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We discovered biallelic intragenic structural variations (SVs) in FGF12 by applying long-read whole genome sequencing to an exome-negative patient with developmental and epileptic encephalopathy (DEE). We also found another DEE patient carrying a biallelic (homozygous) single-nucleotide variant (SNV) in FGF12 that was detected by exome sequencing. FGF12 heterozygous recurrent missense variants with gain-of-function or heterozygous entire duplication of FGF12 are known causes of epilepsy, but biallelic SNVs/SVs have never been described. FGF12 encodes intracellular proteins interacting with the C-terminal domain of the alpha subunit of voltage-gated sodium channels 1.2, 1.5, and 1.6, promoting excitability by delaying fast inactivation of the channels. To validate the molecular pathomechanisms of these biallelic FGF12 SVs/SNV, highly sensitive gene expression analyses using lymphoblastoid cells from the patient with biallelic SVs, structural considerations, and Drosophila in vivo functional analysis of the SNV were performed, confirming loss-of-function. Our study highlights the importance of small SVs in Mendelian disorders, which may be overlooked by exome sequencing but can be detected efficiently by long-read whole genome sequencing, providing new insights into the pathomechanisms of human diseases., (© 2023 Ohori et al.)

In Peru, the number of species of edible seaweeds within the genera Chondracanthus , Porphyra (hereafter P. ), Pyropia (hereafter Py. ), and Ulva has not been fully established, nor is there a significant level of information available related to their chemical and nutritional composition. This study involved the biochemical analysis of species belonging to ten genera of macroalgae, known edible and some of which have the potential to be used as food, including six red ( Callophyllis, Chondracanthus, Mazzaella , Porphyra , Pyropia , and Rhodymenia ), two green ( Ulva and Codium ), and two brown ( Eisenia and Lessonia ) species collected along the Peruvian coast (6°-17° S). In the evaluation of 37 specimens, differences were found in the proximal composition, amino acid composition, and fatty acid profiles, which were specific to subgroups and supported their taxonomic classification, mainly at the order level. The red algae Porphyra/Pyropia (Bangiales) had the highest average percentage of protein (24.10%) and carbohydrates (59.85%) and the lowest percentage of ash (7.95%). Conversely, the brown alga Eisenia (Laminariales) had the lowest average percentage of protein, with different values related to the structure: 14.11% at the level of the frond and 9.46% at the level of the stipe. On the other hand, Bryopsidales green algae showed the highest average percentages of lipids (5.38%). The moisture percentages ranged from 4 to 16%, and no relevant significant differences were shown between the orders. The characteristic amino acids in all of the studied groups were glutamic acid, aspartic acid, alanine, and leucine. The highest average of the essential amino acids ratio was obtained for the Gigartinales red algae (48.65%), and the highest values of the essential amino acid index (EAAI) were obtained for the Ulvales, Laminariales, Gigartinales, and Rhodymeniales algae (EAAI > 0.92). The highest average relative percentage of fatty acids was obtained for polyunsaturated fatty acids, followed by saturated fatty acids. The major component of the ω6 fatty acids from red and brown algae was arachidonic acid (C20:4n - 6). The highest level of ω3 fatty acids was observed for the eicosapentaenoic acids (EPA) in red algae. The highest median ω6/ω3 ratio was displayed by the red alga Callophyllis variegata (Gigartinales). A detailed knowledge of edible seaweeds, and those considered potentially edible, would help to diversify the diet based on macroalgae in Peru.

Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean populations has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2232 single nucleotide polymorphisms (SNPs) to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. Approximate Bayesian Computation (ABC) analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species., (© 2022 John Wiley & Sons Ltd.)

Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, which make this region ideal for assessing genetic attributes of coral populations. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands. By merging newly obtained genome resequencing data with previously published data, we identified more than 4 million genome-wide SNPs in 303 colonies collected at 22 locations, with sequencing coverage ranging from 3.91× to 27.41×. While population structure analyses revealed genetic similarities between the southernmost and northernmost locations, separated by >1000 km, several subpopulations in intermediate locations suggested limited genetic admixture, indicating conflicting migration tendencies in the Nansei Islands. Although migration networks revealed a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, and similar unexpected population complexities may be expected for other marine species with similar reproductive modes., (© 2022 John Wiley & Sons Ltd.)

Aims: Resource-strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings., Methods: We used simple information theory calculations on a brain cancer simulation model and real-world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&E and Olig2 stained images obtained from digital slides. An auto-adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH-mutant tumors., Results: Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH-mutant tumors. The predictive models may facilitate the reduction of false-positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing., Conclusions: We posit that this approach provides an improvement on the cIMPACT-NOW workflow recommendations for IDH-mutant tumors and a framework for future resource and testing allocation., (© 2022 The Authors. Brain Pathology published by John Wiley & Sons Ltd on behalf of International Society of Neuropathology.)

