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PubMed2007

A comparison of the variability spectra of two genomic loci in a European group of individuals reveals fundamental differences pointing to selection or a population bottleneck.

Knowledge about the variability spectra of neutrally evolving sequences in a population is a prerequisite for the identification of genes, which may have been under positive selection during recent human evolution. Here, we report the results of a re-sequencing project of a presumably neutrally evolving chromosome 22 locus with a severely reduced recombination frequency in a group of 24 individuals of German origin. The comparison of these data with the results of a similar analysis of a chromosome 17 locus revealed striking differences, although the same group of individuals was used. For the chromosome 17 locus two well-separated groups of sequences, a positive value of Tajima's D and a TMRCA of 700,000 years were observed. In contrast, the sequences from the chromosome 22 locus were found to be relatively homogeneous, with no deep splits between subgroups; the obtained value for Tajima's D was negative and the TMRCA was only 260,000 years. These discrepancies may be explained by selection or demographic processes. Regarding demography, the most plausible explanation is the assumption of a severe bottleneck in the history of the European population: in the case of the chromosome 17 locus two ancient lineages passed this bottleneck; for the chromosome 22 locus it was only one ancient lineage.

Chromosomes, Human, Pair 17↗
PubMed1997

Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel.

Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand the ecology of these microorganisms, we investigated the relative abundance, distribution, and phylogenetic composition of Archaea in the Santa Barbara Channel. Significant amounts of archaeal rRNA and rDNA (genes coding for rRNA) were detected in all samples analyzed. The relative abundance of archaeal rRNA as measured by quantitative oligonucleotide hybridization experiments was low in surface waters but reached higher values (20 to 30% of prokaryotic rRNA) at depths below 100 m. Probes were developed for the two major groups of marine Archaea detected. rRNA originating from the euryarchaeal group (group II) was most abundant in surface waters, whereas rRNA from the crenarchaeal group (group I) dominated at depth. Clone libraries of PCR-amplified archaeal rRNA genes were constructed with samples from 0 and 200 m deep. Screening of libraries by hybridization with specific oligonucleotide probes, as well as subsequent sequencing of the cloned genes, indicated that virtually all archaeal rDNA clones recovered belonged to one of the two groups. The recovery of cloned rDNA sequence types in depth profiles exhibited the same trends as were observed in quantitative rRNA hybridization experiments. One representative of each of 18 distinct restriction fragment length polymorphism types was partially sequenced. Recovered sequences spanned most of the previously reported phylogenetic diversity detected in planktonic crenarchaeal and euryarchaeal groups. Several rDNA sequences appeared to be harbored in archaeal types which are widely distributed in marine coastal waters. In total, data suggest that marine planktonic crenarchaea and euryarchaea of temperate coastal habitats thrive in different zones of the water column. The relative rRNA abundance of the crenarchaeal group suggests that its members constitute a significant fraction of the prokaryotic biomass in subsurface coastal waters.

Animals↗
PubMed2000

Corneal amyloidosis caused by Leu518Pro mutation of betaig-h3 gene.

AIM: To report a Japanese family diagnosed clinically as having lattice corneal dystrophy type I (LCDI) in which a Leu518Pro mutation in the betaig-h3 gene and not the R124C mutation reported previously was found. METHODS: Molecular genetic analysis was performed on DNA extracted from peripheral leucocytes from four members (three affected and one unaffected) of a family. Exon 4 of the betaig-h3 gene was amplified by PCR and directly sequenced. Histopathological study was performed on the corneal tissue from the proband obtained during deep lamellar keratoplasty. RESULTS: All the affected members were clinically diagnosed as having LCDI, and the pedigree indicated an autosomal dominant inheritance. A heterozygous single base pair transition (CTG to CCG, leucine to proline) was detected in codon 518 of the betaig-h3 gene in the three affected members, and not in the unaffected member. No mutation was found in codon 124. Amyloid deposits were observed between the collagen bundles of the corneal stroma and were seen to extend deep into the stroma. CONCLUSION: The Leu518Pro mutated betaig-h3 forms amyloidogeneic intermediates which precipitate in the cornea and gives rise to a clinical appearance of LCDI.

