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John P Sullivan

Publications and source records attributed to John P Sullivan.

9 recordsLinked to original sources
PubMed2006

A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences.

Higher-level relationships among catfishes were investigated by parsimony, maximum likelihood and Bayesian analyses of two nuclear genes across 110 catfish species representing 36 of 37 families and Conorhynchos (family incertae sedis). Analysis of 3660 aligned base pairs from the rag1 and rag2 genes confirms monophyly of Siluriformes, of most siluriform families and of a number of multifamily groups, some recognized, some novel. South American Loricarioidei are recovered as the sistergroup to other catfishes which are divided into Diplomystidae and Siluroidei. This result contrasts with the prevailing hypothesis that Diplomystidae is the sister to all other catfishes. Monophyly of Siluroidei is supported by rag data including a unique three-codon deletion from rag1. Deep within Siluroidei are 12 large, strongly supported groups with poorly resolved interrelationships. Five are single families: Cetopsidae, Plotosidae, Chacidae, Siluridae and Pangasiidae. Four others are monophyletic taxa ranked here as superfamilies: Clarioidea (Clariidae, Heteropneustidae), Arioidea (Ariidae, Anchariidae), Pimelodoidea (Pimelodidae, Pseudopimelodidae, Heptapteridae, Conorhynchos), Ictaluroidea (Ictaluridae, Cranoglanididae). South American Doradoidea (Doradidae, Auchenipteridae) and Aspredinidae are a sistergroup pair. Sisoroidea (without Aspredinidae), Ailia+Laides, Horabagridae, and Bagridae (without Rita) form a large, predominantly Asian clade, "Big Asia." Mochokidae, Malapteruridae, Amphiliidae, Claroteidae, and African schilbids are united as a species-rich African clade, "Big Africa." The three large continental clades, "Big Asia," "Big Africa" and Neotropical Loricarioidei suggest a prevalence of intracontinental diversification of catfishes. South America is the home of the Gymnotiformes, putative sistergroup of catfishes, plus two of the deepest siluriform clades, Loricarioidei and Diplomystidae, thus suggesting an ancient siluriform presence if not origin there. The rag phylogeny does not identify any African-South American catfish clade. The well-known African-Asian relationships within families Clariidae and Bagridae are confirmed, as is the recently found North American-Asian relationship between Ictaluridae and Cranoglanididae.

Africa↗
PubMed2006

Pressure-sensitive paint as a distributed optical microphone array.

Pressure-sensitive paint is presented and evaluated in this article as a quantitative technique for measurement of acoustic pressure fluctuations. This work is the culmination of advances in paint technology which enable unsteady measurements of fluctuations over 10 kHz at pressure levels as low as 125 dB. Pressure-sensitive paint may be thought of as a nano-scale array of optical microphones with a spatial resolution limited primarily by the resolution of the imaging device. Thus, pressure-sensitive paint is a powerful tool for making high-amplitude sound pressure measurements. In this work, the paint was used to record ensemble-averaged, time-resolved, quantitative measurements of two-dimensional mode shapes in an acoustic resonance cavity. A wall-mounted speaker generated nonlinear, standing acoustic waves in a rigid enclosure measuring 216 mm wide, 169 mm high, and 102 mm deep. The paint recorded the acoustic surface pressures of the (1,1,0) mode shape at approximately 1.3 kHz and a sound pressure level of 145.4 dB. Results from the paint are compared with data from a Kulite pressure transducer, and with linear acoustic theory. The paint may be used as a diagnostic technique for ultrasonic tests where high spatial resolution is essential, or in nonlinear acoustic applications such as shock tubes.

Journal Article↗
PubMed2005

In vivo evaluation of tetrahedral amorphous carbon.

The in vivo behavior and tissue reaction to tetrahedral amorphous carbon (ta-C) has been evaluated for periods of up to 6 months in SV129 mice. Two sample types were tested--silicon die coated with ta-C (n = 53) and micromachined particles (n = 40). The coated samples were compared to uncoated silicon die (n = 22). Die samples were implanted subcutaneously, and tissue reaction and capsule formation were evaluated at various time points. Micromachined particles of 1, 3, 10, and 30 microm were injected adjacent to the sciatic nerve, and tissue samples were examined histologically at various time points (4 days-6 months). Tissue reaction to ta-C was mild and was localized to the area of the injection or implantation. Samples with a higher ratio of 3-fold bonding appeared to shed material during the experiments; this was not observed on samples with a higher level of 4-fold bonding, nor on uncoated silicon die. The results strongly suggest that films with greater 4-fold bonding character (more diamond-like) are more resistant to in vivo fragmentation than films with higher 3-fold character (more graphitic).

Animals↗
PubMed2004

Experimental demonstration of a laterally deformable optical nanoelectromechanical system grating transducer.

We experimentally demonstrate operation of a laterally deformable optical nanoelectromechanical system grating transducer. The device is fabricated in amorphous diamond with standard lithographic techniques. For small changes in the spacing of the subwavelength grating elements, lossy propagating resonant modes in the plane of the grating cause a large change in the optical reflection amplitude. An in-plane motion detection sensitivity of 160 fm/square root(Hz) was measured, exceeding that of any other optical microelectromechanical system transducer to our knowledge. Calculations predict that this sensitivity could be improved to better than 40 fm/square root(Hz) in future designs. In addition to having applications in the field of inertial sensors, this device could also be used as an optical modulator.

Journal Article↗
PubMed2004

Functional genomics of cell elongation in developing cotton fibers.

