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Abstract Prognostic stratification is an urgent concern for patients with colorectal cancer (CRC). The desmoplastic reaction (DR) is speculated to mirror the tumor microenvironment. DR types are considered independent prognostic indicators in CRC, but have not been incorporated in previous prognostic nomograms. We aimed to assess the prognostic significance of a novel approach incorporating histopathological indicators reflecting tumor glandular differentiation and microenvironment. We evaluated 329 consecutive patients with CRC who underwent surgical resection at Kansai Medical University. Histological glandular differentiation was scored as 2 (0 point), 3 (1 point), or 4 (2 points). Tumor buddings (TBs) were classified as TB1 (0 point), TB2 (1 point), or TB3 (2 points). pT1 or 2 was considered as 0 point, pT3 or 4 + DR non-immature type as 1 point, and pT3 or 4 + DR immature type as 2 points. Lymph node metastasis was classified as pN0 (0 point), pN1 (1 point), or pN2 (2 points). The preoperative carcinoembryonic antigen levels were categorized as

Abstract Background Postoperative lymphatic leakage is a complication of ineffective conservative treatment for retroperitoneal mass. Herein, we report a case of lymphatic leakage that arose after retroperitoneal tumor resection and that was treated with retrograde transvenous thoracic duct embolization. Case presentation A 28-year-old man with persistent abdominal pain was diagnosed with a large retroperitoneal metastatic tumor measuring 10 cm and a subdiaphragmatic lymph node originating from a testicular tumor. After high orchidectomy and neoadjuvant chemotherapy, the subdiaphragmatic lymph node and retroperitoneal tumor were resected together with the abdominal aorta; the latter was reconstructed using a prosthetic graft. Postoperatively, the patient developed chylothorax. No improvement was observed after conservative treatment that included fasting and somatostatin therapy. The leakage site could not be identified using antegrade lymphangiography of the bilateral inguinal lymph nodes, but was detected using retrograde transvenous lymphangiography. The leakage site was successfully embolized. Conclusion This case report describes successful treatment with retrograde transvenous thoracic duct embolization for chylothorax following resection of a retroperitoneal tumor and lymph node. This approach is a less invasive and more effective mode of treatment for chylothorax and should be considered before surgical thoracic duct ligation when the leakage point cannot be identified using the antegrade approach.

Abstract Purpose This study aimed to examine the incidence of incisional hernia (IH) in elective laparoscopic colorectal surgery (LC) using regulated computed tomography (CT) images at intervals every 6 months. Methods We retrospectively examined the diagnosis of IH in patients who underwent LC for colorectal cancer at Kansai Medical University Hospital from January 2014 to August 2018. The diagnosis of IH was defined as loss of continuity of the fascia in the axial CT images. Results 470 patients were included in the analysis. IH was diagnosed in 47 cases at 1 year after LC. The IH size was 7.8 cm2 [1.3–55.6]. In total, 38 patients with IH underwent CT examination 6 months after LC, and 37 were already diagnosed with IH. The IH size was 4.1 cm2 [0–58.9]. The IH size increased in 17 cases between 6 months and 1 year postoperatively, and in 1 case, a new IH occurred. 47%(18/38) of them continued to grow until 1 year after LC. A multivariate analysis was performed on the risk of IH occurrence. SSI was most significantly associated with IH occurrence (OR:5.28 [2.14–13.05], p = 0.0003). Conclusion IH occurred in 10% and 7.9% at 1 year and 6 months after LC. By examining CT images taken for the postoperative surveillance of colorectal cancer, we were able to investigate the occurrence of IH in detail.