The Peruvian sea is one of the most productive ecosystems in the world. Phytoplankton production provides food for fish, mammals, mollusks and birds. This trophic network is affected by the presence of toxic phytoplankton species. In July 2017, samples of phytoplankton were obtained from Paracas Bay, an important zone for scallop ( Argopecten purpuratus ) aquaculture in Peru. Morphological analysis revealed the presence of the genus Pseudo-nitzschia , which was isolated and cultivated in laboratory conditions. Subsequently, the monoclonal cultures were observed by scanning electron microscopy (SEM), and identified as P. multistriata , based on both the morphological characteristics, and internal transcribed spacers region (ITS2) sequence phylogenetic analysis. Toxin analysis using liquid chromatography (LC) with high-resolution mass spectrometry (HRMS) revealed the presence of domoic acid (DA) with an estimated amount of 0.004 to 0.010 pg cell -1 . This is the first report of DA from the coastal waters of Peru and its detection in P. multistriata indicates that it is a potential risk. Based on our results, routine monitoring of this genus should be considered in order to ensure public health.

Lessonia spicata (Suhr) Santelices is the most ecologically and economically important kelp from Pacific South America. Here, we contribute to the bioinformatics and evolutionary systematics of the species by performing high throughput sequencing on L. spicata from Valparaiso, Chile. The L. spicata complete mitogenome is 37,097 base pairs (bp) in length and contains 66 genes (GenBank accession MK965907), the complete plastid genome is 130,305 bp and has 173 genes (accession MK965908), and the data assembled 7,630 bp of the nuclear ribosomal cistron (accession MK965909). The organellar genomes are similar in structure and content to others published from the Laminariales., Competing Interests: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Genome evolution and development of unicellular, multinucleate macroalgae (siphonous algae) are poorly known, although various multicellular organisms have been studied extensively. To understand macroalgal developmental evolution, we assembled the ∼26 Mb genome of a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that the diversification of the class Ulvophyceae, including C. lentillifera, occurred before the split of the Chlorophyceae and Trebouxiophyceae. Compared with other green algae, the TALE superclass of homeobox genes, which expanded in land plants, shows a series of lineage-specific duplications in this siphonous macroalga. Plant hormone signalling components were also expanded in a lineage-specific manner. Expanded transport regulators, which show spatially different expression, suggest that the structural patterning strategy of a multinucleate cell depends on diversification of nuclear pore proteins. These results not only imply functional convergence of duplicated genes among green plants, but also provide insight into evolutionary roots of green plants. Based on the present results, we propose cellular and molecular mechanisms involved in the structural differentiation in the siphonous alga., (© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

Foxp3-expressing CD4 + regulatory T (Treg) cells need to differentiate into effector Treg (eTreg) cells to maintain immune homeostasis. T-cell receptor (TCR)-dependent induction of the transcription factor IRF4 is essential for eTreg differentiation, but how IRF4 activity is regulated in Treg cells is still unclear. Here we show that the AP-1 transcription factor, JunB, is expressed in eTreg cells and promotes an IRF4-dependent transcription program. Mice lacking JunB in Treg cells develop multi-organ autoimmunity, concomitant with aberrant activation of T helper cells. JunB promotes expression of Treg effector molecules, such as ICOS and CTLA4, in BATF-dependent and BATF-independent manners, and is also required for homeostasis and suppressive functions of eTreg. Mechanistically, JunB facilitates the accumulation of IRF4 at a subset of IRF4 target sites, including those located near Icos and Ctla4. Thus, JunB is a critical regulator of IRF4-dependent Treg effector programs, highlighting important functions for AP-1 in Treg-mediated immune homeostasis.

Background: The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch., Results: The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes., Conclusions: Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families.

We report the clinical case of an adult patient referred to our hospital because of trismus due to a tumour in the right infratemporal and pterygomaxillary fossa. He referred hyporexia, weight loss and right trigeminal neuralgia. On physical examination, he had trismus and diplopia. On neuroimaging, the tumour invaded the central nervous system affecting the right temporal lobe and orbit, and the sellar region. Tumour biopsy revealed foamy histiocytes and isolated giant multinuclear cells immunoreactive to CD68 and negative to CD1a and S100. A diagnosis of Erdheim-Chester disease was made. Non-evidence of large bone involvement was found in neither plain radiographs nor Technetium 99 m bone scintigraphy. BRAFV600E mutation analysis was negative. Because of raised intracranial pressure, a debulking surgery of the intracranial histiocytic process was performed. The patient improved his symptoms and remains clinically stable after 12 months of treatment with pegylated interferon-α-2a 180 µg/weekly., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

