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1.
PLoS One ; 19(6): e0304858, 2024.
Article in English | MEDLINE | ID: mdl-38837990

ABSTRACT

Link prediction in bipartite networks finds practical applications in various domains, including friend recommendation in social networks and chemical reaction prediction in metabolic networks. Recent studies have highlighted the potential for link prediction by maximal bi-cliques, which is a structural feature within bipartite networks that can be extracted using formal concept analysis (FCA). Although previous FCA-based methods for bipartite link prediction have achieved good performance, they still have the problem that they cannot fully capture the information of maximal bi-cliques. To solve this problem, we propose a novel method for link prediction in bipartite networks, utilizing a BERT-like transformer encoder network to enhance the contribution of FCA to link prediction. Our method facilitates bipartite link prediction by learning more information from the maximal bi-cliques and their order relations extracted by FCA. Experimental results on five real-world bipartite networks demonstrate that our method outperforms previous FCA-based methods, a state-of-the-art Graph Neural Network(GNN)-based method, and classic methods such as matrix-factorization and node2vec.


Subject(s)
Algorithms , Neural Networks, Computer , Humans
2.
Surg Neurol Int ; 15: 167, 2024.
Article in English | MEDLINE | ID: mdl-38840599

ABSTRACT

Background: Although awake surgery is the gold standard for resecting brain tumors in eloquent regions, patients with hearing impairment require special consideration during intraoperative tasks. Case Description: We present a case of awake surgery using sign language in a 45-year-old right-handed native male patient with hearing impairment and a neoplastic lesion in the left frontal lobe, pars triangularis (suspected to be a low-grade glioma). The patient primarily communicated through sign language and writing but was able to speak at a sufficiently audible level through childhood training. Although the patient remained asymptomatic, the tumors gradually grew in size. Awake surgery was performed for tumors resection. After the craniotomy, the patient was awake, and brain function mapping was performed using tasks such as counting, picture naming, and reading. A sign language-proficient nurse facilitated communication using sign language and the patient vocally responded. Intraoperative tasks proceeded smoothly without speech arrest or verbal comprehension difficulties during electrical stimulation of the tumor-adjacent areas. Gross total tumor resection was achieved, and the patient exhibited no apparent complications. Pathological examination revealed a World Health Organization grade II oligodendroglioma with an isocitrate dehydrogenase one mutant and 1p 19q codeletion. Conclusion: Since the patient in this case had no dysphonia due to training from childhood, the task was presented in sign language, and the patient responded vocally, which enabled a safe operation. Regarding awake surgery in patients with hearing impairment, safe tumor resection can be achieved by performing intraoperative tasks depending on the degree of hearing impairment and dysphonia.

3.
Asian J Endosc Surg ; 17(3): e13317, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38692582

ABSTRACT

INTRODUCTION: Robot-assisted nephroureterectomy (RANU) for upper urinary tract urothelial carcinoma is typically performed via the transperitoneal approach because of limited surgical space. However, a retroperitoneal approach may be preferable in patients with a history of abdominal surgery or in those in whom pelvic lymph node dissection is unnecessary. MATERIALS AND SURGICAL TECHNIQUES: RANU via the retroperitoneal approach was selected for two patients diagnosed with high-grade upper urothelial carcinoma with a history of abdominal surgery. Nephrectomy was performed in the 90° flank position, and the bed was tilted at 20°. The retroperitoneal space was extended, and the robot trocar was subsequently repositioned in the left lower quadrant. After redocking the robot, the distal ureter was dissected, and the bladder cuff was resected en bloc along with the kidney and the ureter. Neither patient had any complications within 3 months postoperatively. DISCUSSION: By devising a new technique for trocar placement, total retroperitoneal RANU without repositioning was possible, even in a small patient.


