Phylogenetics of archerfishes (Toxotidae) and evolution of the toxotid shooting apparatus

Archerfishes (Toxotidae) are variously found in the fresh- and brackish-water environments of Asia Pacific and are well known for their ability to shoot water at terrestrial prey. These shots of water are intended to strike their prey and cause it to fall into the water for capture and consumption. While this behavior is well known, there are competing hypotheses (blowpipe vs. pressure tank hypothesis) of how archerfishes shoot and which oral structures are involved. Current understanding of archerfish shooting structures is largely based on two species, Toxotes chatareus and T. jaculatrix. We do not know if all archerfishes possess the same oral structures to shoot water, if anatomical variation is present within these oral structures, or how these features have evolved. Additionally, there is little information on the evolution of the Toxotidae as a whole, with all previous systematic works focusing on the interrelationships of the family. We first investigate the limits of archerfish species using new and previously published genetic data. Our analyses highlight that the current taxonomy of archerfishes does not conform to the relationships we recover. Toxotes mekongensis and T. siamensis are placed in synonymy of T. chatareus, Toxotes carpentariensis is recognized as a species and removed from synonymy of T. chatareus, and the genus Protoxotes is recognized for T. lorentzi based on the results of our analyses. We then take an integrative approach, using a combined analysis of discrete hard- and soft-tissue morphological characters with genetic data, to construct a phylogeny of the Toxotidae. Using the resulting phylogenetic hypothesis, we then characterize the evolutionary history and anatomical variation within the archerfishes. We discuss the variation in the oral structures and the evolution of the mechanism with respect to the interrelationships of archerfishes, and find that the oral structures of archerfishes support the blowpipe hypothesis but soft-tissue oral structures may also play a role in shooting. Finally, by comparing the morphology of archerfishes to their sister group, we find that the Leptobramidae has relevant shooting features in the oral cavity, suggesting that some components of the archerfish shooting mechanism are examples of co-opted or exapted traits.

Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements

Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral-fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.

Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha)

Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.

Anatomy and evolution of bioluminescent organs in the slimeheads (Teleostei: Trachichthyidae)

Bacterial bioluminescent organs in fishes have a diverse range of tissues of origin, patterns of compartmentalization, and associated light-conducting structures. The morphology of the perianal, bacterial bioluminescent organ of Aulotrachichthys prosthemius was described previously, but the light organ in other species of slimeheads, family Trachichthyidae, is poorly known. Here, we describe the anatomy of the bioluminescent organs in trachichthyids and places the evolution of this light-producing system in the context of a new phylogeny of the Trachichthyoidei to test the hypothesis that bioluminescence evolved twice in the suborder and that the light-producing component derives from the perianal ectoderm. We use gross and histological examination to provide the first description of the bioluminescent organ of Paratrachichthys and four additional species of Aulotrachichthys. Observations also strongly suggest the presence of a perianal bioluminescent organ in Sorosichthys ananasa. The updated phylogeny of the Trachichthyoidei is the first to combine morphological and DNA-sequence (11-gene fragments) evidence, and supports a monophyletic Trachichthyidae with component subfamilies Hoplostethinae and Trachichthyinae, supporting continued recognition of the family Anoplogastridae. All bioluminescent trachichthyoids share a similar bioluminescent-organ structure with elongate chambers filled with bacteria and connected to collecting ducts that, in turn, connect to superficial ducts that lead to and have lining epithelia continuous with the epidermis. In the context of the phylogeny, the bioluminescent organ of trachichthyids is inferred to have evolved as an elaboration of the proctodeum in the ancestor of Aulotrachichthys, Paratrachichthys, and Sorosichthys independently from the structurally similar cephalic bioluminescent organs in Anomalopidae and Monocentridae.

