Aerobic degradation of cis-dichloroethene by the marine bacterium Marinobacter salsuginis strain 5N-3.

An aerobic bacterium, designated strain 5N-3 (NBRC 113055), that degrades cis-dichloroethene (cDCE) was isolated from a sea sediment in Japan. Strain 5N-3 was able to degrade a certain amount of cDCE in the presence of pyruvate without the action of inducers. In the presence of inducers, such as phenol and benzene, the strain completely removed cDCE. By the application of 16S ribosomal RNA (16S rRNA) gene sequencing and average nucleotide identity analyses, the strain 5N-3 was identified as Marinobacter salsuginis. On the other hand, identified species of Marinobacter are not known to degrade cDCE at all. A draft genome sequence analysis of the strain 5N-3 suggested that the dmp-homologous operon (operon for phenol degradation) may be contributing to the aerobic degradation of cDCE. This is the first report on an aerobic marine bacterium that has been found to degrade cDCE.

Resecting a giant malignant lung tumor in a patient with unilateral acute interstitial pneumonitis.

Acute interstitial pneumonia is a rare and fulminant form of idiopathic interstitial lung disease. Here, we report a case of a giant malignant sarcomatoid tumor of the left lung with unilateral lung infiltration. The tumor was resected under venovenous extracorporeal membrane oxygenation support. Right middle lung lobe biopsy revealed alveolar epithelial hyperplasia, mild interstitial fibrosis, and interstitial edema. The patient was diagnosed with acute interstitial pneumonitis, and effectively treated with steroid pulse therapy followed by prednisolone. In this case, the contralateral lung expansion accomplished with tumor resection, definitive diagnosis based on lung biopsy, and corticosteroid treatment possibly improved the outcome.

Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique.

PCR clamping by locked nucleic acid (LNA) oligonucleotides is an effective technique for selectively amplifying the community SSU rRNA genes of plant-associated bacteria. However, the original primer set often shows low amplification efficiency. In order to improve this efficiency, new primers were designed at positions to compete with LNA oligonucleotides. Three new sets displayed higher amplification efficiencies than the original; however, efficiency varied among the primer sets. Two new sets appeared to be available in consideration of bacterial profiles by next-generation sequencing. One new set, KU63f and KU1494r, may be applicable to the selective gene amplification of plant-associated bacteria.

Circulating gonadotropins and testicular hormones during sexual maturation and annual changes in male bottlenose dolphins (Tursiops truncatus).

To reveal the reproductive biology in male bottlenose dolphins (Tursiops truncatus), circulating gonadotropins (follicle stimulating hormone [FSH] and luteinizing hormone [LH]) and testicular hormones (testosterone and inhibin) were monitored for 8-12 years in 2 captive bottlenose dolphins (Mars and Regulus). During the study period, Mars was undergoing sexual maturation, whereas Regulus was already mature at the beginning of the study. Assuming that Mars had reached sexual maturity when the significant increase in circulating testosterone levels was observed, serum concentration of inhibin was higher in the sexually immature stage than in the mature stage, whereas the serum concentration of FSH was higher in the sexually mature stage than in the immature stage. No difference was observed in the LH levels between pre- and post-sexual maturation. There was a significant increase in serum concentration of testosterone during spring in both animals. These results suggest that the mechanism responsible for regulating FSH secretion by inhibin functions during the sexually immature stage in this species.

Spontaneous establishing of cross-modal stimulus equivalence in a beluga whale.

Beluga whales use calls to convey various information to group members. Is this communication similar to humans? We addressed this question by using the framework of stimulus equivalence. Stimulus equivalence consists of three phases: if the animal is trained to match A to B and B to C, symmetry is demonstrated by matching BA and CB, transitivity by matching AC, and equivalence by matching CA. We tested the spontaneous establishment of cross-modal stimulus equivalence between visual and auditory symbols in a beluga whale nicknamed Nack. Nack could make symmetrical choices in novel objects untrained. Moreover, visual/auditory cross-modal transitivity was formed spontaneously. Nack succeeded in six tasks, including an untrained task concerning stimulus equivalence. We conclude that Nack spontaneously formed cross-modal stimulus equivalence between visual and auditory symbols. Cross-modal stimulus equivalence was considered to exist only in humans because of linguistic faculty; however, Nack exhibited the same understanding as humans.