CD4 + T-helper cells producing interleukin-17 (IL-17), known as T-helper 17 (T H 17) cells, comprise heterogeneous subsets that exhibit distinct pathogenicity. Although pathogenic and non-pathogenic T H 17 subsets share a common RORγt-dependent T H 17 transcriptional programme, transcriptional regulatory mechanisms specific to each of these subsets are mostly unknown. Here we show that the AP-1 transcription factor JunB is critical for T H 17 pathogenicity. JunB, which is induced by IL-6, is essential for expression of RORγt and IL-23 receptor by facilitating DNA binding of BATF at the Rorc locus in IL-23-dependent pathogenic T H 17 cells, but not in TGF-β1-dependent non-pathogenic T H 17 cells. Junb-deficient T cells fail to induce T H 17-mediated autoimmune encephalomyelitis and colitis. However, JunB deficiency does not affect the abundance of gut-resident non-pathogenic T H 17 cells. The selective requirement of JunB for IL-23-dependent T H 17 pathogenicity suggests that the JunB-dependent pathway may be a therapeutic target for autoimmune diseases.

The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is economically one of the most important edible seaweeds, and is cultivated for market primarily in Okinawa, Japan. C. okamuranus constitutes a significant source of fucoidan, which has various physiological and biological activities. To facilitate studies of seaweed biology, we decoded the draft genome of C. okamuranus S-strain. The genome size of C. okamuranus was estimated as ∼140 Mbp, smaller than genomes of two other brown algae, Ectocarpus siliculosus and Saccharina japonica Sequencing with ∼100× coverage yielded an assembly of 541 scaffolds with N50 = 416 kbp. Together with transcriptomic data, we estimated that the C. okamuranus genome contains 13,640 protein-coding genes, approximately 94% of which have been confirmed with corresponding mRNAs. Comparisons with the E. siliculosus genome identified a set of C. okamuranus genes that encode enzymes involved in biosynthetic pathways for sulfated fucans and alginate biosynthesis. In addition, we identified C. okamuranus genes for enzymes involved in phlorotannin biosynthesis. The present decoding of the Cladosiphon okamuranus genome provides a platform for future studies of mozuku biology., (© The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

Bone involvement of syphilis can be observed in tertiary and congenital syphilis. It is infrequent during the secondary stage. The skull is the most affected bone in secondary syphilis, and its most frequent form of presentation is proliferative osteitis. If the skull is affected, headache is usual and can be as intense as in meningitis. Osteolyitic lesions may be seen in complimentary imaging studies, with a moth eaten aspect. These lesions raise concern over a number of differential diagnoses, among which are infectious, inflammatory and neoplastic diseases. The definitive diagnosis is made by bone biopsy of the compromised bone. Molecular techniques in the affected tissues increases diagnostic performance. There is no standardized treatment protocol for syphilis since there are no guidelines available. We report a case of a 19 year old female, presenting with a unique osteolytic lesion in the skull due to secondary syphilis.

Although BMP4-induced differentiation of glioma stem cells (GSCs) is well recognized, details of the cellular responses triggered by this morphogen are still poorly defined. In this study, we established several GSC-enriched cell lines (GSC-ECLs) from high-grade gliomas. The expansion of these cells as adherent monolayers, and not as floating neurospheres, enabled a thorough study of the phenotypic changes that occurred during their differentiation. Herein, we evaluated GSC-ECLs' behavior toward differentiating conditions by depriving them of growth factors and/or by adding BMP4 at different concentrations. After analyzing cellular morphology, proliferation and lineage marker expression, we determined that GSC-ECLs have distinct preferences in lineage choice, where some of them showed an astrocyte fate commitment and others a neuronal one. We found that this election seems to be dictated by the expression pattern of BMP signaling components present in each GSC-ECL. Additionally, treatment of GSC-ECLs with the BMP antagonist, Noggin, also led to evident phenotypic changes. Interestingly, under certain conditions, some GSC-ECLs adopted an unexpected smooth muscle-like phenotype. As a whole, our findings illustrate the wide differentiation potential of GSCs, highlighting their molecular complexity and paving a way to facilitate personalized differentiating therapies., (© 2015 International Society of Neuropathology.)

Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30 km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI, and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history.

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Cell-surface F1F0-ATP synthase was involved in the cell signaling mediating various biological functions. Recently, we found that cell-surface F1F0-ATP synthase plays a role on intracellular triacylglycerol accumulation in adipocytes, and yet, the underlying mechanisms remained largely unknown. In this study, we investigated the role of extracellular ATP on the intracellular triacylglycerol accumulation. We demonstrated that significant amounts of ATP were produced extracellularly by cultured 3T3-L1 adipocytes and that the antibodies against α and β subunits of F1F0-ATP synthase inhibited the extracellular ATP production. Piceatannol, a F1F0-ATP synthase inhibitor, and apyrase, an enzyme which degrades extracellular ATP, suppressed triacylglycerol accumulation. The selective P2Y1 receptor antagonist MRS2500 significantly inhibited triacylglycerol accumulation, whereas the selective P2X receptor antagonist NF279 has less effect. The present results indicate that cell-surface F1F0-ATP synthase on adipocytes is functional in extracellular ATP production and that the extracellular ATP produced contributes, at least in part, to the cell-surface F1F0-ATP synthase-mediated intracellular triacylglycerol accumulation in adipocytes through P2Y1 receptor.