Subject(s)
Nephroureterectomy , Robotic Surgical Procedures , Humans , Robotic Surgical Procedures/methods , Retroperitoneal Space/surgery , Nephroureterectomy/methods , Male , Aged , Ureteral Neoplasms/surgery , Carcinoma, Transitional Cell/surgery , Carcinoma, Transitional Cell/pathology , Urinary Bladder/surgery , Kidney Neoplasms/surgery , Kidney Neoplasms/pathology , Middle Aged , Female
4.
Surg Neurol Int ; 15: 125, 2024.
Article in English | MEDLINE | ID: mdl-38741987

ABSTRACT

Background: In a 31-year-old male, psoriasis vulgaris (PV) of the skin caused paraparesis attributed to a L3-L4 epidural spinal abscess that required emergent surgical decompression. Case Description: A 31-year-old male presented with lower back pain and cauda equina compression attributed to a magnetic resonance-documented L34 enhancing lesion consistent with a spinal epidural abscess (SEA). The skin over the L3-L4 level revealed severe PV that proved to be the likely etiology of the right-sided paraspinal muscle abscess, infected right L3-L4 facet joint, and SEA. At surgery, the foci of infection were excised/decompressed, and cultures grew methicillin-susceptible Staphylococcus aureus. Following surgery, the patient was improved and was treated with appropriate antibiotic therapy. Conclusion: PV caused a L3-L4 epidural spinal abscess and cauda equina compression in a 31-year-old male who was successfully treated with operative decompression and appropriate antibiotic management.

5.
PLoS One ; 18(8): e0289568, 2023.
Article in English | MEDLINE | ID: mdl-37585433

ABSTRACT

We propose a new method for bipartite link prediction using matrix factorization with negative sample selection. Bipartite link prediction is a problem that aims to predict the missing links or relations in a bipartite network. One of the most popular solutions to the problem is via matrix factorization (MF), which performs well but requires reliable information on both absent and present network links as training samples. This, however, is sometimes unavailable since there is no ground truth for absent links. To solve the problem, we propose a technique called negative sample selection, which selects reliable negative training samples using formal concept analysis (FCA) of a given bipartite network in advance of the preceding MF process. We conduct experiments on two hypothetical application scenarios to prove that our joint method outperforms the raw MF-based link prediction method as well as all other previously-proposed unsupervised link prediction methods.


Subject(s)
Algorithms , Research Design
6.
Clin Case Rep ; 10(4): e05760, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35449773

ABSTRACT

Cardiac perforation by the lead of cardiac implantable electronic devices is a critical complication that often occurs within 24 h after the implantation but can occur later. We report a case of cardiac perforation of the right ventricular wall during the chronic period, 2 years after pacemaker implantation.

7.
Forensic Sci Int ; 335: 111284, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35398634

ABSTRACT

In forensic investigations, it is crucial to detect a suspect's DNA from the available evidence. In an outdoor crime scene, the evidence may be mixed with the soil. However, soil is speculated to inhibit DNA extraction from forensic science samples. In the field of soil microbiology, it is necessary to extract DNA directly from soil to analyse its microbial composition. In this study, we investigated whether skim milk used in procedure of DNA extraction from soil samples could be applied to forensic science to enhance human DNA extraction efficiency from soil mixed with forensic evidence, such as blood, buccal cells, and skin cells. The use of additive reagents, skim milk and bovine serum albumin (BSA), are known to blocking reagent. In the selection of additive reagents experiment, about blood sample, using the skim milk and BSA were found to increase the DNA yield. Therefore, we observed extracted DNA yield from blood, buccal cells, and skin cells when skim milk and BSA were used as additive reagents. The DNA recovery rate was high across all samples upon addition of skim milk. However, in STR analysis, a non-specific peak was detected in the extracted DNA in the presence of skim milk, which was not detected in the presence of BSA, indicating its suitability in forensic analysis. Our study suggests that addition of BSA can efficiently aid the extraction of DNA from forensic evidence mixed with soil.