Development and evaluation of microsatellite markers for the critically endangered birch Betula chichibuensis (Betulaceae).

PREMISE OF THE STUDY: Microsatellite markers were developed and characterized for the critically endangered birch Betula chichibuensis (Betulaceae) to investigate the genetic structure of this species for conservation purposes. METHODS AND RESULTS: Sixteen microsatellite markers with di-, tri-, and tetranucleotide repeat motifs were developed and optimized using MiSeq paired-end sequencing. Of these, 14 were polymorphic, with two to five alleles per locus, in 47 individuals from two newly discovered populations of B. chichibuensis in Japan. Observed and unbiased expected heterozygosities per locus ranged from 0.000 to 0.617 and from 0.000 to 0.629, respectively. These markers were tested for cross-species amplification in B. maximowicziana, B. platyphylla var. japonica, and B. schmidtii. CONCLUSIONS: This set of microsatellite markers, the first developed for B. chichibuensis, will help elucidate spatial patterns of gene flow and levels of inbreeding in this species to aid its conservation.

Interlaboratory validation data on real-time polymerase chain reaction detection for unauthorized genetically modified papaya line PRSV-YK.

This article is referred to research article entitled "Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method" (Nakamura et al., 2016) [1]. Real-time polymerase chain reaction (PCR) detection method for unauthorized genetically modified (GM) papaya (Carica papaya L.) line PRSV-YK (PRSV-YK detection method) was developed using whole genome sequence data (DDBJ Sequenced Read Archive under accession No. PRJDB3976). Interlaboratory validation datasets for PRSV-YK detection method were provided. Data indicating homogeneity of samples prepared for interlaboratory validation were included. Specificity and sensitivity test data for PRSV-YK detection method were also provided.

[Current Status of Preoperative Professional Oral Care by Dentists for Elderly Patients Undergoing Lung Resection and Occurrence of Postoperative Pneumonia].

Pneumonia in elderly people is mainly caused by silent aspiration due to an age-related impairment of cough and swallowing reflexes. Because most of the patients with lung cancer are elderly people, we hypothesized that the age-related impairment of these protective reflexes might exist or occur in patients undergoing lung surgery, and cause postoperative pneumonia. We revealed that many elderly patients showed depressed swallowing reflex even before surgery and transient attenuation of cough reflex after surgery, and that postoperative pneumonia occurred only in the patients whose cough and/or swallowing reflex was abnormal postoperatively. Then, we prospectively showed that 30 elderly patients who received perioperative intensive oral care, including professional assessment of oral status, dental cleaning, and patient education for self-oral care by dentists, followed by intensive oral care by intensive care unit nurses, and encouragement of self-oral care by floor nurses, did not develop pneumonia after lung resection. In this study, we retrospectively reviewed the execution status of professional oral care by dentists and the occurrence of postoperative pneumonia in 159 consecutive patients aged 65 or older undergoing lung resection from 2013 to 2014. Thoracic surgeons in our institute asked dentists to provide professional oral care before lung resection only in 30.3% of the subjects in 2013, and 45.8% in 2014. Postoperative pneumonia occurred in 3 out of 76 subjects(3.9%)in 2013, and 1 out of 83(1.2%) in 2014. In 2013, 1 patient who did not receive preoperative professional oral care developed aspiration pneumonia postoperatively followed by acute exacerbation of idiopathic pulmonary fibrosis and in-hospital death. We need to make an effective system to provide preoperative professional oral care by dentists especially for elderly patients and high-risk patients before lung resection.

Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities.

[Alpha Fetoprotein-producing Lung Adenocarcinoma].

We report a case of alpha fetoprotein (AFP) -producing lung adenocarcinoma. A 53-year-old man was referred to our hospital due to right pneumothorax. Computed tomography showed right moderate pneumothorax, a solid tumor in the upper lobe (S3) and mediastinal lymph node swelling. The serum AFP level was as high as 223.0 ng/ml. Frozen examination revealed a low-differentiated adenocarcinoma. Based on the pathological and immunohistochemical findings, the tumor was diagnosed as AFP-producing lung adenocarcinoma.