The chaperone αB-crystallin (αBC) is a member of the small heat shock protein family and its point or truncated mutants cause the muscular disorder α-crystallinopathy. The illness is histologically characterized by accumulation of protein aggregates in muscle cells. Expression of the myopathy-causing R120G mutant of αBC, harboring an arginine-to-glycine mutation at position 120, results in aggregate formation. We demonstrated that tethering αBC to the endoplasmic reticulum (ER) membrane represses the protein aggregation mediated by the R120G mutant. ER-anchored αBC decreased the amount of the R120G mutant through autophagic proteolysis. In contrast, knockdown of ATG5, an E3 ligase essential for autophagy, in ER-anchored αBC-transfected cells restored the quantity of the R120G mutant. In this context, aggregate formation was still suppressed, indicating that ER-anchored αBC profoundly constrains aggregation competency of the R120G mutant separately from downregulating the abundance of the mutant. We have proposed that protein aggregation is prevented by manipulation of the ER microenvironment with αBC, and have shed light on a novel aspect of the ER as a therapeutic target., (Copyright © 2014 Elsevier Inc. All rights reserved.)

We investigated physical and chemical cues involved in male mating behavior of the white grub beetle, Dasylepida ishigakiensis (Scarabaeidae). When presented with female attractant pheromone (R)-2-butanol lures in a flight tunnel, nearly all males exhibited orientation and touching behaviors to freshly killed males and females and to intact glass models. Males landed and bent their abdomens on male and female bodies, but not on intact glass models. When treated with one female equivalent (FE) extract, washed immature male bodies and glass models both evoked stronger male responses than untreated equivalents, with the former eliciting a greater response than the treated glass models. Male responses to target male and female bodies decreased with increased numbers of washings of target bodies with organic solvents. These results suggest that the chemical factors that elicit male abdominal bending behavior are present on the body surface in both sexes. Washed immature male bodies treated with 1 FE or one male equivalent (ME) of extract induced strong male abdominal bending behavior. Washed mature female bodies treated with 1 ME extract also evoked male responses. Extracts of both sexes included factors eliciting male abdominal bending behavior. These results suggest that both physical and chemical cues derived from conspecifics cooperate to facilitate male mating recognition in D. ishigakiensis. The mating process of this species in the field is highly synchronized. Thus, after orienting to a female-like object, the only information males require by touching is whether the sex attractant pheromone that attracted them is indeed from a conspecific.

Background: Dinoflagellates are known for their capacity to form harmful blooms (e.g., "red tides") and as symbiotic, photosynthetic partners for corals. These unicellular eukaryotes have permanently condensed, liquid-crystalline chromosomes and immense nuclear genome sizes, often several times the size of the human genome. Here we describe the first draft assembly of a dinoflagellate nuclear genome, providing insights into its genome organization and gene inventory., Results: Sequencing reads from Symbiodinium minutum were assembled into 616 Mbp gene-rich DNA regions that represented roughly half of the estimated 1,500 Mbp genome of this species. The assembly encoded ∼42,000 protein-coding genes, consistent with previous dinoflagellate gene number estimates using transcriptomic data. The Symbiodinium genome contains duplicated genes for regulator of chromosome condensation proteins, nearly one-third of which have eukaryotic orthologs, whereas the remainder have most likely been acquired through bacterial horizontal gene transfers. Symbiodinium genes are enriched in spliceosomal introns (mean = 18.6 introns/gene). Donor and acceptor splice sites are unique, with 5' sites utilizing not only GT but also GC and GA, whereas at 3' sites, a conserved G is present after AG. All spliceosomal snRNA genes (U1-U6) are clustered in the genome. Surprisingly, the Symbiodinium genome displays unidirectionally aligned genes throughout the genome, forming a cluster-like gene arrangement., Conclusions: We show here that a dinoflagellate genome exhibits unique and divergent characteristics when compared to those of other eukaryotes. Our data elucidate the organization and gene inventory of dinoflagellates and lay the foundation for future studies of this remarkable group of eukaryotes., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Bone remodeling is regulated by local factors that regulate bone-forming osteoblasts and bone-resorbing osteoclasts, in addition to hormonal activity. Recent studies have shown that reactive oxygen species (ROS) act as an intracellular signal mediator for osteoclast differentiation. However the role of ROS on osteoblast differentiation is poorly understood. Here, we investigated the impact of ROS on osteoblastic differentiation of MC3T3-E1 cells. Osteogenic induction resulted in notable enhancement of mineralization and expression of osteogenic marker gene alkaline phosphatase, which were accompanied by an increase in ROS production. Additionally, we found that mitochondrial morphology dynamically changed from tubular reticulum to fragmented structures during the differentiation, suggesting that mitochondrial morphological transition is a novel osteoblast differentiation index. The antioxidant N-acetyl cysteine prevented not only ROS production but also mineralization and mitochondrial fragmentation. It is therefore suggested that the ROS-dependent signaling pathways play a role in osteoblast differentiation accompanied by mitochondrial morphological transition.

