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PubMed1998

Molecular systematics and biogeography of aridland gnatcatchers (genus Polioptila) and evidence supporting species status of the California gnatcatcher (Polioptila california).

Over 2000 basepairs of mitochondrial DNA (mtDNA) sequences were compared to (1) examine evolution in protein coding versus noncoding [control region (CR)] segments, and (2) test the species-level distinctiveness of the California gnatcatcher (Polioptila californica) and clarify its phylogenetic and biogeographic relationships to other arid-adapted gnatcatchers. Unlike some studies, CR region I (left domain) was not as variable as coding genes. As expected, the central domain of the CR varied little, whereas CR II (right domain) showed high levels of variation. CR sequences tended to be "phylogenetically noisy" as evidenced by lower rescaled consistency indices, relative to those for coding genes. The California gnatcatcher differs from its sister-species, the black-tailed gnatcatcher (P. melanura), by approximately 4.0%, which supports species-level recognition. Two other aridland gnatcatchers, the black-capped gnatcatcher. (P. nigriceps) and white-lored gnatcatcher (P. albiloris), are closely related to the previous two species, also at a level of about 4 to 4.5% sequence divergence. These species evolved over a relatively short time, but prior to the most recent Pleistocene glaciations.

Animals↗
PubMed2005

Systematic analysis of gene expression in human brains before and after death.

BACKGROUND: Numerous studies have employed microarray techniques to study changes in gene expression in connection with human disease, aging and evolution. The vast majority of human samples available for research are obtained from deceased individuals. This raises questions about how well gene expression patterns in such samples reflect those of living individuals. RESULTS: Here, we compare gene expression patterns in two human brain regions in postmortem samples and in material collected during surgical intervention. We find that death induces significant expression changes in more than 10% of all expressed genes. These changes are non-randomly distributed with respect to their function. Moreover, we observe similar expression changes due to death in two distinct brain regions. Consequently, the pattern of gene expression differences between the two brain regions is largely unaffected by death, although the magnitude of differences is reduced by 50% in postmortem samples. Furthermore, death-induced changes do not contribute significantly to gene expression variation among postmortem human brain samples. CONCLUSION: We conclude that postmortem human brain samples are suitable for investigating gene expression patterns in humans, but that caution is warranted in interpreting results for individual genes.

Adolescent↗
PubMed2006

The evolution of activity breaks in the nest cycle of annual eusocial bees: a model of delayed exponential growth.

BACKGROUND: Social insects show considerable variability not only in social organisation but also in the temporal pattern of nest cycles. In annual eusocial sweat bees, nest cycles typically consist of a sequence of distinct phases of activity (queen or workers collect food, construct, and provision brood cells) and inactivity (nest is closed). Since the flight season is limited to the time of the year with sufficiently high temperatures and resource availability, every break reduces the potential for foraging and, thus, the productivity of a colony. This apparent waste of time has not gained much attention. RESULTS: We present a model that explains the evolution of activity breaks by assuming differential mortality during active and inactive phases and a limited rate of development of larvae, both reasonable assumptions. The model predicts a systematic temporal structure of breaks at certain times in the season which increase the fitness of a colony. The predicted pattern of these breaks is in excellent accordance with field data on the nest cycle of the halictid Lasioglossum malachurum. CONCLUSION: Activity breaks are a counter-intuitive outcome of varying mortality rates that maximise the reproductive output of primitively eusocial nests.

Animals↗
PubMed2004

Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition.

Germ-line mutations in the BRCA1 gene predispose affected individuals to breast and ovarian cancer syndromes. In an attempt to systematically analyze a broader spectrum of genetic changes ranging from frequent exon deletions and duplications to amino acid replacements and protein truncations, we isolated and characterized full size BRCA1 homologues from a representative group of non-human primates. Our analysis represents the first comprehensive sequence comparison of primate BRCA1 loci and corresponding proteins. The comparison revealed an unusually high proportion of indels in non-coding DNA. The major force driving evolutionary changes in non-coding BRCA1 sequences was Alu-mediated rearrangements, including Alu transpositions and Alu-associated deletions, indicating that structural instability of this locus may be intrinsic in anthropoids. Analysis of the non-synonymous/synonymous ratio in coding portions of the gene revealed the presence of both conserved and rapidly evolving regions in the BRCA1 protein. Previously, a rapidly evolving region with evidence of positive evolutionary selection in human and chimpanzee had been identified only in exon 11. Here, we show that most of the internal BRCA1 sequence is variable between primates and evolved under positive selection. In contrast, the terminal regions of BRCA1, which encode the RING finger and BRCT domains, experienced negative selection, which left them almost identical between the compared primates. Distribution of the reported missense mutations, but not frameshift and nonsense mutations, is positively correlated with BRCA1 protein conservation. Finally, on the basis of protein sequence conservation, we identified missense changes that are likely to compromise BRCA1 function.

