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PubMed2005

Reassessing Coxcatlan Cave and the early history of domesticated plants in Mesoamerica.

Reanalysis and direct accelerator mass spectrometry radiocarbon dating of the cucurbit assemblage from Coxcatlan Cave provide information on the timing and sequence of the initial appearance of three domesticated plants in the Tehuacán Valley (Puebla, Mexico) and allow reassessment of the overall temporal context of plant domestication in Mexico. Cucurbita pepo is the earliest documented domesticate in the cave, dating to 7,920 calibrated calendrical (cal) years B.P. The bottle gourd (Lagenaria siceraria) is dated at 7,200 cal years B.P. Cucurbita argyrosperma does not appear until 2,065 cal years B.P. The earlier identification of Cucurbita moschata specimens is not confirmed. Seventy-one radiocarbon dates, including 23 accelerator mass spectrometry dates on cucurbits, provide ample evidence of postdepositional vertical displacement of organic materials in the western half of Coxcatlan Cave, but they also indicate that the eastern half of the cave was largely undisturbed.

Archaeology↗
PubMed2006

Revised age estimates for the later Paleogene mammal faunas of Egypt and Oman.

The Jebel Qatrani Formation of northern Egypt has produced Afro-Arabia's primary record of Paleogene mammalian evolution, including the world's most complete remains of early anthropoid primates. Recent studies of Fayum mammals have assumed that the Jebel Qatrani Formation contains a significant Eocene component ( approximately 150 of 340 m), and that most taxa from that succession are between 35.4 and 33.3 million years old (Ma), i.e., latest Eocene to earliest Oligocene in age. Reanalysis of the chronological evidence shared by later Paleogene strata exposed in Egypt and Oman (Taqah and Thaytiniti areas, Dhofar Province) reveals that this hypothesis is no longer tenable. Revised correlation of the Fayum and Dhofar magnetostratigraphies indicates that (i) only the lowest 48 m of the Jebel Qatrani Formation are likely to be Eocene in age; (ii) the youngest Fayum anthropoids, including well known species such as Aegyptopithecus zeuxis and Apidium phiomense, are probably between 30.2 and 29.5 Ma, approximately 3-4 Ma younger than previously thought; (iii) oligopithecid anthropoids did not go extinct at the Eocene-Oligocene boundary but rather persisted for at least another 2.5 Ma; (iv) propliopithecid anthropoids first appear in the Fayum area at approximately 31.5 Ma, long after the Eocene-Oligocene boundary; and (v) the youngest Fayum mammals may be only approximately 1 Ma older than the 28- to 27-Ma mammals from Chilga, Ethiopia, and not 4-5 Ma older, as previously thought. Whatever gap exists in the Oligocene record of Afro-Arabian mammal evolution is now limited primarily to a poorly sampled 27- to 23-Ma window in the latest Oligocene.

Animals↗
PubMed2006

Analysis of Aurignacian interstratification at the Chatelperronian-type site and implications for the behavioral modernity of Neandertals.

The Châtelperronian is a Neandertal-associated archeological culture featuring ornaments and decorated bone tools. It is often suggested that such symbolic items do not imply that Neandertals had modern cognition and stand instead for influences received from coeval, nearby early modern humans represented by the Aurignacian culture, whose precocity would be proven by stratigraphy and radiocarbon dates. The Grotte des Fées at Châtelperron (France) is the remaining case of such a potential Châtelperronian-Aurignacian contemporaneity, but reanalysis shows that its stratification is poor and unclear, the bone assemblage is carnivore-accumulated, the putative interstratified Aurignacian lens in level B4 is made up for the most part of Châtelperronian material, the upper part of the sequence is entirely disturbed, and the few Aurignacian items in levels B4-5 represent isolated intrusions into otherwise in situ Châtelperronian deposits. As elsewhere in southwestern Europe, this evidence confirms that the Aurignacian postdates the Châtelperronian and that the latter's cultural innovations are better explained as the Neandertals' independent development of behavioral modernity.

Anthropology, Physical↗
PubMed2002

Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization.

Microarray analysis of gene expression patterns for thousands of human genes has led to the proposal that a large number of genes are expressed in a cell-cycle-specific manner. The identification of cyclically expressed genes was based on Affymetrix microarray analysis of gene expression after double-thymidine block synchronization. A statistical reanalysis of the original data leads to three principal findings. (i) Randomized data exhibit periodic patterns of similar or greater strength than the experimental data. This finding suggests that all apparent cyclicities in the expression measurements may arise from chance fluctuations. (ii) The presence of cyclicity and the timing of peak cyclicity in a given gene are not reproduced in two replicate experiments. This fact suggests there is an uncontrolled source of experimental variation that is stronger than the innate variation of gene expression in cells over time. (iii) The amplitude of peak expression in the second cycle is not consistently smaller than the corresponding amplitude in the first cycle. This finding places doubt on the assumption that the cells are actually synchronized. We propose that the microarray results do not support the proposal that there are numerous cell-cycle-specifically expressed genes in human cells.