Subject(s)
Mouth Mucosa , Soil , DNA/genetics , Forensic Medicine/methods , Forensic Sciences , Humans
8.
Mol Biol Cell ; 32(19): 1838-1848, 2021 09 01.
Article in English | MEDLINE | ID: mdl-34260260

ABSTRACT

p52SHC (SHC) and GRB2 are adaptor proteins involved in the RAS/MAPK (ERK) pathway mediating signals from cell-surface receptors to various cytoplasmic proteins. To further examine their roles in signal transduction, we studied the translocation of fluorescently labeled SHC and GRB2 to the cell surface, caused by the activation of ERBB receptors by heregulin (HRG). We simultaneously evaluated activated ERK translocation to the nucleus. Unexpectedly, the translocation dynamics of SHC were sustained when those of GRB2 were transient. The sustained localization of SHC positively correlated with the sustained nuclear localization of ERK, which became more transient after SHC knockdown. SHC-mediated PI3K activation was required to maintain the sustainability of the ERK translocation regulating MEK but not RAF. In cells overexpressing ERBB1, SHC translocation became transient, and the HRG-induced cell fate shifted from a differentiation to a proliferation bias. Our results indicate that SHC and GRB2 functions are not redundant but that SHC plays the critical role in the temporal regulation of ERK activation.


Subject(s)
Extracellular Signal-Regulated MAP Kinases/metabolism , MAP Kinase Signaling System , Src Homology 2 Domain-Containing, Transforming Protein 1/metabolism , raf Kinases/metabolism , Cell Differentiation , Cell Proliferation , Enzyme Activation , Extracellular Signal-Regulated MAP Kinases/genetics , GRB2 Adaptor Protein/genetics , GRB2 Adaptor Protein/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Humans , MCF-7 Cells , Microscopy, Fluorescence/methods , Src Homology 2 Domain-Containing, Transforming Protein 1/genetics , raf Kinases/genetics
9.
Biophys Physicobiol ; 18: 1-12, 2021.
Article in English | MEDLINE | ID: mdl-33665062

ABSTRACT

RTK-RAS-MAPK systems are major signaling pathways for cell fate decisions. Among the several RTK species, it is known that the transient activation of ERK (MAPK) stimulates cell proliferation, whereas its sustained activation induces cell differentiation. In both instances however, RAS activation is transient, suggesting that the strict temporal regulation of its activity is critical in normal cells. RAS on the cytoplasmic side of the plasma membrane is activated by SOS through the recruitment of GRB2/SOS complex to the RTKs that are phosphorylated after stimulation with growth factors. The adaptor protein GRB2 recognizes phospho-RTKs both directly and indirectly via another adaptor protein, SHC. We here studied the regulation of GRB2 recruitment under the SHC pathway using single-molecule imaging and fluorescence correlation spectroscopy in living cells. We stimulated MCF7 cells with a differentiation factor, heregulin, and observed the translocation, complex formation, and phosphorylation of cell signaling molecules including GRB2 and SHC. Our results suggest a biphasic regulation of the GRB2/SOS-RAS pathway by SHC: At the early stage (<10 min) of stimulation, SHC increased the amplitude of RAS activity by increasing the association sites for the GRB2/SOS complex on the plasma membrane. At the later stage however, SHC suppressed RAS activation and sequestered GRB2 molecules from the membrane through the complex formation in the cytoplasm. The latter mechanism functions additively to other mechanisms of negative feedback regulation of RAS from MEK and/or ERK to complete the transient activation dynamics of RAS.

