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PubMed2006

[Cine MRI of the thorax in patients with pectus excavatum].

BACKGROUND: Morphologic and dynamic assessment of respiratory chest kinetics was performed in patients with pectus excavatum deformity (PE) using dynamic MRI: cine MRI. MATERIAL AND METHODS: Seven consecutive patients with PE (aged 20.3 years+/-4.0) and ten healthy volunteers of comparable age underwent real-time cine MRI of the chest during breathing on a 1.5 T MR scanner (Magnetom Sonata, Siemens Medical Systems, Erlangen, Germany) using a standard phased array body coil and a half-Fourier single-shot turbo spin echo sequence (HASTE) for dynamic imaging. During deep inspiration and expiration, single-shot sequences were performed in one slice level over 20 s at a frequency of 1 image/s covering the entire thoracic cage in three orientations. Morphology and chest kinetics in patients with PE were analyzed and compared with normal values, and typical patterns of chest kinetics were noted. RESULTS: Three different types of chest morphology in PE were identified: (1) the generally flattened thoracic cage, (2) the "tilted" sternum, and (3) the focally deepened sternum. Three patterns of motion correspond to these morphological types: (1) elevation of the sternum and the anterior thoracic wall, (2) angulated elevation of the parasternal rib cage with persistent deepening of the sternum resembling a "wing beat" movement, and (3) increased diaphragmatic movements with limited chest wall dynamics. CONCLUSIONS: Cine MRI is an adequate radiation-free diagnostic modality for the dynamic imaging of both chest morphology and chest wall kinetics in patients with PE. The pectus severity index can easily be determined and three typical movement patterns of chest wall kinetics identified.

Adolescent↗

PubMed1999

Panning for genes--A visual strategy for identifying novel gene orthologs and paralogs.

We have developed a rapid visual method for identifying novel members of gene families. Starting with an evolutionary tree, 20-50 protein query sequences for a gene family are selected from different branches of the tree. These query sequences are used to search the GenBank and expressed sequence tag (EST) DNA databases and their nightly updates using the tfastx3 or tfasty3 programs. The results of all 20-50 searches are collated and resorted to highlight EST or genomic sequences that share significant similarity with the query sequences. The statistical significance of each DNA/protein alignment is plotted, highlighting the portion of the query sequence that is present in the database sequence and the percent identity in the aligned region. The collated results for database sequences are linked using the WWW to the underlying scores and alignments; these links can also be used to perform additional searches to characterize the novel sequence further. With traditional "deep" scoring matrices (BLOSUM50) one can search for previously unrecognized families of large protein superfamilies. Alternatively, by using query sequences and EST libraries from the same species (e. g., human or mouse) together with "shallow" scoring matrices and filters that remove high-identity sequences, one can highlight new paralogs of previously described subfamilies. Using query sequences from the glutathione transferase superfamily, we identified two novel mammalian glutathione transferase families that were recognized previously only in plants. Using query sequences from known mammalian glutathione transferase subfamilies, we identified new candidate paralogs from the mouse class-mu, class-pi, and class-theta families.

Amino Acid Sequence↗

PubMed2006

Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone.

To examine the occurrence in other deep-sea bacteria of two amino acid substitutions (Ala-180 and His-229) in malate dehydrogenase (MDH) found previously in the deep-sea piezophilic Moritella sp. strain 2D2, we cloned and sequenced MDH genes of deep-sea piezophilic Moritella and Shewanella strains isolated from intestinal contents of deep-sea fishes, as well as other Moritella species from deep-sea water and sediments: M. marina, M. japonica, and M. yayanosii. The piezophilic Moritella strains had a Val residue or an Ala residue at position 180 and all the Moritella strains except for one had a His residue at position 229. However, four piezophilic-strain-specific substitutions at positions 103, 111, 229, and 283 were found to be completely conserved in the MDH of the intestinal Moritella strains of deep-sea fishes, indicating the substitutions may be habitat-specific. The piezophilic Shewanella strains had a Val residue and a Gln residue at positions 180 and 229, respectively. However, the MDHs of the Shewanella strains had five piezophilic-strain-specific substitutions at positions 61, 65, 107, 161, and 202. Therefore, the enzymatic strategies for responding to deep-sea high pressure environments of the MDHs between the genera Moritella and Shewanella are potentially different. Moreover, homology modeling shows these substitutions found in the MDHs of both genera except for position 229 in the subunit interface are located on the exposed region of the MDH molecules, indicating the substitutions may be related to the hydration state of the molecules.

