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Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme.

The formation of individual tertiary contacts of the Tetrahymena L-21 Sca I ribozyme has been monitored by hydroxyl radical footprinting and its global conformation by analytical ultracentrifugation as a function of monovalent ion concentration in the absence of divalent ions. Advanced methods of data analysis, which allow the hydroxyl radical reactivity of every nucleotide to be quantified, permit monitoring of each and every structural element of the RNA. Monovalent ion-mediated global compaction of the ribozyme is accompanied by the formation of native tertiary contacts; most native tertiary contacts are evident except several that are located near where divalent ions are observed in crystallographic structures. Non-native tertiary contacts are also observed at low but not high concentrations of monovalent ions. In light of recent studies that have shown that the presence of monovalent ions greatly accelerates the Mg2+-dependent folding of the Tetrahymena ribozyme, the present studies suggest that Na+ concentration changes not only the starting position of the RNA on its folding funnel but also pushes it deep into the well by forming native tertiary contacts and, thus, favoring fast and correct folding pathways.

Animals↗

Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.

Enhancers control tissue-specific gene expression across animals1. Although deep learning2,3 has enabled enhancer prediction and design in mammalian cell lines and non-mammalian model organisms4-10 (reviewed in a previous publication11), it remains unclear whether such approaches can operate within the regulatory complexity of mammalian genomes and tissues in vivo. Here we present a general strategy for designing tissue-specific enhancers that function reliably in mice. We use deep learning to train compact convolutional neural networks on curated chromatin accessibility data and fine-tune them by transfer learning on validated human and mouse enhancers. Guided by these models, we design 15 synthetic enhancers for the heart, limb and central nervous system in mouse embryos, all of which are active in their intended target tissue. These results demonstrate that mammalian enhancer function can be reliably inferred from DNA sequence alone, enabling the predictive de novo design of tissue-specific synthetic enhancers from modest training sets. This work establishes a generalizable framework for programmable control of mammalian gene expression in vivo, opening new avenues in functional genomics, synthetic biology and gene therapy.

Animals↗

Resurgent current and voltage sensor trapping enhanced activation by a beta-scorpion toxin solely in Nav1.6 channel. Significance in mice Purkinje neurons.

Resurgent currents are functionally crucial in sustaining the high frequency firing of cerebellar Purkinje neurons expressing Na(v)1.6 channels. Beta-scorpion toxins, such as CssIV, induce a left shift in the voltage-dependent activation of Na(v)1.2 channels by "trapping" the IIS4 voltage sensor segment. We found that the dangerous Cn2 beta-scorpion peptide induces both the left shift voltage-dependent activation and a transient resurgent current only in human Na(v)1.6 channels (among 1.1-1.7), whereas CssIV did not induce the resurgent current. Cn2 also produced both actions in mouse Purkinje cells. These findings suggest that only distinct beta-toxins produce resurgent currents. We suggest that the novel and unique selectivity of Cn2 could make it a model drug to replace deep brain stimulation of the subthalamic nucleus in patients with Parkinson disease.

Amino Acid Sequence↗

The evolutionary history of kinetoplastids and their kinetoplasts.