10.
FEBS Open Bio ; 10(11): 2417-2426, 2020 11.
Article in English | MEDLINE | ID: mdl-33022895

ABSTRACT

MicroRNAs (miRNAs) are small noncoding RNA molecules that interact with target mRNAs at specific sites to induce cleavage of the mRNA or inhibit translation. Such miRNAs play a vital role in gene expression and in several other biological processes, including cell death. We have studied the mechanisms regulating cell death (necrosis in original F28-7 cells and apoptosis in their variant F28-7-A cells) in the mouse mammary tumor cell line FM3A using the anticancer agent floxuridine (FUdR). We previously reported that inhibition of heat-shock protein 90 by the specific inhibitor geldanamycin (GA) in F28-7 cells causes a shift from necrosis to apoptosis. In this study, we investigated the intracellular miRNA expression profiles of FUdR-treated F28-7 cells (necrotic condition), GA plus FUdR-treated F28-7 cells (apoptotic condition), and FUdR-treated F28-7-A cells (apoptotic condition) through miRNA microarray analysis. In addition, we knocked down Dicer, a key molecule for the expression of mature miRNAs, in F28-7 cells to examine whether it modulates FUdR-induced cell death. Our analysis revealed that the miRNA expression patterns differ significantly between these cell death conditions. Furthermore, we identified miRNA candidates that regulate cell death. Knockdown of Dicer in FUdR-treated necrosis-fated cells caused a partial shift from necrosis to apoptosis. These findings suggest that modulation of miRNA expression patterns influences the decision of cell death fate toward necrosis or apoptosis. Our findings may serve as a basis for further study of the functions of miRNAs in cell death mechanisms.


Subject(s)
Apoptosis/genetics , Gene Expression Regulation , Intracellular Space/metabolism , MicroRNAs/metabolism , Necrosis/genetics , Animals , Apoptosis/drug effects , Benzoquinones/pharmacology , Cell Line, Tumor , Down-Regulation/drug effects , Floxuridine/pharmacology , Gene Expression Profiling , Gene Expression Regulation/drug effects , Gene Silencing/drug effects , Lactams, Macrocyclic/pharmacology , Mice , MicroRNAs/genetics , Ribonuclease III/metabolism
11.
Yonago Acta Med ; 63(2): 132-134, 2020 May.
Article in English | MEDLINE | ID: mdl-32494220

ABSTRACT

Home oxygen therapy (HOT) is an important treatment for patients with chronic respiratory diseases. Recently, telemonitoring of HOT has been become available. In the present study, we examined whether telemonitoring of HOT could improve health-related quality of life (HRQOL). Twelve patients receiving HOT participated in this study. The oxygen flow rates, use of the oxygen concentrator, and the values of percutaneous arterial oxygen saturation measured by each patient with a pulse oximeter were checked using a telemonitoring system for a period of one month. Interventions based on the results obtained were carried out in order to optimize oxygen use in this patient cohort. We evaluated the results of the SF-36 questionnaire before the initiation of telemonitoring and at 3 months after completion of the study. We identified significant improvements in SF-36 sub-scores after completion of this intervention. We conclude that telemonitoring may be a useful method to improve HRQOL.

12.
Neuropathology ; 40(4): 399-406, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32367540

ABSTRACT

We report a case of early-phase sporadic Creutzfeldt-Jakob disease (sCJD) complicated by intracerebral hemorrhage (ICH), classified as MM1 + 2C-type based on autopsy. A 61-year-old Japanese man presented to our hospital with speaking difficulties including repeated usage of the same words. He was hospitalized on the seventh day after symptom onset, and diffusion-weighted images on magnetic resonance imaging showed hyperintense regions in the frontal cortex and caudate nucleus. On the 11th day after symptom onset, head computed tomography revealed ICH in the right occipital and parietal lobes. Routine laboratory evaluations and angiography revealed no cause of ICH. Myoclonus of the extremities and drowsiness were observed on the 15th day after symptom onset. He reached the state of akinetic mutism approximately two months after symptom onset. The cerebrospinal fluid test revealed positive real-time quaking-induced conversion and 14-3-3 protein. Electroencephalography revealed periodic sharp wave complexes. A clinical diagnosis of probable Creutzfeldt-Jakob disease was made according to the diagnostic criteria. After a relapse of pneumonia, he passed away on the 103rd day after symptom onset. Postmortem examination revealed ICH in the right posterior cingulate gyrus. No pathological change that might have caused ICH was obtained. Although the effect of sCJD on the onset of ICH is undeniable, the cause of ICH was unknown. Prion protein immunohistochemistry revealed the following results: (1) weak synaptic-type deposits in the tissue rarefacted by ICH; (2) synaptic-type deposits in the cerebral cortex, which showed fine vacuoles; and (3) perivacuolar-type deposits in the inferior temporal gyrus and lingual gyrus, which showed frequent large confluent vacuoles. Although it could be considered MM1-type sCJD clinically, this case was neuropathologically diagnosed as having MM1 + 2C-type sCJD. It was shown that ICH may occur in early-phase sCJD. To improve sCJD prognosis, treatment of complications and careful follow up are important. Furthermore, pathological diagnosis is indispensable for sCJD type diagnosis.