Abstract Adjuvant S-1 monotherapy is the standard of care for stage II gastric cancer (GC) after curative resection in Japan, but its efficacy for microsatellite instability–high (MSI-H) tumors has remained unknown. Among a multi-institutional cohort of patients with stage II GC who underwent R0 resection followed by S-1 adjuvant chemotherapy between February 2008 and December 2018, we assessed MSI status with an MSI-IVD Kit (Falco). MSI status was assessable for 184 (88.5%) of the 208 enrolled patients, with MSI-H being identified in 24 (13.0%) individuals. Although neither relapse-free survival (RFS) (hazard ratio [HR] = 1.00, p = 0.997) nor overall survival (OS) (HR = 0.66, p = 0.488) differed between MSI-H versus microsatellite-stable (MSS) patients, MSI-H patients showed a nonsignificant but better RFS (HR = 0.34, p = 0.064) and OS (HR = 0.22, p = 0.057) than did MSS patients after adjustment for background characteristics by propensity score (PS) analysis. Gene expression analysis in the PS-matched cohort suggested that recurrence was associated with the immunosuppressive microenvironment in MSI-H tumors but with expression of cancer/testis antigen genes in MSS tumors. Our data reveal a better adjusted survival for MSI-H versus MSS stage II GC treated with S-1 adjuvant therapy, and they suggest that mechanisms of recurrence differ between MSI-H and MSS tumors.

Abstract Background and Aim The risk of hepatocellular carcinoma (HCC) persists in a condition of sustained virologic response (SVR) after hepatitis C virus (HCV) eradication. Comprehensive molecular analyses were performed to test the hypothesis that epigenetic abnormalities present after an SVR play a role in hepatocarcinogenesis. Methods Whole‐genome methylome and RNA sequencing were performed on HCV, SVR, and healthy liver tissue. Integrated analysis of the sequencing data focused on expression changes in transcription factors and their target genes, commonly found in HCV and SVR. Identified expression changes were validated in demethylated cultured HCC cell lines and an independent validation cohort. Results The coincidence rates of the differentially methylated regions between the HCV and SVR groups were 91% in the hypomethylated and 71% in the hypermethylated regions in tumorous tissues, and 37% in the hypomethylated and 36% in the hypermethylated regions in non‐tumorous tissues. These results indicate that many epigenomic abnormalities persist even after an SVR was achieved. Integrated analysis identified 61 transcription factors and 379 other genes that had methylation abnormalities and gene expression changes in both groups. Validation cohort specified gene expression changes for 14 genes, and gene ontology pathway analysis revealed apoptotic signaling and inflammatory response were associated with these genes. Conclusion This study demonstrates that DNA methylation abnormalities, retained after HCV eradication, affect the expression of transcription factors and their target genes. These findings suggest that DNA methylation in SVR patients may be functionally important in carcinogenesis, and could serve as biomarkers to predict HCC occurrence.

Abstract Background IgG4-related cholecystitis, which is a manifestation of IgG4-related disease in the gallbladder, is associated with autoimmune pancreatitis or IgG4-related sclerosing cholangitis in most cases; isolated gallbladder lesions without systemic manifestations are very rare. Gallbladder wall thickening is often diffuse, but sometimes localized, in which case, differentiation from gallbladder cancer becomes difficult. The characteristic features of IgG4-related cholecystitis on imaging that would enable differentiation from gallbladder cancer remain poorly described. Case presentation We present a rare case of isolated IgG4-related cholecystitis with localized gallbladder wall thickening that was clinically difficult to distinguish from malignancy before resection. An 82-year-old man was referred to our hospital because of gallbladder wall thickening on abdominal ultrasonography without any symptoms. Dynamic computed tomography of the abdomen showed localized wall thickening from the body to the fundus of the gallbladder that was enhanced from an early stage with a prolonged contrast effect. There were no other findings, such as pancreatic enlargement and bile duct dilatation. Magnetic resonance cholangiopancreatography revealed neither dilatation nor stenosis of the bile duct and pancreatic duct. Endoscopic ultrasonography (EUS) showed a smooth layered thickening of the gallbladder wall with a maximum thickness of 6 mm and a well-preserved outermost hyperechoic layer in the same area. Laparoscopic cholecystectomy was performed because malignancy could not be completely ruled out. Pathological examination of a resected specimen revealed IgG4-positive plasma cell infiltration, fibrosis, and phlebitis. Although the serum IgG4 level measured after resection was normal, the condition was ultimately diagnosed as probable IgG4-related cholecystitis according to the 2020 revised comprehensive diagnostic criteria for IgG4-related disease. The EUS images reflected the pathological findings, in which lymphocytic infiltration was distributed in a laminar fashion in the gallbladder wall. Conclusions Although rare, isolated IgG4-related cholecystitis with localized wall thickening mimicking gallbladder cancer remains a clinical problem. A smooth laminar thickening of the gallbladder wall on EUS imaging could be one of the most informative characteristics for differentiating IgG4-related cholecystitis from gallbladder cancer.