Despite extensive phylogenetic analysis of small subunit ribosomal RNA (SSUrRNA) genes, the deep-level relationships among kinetoplastids remain poorly understood, limiting our grasp of their evolutionary history, especially the origins of their bizarre mitochondrial genome organizations. In this study we examine the SSUrRNA data in the light of a new marker--cytoplasmic heat shock protein 90 (hsp90) sequences. Our phylogenetic analyses divide kinetoplastids into four main clades. Clades 1-3 include the various bodonid kinetoplastids. Trypanosomatids comprise the fourth clade. SSUrRNA analyses give vastly different and poorly supported positions for the root of the kinetoplastid tree, depending on the out-group and analysis method. This is probably due to the extraordinary length of the branch between kinetoplastids and any out-group. In contrast, almost all hsp90 analyses place the root between clade 1 (including Dimastigella, Rhynchomonas, several Bodo spp., and probably Rhynchobodo) and all other kinetoplastids. Maximum likelihood and maximum likelihood distance analyses of hsp90 protein and second codon-position nucleotides place trypanosomatids adjacent to Bodo saltans and Bodo cf. uncinatus (clade 3), as (weakly) do SSUrRNA analyses. Hsp90 first codon- plus second codon-position nucleotide analyses return a slightly different topology. We show that this may be an artifact caused, in part, by the different evolutionary behavior of first- and second-codon positions. This study provides the most robust evidence to date that trypanosomatids are descended from within bodonids and that B. saltans is a close relative of trypanosomatids. A total reevaluation of the high-level systematics within kinetoplastids is needed. We confirm that the interlocking network organization of kinetoplast DNA seen in trypanosomatids is a derived condition within kinetoplastids but suggest that open-conformation minicircles may have arisen early in kinetoplastid evolution. Further understanding of the evolution of kinetoplast structure and RNA editing is hampered by a paucity of data from basal (i.e., clade 1) bodonids.

Animals↗

Influence of therapeutic phenobarbital and phenytoin medication on the polygraphic sleep of patients with epilepsy.

Sleep is a modulator of seizure activity, and many antiepileptic drugs are modulators of sleep. Can influences on sleep organization be involved in antiepileptic drug action, and can these partly account for differences in drug response of various epileptic syndromes? Much more exact data must be collected before these questions can be adequately discussed. The polygraphic sleep of 40 unmedicated epileptic patients was recorded and compared with polygraphy after adjustment to therapeutic steady states of phenobarbital (PB) and phenytoin (DPH) (as sequential sole agents in a crossover design with random sequence). With PB, patients fell asleep more rapidly and had fewer movements, movement arousals, and arousal awakenings, all of which could be beneficial, especially for patients with generalized epilepsy. Light sleep was increased, and REM sleep decreased. The usual sleep pattern was altered, with maximal deep sleep early and maximal REM sleep late in the night. PB seemed to have maximal effect in the first REM cycle. With DPH, sleep onset also came sooner, but light sleep was decreased and deep sleep increased, with no alteration of REM sleep. In contrast to PB, the changes in sleep organization were toward leveling the distribution of deep NREM sleep. The maximal alterations were observed in the third REM cycle. With both drugs, there were some differences in the response of generalized as opposed to focal epilepsies, and of awakening as opposed to sleep epilepsies. Thus, the early REM cycles seemed to be more modifiable by drugs in patients with generalized or awakening epilepsies than in patients with focal or sleep epilepsies.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

Three layers of the medial capsular and supporting structures of the knee: MR imaging-anatomic correlation.

The authors used a three-layer approach to correlate the appearance of the capsule and ligaments of the medial side of the knee on magnetic resonance (MR) images with corresponding anatomic slices. MR images of six fresh cadaveric specimens were obtained by using a proton-density-weighted fast spin-echo sequence with a 256 x 512 matrix. Specimens were frozen and sliced with a band saw into 3. 0-mm-thick sections that corresponded to the MR images. Three layers were depicted on both anatomic slices and MR images. Layer 1 consisted of the deep crural fascia; layer 2, the superficial portion of the medial collateral ligament (MCL); and layer 3, the capsule, the deep portion of the MCL, the meniscofemoral and meniscotibial extensions of the deep portion of the MCL, and the patellomeniscal ligament. Along the anterior aspect of the medial side of the knee, layer 1 was fused with layer 2; along the posterior aspect of the knee, layer 2 was fused with layer 3.

Aged↗

Proton magnetic resonance spectroscopy of cerebral lactate and other metabolites in stroke patients.