Amino Acid Sequence↗

PubMed2005

Life at depth: Photobacterium profundum genome sequence and expression analysis.

Deep-sea life requires adaptation to high pressure, an extreme yet common condition given that oceans cover 70% of Earth's surface and have an average depth of 3800 meters. Survival at such depths requires specific adaptation but, compared with other extreme conditions, high pressure has received little attention. Recently, Photobacterium profundum strain SS9 has been adopted as a model for piezophily. Here we report its genome sequence (6.4 megabase pairs) and transcriptome analysis. The results provide a first glimpse into the molecular basis for life in the largest portion of the biosphere, revealing high metabolic versatility.

Adaptation, Physiological↗

PubMed1996

Phylogeny of oral asaccharolytic Eubacterium species determined by 16S ribosomal DNA sequence comparison and proposal of Eubacterium infirmum sp. nov. and Eubacterium tardum sp. nov.

16S rRNA gene sequences of Eubacterium brachy, Eubacterium nodatum, Eubacterium saphenum, Eubacterium timidum, and two previously unnamed taxa were determined. The results of a phylogenetic analysis indicated that all of the strains sequenced belonged to a deep branch of the low-G+C-content gram-positive group. The levels of 16S ribosomal DNA sequence similarity between species were low, suggesting that a number of genera may be represented in this group. The representatives of the two unnamed taxa, which were isolated from patients with periodontitis, were clearly distinct from the previously described species, and, therefore, the following two new species are proposed: Eubacterium infirmum (type strain, NCTC 12940) and Eubacterium tardum (type strain, NCTC 12941).

Base Sequence↗

PubMed1998

Distribution of the pressure-regulated operons in deep-sea bacteria.

DNA regions corresponding to portions of two different pressure-regulated operons previously identified in two deep-sea barophilic bacteria were separately PCR amplified from a variety of deep-sea microorganisms and sequenced. With the two sets of primers employed, amplification was particularly successful from the more barophilic bacteria examined. 16S rRNA sequence analysis revealed that these bacteria are all phylogenetically related and belong in a sub-branch of the genus Shewanella containing only the deep-sea Shewanella barophilic bacteria. We define this sub-branch as the 'Shewanella barophile branch' containing at least two different species. Our results suggest that the DNA sequences of the pressure-regulated operons can be regarded as marker sequences to identify the Shewanella barophilic strains.

Amino Acid Sequence↗

PubMed1997

Cloning, sequencing and overexpression of the gene encoding malate dehydrogenase from the deep-sea bacterium Photobacterium species strain SS9.

The gene encoding malate dehydrogenase (mdhA) was obtained from the psychrophilic, barophilic, deep-sea isolate Photobacterium species strain SS9. The SS9 mdhA gene directed high levels of malate dehydrogenase (MDH) production in Escherichia coli. A comparison of SS9 MDH to three mesophile MDHs, a MDH sequence obtained from another deep-sea bacterium, and to other psychrophile proteins is presented.

Amino Acid Sequence↗

PubMed1989

Amino acid sequence of the dimeric hemoglobin (Hb I) from the deep-sea cold-seep clam Calyptogena soyoae and the phylogenetic relationship with other molluscan globins.

The deep-sea cold-seep clam Calyptogena soyoae has two homodimeric hemoglobins (Hbs I and II) in erythrocytes. The complete amino acid sequence of Hb I has been determined. It is composed of 144 amino acid residues, has a high content of hydrophobic residues, and a calculated molecular weight of 16,350 including a heme group. The sequence of Calyptogena Hb I showed high homology (42% identity) with that of Calyptogena Hb II (Suzuki, T., Takagi T. and Ohta, S. (1989) Biochem. J. 260, 177-182), although it has a long insertion of seven residues in the C-terminal region compared with Hb II. On the other hand, it showed low homology (12-20% identity) with other molluscan globins. As well as Hb II, Calyptogena Hb I lacked the N-terminal extension of 7-9 residues characteristic of molluscan intracellular hemoglobins, and the distal (E7) histidine was replaced by glutamine. A phylogenetic tree was constructed from 13 molluscan globins belonging to the five families Aplysiidae, Galeodidae, Potamididae, Arcidae and Vesicomyidae. The globin sequences of Calyptogena (Vesicomyidae) were found to be rather distant from other globin sequences, suggesting that they might conserve a primitive form of molluscan globins.

Amino Acid Sequence↗

PubMed2000

Analysis of human immunodeficiency virus type 1 gp160 sequences from a patient with HIV dementia: evidence for monocyte trafficking into brain.

