Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases

N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Phylogeny and evolution of mycophagy in the Zygothrica genus group (Diptera: Drosophilidae)

Despite numerous phylogenetic studies on the family Drosophilidae, relationships among some important lineages are still poorly resolved. An example is the equivocal position of the Zygothrica genus group that is mostly comprised of the mycophagous genera Hirtodrosophila, Mycodrosophila, Paramycodrosophila, and Zygothrica. To fill this gap, we conducted a phylogenetic analysis by assembling a dataset of 24 genes from 92 species, including 42 species of the Zygothrica genus group mainly from the Palearctic and Oriental regions. The resulting tree shows that the Zygothrica genus group is monophyletic and places it as the sister to the genus Dichaetophora, and the clade Zygothrica genus group + Dichaetophora is sister to the Siphlodora + Idiomyia/Scaptomyza clade. Within the Zygothrica genus group, the genera Mycodrosophila and Paramycodrosophila are both recognized as monophyletic, while neither the genus Zygothrica nor Hirtodrosophila is monophyletic. We also used this phylogenetic tree to investigate the evolution of mycophagy by reconstructing ancestral food habit in the Drosophilidae. We found that fungus-feeding habit has been gained independently in two lineages. The most recent common ancestor (MRCA) of the subgenus Drosophila was estimated to have acquired mycophagy by expanding its ancestral feeding niche on fermenting fruits to decayed fungi, while the MRCA of the Zygothrica genus group shifted its niche from fruits to fungi as a specialist probably preferring fresh fruiting bodies.

Impact of frailty on super elderly patients with peripheral artery disease from the I-PAD 3 year registry

Background

Unlike age, frailty is often not taken into account in treatment indications of Endovascular treatment (EVT). One of the reason is that there was little known the relationship between frailty and the outcome of EVT for super elderly patients with peripheral artery disease (PAD). We investigate impacts of frailty on the super elderly patient prognosis who underwent EVT.

Purpose

To investigate impacts of frailty on the super elderly patient prognosis who underwent EVT.

Methods

From August 2015 to July 2016, 335 consecutive patients who underwent EVT were enrolled in the I-PAD registry from 7 institutes in Nagano prefecture. Among them, we selected and analyzed 91 super elderly PAD patients (≥80 years-old) and divided them into two groups:those with moderate or higher frailty (Clinical Frailty Scale (CFS) ≥6, n=28) and those without (CFS ≤5, n=63). The primary endpoints were cardiovascular death and major adverse cardiovascular and limb events (MACLE), defined as a composite of cardiovascular death, myocardial infarction, stroke, admission for heart failure, major amputation and revascularization.

Results

The median follow-up period was 2.7 years. Freedom rate from cardiovascular death and MACLE were significantly lower among patients with moderate or higher frailty than among those without (47.0% vs. 58.0%, P=0.03; 39.1% vs. 68.5%, P<0.01).

Conclusion

The prognosis of super elderly patients with moderate or higher frailty is worse than those without.

Funding Acknowledgement

Type of funding source: None

Baseline clinical features in a large-scale registration survey of patient with hypertrophic cardiomyopathy throughout Japan: J-HCM registry study

Background

Hypertrophic cardiomyopathy (HCM) is a most prevalent primary myocardial disorder with heterogeneous clinical features. However, there have been few studies on clinical features of HCM as a prospective cohort. In 2015, we established a large-scale registration survey of patients with HCM throughout Japan, named J-HCM registry study.

Purpose

The aim of this study was to clarify the clinical features of Japanese patients with HCM.

Methods

J-HCM registry study is a prospective, multicenter investigation, consisting of 24 hospitals. This time, we present the baseline clinical characteristics in this survey.

Results

Total 1484 patients were registered. The ages at registration and at diagnosis were 65±15 and 56±17 years, respectively, and 806 patients (54%) were men. Majority of the patients (95%) was NYHA class I or II. With regard to subtypes of HCM, there were 526 patients (36%) in the HCM with left ventricular (LV) outflow tract obstruction, 126 patients (8%) in the mid-ventricular obstruction, 57 patients (4%) in the end-stage phase characterized by LV ejection fraction <50%, and 197 patients (14%) in apical HCM. At registration, 80 patients (6%) had prior successful recovery from sustained ventricular tachycardia or ventricular fibrillation, 162 patients (11%) suffered from heart failure hospitalization, and 64 patients (4%) had history of embolic event. Regarding invasive treatment, 160 patients (10%) had prior septal reduction therapy and 162 patients (11%) had ICD implantation. According to the 2014 European Society of Cardiology Guidelines on sudden cardiac death (SCD) prevention, the study patients were divided into 3 categories by the HCM Risk-SCD calculator: patients distribution, 4% in the high risk group (≥6% calculated HCM Risk-SCD at 5 years), 7% in the intermediate risk group (4% to <6%), 69% in the low risk group (<4%), and 16% in the patients with extreme characteristics (Figure 1).

Conclusions

In this multicenter registration survey of patients with HCM, the baseline clinical characteristics were almost similar to several retrospective large-scale cohorts in Western countries except older age and less symptomatic state. This study will provide important knowledge regarding management of HCM.