Abstract Background Aortic valve neocuspidization (AVNeo) has emerged as a promising aortic valve procedure, and is expected to have a larger effective orifice area (EOA) than commercially available bioprostheses. It is, however, unclear which indices could facilitate left ventricular (LV) reverse remodeling after AVNeo. The aim of this study is to verify the impact of global left ventricular afterload on the LV reverse remodeling following AVNeo. Methods Data-available consecutive 38 patients (median age, 77; interquartile range, 72.8–82.0) undergoing AVNeo for severe aortic stenosis were enrolled in this study. Preoperative and the last follow-up echocardiographic data were retrospectively analyzed including the valvuloarterial impedance (Zva), a marker of global LV afterload. Reduction in LV geometry index (LVGI) and relative wall thickness (RWT) were used as an indicator for LV reverse remodeling. Results The Zva reduced in 24 patients (63.2%) during the follow-up period (median, 12 months). Reduction in Zva significantly correlated to improvement of LV geometry (LVGI (r = 0.400, p = 0.013) and RWT (r = 0.627, p

Abstract. Objective:. No ideal training system exists for pancreaticoduodenectomy (PD). We developed an educational system that uses an objective structured assessment of technical skills. Methods:. This retrospective observational study was conducted using the data of consecutive trainees and patients who underwent PD from 2007 to 2013 in Kansai Medical University Hospital. The total score on the task checklist (21 parameters) for measuring technical performance during PD by self assessment and instructor assessment was compared between junior (JN) and hepatobiliary pancreatic (HBP) trainees at a university hospital. Surgical outcomes of 303 PDs (2007–2013) were also compared among JN trainees, HBP trainees, and instructors, and the present position of the trainees was investigated. This study was approved by the institutional review board of Kansai Medical University on May 26, 2020. Results:. The self-assessment score on the task checklist was significantly higher for the HBP trainees than for the JN trainees on all parts of PD (P

Abstract Background A brachial artery aneurysm (BAA) is a rare condition accounting for 5% of all peripheral arterial aneurysms. More cases of true BAAs after arteriovenous fistula (AVF) closure have been reported in the past two decades. Case presentation A 60-year-old man who underwent AVF closure after renal transplantation had a true BAA on his left elbow that had grown within the past 6 months. We successfully performed an open repair with end-to-end anastomosis. No complications occurred for 1 year. Conclusions High flow due to AVF and some collateral factors such as the use of steroids and immunosuppressants after renal transplantation, arteriosclerosis, and chronic mechanical stimulation might contribute to BAA formation.

Dominant-negative mutations associated with signal transducer and activator of transcription 3 (STAT3) signaling, which controls epithelial proliferation in various tissues, lead to atopic dermatitis in hyper IgE syndrome. This dermatitis is thought to be attributed to defects in STAT3 signaling in type 17 helper T cell specification. However, the role of STAT3 signaling in skin epithelial cells remains unclear. We found that STAT3 signaling in keratinocytes is required to maintain skin homeostasis by negatively controlling the expression of hair follicle-specific keratin genes. These expression patterns correlated with the onset of dermatitis, which was observed in specific pathogen-free conditions but not in germ-free conditions, suggesting the involvement of Toll-like receptor-mediated inflammatory responses. Thus, our study suggests that STAT3-dependent gene expression in keratinocytes plays a critical role in maintaining the homeostasis of skin, which is constantly exposed to microorganisms.

Macrophage-like cells derived from vascular smooth muscle cells (SMCs) play critical roles in atherogenesis, and DNA hydroxymethylation was implicated in transdifferentiation. We examined transcriptomes and (hydroxy)methylomes of human coronary artery SMCs during cholesterol-induced transdifferentiation. A unique approach of exhaustive identification of differentially expressed genes followed by Gene Ontology-centric clustering facilitated deeper understanding of multifaceted modulations of genes involved in extracellular matrix organization, angiogenesis, cell migration, hypoxia response, and cholesterol biosynthesis. Intriguingly, type I interferon response was transiently activated, presumably forming an immuno-metabolic circuit with cholesterol metabolism. Neither global nor DEG-proximal changes were evident in (hydroxy)methylation. These results would not only provide a unique data resource for atherosclerosis research but present a potentially useful approach in transcriptome data interpretation.