[Intrapulmonary Solitary Fibrous Tumor].

We report a case of intrapulmonary solitary fibrous tumor( SFT). A 34-year-old woman was referred to our hospital due to an abnormal shadow on a chest roentgenogram without symptom. Computed tomography showed a circumscribed intrapulmonary tumor with mild uptake on fluorodeoxyglucose (FDG)-positron emission tomography( PET) in the left lower lobe( S6). Frozen examination revealed a mesenchymal tumor. Based on the pathological and immunohistochemical findings, the tumor was diagnosed as intrapulmonary SFT.

[Long-term survival with complete response by gefitinib treatment followed by noncurative operation for lung cancer].

A 54-year-old man was referred to our hospital because of an abnormal shadow on chest X-ray. A computed tomography( CT) scan of the chest revealed a 6.5 cm tumor in the right upper lobe suspected of superior vena cava (SVC) infiltration. He was diagnosed as lung cancer(adenocarcinoma), and the right upper lobectomy with partial resection of SVC was performed. But the pathology confirmed the surgery to be non-curative. Nine months after operation, carcinomatous pleuritis was detected on chest X-ray. Since deoxyribonucleic acid (DNA)analysis revealed a mutation of epidermal growth factor receptor (EGFR) gene in exon 21, gefitinib treatment was started. Nine months later, pleural effusion regressed and his cerum carcinoembrionic antigen( CEA) level was normalized. 4 years later, gefitinib was discontinued by patient's request, however, he is alive without any signs of relapse 9 years after the operation.

[Typical bronchial carcinoid with repeated recurrence observed for 17 years after radical operation].

A 68-years-old male patient had been diagnosed as having bronchial carcinoid in B2 and right upper lobectomy with systematic hiler and mediastinal lymphadenectomy had been performed in 1996. Pathological diagnosis was a typical carcinoid (pT1aN0M0, stage I A). In 2004, 4 tumors were found in the trachea, right bronchial stump, right main bronchi and right B6 orfice. These were diagnosed as typical carcinoids by pathology. In 2005 argon plasma coagration was performed.In 2013, a localized recurrence was found in the right S6 by chest computed tomography (CT). The segmentectomy of the right S6 was performed. Even after radical operation for typical carcinoids, we should conduct long-term observation.

A genome sequence-based approach to taxonomy of the genus Nocardia.

The genus Nocardia includes both pathogens and producers of useful secondary metabolites. Although 16S rRNA analysis is required to accurately discriminate among phylogenetic relationships of the Nocardia species, most branches of 16S rRNA-based phylogenetic trees are not reliable. In this study, we performed in silico analyses of the genome sequences of Nocardia species in order to understand their diversity and classification for their identification and applications. Draft genome sequences of 26 Nocardia strains were determined. Phylogenetic trees were prepared on the basis of multilocus sequence analysis of the concatenated sequences of 12 genes (atpD-dnaJ-groL1-groL2-gyrB-recA-rpoA-secA-secY-sodA-trpB-ychF) and a bidirectional best hit. To elucidate the evolutionary relationships of these genes, the genome-to-genome distance was investigated on the basis of the average nucleotide identity, DNA maximal unique matches index, and genome-to-genome distance calculator. The topologies of all phylogenetic trees were found to be essentially similar to each other. Furthermore, whole genome-derived and multiple gene-derived relationships were found to be suitable for extensive intra-genus assessment of the genus Nocardia.

Circulating testosterone and inhibin levels at different ages in the male beluga (Delphinapterus leucas).