Figure 1

Funding Acknowledgement

Type of funding source: None

Taxonomy and evolution of asymmetric male genitalia in the subgenus <br />Ashima Chen (Diptera: Drosophilidae: Phortica Schiner), with descriptions <br />of seven new species

The taxonomy of the subgenus Ashima of the genus Phortica is revised. A cladistic analysis of 66 morphological characters is conducted, covering 35 species (28 known and 7 new species: Phortica efragmentata sp. nov., P. andreagigoni sp. nov., P. watabei sp. nov., P. halimunensis sp. nov., P. akutsui sp. nov., P. kerinciensis sp. nov., and P. takehiroi sp. nov.) which correspond to 71.4% of 49 total spp. of Ashima. The resulting cladogram shows that the studied species are separated into several clades/subclades/cluster each highly supported with specific synapomorphies. Those clades/subclades/cluster are newly defined as the following species groups, subgroups or complex: the afoliolata, foliiseta, nigrifoliiseta and angulata species groups; the foliiseta, tanabei, nigrifoliiseta and glabra species subgroups; and the foliiseta species complex. The subgenus Ashima is peculiar in having the asymmetric male genitalia as the ground plan and showing the antisymmetry (i.e. intraspecific mirror-image variation) in some species but the directional asymmetry (i.e. side-fixed asymmetry) in others. The evolution of genital asymmetry in this subgenus is estimated by mapping the states (symmetry, directional asymmetry and antisymmetry) of bilateral structures of male genitalia on the cladogram. This ancestral state reconstruction estimates that the directional asymmetry of male genitalia has evolved at the ancestor of this subgenus and then changed to the antisymmetric state independently in two lineages, the angulata + nigrifoliiseta species groups and the foliiseta species complex. In this study, a standardized terminology recently proposed for the male terminalia of Drosophila melanogaster is extendedly adopted to describe the morphology of male terminalia in the subgenus Ashima, one group of the subfamily Steganinae.

P943The impact of diabetes on patients with frail after endovascular treatments: from I-PAD registry

Background

Diabetes mellitus (DM) is known to be one of the risks of arteriosclerosis. However, it is still unknown whether DM is a risk factor also in secondary prevention of frail patients after endovascular treatments (EVT)

Purpose

To investigate impact of diabetes on patients with frail after EVT.

Methods

From July 2015 to July 2016, 371 consecutive PAD patients who performed EVT were enrolled in I-PAD registry. We could conduct follow up survey 361 patients (446 lesions) and divided into 2 groups; with diabetes (185 patients, 226 lesions) or without diabetes (176 patients, 220 lesions) and analyzed. And among them,we selected 96 patients with frail and divided into 2 groups; with diabetes (49 patients, 70 lesions) or without diabetes (46 patients, 58 lesions) and analyzed. We defined frail patients as the patients with Clinical Frailty Scale 5 (mild frail) or higher. The primary end point was all-cause-death and major adverse limb events (MALE: TLR, TVR, major amputations) at 1 year.

Result

At 1 years in the patients group with diabetes, overall survival and freedom from MALE were significantly lower (81.7% vs 95.8% P<0.0001; 80.0% vs 94.6%, P<0.0001) than the group without diabetes.Among the patients with frail, between the patients group with diabetes and the group without, there is no significant differences in overall survival and freedom from MALE (88.2% vs 88.9% P=0.83; 80.7% vs 84.1%, P=0.55) at 5 years.

Conclusion

The prognosis of patients with diabetes after EVT was worse than the patient without. On the other hand, the prognosis of frail patients with diabetes after EVT was no difference with the frail patient without diabetes in this study.

P942Impact of left ventricular ejection fraction in patients with critical limb ischemia: from I-PAD registry

Introduction

In patients with critical limb ischemia (CLI) it is known that malnutrition, low BMI, inflammation and so on are prognostic factors. But, it is unclear whether left ventricular ejection fraction (LVEF) affects prognosis of CLI patients. So we investigated that LVEF affects prognosis of CLI patients.

Methods

From July 2015 to July 2016, 371 consecutive peripheral artery disease patients who performed endovascular treatment (EVT) were enrolled in I-PAD registry. 179 of them were patients with CLI. We could conduct follow up survey about 126 (age 75.5±11.1, men 63.5%) and divided two groups according to their LVEF (group with LVEF≤40%, n=13, group without LVEF≤40%, n=113). The primary end point was major adverse limb events (MALE: TLR, TVR, major amputations) and secondary end point was all-cause death.

Results

The median follow-up period was 11.5±6.7 months. The 18 months MALE rate was significant higher in the group with low LVEF than group without low LVEF (76.9% vs 37.2% p<0.05). The 18months all-cause death tended to be higher in the group with low LVEF, however there was not statistical significance in the two groups (53.8% vs 24.8% p=0.09).

Conclusion

LVEF was associated with MALE in patients with CLI.

P1957Impact of fraility on the super elderly patients with peripheral artery disease

Background

The current consensus is that frail patients have high risks of mortality. However, it remains unclear whether frailty is associated with mortality risks in super-elderly patients with peripheral artery disease (PAD).

