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At least 883 records · Page 49Linked to original sources

Divergence and diversity: lessons from an arctic-alpine distribution (Pardosa saltuaria group, Lycosidae).

The relationship of interpopulation genetic divergence and within-population diversity has been studied for many temperate species in Europe, but not for the cold-adapted fauna. Here we present the first European-wide phylogeographical study of an arctic-alpine distribution in invertebrates, focusing on wolf spiders of the Pardosa saltuaria group. One hundred twenty-seven (127) specimens from 14 populations were examined. Within Europe, these populations were distributed among six high mountain ranges and Scandinavia. We sequenced the whole 921 base pair mitochondrial (mt) ND1 gene. The resulting 55 unique haplotypes form three monophyletic phylogroups of deep divergence: a Pyrenean, a Balkan and a 'northern' clade. Genetic distances (3.6-4.0%) between the major clades indicate that the arctic-alpine range disjunction was initiated by vicariance events, which precede the four major Alpine glaciations. However, low divergence and incomplete lineage sorting within the 'northern clade' suggest a late Pleistocene separation of the Alpine, Scandinavian, Carpathian and Sudetian populations. Thus, we provide evidence for a multiglacial origin of arctic-alpine distributions in Europe, i.e. the current disjunction results from range fragmentation in several glacial cycles. The pattern of genetic diversity within populations seems predominantly determined by historical factors, but is modified by contemporary aspects. Overall, diversity and divergence are negatively correlated. We suggest that low diversity values might result from (i) ancient bottlenecking during warm interglacial periods, as seen in the Pyrenees and Balkans; (ii) recent bottlenecking in small modern areas, as seen in the Giant Mountains and Bohemian Forest; and (iii) dispersal bottlenecking in northern Scandinavia.

Animals↗

A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis.

Trichomonads are anaerobic flagellated protists that, based on analyses of ribosomal RNA sequences, represent one of the earliest branching lineages among the eukaryotes. The absence of mitochondria in these organisms coupled with their deep phylogenetic position has prompted several authors to suggest that trichomonads, along with other deeply-branching amitochondriate protist groups, diverged from the main eukaryotic lineage prior to the endosymbiotic origin of mitochondria. In this report we describe the presence of a gene in Trichomonas vaginalis specifically related to mitochondrial chaperonin 60 (cpn60). A recent study indicates that a protein immunologically related to cpn60 is located in trichomonad hydrogenosomes. Together, these data provide evidence that ancestors of trichomonads perhaps harbored the endosymbiotic progenitors of mitochondria, but that these evolved into hydrogenosomes early in trichomonad evolution.

Animals↗

The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.

Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3'-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs.

Base Sequence↗

Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.

The crystal structure of endo-1,4-beta-xylanase I from Aspergillus niger has been solved by molecular replacement and was refined to 2.4 A resolution. The final R-factor for all data from 6 to 2.4 A is 17.9%. The A. niger xylanase has a characteristic fold which is unique for family G xylanases (root-mean-square deviation = 1.1 A to Trichoderma reesei xylanase I, which has 53% sequence identity). It consists of a single domain composed predominantly of beta-strands. Two beta-sheets are twisted around a deep, long cleft, which is lined with many aromatic amino acid residues and is large enough to accommodate at least four xylose residues. The two conserved glutamate residues, Glu79 and Glu170, which are likely to be involved in catalysis, reach into this cleft from opposite sides. A niger xylanase I is of particular commercial interest because of its low pH optimum. A model is proposed which explains this low pH optimum compared to other members of xylanase family G.

Amino Acid Sequence↗

Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon.