Atonic seizures are epileptic attacks characterised by a sudden loss or diminution of muscle tone. Structures corresponding to inhibitory cortical areas, such as the primary negative motor area or the supplementary negative motor area, could be responsible. We present findings observed in a patient with atonic seizures due to focal epilepsy, who underwent intracranial video-EEG monitoring and epilepsy surgery, and discuss possible underlying mechanisms. [Published with video sequences].

Objective: The objectives of this study were to present a case of a solitary intraventricular schwannoma with a review of the literature and to analyse the current theories of its origin., Description: A 16-year-old male patient, without any pathological, genetic or familial history of significance, presented with symptoms of intracranial hypertension and progressive left brachiocrural paresis. The magnetic resonance image showed a bulky intraventricular space-occupying lesion emerging from the posterior horn of the right lateral ventricle, with an irregular nodular component intimately connected to the choroid plexus, and a multiloculated cystic component extending beyond the ventricle., Surgical Approach: A right parietal craniotomy was performed, revealing a multiloculated cyst with xantochromic fluid and a soft brownish red nodule. The lesion was dissected surrounding the periphery and coagulating a vascular pedicle related to the wall of the right lateral ventricle and its choroid plexus. Total excision was achieved. The pathological exam reported an intraventricular schwannoma (WHO grade 1). The patient evolved favourably, with no recurrence at 36-month follow-up., Conclusion: The literature describes less than 45 cases of schwannomas not associated to cranial nerves of the following locations: intramedullary, leptomeningeal and only 12 intraventricular cases. The three theories explaining the origin of this last group describe: (1) a neoplastic transformation of peripheral nerve fibres, (2) a neoplastic transformation of autonomic neural tissue located within the intraventricular choroid plexus and (3) an abnormal embryogenesis leading to a failed migration of the neural crest cells. Complete resection is the therapeutic goal for this benign pathology to avoid recurrence.

Synthesis of four water-soluble resveratrol and piceatannol derivatives bearing symmetrically branched glyceryl trimer (BGL003) with a non-biocleavable linkage, and their biological evaluation as a mitochondrial fusion-inducing agent with cellular fat-reducing effect from cells, is described. The effect of Piceatannol-BGL003 conjugate was as high as that of original stilbenoids., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

In Rosai-Dorfman disease (RDD), exclusive extranodal involvement with lesions limited to the kidneys is very uncommon and has been described only in adult patients. Occasionally, human herpesvirus 6 (HHV-6) has also been detected in RDD tissue samples. We present the case of a 7-year-old boy referred to our center presenting a single solid mass in the right kidney measuring 3.4 cm, detected both on contrast computed tomography and magnetic resonance imaging. Surgical excision was successfully completed, and the pathology report informed characteristic histopathology and immmunohistochemistry features of RDD. Human herpesvirus 6 was detected and amplified by polymerase chain reaction, as well as by immunohistochemistry. We discuss imaging and histology-based differential diagnoses in the pediatric age group. Although RDD is a rare histiocytic disorder of unknown etiology and pathogenesis, the presence of HHV-6 observed in this case supports the possibility of an abnormal immunologic response linked to viral presence.

Pseudomonas aeruginosa causes both invasive (bacteremic) and chronic noninvasive infections. An increase in intestinal epithelial permeability is a characteristic of severe sepsis. Alterations in the normal barrier function of the gut mucosa may result in the translocation of microbial cells and products. On the otherhand, it has been demonstrated that statin use is associated with a lower risk of mortality from bloodstream infections. Therefore, we investigated the ability of P. aeruginosa PAO1 to translocate across the Madin-Darby canine kidney (MDCK) cell monolayers in the presence and absence of simvastatin. The bacteria readily translocated across MDCK cell monolayers after 3 h of infection irrespective of the presence or absence of the drug in the medium. However, the bacteria were less able to penetrate the MDCK monolayers in the presence of simvastatin than in its absence. A gentamicin survival assay demonstrated that simvastatin did not affect the bacteria's invasive behavior in the MDCK cells.

