction with Smc1/3 heterodimers and eliminates cohesin function. Interaction of Scc1's N terminus with Smc3 depends on prior C terminus connection with Smc1. There is little or no turnover of Smc1-Scc1 interactions within cohesin complexes in vivo because expression of noncleavable Scc1 after DNA replication does not hinder anaphase.

Adenosine Triphosphatases↗

PubMed2004

Folate deficiency induces aneuploidy in human lymphocytes in vitro-evidence using cytokinesis-blocked cells and probes specific for chromosomes 17 and 21.

Folate plays a critical role in the prevention of chromosome breakage and hypomethylation of DNA. Deficiency in this vitamin may lead to demethylation of heterochromatin causing structural centromere defects that could induce abnormal distribution of replicated chromosomes during nuclear division. Because aneuploidy of chromosomes 17 and 21 is often observed in breast cancer and leukaemia and increased risk for these cancers is associated with folate deficiency, we hypothesized that folate deficiency may lead to aneuploidy of chromosomes 17 and 21. To test these hypotheses we cultured lymphocytes from eight female volunteers (aged 40-48 years) in RPMI 1640 medium containing 12 or 120nM of folic acid (FA) or 5-methyltetrahydrofolate (MF) for 9 days. Chromosomes 17 and 21 aneuploidies induced by folate deficiency were measured in mononucleated (MONO) and cytokinesis-blocked binucleated (BN) lymphocytes after dual-color fluorescent in situ hybridization (FISH) with a digoxigenin-labeled probe for the alphoid satellite sequence of chromosome 17 and a biotin-labeled probe for the pericentric region of chromosome 21. The results showed that 12nm of MF or FA caused a significant 26-35% increment in frequency of aneuploidy of chromosome 17 (P = 0.0017) and aneupoidy of chromosome 21 (P = 0.0008) relative to 120nM MF or FA. The pattern of aneuploidy in binucleated cells was significantly correlated with that observed in mononucleated cells (R = 0.51-0.75, P < 0.0004) and was consistent with a model based on chromosome loss or partial aneusomy rescue as the cause rather than non-disjunction, although the latter mechanism could not be excluded. MF was not more efficient than FA in preventing aneuploidy in this in vitro system. We conclude that folate deficiency is a risk factor for chromosomes 17 and 21 aneuploidy.

Aneuploidy↗

PubMed2006

The use of the in vitro micronucleus assay to detect and assess the aneugenic activity of chemicals.

The successful validation of the in vitro micronucleus assay by the SFTG now provides the opportunity for this highly cost effective assay to be used to screen chemicals for their ability to induce both structural (clastogenic) and numerical (aneugenic) chromosome changes using interphase cells. The use of interphase cells and a relatively simple experimental protocol provides the opportunity to greatly increase the statistical power of cytogenetic studies on chemical interactions. The application of molecular probes capable of detecting kinetochores and centromeres provides the opportunity to classify mechanisms of micronucleus induction into those which are primarily due to chromosome loss or breakage. When a predominant mechanism of micronucleus induction has been shown to be based upon chromosome loss then further investigation can involve the determination of the role of non-disjunction in the induction of aneuploidy. The binucleate cell modification of the in vitro micronucleus assay can be combined with the use of chromosome specific centromere probes to determine the segregation of individual chromosomes into daughter nuclei. The combination of these methods provides us with powerful tools for the investigation of mechanisms of genotoxicity particularly in the low dose regions.

Aneugens↗

PubMed2005

Susceptibility to chromosome malsegregation in lymphocytes of women who had a Down syndrome child in young age.

Recent findings seem to converge towards a unified hypothesis trying to relate Down's syndrome (DS), trisomy 21 and Alzheimer's disease (AD). The majority of DS individuals develop neuropathological characteristics of AD by the age of 40. Previous cytogenetic studies performed by us showed an increased frequency of aneuploidy in peripheral lymphocytes and fibroblasts of AD patients and a preferential occurrence of chromosome 21 in malsegregation events. An increased frequency of AD among young mothers of individuals with DS (MDS) is reported. This study investigates the cytogenetic characteristics and the predisposition to chromosome malsegregation of peripheral blood lymphocytes in a group of women (n = 35) who had a Down syndrome child in young age (<35 years) and in a control group (n = 30). We applied the micronucleus assay and the dual-color FISH in order to assess the susceptibility to malsegregation events. The results indicate a higher frequency of binucleated micronucleated cells in MDS in respect to the control group (16.1+/-9.1 per thousand versus 8.7+/-5.4 per thousand). Moreover, our data reveal that peripheral lymphocytes of MDS are more prone to chromosome non-disjunction with both chromosomes, 13 and 21, equally involved.