Cotton fibers are single-celled seed trichomes of major economic importance. Factors that regulate the rate and duration of cell expansion control fiber morphology and important agronomic traits. For genetic characterization of rapid cell elongation in cotton fibers, approximately 14,000 unique genes were assembled from 46,603 expressed sequence tags (ESTs) from developmentally staged fiber cDNAs of a cultivated diploid species ( Gossypium arboreum L.). Conservatively, the fiber transcriptome represents 35-40% of the genes in the cotton genome. In silico expression analysis revealed that rapidly elongating fiber cells exhibit significant metabolic activity, with the bulk of gene transcripts, represented by three major functional groups - cell wall structure and biogenesis, the cytoskeleton and energy/carbohydrate metabolism. Oligonucleotide microarrays revealed dynamic changes in gene expression between primary and secondary cell wall biogenesis showing that fiber genes in the dbEST are highly stage-specific for cell expansion - a conclusion supported by the absence of known secondary cell wall-specific genes from our fiber dbEST. During the developmental switch from primary to secondary cell wall syntheses, 2553 "expansion-associated" fiber genes are significantly down regulated. Genes (81) significantly up-regulated during secondary cell wall synthesis are involved in cell wall biogenesis and energy/carbohydrate metabolism, which is consistent with the stage of cellulose synthesis during secondary cell wall modification in developing fibers. This work provides the first in-depth view of the genetic complexity of the transcriptome of an expanding cell, and lays the groundwork for studying fundamental biological processes in plant biology with applications in agricultural biotechnology.

Cell Growth Processes↗
PubMed2004

Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei).

Fishes of the Superorder Osteoglossomorpha (the "bonytongues") constitute a morphologically heterogeneous group of basal teleosts, including highly derived subgroups such as African electric fishes, the African butterfly fish, and Old World knifefishes. Lack of consensus among hypotheses of osteoglossomorph relationships advanced during the past 30 years may be due in part to the difficulty of identifying shared derived characters among the morphologically differentiated extant families of this group. In this study, we present a novel phylogenetic hypothesis for this group, based on the analysis of more than 4000 characters from five molecular markers (the mitochondrial cytochrome b, 12S and 16S rRNA genes, and the nuclear genes RAG2 and MLL). Our taxonomic sampling includes one representative of each extant non-mormyrid osteoglossomorph genus, one representative for the monophyletic family Mormyridae, and four outgroup taxa within the basal Teleostei. Maximum parsimony analysis of combined and equally weighted characters from the five molecular markers and Bayesian analysis provide a single, well-supported, hypothesis of osteoglossomorph interrelationships and show the group to be monophyletic. The tree topology is the following: (Hiodon alosoides, (Pantodon buchholzi, (((Osteoglossum bicirrhosum, Scleropages sp.), (Arapaima gigas, Heterotis niloticus)), ((Gymnarchus niloticus, Ivindomyrus opdenboschi), ((Notopterus notopterus, Chitala ornata), (Xenomystus nigri, Papyrocranus afer)))))). We compare our results with previously published phylogenetic hypotheses based on morpho-anatomical data. Additionally, we explore the consequences of the long terminal branch length for the taxon Pantodon buchholzi in our phylogenetic reconstruction and we use the obtained phylogenetic tree to reconstruct the evolutionary history of electroreception in the Notopteroidei.

Animals↗
PubMed2004

AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei).

Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.

Animal Communication↗
PubMed2002

Discovery and phylogenetic analysis of a riverine species flock of African electric fishes (Mormyridae: Teleostei).

The evolution of species-specific mate recognition signals is of particular interest within speciose monophyletic groups with restricted distributions (known as "species flocks"). However, the explosive nature of speciation in these clades makes difficult the reconstruction of their phylogenetic history. Here we describe a species flock of riverine mormyrid fishes from west-central Africa in which electric signals may play a role in the reproductive isolation of sympatric species. In our recent field collections, totaling more than 1400 specimens from many localities, we recognize 38 forms that are distinct in their morphologies and electric organ discharge (EOD) characteristics. Of these 38, only four clearly correspond to described species. Here we treat these forms as operational taxonomic units (OTUs) in a phylogenetic analysis of cytochrome b sequence data from a sample of 86 specimens. We examined support in the molecular data for the monophyly of these 38 OTUs considered together, the monophyly of each phenotypically delimited OTU considered individually, and for relationships among OTUs congruent with those inferred from the distribution of morphological and EOD character states. Trees obtained by both maximum-parsimony and maximum-likelihood analyses, rooted with sequence data from outgroup taxa, provide evidence for the monophyly of these 38 OTUs with respect to other mormyrid fishes. The small genetic distances between many distinct forms suggest their recent divergence. However, in many instances the cytochrome b tree topology fails to support the monophyly of individual OTUs and close relationships between OTUs that are similar in morphology and EOD characteristics. In other cases, individuals from distinct OTUs share identical or nearly identical haplotypes. Close examination of these cases suggests that unnatural OTU definition is not the sole cause of this pattern, and we infer an incongruence between the mitochondrial gene tree and the organismal phylogeny caused by incomplete mitochondrial lineage sorting and/ or introgression across forms. The apparently rapid diversification in this clade of riverine electric fishes and the problems associated with recovering a meaningful species-level phylogeny from mitochondrial data parallel findings in other species flocks. Selection on EOD waveforms as mate recognition signals may be involved in the radiation of these fishes. This is the first description of a freshwater fish species flock from a riverine, as opposed to a lacustrine, environment.

Animals↗