Subject(s)
Cerebral Hemorrhage/etiology , Cerebral Hemorrhage/pathology , Creutzfeldt-Jakob Syndrome/complications , Creutzfeldt-Jakob Syndrome/pathology , Humans , Male , Middle Aged
13.
World J Microbiol Biotechnol ; 35(11): 176, 2019 Oct 31.
Article in English | MEDLINE | ID: mdl-31673867

ABSTRACT

The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.


Subject(s)
Bacteria/classification , Bacteria/metabolism , Climate , Endophytes/classification , Ipomoea batatas/microbiology , Metagenome , Microbiota , Soil/chemistry , Bacteria/genetics , Base Sequence , Biodiversity , DNA, Bacterial/analysis , DNA, Mitochondrial/analysis , Endophytes/genetics , Microbiota/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Soil Microbiology
14.
Mol Clin Oncol ; 11(5): 439-446, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31616560

ABSTRACT

Immune checkpoint inhibitors (ICIs), including nivolumab, have exhibited substantial benefits in the treatment of several types of cancers. However, treatment with ICIs is often accompanied by immune-related adverse events (irAEs), and a clear understanding of the precise indications and management of irAEs is important for harnessing the full potential of these agents. While skin- or gastrointestinal-associated irAEs have been relatively well studied, there are few reports regarding nivolumab-induced cholangitis. We retrospectively reviewed data from patients with advanced or recurrent non-small cell lung cancer who were treated with nivolumab between December 2015 and December 2018 at Tottori University in Japan. Among the 59 patients, we identified four patients who experienced nivolumab-induced cholangitis. Of these four patients, stable disease (SD) was observed in two patients (50%), while partial response (PR) was achieved in two patients (50%) under nivolumab treatment. Patients were treated with corticosteroid alone (n=2) or in combination with mycophenolate mofetil (MMF) (n=2); these treatments resulted in improvements in nivolumab-induced cholangitis in three patients. In conclusion, the present retrospective study identified four cases of nivolumab-induced cholangitis. The combination of corticosteroid and MMF was effective in two cases with grade 4 nivolumab-induced cholangitis. Further reports are needed to establish the optimal management of patients with this irAE.