Adult↗

PubMed2006

Characterizing rule-based category learning deficits in patients with Parkinson's disease.

Parkinson's disease (PD) patients and normal controls were tested in three category learning experiments to determine if previously observed rule-based category learning impairments in PD patients were due to deficits in selective attention or working memory. In Experiment 1, optimal categorization required participants to base their decision on a single stimulus dimension and ignore irrelevant variation on another dimension, thus emphasizing selective attention processes. In Experiment 2, optimal categorization required participants to base their decision on both stimulus dimensions using a conjunction of unidimensional decisions. Thus, this task placed less emphasis on selective attention and more on working memory. In Experiment 3, optimal categorization again required participants to base their decision on both stimulus dimensions using a disjunction of two unidimensional decisions in which an additional verbal operation was needed, thereby placing even greater emphasis on working memory. Results indicated that PD patients were impaired in the unidimensional rule-based condition, but not the other two rule-based conditions. These results are consistent with previous studies that demonstrate that PD patients are impaired in learning rule-based categories when selective attention demands are greatest, whereas these patients are normal in learning rule-based tasks when working memory demands are emphasized. Overall, these findings help to delineate the conditions under which PD patients display rule-based category learning deficits.

Aged↗

PubMed2005

Eye movements evoked by electrical microstimulation of the mesencephalic reticular formation in goldfish.

Anatomical studies in goldfish show that the tectofugal axons provide a large number of boutons within the mesencephalic reticular formation. Electrical stimulation, reversible inactivation and cell recording in the primate central mesencephalic reticular formation have suggested that it participates in the control of rapid eye movements (saccades). Moreover, the role of this tecto-recipient area in the generation of saccadic eye movements in fish is unknown. In this study we show that the electrical microstimulation of the mesencephalic reticular formation of goldfish evoked short latency saccadic eye movements in any direction (contraversive or ipsiversive, upward or downward). Movements of the eyes were usually disjunctive. Based on the location of the sites from which eye movements were evoked and the preferred saccade direction, eye movements were divided into different groups: pure vertical saccades were mainly elicited from the rostral mesencephalic reticular formation, while oblique and pure horizontal were largely evoked from middle and caudal mesencephalic reticular formation zones. The direction and amplitude of pure vertical and horizontal saccades were unaffected by initial eye position. However the amplitude, but not the direction of most oblique saccades was systematically modified by initial eye position. At the same time, the amplitude of elicited saccades did not vary in any consistent manner along either the anteroposterior, dorsoventral or mediolateral axes (i.e. there was no topographic organization of the mesencephalic reticular formation with respect to amplitude). In addition to these groups of movements, we found convergent and goal-directed saccades evoked primarily from the anterior and posterior mesencephalic reticular formation, respectively. Finally, the metric and kinetic characteristics of saccades could be manipulated by changes in the stimulation parameters. We conclude that the mesencephalic reticular formation in goldfish shares physiological functions that correspond closely with those found in mammals.

Animals↗

PubMed2005

Antipsychotic-associated neuronal changes in the brain: toxic, therapeutic, or irrelevant to the long-term outcome of schizophrenia?

The increasingly wide-spread use of antipsychotics in both adults and children calls for a detailed examination of antipsychotic-associated neuronal changes in the brain, and whether these changes are toxic, therapeutic, or perhaps irrelevant to the outcome of major psychiatric disorders, especially schizophrenia. In this review we will examine the extensive evidence demonstrating both acute and longer-term antipsychotic-associated neurotoxicity and neuroplasticity, as well as the more specific cellular changes that appear to underlie these phenomena. These include changes in proteins affecting cell survival, impairment of the mitochondrial respiratory chain, increases in DNA fragmentation, injury to dendritic microtubules, increases in dopamine-generated reactive oxygen species, changes in cell morphology, and rapid induction of apoptosis. We shall also examine the correlation between these changes and alterations in gross brain structure. There appears to be a disjunction between the widespread cellular and gross structural brain changes in schizophrenia, and the duration of illness, expression of symptoms, and response to treatment. We shall explore possible explanations for this apparent paradox.

Animals↗

PubMed2005

Comparative genomic hybridization pattern of non-anaplastic and anaplastic oligodendrogliomas--a meta-analysis.

