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1.  Phylogenetic Analysis of Algal Symbionts Associated with Four North American Amphibian Egg Masses 
PLoS ONE  2014;9(11):e108915.
Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga “Oophila amblystomatis” (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these questions, we conducted a phylogeographic study of algae sampled from egg capsules of A. maculatum, its allopatric congener A. gracile, and two frogs: Lithobates sylvatica and L. aurora. All of these North American amphibians form associations with algae in their egg capsules. We sampled algae from egg capsules of these four amphibians from localities across North America, established representative algal cultures, and amplified and sequenced a region of 18S rDNA for phylogenetic analysis. Our combined analysis shows that symbiotic algae found in egg masses of four North American amphibians are closely related to each other, and form a well-supported clade that also contains three strains of free-living chlamydomonads. We designate this group as the ‘Oophila’ clade, within which the symbiotic algae are further divided into four distinct subclades. Phylogenies of the host amphibians and their algal symbionts are only partially congruent, suggesting that host-switching and co-speciation both play roles in their associations. We also established conditions for isolating and rearing algal symbionts from amphibian egg capsules, which should facilitate further study of these egg mass specialist algae.
PMCID: PMC4230919  PMID: 25393119
2.  Hemorrhagic shock occurring due to a concealed hematoma after insertion of a subclavian venous catheter in a patient undergoing anticoagulation therapy: a case report 
Korean Journal of Anesthesiology  2014;67(5):358-362.
A 74-year-old man who had been receiving warfarin for atrial fibrillation, underwent emergency thrombectomy. A central venous catheter (CVC) was inserted via the left subclavian vein, and heparin was administered to prevent preoperative and postoperative thrombotic events. After an uneventful thrombectomy, the patient was transferred to the intensive care unit (ICU). On the second postoperative day, the patient developed syncope and his blood pressure and oxygen saturation decreased. A computed tomography (CT) revealed a huge hematoma under the pectoralis major muscle. The patient was then treated with continuous renal replacement therapy and mechanical ventilation for multiorgan dysfunction syndrome, which developed due to hemorrhagic shock in the ICU. These findings suggest that when a CVC is inserted in patients requiring anticoagulant therapy, the possible risk of excessive bleeding must be carefully considered. Further, choosing a proper insertion site and performing an ultrasound-guided aspiration may be helpful in preventing these complications.
PMCID: PMC4252351  PMID: 25473468
Anticoagulants; Central venous catheter; Hematoma; Hemorrhagic shock
3.  Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista 
Scientific Reports  2014;4:4641.
Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution of these two eukaryotic assemblages have yet to be fully elucidated, and P. bilix may be a key lineage in tracing those groups' early evolution. In the present study, we analyzed a ‘phylogenomic' alignment of 157 genes to clarify the position of P. bilix in eukaryotic phylogeny. In the 157-gene phylogeny, P. bilix was found to be basal to a clade of cryptophytes, goniomonads and kathablepharids, collectively known as Cryptista, which is proposed to be a part of the larger taxonomic assemblage Hacrobia. We here discuss the taxonomic assignment of P. bilix, and character evolution in Cryptista.
PMCID: PMC3982174  PMID: 24717814
4.  Oxycodone vs. Fentanyl Patient-Controlled Analgesia after Laparoscopic Cholecystectomy 
Objectives Oxycodone is semi-synthetic opioid, oral and parenteral preparations have been widely used for acute and chronic pain. The aim of this study was to assess the efficacy and side effects of oxycodone and fentanyl in patient controlled analgesia (PCA) after laparoscopic cholecystectomy.
Methods A prospective, randomized, double-blind study was conducted. 81 patients were randomly divided into two groups; fentanyl (10 mcg fentanyl and 1.5 mg ketorolac) and oxycodone group (1 mg oxycodone and 1.5 mg ketorolac). After the operation, a blinded observer assessed pain using a numerical rating scale (NRS), infused PCA dose, side effects, sedation levels, and satisfaction.