Adolescent↗
PubMedDate not supplied

Collateral ligaments of the ankle: high-resolution MR imaging with a local gradient coil and anatomic correlation in cadavers.

Findings at high-resolution magnetic resonance (MR) imaging of the lateral and medial collateral ligaments of the ankle were compared with findings in anatomic sections from cadavers. MR imaging of six cadaveric feet was performed with a newly developed local gradient coil and axial and coronal T1-weighted spin-echo sequences. Axial imaging provided optimum views of the anterior and posterior talofibular ligaments, the deep layers of the medial collateral ligament, and the tibionavicular ligament. Coronal imaging allowed complete visualization of the calcaneofibular, posterior talofibular, tibiocalcaneal, and posterior tibiotalar ligaments. In both imaging planes, differentiation of the deep and superficial layers of the medial collateral ligament was possible. Differentiation between the syndesmotic complex and the lateral collateral ligament was accomplished easily; in particular, differentiation of the posterior tibiofibular ligament from the posterior talofibular ligament was not difficult because of the differing insertions of these ligaments. The inhomogeneous appearance of the medial collateral ligament and the posterior talofibular ligament on MR images correlated with areas of fatty tissue on corresponding microscopic sections. High-resolution MR imaging with a newly developed local gradient coil allows excellent visualization of the lateral and medial collateral ligaments of the ankle.

Adipose Tissue↗
PubMed2001

V beta 6+ T cells are obligatory for vaccine-induced immunity to Histoplasma capsulatum.

We examined TCR usage to a protective fragment of heat shock protein 60 from the fungus, Histoplasma capsulatum. Nearly 90% of T cell clones from C57BL/6 mice vaccinated with this protein were Vbeta6+; the remainder were Vbeta14+. Amino acid motifs of the CDR3 region from Vbeta6+ cells were predominantly IxGGG, IGG, or SxxGG, whereas it was uniformly SFSGG for Vbeta14+ clones. Short term T cell lines from Vbeta6+-depleted mice failed to recognize Ag, and no T cell clones could be generated. To determine whether Vbeta6+ cells were functionally important, we eliminated them during vaccination. Depletion of Vbeta6+ cells abrogated protection in vivo and upon adoptive transfer of cells into TCR alphabeta(-/-) mice. Transfer of a Vbeta6+, but not a Vbeta14+, clone into TCR alphabeta(-/-) mice prolonged survival. Cytokine generation by Ag-stimulated splenocytes from immunized mice depleted of Vbeta6+ cells was similar to that of controls. The efficacy of the Vbeta6+ clone was associated with elevated production of IFN-gamma, TNF-alpha, and GM-CSF compared with that of the Vbeta14+ clone. More Vbeta6+ cells were present in lungs and spleens of TCR alphabeta(-/-) on day 3 postinfection compared with Vbeta14+ cells. Thus, a single Vbeta family was essential for vaccine-induced immunity. Moreover, the mechanism by which Vbeta6+ contributed to protective immunity differed between unfractionated splenocytes and T cell clones.

Adoptive Transfer↗
PubMed1981

Time of origin of neurons of the rat superior colliculus in relation to other components of the visual and visuomotor pathways.

Groups of pregnant rats were injected with two successive daily doses of 3H-thymidine from gestational day 12 and 13 (E12 + E13) until the day before parturition (E21 + 22) in order to label all the multiplying precursors of neurons. At 60 days of age the proportion of neurons generated (or no longer labelled) on specific days was determined in the separate layers of the superiorr colliculus. Neurogenesis begins with layers V and IV on day E12; the bulk (87%) of these cells are generated on day E13. This early-produced band of large neurons, the intermediate magnocellular zone, divides the superior colliculus into two cytogenetically distinct regions. In both the deep and the superficial superior colliculus neuron production is relatively protracted. In the deep superior colliculus neuron production peaks on day E15 in lay VII, on day E15 and E16 in lay VI, and on day E16 (the large neurons excluded) in layer V, indicating an inside-out sequence. In the superficial superio coliculus peak production time of both layer I and II is on day E16 but in the latter region neuron production is more prolonged and ends on day E18. One interpretation of these results is that the two pairs of superficial layers are produced in an outside-in sequence. These three cytogenetic subdivisions of the superior colliculus may be correlated with its structural-functional parcellation into an efferent spinotectal, a deep somatomotor and a superficial visual component. A comparison of neurogenesis in different components of the visuomotor and visual pathways of the rat indicates that the motor neurons of the extraocular muscles, the abducens, trochlear and oculomotor nuclei, and neurons of the nucleus of Darkschewitsch are produced first. Next in line are source neurons of efferents to the bulb and the spinal cord: those of the Edinger-Westphal nucleus and the intermediate magnocellular zone of the superior colliculus. These are followed by the relay neurons of the dorsal nucleus of the lateral geniculate body. The neurons of the superficial superior colliculus and of the visual cortex implicated in visual sensori-motor integrations are produced last.