This study is the first report on circulating testosterone and inhibin levels in a species of whales, the beluga. Circulating testosterone and immunoreactive (ir-) inhibin levels in two captive male belugas ("Nack", originally from Canada and "Duke", from the Okhotsk Sea) were measured every month for 9 years between 1995 and 2003. Assuming that clearly increased testosterone levels in the circulation indicates that the belugas had reached sexual maturity, at the ages of 10 ("Nack") and 11 years old ("Duke"). Their testosterone levels before the significant increase (pre-pubertal) were 0.42 ± 0.07 ng/ml (n=18) and 0.35 ± 0.10 ng/ml (n=18) and, those of after the increase (maturity) were 1.65 ± 0.14 ng/m l (n=74) and 2.06 ± 0.14 ng/ml (n=74). Circulating ir-inhibin levels before sexual maturity were 0.78 ± 0.04 ng/ml (n=18) and 0.64 ± 0.04 ng/ml (n=15) and, after sexual maturity were 0.52 ± 0.02 ng/ml (n=56) and 0.43 ± 0.02 ng/ml (n=67). Seasonal changes were observed in the testosterone levels after sexual maturity and the levels increased during March and April in Canadian origin "Nack", and peaked in February in Okhotsk origin "Duke". Circulating ir-inhibin level gradually decreased as they aged. A negative correlation between the circulating testosterone and ir-inhibin was observed. No seasonal changes were observed in the ir-inhibin levels after sexual maturity. These data will surely correspond to clarification of endocrinology and the successful reproduction of the beluga.

Changes in gene expression for GH/PRL/SL family hormones in the pituitaries of homing chum salmon during ocean migration through upstream migration.

Gene expression for growth hormone (GH)/prolactin (PRL)/somatolactin (SL) family hormones in the pituitaries of homing chum salmon were examined, because gene expression for these hormones during ocean-migrating phases remains unclear. Fish were collected in the winter Gulf of Alaska, the summer Bering Sea and along homing pathway in the Ishikari River-Ishikari Bay water system in Hokkaido, Japan in autumn. The oceanic fish included maturing adults, which had developing gonads and left the Bering Sea for the natal river by the end of summer. The absolute amounts of GH, PRL and SL mRNAs in the pituitaries of the maturing adults in the summer Bering Sea were 5- to 20-fold those in the winter Gulf of Alaska. The amount of GH mRNA in the homing adults at the coastal seawater (SW) areas was smaller than that in the Bering fish, while the amount of PRL mRNA remained at the higher level until fish arrived at the Ishikari River. The gill Na(+),K(+)-ATPase activity in the coastal SW fish and the plasma Na(+) levels in the brackish water fish at the estuary were lowered to the levels that were comparable to those in the fresh water (FW) fish. In conclusion, gene expression for GH, PRL and SL was elevated in the pituitaries of chum salmon before initiation of homing behavior from the summer Bering Sea. Gene expression for GH is thereafter lowered coincidently with malfunction of SW adaptability in the breeding season, while gene expression for PRL is maintained high until forthcoming FW adaptation.

Changes in the plasma levels of insulin-like growth factor-I from the onset of spawning migration through upstream migration in chum salmon.

An increase in activity of the pituitary-gonadal axis (PG-axis) and gonadal development are essential for the onset of spawning migration of chum salmon from the Bering Sea. In the Bering Sea, fish with larger body sizes initiated gonadal development and commenced spawning migration to the natal river by the end of summer. We thus hypothesized that insulin-like growth factor-I (IGF-I), a somatotropic signal that interacts with the PG-axis, can be one of such factors responsible for the onset of migration, and examined changes in plasma levels and hepatic expression of IGF-I gene in oceanic and homing chum salmon in 2001-2003. The plasma IGF-I levels and corresponding body sizes in maturing adults, which had developing gonads, were significantly higher than those in immature fish in all years examined. Such increase in the plasma IGF-I levels in maturing fish was observed even in the Gulf of Alaska during February 2006, while coincident increase was not observed in the hepatic amounts of IGF-I mRNA. In autumn, the plasma IGF-I levels in homing adults decreased during upstream migration in the Ishikari River-Ishikari bay water system in Hokkaido, Japan. In conclusion, the plasma IGF-I levels increased with gonadal development when chum salmon migrated from the winter Gulf of Alaska to the summer Bering Sea. Circulating IGF-I may interact with the PG-axis and promote gonadal development that is inseparable from the onset of spawning migration. Circulating IGF-I levels were thereafter lowered in accordance with final maturation during upstream migration in the breeding season.

Activity of the pituitary-gonadal axis is increased prior to the onset of spawning migration of chum salmon.