The evolution of specialized dentition in the deep-sea lanternfishes (Myctophiformes)

The evolution of heterodonty, the possession of varied tooth morphologies on the jaws of animals, has been relatively unexplored in ray-finned fishes compared to terrestrial vertebrates, and to an even lesser degree in deep-sea fish lineages. Lanternfishes (Myctophiformes) are an abundant and species-rich group endemic to deep-sea pelagic habitats. In this study, we document the presence of heterodonty on the oral jaws of lanternfishes, identifying differing anatomical and positional variations of dentition. We survey the anatomical variation in tooth morphology on the oral jaws of 114 lanternfish species across 37 genera and integrate our findings with a hypothesis of evolutionary relationships of lanternfishes to infer the number of times heterodonty evolved in this lineage. Our results indicate that heterodonty evolved at least six separate times on the oral jaws of lanternfishes, occurring as variable tooth morphologies in combination with villiform teeth. These combinations of tooth types include villiform plus hooked teeth, villiform plus hooked and recurved teeth, villiform plus spade, tricuspid, and hooked teeth, and villiform plus caniniform teeth. The reoccurring evolution of hooked teeth on the premaxilla and dentary in lanternfishes suggests heterodonty may serve an important functional role in their pelagic deep-sea environment. Hooked teeth could aid in securing and retaining prey in the oral cavity and allow for species to specialize on differing food resources, vital attributes for organisms living in open-ocean habitats.

Salamanders and other amphibians are aglow with biofluorescence

Biofluorescence is the absorption of electromagnetic radiation (light) at one wavelength followed by its reemission at a lower energy and longer wavelength by a living organism. Previous studies have documented the widespread presence of biofluorescence in some animals, including cnidarians, arthropods, and cartilaginous and ray-finned fishes. Many studies on biofluorescence have focused on marine animals (cnidarians, cartilaginous and ray-finned fishes) but we know comparatively little about the presence of biofluorescence in tetrapods. We show for the first time that biofluorescence is widespread across Amphibia, with a focus on salamanders (Caudata), which are a diverse group with a primarily Holarctic distribution. We find that biofluorescence is not restricted to any particular family of salamanders, there is striking variation in their fluorescent patterning, and the primary wavelengths emitted in response to blue excitation light are within the spectrum of green light. Widespread biofluorescence across the amphibian radiation is a previously undocumented phenomenon that could have significant ramifications for the ecology and evolution of these diverse and declining vertebrates. Our results provide a roadmap for future studies on the characterization of molecular mechanisms of biofluorescence in amphibians, as well as directions for investigations into the potential impact of biofluorescence on the visual ecology and behavior of biofluorescent amphibians.

The first evidence of intrinsic epidermal bioluminescence within ray-finned fishes in the linebelly swallower Pseudoscopelus sagamianus (Chiasmodontidae)

External and histological examination of the photophores of the linebelly swallower Pseudoscopelus sagamianus reveal three epidermal layers of cells that form the light-producing and light-transmitting components of the photophores. Photophores among the examined photophore tracts are not significantly different in structure but the presence of mucous cells in the superficial layers of the photophore suggest continued function of the epidermal photophore in contributing to the mucous coat. This is the first evidence of intrinsic bioluminescence in primarily epidermal photophores reported in ray-finned fishes.

Impact of hydraulic residence time on nitrate removal in pilot-scale woodchip bioreactors

Nitrate (NO₃^-N) export from row crop agricultural systems with subsurface tile drainage continues to be a major water quality concern. Woodchip bioreactors are an effective edge-of-field practice designed to remove NO₃^-N from tile drainage. The NO₃^-N removal rate of woodchip bioreactors can be impacted by several factors, including hydraulic residence time (HRT). This study examined the impact of three HRTs, 2 h, 8 h, and 16 h, on NO₃^-N removal in a set of nine pilot-scale woodchip bioreactors in Central Iowa. NO₃^-N concentration reduction from the inlet to the outlet was significantly different for all HRTs (p < 0.05). The 16 h HRT removed the most NO₃^-N by concentration (7.5 mg L^-1) and had the highest removal efficiency at 53.8%. The 8 h HRT removed an average of 5.5 mg L^-1 NO₃^-N with a removal efficiency of 32.1%. The 2 h HRT removed an average of 1.3 mg L^-1 NO₃^-N with a removal efficiency of 9.0%. The 2 h HRT had the highest NO₃^-N mass removal rate (MRR) at 9.0 g m^-3 day^-1, followed by the 8 h HRT at 8.5 g m^-3 day^-1, and the 16 h HRT at 7.4 g m^-3 day^-1, all of which were statistically different (p < 0.05). Significant explanatory variables for removal efficiency were HRT (p < 0.001) and influent NO₃^-N concentration (p < 0.001), (R² = 0.80), with HRT accounting for 93% contribution. When paired with results from a companion study, the ideal HRT for the bioreactors was 8 h to achieve maximum NO₃^-N removal while reducing the impact from greenhouse gas emissions.