Methods

The I-PAD registry was a prospective multicenter observational study involving 12 institutions in Nagano prefecture in Japan. From July 2015 to July 2016, the I-PAD registry enrolled 371 consecutive PAD patients who had undergone endovascular therapy (EVT). Among them, we selected and analysed 109 PAD patients who were >80 years old when they had undergone EVT and divided them into two groups: those with frailty (Clinical Frailty Scale≥5, n=47) and those without frailty (Clinical Frailty Scale≤4, n=62). The primary endpoints were overall survival and major adverse limb events (MALE), defined as a composite of all-cause death, major amputation and revascularization.

Results

The median follow-up period was 1.58±0.3 years. Overall, 109 patients with a mean age of 84.8±4.0 years, of whom 63.3% were men, were included. Overall survival and freedom from MALE were significantly lower among patients with frailty than among those without frailty (60.5% vs. 91.6%, P<0.001; 51.4% vs. 87.5%, P<0.001; respectively).

Conclusion

The prognosis of super-elderly patients with frailty is worse than that of patients without frailty.

P936Impact of left ventricular ejection fraction in patients with peripheral artery disease: from I-PAD registry

Introduction

In patients with peripheral artery disease (PAD) it is known that CVD is one of prognostic factors. But, it is unclear whether left ventricular ejection fraction (LVEF) affects prognosis of PAD patients. So we investigated that LVEF affects prognosis of PAD patients.

Methods

From July 2015 to July 2016, 371 consecutive PAD patients who performed endovascular treatment (EVT) were enrolled in I-PAD registry. We could conduct follow up survey about 337 (age 73.8±9.6, men 72.4%) patients and divided two groups according to their LVEF (group with LVEF≤40%, n=18, group without LVEF≤40%, n=319). The primary end point was major adverse limb events (MALE: TLR, TVR, major amputations) and secondary end point was all-cause death.

Results

The median follow-up period was 13.6±5.7 months. The 18 months MALE and all-cause death rate were significantly higher in the group with low LVEF than group without low LVEF (61.1% vs 21.6% p<0.001, 44.4% vs 11.6% p<0.001).

Conclusion

LVEF was significantly associated with MALE and all-cause death in patients with PAD.

Evolution and diversity of the courtship repertoire in the Drosophila montium species group (Diptera: Drosophilidae)

Changes in elements of courtship behaviour can influence sexual isolation between species. Large-scale analyses of changes, including loss and gain of courtship elements, across a relatively complete phylogenetic group are rare but needed to understand the significance of such changes, for example whether the gain and loss of courtship elements are essentially arbitrary or equally reversible. In most species of Drosophila, courtship, including singing, mainly occurs before mounting as premounting courtship. The Drosophila montium species group is unusual because loss of premounting courtship and gain of post-mounting one has been detected in this group. Here, we provide an extensive analysis on the courtship repertoire and songs of 42 species in this group. Synchronously captured video and audio recordings were analysed to describe courtship patterns and male courtship songs, and changes were analysed in a phylogenetic context. Ancestral state reconstruction suggests that a gain of post-mounting courtship singing at the ancestor of this species group has been accompanied by a concurrent decrease in the incidence of premounting courtship singing and has led to subsequent further decrease and eventually complete loss of premounting courtship song in several lineages. Alongside this evolutionary trend towards post-mounting courtship, sine song and a special type of "high pulse repetition song" have become more widely used for courtship during species diversification in the montium group. It is likely that the elaboration of post-mounting courtship behaviours is associated with changes in the relative importance of pre- and post-mounting components of mating systems, such as sperm competition or cryptic female choice.

Di-(2-ethylhexyl) phthalate suppresses IL-12p40 production by GM-CSF-dependent macrophages via the PPARα/TNFAIP3/TRAF6 axis after lipopolysaccharide stimulation

Activation of peroxisome proliferator-activated receptor α (PPARα) by di-(2-ethylhexyl) phthalate (DEHP) has an anti-inflammatory effect. This study investigated the potential combined influence of PPARα, tumor necrosis factor α-induced protein 3 (TNFAIP3/A20), and tumor necrosis factor receptor-associated factor 6 (TRAF6) on interleukin (IL)-12p40 production by macrophages exposed to DEHP and stimulated with lipopolysaccharide (LPS). LPS upregulated IL-12p40 expression by granulocyte-macrophage colony-stimulating factor-dependent macrophages (on day 9 of culture), whereas adding DEHP to cultures significantly attenuated the response of IL-12p40 to LPS stimulation. PPARα protein was also reduced by DEHP. Interestingly, transfection of macrophages with small interfering RNA (siRNA) duplexes for PPARα, TNFAIP3/A20, or dual oxidase 2 restored the response of IL-12p40 protein to LPS stimulation in the presence of DEHP. siRNAs for various protein kinase Cs (PKCs) (α, β, γ, or δ) also restored IL-12p40 production by macrophages exposed to LPS and DEHP. While LPS upregulated both IL-12p40 and TNFAIP3/A20 production, adding DEHP to cultures dramatically reduced IL-12p40 and TNFAIP3/A20 levels. Silencing of PKCα reduced TNFAIP3/A20 production, whereas PKCγ siRNA (but not PKCβ or δ siRNA) significantly increased TNFAIP3/A20. TRAF6 was also attenuated by macrophages with DEHP. The PPARα/TNFAIP3/TRAF6 axis may have an important role in the mechanism through which DEHP reduces IL-12p40 production by LPS-stimulated macrophages.