Alu Elements↗
PubMed2002

Archaeology and cognitive evolution.

Archaeology can provide two bodies of information relevant to the understanding of the evolution of human cognition--the timing of developments, and the evolutionary context of these developments. The challenge is methodological. Archaeology must document attributes that have direct implications for underlying cognitive mechanisms. One example of such a cognitive archaeology is found in spatial cognition. The archaeological record documents an evolutionary sequence that begins with ape-equivalent spatial abilities 2.5 million years ago and ends with the appearance of modern abilities in the still remote past of 400,000 years ago. The timing of these developments reveals two major episodes in the evolution in spatial ability, one, 1.5 million years ago and the other, one million years later. The two episodes of development in spatial cognition had very different evolutionary contexts. The first was associated with the shift to an open country adaptive niche that occurred early in the time range of Homo erectus. The second was associated with no clear adaptive shift, though it does appear to have coincided with the invasion of more hostile environments and the appearance of systematic hunting of large mammals. Neither, however, occurred in a context of modern hunting and gathering.

Animals↗
PubMed2005

The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny.

BACKGROUND: Evolutionary analyses of the largest subunit of RNA polymerase II (RPB1) have yielded important and at times provocative results. One particularly troublesome outcome is the consistent inference of independent origins of red algae and green plants, at odds with the more widely accepted view of a monophyletic Plantae comprising all eukaryotes with primary plastids. If the hypothesis of a broader kingdom Plantae is correct, then RPB1 trees likely reflect a persistent phylogenetic artifact. To gain a better understanding of RNAP II evolution, and the presumed artifact relating to green plants and red algae, we isolated and analyzed RPB1 from representatives of Glaucocystophyta, the third eukaryotic group with primary plastids. RESULTS: Phylogenetic analyses incorporating glaucocystophytes do not recover a monophyletic Plantae; rather they result in additional conflicts with the most widely held views on eukaryotic relationships. In particular, glaucocystophytes are recovered as sister to several amoebozoans with strong support. A detailed investigation shows that this clade can be explained by what we call "short-branch exclusion," a phylogenetic artifact integrally associated with "long-branch attraction." Other systematic discrepancies observed in RPB1 trees can be explained as phylogenetic artifacts; however, these apparent artifacts also appear in regions of the tree that support widely held views of eukaryotic evolution. In fact, most of the RPB1 tree is consistent with artifacts of rate variation among sequences and co-variation due to functional constraints related to C-terminal domain based RNAP II transcription. CONCLUSION: Our results reveal how subtle and easily overlooked biases can dominate the overall results of molecular phylogenetic analyses of ancient eukaryotic relationships. Sources of potential phylogenetic artifact should be investigated routinely, not just when obvious "long-branch attraction" is encountered.

Bayes Theorem↗
PubMed2000

In vitro stability of plasma-sprayed hydroxyapatite coatings on Ti-6Al-4V implants under cyclic loading.

The success of hydroxyapatite (HA)-coated Ti-6Al-4V implants relies on the long-term stability of HA coatings. In this study, the mechanical stability of plasma-sprayed HA coatings on Ti-6Al-4V implants under four-point cyclic bending was systematically investigated in both air and simulated body fluid (SBF) environments at room temperature. To have a clear view of the microscale damage evolution, the surface morphology change of HA coatings during cyclic loading was carefully examined by scanning electron microscopy at the same locations on the coating surfaces after four-point bending for 4, 6.5, 8.5, and 10 million cycles. Also, possible changes of other characteristics such as thickness, weight, crystallinity, and residual stress of HA coatings were measured as a function of loading cycles. Up to 10 million cycles of bending in air and SBF, we found no significant microcracking or coating spalling on the surface of coatings, and no significant changes in thickness, weight, crystallinity, or residual stress of the plasma-sprayed HA coatings. The experiment results indicate that thickness and crystallinity had no effects on the stability of the HA coatings. HA coating resistance to the cyclic four-point bending might result from the stress shielding effects of preexisting microcracks in the coatings.

Biocompatible Materials↗
PubMed2000

Pure-exchange solid-state NMR.