Abstract Aim The present study aimed to evaluate the efficacy of short‐term nutritional intervention with an oral elemental diet (ED; Elental; EA Pharma Co., Ltd, Tokyo, Japan) at 300 kcal/day for 6‐8 weeks in the early post‐gastrectomy period on postoperative long‐term body weight loss (BWL). Methods We analyzed consecutive patients who were randomly divided to receive the regular diet with or without ED. The control group received regular diet alone post‐gastrectomy, whereas the ED group received 300 kcal ED plus regular diet for 6‐8 weeks. Primary endpoint was percentage (%) BWL (body weight loss; body weight before surgery minus that at postoperative 1 year) by surgical type. Secondary endpoints included changes in nutrition‐related blood parameters. Results Of the patients in the original trial, 106 were eligible for efficacy analyses. %BWL at postoperative 1 year was significantly lower in the ED group than in the control group among patients who underwent total gastrectomy (TG) (n = 19 and n = 17, respectively; 9.66 ± 5.98% [95% confidence interval, CI: 6.77‐12.54] vs 15.11 ± 6.78% [95% CI: 11.63‐18.60], P = .015), but not in patients who underwent distal gastrectomy (n = 38 and n = 32, respectively; 5.81 ± 7.91% [95% CI: 3.21‐8.41] vs 5.96 ± 6.20% [95% CI: 3.72‐8.19], P = .933). In multivariate analysis, ED was the only factor affecting %BWL at postoperative 1 year among patients who underwent TG. Conclusions Daily nutritional intervention (300 kcal/day ED) for 6‐8 weeks reduced %BWL not only at postoperative 6‐8 weeks but also at 1 year in patients who underwent TG.

Summary: Background: Post-operative pancreatic fistula (POPF) is one of the most common and serious complications after pancreaticoduodenectomy (PD). The aim of this study is to retrospectively compare clinically relevant (CR) POPF and other complications after pacreaticojejunostomy (PJ) after modified Kakita (m-Kakita) or modified Blumgart (m-Blumgart) anastomoses without stenting in a single institution. Methods: One hundred twenty-eight patients underwent PJ using m-Kakita anastomoses (two interrupted penetrating sutures) between January 2009 and December 2011. One hundred eighteen patients underwent m-Blumgart anastomoses (two transpancreatic/jejunal seromuscular sutures to cover the pancreatic stump with jejunal serosa) between January 2014 and December 2015. Demographics, clinical characteristics, and post-operative mortality and morbidity were retrospectively compared between the two groups. Results: There were no significant differences in demographics or clinical characteristics between the two groups except operative time. A significantly lower rate of CR-POPF was found in the m-Blumgart group relative to the m-Kakita group (10% vs. 19%, p = 0.038). Univariate and multivariate analyses revealed that the m-Blumgart anastomosis and fistula risk category (Negligible, Low) were independently protective against CR-POPF (p

Background Angiotensin II (Ang II) can cause hypertension and tissue impairment via AGTR1 (Ang II receptor type 1), particularly in renal proximal tubule cells, and can cause DNA damage in renal cells via nicotinamide adenine dinucleotide phosphate oxidase. BubR1 (budding uninhibited by benzimidazole‐related 1) is a multifaceted kinase that functions as a mitotic checkpoint. BubR1 expression can be induced by Ang II in smooth muscle cells in vitro, but the relationship between systemic BubR1 expression and the Ang II response is unclear. Methods and Results Twenty 24‐week‐old male BubR1 low‐expression mice (BubR1L/L mice) and age‐matched BubR1+/+ mice were used in this study. We investigated how Ang II stimulation affects BubR1L/L mice. The elevated systolic blood pressure caused by Ang II stimulation in BubR1+/+ mice was significantly attenuated in BubR1L/L mice. Additionally, an attenuated level of Ang II–induced perivascular fibrosis was observed in the kidneys of BubR1L/L mice. Immunohistochemistry revealed that the overexpression of AGTR1 induced by Ang II stimulation was repressed in BubR1L/L mice. We evaluated AGTR1 and Nox‐4 (nicotinamide adenine dinucleotide phosphate oxidase‐4) levels to determine the role of BubR1 in the Ang II response. Results from in vitro assays of renal proximal tubule cells suggest that treatment with small interfering RNA targeting BubR1 suppressed Ang II‐induced overexpression of AGTR1. Similarly, the upregulation in Nox4 and Jun N‐terminal kinase induced by Ang II administration was repressed by treatment with small interfering RNA targeting BubR1. Conclusions Ang II–induced hypertension is caused by AGTR1 overexpression in the kidneys via the upregulation of BubR1 and Nox4.

