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Sequences of rDNA internal transcribed spacers from the chloroplast DNA of 26 bryophytes: properties and phylogenetic utility.

We determined the sequence of the region of the chloroplast DNA inverted repeat spanning from the 3'-terminus of the 23S rRNA gene to the 5'-terminus of the tRNA[Arg](ACG) gene (about 700 bp) from 25 bryophytes and from the charophycean alga Chara australis. Phylogenetic analysis of these sequences using the neighbor-joining method suggests an early dichotomy of bryophytes and their paraphyly relative to the tracheophyte lineage. A monophyly of liverworts (Marchantiidae plus Jungermanniidae), a deep divergence of Metzgeriales among Jungermanniidae and a close affinity of the two subclasses of mosses, Sphagnidae and Andreaeidae, are evident. The branching pattern observed is consistent with the phylogenetic distribution of several prominent indels observed in the alignment.

Base Sequence↗

Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data.

To test hypotheses about the origin of modern humans, we analyzed mtDNA sequences, 30 nuclear restriction-site polymorphisms (RSPs), and 30 tetranucleotide short tandem repeat (STR) polymorphisms in 243 Africans, Asians, and Europeans. An evolutionary tree based on mtDNA displays deep African branches, indicating greater genetic diversity for African populations. This finding, which is consistent with previous mtDNA analyses, has been interpreted as evidence for an African origin of modern humans. Both sets of nuclear polymorphisms, as well as a third set of trinucleotide polymorphisms, are highly consistent with one another but fail to show deep branches for African populations. These results, which represent the first direct comparison of mtDNA and nuclear genetic data in major continental populations, undermine the genetic evidence for an African origin of modern humans.

Africa↗

Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting deep-sea hydrothermal ecosystems.

The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Additional sequences phylogenetically related to Thermococcus and epsilon-Proteobacteria were detected by cloning and sequencing of 16S rDNA from two samples of the enrichment culture. In comparison, the sequences retrieved from cloning analysis from an enrichment culture performed in a flask (batch condition) using the same culture medium showed that only members of the genus Thermococcus were cultivated. Therefore, continuous enrichment culture using the gas-lift bioreactor can be considered as an efficient and improved method for investigating microbial communities originating from deep-sea hydrothermal vents.

Atlantic Ocean↗

The position of the cell penetrating peptide penetratin in SDS micelles determined by NMR.

Penetratin is a 16 residue peptide, RQI KIWFQ NRRMK WKK-amide, with the ability to penetrate cell membranes and a sequence taken from the homeodomain of the Drosophila Antennapedia transcription factor. 600 MHz 1H-nuclear magnetic resonance has been used to study the structure and location of penetratin interacting with a sodium dodecyl sulphate micelle. The positioning of penetratin in the micelle was studied by adding paramagnetic probes (Mn2+ ions, 5-doxyl and 12-doxyl stearic acid) to the solvent. The results show that the peptide is a straight helix positioned with its C-terminus deep inside the micelle and its N-terminus near the surface of the micelle.

Amino Acid Sequence↗

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum.

We have determined the crystal structure of nicotinate phosphoribosyltransferase from Themoplasma acidophilum (TaNAPRTase). The TaNAPRTase has three domains, an N-terminal domain, a central functional domain, and a unique C-terminal domain. The crystal structure revealed that the functional domain has a type II phosphoribosyltransferase fold that may be a common architecture for both nicotinic acid and quinolinic acid (QA) phosphoribosyltransferases (PRTase) despite low sequence similarity between them. Unlike QAPRTase, TaNAPRTase has a unique extra C-terminal domain containing a zinc knuckle-like motif containing 4 cysteines. The TaNAPRTase forms a trimer of dimers in the crystal. The active site pocket is formed at dimer interfaces. The complex structures with phosphoribosylpyrophosphate (PRPP) and nicotinate mononucleotide (NAMN) showed, surprisingly, that functional residues lining on the active site of TaNAPRTase are quite different from those of QAPRTase, although their substrates are quite similar to each other. The phosphate moiety of PRPP and NAMN is anchored to the phosphate-binding loops formed by backbone amides, as found in many alpha/beta barrel enzymes. The pyrophosphate moiety of PRPP is located at the entrance of the active site pocket, whereas the nicotinate moiety of NAMN is located deep inside. Interestingly, the nicotinate moiety of NAMN is intercalated between highly conserved aromatic residues Tyr(21) and Phe(138). Careful structural analyses combined with other NAPRTase sequence subfamilies reveal that TaNAPRTase represents a unique sequence subfamily of NAPRTase. The structures of TaNAPRTase also provide valuable insight for other sequence subfamilies such as pre-B cell colony-enhancing factor, known to have nicotinamide phosphoribosyltransferase activity.