Despite increasing threats to the marine environment, only a fraction of the biodiversity of the oceans has been described, owing in part to the widespread occurrence of cryptic species. DNA-based barcoding through screening of an orthologous reference gene has been proposed as a powerful tool to uncover biological diversity in the face of dwindling taxonomic expertise and the limitations of traditional species identification. Although DNA barcoding should be particularly useful in the sea, given the prevalence of marine cryptic species, the link between taxa identified through DNA barcodes and reproductively isolated taxa (biological species) has rarely been explicitly tested. Here, we use an integrated framework comparing breeding compatibility, morphology and mitochondrial (cytochrome c oxidase 1) and nuclear (elongation factor-1-alpha) DNA sequence variation among globally distributed samples of the cosmopolitan marine bryozoan Celleporella hyalina (L.). Our results reveal that C. hyalina comprises numerous deep, mostly allopatric, genetic lineages that are reproductively isolated, yet share very similar morphology, indicating rampant cryptic speciation. The close correspondence between genetic lineages and reproductively isolated taxa in the context of minimal morphological change suggests that DNA barcoding will play a leading role in uncovering the hidden biodiversity of the oceans and that the sole use of morphologically based taxonomy would grossly underestimate the number of marine species.

Animals↗

The relation of White Matter Hyperintensities to implicit learning in healthy older adults.

OBJECTIVE: This study examined whether MRI evidence of cerebrovascular disease in the form of white matter hyperintensities (WMH) was associated with decreased implicit sequence learning performance in a high-functioning group of normal elderly volunteers. METHOD: One hundred and eight community-dwelling elderly individuals received an MRI and performed an implicit sequence learning task, the serial reaction time (SRT) task. RESULTS: Hyperintensities present in the white matter were associated with a decreased learning effect. This association was found with both deep white matter and periventricular changes. Other factors affecting SRT performance (i.e., baseline reaction time and switch-cost) were not significantly related to the presence of WMH. CONCLUSIONS: The results indicate that in addition to previously identified generalized cognitive deficits, WMH are also associated with a specific decrease in the implicit learning of sequences.

Aged↗

Saami mitochondrial DNA reveals deep maternal lineage clusters.

The mitochondrial DNA of 62 Saami from the north of Norway was analyzed in the D loop hypervariable region I and II and sequences were compared to other gene pools. Two major (lineage 1 and 2) and two minor (lineage 3 and 4) maternal lineage clusters were found. Lineage 1 (56.9% of all hitherto analyzed Saami samples) contains a substantial number of branching haplotypes which are unknown in European gene pools. Lineage 2 (31.5%) and lineage 4 (3.6%) have few branching points and are present at a low rate throughout European gene pools. Lineage 3 (4.7%) has polymorphisms characteristic of circumpolar lineages.

Base Sequence↗

Diffusion-weighted MR imaging in closed head injury: high correlation with initial glasgow coma scale score and score on modified Rankin scale at discharge.

PURPOSE: To determine whether diffusion-weighted magnetic resonance (MR) imaging findings and conventional MR imaging findings correlate with initial Glasgow Coma Scale score and score on modified Rankin scale at discharge. MATERIALS AND METHODS: Twenty-six patients (18 male and eight female patients; mean age, 25.2 years; age range, 4-72 years) with diffuse axonal injury were examined with diffusion-weighted MR imaging and with fluid-attenuated inversion recovery, T2-weighted fast spin-echo, and T2*-weighted gradient-echo sequences. All images were evaluated by two neuroradiologists in consensus. Tissue volume with trauma-related signal-intensity abnormality on images from each sequence, number of lesions for each sequence, number of lesions for all sequences, and number of lesions with reduced apparent diffusion coefficient were correlated with scores on Glasgow Coma Scale and modified Rankin scale. Involvement of brainstem, deep gray matter, and corpus callosum were also correlated with clinical scores. Spearman rank correlation coefficients (r) were calculated. RESULTS: The strongest correlation was between signal-intensity abnormality volume on diffusion-weighted images and modified Rankin score (r = 0.772, P <.001). The strength of this correlation did not improve when only volume of lesions with decreased apparent diffusion coefficient was considered. For lesion number, the strongest correlation was between lesion number on images acquired with all sequences and modified Rankin score (r = 0.662, P <.001). For lesion location, the strongest correlation was between lesion location in the corpus callosum and modified Rankin score (r = 0.513, P =.007). CONCLUSION: Volume of lesions on diffusion-weighted MR images provides the strongest correlation with a score of subacute on modified Rankin scale at discharge. Total lesion number also correlates well with modified Rankin score. In future, diffusion-weighted images may be useful in determining treatment strategies for acute head injury.

Adolescent↗

A novel transformer model of protein domains for viral taxonomy classification.