Results Cumulative PCA dose of oxycodone group at 48 h (31.4 ± 16.0 ml) was significantly less than that of fentanyl group (43.8 ± 23.1 ml, P = 0.009). Oxycodone group showed more nausea at 6 - 24 h after the operation (P = 0.001), but there was no difference in satisfaction score (P = 0.073). There were no significant differences in other side effects, sedation and NRS scores between two groups.
Conclusion Oxycodone showed comparable effects for pain relief compared to fentanyl in spite of less cumulative PCA dose. Based on these results, we could conclude that oxycodone may be useful as an alternative to fentanyl for PCA after laparoscopic cholecystectomy.
PMCID: PMC4025163  PMID: 24843313
Fentanyl; Laparoscopic cholecystectomy surgery; Oxycodone; Patient-controlled analgesia; Postoperative pain.
5.  A Broad Phylogenetic Survey Unveils the Diversity and Evolution of Telomeres in Eukaryotes 
Genome Biology and Evolution  2013;5(3):468-483.
Telomeres, ubiquitous and essential structures of eukaryotic chromosomes, are known to come in a variety of forms, but knowledge about their actual diversity and evolution across the whole phylogenetic breadth of the eukaryotic life remains fragmentary. To fill this gap, we employed a complex experimental approach to probe telomeric minisatellites in various phylogenetically diverse groups of algae. Our most remarkable results include the following findings: 1) algae of the streptophyte class Klebsormidiophyceae possess the Chlamydomonas-type telomeric repeat (TTTTAGGG) or, in at least one species, a novel TTTTAGG repeat, indicating an evolutionary transition from the Arabidopsis-type repeat (TTTAGGG) ancestral for Chloroplastida; 2) the Arabidopsis-type repeat is also present in telomeres of Xanthophyceae, in contrast to the presence of the human-type repeat (TTAGGG) in other ochrophytes studied, and of the photosynthetic alveolate Chromera velia, consistent with its phylogenetic position close to apicomplexans and dinoflagellates; 3) glaucophytes and haptophytes exhibit the human-type repeat in their telomeres; and 4) ulvophytes and rhodophytes have unusual telomere structures recalcitrant to standard analysis. To obtain additional details on the distribution of different telomere types in eukaryotes, we performed in silico analyses of genomic data from major eukaryotic lineages, utilizing also genome assemblies from our on-going genome projects for representatives of three hitherto unsampled lineages (jakobids, malawimonads, and goniomonads). These analyses confirm the human-type repeat as the most common and possibly ancestral in eukaryotes, but alternative motifs replaced it along the phylogeny of diverse eukaryotic lineages, some of them several times independently.
PMCID: PMC3622300  PMID: 23395982
algae; telomerase activity; Excavata; comparative genomics; Goniomonas
6.  Correlation between Intake of Dietary Fiber and Adherence to the Korean National Dietary Guidelines in Adolescents from Jeonju 
This study surveyed dietary intake and adherence to the Korean national dietary guidelines in Korean adolescents. To elucidate basic data for use in nutrition education, which aims to improve adolescent compliance with the national dietary guidelines and to increase the intake of dietary fiber, we evaluated the sources of fiber in adolescent diets. This study included 182 male and 212 female students from 2 middle schools in the Jeonju province. From November 15~20, 2011, we surveyed the students for general characteristics, adherence to the Korean national dietary guidelines, and dietary intake. Dietary fiber intake was 16.57 ± 6.95 g/day for male students and 16.14 ± 7.11 g/day for female students. The food groups that contributed most to dietary fiber intake were (in descending order) cereals, vegetables, seasoning, and fruits. The fiber-containing food items consumed most were cabbage- kimchi, cooked rice, instant noodles, and cabbage. Based on adherence to the Korean national dietary guidelines, the vegetable-based intake of dietary fiber in groups 1 (score 15~45), 2 (score 46~52), and 3 (score 53~75) were 4.41 ± 2.595 g/day, 4.12 ± 2.692 g/day, and 5.49 ± 3.157 g/day, respectively (p<0.001). In addition, the total intake of dietary fiber varied significantly among the three groups (p<0.001) as follows: Group 1, 14.99 ± 6.374 g/day; Group 2, 15.32 ± 6.772 g/day; and Group 3, 18.79 ± 7.361 g/day. In this study, we discovered that adherence to the Korean national dietary guidelines correlates with improved intake of dietary fiber. Therefore, marketing and educational development is needed to promote adherence to the Korean national dietary guidelines. In addition, nutritional education is needed to improve dietary fiber consumption through the intake of vegetables and fruits other than kimchi.