Towards understanding the pathogenesis of HIV dementia, we molecularly cloned and sequenced human immundeficiency virus type 1 (HIV-1) gp160 genes from uncultured post-mortem tissues collected from a patient with HIV dementia. Sequences from bone marrow, lymph node, lung, and four regions of brain - the deep white matter, head of caudate, choroid plexus and meninges - were compared. Also included were gp160 sequences recovered from blood monocytes collected 5 months prior to death. Phylogenetic analyses showed that the sequences from deep white matter were more closely related to those from bone marrow, than to those from the other tissues, and moreover, were most closely related to sequences from the blood monocytes. These findings suggest trafficking of bone marrow-derived monocytes into the deep white matter during this late stage of infection. Another cluster included sequences from choroid plexus, meninges and lymph node, and interestingly, identical patterns of four or nine stop codons were shared among these tissues. These mutations appear to be the consequence of G-->A hypermutation, and could reflect independent events, or the movement of virions or infected cells, from the choroid plexus into the cerebrospinal fluid and ultimately, into the lymph node. We propose that a critical step towards the development of HIV dementia is an increase in monocyte trafficking into the brain, and that this process is either initiated and/or accelerated during late-stage infection, which could explain why dementia occurs primarily during this time.

AIDS Dementia Complex↗

PubMed1984

The ribonucleotide sequence of 5s rRNA from two strains of deep-sea barophilic bacteria.

Deep-sea bacteria were isolated from the digestive tract of animals inhabiting depths of 5900 m in the Puerto Rico Trench and 4300 m near the Walvis Ridge. Growth of two bacterial strains was measured in marine broth and in solid media under a range of pressures and temperatures. Both strains were barophilic at 2 degrees C (+/- 1 degrees C) with an optimal growth rate of 0.22 h-1 at a pressure 30% lower than that encountered in situ. At 1 atm they grew at temperatures ranging from 1.2 to 18.2 degrees C (+/- 0.3 degrees C), while in situ pressures increased the upper temperature limit to 23.3 degrees C. Both strains were identified as members of the genus Vibrio, based on standard taxonomic tests and mol% G + C values (47.0 and 47.1). Ribonucleotide sequences determined for 5S ribosomal RNA from each strain confirmed relationship to the Vibrio-Photobacterium group, as represented by V. harveyi and P. phosphoreum, but the barophiles were clearly distinct from these species. Secondary structure conformed to the established model for eubacterial 5S rRNA.

Animals↗

PubMed2005

Comparing white matter lesions on T2 and FLAIR MRI in the Sydney Older Persons Study.

There is suggestion that magnetic resonance imaging (MRI) fluid-attenuated inversion recovery (FLAIR) sequence may be more accurate than T2 images in detecting white matter lesions (WML) in older people. Comparative ratings of these two image sequences have not been directly investigated in very old individuals to date. We compared the ratings of periventricular and deep WML on these two sequences in a sample of 111 community dwellers (mean age 85.5 years) using semiquantitative methods. Periventricular WML were as commonly detected on T2 as on FLAIR but were more severely rated on the latter sequence. No such bias was observed for the deep WML. With one exception, correlations between the two sets of measures were significant at the P < 0.001 level (range: 0.34-0.75). Intrarater reliability coefficients were moderate to excellent for most ratings. These results suggest that ratings performed on T2-weighted images to detect WML in very old individuals are very comparable with those performed on FLAIR images although FLAIR may allow a finer grading of periventricular lesions. Absence of FLAIR does not preclude the identification of WML in this population. These findings have clinical and epidemiological relevance where the acquisition of supplementary MRI data may not always be possible.

Aged↗

PubMed2005

Chewing activities and oesophageal motility during feed intake, rumination and eructation in camels.

It was the aim of this study to characterize rumination behaviour, eructation and oesophageal motility in camels to identify similarities and differences between camels and domestic ruminants. Recordings were carried out in five camels fed on a hay-based diet. On an average, the duration of rumination, feeding and resting was 8.3, 5.6 and 10.1 h per 24 h, respectively. Rumination activity peaked in the morning between 9:00 and 11:00 and in the night between 02:00 and 04:00 a.m. During rumination periods, on an average 67 boluses were regurgitated per hour. Each bolus was chewed for an average of 45 s with 68 chews per min. The pause between two rumination cycles lasted on an average 9 s. Hay intake took 61 min/kg dry matter (DM), rumination lasted 71 min/kg DM of hay consumed. The regurgitation of a bolus started with a contraction of cranial compartment 1 (C 1) during a B-sequence, followed by a deep inspiration with closed glottis. Digesta enters the oesophagus, and an antiperistaltic wave transported the bolus orally. Eructation starts with a contraction of the caudal C1 during a B-sequence when the cranial C1 is relaxed. After entering the oesophagus, a rapid antiperistaltic wave transports the gas orally. Results revealed that the parameter values obtained in the camels were remarkably similar to those in domestic ruminants despite profound morphological differences and different patterns of forestomach motility.