BACKGROUND AND PURPOSE: Proton magnetic resonance spectroscopy can measure in vivo brain lactate and other metabolites noninvasively. We measured the biochemical changes accompanying stroke in 16 human subjects with cortical or deep cerebral infarcts within the first 3 weeks after symptom onset, and performed follow-up studies on six. METHODS: One-dimensional proton spectroscopic imaging encompassing the infarct region was performed with a 2.1-T whole-body magnet using the stimulated echo pulse sequence and an echo time of 270 msec. RESULTS: All but one of the cortical stroke patients had increased lactate within or near the infarct. Persistently elevated cerebral lactate was documented in five of six cases studied serially as long as 251 days after infarction. N-acetylaspartate levels were decreased in most cortical strokes. Elevated lactate, accompanied by minimal reduction in N-acetylaspartate, was recorded in two of four patients in the first week following a small subcortical infarct. CONCLUSIONS: Long-term elevation of lactate commonly occurs after stroke. This lactate may arise from ongoing ischemia or infiltrating leukocytes, or it may be a residual of the lactate formed during the initial insult. The ability to observe stroke-elevated lactate pools at any time after lesion onset provides an approach to distinguishing among these possibilities in the future.

Aspartic Acid↗

Increased damage to type II collagen in osteoarthritic articular cartilage detected by a new immunoassay.

A new immunoassay was developed to detect denaturation of type II collagen in osteoarthritis (OA). A peptide, alpha 1 (II)-CB11B, located in the CB11 peptide of type II collagen, was synthesized and used to produce a monoclonal antibody (COL2-3/4m) of the IgG1 (kappa) isotype. This reacts with a defined epitope in denatured but not native type II collagen and the alpha 3 chain of type XI collagen. The latter is present in very small amounts (about 1% wt/wt) in cartilage relative to the alpha 1 (II) chain. By using an enzyme-linked immunosorbent assay, type II collagen denaturation and total type II collagen content were determined. The epitope recognized by the antibody was resistant to cleavage by alpha-chymotrypsin and proteinase K which were used to extract alpha 1 (II)-CB11B from the denatured (alpha-chymotrypsin soluble) and residual native (proteinase K soluble) collagen alpha-chains, respectively, present in human femoral articular cartilage. Type II collagen content was significantly reduced from a mean (range) of 14% (9.2-20.8%) of wet weight in 8 normal cartilages to 10.3% (7.4-15.0%) in 16 OA cartilages. This decrease, which may result in part from an increased hydration, was accompanied by an increase in the percent denaturation of type II collagen in OA to 6.0% of total type II collagen compared with 1.1% in normal tissue. The percent denaturation was ordinarily greater in the more superficial zone than in the deep zone of OA cartilage.

Adult↗

The urinary system in Down syndrome: a study of 124 autopsy cases.

We examined 124 autopsy cases of Down syndrome for the presence of renal and urinary tract abnormalities. The cases were divided into three groups: (I) fetuses of 16-22 weeks gestation (n = 18), (II) stillborns or newborns who died on the first day of life (n = 9), and (III) Down patients 1 day to 25 years of age (n = 97). Kidney weight was reduced by a mean of 14.4% compared with expected values. Renal hypoplasia, defined as kidney weight less than two-thirds expected, was found in 18 cases. Glomerular microcysts were found in 23 of 97 cases in group III. Focal dilatation of tubules was found in 10, simple cysts in 7, and immature glomeruli deep in the renal cortex in 18 cases. Obstructive uropathy occurred in 2 of 18 (11.1%) in group I, 2 of 9 (22.2%) in group II, and 4 of 97 (4.1%) in group III. Obstructive uropathy with bilateral cystic dysplastic kidneys resulted in Potter's sequence. We suggest that obstructive uropathy is associated with Down syndrome. When severe, it results in Potter's sequence and an early perinatal death. A chromosomal analysis is recommended in any case of obstructive uropathy in the fetal or neonatal period.

Adolescent↗

Liver enzymes after retropubic prostatectomy in patients receiving continuous lumbar epidural analgesia or general anaesthesia.

