The Convective Transport of Active Species in the Tropics (CONTRAST) Experiment.

The Convective Transport of Active Species in the Tropics (CONTRAST) experiment was conducted from Guam (13.5° N, 144.8° E) during January-February 2014. Using the NSF/NCAR Gulfstream V research aircraft, the experiment investigated the photochemical environment over the tropical western Pacific (TWP) warm pool, a region of massive deep convection and the major pathway for air to enter the stratosphere during Northern Hemisphere (NH) winter. The new observations provide a wealth of information for quantifying the influence of convection on the vertical distributions of active species. The airborne in situ measurements up to 15 km altitude fill a significant gap by characterizing the abundance and altitude variation of a wide suite of trace gases. These measurements, together with observations of dynamical and microphysical parameters, provide significant new data for constraining and evaluating global chemistry climate models. Measurements include precursor and product gas species of reactive halogen compounds that impact ozone in the upper troposphere/lower stratosphere. High accuracy, in-situ measurements of ozone obtained during CONTRAST quantify ozone concentration profiles in the UT, where previous observations from balloon-borne ozonesondes were often near or below the limit of detection. CONTRAST was one of the three coordinated experiments to observe the TWP during January-February 2014. Together, CONTRAST, ATTREX and CAST, using complementary capabilities of the three aircraft platforms as well as ground-based instrumentation, provide a comprehensive quantification of the regional distribution and vertical structure of natural and pollutant trace gases in the TWP during NH winter, from the oceanic boundary to the lower stratosphere.

Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study.

The analysis of volatile organic compounds (VOC) as biomarkers of cancer is both promising and challenging. In this pilot study, we used an untargeted approach to compare volatile metabolomic signatures of melanoma and matched control non-neoplastic skin from the same patient. VOC from fresh (non-fixed) biopsied tissue were collected using the headspace solid phase micro extraction method (HS SPME) and analyzed by gas chromatography and mass spectrometry (GCMS). We applied the XCMS analysis platform and MetaboAnalyst software to reveal many differentially expressed metabolic features. Our analysis revealed increased levels of lauric acid (C12:0) and palmitic acid (C16:0) in melanoma. The identity of these compounds was confirmed by comparison with chemical standards. Increased levels of these fatty acids are likely to be a consequence of up-regulated de novo lipid synthesis, a known characteristic of cancer. Increased oxidative stress is likely to cause an additional increase in lauric acid. Implementation of this study design on larger number of cases will be necessary for the future metabolomics biomarker discovery applications.

Intercomparison of volatile organic carbon measurement techniques and data at La Porte during the TexAQS2000 Air Quality Study.

The Texas Air Quality Study 2000 (TexAQS2000) investigated the photochemical production of ozone and the chemistry of related precursors and reaction products in the vicinity of Houston, TX. The colocation of four instruments for the measurement of volatile organic carbon compounds (VOCs) allowed a unique opportunity for the intercomparison of the different in-situ measuring techniques. The instruments included three gas chromatographs, each with a different type of detector, and a Proton-Transfer-Reaction Mass Spectrometer (PTR-MS) with each system designed to measure a different suite of VOCs. Correlation plots and correlation statistics are presented for species measured by more than one of these instruments. The GC instruments were all in agreement to within 10-20% (slope) with coefficients of variation (r2) of > or = 0.85. The PTR-MS agreement with other instruments was more dependent on species with some very good agreements (r2 values of approximately 0.95 for some aromatics), but isoprene, acetaldehyde and propene were substantially less highly correlated (0.55 < r2 < 0.80). At least part of these differences were undoubtedly due to the timing of sample acquisition in an environment in which VOC levels changed very rapidly on both quantitative and temporal scales.

The role of integrated myocardial management in reoperative coronary surgery.