15.
Plant Cell Physiol ; 60(10): 2255-2262, 2019 Oct 01.
Article in English | MEDLINE | ID: mdl-31198958

ABSTRACT

Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), comprising an RNA-guided DNA endonuclease and a programmable guide RNA (gRNA), is currently recognized to be a powerful genome-editing tool and is widely used in biological science. Despite the usefulness of the system, a protospacer-adjacent motif (PAM) immediately downstream of the target sequence needs to be taken into account in the design of the gRNA, a requirement which limits the flexibility of the CRISPR-based genome-editing system. To overcome this limitation, a Cas9 isolated from Streptococcus pyogenes, namely SpCas9, engineered to develop several variants of Cas9 nuclease, has been generated. SpCas9 recognizes the NGG sequence as the PAM, whereas its variants are capable of interacting with different PAMs. Despite the potential advantage of the Cas9 variants, their functionalities have not previously been tested in the widely used model plant, Arabidopsis thaliana. Here, we developed a plant-specific vector series harboring SpCas9-VQR (NGAN or NGNG) or SpCas9-EQR (NGAG) and evaluated their functionalities. These modified Cas9 nucleases efficiently introduced mutations into the CLV3 and AS1 target genes using gRNAs that were compatible with atypical PAMs. Furthermore, the generated mutations were passed on to their offspring. This study illustrated the usefulness of the SpCas9 variants because the ability to generate heritable mutations will be of great benefit in molecular genetic analyses. A greater number of potential SpCas9-variant-recognition sites in these genes are predicted, compared with those of conventional SpCas9. These results demonstrated the usefulness of the SpCas9 variants for genome editing in the field of plant science research.


Subject(s)
Arabidopsis/genetics , CRISPR-Associated Protein 9/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Gene Editing , RNA, Guide, Kinetoplastida/genetics , Streptococcus pyogenes/enzymology , CRISPR-Associated Protein 9/metabolism , CRISPR-Cas Systems , Mutagenesis , Mutation , Species Specificity , Streptococcus pyogenes/genetics
16.
ISME J ; 13(8): 1899-1910, 2019 08.
Article in English | MEDLINE | ID: mdl-30809012

ABSTRACT

Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.


Subject(s)
Chlorophyll/metabolism , Eukaryota/metabolism , Oxygen/metabolism , Chloroplasts/metabolism , Ecosystem , Eukaryota/classification , Eukaryota/genetics , Microalgae/classification , Microalgae/genetics , Microalgae/metabolism , Photosynthesis , Phylogeny , Symbiosis
17.
Ann Vasc Dis ; 12(4): 456-459, 2019 Dec 25.
Article in English | MEDLINE | ID: mdl-31942202

ABSTRACT

Spontaneous isolated dissection of the superior mesenteric artery (SMAD) is not still well known. We retrospectively analyzed our 30 patients with SMAD to elucidate the treatment strategy and long-term follow-up outcomes. Due to severe abdominal symptom we performed a stents deployment and surgical reconstructive surgery for each one case. Anerysmectomy and bypass surgery was performed for a patient with aneurysmal change. Other 27 patients were managed conservatively. SMAD patients had only two vascular events (renal infarction and graft occlusion), and showed good prognosis for 6-146 (mean 69) months follow-up. We found that there is a few SMAD patients necessary of invasive management at acute phase and that most patients are safely conservatively treated with good prognosis. (This is a translation of J Jpn Coll Angiol 2018; 58: 195-199.).

18.
Heliyon ; 4(11): e00921, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30480155

ABSTRACT

One of the strategies that is commonly used in the Philippines to improve the production of soybean is by inoculation. However, this technique often fails mainly due to the lack of information about the indigenous soybean rhizobia in the Philippines soil. In this study, the diversity of indigenous bradyrhizobia collected from the non-flooded and flooded soil conditions at 11 locations in the country was investigated using a local soybean cultivar as the host plant. The genetic variation among the 424 isolates was detected through Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment and sequence analysis for 16S rRNA gene, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene. All the isolates were classified under the Bradyrhizobium species namely B. elkanii, B. diazoefficiens, B. japonicum, B. yuanmingense and a considerable proportion of the isolates were clustered under Bradyrhizobium sp. The isolates which were classified under Bradyrhizobium sp. were thought to be endemic to Philippines soil as evidenced by their nucleotide divergence against the known rhizobia and the historical absence of rhizobia inoculation in the collection sites. The major influence on the distribution and diversity of soybean bradyrhizobia is attributed to the difference in the flooding period, followed by soil properties such as pH, soil type, and nutrient content. As determined, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.