In 38 patients subjected to retropubic prostatectomy the effects of continuous lumbar epidural analgesia for 24 hours and the thiopentone- oxygen-nitrous oxide- alcuronium-pethidine sequence with artificial ventilation on the serum activities of aspartate aminotransferase (ASAT), alanine aminotransferase (ALAT), alpha-hydroxybutyrate dehydrogenase (HBD), and alkaline phosphatase (AP) have been studied. Per- and postoperative complications were recorded according to a prearranged plan designed to quantify the peroperative haemorrhage, postoperative deep vein thrombosis, pulmonary, circulatory and infectious complications. ASAT, ALAT and AP in the general group and ALAT in the epidural group showed significant increases on the 5th and 7th postoperative days. There existed no statistically significant difference between the groups. 82% of the patients with documented postoperative complications combined with hypoxaemia showed a pathologic liver enzyme pattern in contrast to 9% of the patients with uneventful postoperative course. It is concluded that the method of anaesthesia did not have an effect on the liver enzymes. Complications combined with postoperative hypoxaemia seemed to be the factors responsible for the increases of liver enzymes.

Aged↗

Parapinopsin, a novel catfish opsin localized to the parapineal organ, defines a new gene family.

Multiple sites of extraretinal photoreception are present in vertebrates, but the molecular basis of extraretinal phototransduction is poorly understood. This study reports the cloning of the first opsin specifically expressed in the directly photosensitive pineal and parapineal of cold-blooded vertebrates. This opsin, identified in channel catfish and termed parapinopsin, defines a new gene family of vertebrate photopigments and is expressed in a majority of parapinealocytes and a subset of pineal photoreceptor cells. Parapinopsin shows a caudal-rostral gradient of expression within the pineal organ. This study also reports the cloning of partial cDNAs encoding the channel catfish orthologues of rhodopsin and the red cone pigment-the full complement of retinal opsins in the species. In situ hybridization studies using probes derived from these retinal opsins, together with parapinopsin, reveal no expression of retinal opsins in pineal and parapineal organ and no expression of any opsin tested in the "deep brain," iris, or dermal melanophores. These data imply that phototransduction in these sites of extraretinal photoreception must be mediated by novel opsins.

Amino Acid Sequence↗

Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans.

To understand how allopatric speciation proceeds, we need information on barriers to gene flow, their antiquity, and their efficacy. For marine organisms with planktonic larvae, much of this information can only be obtained through the determination of divergence between populations. We evaluated the importance of ocean barriers by studying the mitochondrial DNA phylogeography of Tripneustes, a pantropical genus of shallow water sea urchin. A region of cytochrome oxidase I (COI) was sequenced in 187 individuals from locations around the globe. The COI phylogeny agreed with a previously published phylogeny of bindin that barriers important to the evolution of Tripneustes are: (1) the cold water upwelling close to the tip of South Africa, (2) the Isthmus of Panama, (3) the long stretch of deep water separating the eastern from the western Atlantic, and (4) the freshwater plume of the Orinoco and the Amazon rivers between the Caribbean and the coast of Brazil. These barriers have previously been shown to be important in at least a subset of the shallow water marine organisms in which phylogeography has been studied. In contrast, the Eastern Pacific Barrier, 5000 km of deep water between the central and the eastern Pacific that has caused the deepest splits in other genera of sea urchins, is remarkably unimportant as a cause of genetic subdivision in Tripneustes. There is also no discernible subdivision between the Pacific and Indian Ocean populations of this genus. The most common COI haplotype is found in the eastern, central, and western Pacific as well as the Indian Ocean. Morphology, COI, and bindin data agree that T. depressus from the eastern Pacific and T. gratilla from the western Pacific are, in fact, the same species. The distribution of haplotype differences in the Indo-Pacific exhibits characteristics expected from a sea urchin genus with ephemeral local populations, but with high fecundity, dispersal, and growth: there is little phylogenetic structure, and mismatch distributions conform to models of recent population expansion on a nearly global scale. Yet, comparisons between local populations produce large and significant F(ST) values, indicating nonrandom haplotype distribution. This apparent local differentiation is only weakly reflected in regional divergence, and there is no evidence of isolation by distance in correlations between F(ST) values and either geographical or current distance. Thus, Tripneustes in the Indo-Pacific (but not in the Atlantic) seems to be one large metapopulation spanning two oceans and containing chaotic, nonequilibrium local variation, produced by the haphazard arrival of larvae or by unpredictable local extinction.