Many oligodendrogliomas (ODG) have been investigated by comparative genomic hybridization (CGH). To visualize characteristic aberration profiles of non-anaplastic in a comparison with anaplastic ODGs, we performed a meta-analysis of the CGH results of all 89 cases published so far. Therefore, we expanded all given aberrations to the maximum of 850 GTG band resolution. The frequencies of each chromosomal band affected by a genetic imbalance were calculated for WHO grades II and III separately. In non-anaplastic ODGs, -1p and -19q were the most prominent aberrations. In anaplastic ODGs, +7, -4q, -9p, -10, and -15q emerged additionally. We could confirm the existence of three disjunct genetically defined subgroups of ODGs, characterized by -1p/-19q (n=58, 65%, subgroup A), +7/-10 (n=6, 7%, subgroup B) or the absence of either of the two patterns (n=25, 28%, subgroup C). Interestingly, we found a unique aberration pattern in subgroup C (-1p31, -4q, -11p15, -18q, -22q, +17p, +17q) that was different from subgroups A and B, which could indicate a unique molecular carcinogenetic pathway of this ODG subset. Scrutinizing published putative progression markers of ODG, we found that only +7, -10, and -15q significantly correlated with a higher grade of malignancy. Summing up, the expansion of the CGH results to the 850 GTG band resolution enabled a meta-analysis to visualize WHO grade-specific aberration profiles in ODG for the first time.

Chromosome Aberrations↗

PubMed2006

Community participation in AIDS vaccine trials: empowerment or science?

For future AIDS vaccines to be successfully tested and implemented, extensive participation in vaccine trials will be necessary. Central to the challenges associated with such participation is concern for protection of participant wellbeing. This short report examines the tension that is sometimes found between the pragmatic need for recruitment into trials, and a more general social good concerning community participation in health. Community empowerment and trial participation are sometimes assumed to go hand in hand, but are potentially contradictory. Recognizing the possible disjunction between empowerment and trial participation allows for clearer discussion of and planning for ethical, scientifically valid trials.

AIDS Vaccines↗

PubMed2005

Cognitive and affective development in adolescence.

Questions about the nature of normative and atypical development in adolescence have taken on special significance in the last few years, as scientists have begun to recast old portraits of adolescent behavior in the light of new knowledge about brain development. Adolescence is often a period of especially heightened vulnerability as a consequence of potential disjunctions between developing brain, behavioral and cognitive systems that mature along different timetables and under the control of both common and independent biological processes. Taken together, these developments reinforce the emerging understanding of adolescence as a critical or sensitive period for a reorganization of regulatory systems, a reorganization that is fraught with both risks and opportunities.

Adolescent↗

PubMed2004

Carcinogenicity categorization of chemicals-new aspects to be considered in a European perspective.

Existing systems of classification of carcinogens are a matter of discussion, world-wide. There is agreement that it should be distinguished between genotoxic and non-genotoxic chemicals. The risk assessment approach used for non-genotoxic chemicals is similar among different regulatory bodies: insertion of an uncertainty (safety) factor permits the derivation of permissible exposure levels at which no relevant human cancer risks are anticipated. For genotoxic carcinogens, case studies of chemicals point to a whole array of possibilities. Positive data of chromosomal effects only, in the absence of mutagenicity, may support the characterization of a compound that produces carcinogenic effects only at high, toxic doses. Non-DNA-reactive genotoxins, such as topoisomerase inhibitors or inhibitors of the spindle apparatus are considered in this respect. In such cases, arguments are in favour of the existence of "practical" thresholds. Taking existing concepts together, it is proposed to basically distinguish between "perfect" and "practical" thresholds. There is a wide consensus that for non-DNA-reactive genotoxins such as aneugens (aneuploidy, chromosome loss, non-disjunction) thresholds should be defined. It is being discussed as to whether the identification of possible threshold effects should also include other mechanisms of genotoxicity, in addition to aneugenic effects. Specific mechanisms of clastogenicity have been repeatedly addressed as also having thresholds, such as topoisomerase II poisons or mechanisms based on reactive oxygen. Oxidative stress as an important mechanism is triggered by exposure to exogenous factors such as ultraviolet (UV) and ionizing radiation, anoxia and hyperoxia, and by chemicals producing reactive oxygen species. The idea is receiving increased support that reactive oxygen species (ROS)-mediated processes of carcinogenesis have practical thresholds. Since reactive oxygen species are genotoxic in principle, questions arise whether chemicals that increase ROS production will superimpose to an endogenously produced background level of DNA lesions, related to mechanisms that may result in non-linear dose-effect relationships. The existence of "endogenous" DNA adducts has been generally accepted, and possible regulatory implications of the presence of endogenous carcinogens have been discussed. It is now becoming evident that a diversity of methods of carcinogenic risk extrapolation to low doses must be considered, dependent on the mode of action. Although there is an increasing international awareness of these developments, the system of classification of carcinogens of the European Union still remains static. This should be changed, as the philosophy of separation of a strictly sequential "hazard assessment" and "risk assessment" appears out-of-date.