Afferent Pathways↗
PubMed2002

Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies.

Phylogenetic relationships among the NBS-LRR (nucleotide binding site-leucine-rich repeat) resistance gene homologues (RGHs) from 30 genera and nine families were evaluated relative to phylogenies for these taxa. More than 800 NBS-LRR RGHs were analyzed, primarily from Fabaceae, Brassicaceae, Poaceae, and Solanaceae species, but also from representatives of other angiosperm and gymnosperm families. Parsimony, maximum likelihood, and distance methods were used to classify these RGHs relative to previously observed gene subfamilies as well as within more closely related sequence clades. Grouping sequences using a distance cutoff of 250 PAM units (point accepted mutations per 100 residues) identified at least five ancient sequence clades with representatives from several plant families: the previously observed TIR gene subfamily and a minimum of four deep splits within the non-TIR gene subfamily. The deep splits in the non-TIR subfamily are also reflected in comparisons of amino acid substitution rates in various species and in ratios of nonsynonymous-to-synonymous nucleotide substitution rates ( K(A)/ K(S) values) in Arabidopsis thaliana. Lower K(A)/ K(S) values in the TIR than the non-TIR sequences suggest greater functional constraints in the TIR subfamily. At least three of the five identified ancient clades appear to predate the angiosperm-gymnosperm radiation. Monocot sequences are absent from the TIR subfamily, as observed in previous studies. In both subfamilies, clades with sequences separated by approximately 150 PAM units are family but not genus specific, providing a rough measure of minimum dates for the first diversification event within these clades. Within any one clade, particular taxa may be dramatically over- or underrepresented, suggesting preferential expansions or losses of certain RGH types within particular taxa and suggesting that no one species will provide models for all major sequence types in other taxa.

Amino Acid Sequence↗
PubMed1999

Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin.

A group of seven Sm proteins forms a complex that binds to several RNAs in metazoans. All Sm proteins contain a sequence signature, the Sm domain, also found in two yeast Sm-like proteins associated with the U6 snRNA. We have performed database searches revealing the presence of 16 proteins carrying an Sm domain in the yeast genome. Analysis of this protein family confirmed that seven of its members, encoded by essential genes, are homologues of metazoan Sm proteins. Immunoprecipitation revealed that an evolutionarily related subgroup of seven Sm-like proteins is directly associated with the nuclear U6 and pre-RNase P RNAs. The corresponding genes are essential or required for normal vegetative growth. These proteins appear functionally important to stabilize U6 snRNA. The two last yeast Sm-like proteins were not found associated with RNA, and neither was essential for vegetative growth. To investigate whether U6-associated Sm-like protein function is widespread, we cloned several cDNAs encoding homologous human proteins. Two representative human proteins were shown to associate with U6 snRNA-containing complexes. We also identified archaeal proteins related to Sm and Sm-like proteins. Our results demonstrate that Sm and Sm-like proteins assemble in at least two functionally conserved complexes of deep evolutionary origin.

Animals↗
PubMed1996

Glycosylated threonine but not 4-hydroxyproline dominates the triple helix stabilizing positions in the sequence of a hydrothermal vent worm cuticle collagen.