PMCID: PMC3866727  PMID: 24471093
adolescents; dietary fiber; guideline adherence
7.  Genomic Characterization of Neoparamoeba pemaquidensis (Amoebozoa) and Its Kinetoplastid Endosymbiont▿ 
Eukaryotic Cell  2011;10(8):1143-1146.
We have performed a genomic characterization of a kinetoplastid protist living within the amoebozoan Neoparamoeba pemaquidensis. The genome of this “Ichthyobodo-related organism” was found to be unexpectedly large, with at least 11 chromosomes between 1.0 and 3.5 Mbp and a total genome size of at least 25 Mbp.
PMCID: PMC3165438  PMID: 21666073
8.  Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen 
Biology Direct  2012;7:5.
Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes.
This article was reviewed by Eric Bapteste and Eugene Koonin.
PMCID: PMC3317845  PMID: 22296756
eukaryotes; lateral gene transfer; phagocytosis; sterols; tetrahymanol
9.  The CIL-1 phosphoinositide 5-phosphatase regulates ciliary localization of the TRP polycystins and sperm function in C. elegans 
Current biology : CB  2009;19(19):1599-1607.
C. elegans male sexual behaviors include chemotaxis and response to hermaphrodites, backing/turning, vulva location, spicule insertion and sperm transfer, culminating in cross fertilization of hermaphrodite oocytes with male sperm. The LOV-1 and PKD-2 transient receptor potential polycystin (TRPP) complex localizes to ciliated endings of C. elegans male-specific sensory neurons and mediates several aspects of male mating behavior. TRPP complex ciliary localization and sensory function is evolutionarily conserved. A genetic screen for C. elegans mutants with PKD-2 ciliary localization (Cil) defects led to the isolation of a mutation in the cil-1 gene.
Here, we report that a phosphoinositide (PI) 5-phosphatase CIL-1 regulates TRPP complex ciliary receptor localization and sperm activation. cil-1 does not regulate the localization of other ciliary proteins, including intraflagellar transport (IFT) components, sensory receptors, or other TRP channels in different cell types. Rather, cil-1 specifically controls TRPP complex trafficking in male-specific sensory neurons and does so in a cell autonomous fashion. In these cells, cil-1 is required for normal PI(3)P distribution, indicating that a balance between PI(3,5)P2 and PI(3)P is important for TRPP localization. cil-1 mutants are infertile due to sperm activation and motility defects. In sperm, the CIL-1 5-phosphatase and a wortmannin sensitive PI 3-kinase act antagonistically to regulate the conversion of sessile spermatids into motile spermatozoa, implicating PI(3,4,5)P3 signaling in nematode sperm activation.
Our studies identify the CIL-1 5-phosphatase as key regulator of PI metabolism in cell types that are important in several aspects of male reproductive biology.
PMCID: PMC2762383  PMID: 19781942
10.  Plastid evolution: gene transfer and the maintenance of 'stolen' organelles 
BMC Biology  2010;8:73.
Many heterotrophic organisms sequester plastids from prey algae and temporarily utilize their photosynthetic capacity. A recent article in BMC Genomics reveals that the dinoflagellate Dinophysis acuminata has acquired photosynthesis-related genes by horizontal gene transfer, which might explain its ability to retain 'stolen' plastids for extended periods of time.
See research article
PMCID: PMC2883544  PMID: 20594287
11.  EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata 
PLoS ONE  2008;3(7):e2621.