Animals↗

Characterization of two novel yeast strains used in mediated biosensors for wastewater.

After isolation from a pulp mill wastewater treatment facility, two yeast strains, designated SPT1 and SPT2, were characterized and used in the development of mediated biochemical oxygen demand (BOD) biosensors for wastewater. 18S rRNA gene sequence analysis revealed a one nucleotide difference between the sequence of SPT1 and those of Candida sojae and Candida viswanthii. While SPT2 had the highest overall homology to Pichia norvegensis, at only 73.5%, it is clearly an ascomycete, based on BLAST comparisons and phylogenetic analyses. Neighbor-joining dendrograms indicated that SPT1 clustered with several Candida spp., and that SPT2 clustered with Starmera spp., albeit as a very deep branch. Physiological tests, microscopic observations, and fatty acid analysis confirmed that SPT1 and SPT2 are novel yeast strains. Physiological tests also indicated that both strains had potential for use in mediated biosensors for estimation of BOD in wastewater. The lower detection limits of SPT1- and SPT2-based K3Fe(CN)6-mediated biosensors for a pulp-mill effluent were 2 and 1 mg BOD/L, respectively. Biosensor-response times for effluents from eight different pulp mills were in the range of 5 min. Reliability and sensitivity of the SPT1- and SPT2-based biosensors were good, but varied with the wastewater.

Ascomycota↗

Importance of lipooligosaccharide structure in determining gonococcal resistance to hydrophobic antimicrobial agents resulting from the mtr efflux system.

Levels of gonococcal resistance to antimicrobial hydrophobic agents (HAs) are controlled by the mtr (multiple transferrable resistance) system, composed of the mtrRCDE genes. The mtrR gene encodes a transcriptional repressor that appears to regulate expression of the upstream and divergent mtrCDE operon. The mtrCDE genes encode membrane proteins analogous to the MexABOprK proteins of Pseudomonas aeruginosa that mediate export of structurally diverse antimicrobial agents. In this study we found that a single base pair deletion in a 13 bp inverted repeat sequence within the mtrR promoter resulted in increased resistance of gonococci to both crystal violet (CV) and erythromycin (ERY) as well as to the more lipophilic non-ionic detergent Triton X-100 (TX-100). However, this cross-resistance was contingent on the production of a full-length lipooligosaccharide (LOS) by the recipient strain used in transformation experiments. Introduction of this mutation (mtrR-171) into three chemically distinct deep-rough LOS mutants by transformation resulted in a fourfold increase in resistance to TX-100 compared with a 160-fold increase in an isogenic strain producing a full-length LOS. However, both wild-type and deep-rough LOS strains exhibited an eightfold increase in resistance to CV and ERY as a result of the mtrR-171 mutation. This suggests that gonococci have different LOS structural requirements for mtr-mediated resistance to HAs that differ in their lipophilic properties. Evidence is presented that gonococci exclude HAs by an energy-dependent efflux process mediated by the mtr system.

Bacterial Proteins↗

Structure of a specific peptide complex of the carboxy-terminal SH2 domain from the p85 alpha subunit of phosphatidylinositol 3-kinase.

We have determined the solution structure of the C-terminal SH2 domain of the p85 alpha subunit of human phosphatidylinositol (PI) 3-kinase (EC 2.7.1.137) in complex with a phosphorylated tyrosine pentapeptide sequence from the platelet-derived growth factor receptor using heteronuclear nuclear magnetic resonance spectroscopy. Overall, the structure is similar to other SH2 domain complexes, but displays different detail interactions within the phosphotyrosine binding site and in the recognition site for the +3 methionine residue of the peptide, the side chain of which inserts into a particularly deep and narrow pocket which is displaced relative to that of other SH2 domains. The contacts made within this +3 pocket provide the structural basis for the strong selection for methionine at this position which characterizes the SH2 domains of PI3-kinase. Comparison with spectral and structural features of the uncomplexed domain shows that the long BG loop becomes less mobile in the presence of the bound peptide. In contrast, extreme resonance broadening encountered for most residues in the beta D', beta E and beta F strands and associated connecting loops of the domain in the absence of peptide persists in the complex, implying conformational averaging in this part of the molecule on a microsecond-to-millisecond time scale.