Amino Acid Sequence↗

Changes in rat retinal ganglion neuronotrophic factor and its mRNA during postnatal development.

The monoclonal antibody specific to the retinal ganglion neuronotrophic factor (RGNTF) was used to localize and quantify the presence and amount of RGNTF during the postnatal development of the visual system in the rat. The results showed that in the 0-1-day age group, neurons at the superficial layers and deep part of superior colliculus, and as well as retinal ganglion cells were strongly stained with their RGNTF contents quantified to be 88%, 100% and 100%, respectively. In the 5-6-day age group, RGNTF contents were significantly reduced to merely 50%, 30% and 80%, respectively. The RGNTF contents reduced further to 0% as age increased to 2 years old. A 32P-DNA probe specific to the first 7 amino acid sequence of RGNTF at its N-terminal end was synthesized and used for in situ hybridization studies. The results revealed that strong hybridized signals (i.e. mRNA of RGNTF) were localized in the same neurons in the superficial layers and deep part of the superior colliculus only in the 0-1-day age group, and that no signals were found in retinae of all postnatal age groups. The significant reduction of RGNTF may be related to the RGC death during postnatal development. Neurons at the superficial layers and deep part of the superior colliculus are the sources of RGNTF for RGCs in the postnatal retina.

Age Factors↗

A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples.

The Cariaco Basin off the Venezuelan coast in the Caribbean Sea is the world's largest truly marine body of anoxic water. The first rRNA survey of microbial eukaryotes in this environment revealed a number of novel lineages, but sampled only a fraction of the entire diversity. The goal of this study was to significantly improve recovery of protistan rRNA from the Basin. This was achieved by a systematic application of multiple PCR primer sets and substantially larger sequencing efforts. We focused on the most diverse habitat in the basin, anoxic waters approximately 100m below the oxic-anoxic interface, and detected novel lineages that escaped the single PCR primer approach. All clones obtained proved unique. A 99% sequence similarity cut-off value combined these clones into operational taxonomic units (OTUs), over 75% of which proved novel. Some of these OTUs form deep branches within established protistan groups. Others signify discovery of novel protistan lineages that appear unrelated to any known microeukaryote. Surprisingly, even this large-scale multi-primer rRNA approach still missed a substantial part of the samples' rRNA diversity. The overlap between the species lists obtained with different primers is low, with only 4% of OTUs shared by all three libraries, and the number of species detected only once is large (55%). This strongly indicates that, at least in anoxic environments, protistan diversity may be much larger than is commonly thought. A single sample appears to contain thousands of largely novel protistan species. Multiple PCR primer combinations may be needed to capture these species.

Animals↗

Evidence-based compression: prevention of stasis and deep vein thrombosis.

OBJECTIVE: To summarize the currently published scientific evidence for the venous flow effects of mechanical devices, particularly intermittent pneumatic compression, and the relation to prevention of deep vein thrombosis (DVT). SUMMARY BACKGROUND DATA: While intermittent pneumatic compression is an established method of DVT prophylaxis, the variety of systems that are available can use very different compression techniques and sequences. In order for appropriate choices to be made to provide the optimum protection for patients, the general performance of systems, and physiological effects of particular properties, must be analyzed objectively. METHODS: Medline was searched from 1970 to 2002, and all relevant papers were searched for further appropriate references. Papers were selected for inclusion when they addressed specifically the questions posed in this review. RESULTS: All the major types of intermittent compression systems are successful in emptying deep veins of the lower limb and preventing stasis in a variety of subject groups. Compression stockings appear to function more by preventing distension of veins. Rapid inflation, high pressures, and graded sequential intermittent compression systems will have particular augmentation profiles, but there is no evidence that such features improve the prophylactic ability of the system. CONCLUSIONS: The most important factors in selecting a mechanical prophylactic system, particularly during and after surgery, are patient compliance and the appropriateness of the site of compression. There is no evidence that the peak venous velocity produced by a system is a valid measure of medical performance.