Three exchange nuclear magnetic resonance (NMR) techniques are presented that yield (13)C NMR spectra exclusively of slowly reorienting segments, suppressing the often dominant signals of immobile components. The first technique eliminates the diagonal ridge that usually dominates two-dimensional (2D) exchange NMR spectra and that makes it hard to detect the broad and low off-diagonal exchange patterns. A modulation of the 2D exchange spectrum by the sine-square of a factor which is proportional to the difference between evolution and detection frequencies is generated by fixed additional evolution and detection periods of duration tau, yielding a 2D pure-exchange (PUREX) spectrum. Smooth off-diagonal intensity is obtained by systematically incrementing tau and summing up the resulting spectra. The related second technique yields a static one-dimensional (1D) spectrum selectively of the exchanging site(s), which can thus be identified. Efficient detection of previously almost unobservable slow motions in a semicrystalline polymer is demonstrated. The third approach, a 1D pure-exchange experiment under magic-angle spinning, is an extension of the exchange-induced sideband (EIS) method. A TOSS (total suppression of sidebands) spectrum obtained after the same number of pulses and delays, with a simple swap of z periods, is subtracted from the EIS spectrum, leaving only the exchange-induced sidebands and a strong, easily detected centerband of the mobile site(s).

Carbon Isotopes↗
PubMed1997

Simulation of nonstationary EEG.

In this paper we present a systematic method for generating simulations of nonstationary EEG. Such simulations are needed, for example, in the evaluation of tracking algorithms. First a state evolution process is simulated. The states are initially represented as segments of stationary autoregressive processes which are described with the corresponding predictor coefficients and prediction error variances. These parameters are then concatenated to give a piecewise time-invariant parameter evolution. The evolution is projected onto an appropriately selected set of smoothly time-varying functions. This projection is used to generate the final EEG simulation. As an example we use this method to simulate the EEG of a drowsy rat. This EEG can be described as toggling between two states that differ in the degree of synchronization of the activity-inducing neuron clusters.

Algorithms↗
PubMed1991

Developmental and age-related changes in reflexes of the human jaw-closing system.

Reflex responses of the jaw-closing system to innocuous mechanical stimulation of the tongue and palate were examined in a group of 25 girls aged 7-8 years and in a group of 25 women aged 70-80 years. Responses were measured both as changes in background biting force and from bilateral recordings of masseter EMGs. For comparative purposes, results from an earlier study of 35 young adult women (aged 18-25 years) were available. Compared to younger groups of subjects, reflex responses of the elderly were reduced in numbers and amplitude, were characterized by fewer initial excitatory component responses, and had longer latency to onset. Analyses of responses of the children indicated that age 7-8 years is a transitional period. Some children show adult-like responses, while others display responses that appear to represent earlier forms or transitional responses. These results suggest that oral-motor reflexes are not fixed response patterns upon which more complex motor skills, such as speech, are built. Rather, oral reflex development appears to occur in concert with the acquisition of complex motor skills. Systematic changes in reflex responses also occur in the period from young adulthood to seventh decade of life. This result indicates a continuous evolution of oral sensorimotor systems throughout the human life span.

Adult↗
PubMed2026

Early infantile developmental and epileptic encephalopathy: clinical spectrum, diagnosis, outcomes, and evolving treatment strategies.

Early infantile developmental and epileptic encephalopathy (EIDEE) is among the most severe epilepsy syndromes, with onset before three months of age and an estimated incidence of approximately 10 per 100,000 live births. The 2022 International League Against Epilepsy classification unified the historically distinct Ohtahara syndrome and early myoclonic encephalopathy under a single diagnostic framework defined by frequent drug-resistant tonic and/or myoclonic seizures, an abnormal neurological examination, and an abnormal interictal electroencephalogram-most characteristically a burst-suppression pattern. This narrative review synthesizes the clinical, electrophysiological, neuroimaging, genetic, and therapeutic literature within the EIDEE framework. The clinical phenotype is characterized by central hypotonia, postnatal microcephaly, cortical visual impairment, and age-dependent syndromic evolution toward infantile epileptic spasms syndrome or Lennox-Gastaut syndrome in the majority of patients. Electroencephalography remains essential for syndromic classification, while systematic metabolic screening and early trio whole-exome or whole-genome sequencing are central to the etiologic workup, achieving diagnostic yields of 60-65%. The most commonly identified genetic causes include STXBP1, KCNQ2, and SCN2A variants. Outcomes are poor overall and strongly etiology-dependent: vitamin-responsive disorders carry a substantially more favorable prognosis, whereas mortality reaches 25% in genetic cohorts. Genotype-guided pharmacotherapy is now applicable to a clinically meaningful subset of patients, with sodium channel blockers, potassium channel openers, and emerging antisense oligonucleotide therapies representing important therapeutic advances. Gene therapy trials are underway but have encountered early safety signals, underscoring the vulnerability of this population. Critical unmet needs include earlier molecular diagnosis, precision therapies targeting developmental outcomes beyond seizure control, and prospective international registries to characterize the long-term natural history of EIDEE.

Humans↗
PubMed1999

DNA markers in plant improvement: an overview.