Introgression and Habitat Segregation in a Pair of Ladybird Beetle Species in the Genus Propylea (Coccinellidae, Coccinellinae) in Northern Japan

The ladybird beetles Propylea quatuordecimpunctata and P. japonica have largely overlapping distributions in northern Japan, and in the laboratory produce fertile hybrids. In this study, we surveyed the distribution and morphological differentiation of these species and the hybrids in natural populations, with a focus on western Hokkaido, northern Japan. Phenotypic analyses were conducted for 987 individuals collected at 90 localities. In addition, the nuclear internal transcribed spacer-II (ITS2) region (549 bp) and part of the mitochondrial cytochrome c oxidase subunit I (COI) gene (700 bp) were sequenced for 620 individuals from 53 localities. Analyses of both phenotypic and genotypic features discriminated two distinct entities assignable to P. quatuordecimpunctata and P. japonica. However, individuals with intermediate phenotypes and/or genotypes also occurred extensively, indicating natural hybridization. Putative P. quatuordecimpunctata individuals were collected across a wide range of altitudes (30-600 m), whereas those of P. japonica were found mostly lower than 300 m alt. In addition, P. quatuordecimpunctata was dominant in semi-open habitats shaded by canopy foliage, whereas P. japonica was frequent in more open habitats. The perceived altitudinal difference in the distributions may thus in part be a consequence of this different habitat preference, as open habitats are more common at lower altitudes in the study area.

Molecular Phylogeny of Cypridoid Freshwater Ostracods (Crustacea: Ostracoda), Inferred from 18S and 28S rDNA Sequences

With the aim of exploring phylogenetic relationships within Cypridoidea, the most species-rich superfamily among the podocopidan ostracods, we sequenced nearly the entire 18S rRNA gene (18S) and part of the 28S rRNA gene (28S) for 22 species in the order Podocopida, with representatives from all the major cypridoid families. We conducted phylogenetic analyses using the methods of maximum likelihood, minimum evolution, and Bayesian analysis. Our analyses showed monophyly for Cyprididae, one of the four families currently recognized in Cypridoidea. Candonidae turned out to be paraphyletic, and included three clades corresponding to the subfamilies Candoninae, Paracypridinae, and Cyclocypridinae. We propose restricting the name Candonidae s. str. to comprise what is now Candoninae, and raising Paracypridinae and Cyclocyprininae to family rank within the superfamily Cypridoidea.

Phylogeography of the Subgenus Drosophila (Diptera: Drosophilidae): Evolutionary History of Faunal Divergence between the Old and the New Worlds

The current subgenus Drosophila (the traditional immigrans-tripunctata radiation) includes major elements of temperate drosophilid faunas in the northern hemisphere. Despite previous molecular phylogenetic analyses, the phylogeny of the subgenus Drosophila has not fully been resolved: the resulting trees have more or less varied in topology. One possible factor for such ambiguous results is taxon-sampling that has been biased towards New World species in previous studies. In this study, taxon sampling was balanced between Old and New World species, and phylogenetic relationships among 45 ingroup species selected from ten core species groups of the subgenus Drosophila were analyzed using nucleotide sequences of three nuclear and two mitochondrial genes. Based on the resulting phylogenetic tree, ancestral distributions and divergence times were estimated for each clade to test Throckmorton’s hypothesis that there was a primary, early-Oligocene disjunction of tropical faunas and a subsequent mid-Miocene disjunction of temperate faunas between the Old and the New Worlds that occurred in parallel in separate lineages of the Drosophilidae. Our results substantially support Throckmorton’s hypothesis of ancestral migrations via the Bering Land Bridge mainly from the Old to the New World, and subsequent vicariant divergence of descendants between the two Worlds occurred in parallel among different lineages of the subgenus Drosophila. However, our results also indicate that these events took place multiple times over a wider time range than Throckmorton proposed, from the late Oligocene to the Pliocene.

Development of a microwave ion source for ion implantations

A microwave ion source is expected to have a long lifetime, as it has fewer consumables. Thus, we are in the process of developing a microwave ion source for ion implantation applications. In this paper, we report on a newly developed plasma chamber and the extracted P(+) beam currents. The volume of the plasma chamber is optimized by varying the length of a boron nitride block installed within the chamber. The extracted P(+) beam current is more than 30 mA, at a 25 kV acceleration voltage, using PH3 gas.