The Interior Highlands, in southern North America, possesses a distinct fauna with numerous endemic species. Many freshwater taxa from this area exhibit genetic structuring consistent with biogeography, but this notion has not been explored in freshwater snails. Using mitochondrial 16S DNA sequences and ISSRs, we aimed to examine genetic structuring in the Pyramid Elimia, Elimia potosiensis, at various geographic scales. On a broad scale, maximum likelihood and network analyses of 16S data revealed a high diversity of mitotypes lacking biogeographic patterns across the range of E. potosiensis. On smaller geographic scales, ISSRs revealed significant population structure, even over the distance of a few hundred meters. Unlike other freshwater mollusks like mussels, E. potosiensis showed no evolutionary patterns relating to biogeography. The species does show population-level genetic structure, which may have implications in conservation efforts.

Abstract Background Primary hepatic neuroendocrine carcinomas are extremely rare. Because of the rarity of PHNEC, its clinical features and treatment outcomes are not well understood. A proper diagnosis and the correct therapeutic approach therefore remain clinically challenging. Case presentation A 67-year-old man was admitted to our department because of a liver tumor. Computed tomography revealed a single liver tumor 50 mm in diameter and located in the S3 region. Biopsy and imaging findings resulted in a diagnosis of primary hepatic neuroendocrine carcinoma. Left lateral segmentectomy was performed. Immunohistochemically, the tumor cells were positive for synaptophysin, chromogranin A, and CD56. Ki-67 was positive in > 90% of the tumor cells. The final diagnosis was primary hepatic neuroendocrine carcinoma. The patient suffered two episodes of lymph node recurrence. Nonetheless, the tumor was excised to prolong survival. Thus, after lymphadenectomy, he received adjuvant chemotherapy for 6 months. Two years after surgery, the patient remains alive and in good general condition. Conclusions In most cases, primary hepatic neuroendocrine carcinoma, while extremely rare, has a poor prognosis. At present, surgical resection is a priority for curative treatment, but in patients with recurrence, combined therapies are recommended.

Mathematical models for signaling pathways are helpful for understanding molecular mechanism in the pathways and predicting dynamic behavior of the signal activity. To analyze the robustness of such models, local sensitivity analysis has been implemented. However, such analysis primarily focuses on only a certain parameter set, even though diverse parameter sets that can recapitulate experiments may exist. In this study, we performed sensitivity analysis that investigates the features in a system considering the reproducible and multiple candidate values of the model parameters to experiments. The results showed that although different reproducible model parameter values have absolute differences with respect to sensitivity strengths, specific trends of some relative sensitivity strengths exist between reactions regardless of parameter values. It is suggested that (i) network structure considerably influences the relative sensitivity strength and (ii) one might be able to predict relative sensitivity strengths specified in the parameter sets employing only one of the reproducible parameter sets.

Correct identification of sex is an important component of wildlife management because changes in sex ratios can affect population viability. Identification of sex often relies on external morphology, which can be biased by intermediate or nondistinctive morphotypes and observer experience. For unionid mussels, research has demonstrated that species misidentification is common but less attention has been given to the reliability of sex identification. To evaluate whether this is an issue, we surveyed 117 researchers on their ability to correctly identify sex of Lampsilis teres (Yellow Sandshell), a wide ranging, sexually dimorphic species. Personal background information of each observer was analyzed to identify factors that may contribute to misidentification of sex. We found that median misidentification rates were ~20% across males and females and that observers falsely identified the number of female specimens more often (~23%) than males (~10%). Misidentification rates were partially explained by geographic region of prior mussel experience and where observers learned how to identify mussels, but there remained substantial variation among observers after controlling for these factors. We also used three morphometric methods (traditional, geometric, and Fourier) to investigate whether sex could be more correctly identified statistically and found that misidentification rates for the geometric and Fourier methods (which characterize shape) were less than 5% (on average 7% and 2% for females and males, respectively). Our results show that misidentification of sex is likely common for mussels if based solely on external morphology, which raises general questions, regardless of taxonomic group, about its reliability for conservation efforts.