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences. In brief, miRNAs usually have a well-defined 5′ end and a more flexible 3′ end with the possibility of 3′ tailing events, such as uridylation. Previous approaches to the prediction of novel miRNAs usually involve the analysis of structural features of miRNA precursor hairpin sequences obtained from genome sequence. We surmised that it may be possible to identify miRNAs by using these biogenesis features observed directly from sequenced reads, solely or in addition to structural analysis from genome data. To this end, we have developed mirnovo, a machine learning based algorithm, which is able to identify known and novel miRNAs in animals and plants directly from small RNA-Seq data, with or without a reference genome. This method performs comparably to existing tools, however is simpler to use with reduced run time. Its performance and accuracy has been tested on multiple datasets, including species with poorly assembled genomes, RNaseIII (Drosha and/or Dicer) deficient samples and single cells (at both embryonic and adult stage).

A high-resolution mRNA expression time course of embryonic development in zebrafish

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis

MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs. Herein, we focus on Human and Mouse for which the majority of data are available. We reanalyse sequencing data from 461 samples into a coordinated catalog of microRNA expression. We use this to perform large-scale analyses of miRNA function and biogenesis. These analyses include global expression comparison, co-expression of miRNA clusters and the prediction of miRNA strand-specificity and underlying constraints. Additionally, we report for the first time a global analysis of miRNA epi-transcriptomic modifications and assess their prevalence across tissues, samples and families. Finally, we report a list of potentially mis-annotated miRNAs in miRBase based on their aggregated modification profiles. The results have been collated into a comprehensive online repository of miRNA expression and features such as modifications and RNA editing events, which is available at: http://wwwdev.ebi.ac.uk/enright-dev/miratlas. We believe these findings will further contribute to our understanding of miRNA function in animals and benefit the miRNA community in general.

Relationship between residual feed intake and lymphocyte mitochondrial complex protein concentration and ratio in crossbred steers

Rate of oxygen uptake by muscle mitochondria and respiratory chain protein concentrations differed between high- and low-residual feed intake (RFI) animals. The hypothesis of this research was that complex I (CI), II (CII), and III (CIII) mitochondria protein concentrations in lymphocyte (blood) mitochondria were related to the RFI phenotype of beef steers. Daily feed intake (ADFI) was individually recorded for 92 Hereford-crossbreed steers over 63 d using GrowSafe individual feed intake system. Predicted ADFI was calculated as the regression of ADFI on ADG and midtest BW. Difference between ADFI and predicted ADFI was RFI. Lymphocytes were isolated from low-RFI (-1.32 ± 0.11 kg/d; = 10) and high-RFI (1.34 ± 0.18 kg/d; = 8) steers. Immunocapture of CI, CII, and CIII proteins from the lymphocyte was done using MitoProfile CI, CII, and CIII immunocapture kits (MitoSciences Inc., Eugene, OR). Protein concentrations of CI, CII, and CIII and total protein were quantified using bicinchoninic acid colorimetric procedures. Low-RFI steers consumed 30% less ( = 0.0004) feed and had a 40% improvement ( < 0.0001) in feed efficiency compared with high-RFI steers with similar growth ( = 0.78) and weight measurements ( > 0.65). High- and low-RFI steers did not differ in CI ( = 0.22), CII ( = 0.69), and CIII ( = 0.59) protein concentrations. The protein concentration ratios for CI to CII ( = 0.03) were 20% higher and the ratios of CI to CIII ( = 0.01) were 30% higher, but the ratios of CII to CIII ( = 0.89) did not differ when comparing low-RFI steers with high-RFI steers. The similar magnitude difference in feed intake, feed efficiency measurements, and CI-to-CIII ratio between RFI phenotypes provides a plausible explanation for differences between the phenotypes. We also concluded that mitochondria isolated from lymphocytes could be used to study respiratory chain differences among differing RFI phenotypes. Further research is needed to determine if lymphocyte mitochondrial complex proteins can be used for identification of RFI phenotype.

Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution

Spermatogenesis is associated with major and unique changes to chromosomes and chromatin. Here, we sought to understand the impact of these changes on spermatogenic transcriptomes. We show that long terminal repeats (LTRs) of specific mouse endogenous retroviruses (ERVs) drive the expression of many long non‐coding transcripts (lncRNA). This process occurs post‐mitotically predominantly in spermatocytes and round spermatids. We demonstrate that this transposon‐driven lncRNA expression is a conserved feature of vertebrate spermatogenesis. We propose that transposon promoters are a mechanism by which the genome can explore novel transcriptional substrates, increasing evolutionary plasticity and allowing for the genesis of novel coding and non‐coding genes. Accordingly, we show that a small fraction of these novel ERV‐driven transcripts encode short open reading frames that produce detectable peptides. Finally, we find that distinct ERV elements from the same subfamilies act as differentially activated promoters in a tissue‐specific context. In summary, we demonstrate that LTRs can act as tissue‐specific promoters and contribute to post‐mitotic spermatogenic transcriptome diversity.

The taxonomic placement of three fossil <i>Fundulus</i> species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)

The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53-23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys.

Repeated and Widespread Evolution of Bioluminescence in Marine Fishes

Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.

Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology

Biofluorescence has recently been found to be widespread in marine fishes, including sharks. Catsharks, such as the Swell Shark (Cephaloscyllium ventriosum) from the eastern Pacific and the Chain Catshark (Scyliorhinus retifer) from the western Atlantic, are known to exhibit bright green fluorescence. We examined the spectral sensitivity and visual characteristics of these reclusive sharks, while also considering the fluorescent properties of their skin. Spectral absorbance of the photoreceptor cells in these sharks revealed the presence of a single visual pigment in each species. Cephaloscyllium ventriosum exhibited a maximum absorbance of 484 ± 3 nm and an absorbance range at half maximum (λ1/2max) of 440-540 nm, whereas for S. retifer maximum absorbance was 488 ± 3 nm with the same absorbance range. Using the photoreceptor properties derived here, a "shark eye" camera was designed and developed that yielded contrast information on areas where fluorescence is anatomically distributed on the shark, as seen from other sharks' eyes of these two species. Phylogenetic investigations indicate that biofluorescence has evolved at least three times in cartilaginous fishes. The repeated evolution of biofluorescence in elasmobranchs, coupled with a visual adaptation to detect it; and evidence that biofluorescence creates greater luminosity contrast with the surrounding background, highlights the potential importance of biofluorescence in elasmobranch behavior and biology.

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells

The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-γ) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-γ bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-γ/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-γ/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system.

Maintenance energy requirements of beef cows and relationship with cow and calf performance, metabolic hormones, and functional proteins