Cell Cycle↗
PubMed2000

Inverse radiation dose-rate effects on somatic and germ-line mutations and DNA damage rates.

The mutagenic effect of low linear energy transfer ionizing radiation is reduced for a given dose as the dose rate (DR) is reduced to a low level, a phenomenon known as the direct DR effect. Our reanalysis of published data shows that for both somatic and germ-line mutations there is an opposite, inverse DR effect, with reduction from low to very low DR, the overall dependence of induced mutations being parabolically related to DR, with a minimum in the range of 0.1 to 1.0 cGy/min (rule 1). This general pattern can be attributed to an optimal induction of error-free DNA repair in a DR region of minimal mutability (MMDR region). The diminished activation of repair at very low DRs may reflect a low ratio of induced ("signal") to spontaneous background DNA damage ("noise"). Because two common DNA lesions, 8-oxoguanine and thymine glycol, were already known to activate repair in irradiated mammalian cells, we estimated how their rates of production are altered upon radiation exposure in the MMDR region. For these and other abundant lesions (abasic sites and single-strand breaks), the DNA damage rate increment in the MMDR region is in the range of 10% to 100% (rule 2). These estimates suggest a genetically programmed optimatization of response to radiation in the MMDR region.

Animals↗
PubMed2002

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains.

Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two "gapped" Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an "in silico" cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.

Bacterial Proteins↗
PubMed2001

Neuroinvasion by a Creutzfeldt-Jakob disease agent in the absence of B cells and follicular dendritic cells.

With the potential spread of bovine spongiform encephalopathy to people as a variant Creutzfeldt-Jakob disease (CJD), it becomes critical to identify cells in the periphery that carry infection. Initial work with scrapie agents suggested that B cells were central vectors for neuroinvasion. Subsequent studies indicated that B cells played an indirect role by promoting the development of follicular dendritic cells (FDCs) that accumulate abnormal prion protein (PrP). The mechanism for the role of FDCs, however, has not been clear. To further dissect potential B cell functions that contribute to neuroinvasion, we inoculated a CJD agent into mutant mice that (i) lacked B cells, (ii) had B cells unable to secrete Ig, or (iii) could secrete only IgM. Remarkably, all these mice developed disease with practically indistinguishable incubation times. The demonstration that neither immune complexes nor B cells were required for neuroinvasion from the periphery mandates a reanalysis of the accepted view of the essential role of B cells and FDC in these infections. Moreover, immune complexes were not required for the accumulation of pathologic PrP on the surface of FDCs, suggesting that PrP can bind to FDCs autonomously or by means of another factor. Wild-type mice had incubation times approximately 50 days less than all mutant mice at the same peripheral doses, indicating that an intact immune system may increase agent uptake and delivery, but this condition is not essential. Specifically, the evidence to date suggests that IgG may enhance pivotal agent interactions with migratory myeloid cells.

Animals↗
PubMed2000

Predicting the local dynamics of epizootic rabies among raccoons in the United States.

Mathematical models have been developed to explore the population dynamics of viral diseases among wildlife. However, assessing the predictions stemming from these models with wildlife databases adequate in size and temporal duration is uncommon. An epizootic of raccoon rabies that began in the mid-Atlantic region of the United States in the late 1970s has developed into one of the largest and most extensive in the history of wildlife rabies. We analyzed the dynamics of local epizootics at the county level by examining a database spanning more than 20 years and including 35,387 rabid raccoons. The size, number, and periodicity of rabies epizootics among raccoons were compared with predictions derived from a susceptible, exposed, infectious, and recovered model of raccoon rabies [Coyne, J., Smith, G. & McAllister, F. E. (1989) Am. J. Vet. Res. 50, 2148-2154]. After our methods for defining epizootics were applied to solutions of the model, the time series revealed recurrent epizootics in some counties, with a median first epizootic period of 48 months. Successive epizootics declined in size and the epizootic period progressively decreased. Our reanalysis of the model predicted the initial-epizootic period of 4-5 years, with a progressive dampening of epizootic size and progressive decrease in epizootic period. The best quantitative agreement between data and model assumed low levels of immunity (1-5%) within raccoon populations, suggesting that raccoons develop little or no rabies immune class. These results encourage the use of data obtained through wildlife surveillance in assessing and refining epidemic models for wildlife diseases.