Toc75 plays a central role in chloroplast biogenesis in plants as the membrane channel of the protein import translocon at the outer envelope of chloroplasts (TOC). Toc75 is a member of the Omp85 family of bacterial and organellar membrane insertases, characterized by N-terminal POTRA (polypeptide-transport associated) domains and C-terminal membrane-integrated β-barrels. We demonstrate that the Toc75 POTRA domains are essential for protein import and contribute to interactions with TOC receptors, thereby coupling preprotein recognition at the chloroplast surface with membrane translocation. The POTRA domains also interact with preproteins and mediate the recruitment of molecular chaperones in the intermembrane space to facilitate membrane transport. Our studies are consistent with the multi-functional roles of POTRA domains observed in other Omp85 family members and demonstrate that the domains of Toc75 have evolved unique properties specific to the acquisition of protein import during endosymbiotic evolution of the TOC system in plastids.

Abnormal cardiac uptake of 123I-metaiodobenzylguanidine (123I-MIBG) is a diagnostic marker of Lewy body diseases (LBDs), e.g., Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Planar imaging is generally used to assess cardiac sympathetic dysfunction in 123I-MIBG scintigraphy; however, its clinical utility requires further improvement. We hypothesized that the co-registration of single-photon emission tomography (SPECT) and computed tomography (CT) images would improve the diagnostic accuracy of 123I-MIBG cardiac scintigraphy for LBDs. This study sought to evaluate the effects of SPECT/CT imaging on 123I-MIBG cardiac scintigraphy for diagnosing LBDs.We retrospectively investigated data of 54 patients (consecutive 18 patients in each PD, DLB, and idiopathic normal pressure hydrocephalus [iNPH] groups) who underwent 123I-MIBG cardiac scintigraphy (planar and SPECT/CT) because of suspected LBDs at the Tohoku University hospital from June 2012 to June 2015. We compared the diagnostic accuracies of the conventional planar 123I-MIBG method and SPECT/CT methods (manual and semi-automatic).In the conventional planar analysis, 123I-MIBG uptake decreased only in the DLB group compared with the iNPH group. In contrast, the SPECT/CT analysis revealed significantly lower 123I-MIBG uptake in both the PD and DLB groups compared with the iNPH group. Furthermore, a receiver operating characteristic analysis revealed that both the manual and semi-automatic SPECT/CT methods were superior to the conventional planar method in differentiating the 3 disorders.SPECT/CT 123I-MIBG cardiac scintigraphy can detect mild cardiac sympathetic dysfunction in LDBs. Our results suggest that the SPECT/CT technique improves diagnostic accuracy for LBDs.

PolyGly is present in many proteins in various organisms. One example is found in a transmembrane β-barrel protein, translocon at the outer-envelope-membrane of chloroplasts 75 (Toc75). Toc75 requires its N-terminal extension (t75) for proper localization. t75 comprises signals for chloroplast import (n75) and envelope sorting (c75) in tandem. n75 and c75 are removed by stromal processing peptidase and plastidic type I signal peptidase 1, respectively. PolyGly is present within c75 and its deletion or substitution causes mistargeting of Toc75 to the stroma. Here we have examined the properties of polyGly-dependent protein targeting using two soluble passenger proteins, the mature portion of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (mSS) and enhanced green fluorescent protein (EGFP). Both t75-mSS and t75-EGFP were imported into isolated chloroplasts and their n75 removed. Resultant c75-mSS was associated with the envelope at the intermembrane space, whereas c75-EGFP was partially exposed outside the envelope. Deletion of polyGly or substitution of tri-Ala for the critical tri-Gly segment within polyGly caused each passenger to be targeted to the stroma. Transient expression of t75-EGFP in Nicotiana benthamiana resulted in accumulation of c75-EGFP exposed at the surface of the chloroplast, but the majority of the EGFP passenger was found free in the cytosol with most of its c75 attachment removed. Results of circular dichroism analyses suggest that polyGly within c75 may form an extended conformation, which is disrupted by tri-Ala substitution. These data suggest that polyGly is distinct from a canonical stop-transfer sequence and acts as a rejection signal at the chloroplast inner envelope.