Bandages↗

Salmonid opsin sequences undergo positive selection and indicate an alternate evolutionary relationship in oncorhynchus.

Positive selection can be demonstrated by statistical analysis when non-synonymous nucleotide substitutions occur more frequently than synonymous substitutions (dN>dS). This pattern of sequence evolution has been observed in the rhodopsin gene of cichlids. Mutations in opsin genes resulting in amino acid (AA) replacement appear to be associated with the evolution of specific color patterns and the evolution of courtship behaviors. Within fish, AA replacements in opsin proteins have improved vision at great depths and have occurred in deep-sea species. Salmonids experience diverse photic environments during their life history. Furthermore, sexual selection has resulted in species-specific male and female coloration during spawning. To look for evidence of positive selection in salmonid opsins, we sequenced the RH1, RH2, LWS, SWS1, and SWS2 genes from six Pacific salmon species as well as the Atlantic salmon. These salmonids include landlocked and migratory species and species that vary in their coloration during spawning. In each opsin gene comparison from all species sampled, traditional dN:dS analysis did not indicate positive selection. However, the more sensitive Creevey-McInerney statistical analysis indicates that RH1 and RH2 experienced positive selection early in the evolution and speciation of salmonids.

Animals↗

Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote.

The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents.

Archaea↗

Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang.

The phylogenetic relationships among major eukaryotic protist lineages are largely uncertain. Two significant obstacles in reconstructing eukaryotic phylogeny are long-branch attraction (LBA) effects and poor taxon sampling of free-living protists. We have obtained and analyzed gene sequences encoding the largest subunit of RNA Polymerase II (RPB1) from Naegleria gruberi (a heterolobosean), Cercomonas ATCC 50319 (a cercozoan), and Ochromonas danica (a heterokont); we have also analyzed the RPB1 gene from the nucleomorph (nm) genome of Guillardia theta (a cryptomonad). Using a variety of phylogenetic methods our analysis shows that RPB1s from Giardia intestinalis and Trichomonas vaginalis are probably subject to intense LBA effects. Thus, the deep branching of these taxa on RPB1 trees is questionable and should not be interpreted as evidence favoring their early divergence. Similar effects are discernable, to a lesser extent, with the Mastigamoeba invertens RPB1 sequence. Upon removal of the outgroup and these problematic sequences, analyses of the remaining RPB1s indicate some resolution among major eukaryotic groups. The most robustly supported higher-level clades are the opisthokonts (animals plus fungi) and the red algae plus the cryptomonad nm-the latter result gives added support to the red algal origin of cryptomonad chloroplasts. Clades comprising Dictyostelium discoideum plus Acanthamoeba castellanii (Amoebozoa) and Ochromonas plus Plasmodium falciparum (chromalveolates) are consistently observed and moderately supported. The clades supported by our RPB1 analyses are congruent with other data, suggesting that bona fide phylogenetic relationships are being resolved. Thus, the RPB1 gene has apparently retained some phylogenetically meaningful signal, making it worthwhile to obtain sequences from more diverse protist taxa. Additional RPB1 data, especially in combination with other genes, should provide further resolution of branching orders among protist groups within the apparently rapid early divergence of eukaryotes.

Evolution, Molecular↗

Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology.

The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree.

Animals↗

beta-Amyloid peptide free radical fragments initiate synaptosomal lipoperoxidation in a sequence-specific fashion: implications to Alzheimer's disease.