Animals↗
PubMed1987

Metabolism of 5-fluorouracil to an N-cholyl-2-fluoro-beta-alanine conjugate: previously unrecognized role for bile acids in drug conjugation.

Recently we demonstrated clinically significant levels of a previously unrecognized metabolite of the anticancer drug 5-fluorouracil (FUra) in bile of cancer patients. In the present study, reanalysis of bile from these patients demonstrated the presence of not one but two previously unrecognized metabolites. The major unrecognized metabolite was purified by reversed-phase HPLC, after which its molecular weight was determined by fast-atom-bombardment mass spectrometry to be 497. The similarity in HPLC retention times and molecular weights of this FUra derivative and the bile acids N-cholylglycine (Mr 465) and N-cholyltaurine (Mr 515), along with the structural similarity of the FUra catabolite 2-fluoro-beta-alanine and the amino acids glycine and taurine, led to the hypothesis that this metabolite could be a conjugate of 2-fluoro-beta-alanine and cholic acid. This hypothesis was tested and confirmed by hydrolyzing the purified metabolite by cholylglycine hydrolase after which: 2-fluoro-beta-alanine was demonstrated by using a sensitive HPLC technique capable of resolving all of the known putative FUra metabolites, and unconjugated cholic acid was identified by both GC and GC-MS. Additionally, chemically synthesized N-cholyl-2-fluoro-beta-alanine was shown to cochromatograph on HPLC and TLC with the purified biliary metabolite. In summary, this study demonstrates a unique, so far as we know, pathway of drug metabolism in man in which an amino acid drug metabolite is conjugated with cholic acid and eliminated into the bile. Furthermore, the finding that 2-fluoro-beta-alanine is conjugated to bile acids may provide some insight into the mechanism of cholestasis that is frequently observed after administration of fluoropyrimidine by hepatic arterial infusion.

Alanine↗
PubMed1995

Flightless brown kiwis of New Zealand possess extremely subdivided population structure and cryptic species like small mammals.

Using allozymes and mtDNA sequences from the cytochrome b gene, we report that the brown kiwi has the highest levels of genetic structuring observed in birds. Moreover, the mtDNA sequences are, with two minor exceptions, diagnostic genetic markers for each population investigated, even though they are among the more slowly evolving coding regions in this genome. A major unexpected finding was the concordant split in molecular phylogenies between brown kiwis in the southern South Island and elsewhere in New Zealand. This basic phylogeographic boundary halfway down the South Island coincides with a fixed allele difference in the Hb nuclear locus and strongly suggests that two morphologically cryptic species are currently merged under one polytypic species. This is another striking example of how molecular genetic assays can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. However, reanalysis of the morphological characters by using phylogenetic methods revealed that the reason for this discordance is that most are primitive and thus are phylogenetically uninformative. Shared-derived morphological characters support the same relationships evident in the molecular phylogenies and, in concert with the molecular data, suggest that as brown kiwis colonized northward from the southern South Island, they retained many primitive characters that confounded earlier systematists. Strong subdivided population structure and cryptic species in brown kiwis seem to have evolved relatively recently as a consequence of Pleistocene range disjunctions, low dispersal power, and genetic drift in small populations.

Animals↗
PubMed1995

Cytochrome b-245 of the neutrophil superoxide-generating system contains two nonidentical hemes. Potentiometric studies of a mutant form of gp91phox.

Analysis of potentiometric titrations of the cytochrome b-245 from a X+ chronic granulomatous disease patient with an Arg54 --> Ser mutation in gp91phox indicates that the mutant form of the cytochrome contains two nonidentical hemes with midpoint potentials of Em7 = -220 and Em7 = -300 mV. In the light of this information, reanalysis of redox titrations of wild-type cytochrome b-245 implies that it probably also contains two separate heme centers with midpoint potentials of Em7 = -225 and Em7 = -265 mV. The effect of the Arg54 --> Ser substitution is to reduce the midpoint potential of one of the heme centers by approximately 35 mV and suggests possible interaction between Arg54 and a heme propionate side chain.

Cytochrome b Group↗
PubMed1999

The structural and functional analysis of the hemoglobin D component from chicken.