Gestating Angus, nonlactating, spring-calving cows were used to determine variation in maintenance energy requirements (MR); to evaluate the relationship among MR and cow and calf performance, plasma concentrations of IGF-I, T4, glucose, insulin, and ruminal temperature; and to describe the LM proteome and evaluate protein abundance in cows with different MR. Cows (4 to 7 yr of age) with a BCS of 5.0 ± 0.2 and BW of 582 ± 37 kg in the second to third trimester of gestation were studied in 3 trials (trial 1, n = 23; trial 2, n = 32; trial 3, n = 38). Cows were individually fed a complete diet in amounts to meet predicted MR (Level 1 Model of NRC), and feed intake was adjusted weekly until constant BW was achieved for at least 21 d (maintenance). Cows were classified on the basis of MR as low (>0.5 SD less than mean, LMR), moderate (±0.5 SD of mean, MMR), or high (>0.5 SD more than mean, HMR) MR. Blood samples were taken at maintenance and at 2 mo postpartum in trial 2. Muscle biopsies were taken from LMR and HMR after cows consumed actual MR for 28 d (trial 2) or 21 d (trial 3). Proteins from LM were separated by 2-dimensional difference gel electrophoresis and were identified, and abundance was quantified and compared. The greatest differences in MR between cows were 29%, 24%, and 25% in trials 1, 2, and 3, respectively. Daily MR (NEm, kcal·BW(-0.75)·d(-1)) averaged 89.2 ± 6.3, 93.0 ± 4.9, and 90.4 ± 4.6 in trials 1, 2, and 3, respectively. Postpartum BW and BCS, calf birth and weaning weights, postpartum luteal activity, and ruminal temperature were not influenced by MR of the cows. Concentrations of IGF-I were greater (P = 0.001) in plasma of MMR compared with LMR cows consuming predicted MR diets, and MR was negatively correlated with concentrations of IGF-I in plasma (r = -0.38; P = 0.05) at 2 mo postpartum. A total of 103 proteins were isolated from LM; 52 gene products were identified. Abundance of specific proteins in the LM was not influenced (P > 0.11) by MR. Variation in MR of cows will make it possible to improve feed efficiency by selection. Identification of biomarkers for MR will allow selection of more efficient cows, which consume less feed and produce calves with similar weaning weights. Productive cows that require less feed for maintenance will improve efficiency of production and enhance sustainability of the environment.

Species-specific bioluminescence facilitates speciation in the deep sea

The vast darkness of the deep sea is an environment with few obvious genetic isolating barriers, and little is known regarding the macroevolutionary processes that have shaped present-day biodiversity in this habitat. Bioluminescence, the production and emission of light from a living organism through a chemical reaction, is thought to occur in approximately 80 % of the eukaryotic life that inhabits the deep sea (water depth greater than 200 m). In this study, we show, for the first time, that deep-sea fishes that possess species-specific bioluminescent structures (e.g., lanternfishes, dragonfishes) are diversifying into new species at a more rapid rate than deep-sea fishes that utilize bioluminescence in ways that would not promote isolation of populations (e.g., camouflage, predation). This work adds to our understanding of how life thrives and evolution shaped present-day biodiversity in the deep sea, the largest and arguably least explored habitat on earth.

The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon

The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.

Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae)

The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.

The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites

We show using the most complete phylogeny of one of the most species-rich orders of vertebrates (Gobiiformes), and calibrations from the rich fossil record of teleost fishes, that the genus Typhleotris, endemic to subterranean karst habitats in southwestern Madagascar, is the sister group to Milyeringa, endemic to similar subterranean systems in northwestern Australia. Both groups are eyeless, and our phylogenetic and biogeographic results show that these obligate cave fishes now found on opposite ends of the Indian Ocean (separated by nearly 7,000 km) are each others closest relatives and owe their origins to the break up of the southern supercontinent, Gondwana, at the end of the Cretaceous period. Trans-oceanic sister-group relationships are otherwise unknown between blind, cave-adapted vertebrates and our results provide an extraordinary case of Gondwanan vicariance.

VUV photoabsorption spectroscopy of sulfur dioxide ice

In this paper we present the first study of the VUV photoabsorption spectrum of condensed phase SO(2) recorded over the VUV region 120 to 320 nm (10.33 to 3.64 eV). Distinct spectral features were observed that can be used to distinguish between the formation of amorphous and crystalline ice structures. These signatures may then be used to probe the formation of different ice structures as a function of both deposition rate and substrate temperature.

A genome annotation-driven approach to cloning the human ORFeome

We have developed a systematic approach to generating cDNA clones containing full-length open reading frames (ORFs), exploiting knowledge of gene structure from genomic sequence. Each ORF was amplified by PCR from a pool of primary cDNAs, cloned and confirmed by sequencing. We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined.