MOTIVATION: Viruses with carefully curated taxonomic assignments (such as those in the ICTV taxonomy) still represent only a small fraction of viruses identified through sequencing data from virome or microbiome projects. It is therefore critical to develop methods that can assign viruses at multiple taxonomic ranks, so that a virus deemed novel at a given rank may still be placed into a higher-level taxon. Sequence-similarity-based approaches can classify viruses that share substantial genomic similarity with known viruses (e.g. those belonging to the same species or genus); however, their performance drops significantly when applied to more divergent viruses. Recent deep learning models, such as ViTax, which utilize DNA language models, aim to address these limitations, but their performance also degrades when applied to novel viruses lacking genus-level similarity to known references. Proteins are more conserved than genomic sequences, and the multiple proteins encoded by a virus can be leveraged to reveal evolutionary relationships among viruses. RESULTS: We propose a new tool, D2T (Domain-to-Taxonomy), that leverages recent advances in protein language models to improve viral taxonomic assignment. D2T represents a virus as a sequence of protein domain tokens and learns a transformer-based model for taxonomic classification. Experiments on multiple closed-set and open-set datasets show that D2T excels at assigning higher-level taxonomic labels (family and above). Furthermore, by combining D2T with Kraken2, which performs well at the genus level, the hybrid method (K+D2T) achieves accurate viral taxonomic classification across multiple taxonomic ranks. AVAILABILITY AND IMPLEMENTATION: D2T is available as a GitHub repository at https://github.com/mgtools/D2T.

Viruses↗

Measurement of magnetization transfer in different stages of neurocysticercosis.

The purpose of this study was to establish magnetization transfer ratio (MTR) in different stages of neurocysticercosis. A total 2,532 cysticerci were studied prospectively in 15 cases. MTR from different regions of the lesions (ie, the cyst, the protoscolex or mural nodule, the granuloma wall) were calculated in different stages of evolution/degeneration in all cases. Of a total 2,532 lesions studied, 2,261 (89.29%) were seen on routine spin-echo (SE) imaging. The rest of the lesions were only seen on magnetization transfer (MT) SE imaging. Maximum MTR was calculated from healing lesions (mean + SD = 31.0+/-2.8) and from the core of SE invisible lesions (30.0+/-5.1). Innocuous cystic lesions, which were hyperintense on T2-weighted images, did not show any MT (MTR = 5.10+/-1.2), whereas degenerating T2 hyperintense lesions showed MTR of 26.40+/-2.7. Nondegenerating and degenerating scolices showed an intermediate MTR of 21.7+/-3.3 and 15.0+/-4.5, respectively. MT varies between different parts of the lesion and also from the same part in different stages of evolution/degeneration of the lesion. The visibility of a lesion on MT-SE sequence was dependent on its MTR and its location at a particular site (cortical gray matter, white matter, or deep gray matter). The difference in MTR of the lesion and the surrounding brain parenchyma decides the resulting contrast and visibility of the lesion.

Adolescent↗

Mapping of septal ventricular tachycardia: clinical and experimental correlations.