Immunological memory has been believed to be a feature of the adaptive immune system for long period, but recent reports suggest that the innate immune system also exhibits memory-like reaction. Although evidence of innate immune memory is accumulating, no in vivo experimental data has clearly implicated a molecular mechanism, or even a cell-type, for this phenomenon. In this study of data deposited into Gene Expression Omnibus (GEO) under GSE71111, we analyzed the expression profile of peritoneal macrophages isolated from mice pre-administrated with toll-like receptor (TLR) ligands, mimicking pathogen infection. In these macrophages, increased expression of a group of innate immunity-related genes was sustained over a long period of time, and these genes overlapped with ATF7-regulated genes. We conclude that ATF7 plays an important role in innate immune memory in macrophages. Keywords: Macrophage, ATF7, Innate immune memory, Microarray

Phosphatidylethanolamine N-methyltransferase (Pemt) catalyzes the methylation of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) mainly in the liver. Under an obese state, the upregulation of Pemt induces endoplasmic reticulum (ER) stress by increasing the PC/PE ratio in the liver. We targeted the Pemt gene in mice to explore the therapeutic impact of Pemt on the progression of diabetic nephropathy and diabetes, which was induced by the injection of streptozotocin (STZ). Although the blood glucose levels were similar in STZ-induced diabetic Pemt+/+ and Pemt-/-mice, the glomerular hypertrophy and albuminuria in Pemt-/- mice were significantly reduced. Pemt deficiency reduced the intraglomerular F4/80-positive macrophages, hydroethidine fluorescence, tubulointerstitial fibrosis and tubular atrophy. The expression of glucose-regulated protein-78 (GRP78) was enriched in the renal tubular cells in STZ-induced diabetic mice, and this was ameliorated by Pemt deficiency. In mProx24 renal proximal tubular cells, the treatment with ER-stress inducers, tunicamycin and thapsigargin, increased the expression of GRP78, which was reduced by transfection of a shRNA lentivirus for Pemt (shRNA-Pemt). The number of apoptotic cells in the renal tubules was significantly reduced in Pemt-/- diabetic mice, and shRNA-Pemt upregulated the phosphorylation of Akt and decreased the cleavage of caspase 3 and 7 in mProx24 cells. Taken together, these findings indicate that the inhibition of Pemt activity ameliorates the ER stress associated with diabetic nephropathy in a model of type 1 diabetes and corrects the functions of the three major pathways downstream of ER stress, i.e. oxidative stress, inflammation and apoptosis.

We analyzed the urine samples of patients with type 2 diabetes at various stages of diabetic nephropathy by lectin microarray to identify a biomarker to predict the progression of diabetic nephropathy. Japanese patients with type 2 diabetes at various stages of nephropathy were enrolled and we performed lectin microarray analyses (n = 17) and measured urinary excretion of fetuin-A (n = 85). The increased signals of urine samples were observed in Siaα2-6Gal/GalNAc-binding lectins (SNA, SSA, TJA-I) during the progression of diabetic nephropathy. We next isolated sialylated glycoproteins by using SSA-lectin affinity chromatography and identified fetuin-A by liquid chromatography-tandem mass spectrometer. Urinary excretion of fetuin-A significantly increased during the progression of albuminuria (A1, 0.40 ± 0.43; A2, 0.60 ± 0.53; A3 1.57 ± 1.13 ng/gCr; p = 7.29 × 10(-8)) and of GFR stages (G1, 0.39 ± 0.39; G2, 0.49 ± 0.45; G3, 1.25 ± 1.18; G4, 1.34 ± 0.80 ng/gCr; p = 3.89 × 10(-4)). Multivariate logistic regression analysis was employed to assess fetuin-A as a risk for diabetic nephropathy with microalbuminuria or GFR

BACKGROUND: For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. RESULTS: We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. CONCLUSIONS: Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