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species, Curtos costipennis and C. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups, C. costipennis in the Amami region, C. okinawanus in the Okinawa region, and C. costipennis in the Sakishima region. Their mtDNA sequences suggested that ancestral C. costipennis population was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided between C. costipennis in the Amami and C. okinawanus in the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0-1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

Malignant gliomas are the most common subtype of primary central nervous system (CNS) tumors. Their pathological classification, however, remains subjective, stimulating researchers to actively seek objective molecular markers to discover alternative and more reproducible tools for improved subtypification. Herein, we present a global survey of genomic alterations in oligodendroglial tumors (OT). Genetic and epigenetic alterations identified in this study are correlated with OT molecular groups we have recently reported: a neurogenic group composed of tumors with loss of heterozygosity (LOH) at 1p-19q, IDH1 mutations, and MGMT promoter methylation, showing good prognosis; an intermediate group, presenting TP53 mutations or LOH at 17p, IDH1 mutations, and GSTP1 promoter methylation; and a proliferative group, presenting major genetic alterations (LOH at 10q, EGFR amplification, and CDKN2A/ARF deletion) and poor prognosis. These results allowed us to refine our molecular characterization associated with prognosis, referring exclusively to oligodendroglial tumors.

Background: Hepatocyte growth factor (HGF) is known to be involved in the resolution of pulmonary inflammation and repair of acute lung injury. Legionella pneumonia is sometimes complicated by acute lung injury. Our study aimed to determine the role of serum HGF levels in Legionella pneumonia., Methods: Sera from patients with Legionella pneumonia (42 cases), other bacterial pneumonia (33 cases), pulmonary tuberculosis (19 cases), and normal controls (29 cases) were collected. The serum HGF levels for each serum sample were determined by sandwich ELISA. Clinical and laboratory data were collected by reviewing the medical charts., Results: Serum HGF levels were higher in patients with Legionella pneumonia than in those with other bacterial pneumonia, pulmonary tuberculosis, and controls. The HGF levels were compared with white blood cell counts, C-reactive protein, Alanine amino-transferase, and lactate dehydrogenase (LDH). The HGF levels were correlated to serum LDH levels. Moreover, serum HGF levels were significantly higher in non-survivors than in survivors., Conclusions: HGF levels increased in severer pneumonia caused by Legionella, suggesting that HGF might play a significant role in the Legionella pneumonia.

An effective malaria vaccine is a public health priority. Proteins expressed during the blood-stage of the parasite life cycle have been proposed as good vaccine candidates. No such blood-stage vaccine, however, is available against Plasmodium falciparum, the deadliest Plasmodium species. We show here that P. falciparum serine repeat antigen 5 (SERA5) is a potential vaccine immunogen. We have constructed a new recombinant molecule of SERA5, namely SE36, based on previously reported SE47' molecule by removing the serine repeats. Epidemiological study in the holo-endemic population of Solomon Islands shows highly significant correlation of sero-conversion and malaria protective immunity against this antigen. Animal experiments using non-human primates, and a human phase 1a clinical trial assessed SE36 vaccine immunogenicity. Vaccination of squirrel monkeys with SE36 protein and aluminum hydroxyl gel (SE36/AHG) conferred protection against high parasitemia and boosted serum anti-SE36 IgG after P. falciparum parasite challenge. SE36/AHG was highly immunogenic in chimpanzees, where serum anti-SE36 IgG titers last more than one year. Phase 1a clinical trial (current controlled trials, ISRCTN78679862) demonstrated the safety and immunogenicity of SE36/AHG with 30 healthy adults and 10 placebo controls. Three subcutaneous administrations of 50 and 100microg dose of SE36/AHG were well-tolerated, with no severe adverse events; and resulted in 100% sero-conversion in both dose arms. The current research results for SE36/AHG provide initial clinical validation for future trials and suggest clues/strategies for further vaccine development.

Pigment epithelium-derived factor (PEDF), a potent blocker of angiogenesis in vivo, and of endothelial cell migration and tubule formation, binds with high affinity to an as yet unknown protein on the surfaces of endothelial cells. Given that protein fingerprinting suggested a match of a approximately 60 kDa PEDF-binding protein in bovine retina with Bos taurus F(1)-ATP synthase beta-subunit, and that F(1)F(o)-ATP synthase components have been identified recently as cell-surface receptors, we examined the direct binding of PEDF to F(1). Size-exclusion ultrafiltration assays showed that recombinant human PEDF formed a complex with recombinant yeast F(1). Real-time binding as determined by surface plasmon resonance demonstrated that yeast F(1) interacted specifically and reversibly with human PEDF. Kinetic evaluations revealed high binding affinity for PEDF, in agreement with PEDF affinities for endothelial cell surfaces. PEDF blocked interactions between F(1) and angiostatin, another antiangiogenic factor, suggesting overlapping PEDF-binding and angiostatin-binding sites on F(1). Surfaces of endothelial cells exhibited affinity for PEDF-binding proteins of approximately 60 kDa. Antibodies to F(1)beta-subunit specifically captured PEDF-binding components in endothelial plasma membranes. The extracellular ATP synthesis activity of endothelial cells was examined in the presence of PEDF. PEDF significantly reduced the amount of extracellular ATP produced by endothelial cells, in agreement with direct interactions between cell-surface ATP synthase and PEDF. In addition to demonstrating that PEDF binds to cell-surface F(1), these results show that PEDF is a ligand for endothelial cell-surface F(1)F(o)-ATP synthase. They suggest that PEDF-mediated inhibition of ATP synthase may form part of the biochemical mechanisms by which PEDF exerts its antiangiogenic activity.