Phylogeny of epilachna, henosepilachna, and some minor genera of phytophagous ladybird beetles (coleoptera: coccinellidae: coccinellinae: epilachnini), with an analysis of ancestral biogeography and host-plant utilization

Ladybird beetles in the tribe Epilachnini include notorious crop pests and model species studied intensively in various fields of evolutionary biology. From a combined dataset of mitochondrial (ND2) and nuclear (28S) DNA sequences, we reconstructed the phylogeny of 46 species of Epilachnini from Asia, Africa, America, and the Australian region: 16 species in Epilachna, 24 species in Henosepilachna, and one species each in Adira, Afidenta, Afidentula, Afissula, Chnootriba, and Epiverta. In our phylogenetic trees, both Epilachna and Henosepilachna were reciprocally polyphyletic. Asian Epilachna species were monophyletic, except for the inclusion of Afissula sp. Asian and Australian Henosepilachna species likewise formed a monophyletic group, excluding H. boisduvali. African Epilachna and Henosepilachna species did not group with their respective Asian and American congeners, but were paraphyletic to other clades (Epilachna species) or formed a separate monophyletic group (Henosepilachna species) together with Chnootriba similis. The American Epilachna species were monophyletic and formed a clade with American Adira clarkii and Asian Afidentula manderstjernae bielawskii; this clade was the sister group to Asian and Australian Henosepilachna, but was distant from Asian Epilachna. Chnootriba was embedded in the African Henosepilachna clade, and Afissula in the Asian Epilachna clade. Epiverta, which is morphologically unique, was the sister group to Asian Epilachna, although with weak support. From reconstructions of biogeographical distribution and host-plant utilization at ancestral nodes, we inferred an African origin for the common ancestor of the species studied, and found the frequency of host shifts to differ greatly between the two major lineages of Epilachnini examined.

Description and molecular phylogeny of a new species of Phoronis (Phoronida) from Japan, with a redescription of topotypes of P. ijimai Oka, 1897

We describe Phoronis emigisp. n. as the eighth member of the genus based on specimens collected from a sandy bottom at 33.2 m depth in Tomioka Bay, Amakusa, Japan. The new species is morphologically similar to P. psammophila Cori, 1889, but can be distinguished from the latter by the number of longitudinal muscle bundles in the body wall (56–72 vs. 25–50 in P. psammophila) and the position of the nephridiopores (situated level with the anus vs. lower than the anus in P. psammophila). Using sequences of the nuclear 18S and 28S rRNA genes and the mitochondrial cytochrome c oxidase subunit I (COI) gene, we inferred the relationship of P. emigi to other phoronids by the maximum likelihood method and Bayesian analysis. The analyses showed that P. emigi is closely related to P. hippocrepia Wright, 1856 and P. psammophila Cori, 1889. We describe the morphology of the topotypes and additional material for P. ijimai Oka, 1897. Neither our morphological observations of P. ijimai, nor the phylogenetic analyses based on 18S and COI sequences, contradicts that P. vancouverensis Pixell, 1912 is conspecific with P. ijimai, a synonymy that has long been disputed.

Divergence of East Asians and Europeans estimated using male- and female-specific genetic markers

To study the male and female lineages of East Asian and European humans, we have sequenced 25 short tandem repeat markers on 453 Y-chromosomes and collected sequences of 72 complete mitochondrial genomes to construct independent phylogenetic trees for male and female lineages. The results indicate that East Asian individuals fall into two clades, one that includes East Asian individuals only and a second that contains East Asian and European individuals. Surprisingly, the European individuals did not form an independent clade, but branched within in the East Asians. We then estimated the divergence time of the root of the European clade as ∼41,000 years ago. These data indicate that, contrary to traditional views, Europeans diverged from East Asians around that time. We also address the origin of the Ainu lineage in northern Japan.

Development of microwave ion source for industrial applications

A microwave ion source is one of the long-life ion sources. In this paper, we report on the characteristics of the extracted Ar ion beam produced by a microwave ion source under various conditions, in terms of magnetic flux distribution and mass flow, and the stability of the ion beam. The measured spectra show that, under the experimental condition, almost all of produced ions were Ar(+) ions. For more than 6 h, the ion beam was stable.

A preliminary study to determine the diagnostic reference level using dose-area product for limited-area cone beam CT

OBJECTIVES

The aim of this study was to measure the dose-area product (DAP) of limited-area cone beam CT (CBCT) units used by dental offices, and to evaluate the rationale of the DAP with an aid of optically stimulated luminescence (OSL) dosemeter in measuring radiation dose.

METHOD

The DAPs of 21 CBCT units used in the dental offices of Tokyo and the surrounding areas from five different manufacturers were measured using OSL nanoDot dosemeter. An assembly of OSL dosemeters with an X-ray film was exposed by CBCT units at exposure parameters commonly used in each dental office. DAP values were then calculated as expressed in mGy cm(2).

RESULTS

DAP values ranged from 126.7 mGy cm(2) to 1476.9 mGy cm(2), depending on the units used.

CONCLUSION

OSL dosemeter coupled with film can be utilized for a large-scale study to measure DAP. The DAP values for individual CBCT units depend not only on the field of view, but also on the exposure parameters adapted by the dental offices.