Carcinogenicity Tests↗

PubMed2004

The resurrection of oceanic dispersal in historical biogeography.

Geographical distributions of terrestrial or freshwater taxa that are broken up by oceans can be explained by either oceanic dispersal or vicariance in the form of fragmentation of a previously contiguous landmass. The validation of plate-tectonics theory provided a global vicariance mechanism and, along with cladistic arguments for the primacy of vicariance, helped create a view of oceanic dispersal as a rare phenomenon and an explanation of last resort. Here, I describe recent work that suggests that the importance of oceanic dispersal has been strongly underestimated. In particular, molecular dating of lineage divergences favors oceanic dispersal over tectonic vicariance as an explanation for disjunct distributions in a wide variety of taxa, from frogs to beetles to baobab trees. Other evidence, such as substantial gene flow among island populations of Anolis lizards, also indicates unexpectedly high frequencies of oceanic dispersal. The resurrection of oceanic dispersal is the most striking aspect of a major shift in historical biogeography toward a more even balance between vicariance and dispersal explanations. This new view implies that biotas are more dynamic and have more recent origins than had been thought previously. A high frequency of dispersal also suggests that a fundamental methodological assumption of many biogeographical studies--that vicariance is a priori a more probable explanation than dispersal--needs to be re-evaluated and perhaps discarded.

Journal Article↗

PubMed2005

A simple technique to facilitate the Le Fort I osteotomy downfracture.

In order to mobilize and reposition the maxilla when treating dentofacial deformities, the Le Fort I maxillary osteotomy is commonly used. Like other surgical procedures, this procedure is not without inherent difficulties. At times, it may be difficult to initially mobilize the maxilla after performing the osteotomies. Techniques used to help in the initial mobilization and downfracture of the maxilla from the pterygoid plates include digital pressure to the dentoalveolus, disimpaction forceps, spreaders, and other instruments. These techniques are similar in that they all apply a unidirectional downward vector of force on the maxilla and have various drawbacks. We present a technique that uses a 0.5-mm stainless steel traction wire to facilitate Le Fort I maxillary downfracturing by applying a forward and downward vector of force simultaneously. After vertical downfracture of the maxilla, lateral traction on the wire can be used to complete the pterygomaxillary disjunction. This technique has several advantages and is atraumatic, and requires no special instrumentation; thus, downfracturing of the maxilla is done with relatively little effort and minimal risk.

Biomechanical Phenomena↗

PubMed2004

Attenuation of perceived motion smear during vergence and pursuit tracking.

When the eyes move, the images of stationary objects sweep across the retina. Despite this motion of the retinal image and the substantial integration of visual signals across time, physically stationary objects typically do not appear to be smeared during eye movements. Previous studies indicated that the extent of perceived motion smear is smaller when a stationary target is presented during pursuit or saccadic eye movements than when comparable motion of the retinal image occurs during steady fixation. In this study, we compared the extent of perceived motion smear for a stationary target during smooth pursuit and vergence eye movements with that for a physically moving target during fixation. For a target duration of 100 ms or longer, perceived motion smear is substantially less when the motion of the retinal image results from vergence or pursuit eye movements than when it results from the motion of a target during fixation. The reduced extent of perceived motion smear during eye movements compared to fixation cannot be accounted for by different spatio-temporal interactions between visual targets or by unequal attention to the moving test spot under these two types of conditions. We attribute the highly similar attenuation of perceived smear during vergence and pursuit to a comparable action of the extra-retinal signals for disjunctive and conjugate eye movements.

Convergence, Ocular↗

PubMed2004

Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex.