In patients with chronic myocardial infarction, ventricular tachycardia originating in the interventricular septum may account for a significant number of arrhythmia recurrences after direct ablative operations. We used total computer-assisted cardiac mapping (epicardial sock, left and right ventricular endocardial balloon electrode arrays) to assess whether tachycardia originating in deep or right-sided layers of the interventricular septum is associated with a specific pattern of epicardial activation sequence. We performed these studies during operations in 18 patients and during experiments in 12 dogs in which a septal myocardial infarction was produced by ligating the anterior septal coronary artery. Intraseptal needle electrodes were plunged into the septum of all animal preparations to generate pace-mapping data and to obtain intraseptal recordings (six preparations) during reentrant ventricular tachycardia induced by programmed stimulation. In addition, pace-mapping data of infarcted canine heart preparations were compared with those of nine healthy heart preparations. In the clinical study, 31 ventricular tachycardias with a septal site of origin were analyzed. Twenty tachycardias displayed an epicardial breakthrough in the area of the interventricular groove, whereas 11 had an epicardial breakthrough in the right ventricular free wall. Biventricular endocardial mapping revealed that left septal endocardial activation preceded right septal activation in the former and that right septal activation occurred earlier in the latter. In the experimental study, 14 ventricular tachycardias (cycle length 146 +/- 34 msec) were induced by programmed stimulation in 11 infarcted heart preparations. Eight tachycardias displaying an epicardial breakthrough on the right ventricle were found to originate in the right ventricular septal subendocardial layers, whereas six tachycardias in which the epicardial breakthrough occurred on the anterior interventricular groove originated in the left ventricular septal subendocardial layers. The epicardial breakthrough preceded the left ventricular endocardial breakthrough in six tachycardias (85.7%) originating in intermediate or right ventricular septal layers, but in only one of five tachycardias originating in the left ventricular septal layers. In the pace-mapping study, the epicardial breakthrough shifted progressively from the right ventricular free wall toward the interventricular groove area in response to pacing from the right, intermediate, and left ventricular thirds of the basal septum. This relationship was similar for infarcted and noninfarcted hearts, although transseptal conduction time was prolonged in infarcted hearts (45 +/- 10 msec vs 33 +/- 7 msec, p < 0.01). Therefore the information integrated from the localization of the epicardial breakthrough and the relative timing between the epicardial and the left ventricular endocardial breakthroughs can be used to estimate the depth of the site of origin of septal ventricular tachycardias. This study confirms that a three-dimensional view of the substratum of ventricular tachycardia can be derived from simultaneous epicardial and left ventricular endocardial mapping and can provide a superior basis for therapeutic interventions.

Animals↗

Failure in the detection of aberrant mRNA from the heterozygotic splice site mutant allele for protein S in a patient with protein S deficiency.

A 29-year-old male patient with acute arterial obstruction and a medical history including thrombosis in the deep veins and pulmonary infarction presented with a reduced level of both protein S (PS) activity and free PS. Sequencing of the genomic PS gene in this patient revealed that the patient was heterozygous for the mutant PS allele, in which a nucleotide substitution occurred at the donor splice site in intron 12 (GT to GA). The patient was heterozygous for PS genes having dimorphic codons for Pro626 (CCA/CCG) and the aberrant allele in this patient was associated with the CCA form. Allelic exclusion of PS expression was demonstrated by use of Pro626 (CCA/CCG) dimorphism and only a normal mRNA sequence derived from the CCG-allele was identified in the patient. These findings suggested that the mutation at the splice site in the PS gene caused either defective production of mRNA or the gene may have produced extremely unstable RNA products, leading to reduced levels of PS activity and free PS in this patient.

Adult↗

Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America.

The yellow-pine chipmunk, Tamias amoenus, is common in xerophytic forests throughout much of northwest North America. We analyzed cytochrome b sequence variation from 155 individuals representing 57 localities across the distribution of T. amoenus including 10 additional species of Tamias. Maximum likelihood and parsimony tree estimation methods were used in conjunction with nested clade analysis to infer both deep and population-level processes. Our results indicate that two currently recognized subspecies of T. amoenus (T. a. canicaudus and T. a. cratericus) are not nested within other samples of T. amoenus. Maximum uncorrected levels of intraspecific sequence divergence within remaining samples of T. amoenus are >7%. Substantial geographic variation is characterized by 12 well-supported clades that correspond to distinct mountain ranges, but do not necessarily follow existing subspecific taxonomy. Significant association between geography and genealogy was detected within many of these clades and can be attributed to different population-level processes including past fragmentation, recent range expansion, and isolation by distance.

Animals↗

Environmental Gradients as a Dominant Force in the Macroevolution of a Host-Associated Marine Bacterium.

Natural selection is imposed by both abiotic environmental filtering and biotic interactions, yet their relative roles in shaping the deep phylogeny of widespread, generalist host-associated bacteria remain unclear. Here, we integrate large-scale phylogenomics, environmental sequencing, functional genomics, and global metagenomic analysis to demonstrate that tidal zonation overrides host association as the dominant macroevolutionary force structuring the marine bacterial genus Ruegeria. Analysis of 533 genomes and 74 global coastal metagenomes reveals that the intertidal-subtidal boundary structures the deepest phylogenetic splits, driving the repeated evolution of distinct ecotypes through independent zonation transitions across global coastlines. These ecotypes possess divergent genomic toolkits: intertidal strains are enriched for genes coding for stress resistance and anaerobic metabolism, whereas subtidal strains specialize in high-affinity nutrient scavenging. Our findings establish that predictable physicochemical gradients act as filters that generate foundational diversity from which specialized host symbionts subsequently emerge, reframing how environmental gradients shape microbial evolution at the eco-evolutionary interface.