Community structure is a universal and significant feature of many complex networks in biology, society, and economics. Community structure has also been revealed in human brain structural and functional networks in previous studies. However, communities overlap and share many edges and nodes. Uncovering the overlapping community structure of complex networks remains largely unknown in human brain networks. Here, using regional gray matter volume, we investigated the structural brain network among 90 brain regions (according to a predefined anatomical atlas) in 462 young, healthy individuals. Overlapped nodes between communities were defined by assuming that nodes (brain regions) can belong to more than one community. We demonstrated that 90 brain regions were organized into 5 overlapping communities associated with several well-known brain systems, such as the auditory/language, visuospatial, emotion, decision-making, social, control of action, memory/learning, and visual systems. The overlapped nodes were mostly involved in an inferior-posterior pattern and were primarily related to auditory and visual perception. The overlapped nodes were mainly attributed to brain regions with higher node degrees and nodal efficiency and played a pivotal role in the flow of information through the structural brain network. Our results revealed fuzzy boundaries between communities by identifying overlapped nodes and provided new insights into the understanding of the relationship between the structure and function of the human brain. This study provides the first report of the overlapping community structure of the structural network of the human brain.

Thylakoidal processing peptidase (TPP) is responsible for removing amino-terminal thylakoid-transfer signals from several proteins in the thylakoid lumen. Three TPP isoforms are encoded by the nuclear genome of Arabidopsis thaliana. Previous studies showed that one of them termed plastidic type I signal peptidase 1 (Plsp1) was necessary for processing three thylakoidal proteins and one protein in the chloroplast envelope in vivo. The lack of Plsp1 resulted in seedling lethality, apparently due to disruption of proper thylakoid development. The physiological roles of the other two TPP homologs remain unknown. Here we show that the three A. thaliana TPP isoforms evolved to acquire diverse functions. Phylogenetic analysis revealed that TPP may have originated before the endosymbiotic event, and that there are two groups of TPP in seed plants: one includes Plsp1 and another comprises the other two A. thaliana TPP homologs, which are named as Plsp2A and Plsp2B in this study. The duplication leading to the two groups predates the gymnosperm-angiosperm divergence, and the separation of Plsp2A and Plsp2B occurred after the Malvaceae-Brassicaceae diversification. Quantitative reverse transcription-PCR assay revealed that the two PLSP2 genes were co-expressed in both photosynthetic tissues and roots, whereas the PLSP1 transcript accumulated predominantly in photosynthetic tissues. Both PLSP2 genes were expressed in the aerial parts of the plsp1-null mutant at levels comparable to those in wild-type plants. The seedling-lethal phenotype of the plsp1-null mutant could be rescued by a constitutive expression of Plsp1 cDNA but not by that of Plsp2A or Plsp2B. These results indicate that Plsp1 and Plsp2 evolved to function differently, and that neither of the Plsp2 isoforms is necessary for proper thylakoid development in photosynthetic tissues.

BACKGROUND: A goal of systems biology is to analyze large-scale molecular networks including gene expressions and protein-protein interactions, revealing the relationships between network structures and their biological functions. Dividing a protein-protein interaction (PPI) network into naturally grouped parts is an essential way to investigate the relationship between topology of networks and their functions. However, clear modular decomposition is often hard due to the heterogeneous or scale-free properties of PPI networks. METHODOLOGY/PRINCIPAL FINDINGS: To address this problem, we propose a diffusion model-based spectral clustering algorithm, which analytically solves the cluster structure of PPI networks as a problem of random walks in the diffusion process in them. To cope with the heterogeneity of the networks, the power factor is introduced to adjust the diffusion matrix by weighting the transition (adjacency) matrix according to a node degree matrix. This algorithm is named adjustable diffusion matrix-based spectral clustering (ADMSC). To demonstrate the feasibility of ADMSC, we apply it to decomposition of a yeast PPI network, identifying biologically significant clusters with approximately equal size. Compared with other established algorithms, ADMSC facilitates clear and fast decomposition of PPI networks. CONCLUSIONS/SIGNIFICANCE: ADMSC is proposed by introducing the power factor that adjusts the diffusion matrix to the heterogeneity of the PPI networks. ADMSC effectively partitions PPI networks into biologically significant clusters with almost equal sizes, while being very fast, robust and appealing simple.