Efficacy of adding sodium alginate to omeprazole in patients with nonerosive reflux disease: a randomized clinical trial

Nonerosive reflux disease (NERD) is the most common form of gastroesophageal reflux disease. Patients with NERD have a lower response rate to proton pump inhibitors (PPIs) than patients with erosive esophagitis when gauged from relief of heartburn. Sodium alginate decreases the acidity of refluxate and protects the esophageal mucosa. However, whether the addition of sodium alginate to PPI therapy can improve NERD symptoms remains unknown. Accordingly, the aim of this study was to evaluate the efficacy of adding sodium alginate to basal PPI therapy for NERD. Patients who had experienced heartburn on at least 2 days per week during the 1-month period before entering the study and had no endoscopic mucosal breaks (grade M or N according to Hoshihara's modification of the Los Angeles classification) were randomized to one of two treatments for 4 weeks: omeprazole (20 mg once daily) plus sodium alginate (30 mL four times a day) (group A) or omeprazole (20 mg once daily) alone (group B). Eighty-seven patients were enrolled, and 76 patients were randomly assigned to group A (n = 36) or group B (n = 40). Complete resolution of heartburn for at least 7 consecutive days by the end of treatment was significantly more common in group A (56.7%) than in group B (25.7%). One patient from group A had mild drug-related diarrhea that was not clinically serious. In conclusion, omeprazole combined with sodium alginate was better than omeprazole alone in Japanese patients with NERD.

Three species of Amphicorina (Annelida, Sabellida, Sabellidae) from Japan, with descriptions of two new species

We describe two new species and redescribe one in the polychaete genus Amphicorina Claparède, 1864 (Sabellidae) from Hokkaido, Japan. Amphicorina ascidicolasp. n. differs from its 38 congeners chiefly in the reduction of the collar, but also in having three pairs of radioles, one pair of ventral radiolar appendages, a bifurcate ventral lobe on the anterior peristomial ring, six abdominal chaetigers, and a large anterior tooth on the abdominal uncini. Amphicorina ezoensissp. n. has a crenulated collar, three pairs of radioles, and more than eight (12) abdominal chaetigers; Amphicorina ezoensis shares these character states with Amphicorina anneae (Rouse, 1994), Amphicorina eimeri (Langerhans, 1880), and Amphicorina persinosa (Ben-Eliahu, 1975), but differs from them in having two pairs of ventral radiolar appendages and a non-oblique collar. Amphicorina mobilis (Rouse, 1990) was previously known only from the type locality (New South Wales, Australia), but we identify our Japanese material as conspecific on the basis of morphological and molecular similarity.

Characterization of optically stimulated luminescence dosemeters to measure organ doses in diagnostic radiology

OBJECTIVE

The aim of this study was to assess the characteristics of an optically stimulated luminescence dosemeter (OSLD) for use in diagnostic radiology and to apply the OSLD in measuring the organ doses by panoramic radiography.

METHODS

The dose linearity, energy dependency and angular dependency of aluminium oxide-based OSLDs were examined using an X-ray generator to simulate various exposure settings in diagnostic radiology. The organ doses were then measured by inserting the dosemeters into an anthropomorphic phantom while using three panoramic machines.

RESULTS

The dosemeters demonstrated consistent dose linearity (coefficient of variation<1.5%) and no significant energy dependency (coefficient of variation<1.5%) under the applied exposure conditions. They also exhibited negligible angular dependency (≤ 10%). The organ doses of the X-ray as a result of panoramic imaging by three machines were calculated using the dosemeters.

CONCLUSION

OSLDs can be utilized to measure the organ doses in diagnostic radiology. The availability of these dosemeters in strip form proves to be reliably advantageous.

Population-based study of asymptomatic infection with Chlamydia trachomatis among female and male students

There are few epidemiological studies of asymptomatic chlamydial infection among students in non-medical settings with minimal bias and improved accuracy; thus, useful data from screening among students are limited. We aimed to obtain accurate epidemiological information about asymptomatic chlamydial infection among students in non-medical settings. A population-based cross-sectional survey of 10,440 >or=18-year-old asymptomatic students who volunteered for a urine screening test for chlamydia was conducted. The prevalences of asymptomatic infection were 9.5% for women and 6.7% for men. Multivariate analysis revealed the risk factors to be a lifetime history of >or=4 sexual partners for women (odds ratio [OR] 3.17) and inconsistent condom use for men (OR 4.18). For both sexes, younger age at first intercourse was associated with a higher rate of inconsistent condom use. This study produced accurate epidemiological information on asymptomatic chlamydial infection. These results may contribute to the establishment of preventive countermeasures against such infection.

"Living electrode" as a long-lived photoconverter for biophotolysis of water

Living blue-green algae (Mastigocladus laminosus), immobilized on an SnO(2) optically transparent electrode with calcium alginate, functioned as an anodic photoelectrode on continuous illumination for periods of time adequate for use in a conventional electrochemical cell. This "living electrode" shows promise of use as a long-lived photoconverter of solar radiant energy to electric energy and as a suitable replacement for unstable chloroplast systems.

[Thymic cancer with superior vena cava invasion reconstructed by ready-made Y-graft]

A 57-year-old woman was admitted to our hospital with a complaint of left supraclavicular lymph node's swelling in January 2007. Computed tomography (CT) showed the lobulated tumor suspected of superior vena cava (SVC) invasion, located in the anterior mediastinum, 5 x 3 cm in size. The patient underwent thymectomy, resection of SVC, and partial resection of the right upper lobe. SVC was reconstructed by ready-made Y-graft (Hemashied phi 18 x 9 mm). Histopathological diagnosis was thymic cancer, poorly differentiated squamous cell carcinoma. The patient was discharged on 21st postoperative day. Postoperative radiotherapy (RT : 12.6 Gy) was canceled for the side effect. Alternatively, adjuvant chemotherapy [carboplatin (CBDCA) +paclitaxel (PTX)] was administered. Additional RT (50 Gy) was given to the lesion of local recurrence 1 and half year after the operation. The patient was alive without any signs of recurrence after RT. Left side bypass graft was patent at 8 months postoperatively, but was obliterated thereafter. Right side bypass is patent at more than 2 years postoperatively. Ready-made Y-graft can be one of the choices of SVC reconstruction.