19.
Exp Cell Res ; 366(2): 172-180, 2018 05 15.
Article in English | MEDLINE | ID: mdl-29555369

ABSTRACT

Apical and basolateral cell membranes are separated by tight junctions (TJs). Microvilli are limited to the apical cell membrane. TJs and microvilli are the landmarks for epithelial cell polarity. However, the direct relationship between TJ proteins (TJPs) and the components of microvilli remains unclear. In this study, we investigated whether occludin, which is considered to be a functional TJP, is involved in microvillus formation. In occludin knockout mouse hepatic cells (OcKO cells), the microvillus density was less than that in wild-type (WT) cells and the length of microvilli was short. Immunoreactivity of ezrin was decreased in OcKO cells compared with that in WT cells. Although there was no change in the expression level of ezrin, phosphorylation of ezrin was decreased in OcKO cells. The microvillus density and the length of microvilli were increased in OcKO cells by transfection of full-length mouse occludin and COOH-terminal domains of occludin. These results suggested that occludin induced microvillus formation via phosphorylation of ezrin and that the COOH-terminal domain of occludin, which is localized in non-TJ areas, might be able to induce microvilli formation. Our results provide new insights into the function of occludin.


Subject(s)
Cytoskeletal Proteins/metabolism , Epithelial Cells/cytology , Hepatocytes/cytology , Microvilli/physiology , Occludin/physiology , Phosphoproteins/metabolism , Tight Junctions/physiology , Animals , Cell Polarity , Cells, Cultured , Epithelial Cells/metabolism , Hepatocytes/metabolism , Mice , Mice, Knockout , Phosphorylation
20.
Yonago Acta Med ; 61(1): 8-18, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29599617

ABSTRACT

BACKGROUND: Resolvin E1 (RvE1) derived from the ω-3 polyunsaturated fatty acid eicosapentaenoic acid is known to be a potent pro-resolving lipid mediator that prevents chronic inflammation and osteoclastogenesis. We investigated the inhibitory effects of RvE1 on osteoclastogenesis and bone resorption to clarify its therapeutic potential for rheumatoid arthritis (RA). METHODS: Receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast differentiation was assessed with tartrate-resistant acid phosphatase staining. RANKL-induced bone resorption was assessed by the measurement of pit formation using calcium phosphate-labeled fluorescent polyanionic molecules in RAW264.7 cells as osteoclast precursors. The effects of RvE1 on the RANKL-induced mRNA expression of osteoclast-specific genes and transcriptional factors such as c-fos and nuclear factor of activated T cells c1 (NFATc1) in RAW264.7 cells were measured by quantitative real-time PCR. The distribution of NFATc1 induced by RANKL was evaluated by immunofluorescence staining in RAW264.7 cells. To analyze the mechanism of the inhibitory effect of RvE1 on osteoclastogenesis, we measured IL-17-induced RANKL mRNA expression in MC3T3-E1 osteoblast cells treated with RvE1 using quantitative real-time PCR and determined the level of prostaglandin E2 (PGE2) production by enzyme-linked immunosorbent assay. RESULTS: RvE1 significantly suppressed RANKL-induced osteoclast differentiation and bone resorption. RvE1 inhibited the RANKL-induced mRNA expression of osteoclast-specific genes along with the transcription factors NFATc1 and c-fos. Moreover, NFATc1 translocation from the cytoplasm to the nucleus of RAW264.7 cells was suppressed following RvE1 treatment. RvE1 also inhibited IL-17-induced RANKL mRNA expression and PGE2 production in MC3T3-E1 cells. CONCLUSION: RvE1 inhibited osteoclastogenesis and bone resorption by suppressing RANKL-induced NFATc1 and c-fos expression in osteoclasts and IL-17-induced RANKL expression through the autocrine action of PGE2 in osteoblasts. Our data suggest RvE1 as a new therapeutic target of RA.

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