Trends in antimicrobial prescribing for bronchitis and upper respiratory infections among adults and children

OBJECTIVES

This study examined antimicrobial prescribing patterns for adults and children with bronchitis or upper respiratory infections (URIs) before and after release of nationally disseminated pediatric practice recommendations.

METHODS

Data from the 1993, 1995, 1997, and 1999 National Ambulatory Medical Care Survey were used to evaluate prescriptions for antimicrobials for URIs and bronchitis.

RESULTS

From 1993 to 1999, the proportion of children receiving antimicrobials after visits for URIs and bronchitis decreased. However, the use of broad-spectrum antimicrobials rose from 10.6% of bronchitis visits to 40.5%. Prescriptions of antimicrobials for adults with URIs or bronchitis showed a decrease between 1993 and 1999.

CONCLUSIONS

Although antimicrobial prescribing for URIs and bronchitis has decreased for both children and adults, the prescribing of broad-spectrum antibiotics among children has shown a proportional rise.

Use of complementary and alternative medicine by children in the United States

BACKGROUND

Current estimates of pediatric complementary and alternative medicine (CAM) use range from 10% to 15%. These estimates are derived from children sampled at health care facilities, with chronic conditions, and/or from countries other than the United States.

OBJECTIVE

To provide a population-based estimate of the prevalence of pediatric CAM use in the United States.

DESIGN

We used the 1996 Medical Expenditure Panel Survey (MEPS), a nationally representative survey of the noninstitutionalized US population. The survey asks parents if their children used alternative care practitioners within the previous year. Our analysis included children younger than 18 years and accounted for the complex sampling design of MEPS.

RESULTS

Weighted for the US population, pediatric CAM use was 1.8% (95% confidence interval, 1.3%-2.3%). Participants who used CAM were found in each age category, and the mean age was 10.3 years; 76.8% were white, 54% were female, 32% lived in the West, 66% lived in a metropolitan statistical area, and 36% lived at 100% to 199% of the poverty level. Bivariate chi2 analysis shows that CAM use increased with age (P =.006) and was twice as common in children not living in a metropolitan statistical area (P =.02).

CONCLUSIONS

The use of CAM among US children, as measured by the MEPS, is far less prevalent than has previously been asserted. With such disparate estimates, future CAM research efforts would benefit from a consensus regarding what practices constitute CAM and how these practices should be measured.

A phase II study of methylphenidate for depression in advanced cancer

This study evaluated the use of methylphenidate for depression in advanced cancer

DESIGN

Phase II open-label prospective study.

ELIGIBILITY CRITERIA

No previous use of methylphenidate or current use of other antidepressants.

EVALUATION

Depression and response to treatment were determined by asking the patient: "are you depressed?" Patients were assessed at baseline and at days 3, 5, and 7.

TREATMENT

Starting dose was 5 mg at 8:00 a.m. and 12:00 noon. The dose was titrated for lack of response on any of the assessment days. RESPONSE CRITERIA: A negative response to the question: "are you depressed?"

RESULTS

Some 41 patients were enrolled and 30 (15 men, 15 women) completed the study. Median age was 68 years (range: 30-90). Methylphenidate was stopped for six patients because of side effects and five were not evaluable; 21 responded to 10 mg/day on day 3; the other nine responded to 20 mg/day on day 5, 29 maintained their positive response through day 7. Anorexia, fatigue, concentration, and sedation also improved in some. All who completed the study had tolerable side effects, none of which caused treatment to stop.

CONCLUSIONS

Methylphenidate is effective for depression in advanced cancer A starting dose of 10 mg in divided doses is effective in most patients. Dose escalation may be needed. Improvement occurs within three days. Close monitoring of side effects is recommended.

Dying at home: emergency medications for terminal symptoms

This article discusses the use of a medication kit at home for terminal symptoms. This innovation has been in place for more than two years at the Hospice of the Cleveland Clinic. There is no previously published information on this innovation in the literature.