We have previously reported (Hensley et al., Proc. Natl. Acad. Sci. USA (1994) in press) that beta-amyloid peptide fragments in aqueous media, in a metal-independent reaction, produce reactive peptide free radicals and reactive oxygen species. In contrast to the hours or days necessary to produce neurotoxicity and a detectable free radical for beta-amyloid, the extremely neurotoxic A beta(25-35) fragment of beta-amyloid peptide produces a detectable radical in minutes. We now report that A beta(25-35) is a potent lipoperoxidation initiator, as inferred from peptide-mediated reduction of nitroxyl stearate spin labels bound to rodent neocortical synaptosomal membranes. A beta(25-35) rapidly quenches the paramagnetism of membrane-bound 12-nitroxyl stearate spin probe deep within the lipid bilayer, but reacts poorly with the 5-nitroxyl isomer whose paramagnetic center is near the lipid/water interface. A beta(35-25), the non-neurotoxic reverse sequence of A beta(25-35), shows little proclivity to reduce either spin label. These findings are formulated into a "molecular shrapnel" model of neuronal membrane damage in Alzheimer's disease.

Alzheimer Disease↗

Input-output relationships of the primary face motor cortex in the monkey (Macaca fascicularis).

1. Somatosensory afferent input and its relationship with efferent output were examined in the primary face motor cortex (MI) and adjacent cerebral cortical areas. Excitatory afferent inputs were tested in a total of 1,654 single neurons recorded in awake or anesthetized monkeys (Macaca fascicularis), and output was characterized in these same monkeys by the movement and EMG responses evoked by intracortical microstimulation (ICMS) at the neuronal recording sites. 2. Most neurons in the MI area responded to light tactile stimulation of the orofacial region, especially the upper lip, lower lip, and tongue. Although contralateral afferent inputs predominated, 21% of the neurons received ipsilateral or bilateral orofacial inputs. The afferent input evoked by tactile stimulation of the upper and lower lips was represented especially at the medial border and the input from the tongue at the lateral border of MI. However, in most regions of MI between the medial and lateral borders, an intermingling of tactile inputs from different orofacial areas occurred. Multiple representation of tactile input from the same orofacial area was found in several, often quite separate, intracortical sites in MI. 3. Only a small proportion of the MI neurons could be activated by the deep stimuli used (e.g., stretch and pressure applied to muscle, passive jaw movement, low-intensity stimulation of hypoglossal nerve) from the orofacial region. Those neurons which did respond to these low-threshold deep inputs were not clearly segregated from those which responded to tactile input, although most of the neurons receiving deep input were located in the rostral part of MI. 4. A somatotopic pattern of representation of orofacial tactile input was more obvious in the primary face somatosensory cortex (SI). At the medial border of SI, the periorbital area was represented, then followed laterally in sequence the tactile representation of the upper lip, lower lip, and intraoral area. Contralateral afferent inputs predominated, but as in MI, a considerable proportion of SI neurons received ipsilateral or bilateral orofacial inputs. Few neurons in the region explored (areas 3b, 1, and 2) responded to deep orofacial stimuli. 5. Tactile input also dominated the input patterns of neurons in the premotor cortex (PM). Most neurons received ipsilateral or bilateral orofacial afferent inputs and no clear somatotopic pattern was noted. Several PM neurons were also activated by visual stimuli. 6. Muscle twitches evoked by ICMS were limited to MI.(ABSTRACT TRUNCATED AT 400 WORDS)

Afferent Pathways↗

Lawsonella clevelandensis: a normal flora that bites deep.