Amino Acid Sequence↗

Mitogenomic analyses of deep gnathostome divergences: a fish is a fish.

It is commonly accepted that among recent fishes the lungfishes are the closest relatives of the tetrapods. According to this hypothesis, the tetrapods, lungfishes and coelacanths constitute a group of specialized fishes (Sarcopterygii) to the exclusion of other bony fishes. Here, we describe basal relationships among gnathostome (jawed) vertebrates as reconstructed by analysis of complete mitochondrial DNA sequences. The study includes all major extant groups of both tetrapods and fishes and uses agnathan (jawless) vertebrates as an outgroup to root the trees. The analyses split extant gnathostomes into two monophyletic groups: tetrapods and fishes (including cartilaginous fishes). Cladistia (bichirs, ropefish) is in a basal position on the piscine branch. Thus, contrary to the traditional view, the mitogenomic results suggest that among living gnathostomes a tetrapod is a tetrapod and a fish, a fish. Similarly, analyses of 18S and 28S rRNA genes (both nuclear) do not support the commonly accepted tree.

Animals↗

Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa.

The deepest-level relationships amongst Euglenozoa remain poorly resolved, despite a rich history of morphological examination and numerous molecular phylogenetic studies of small subunit ribosomal RNA (SSU rRNA) data. We address this question using two nuclear-encoded proteins, the cytosolic isoforms of heat shock protein 90 (hsp90) and heat shock protein 70 (hsp70). For both proteins we examined sequences from the three primary groups within Euglenozoa (euglenids, diplonemids, and kinetoplastids), and from their close relatives, Heterolobosea. Maximum likelihood (ML) and ML distance analyses of these proteins support a close relationship between diplonemids and kinetoplastids to the exclusion of the euglenid Euglena gracilis. In hsp90 and combined protein analyses bootstrap support is very strong and alternative topologies are generally rejected by 'approximately unbiased' (AU) tests. This result is consistent with recent molecular biological and morphological data, but contradicts early structural accounts and many SSU rRNA analyses that favour a closer relationship between diplonemids and euglenids. However, a re-examination of an important SSU rRNA data set highlights the instability of the inferences from this marker. The protein analyses also suggest that bodonids are paraphyletic, with trypanosomatids grouping with 'clade 2' and 'clade 3' bodonids to the exclusion of 'clade 1' bodonids.

Animals↗

Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake.

This study presents an original 18S rRNA PCR survey of the freshwater picoeukaryote community, and was designed to detect unidentified heterotrophic picoflagellates (size range 0.6-5 microm) which are prevalent throughout the year within the heterotrophic flagellate assemblage in Lake Pavin. Four clone libraries were constructed from samples collected in two contrasting zones in the lake. Computerized statistic tools have suggested that sequence retrieval was representative of the in situ picoplankton diversity. The two sampling zones exhibited similar diversity patterns but shared only about 5% of the operational taxonomic units (OTUs). Phylogenetic analysis clustered our sequences into three taxonomic groups: Alveolates (30% of OTUs), Fungi (23%) and Cercozoa (19%). Fungi thus substantially contributed to the detected diversity, as was additionally supported by direct microscopic observations of fungal zoospores and sporangia. A large fraction of the sequences belonged to parasites, including Alveolate sequences affiliated to the genus Perkinsus known as zooparasites, and chytrids that include host-specific parasitic fungi of various freshwater phytoplankton species, primarily diatoms. Phylogenetic analysis revealed five novel clades that probably include typical freshwater environmental sequences. Overall, from the unsuspected fungal diversity unveiled, we think that fungal zooflagellates have been misidentified as phagotrophic nanoflagellates in previous studies. This is in agreement with a recent experimental demonstration that zoospore-producing fungi and parasitic activity may play an important role in aquatic food webs.

Chlorophyll↗