Thalidomide: dual benefits in palliative medicine and oncology

Thalidomide is an immunomodulator, anti-angiogenic agent, anti-cytokine, and anti-integrin. Alone or in combination with other drugs, thalidomide has also demonstrated anti-cachexin and anti-neoplastic properties. Anorexia and cachexia are common symptoms of advanced cancer. Since certain cytokines also promote tumor growth, we may have a class of agents with palliative and anti-tumor benefits in combination with anti-neoplastics and anti-cytokines, such as thalidomide.

The importance of cytochrome P450 monooxygenase CYP2D6 in palliative medicine

The enzymes in the cytochrome p450 monooxygenase system (CYP) are the major enzymes responsible for metabolizing medications. The CYP2D6 isomer is responsible for metabolizing certain opioids, neuroleptics, antidepressants and cardiac medications. Owing to CYP2D6's low capacity and high affinity it is easily saturated by substrate and/or inhibited, resulting in pharmacokinetic interactions. Polymorphisms of the structural gene are common, leading to wide inter-individual and ethnic differences in drug metabolism. Clinically important drug interactions, which may be anticipated in the palliative medicine population, are reviewed.

Assessment of delirium in advanced cancer: the use of the bedside confusion scale

We conducted a prospective assessment of 50 consecutive admissions to an acute palliative medicine unit, using the bedside confusion scale (BSCS). Information including age, gender, diagnosis, and the presence or absence of brain metastasis was collected. Possible predisposing factors for delirium were recorded. Forty-one of 50 consecutive admissions were screened. There were 18 men and 23 women with a median age of 65 years (average: 60-75). The most common diagnoses among all were lung and breast cancer. Thirteen patients were delirious (BSCS score of > or = 2), 10 borderline (BSCS score = 1), and 21 normal (BSCS score = 0). Brain metastases and drugs appeared to be the most common predisposing factors of delirium. Forty percent of those that were delirious received haloperidol as symptomatic treatment. The BSCS is simple, portable, valid, quick, and easy to use by any medical team member. Delirium is common in hospitalized patients with advanced cancer.

The terminally ill Muslim: death and dying from the Muslim perspective

Islam holds life as sacred and belonging to God and that all creatures will die one day. Suicide is forbidden. Muslims believe death is only a transition between two different lives. The terminally ill Muslim desires to perform five ritual requirements. Do not resuscitate (DNR) orders are acceptable. A deceased Muslim must always be buried after being ritually washed and wrapped. There are different Muslim schools of thought, but they are united regarding their views on death and dying.

Modern management of cancer-related intestinal obstruction

Malignant-associated bowel obstruction remains a common and perplexing problem for patients with advanced gynecologic and gastrointestinal malignancies. The ability to locate and define its cause preoperatively has improved with the advent of computed tomography. Initial clinical experience with half-Fourier acquisition single-shot turbo spin-echo magnetic resonance imaging (HASTE MRI) and virtual colonoscopy is exciting. The surgical approach for primary obstructing colon cancer has become more aggressive, with experienced surgical groups doing one-stage procedures. Yet to be defined are guidelines for surgical management of obstructions occurring in the face of recurrent disease. Stent placement for upper and lower bowel obstructions is an option in nonoperable patients. Pharmacologic symptom management for intestinal obstructions consists of an opioid, an anticholinergic, and an antiemetic. Octreotide, either alone or added to the original regimen, will palliate symptoms that are resistant to the three-drug combination.

Methylphenidate for fatigue in advanced cancer: a prospective open-label pilot study

Psychostimulants such as methylphenidate are used for fatigue in cancer patients. We report a prospective, open-label, pilot study of the successful use of methylphenidate to treat fatigue in nine of 11 consecutive patients with advanced cancer. Seven had received radiation or chemotherapy, a median of three weeks (range from one to 30 weeks) prior to methylphenidate. A rapid onset of benefit was noted, even in the presence of mild anemia. Sedation and pain also improved in some. Only one patient had side effects severe enough to stop the medication.