Oxygen binding by chicken blood shows enhanced cooperativity at high levels of oxygen saturation. This implies that deoxy hemoglobin tetramers self-associate. The crystal structure of an R-state form of chicken hemoglobin D has been solved to 2.3-A resolution using molecular replacement phases derived from human oxyhemoglobin. The model consists of an alpha2 beta2 tetramer in the asymmetric unit and has been refined to a R-factor of 0.222 (R-free = 0.257) for 29,702 reflections between 10.0- and 2.3-A resolution. Chicken Hb D differs most from human oxyhemoglobin in the AB and GH corners of the alpha subunits and the EF corner of the beta subunits. Reanalysis of published oxygen binding data for chicken Hbs shows that both chicken Hb A and Hb D possess enhanced cooperativity in vitro when inositol hexaphosphate is present. The electrostatic surface potential for a calculated model of chicken deoxy-Hb D tetramers shows a pronounced hydrophobic patch that involves parts of the D and E helices of the beta subunits. This hydrophobic patch is a promising candidate for a tetramer-tetramer interface that could regulate oxygen binding via the distal histidine.

Animals↗
PubMed2006

Crystal structures of expressed non-polymerizable monomeric actin in the ADP and ATP states.

Actin filament growth and disassembly, as well as affinity for actin-binding proteins, is mediated by the nucleotide-bound state of the component actin monomers. The structural differences between ATP-actin and ADP-actin, however, remain controversial. We expressed a cytoplasmic actin in Sf9 cells, which was rendered non-polymerizable by virtue of two point mutations in subdomain 4 (A204E/P243K). This homogeneous monomer, called AP-actin, was crystallized in the absence of toxins, binding proteins, or chemical modification, with ATP or ADP at the active site. The two surface mutations do not perturb the structure. Significant differences between the two states are confined to the active site region and sensor loop. The active site cleft remains closed in both states. Minor structural shifts propagate from the active site toward subdomain 2, but dissipate before reaching the DNase binding loop (D-loop), which remains disordered in both the ADP and ATP states. This result contrasts with previous structures of actin made monomeric by modification with tetramethylrhodamine, which show formation of an alpha-helix at the distal end of the D-loop in the ADP-bound but not the ATP-bound form (Otterbein, L. R., Graceffa, P., and Dominguez, R. (2001) Science 293, 708-711). Our reanalysis of the TMR-modified actin structures suggests that the nucleotide-dependent formation of the D-loop helix may result from signal propagation through crystal packing interactions. Whereas the observed nucleotide-dependent changes in the structure present significantly different surfaces on the exterior of the actin monomer, current models of the actin filament lack any actin-actin interactions that involve the region of these key structural changes.

Actins↗
PubMed2003

Analysis of the subunit composition of complex I from bovine heart mitochondria.

Complex I purified from bovine heart mitochondria is a multisubunit membrane-bound assembly. In the past, seven of its subunits were shown to be products of the mitochondrial genome, and 35 nuclear encoded subunits were identified. The complex is L-shaped with one arm in the plane of the membrane and the other lying orthogonal to it in the mitochondrial matrix. With mildly chaotropic detergents, the intact complex has been resolved into various subcomplexes. Subcomplex Ilambda represents the extrinsic arm, subcomplex Ialpha consists of subcomplex Ilambda plus part of the membrane arm, and subcomplex Ibeta is another substantial part of the membrane arm. The intact complex and these three subcomplexes have been subjected to extensive reanalysis. Their subunits have been separated by three independent methods (one-dimensional SDS-PAGE, two-dimensional isoelectric focusing/SDS-PAGE, and reverse phase high pressure liquid chromatography (HPLC)) and analyzed by tryptic peptide mass fingerprinting and tandem mass spectrometry. The masses of many of the intact subunits have also been measured by electrospray ionization mass spectrometry and have provided valuable information about post-translational modifications. The presence of the known 35 nuclear encoded subunits in complex I has been confirmed, and four additional nuclear encoded subunits have been detected. Subunits B16.6, B14.7, and ESSS were discovered in the SDS-PAGE analysis of subcomplex Ilambda, in the two-dimensional gel analysis of the intact complex, and in the HPLC analysis of subcomplex Ibeta, respectively. Despite many attempts, no sequence information has been obtained yet on a fourth new subunit (mass 10,566+/-2 Da) also detected in the HPLC analysis of subcomplex Ibeta. It is unlikely that any more subunits of the bovine complex remain undiscovered. Therefore, the intact enzyme is a complex of 46 subunits, and, assuming there is one copy of each subunit in the complex, its mass is 980 kDa.

Animals↗
PubMed2002

Sex differences in cognitive impairment in multiple sclerosis.