Animals↗

PubMed2026

Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.

Protein structure bridges the sequence-function relationship, enabling deep exploration of biological processes across diverse organisms. Insects, the most diverse animal lineage, accounting for over 50% of all described animal species, provide an exceptional system for exploring sequence-structure-function relationships. Here, we reconstructed a comprehensive and well-resolved phylogeny of 4854 insects, spanning all orders. Leveraging this framework, we created an atlas of 13.29 million predicted protein structures from 824 representative species, including 11.63 million newly predicted structures. Structural clustering revealed that proteins with divergent sequences but similar structures could be effectively grouped together. Structural similarity searches against proteins with well-characterized functions yielded annotations for 7.61 million insect proteins, including up to 14% of previously unannotated proteins. We further identified 750 million remote homologs between insect proteins, many of which trace back to ancient branches of the insect phylogeny. Remarkably, despite extensive sequence divergence, cGAS-like receptors (cGLRs) were structurally conserved across all 824 insects. Experimental assays demonstrated that these structurally identified cGLRs play a crucial role in antiviral defense in the yellow fever mosquito. Our findings highlight the significance of structural genomics for understanding protein function and evolution across the tree of life.

Animals↗

PubMed2005

Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge.

Two sediment cores were collected in an inactive area of the deep-sea hydrothermal vent field Rainbow (36 degrees N on the Mid-Atlantic Ridge). Metals and carbonates were abundant throughout the cores; calcite (CaCO3) was found throughout the cores while dolomite [CaMg(CO3)2] and siderite (FeCO3) were only found in deeper layers. Using polymerase chain reaction (PCR)-amplified 16S rRNA gene sequence analysis, we examined the bacterial and archaeal diversity in a sediment layer that contained the three carbonates. The retrieved bacterial and archaeal sequences were new and less than 4% of the sequences exhibited 94% or more identity with that of cultured organisms. The analysis of the composition of the bacterial library revealed a high diversity of sequences. Half of the bacterial clones was affiliated to the gamma-Proteobacteria. Most of them had environmental sequences retrieved from deep-sea sediments as closest relatives, some of which being distantly related to free-living and symbiotic sulfur-oxidizers. Other sequences clustered in the alpha-, delta- and epsilon-Proteobacteria, the 'Bacteroidetes', the 'Planctomycetes', the 'Nitrospirae', the 'Actinobacteria', the 'Chlorobi ' and the 'Verrumicrobia'. Based on clonal abundance and sequence comparisons, phylotype groups putatively involved in the oxydation of sulfur compounds appeared to dominate in the studied sample. The majority of the archaeal sequences clustered in an euryarchaeotic lineage recently identified in the walls of black smokers suggesting a possible thermophilic way of life of these uncultured microorganisms. Oxygen isotopic composition of siderite and dolomite indicated that they were formed at 67 degrees C and 94 degrees C respectively. Together with chemical and microbiological data, this suggested that hydrothermal fluids may have circulated through this sediment.

Archaea↗

PubMed2023

Active learning of enhancer and silencer regulatory grammar in photoreceptors.

Cis-regulatory elements (CREs) direct gene expression in health and disease, and models that can accurately predict their activities from DNA sequences are crucial for biomedicine. Deep learning represents one emerging strategy to model the regulatory grammar that relates CRE sequence to function. However, these models require training data on a scale that exceeds the number of CREs in the genome. We address this problem using active machine learning to iteratively train models on multiple rounds of synthetic DNA sequences assayed in live mammalian retinas. During each round of training the model actively selects sequence perturbations to assay, thereby efficiently generating informative training data. We iteratively trained a model that predicts the activities of sequences containing binding motifs for the photoreceptor transcription factor Cone-rod homeobox (CRX) using an order of magnitude less training data than current approaches. The model's internal confidence estimates of its predictions are reliable guides for designing sequences with high activity. The model correctly identified critical sequence differences between active and inactive sequences with nearly identical transcription factor binding sites, and revealed order and spacing preferences for combinations of motifs. Our results establish active learning as an effective method to train accurate deep learning models of cis-regulatory function after exhausting naturally occurring training examples in the genome.