The cuticle collagen of the vestimentiferan Riftia pachyptila, an organism which is endemic to deep-sea hydrothermal vents, has several unusual properties including an extraordinary length (1.5 microns), a high thermal stability (37 degrees C) in spite of a low 4-hydroxyproline content and an atypically high threonine content (20 mol%). We have now purified the constituent chain of cuticle collagen and show that it contains about 40% carbohydrate, which is mainly galactose, indicating that the chain has a molecular mass of approximately 750 kDa. Several large (30 to 150 kDa) fragments, which all contained carbohydrate, could be produced by cleavage with endoproteinase Lys-C, bacterial collagenase and cyanogen bromide (CNBr). Edman degradation of these and several smaller fragments was used to determine about 3000 sequence positions comprising 60% of the total triple-helical sequence. This demonstrated mainly typical Gly-X-Y triplet repeats with a few imperfections and a longer N-terminal non-triplet sequence. Most of the 4-hydroxyproline was found in triplet position X, where it decreases the stability of the triple helix. About 40% of the Y positions could not be identified, which correlated with a low abundance of threonine in the sequence and the demonstration of threonine in these positions after deglycosylation of several peptides by treatment with hydrofluoric acid. Matrix-assisted laser desorption ionisation mass spectrometry of selected peptides indicated that the blocked threonine residues are occupied by chains of one, two or three hexoses (presumably galactose). These glycosylated threonine residues in Y positions are therefore likely to replace 4-hydroxyproline as the major contributor to triple helix stabilization. Studies with a synthetic (Gly-Pro-Thr)10 oligopeptide demonstrated a low thermal stability of its triple helix which emphasizes a crucial role of glycosylation for stabilization.

Amino Acid Sequence↗
PubMed1994

A molecular genetic study of intracerebral hemorrhage.

BACKGROUND: Two forms of inherited intracerebral hemorrhage (ICH) are associated with an amyloid angiopathy caused by mutations in the genes for the amyloid precursor protein or cystatin C. The purpose of this study was to determine whether patients with sporadic ICH have mutations in the amyloid precursor protein or cystatin C genes. METHODS: Consecutive patients with ICH admitted to the neurology or neurosurgery services at Duke University Hospital, Durham, NC, were studied. Using the polymerase chain reaction, we amplified exons 16 and 17 of the amyloid precursor protein and exon 2 of cystatin C and sequenced the products. Twenty-six men and 22 women were studied. The ICH location was deep in 29 patients, lobar in 16, cerebellar in two, and brain stem in one. There were 30 patients (63%) with a positive family history of stroke; seven of them (15%) had a family history of ICH. CONCLUSIONS: Mutations previously reported to cause familial forms of ICH were not found in this group of patients.

Adult↗
PubMed2025

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.

Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they enable researchers to create accurate models with minimal effort and computational resources. Large scale genomics deep learning models come in two flavors: the first are large language models of DNA sequences trained in a self-supervised fashion, similar to the corresponding natural language models; the second are supervised learning models that leverage large scale genomics datasets from ENCODE and other sources. We argue that these models are the equivalent of foundation models in natural language processing in their utility, as they encode within them chromatin state in its different aspects, providing useful representations that allow quick deployment of accurate models of gene regulation. We demonstrate this premise by leveraging the recently created Sei model to develop simple, interpretable models of intron retention, and demonstrate their advantage over models based on the DNA language model DNABERT-2. Our work also demonstrates the impact of chromatin state on the regulation of intron retention. Using representations learned by Sei, our model is able to discover the involvement of transcription factors and chromatin marks in regulating intron retention, providing better accuracy than a recently published custom model developed for this purpose.

Deep Learning↗
PubMed2005

Searching for the IRA "disappeared": ground-penetrating radar investigation of a churchyard burial site, Northern Ireland.