Multiple sclerosis (MS) is twice as prevalent in females as in males, but the possibility of sex differences in the cognitive sequellae of the disease has not been considered. In this study male patients with MS performed more poorly than female patients on tests of verbal and nonverbal memory, visuospatial construction, and on the Mini Mental State Exam (MMSE) and the Wisconsin Card Sorting Test (WCST). The groups of male and female patients were similar in age, education, and on several measures of neurologic and emotional disturbance. Among normals there are no sex differences on the MMSE and WCST. Sex differences on the memory and visuospatial construction tests were larger in magnitude for the patients than for normal controls, implying that male patients are somehow especially vulnerable to cognitive deficits. Reanalysis of existing databases could clarify questions about the existence and source of cognitive sex differences in MS.

Cognition Disorders↗
PubMed2003

Feeding in Atractaspis (Serpentes: Atractaspididae): a study in conflicting functional constraints.

African fossorial colubroid snakes of the genus Atractaspis have relatively long fangs on short maxillae, a gap separating the pterygoid and palatine bones, a toothless pterygoid, and a snout tightly attached to the rest of the skull. They envenomate prey with a unilateral backward stab of one fang projected from a closed mouth. We combined structural reanalysis of the feeding apparatus, video records of prey envenomation and transport, and manipulations of live and dead Atractaspis to determine how structure relates to function in this unusual genus of snakes. Unilateral fang use in Atractaspis is similar to unilateral slashing envenomation by some rear-fanged snakes, but Atractaspis show no maxillary movement during prey transport. Loss of pterygoid teeth and maxillary movement during transport resulted in the inability to perform. 'pterygoid walk' prey transport. Atractaspis transport prey through the oral cavity using movement cycles in which mandibular adduction, anterior trunk compression, and ventral flexion of the head alternate with mandibular abduction and extension of head and anterior trunk over the prey. Inefficiencies in manipulation and early transport of prey are offset by adaptability of the envenomating system to various prey types in both enclosed and open spaces and by selection of prey that occupy burrows or tunnels in soil. Atractaspis appears to represent the evolutionary endpoint of a functional conflict between envenomation and transport in which a rear-fanged envenomating system has been optimized at the expense of most, if not all, palatomaxillary transport function.

Journal Article↗
PubMed2000

Predilection of otosclerotic foci related to the bone turnover in the otic capsule.

Using multiple fluorochrome tagging of eight mongrel dogs and a newly established methodology of measuring bone turnover (BTO) in the otic capsule, it has previously been demonstrated that BTO in the canine otic capsule is highly reduced close to the perilymphatic spaces (PLS) compared to the normal level of BTO in the periphery. Reanalysis of these data shows that this inhibition of BTO is far more pronounced around the cochlea and vestibule than around the semicircular canals. Similar tendencies are seen for the numerical density and mean label area of the bone remodelling units. With increasing distance to the PLS, these patterns are weakened, but still recognizable. In otosclerosis, foci of abnormal bone deposition are particularly frequent around the oval and round windows and in the cochlear capsule, i.e. where inhibition of bone remodelling is most prominent. A surpassing (or failure) of this pronounced inhibition must precede the tumultuous but delimited osteogenesis of otosclerosis. Otosclerosis may be a deviation of the normal BTO process in an osteometabolically abnormal site, perhaps initiated as an osteogenetic response to abnormal stress exposure.

Animals↗
PubMed2001

Development of a brief form of the Life Skills Profile: the LSP-20.

OBJECTIVE: To develop a brief form of the Life Skills Profile (LSP) that incorporates all five subscales of the full form. METHOD: A new short form of the LSP (LSP-20) was developed to incorporate all five subscales of the full form. The LSP-20 development was based on a reanalysis of data from previously published studies. These data sets were also reanalysed to determine any differential effects of numbers and percentages of items in the LSP-39, LSP-16 and LSP-20, comparability of scores of the different forms, of test-retest and interrater reliability, and validity of the LSP-20 by comparison with the Positive and Negative Syndrome Scale (PANSS). RESULTS: A twenty-item short form of the LSP-39 (LSP-20) is described which retains 16 items of an earlier short form but which also reproduces the subscale concerned with disability associated with positive psychotic phenomena. The subscales correlated highly with their counterparts in the full form, interrater and test-retest reliabilities were comparable, and concurrent validity was good. CONCLUSIONS: The LSP-20 is a brief form of a widely used instrument that offers equivalent coverage to the full form with sound empirical properties, though unlike the LSP-39, it can be scored in the direction of impairments or strengths. Therefore the LSP-20 may be more suited to routine service disability and aggregated outcome assessments, but less suited than the LSP-39 to detailed research, or to interactive use as part of service user's individual care planning and review.

Adult↗