Species with fragmented distributions are particularly useful models for investigating processes underlying biological diversification in the Neotropics. The Phaeothlypis wood-warbler complex (Aves: Parulidae) is comprised of six disjunct or parapatric populations. The geographic distribution of these six populations mirrors the classic map of Neotropical areas of endemism that were originally proposed as putative Pleistocene forest refugia, but the magnitude of mitochondrial DNA divergence between these populations suggests that they are each substantially older, with origins in the late Pliocene. Phylogenetic reconstructions based on long mtDNA coding sequences show that the Guiana Shield and Atlantic Forest populations are sister lineages, and group this combined lineage and the remaining four population-specific lineages in a five-way hard polytomy. MtDNA-based phylogenetic reconstructions provide no evidence that the three populations with conspicuous yellow rump and tail feathers currently grouped as the Buff-rumped Warbler (P. fulvicauda) form a monophyletic group. Furthermore, there is a broad discordance between mtDNA and plumage along a transect just east of the Andes, where the contact zone between highly divergent mtDNA clades is more than 1000 km north of the phenotypic hybrid zone between the bright and dark plumage forms. This discordance between mtDNA genotype and plumage phenotype is similar to patterns seen on a finer geographic scale in other avian hybrid zones and may result from asymmetric introgression of the bright plumage trait.

Animal Communication↗

PubMed2004

Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a tertiary relict distribution.

Rhododendron subgenus Hymenanthes subsection Pontica is exceptional among Tertiary relict groups in having a high proportion of species (4 of 11) native to SW Eurasia. A phylogeny based on cpDNA matK and trnL-F indicated that multiple Pontica lineages colonised each of SW Eurasia, SE North America, and NE Asia, with little or no speciation within regions thereafter. Therefore, multiple (3-4) Pontica lineages survived the Quaternary in SW Eurasia, in contrast to other Tertiary relict genera. Pontica comprises two major clades, one of which is wholly Eurasian, and paraphyletic with respect to at least some of the remaining 200 species of subgenus Hymenanthes, which are all distributed in SE Asia. The other clade has species from W and SE North America, SW Eurasia, and NE Asia. According to synonymous matK substitution data, the two clades diverged 9-6 million years ago (mya), whereas most divergence within them happened 5-3 mya. Although the phylogeny indicates probable trans-Atlantic migration for one of two America-Eurasia disjunctions in Pontica, the timing supports migration via Beringia for both.

DNA, Chloroplast↗

PubMed2004

Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere.

Sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA, the chloroplast ndhF gene, and chloroplast trnL-F regions (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) were used for phylogenetic analyses of Rhus, a genus disjunctly distributed in Asia, Europe, Hawaii, North America, and Northern Central America. Both ITS and cpDNA data sets support the monophyly of Rhus. The monophyly of subgenus Rhus was suggested by the combined cpDNA and ITS data, and largely supported in the cpDNA data except that Rhus microphylla of subgenus Lobadium was nested within it. The monophyly of subgenus Lobadium was strongly supported in the ITS data, whereas the cpDNA data revealed two main clades within the subgenus, which formed a trichotomy with the clade of subgenus Rhus plus R. microphylla. The ITS and cpDNA trees differ in the positions of Rhus michauxii, R. microphylla, and Rhus rubifolia, and hybridization may have caused this discordance. Fossil evidence indicates that Rhus dates back to the early Eocene. The penalized likelihood method was used to estimate divergence times, with fossils of Rhus subgenus Lobadium, Pistacia and Toxicodendron used for age constraints. Rhus diverged from its closest relative at 49.1+/-2.1 million years ago (Ma), the split of subgenus Lobadium and subgenus Rhus was at 38.1+/-3.0 Ma. Rhus most likely migrated from North America into Asia via the Bering Land Bridge during the Late Eocene (33.8+/-3.1 Ma). Rhus coriaria from southern Europe and western Asia diverged from its relatives in eastern Asia at 24.4+/-3.2 Ma. The Hawaiian Rhus sandwicensis diverged from the Asian Rhus chinensis at 13.5+/-3.0 Ma. Subgenus Lobadium was inferred to be of North American origin. Taxa of subgenus Lobadium then migrated southward to Central America. Furthermore, we herein make the following three nomenclatural combinations: (1) Searsia leptodictya (Diels) T. S. Yi, A. J. Miller and J. Wen, comb. nov., (2) Searsia pyroides (A. Rich.) T. S. Yi, A. J. Miller and J. Wen, comb. nov., and (3) Searsia undulata (Jacq.) T. S. Yi, A. J. Miller and J. Wen, because our analyses support the segregation of Searsia from Rhus.

Biological Evolution↗