A search for the body of a victim of terrorist abduction and murder was made in a graveyard on the periphery of a major conurbation in Northern Ireland. The area is politically sensitive and the case of high profile. This required non-invasive, completely non-destructive and rapid assessment of the scene. A MALA RAMAC ground-penetrating radar system was used to achieve these objectives. Unprocessed and processed 400 MHz data show the presence of a collapse feature above and around a known 1970s burial with no similar collapse above the suspect location. In the saturated, clay-rich sediments of the site, 200 MHz data offered no advantage over 400 MHz data. Unprocessed 100 MHz data shows a series of multiples in the known burial with no similar features in the suspect location. Processed 100 MHz lines defined the shape of the collapse around the known burial to 2 m depth, together with the geometry of the platform (1 m depth) the gravedigger used in the 1970s to construct the site. In addition, processed 100 MHz data showed both the dielectric contrast in and internal reflection geometry of the soil imported above the known grave. Thus the sequence, geometry, difference in infill and infill direction of the grave was reconstructed 30 years after burial. The suspect site showed no evidence of shallow or deep inhumation. Subsequently, the missing person's body was found some distance from this site, vindicating the results and interpretation from ground-penetrating radar. The acquisition, processing, collapse feature and sequence stratigraphic interpretation of the known burial and empty (suspect) burial site may be useful proxies for other, similar investigations. GPR was used to evaluate this site within 3 h of the survey commencing, using unprocessed data. An additional day of processing established that the suspect body did not reside here, which was counter to police and community intelligence.

Burial↗
PubMed1992

DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities.

A protocol was devised which permitted the extraction of DNA from deep marine sediments up to 503 m below the sea floor. These sediments have been laid down over the last 3 million years. 16S rRNA gene sequences were amplified from the DNA by the polymerase chain reaction. The details of the successful extraction and polymerase chain reaction methodology varied between samples from different depths. This emphasizes the attention to detail required to allow the diversity of bacteria in these deep sediments to be studied.

Bacteria↗
PubMed2025

DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning.

Spatiotemporal gene expression shapes key agronomic traits, yet tissue-specific prediction remains challenging in complex crops. We present DeepWheat, a broadly applicable deep learning framework comprising DeepEXP and DeepEPI, for accurate, tissue-specific gene expression prediction. DeepEXP integrates sequence and epigenomic features to predict gene expression (PCC 0.82-0.88), while DeepEPI predicts epigenomic maps from DNA sequence to support model transfer across varieties. Validations in five wheat cultivars confirm robustness and accuracy. DeepWheat also identifies regulatory variants with strong expression effects, enabling targeted cis-regulatory elements editing and offering a powerful tool for crop functional genomics and breeding.

Triticum↗
PubMed1993

High-throughput purification of M13 templates for DNA sequencing.

Two variants of methods for high-throughput preparation of single-stranded M13 DNA are described. Both variants are derived from previously described chemistry and are appropriate for purification of M13 templates in 96-deep well plates. In both variants, phenol extraction is replaced by treatment with sodium iodide to disrupt phage proteins prior to ethanol precipitation of M13 DNA. In one of the variants, nonderivatized paramagnetic particles are employed to collect aggregated M13 phage particles and DNA, thereby replacing the need for centrifugation. The other variant omits the magnetic particles and utilizes a centrifuge that can accommodate the 96-deep well plates. Although the purification scheme that uses magnetic separation results in a decreased yield of M13 DNA, it is amenable to robotic automation strategies and thus will be useful for genomic sequencing projects. Performed manually, either method can easily produce 192 templates in a few hours. Although both variants produce DNA of sufficient quantity for automated fluorescent DNA sequencing, the procedure that utilizes magnetic separation provides template DNA of higher quality.

Autoanalysis↗
PubMed1997

Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA.

Retroviruses encapsidate two molecules of genomic RNA that are noncovalently linked close to their 5' ends in a region called the dimer linkage structure (DLS). The dimerization initiation site (DIS) of human immunodeficiency virus type 1 (HIV-1) constitutes the essential part of the DLS in vitro and is crucial for efficient HIV-1 replication in cell culture. We previously identified the DIS as a hairpin structure, located upstream of the major splice donor site, that contains in the loop a six-nucleotide self-complementary sequence preceded and followed by two and one purines, respectively. Two RNA monomers form a kissing loop complex via intermolecular interactions of the six nucleotide self-complementary sequence. Here, we introduced compensatory mutations in the self-complementary sequence and/or a mutation in the flanking purines. We determined the kinetics of dimerization, the thermal stabilities and the apparent equilibrium dissociation constants of wild-type and mutant dimers and used chemical probing to obtain structural information. Our results demonstrate the importance of the 5'-flanking purine and of the two central bases of the self-complementary sequence in the dimerization process. The experimental data are rationalized by triple interactions between these residues in the deep groove of the kissing helix and are incorporated into a three-dimensional model of the kissing loop dimer. In addition, chemical probing and molecular modeling favor the existence of a non-canonical interaction between the conserved adenine residues at the first and last positions in the DIS loop. Furthermore, we show that destabilization of the kissing loop complex at the DIS can be compensated by interactions involving sequences located downstream of the splice donor site of the HIV-1 genomic RNA.