Solubilization of excess sludge in activated sludge process using the solar photo-Fenton reaction

The solubilization of excess sludge by the solar photo-Fenton reaction has been investigated for the reduction of excess sludge in the activated sludge process. The solubilization kinetics depended on the dosages of the Fenton reagents, Fe and H(2)O(2). Increases of initial Fe and H(2)O(2) concentrations in their ranges studied in this work continuously enhanced the sludge solubilization. Cell lysis by the photo-Fenton reaction caused the increase in dissolved chemical oxygen demand (COD) in the first step of sludge solubilization. The further oxidative decomposition of the discharged organic compounds by the photo-Fenton reaction led to the decrease in the dissolved COD as the second step of sludge solubilization. The increase of dissolved COD in the first step of sludge solubilization and the consumption of H(2)O(2) could be described by the pseudo-zero order kinetics based on the accumulated light energy. About 40% reduction of mixed-liquor suspended solids (MLSS) by the solar photo-Fenton reaction was found. It was found that solar light used as a light energy source instead of costly and hazardous artificial UV light was very effective. The dissolved COD for solar photo-Fenton reaction increased faster and by 1.5 times as compared with that by artificial UV light.

Tachycardia-dependent right bundle-branch block with supernormal conduction

This paper reports the case of a 76-year-old man in whom atrial flutter with varying atrioventricular block and intermittent right bundle-branch block was found. This is the first report on tachycardia-dependent right bundle-branch block associated with supernormal conduction in a case of atrial flutter. When an impulse is conducted to the ventricles beyond 0.72 s after a QRS complex of right bundle-branch block configuration, the impulse falls after the abnormally long effective refractor period of the right bundle branch and passes through the right bundle branch. When the conducted impulse occurs within 0.72 s after a QRS complex of right bundle-branch block configuration, the impulse usually falls in the refractory period and is blocked in the right bundle branch; however, only when the impulse occurs 0.48 or 0.49 s after that does it fall in the supernormal period and passes through the right bundle branch. The findings in the present report strengthen our previous suggestion that the presence of supernormal conduction plays an important role in the initiation of reentrant ventricular tachycardia.

Phylogeny of the Drosophila immigrans species group (Diptera: Drosophilidae) based on Adh and Gpdh sequences

The immigrans species group in the Drosophilinae is one of the representative species groups of Drosophila in East Asia. Although this group constitutes a significant part of the drosophilid fauna in the Old World, only a few species have been analyzed in previous molecular phylogenetic studies. To study the phylogeny of the immigrans group, we analyzed the nucleotide sequences of two nuclear genes, alcohol dehydrogenase (Adh) and glycerol-3-phosphate dehydrogenase (Gpdh), for 36 drosophilid species, including 12 species of the immigrans group. In the resultant phylogenetic trees, 10 species of the immigrans group (D. immigrans, D. formosana, D. ruberrima, D. albomicans, D. nasuta, D. neonasuta, D. pallidifrons, D. hypocausta, D. neohypocausta, D. siamana) consistently formed a clade (the immigrans group proper), although the phylogeny within this clade did not exactly correspond to the classification of species subgroups. However, D. annulipes and D. quadrilineata, both of which belong to the quadrilineata subgroup of the immigrans group, were not included in the immigrans group proper. Furthermore, we obtained the unexpected result that D. annulipes was included in a clade comprising Scaptomyza and Hawaiian Drosophila, together with D. maculinotata of the funebris group, although the phylogenetic relationships within this clade remain uncertain and need to be substantiated with further studies. Thus, according to the present study, the immigrans group is polyphyletic.

Genetic features of Khoton Mongolians revealed by SNP analysis of the X chromosome

The Khoton Mongolian population is a small and relatively isolated ethnic group residing predominantly in the northwestern part of Mongolia. A recent genetic study of the Y chromosome revealed that the major Mongolian ethnic groups have a relatively close genetic affinity to populations in the northern part of East Asia, while the Khoton population reflected an apparent genetic differentiation from the other Mongolian populations. To further investigate the genetic features of the Khoton and the other Mongolian populations, we analyzed the single nucleotide polymorphisms (SNPs) in the Xq13.3 region, which is thought to have an extremely low level of recombination in the human X chromosome. We found that the frequency distribution of Xq13.3 haplotypes in the Khoton population was substantially different from those in three other Mongolian populations (Khalkh, Uriankhai, and Zakhchin). The same relationship was also revealed by the results from the population tree and principal-component (PC) analysis based on the allele frequencies. These results are largely consistent with the hypothesis that the Khoton population descended from a nomadic tribe of Turkish origin, which has been supported by previous anthropological, historical, and Y-chromosome studies. However, the population structure analysis produced an additional finding, namely, that the Khoton population is likely to be an admixed population.