Classification of eukaryotes provides a fundamental phylogenetic framework for ecological, medical, and industrial research. In recent years eukaryotes have been classified into six major supergroups: Amoebozoa, Archaeplastida, Chromalveolata, Excavata, Opisthokonta, and Rhizaria. According to this supergroup classification, Archaeplastida and Chromalveolata each arose from a single plastid-generating endosymbiotic event involving a cyanobacterium (Archaeplastida) or red alga (Chromalveolata). Although the plastids within members of the Archaeplastida and Chromalveolata share some features, no nucleocytoplasmic synapomorphies supporting these supergroups are currently known.
Methodology/Principal Findings
This study was designed to test the validity of the Archaeplastida and Chromalveolata through the analysis of nucleus-encoded eukaryotic translation elongation factor 2 (EEF2) and cytosolic heat-shock protein of 70 kDa (HSP70) sequences generated from the glaucophyte Cyanophora paradoxa, the cryptophytes Goniomonas truncata and Guillardia theta, the katablepharid Leucocryptos marina, the rhizarian Thaumatomonas sp. and the green alga Mesostigma viride. The HSP70 phylogeny was largely unresolved except for certain well-established groups. In contrast, EEF2 phylogeny recovered many well-established eukaryotic groups and, most interestingly, revealed a well-supported clade composed of cryptophytes, katablepharids, haptophytes, rhodophytes, and Viridiplantae (green algae and land plants). This clade is further supported by the presence of a two amino acid signature within EEF2, which appears to have arisen from amino acid replacement before the common origin of these eukaryotic groups.
Our EEF2 analysis strongly refutes the monophyly of the Archaeplastida and the Chromalveolata, adding to a growing body of evidence that limits the utility of these supergroups. In view of EEF2 phylogeny and other morphological evidence, we discuss the possibility of an alternative eukaryotic supergroup.
PMCID: PMC2440802  PMID: 18612431
12.  Widespread distribution of a unique marine protistan lineage 
Environmental Microbiology  2008;10(6):1621-1634.
Unicellular eukaryotes (protists) are key components of marine food webs, yet knowledge of their diversity, distributions and respective ecologies is limited. We investigated uncultured protists using 18S rRNA gene sequencing, phylogenetic analyses, specific fluorescence in situ hybridization (FISH) probes and other methods. Because few studies have been conducted in warm water systems, we focused on two Atlantic subtropical regions, the Sargasso Sea and the Florida Current. Cold temperate waters were also sampled. Gene sequences comprising a unique eukaryotic lineage, herein termed ‘biliphytes’, were identified in most samples, whether from high- (30°C) or from low- (5°C) temperature waters. Sequences within this uncultured group have previously been retrieved from high latitudes. Phylogenetic analyses suggest biliphytes are a sister group to the cryptophytes and katablepharids, although the relationship is not statistically supported. Bootstrap-supported subclades were delineated but coherence was not obvious with respect to geography or physicochemical parameters. Unlike results from the initial publication on these organisms (therein ‘picobiliphytes’), we could not detect a nucleomorph, either visually, or by targeted primers. Phycobilin-like fluorescence associated with biliphyte-specific FISH-probed cells supports the hypothesis that they are photosynthetic. Our data indicate the biliphytes are nanoplanktonic in size, averaging 4.1 ± 1.0 × 3.5 ± 0.8 μm (±SD) for one probed group, and 3.5 ± 0.9 × 3.0 ± 0.9 μm (±SD) for another. We estimate biliphytes contributed 28 (±6)% of the phytoplanktonic biomass in tropical eddy-influenced surface waters. Given their broad thermal and geographic distribution, understanding the role these protists play in biogeochemical cycling within different habitats is essential.
PMCID: PMC2408648  PMID: 18341584
13.  Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae) 
BMC Genomics  2008;9:215.
Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented.
The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages.
Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.
PMCID: PMC2397417  PMID: 18474103

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