Using liposome systems, we found that gallates with short alkyl chains were located in the external medium and those with longer alkyl chains were located in the surface region of lipid bilayer. Combinations of these gallates remarkably reduced oxacillin MICs against methicillin-resistant Staphylococcus aureus to below the antibiotic breakpoint (< or = 2 microg/ml).

A mating disruption experiment to control Melanotus okinawensis Ohira (Coleoptera: Elateridae) was conducted at a sugarcane (Saccharum spp.) field and a wild Japanese pampas, Miscanthus sinensis Anderss, grassland on Minami-Daito Island (3,057 ha) from 2001 to 2007. The sugarcane field and the pampas grassland were treated with synthetic sex pheromone that evaporated from a polyethylene tube dispenser. The mean total catches obtained by monitoring traps in the sugarcane fields decreased by 96.1% in 2001 from the previous year on Minami-Daito Island. The mean total trap catches in the treated area further decreased by 74.0% from 2001 until 2007 as cumulative effects. Simultaneously, the number of adults captured by hand decreased from 4.7 per sugarcane field in 2001 to 0.5 in 2007 (89.3% reduction), whereas those captured in the untreated area (Miyagi Island) did not show such a decrease. The mating rates were significantly lower in the females captured in the treated area (14.3-71.4%) than those in the untreated area (96.9-100%). However, the amount of the decrease in the trap catches was relatively small at first (39.6% reduction) in the Japanese pampas grassland on the periphery of the Island. This was probably due to the loss of pheromone substance caused by the strong seasonal wind in the periphery. However, mean total trap catches at the periphery also decreased within several years; significant decreases were detected until 2003, 2006, and 2007. These results indicated that the mating disruption effectively reduced an isolated population of M. okinawensis.

After establishing a linear relationship between the amount of penicillin-binding protein (PBP) 2a and membrane proteins of methicillin-resistant Staphylococcus aureus (MRSA) COL by dot-blot analysis using an antibody against PBP 2a, we determined the PBP 2a quantities in membrane fractions prepared from 14 different MRSA cells. Methicillin-sensitive S. aureus ATCC 6538P was used as a quality control strain. The amounts of PBP 2a diverged among the strains, and no relationship to beta-lactam MIC values were observed in the corresponding strains.

Migration inhibitory factor-related protein 8 (MRP8) and MRP14 are expressed by myeloid cells and especially known as marker proteins of an immature and inflammatory subtype of macrophages. In this study, we immunohistochemically examined an accumulation of MRP8+ and MRP14+ macrophages in skin lesions during Leishmania major infection in susceptible BALB/c and RAG-2-/- mice. L. major infection caused the development of a nodular type of skin lesion at the infection site in mice and a massive accumulation of macrophages was observed in the lesions at four weeks after the infection. Immunohistochemical analyses showed MRP8+ and MRP14+ macrophages are predominant cell types in the skin lesions in both mouse strains. In contrast, F4/80+ cells, which correspond to mature macrophages, were rarely found in the skin lesions. These data suggest that the accumulation of inflammatory subtype of macrophages in BALB/c mice during L. major infection can be induced without acquired immune responses.

Here we show that the cell-surface expression of the alpha subunit of H(+)-ATP synthase is markedly increased during adipocyte differentiation. Treatment of differentiated adipocytes with small molecule inhibitors of H(+)-ATP synthase or antibodies against alpha and beta subunits of H(+)-ATP synthase leads to a decrease in cytosolic lipid droplet accumulation. Apolipoprotein A-I, which has been shown to bind to the ectopic beta-chain of H(+)-ATP synthase and inhibit the activity of cell-surface H(+)-ATP synthase, also was found to inhibit cytosolic lipid accumulation. These results suggest that the cell-surface H(+)-ATP synthase has a previously unsuspected role in lipid metabolism in adipocytes.

A 55-year-old woman was admitted to our hospital because of dyspnea on exertion. Hypoxemia and restrictive ventilatory impairment were observed on admission. Chest radiographs showed diffuse patchy infiltration shadows in both lungs. We suspected drug-induced pneumonitis, because her history of fever seemed to be related to drug administration for sinusitis. Her symptoms and findings were gradually decreased by discontinuation of the drugs. Transbronchial lung biopsy specimens showed lymphocyte dominant infiltration in the alveolar septa and Masson bodies. Drug lymphocyte stimulation tests were positive for levofloxacin and shin-i-seihai-to, a kampo medicine. On the basis of these findings, we arrived at a diagnosis of drug-induced pneumonitis caused by these drugs.