Since its formal description in 2016, Lawsonella clevelandensis-a strictly anaerobic, partially acid-fast bacterium-has been increasingly recognized as a cause of deep-seated abscesses, yet its fastidious nature and absence from routine diagnostic databases contribute to significant underdiagnosis. This narrative review synthesizes current knowledge on its microbiology, expanding clinical spectrum, diagnostic strategies, and treatment, based on a literature search of PubMed and Web of Science up to April 2026. Analysis of 27 documented publications, comprising 18 clinical cases, reveals a potential association with host risk factors including diabetes, immunosuppression, and prior surgical procedures, alongside a notable predilection for fat-rich tissues such as the breast and abdomen. While metagenomic next-generation sequencing and 16S rRNA gene amplification have become indispensable for definitive identification, antimicrobial susceptibility data-derived primarily from a single strain-demonstrate uniformly low minimum inhibitory concentrations for penicillins, carbapenems, clindamycin, and metronidazole, with no acquired resistance genes identified by whole-genome sequencing. However, the absence of established clinical breakpoints and limited tested isolates precludes definitive conclusions about universal susceptibility. Clinicians should maintain a high index of suspicion for L. clevelandensis in culture-negative deep abscesses, particularly those with acid-fast rods, as prompt diagnosis and empirical therapy with β-lactam/β-lactamase inhibitors or carbapenems appear reasonable based on current in vitro and clinical evidence, though further susceptibility surveillance is essential.

Humans↗

A novel deep intronic EIF2AK3 variant disrupts splicing and causes Wolcott-Rallison syndrome.

AIM: Deep intronic variants can disrupt splicing and cause monogenic disease but are missed by routine genetic testing. This study assessed the contribution of deep intronic variants to Wolcott-Rallison syndrome (WRS), a recessive disorder characterized by early-onset diabetes and progressive multisystem disease caused by loss-of-function EIF2AK3 variants. METHODS: We investigated a cohort of 116 individuals referred to the Exeter Genomics Laboratory for genetic testing who had diabetes diagnosed at ≤2 years and at least one additional feature consistent with WRS: hepatic dysfunction, skeletal abnormalities or developmental delay. No genetic cause had been identified after testing all known early-onset diabetes genes. We screened genome-sequencing data for rare homozygous intronic EIF2AK3 variants. Candidate variants predicted to affect splicing by SpliceAI were assessed using a minigene exon-trapping assay. RESULTS: We identified two rare homozygous intronic EIF2AK3 variants in two siblings. Only one variant, c.1651-180G>T, was predicted to disrupt splicing in silico. The two children, born to consanguineous parents, were diagnosed with early-onset diabetes (diagnosed at 1 year and 21 weeks), hepatic dysfunction, skeletal abnormalities, developmental delay, thyroid dysfunction, hip dysplasia and gait abnormalities. The minigene assay showed that c.1651-180G>T creates a cryptic donor splice site within intron 9, resulting in inclusion of a 79-nucleotide pseudoexon, causing a frameshift and premature stop codon. Using this evidence, the variant was reclassified as likely pathogenic according to ACMG/ACGS guidelines. CONCLUSIONS: We report the first deep intronic EIF2AK3 variant causing WRS, highlighting the need to consider systematic intronic analysis in unresolved cases.

EIF2AK3↗

Retinal vasculature of the fovea of the squirrel monkey, Saimiri sciureus: three-dimensional architecture, visual screening, and relationships to the neuronal layers.

The retinal vasculature of the fovea of squirrel monkeys was studied in retinal whole mounts and in sections of the same retinas. At the center of the fovea there is an approximately circular avascular zone surrounded by a set of terminal capillaries in the inner nuclear layer. Within the foveal depression, four capillary planes that bear a precise relationship to the neuronal organization appear in a specific sequence with increasing eccentricity. The first plane to be established is the dominant, most voluminous one, located closest to the photoreceptors at the deep (sclerad) border of the inner nuclear layer. A second major plane appears next at the sclerad border of the ganglion cell layer. The two remaining, less voluminous planes occur at a slightly greater eccentricity. One of these, located at the shallow (vitread) border of the inner nuclear layer, often drains into the ganglion cell plane. The fourth plane is initially situated at the vitread border of the ganglion cell layer; with increasing eccentricity it moves into the nerve fiber layer. These capillaries are oriented like the nerve fibers with which they travel. Both the shallow inner nuclear and nerve fiber planes of capillaries show marked regional variations. The capillary planes are within or adjacent to regions of high cytochrome oxidase activity. The retinal vascular network is an unrecognized contributor to the optical filtering properties of the eye. In much of the central retina, a photon has a 40-50% chance of encountering one or more capillaries before it reaches a photoreceptor.

Animals↗