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

Journal Article↗
PubMed2005

Molecular and morphological supertree of stony corals (Anthozoa: Scleractinia) using matrix representation parsimony.

The supertree algorithm matrix representation with parsimony was used to combine existing hypotheses of coral relationships and provide the most comprehensive species-level estimate of scleractinian phylogeny, comprised of 353 species (27% of extant species), 141 genera (63%) and 23 families (92%) from all seven suborders. The resulting supertree offers a guide for future studies in coral systematics by highlighting regions of concordance and conflict in existing source phylogenies. It should also prove useful in formal comparative studies of character evolution. Phylogenetic effort within Scleractinia has been taxonomically uneven, with a third of studies focussing on the Acroporidae or its most diverse genera. Sampling has also been geographically non-uniform, as tropical, reef-forming taxa have been considered twice as often as non-reef species. The supertree indicated that source trees concur on numerous aspects of coral relationships, such as the division between robust versus complex corals and the distant relationship between families in Archaeocoeniina. The supertree also supported the existence of a large, taxonomically diverse and monophyletic group of corals with many Atlantic representatives having exsert corallites. Another large, unanticipated clade consisted entirely of solitary deep-water species from three families. Important areas of ambiguity include the relationship of Astrocoeniidae to Pocilloporidae and the relative positions of several, mostly deep-water genera of Caryophylliidae. Conservative grafting of species at the base of congeneric groups with uncontroversial monophyletic status resulted in a more comprehensive, though less resolved tree of 1016 taxa.

Animals↗
PubMed2003

High-resolution record of pyrogenic polycyclic aromatic hydrocarbon deposition during the 20th century.

A high-resolution record of polycyclic aromatic hydrocarbon (PAH) deposition in Rhode Island over the past approximately 180 years was constructed using a sediment core from the anoxic Pettaquamscutt River basin. The record showed significantly more structure than has hitherto been reported and revealed four distinct maxima in PAH flux. The characteristic increase in PAH flux at the turn of the 20th century was captured in detail, leading to an initial maximum prior to the Great Depression. The overall peak in PAH flux in the 1950s was followed by a maximum that immediately preceded the 1973 Organization of Petroleum Exporting Countries (OPEC) oil embargo. During the most recent portion of the record, an abrupt increase in PAH flux between 1996 and 1999 has been found to follow a period of near constant fluxes. Because source-diagnostic ratios indicate that petrogenic inputs are minor throughout the record, these trends are interpreted in terms of past variations in the magnitude and type of combustion processes. For the most recent PAH maximum, energy consumption data suggest that diesel fuel combustion, and hence traffic of heavier vehicles, is the most probable cause for the increase in PAH flux. Systematic variations in the relative abundance of individual PAHs in conjunction with the above changes in flux are interpreted in relation to the evolution of combustion processes. Coronene, retene, and perylene are notable exceptions, exhibiting unique down-core profiles.

Environmental Monitoring↗
PubMed2026

Advances in genomics-driven genetic decoding and genomic design breeding in tomato.

Tomatoes are highly nutritious and represent one of the important vegetable fruits worldwide. Both historically and moving forward, genetic decoding and precision breeding remain fundamental to tomato improvement. Here, we summarize pivotal advances in decoding tomato genomes across domestication, improvement and evolution processes and provide a perspective on future breeding through precision design. In-depth population genetic studies have revealed how artificial selection systematically prioritized yield-related alleles at the cost of narrowing genetic diversity, especially at flavor-related loci-highlighting the urgent need to reconcile these trade-offs. Comparative genomics across species, viewed through an evolutionary lens, has uncovered critical insights into functional genes, deepening our understanding of the genetic architecture and regulatory mechanisms underlying key traits. Collectively, these advances have enabled precise identification and functional characterization of key genetic elements, paving the way for systematic redomestication of tomato through precision genomic design. Looking ahead, more efficient and precise breeding strategies will be required to accelerate genetic gains in tomato in the coming decades. The integration of recent genomic advances, coupled with genomic selection and artificial intelligence, into genomic design breeding offers a transformative framework, unlocking unprecedented opportunities for developing highly flavorful and consumer-customized tomato varieties.

Journal Article↗
PubMed2005

Evolution of small copper clusters and dissociative chemisorption of hydrogen.

The structural evolution of small copper clusters of up to 15 atoms and the dissociative chemisorption of H2 on the minimum energy clusters are studied systematically using density functional theory. The preferred copper sites for chemisorption are identified and the transition state structures and activation barriers for clusters four to nine atoms are determined and found to be inconsistent with the empirical Bronsted-Evans-Polanyi relationship. The physicochemical properties of the clusters are computed and compared with the bulk and surface values. The results indicate that a phase transition must occur in the going from cluster to bulk.

Journal Article↗