This article identifies the effect of integrated myocardial protection on outcomes after first-time repeat coronary artery bypass grafting (CABG). A consecutive series of 124 repeat CABG procedures were performed between January 1996 and December 1999 with single aortic cross-clamping for all anastomoses and integrated myocardial protection. This included ischemia for heart dissection and distal grafting, and perfusion throughout the remainder of aortic clamping (including warm/cold, substrate/nonsubstrate-enhanced blood cardioplegia, delivered antegrade/retrograde, continuously/intermittently). Mean patient age was 67 +/ - 10 years (median 68) with 61% in New York Heart Association class IV and 23% in class III. Mean ejection fraction (EF) was 45 +/- 10.6% with EF 40% or less in 33% of patients and 30% or less in 20%. An average of 2.5 +/- 0.9 grafts were constructed. Cross-clamp times averaged 72 +/- 22 min and cardiopulmonary bypass time averaged 91 +/- 27 min. The average time from release of cross-clamp it disconnection from cardiopulmonary bypass (CPB) was 10 min. Median postoperative hospital stay was 6 days. hospital mortality was 2.4%, intra-aortic balloon pump (IABP) use 3.2%, stroke 0.8%, atrial fibrillation 11%, and reexploration for bleeding 2.4%. Integrated myocardial protection with blood cardioplegia is safe during reoperative coronary surgery. It allows rapid separation from CPB, limited IABP use, and low morbidity and mortality.

Essential roles for Caenorhabditis elegans lamin gene in nuclear organization, cell cycle progression, and spatial organization of nuclear pore complexes.

Caenorhabditis elegans has a single lamin gene, designated lmn-1 (previously termed CeLam-1). Antibodies raised against the lmn-1 product (Ce-lamin) detected a 64-kDa nuclear envelope protein. Ce-lamin was detected in the nuclear periphery of all cells except sperm and was found in the nuclear interior in embryonic cells and in a fraction of adult cells. Reductions in the amount of Ce-lamin protein produce embryonic lethality. Although the majority of affected embryos survive to produce several hundred nuclei, defects can be detected as early as the first nuclear divisions. Abnormalities include rapid changes in nuclear morphology during interphase, loss of chromosomes, unequal separation of chromosomes into daughter nuclei, abnormal condensation of chromatin, an increase in DNA content, and abnormal distribution of nuclear pore complexes (NPCs). Under conditions of incomplete RNA interference, a fraction of embryos escaped embryonic arrest and continue to develop through larval life. These animals exhibit additional phenotypes including sterility and defective segregation of chromosomes in germ cells. Our observations show that lmn-1 is an essential gene in C. elegans, and that the nuclear lamins are involved in chromatin organization, cell cycle progression, chromosome segregation, and correct spacing of NPCs.

Tunicates have unusual nuclear lamins with a large deletion in the carboxyterminal tail domain.

Lamins are essential proteins of metazoa. They give rise to the nuclear lamina lining the nucleoplasmic face of the inner nuclear membrane. Here we report the isolation of complete lamin cDNA clones from three urochordate (tunicate) libraries - adult Ciona intestinalis, the tailbud stage of Styela clava and the gastrula stage of Molgula oculata. Lamins L1 and L2 of adult Ciona are derived from two distinct genes. The sequence of the 3' part of the Ciona lamin L1 gene shows that the alpha and beta variants of lamin L1 in Ciona and Styela arise by alternative choice of the 5' splice site at the last intron. Strikingly, all urochordate sequences reveal a 90 residue deletion which removes nearly the entire 105-box. This region is the only long sequence homology segment in the carboxyterminal tail domain of lamins from animals as diverse as Hydra, Drosophila, Priapulus, Caenorhabditis elegans, several echinoderms, the cephalochordate Branchiostoma and various vertebrates. We discuss this unexpected plasticity of lamin sequences as a urochordate specific marker. To increase the database for the chordates we completed the partial sequence of the Branchiostoma lamin by the N-terminal head and central rod domains. The molecular phylogenetic analysis of the metazoan lamin sequences emphasises the monophyletic nature of the chordates in line with the morphological evidence.

The epidermal intermediate filament proteins of tunicates are distant keratins; a polymerisation-competent hetero coiled coil of the Styela D protein and Xenopus keratin 8.

Two novel cytoplasmic intermediate filament (IF) proteins (C and D) from the tunicate (urochordate) Styela are characterised as putative keratin orthologs. The coexpression of C and D in all epidermal cells and the obligatory heteropolymeric IF assembly of the recombinant proteins argue for keratin orthologs, but the sequences do not directly reveal which protein behaves as a keratin I or II ortholog. This problem is solved by the finding that keratin 8, a type II keratin from man or Xenopus, forms chimeric IF when mixed with Styela D. Mutant proteins of Styela D and keratin 8 with a single cysteine in equivalent positions show that these chimeric IF are, like vertebrate keratin filaments, based on the hetero coiled coil. We propose that Styela D retains, in spite of its strong sequence drift, important molecular features of type I keratins. By inference Styela C reflects a type II ortholog. We discuss that type I to III IF proteins are expressed along the chordate branch of metazoa.