Initial functional status predicts infections during steroid therapy for renal diseases

BACKGROUND AND AIM

Corticosteroid therapy is an effective way of treatment for many renal diseases, however, it is sometimes associated with infections. Our aim is to identify useful predictive markers of infection during steroid therapy.

METHODS

We examined 121 patients (M/F = 71/50, mean age 43.8, range 15 - 82 years) who were treated with corticosteroids (IgA nephropathy in 51, minimal-change disease in 17, membranous nephropathy in 16 rapidly progressive glomerulonephritis (RPGN) in 13, lupus nephritis in 12 and other disorders in 12). Karnofsky's performance score (KPS) was employed to assess the physical functional status at the time of diagnosis. Infections were defined as conditions that required more than 1-week care, and those that caused the patient's death.

RESULTS

Nineteen patients (15.7%) had infections during treatment. A logistic multivariate analysis showed significant correlations between infection and the use of immunosuppressive agents (relative risk RR = 7.7, p = 0.0265), ages of 52.9 years or more (RR = 13.5, p = 0.0026), initial number of lymphocytes (Lym) less than 1.250/microl (RR = 14.2, p = 0.0011), and KPS less than 77.4 (RR = 12.1, p = 0.0020). All correlations with infection were independent of all the other variables listed above.

CONCLUSION

KPS, along with age, Lym and the use of immunosuppressive agents, are useful for the prediction of infectious complications during steroid therapy.

Glutathione S-transferase (GST) M1, T1 and N-acetyltransferase 2 (NAT2) polymorphisms and urothelial cancer risk with tobacco smoking

The objective of this study was to examine the association between the genetic polymorphism of glutathione S-transferase (GST) M1, T1 and N-acetyltransferase 2 (NAT2) genes and urothelial cancer risk in relation to smoking status. In this study, 325 Japanese patients with urothelial transitional cell carcinoma and 325 healthy controls were compared for frequencies of GSTM1, T1 and NAT2 genotypes. The frequencies of GSTM1 null genotype and NAT2 slow genotype were significantly higher in the cases than in the controls (adjusted odds ratio (OR) 1.37, 95% confidence interval (CI) 1.01-1.87, adjusted OR 3.09, 95% CI 1.69-5.63, individually). Furthermore, the risk of GSTM1 null genotype and NAT2 slow genotype was higher among smokers (adjusted OR 1.48, 95% CI 1.01-2.15, adjusted OR 4.28, 95% CI 1.96-9.36, individually). The regression analysis of cancer risk as a function of the amount of smoking showed that the susceptibility of people who had GSTM1 null genotype increased from 45 pack-years, while the susceptibility of people with NAT2 intermediate or slow genotype increased rapidly from 25 pack-years, compared with non-smokers. A multiplicative interaction between NAT2 intermediate or slow genotype and pack-years of smoking was found (P<0.001), but GSTM1 null genotype was not (P=0.06). Our results indicate that the GSTM1 null genotype and NAT2 intermediate or slow genotype are associated with an increased risk of urothelial cancer in relation to smoking amounts. Furthermore, the interaction between NAT2 intermediate or slow genotype and pack-years of smoking has a strong impact on urothelial cancer.

Phylogeny and Evolution of Butterflies of the Genus Parnassius: Inferences from Mitochondrial 16S and ND1 Sequences

Phylogenetic relationships among species of the genus Parnassius and its related taxa were analyzed by comparing nucleotide sequences of mitochondrial 16S ribosomal RNA (504 sites) and NADH-dehydrogenase subunit 1 (469 sites). In the phylogenetic trees, Parnassius was found to be most closely related to Hypermnestra helios, whereas Archon apollinus, which has been classified in the tribe Parnassiini together with Parnassius and Hypermnestra, was more closely related to members of the tribe Zerynthiini. Within the Parnassius clade, six major clades corresponding to species groups were well supported, although the phylogenetic relationships among them were not clear. Although the results of the present study were in agreement with those of a previous phylogenetic study based on mitochondrial NADH-dehydrogenase subunit 5 sequences, our study strongly supported a close relationship between Parnassius and Hypermnestra, which was not well supported in the previous study.

Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis

About 20 ethnic groups reside in Mongolia. On the basis of genetic and anthropological studies, it is believed that Mongolians have played a pivotal role in the peopling of Central and East Asia. However, the genetic relationships among these ethnic groups have remained obscure, as have their detailed relationships with adjacent populations. We analyzed 16 binary and 17 STR polymorphisms of human Y chromosome in 669 individuals from nine populations, including four indigenous ethnic groups in Mongolia (Khalkh, Uriankhai, Zakhchin, and Khoton). Among these four Mongolian populations, the Khalkh, Uriankhai, and Zakhchin populations showed relatively close genetic affinities to each other and to Siberian populations, while the Khoton population showed a closer relationship to Central Asian populations than to even the other Mongolian populations. These findings suggest that the major Mongolian ethnic groups have a close genetic affinity to populations in northern East Asia, although the genetic link between Mongolia and Central Asia is not negligible.