Journal Article↗

Technique on restoring sub-gingival cervical lesion.

This article outlines an atraumatic isolation approach and a conservative instrumentation sequence, followed by use of a highly viscous, rapid-setting, capsulated glass ionomer cement to manage a difficult deep proximal-cervical Class V lesion.

Aged↗

Sequential staining of DNA-aldehyde with Schiff's reagent and acriflavine-SO2.

Acid hydrolysed DNA of rat liver was stained with Schiff's reagent at pHs 1.7 or 3.0 followed by staining with acriflavine-SO2 at pH 2.0 as well as with acriflavine-SO2 followed by Schiff's reagent at pH 1.7 or 3.0. Nuclei stained with Schiff's reagent at pH 1.7 were brown-yellow and an analysis of their absorption characteristics revealed two peaks--one at 470 nm and the other at 570 nm. Although nuclei stained with Schiff's reagent at pH 3.0 followed by acriflavine-SO2 were deep magenta in colour, they also showed similar peaks of maximum absorption. Identical peaks were also seen when the sequence of staining was reversed. It is suggested that in the conventional Feulgen-type reactions only some of the DNA-aldehyde molecules are stained; the remaining molecules can be stained by sequential application of another Schiff or Schiff-type reagent such as acriflavine-SO2. The possible mechanism of staining in these cases has been discussed.

Acridines↗

[Posterosuperior glenoid rim impingement in athletes: the diagnostic value of traditional radiology and magnetic resonance].

First described by Walch in 1991, the posterosuperior glenoid rim impingement syndrome is a major condition in the differential diagnosis of shoulder pain occurring in the athletes engaged in repetitive and loading movements of abduction and extra-rotation of the dominant upper limb. Thirty-eight athletes with these dynamic athletic characteristics, referred for unexplained shoulder pain and with a clinical diagnosis of posterosuperior glenoid rim impingement syndrome, underwent radiography and MR examinations, with excellent final results. Radiography was capable of depicting the abnormal skeletal features of this kind of impingement, thus allowing a preliminary diagnosis to be made. MRI excelled in diagnosing the lesions in the deep surface of the supraspinatus tendon and in the posterior labrum secondary to impingement. The static and the kinematic sequences with the arm in abduction and extrarotation proved to be the best ones to define the physiopathologic phases of impingement. Thus, we conclude that invasive diagnostic procedures are not necessary for the correct and unquestionable diagnosis of posterosuperior glenoid rim impingement syndrome.

Adolescent↗

[Deep white matter hyperintensity in occipital lobe on T2 weighted magnetic resonance imaging].

Magnetic resonance imaging (MRI) was performed in 270 patients with various neurologic complaints (1-15 Y) with a 0.5 tesla superconducting imaging system (MRT-50 A, Toshiba Co.) using a field echo sequence (TR/TE: 300 ms/14 ms) and a spine echo sequence (TR/TE: 2,000 ms/100 ms or 2,000 ms/120 ms, and 2,000 ms/30 ms). The slice thickness was 10 mm. Hyperintensity areas on T2-weighted images were noted at the occipital lobe in 33 patients (12.2%). Twenty-seven of them had hyperintensity within the deep white matter, which revealed iso- or hypointensity on T1-weighted images. The diagnosis for the 27 patients included medulloblastoma after multidisciplinary therapy (1), congenital heart disease (1), neurofibromatosis (1), tuberous sclerosis (1), congenital muscular dystrophy (1), congenital myotonic dystrophy (2), febrile convulsion (2), autism (3), epilepsy (9) and unknown causes (6). Because the hyperintensity areas are age-dependent, they may result from delayed myelination in the central nervous system.

Adolescent↗