Characterisation and tissue-specific expression of the two keratin subfamilies of intermediate filament proteins in the cephalochordate Branchiostoma.

The cloning of three intermediate filament proteins expressed at the gastrula stage (kl, Y1, X1) extends the size of the IF multigene family of Branchiostoma to at least 13 members. This is one of the largest protein families established for the lancelet. Sequence comparisons indicate five keratin orthologs, three of type I (E1, k1, Y1) and two of type II (E2, D1). This assignment is confirmed by the obligatory heteropolymeric polymerisation behaviour of the recombinant proteins. In line with the hetero-coiled-coil principle IF are formed by any stoichiometric mixture of type I and II keratin orthologs. In spite of the strong sequence drift chimeric IF are formed between K8, a human keratin II, and two of the lancelet type I keratins. We discuss whether the remaining 8 IF proteins reflect three additional and potentially cephalochordate-specific subfamilies. The tissue-specific expression patterns of the 5 keratins and some other IF proteins were analysed by immunofluorescence in the adult. Keratins are primarily present in ectodermally derived tissues. Developmental control of the expression of some IF proteins is observed, but three keratins (k1, Y1, D1) and an additional IF protein (X1) detected at the gastrula stage are expressed throughout the life cycle.

Translocation of C. elegans CED-4 to nuclear membranes during programmed cell death.

The Caenorhabditis elegans Bcl-2-like protein CED-9 prevents programmed cell death by antagonizing the Apaf-1-like cell-death activator CED-4. Endogenous CED-9 and CED-4 proteins localized to mitochondria in wild-type embryos, in which most cells survive. By contrast, in embryos in which cells had been induced to die, CED-4 assumed a perinuclear localization. CED-4 translocation induced by the cell-death activator EGL-1 was blocked by a gain-of-function mutation in ced-9 but was not dependent on ced-3 function, suggesting that CED-4 translocation precedes caspase activation and the execution phase of programmed cell death. Thus, a change in the subcellular localization of CED-4 may drive programmed cell death.

Characterization of the Hydra lamin and its gene: A molecular phylogeny of metazoan lamins.

We report sequences for nuclear lamins from the teleost fish Danio and six invertebrates. These include two cnidarians (Hydra and Tealia), one priapulid, two echinoderms, and the cephalochordate Branchiostoma. Combining these results with earlier data on Drosophila, Caenorhabditis elegans, and various vertebrates, the following conclusions on lamin evolution can be drawn. First, all invertebrate lamins resemble in size the vertebrate B-type lamin. Second, all lamins described previously for amphibia, birds and mammals as well as the first lamin of a fish, characterized here, show a cluster of 7 to 12 acidic residues in the tail domain. Since this acidic cluster is absent from all invertebrate lamins including that of the cephalochordate Branchiostoma, it was acquired with the vertebrate lineage. The larger A-type lamin of differentiated cells must have arisen subsequently by gene duplication and insertion of an extra exon. This extra exon of the vertebrate A-lamins is the only major change in domain organization in metazoan lamin evolution. Third, the three introns of the Hydra and Priapulus genes correspond in position to the last three introns of vertebrate B-type lamin genes. Thus the entirely different gene organization of the C. elegans and Drosophila Dmo genes seems to reflect evolutionary drift, which probably also accounts for the fact that C. elegans has the most diverse lamin sequence. Finally we discuss the possibility that two lamin types, a constitutively expressed one and a developmentally regulated one, arose independently on the arthropod and vertebrate lineages.

Molecular phylogeny of metazoan intermediate filament proteins.

We have cloned cytoplasmic intermediate filament (IF) proteins from a large number of invertebrate phyla using cDNA probes, the monoclonal antibody IFA, peptide sequence information, and various RT-PCR procedures. Novel IF protein sequences reported here include the urochordata and nine protostomic phyla, i.e., Annelida, Brachiopoda, Chaetognatha, Echiura, Nematomorpha, Nemertea, Platyhelminthes, Phoronida, and Sipuncula. Taken together with the wealth of data on IF proteins of vertebrates and the results on IF proteins of Cephalochordata, Mollusca, Annelida, and Nematoda, two IF prototypes emerge. The L-type, which includes 35 sequences from 11 protostomic phyla, shares with the nuclear lamins the long version of the coil 1b subdomain and, in most cases, a homology segment of some 120 residues in the carboxyterminal tail domain. The S-type, which includes all four subfamilies (types I to IV) of vertebrate IF proteins, lacks 42 residues in the coil 1b subdomain and the carboxyterminal lamin homology segment. Since IF proteins from all three phyla of the chordates have the 42-residue deletion, this deletion arose in a progenitor prior to the divergence of the chordates into the urochordate, cephalochordate, and vertebrate lineages, possibly already at the origin of the deuterostomic branch. Four phyla recently placed into the protostomia on grounds of their 18S rDNA sequences (Brachiopoda, Nemertea, Phoronida, and Platyhelminthes) show IF proteins of the L-type and fit by sequence identity criteria into the lophotrochozoic branch of the protostomia.