Journal Article↗

PubMed1989

Growth-rate-dependent regulation of 6-phosphogluconate dehydrogenase level mediated by an anti-Shine-Dalgarno sequence located within the Escherichia coli gnd structural gene.

Previous work has shown that in Escherichia coli K-12 growth-rate-dependent regulation of expression of 6-phosphogluconate dehydrogenase, encoded by the gnd gene, occurs at the posttranscriptional level and is mediated by a negative control element that lies deep in the coding sequence, somewhere between codons 48 and 118. Deletion analysis of a growth-rate-regulated gnd-lacZ translational fusion showed that the element is the segment of gnd mRNA between codons 67 and 78 that is complementary to an extensive portion of the gnd ribosome-binding site, including its Shine-Dalgarno sequence. The boundaries of the element were further defined by the cloning of a synthetic "internal complementary sequence." The core internal complementary sequence element effected growth-rate-dependent regulation when placed at several sites between codon 40 and codon 69, but it severely reduced gene expression when moved to codon 13. The effect on regulation of single and double mutations introduced into the element by site-directed mutagenesis correlated with the ability of the respective mRNAs to fold into secondary structures that sequester the ribosome-binding site. Thus the gnd gene's internal regulatory element appears to function as a cis-acting antisense RNA.

Base Sequence↗

PubMed2004

Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences.

The Mollusca represent one of the most morphologically diverse animal phyla, prompting a variety of hypotheses on relationships between the major lineages within the phylum based upon morphological, developmental, and paleontological data. Analyses of small-ribosomal RNA (SSU rRNA) gene sequence have provided limited resolution of higher-level relationships within the Mollusca. Recent analyses suggest large-subunit (LSU) rRNA gene sequences are useful in resolving deep-level metazoan relationships, particularly when combined with SSU sequence. To this end, LSU (approximately 3.5 kb in length) and SSU (approximately 2 kb) sequences were collected for 33 taxa representing the major lineages within the Mollusca to improve resolution of intraphyletic relationships. Although the LSU and combined LSU+SSU datasets appear to hold potential for resolving branching order within the recognized molluscan classes, low bootstrap support was found for relationships between the major lineages within the Mollusca. LSU+SSU sequences also showed significant levels of rate heterogeneity between molluscan lineages. The Polyplacophora, Gastropoda, and Cephalopoda were each recovered as monophyletic clades with the LSU+SSU dataset. While the Bivalvia were not recovered as monophyletic clade in analyses of the SSU, LSU, or LSU+SSU, the Shimodaira-Hasegawa test showed that likelihood scores for these results did not differ significantly from topologies where the Bivalvia were monophyletic. Analyses of LSU sequences strongly contradict the widely accepted Diasoma hypotheses that bivalves and scaphopods are closely related to one another. The data are consistent with recent morphological and SSU analyses suggesting scaphopods are more closely related to gastropods and cephalopods than to bivalves. The dataset also presents the first published DNA sequences from a neomeniomorph aplacophoran, a group considered critical to our understanding of the origin and early radiation of the Mollusca.

Animals↗

PubMed2004

Reinekea marinisedimentorum gen. nov., sp. nov., a novel gammaproteobacterium from marine coastal sediments.

A Gram-negative, oxidase- and catalase-positive, rod-shaped bacterium, designated strain KMM 3655(T), was isolated from a coastal marine sediment sample. The novel bacterium required sodium ions for growth and grew between 0.5 and 5 % NaCl and at 4-37 degrees C, but not at 40 degrees C. It reduced nitrate, formed acids from glucose under aerobic and anaerobic conditions, utilized a limited spectrum of organic substrates and did not produce gelatinase, caseinase, amylase or chitinase. The major isoprenoid quinone was Q8. Polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. Fatty acid analysis of strain KMM 3655(T) revealed C(16 : 0), C(16 : 1)omega7c and C(18 : 1)omega7c as predominant components. The G+C content of the DNA was 51.1 mol%. Phylogenetic analysis of the 16S rDNA sequence placed the new isolate within the gamma-Proteobacteria as a separate deep branch, with about 90 % sequence similarity to representatives of the genus Oceanospirillum and other remotely related genera. Combined phylogenetic and physiological data show that the new marine sediment isolate, KMM 3655(T), represents a novel genus and species, for which the name Reinekea marinisedimentorum gen. nov., sp. nov. is proposed. The type strain is KMM 3655(T) (=DSM 15388(T)).

Base Composition↗