Dimerization↗
PubMed2002

Thioalkalispira microaerophila gen. nov., sp. nov., a novel lithoautotrophic, sulfur-oxidizing bacterium from a soda lake.

An anaerobic enrichment medium (pH 10) with thiosulfate as electron donor and nitrate as electron acceptor was inoculated with sediment from soda lake Fazda (Wadi Natrun, Egypt); a novel strain, ALEN 1(T), was isolated from the subsequent enrichment culture. Cells of strain ALEN 1(T) had a spiral morphology (0.3-0.45 x 1-4 microm), were motile and had a single polar flagellum. Sphaeroplasts were formed by the cells and were rapidly lysed during prolonged aerobic incubation of cultures. Cells of strain ALEN 1(T) contained a membrane-associated yellow pigment. The metabolism of this novel organism was obligately chemolithoautotrophic, and thiosulfate or sulfide were utilized as electron donors. Washed cells of strain ALEN 1(T) oxidized thiosulfate, sulfide, polysulfide and elemental sulfur to sulfate. Best growth was observed when the strain was grown under micro-oxic conditions (1-2% O2 in gas phase), whereas growth was inhibited under fully oxic conditions. Nitrate was reduced to nitrite without growth of the novel organism, but other nitrogen oxides were not utilized as electron acceptors. Strain ALEN 1(T) was alkaliphilic and moderately halophilic. It grew between pH 8 and 10.4 (optimum around pH 10) with a salt concentration of between 0.3 and 1.5 M Na+ (optimum 0-5 M). The maximum growth rate (0.08 h(-1)) of the organism was achieved in a thiosulfate-limited micro-oxic continuous culture (pH 10). Phylogenetic analyses of the 16S rDNA sequences of strain ALEN 1(T) and its closest relatives demonstrated that this strain formed a deep branch within the gamma-Proteobacteria, with no obvious association to any described cluster of species/genera. On the basis of its unique physiological properties and distinct phylogenetic position, it is proposed that strain ALEN 1(T) (= DSM 14786(T) = UNICEM 212(T)) represents a novel genus within the gamma-Proteobacteria, for which the name Thioalkalispira is proposed. It is also proposed that the type species of this novel genus be named Thioalkalispira microaerophila.

Base Sequence↗
PubMed1998

Gliomatosis cerebri: a rare cause of progressive headache.

A 49-year-old right-handed woman was admitted for an 8-month history of unusual headache and transient diplopia. Clinical examination and brain CT scan were normal. Two months later, symptoms of raised intracranial pressure developed and a brain CT scan showed small lateral ventricles and sulci without any abnormal contrast enhancement or tumor mass. Brain MRI with T2-weighted spin echo sequences revealed a hyperintense signal in the right temporoparietal region, whereas only a slight enlargement of this region was noted on T1 spin echo. The patient deteriorated rapidly and died with uncontrollable raised cerebrospinal fluid pressure. The diagnosis of gliomatosis cerebri was made at necropsy. Gliomatosis cerebri is a rare intracranial neoplasm of neuroepithelial origin. Spread of this tumor is particularly fast in the white matter compared with the gray matter and nuclei. Clinical symptoms are not specific. The diagnosis can be suspected by MFU showing an isointense or hypointense signal in the deep white matter on T1-weighted images, and largely a hyperitense signal on T2-weighted sequences. The diagnosis is confirmed by stereotactic biopsy or necropsy. No curative treatment is currently available. Radiotherapy can delay the rapidly fatal outcome. Our case illustrates the possible onset of this rare disease by isolated cephalgia with normal early CT scan.

Brain Neoplasms↗