Homologues of vertebrate type I, II and III intermediate filament (IF) proteins in an invertebrate: the IF multigene family of the cephalochordate Branchiostoma.

We searched for functional homologues of the four subfamilies of vertebrate cytoplasmic intermediate filament (IF) proteins in the cephalochordate Branchiostoma. The epidermis contains in addition to IF proteins C2 and D1 two novel IF proteins E1 and E2. Both sequence comparisons as well as the obligatory heteropolymer formation by the recombinant proteins identify E1 as a type I keratin and E2 and D1 as type II keratins. In contrast the non-epidermal B1 forms as type III homologue homopolymeric IF. We propose that type I-III diversification of IF proteins is a property of the chordate branch of metazoa and discuss a possible origin of type IV neurofilaments.

Common and variant properties of intermediate filament proteins from lower chordates and vertebrates; two proteins from the tunicate Styela and the identification of a type III homologue.

The chordates combine the vertebrates and the invertebrate phyla of the cephalo- and urochordates (tunicates). Two cytoplasmic intermediate filament (IF) proteins of the urochordate Styela plicata are characterized by cDNA cloning, gene organization, tissue specific expression patterns in the adult animal and the self assembly properties of the recombinant proteins. In line with metazoan phylogeny St-A and St-B have the short length version of the coil 1b domain found in all vertebrate and cephalochordate IF proteins while protostomic IF proteins have the longer length version with an extra 42 residues. St-A is the first IF protein from a lower chordate which can be unambiguously related to a particular vertebrate IF subfamily. St-A shares 46% sequence identity with desmin, displays the N-terminal motif necessary for filament assembly of type III proteins and forms normal homopolymeric 10 nm filaments in vitro. St-A but not St-B is present in smooth muscle cells of the body wall musculature. St-A and St-B are found as separate networks in some interior epithelia. St-B shares 30 to 35% identity with keratin 8, St-A and desmin and does not form IF under in vitro assembly conditions. Its relation to a particular vertebrate IF type or to the eight currently known IF proteins from the cephalochordate Branchiostoma remains unresolved. The striking relation between St-A and desmin predicts that the common progenitor of the urochordate (tunicate) and the cephalochordate/vertebrate lineages already possessed a type III homologue. Unlike in vertebrates intron patterns cannot be used to classify the tunicate IF genes. Although St-A is a type III homologue its gene shows an intron position which in vertebrates is restricted to keratin type II genes.

Analysis of eight cDNAs and six genes for intermediate filament (IF) proteins in the cephalochordate Branchiostoma reveals differences in the IF multigene families of lower chordates and the vertebrates.

We report the sequences of seven new cytoplasmic intermediate filament (IF) proteins of the cephalochordate Branchiostoma. The eight sequences currently known describe four subfamilies (A, B, C and D). All eight IF proteins show the short-length version of the coil 1b subdomain found in vertebrates and lack the additional 42 residues present in all nuclear lamins and the protostomic IF proteins. Although the lancelet is considered to be the closest relative of the vertebrates, it is difficult to relate its IF subfamilies unambiguously to a particular type I-IV subfamily of vertebrates. C1 and C2 have tail domains with two 64 residue repeats of coiled coil-forming ability, a structural feature unknown for IF proteins from vertebrates or protostomia. The epidermal protein D1 shows only a slightly better identity score with vertebrate type II keratins than with type III proteins, but the D1 gene organization is that of type III proteins. The same holds for A1, A2, B1, B2 and C2 genes, although the latter has an additional and uniquely positioned intron. Antibodies (Ab) raised against recombinant C2 and D1 proteins reveal these proteins in epidermis, some internal epithelia and parts of the spinal cord. The results on exonic sequences, gene organization and expression suggest that Branchiostoma IF proteins may retain a largely archetypal condition, whereas the vertebrates have established the well-known type I-IV IF system.