The activity of the pituitary-gonadal axis (PG axis) in pre-migratory and homing chum salmon was examined because endocrine mechanisms underlying the onset of spawning migration remain unknown. Pre-migratory fish were caught in the central Bering Sea in June, July and September 2001, 2002 and 2003, and in the Gulf of Alaska in February 2006. They were classified into immature and maturing adults on the basis of gonadal development. The maturing adults commenced spawning migration to coastal areas by the end of summer, because almost all fish in the Bering Sea were immature in September. In the pituitaries of maturing adults, the copy numbers of FSHbeta mRNA and the FSH content were 2.5- to 100-fold those of the immature fish. Similarly, the amounts of LHbeta mRNA and LH content in the maturing adults were 100- to 1000-fold those of immature fish. The plasma levels of testosterone, 11-ketotestosterone and estradiol were higher than 10 nmol l(-1) in maturing adults, but lower than 1.0 nmol l(-1) in immature fish. The increase in the activity of the PG-axis components had already initiated in the maturing adults while they were still in the Gulf of Alaska in winter. In the homing adults, the pituitary contents and the plasma levels of gonadotropins and plasma sex steroid hormones peaked during upstream migration from the coast to the natal hatchery. The present results thus indicate that the seasonal increase in the activity of the PG axis is an important endocrine event that is inseparable from initiation of spawning migration of chum salmon.

Characterization of the class IV homeodomain-Leucine Zipper gene family in Arabidopsis.

The Arabidopsis (Arabidopsis thaliana) genome contains 16 genes belonging to the class IV homeodomain-Leucine zipper gene family. These include GLABRA2, ANTHOCYANINLESS2, FWA, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), and PROTODERMAL FACTOR2 (PDF2). Our previous study revealed that atml1 pdf2 double mutants have severe defects in the shoot epidermal cell differentiation. Here, we have characterized additional members of this gene family, which we designated HOMEODOMAIN GLABROUS1 (HDG1) through HDG12. Analyses of transgenic Arabidopsis plants carrying the gene-specific promoter fused to the bacterial beta-glucuronidase reporter gene revealed that some of the promoters have high activities in the epidermal layer of the shoot apical meristem and developing shoot organs, while others are temporarily active during reproductive organ development. Expression profiles of highly conserved paralogous gene pairs within the family were found to be not necessarily overlapping. Analyses of T-DNA insertion mutants of these HDG genes revealed that all mutants except hdg11 alleles exhibit no abnormal phenotypes. hdg11 mutants show excess branching of the trichome. This phenotype is enhanced in hdg11 hdg12 double mutants. Double mutants were constructed for other paralogous gene pairs and genes within the same subfamily. However, novel phenotypes were observed only for hdg3 atml1 and hdg3 pdf2 mutants that both exhibited defects in cotyledon development. These observations suggest that some of the class IV homeodomain-Leucine zipper members act redundantly with other members of the family during various aspects of cell differentiation. DNA-binding sites were determined for two of the family members using polymerase chain reaction-assisted DNA selection from random oligonucleotides with their recombinant proteins. The binding sites were found to be similar to those previously identified for ATML1 and PDF2, which correspond to the pseudopalindromic sequence 5'-GCATTAAATGC-3' as the preferential binding site.

Basal body temperature method for detecting ovarian cycle in the Captive Beluga (Delphinapterus leucas).

The relationship between basal body temperature and circulating progesterone levels were investigated in a female beluga. Body temperature and serum concentrations of progesterone were measured daily and at 2-4 week intervals respectively, in a female beluga that was in captivity for 7 years between 1996 and 2003. The beluga first ovulated in April, 2000 (13 years old). Thereafter, serum concentrations of progesterone showed cyclic changes, indicating that the ovulatory cycle had started. Serum concentrations of progesterone ranged from 0.1 ng/ml to 15.7 ng/ml. Body temperature also showed cyclic changes during the estrous cycle. Body temperature ranged from 34.9 to 35.9 C, and tended to reach the peak during the high progesterone phase. Mating behavior was observed during the low body temperature phase. The changes in body temperature positively correlated with the circulating progesterone levels. The length of the estrous cycle was 36.7 +/- 3.9 (mean +/- SEM) days based on the intervals between the days of mating behavior. This is the first report demonstrating that body temperature clearly changes during the estrous cycle in a captive female beluga. The present finding suggests that measurement of body temperature is a useful method for detecting the ovarian cycle of the beluga in captivity.