Mitochondria are highly dynamic organelles in eukaryotic cells. Although the role of mitochondria in metabolism, ATP production and apoptosis is more widely recognized, alterations in mitochondrial morphology and abundance are also important for cellular functions. Here we investigated mitochondrial dynamics in synchronized HeLa cells in which the major stages of the cell cycle of the observed cells were resolved by staining phosphorylate histones H1 and H3, and showed that mitochondria exist as filamentous network structures throughout the cell cycle progression, changing their morphology, distribution, and abundance. The current results suggest that mitochondrial condensation occurred at prophase is required for the proper progression of mitochondrial division.

We found that a mouse homolog of human DNA polymerase delta interacting protein 38, referred to as Mitogenin I in this paper, and mitochondrial single-stranded DNA-binding protein (mtSSB), identified as upregulated genes in the heart of mice with juvenile visceral steatosis, play a role in the regulation of mitochondrial morphology. We demonstrated that overexpression of Mitogenin I or mtSSB increased elongated or fragmented mitochondria in mouse C2C12 myoblast cells, respectively. On the other hand, the silencing of Mitogenin I or mtSSB by RNA interference led to an increase in fragmented or elongated mitochondria in the cells, respectively, suggesting that Mitogenin I and mtSSB are involved in the processes of mitochondrial fusion and fission, respectively. In addition, we showed that the silencing of Mitogenin I resulted in an increase in the number of trypan blue-positive cells and the silencing of mtSSB resulted in an enhancement of the sensitivity of the cells to apoptotic stimulation by etoposide. The present results demonstrated that these proteins play a role in cell survival.

Two distinct electroantennographycally active (EAG-active) components, A and B, and a weakly active component C were found in a solvent extract from virgin females of the Ishigaki strain of the tussock moth, Orgyia postica (Walker). Components A, B, and C were found in the extract of the females at 4.0, 0.5, and 4.0 ng/female respectively. Components A, B, and C were identified as (6Z,9Z,11S,12S)-11,12-epoxyhenicosa-6,9-diene [(11S,12S)-1: posticlure], (6Z)-henicos-6-en-11-one (2), and (6Z,9Z)-henicosa-6,9-diene (3), respectively. Component B was absent in the extract from the Okinawa strain, in which components A and C were present at 2.0 and 1.5 ng/female respectively. (11S,12S)-1 and the racemic mixture showed attractiveness for both the Okinawa and Ishigaki strains, whereas (11R,12R)-1 did not. The addition of 2 significantly reduced the trap catches with (11S,12S)-1 on the Okinawa strain which lacked 2, while there was no significant inhibitory effect on the Ishigaki strain. The addition of 3 to (11S,12S)-1 did not significantly affect trap catches at Ishigaki or Okinawa. This confirmed that the attractant pheromone of O. postica of the Ishigaki strain is also (11S,12S)-1.

A single component in extracts of virgin female Milionia basalis pryeri moths elicited responses from male moth antennae. This compound (ca. 7 ng/female) was identified as (Z,Z)-(3S,4R)-3,4-epoxynonadeca-6,9-diene by GC-MS and NMR analyses, microchemical reactions, and comparative chiral HPLC. In a field test, synthetic (Z,Z)-(3S,4R)-3,4-epoxynonadeca-6,9-diene attracted male moths. The opposite enantiomer, the racemic mixture, and virgin female moths held in small cages attracted no more moths than the solvent controls.

We found that ethyl gallate purified from a dried pod of tara (Caesalpinia spinosa) intensified beta-lactam susceptibility in methicillin-resistant and methicillin-sensitive strains of Staphylococcus aureus (MRSA and MSSA strains, respectively). This compound and several known alkyl gallates were tested with MRSA and MSSA strains to gain new insights into their structural functions in relation to antimicrobial and beta-lactam susceptibility-intensifying activities. The maximum activity of alkyl gallates against MRSA and MSSA strains occurred at 1-nonyl and 1-decyl gallate, with an MIC at which 90% of the isolates tested were inhibited of 15.6 microg/ml. At concentrations lower than the MIC, alkyl gallates synergistically elevated the susceptibility of MRSA and MSSA strains to beta-lactam antibiotics. Such a synergistic activity of the alkyl gallates appears to be specific for beta-lactam antibiotics, because no significant changes were observed in the MICs of other classes of antibiotics examined in this study. The length of the alkyl chain was also associated with the modifying activity of the alkyl gallates, and the optimum length was C5 to C6. The present work clearly demonstrates that the length of the alkyl chain has a key role in the elevation of susceptibility to beta-lactam antibiotics.