The single calmodulin gene of the cephalochordate Branchiostoma.

The cDNA and gene for calmodulin (CaM) from the cephalochordate Branchiostoma were isolated and characterized. The nucleotide sequence of the Branchiostoma CaM cDNA is about 80% identical to the CaM of Drosophila and Aplysia. However, all nucleotide substitutions are silent, therefore the amino acid sequences of all these CaMs are identical. Branchiostoma and Aplysia CaM genes have the same exon/intron organization. PCR, Northern and genomic Southern analyses showed that Branchiostoma CaM is encoded by a single copy gene, while fish are known to have at least four CaM genes. These results fit the hypothesis that major gene duplication events occurred close to the origin of vertebrates, i.e., after the divergence of the cephalochordate lineage.

Expression of Drosophila lamin C is developmentally regulated: analogies with vertebrate A-type lamins.

Vertebrate nuclear lamins form a multigene family with developmentally controlled expression. In contrast, invertebrates have long been thought to contain only a single lamin, which in Drosophila is the well-characterized lamin Dm0. Recently, however, a Drosophila cDNA clone (pG-IF) has been identified that codes for an intermediate filament protein which harbors a nuclear localization signal but lacks a carboxy-terminal CAAX motif. Based on these data the putative protein encoded by pG-IF was tentatively called Drosophila lamin C. To address whether the pG-IF encoded protein is expressed and whether it encodes a cytoplasmic intermediate filament protein or a nuclear lamin we raised antibodies against the recombinant pG-IF protein. The antibodies decorate the nuclear envelope in Drosophila Kc tissue culture cells as well as in salivary and accessory glands demonstrating that pG-IF encodes a nuclear lamin (lamin C). Antibody decoration, in situ hybridization, western and northern blotting studies show that lamin C is acquired late in embryogenesis. In contrast, lamin Dm0 is constitutively expressed. Lamin C is first detected in late stage 12 embryos in oenocytes, hindgut and posterior spiracles and subsequently also in other differentiated tissues. In third instar larvae lamins C and Dm0 are coexpressed in all tissues tested. Thus, Drosophila has two lamins: lamin Dm0, containing a CaaX motif, is expressed throughout, while lamin C, lacking a CaaX motif, is expressed only later in development. Expression of Drosophila lamin C is similar to that of vertebrate lamin A (plus C), which loses its CaaX motif during incorporation into the lamina.

The sequence of a cytoplasmic intermediate filament (IF) protein from the annelid Lumbricus terrestris emphasizes a distinctive feature of protostomic IF proteins.

The complete cDNA clone for a cytoplasmic intermediate filament (IF) protein from the annelid Lumbricus terrestris reported here, shows an extra 42 residues in the coil 1b subdomain of the central rod, as do the IF proteins from nematodes and molluscs. These extra six heptads are also present in all nuclear lamins but not in any known vertebrate cytoplasmic IF protein. Thus, it seems that protostomic metazoa conserve a lamin-like structural element in their cytoplasmic IF proteins, which was lost in the deuterostomic metazoan branch leading to the vertebrates.

Eight genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmic intermediate filament proteins in the nematode Caenorhabditis elegans.

Cytoplasmic intermediate filament (IF) proteins of Caenorhabditis elegans are encoded by a dispersed multigene family comprising at least eight genes which map to three linkage groups. Exon sequences and intron patterns define three distinct subfamilies. While all eight IF genes display the long coil 1b subdomain of nuclear lamins, only six genes (a1-a4, b1 and b2) retain a lamin-like tail domain. Two genes (c1 and c2) have acquired entirely novel tail domains. The overall sequence identity of the rod domains is only 29%. The gene structures show a strong drift in number and positions of introns, none of which are common to all genes. Individual genes share only one to four intron locations with the Helix aspersa IF gene, but all eight nematode genes together account for nine of the 10 introns of the gastropod gene. All C.elegans IF genes are transcribed and all except gene c2 produce trans-spliced mRNAs. Alternatively spliced mRNAs arise from genes a1, b2 and c2 through several mechanisms acting at the transcriptional and posttranscriptional levels. These involve the alternative use of distinct promoters, polyadenylation sequences and both cis and trans RNA splice sites. The resulting sequence variations are restricted to the non-helical end domains. Minimally 12 distinct IF proteins are encoded by the various mRNAs. Different abundances in mixed-stage nematode populations suggest cell type- and/or stage-specific expression of individual mRNAs.