Reconstruction of insulin signal flow from phosphoproteome and metabolome data

Cellular homeostasis is regulated by signals through multiple molecular networks that include protein phosphorylation and metabolites. However, where and when the signal flows through a network and regulates homeostasis has not been explored. We have developed a reconstruction method for the signal flow based on time-course phosphoproteome and metabolome data, using multiple databases, and have applied it to acute action of insulin, an important hormone for metabolic homeostasis. An insulin signal flows through a network, through signaling pathways that involve 13 protein kinases, 26 phosphorylated metabolic enzymes, and 35 allosteric effectors, resulting in quantitative changes in 44 metabolites. Analysis of the network reveals that insulin induces phosphorylation and activation of liver-type phosphofructokinase 1, thereby controlling a key reaction in glycolysis. We thus provide a versatile method of reconstruction of signal flow through the network using phosphoproteome and metabolome data.

Incidence of and risk factors for incisional hernia after abdominal surgery

BACKGROUND

Few larger studies have estimated the incidence of incisional hernia (IH) after abdominal surgery.

METHODS

Patients who had abdominal surgery between November 2009 and February 2011 were included in the study. The incidence rate and risk factors for IH were monitored for at least 180  days.

RESULTS

A total of 4305 consecutive patients were registered. Of these, 378 were excluded because of failure to complete follow-up and 3927 patients were analysed. IH was diagnosed in 318 patients. The estimated incidence rates for IH were 5·2 per cent at 12  months and 10·3 per cent at 24 months. In multivariable analysis, wound classification III and IV (hazard ratio (HR) 2·26, 95 per cent confidence interval 1·52 to 3·35), body mass index of 25 kg/m(2) or higher (HR 1·76, 1·35 to 2·30), midline incision (HR 1·74, 1·28 to 2·38), incisional surgical-site infection (I-SSI) (HR 1·68, 1·24 to 2·28), preoperative chemotherapy (HR 1·61, 1·08 to 2·37), blood transfusion (HR 1·46, 1·04 to 2·05), increasing age by 10-year interval (HR 1·30, 1·16 to 1·45), female sex (HR 1·26, 1·01 to 1·59) and thickness of subcutaneous tissue for every 1-cm increase (HR 1·18, 1·03 to 1·35) were identified as independent risk factors. Compared with superficial I-SSI, deep I-SSI was more strongly associated with the development of IH.

CONCLUSION

Although there are several risk factors for IH, reducing I-SSI is an important step in the prevention of IH.

REGISTRATION NUMBER

UMIN000004723 (University Hospital Medical Information Network, http://www.umin.ac.jp/ctr/index.htm).

The development and initial validation of a virtual dripping sweat rate and a clothing wetness ratio for use in predictive heat strain models

This paper applies the heat balance equation (HBE) for clothed subjects as a linear function of mean skin temperature (t sk ) by a new sweating efficiency (η sw ) and an approximation for the thermoregulatory sweat rate. The equation predicting t sk in steady state conditions was derived as the solution of the HBE and used for a predictive heat strain scale. The heat loss from the wet clothing (WCL) area was identified with a new variable of 'virtual dripping sweat rate VDSR' (S wdr ). This is a subject's un-evaporated sweat rate in dry clothing from the regional sweat rate exceeding the maximum evaporative capacity, and adds the moisture to the clothing, reducing the intrinsic clothing insulation. The S wdr allowed a mass balance analysis of the wet clothing area identified as clothing wetness (w cl ). The w cl was derived by combining the HBE at the WCL surface from which the evaporation rate and skin heat loss from WCL region are given. Experimental results on eight young male subjects wearing typical summer clothing, T-shirt and trousers verified the model for predicting t sk with WCL thermal resistance (R cl,w ) identified as 25 % of dry clothing (R cl,d ).

Highly sensitive nanoscale spin-torque diode

Highly sensitive microwave devices that are operational at room temperature are important for high-speed multiplex telecommunications. Quantum devices such as superconducting bolometers possess high performance but work only at low temperature. On the other hand, semiconductor devices, although enabling high-speed operation at room temperature, have poor signal-to-noise ratios. In this regard, the demonstration of a diode based on spin-torque-induced ferromagnetic resonance between nanomagnets represented a promising development, even though the rectification output was too small for applications (1.4 mV mW(-1)). Here we show that by applying d.c. bias currents to nanomagnets while precisely controlling their magnetization-potential profiles, a much greater radiofrequency detection sensitivity of 12,000 mV mW(-1) is achievable at room temperature, exceeding that of semiconductor diode detectors (3,800 mV mW(-1)). Theoretical analysis reveals essential roles for nonlinear ferromagnetic resonance, which enhances the signal-to-noise ratio even at room temperature as the size of the magnets decreases.

Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota

Objectives

Bifidobacterium species are one of the major components of the infant's intestine microbiota. Colonization with bifidobacteria in early infancy is suggested to be important for health in later life. However, information remains limited regarding the source of these microbes. Here, we investigated whether specific strains of bifidobacteria in the maternal intestinal flora are transmitted to their infant's intestine.

Materials and Methods

Fecal samples were collected from healthy 17 mother and infant pairs (Vaginal delivery: 12; Cesarean section delivery: 5). Mother's feces were collected twice before delivery. Infant's feces were collected at 0 (meconium), 3, 7, 30, 90 days after birth. Bifidobacteria isolated from feces were genotyped by multilocus sequencing typing, and the transitions of bifidobacteria counts in infant's feces were analyzed by quantitative real-time PCR.

Results

Stains belonging to Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum subsp. longum, and Bifidobacterium pseudocatenulatum, were identified to be monophyletic between mother's and infant's intestine. Eleven out of 12 vaginal delivered infants carried at least one monophyletic strain. The bifidobacterial counts of the species to which the monophyletic strains belong, increased predominantly in the infant's intestine within 3 days after birth. Among infants delivered by C-section, monophyletic strains were not observed. Moreover, the bifidobacterial counts were significantly lower than the vaginal delivered infants until 7 days of age.

Conclusions

Among infants born vaginally, several Bifidobacterium strains transmit from the mother and colonize the infant's intestine shortly after birth. Our data suggest that the mother's intestine is an important source for the vaginal delivered infant's intestinal microbiota.

The extraction of simple relationships in growth factor-specific multiple-input and multiple-output systems in cell-fate decisions by backward elimination PLS regression

Cells use common signaling molecules for the selective control of downstream gene expression and cell-fate decisions. The relationship between signaling molecules and downstream gene expression and cellular phenotypes is a multiple-input and multiple-output (MIMO) system and is difficult to understand due to its complexity. For example, it has been reported that, in PC12 cells, different types of growth factors activate MAP kinases (MAPKs) including ERK, JNK, and p38, and CREB, for selective protein expression of immediate early genes (IEGs) such as c-FOS, c-JUN, EGR1, JUNB, and FOSB, leading to cell differentiation, proliferation and cell death; however, how multiple-inputs such as MAPKs and CREB regulate multiple-outputs such as expression of the IEGs and cellular phenotypes remains unclear. To address this issue, we employed a statistical method called partial least squares (PLS) regression, which involves a reduction of the dimensionality of the inputs and outputs into latent variables and a linear regression between these latent variables. We measured 1,200 data points for MAPKs and CREB as the inputs and 1,900 data points for IEGs and cellular phenotypes as the outputs, and we constructed the PLS model from these data. The PLS model highlighted the complexity of the MIMO system and growth factor-specific input-output relationships of cell-fate decisions in PC12 cells. Furthermore, to reduce the complexity, we applied a backward elimination method to the PLS regression, in which 60 input variables were reduced to 5 variables, including the phosphorylation of ERK at 10 min, CREB at 5 min and 60 min, AKT at 5 min and JNK at 30 min. The simple PLS model with only 5 input variables demonstrated a predictive ability comparable to that of the full PLS model. The 5 input variables effectively extracted the growth factor-specific simple relationships within the MIMO system in cell-fate decisions in PC12 cells.

Robustness and compensation of information transmission of signaling pathways

Robust transmission of information despite the presence of variation is a fundamental problem in cellular functions. However, the capability and characteristics of information transmission in signaling pathways remain poorly understood. We describe robustness and compensation of information transmission of signaling pathways at the cell population level. We calculated the mutual information transmitted through signaling pathways for the growth factor-mediated gene expression. Growth factors appeared to carry only information sufficient for a binary decision. Information transmission was generally more robust than average signal intensity despite pharmacological perturbations, and compensation of information transmission occurred. Information transmission to the biological output of neurite extension appeared robust. Cells may use information entropy as information so that messages can be robustly transmitted despite variation in molecular activities among individual cells.

Ethnic diversity of gut microbiota: species characterization of Bacteroides fragilis group and genus Bifidobacterium in healthy Belgian adults, and comparison with data from Japanese subjects

The composition of the human gut microbiota is related to host health, and it is thought that dietary habits may play a role in shaping this composition. Here, we examined the population size and prevalence of six predominant bacterial genera and the species compositions of genus Bifidobacterium (g-Bifid) and Bacteroides fragilis group (g-Bfra) in 42 healthy Belgian adults by quantitative PCR (qPCR) over a period of one month. The population sizes and prevalence of these bacteria were basically stable throughout the study period. The predominant g-Bifid species were Bifidobacterium adolescentis and Bifidobacterium longum ss. longum, and the predominant g-Bfra species were Bacteroides vulgatus, Bacteroides uniformis, and Bacteroides ovatus. The Belgian gut microbiota data were then compared with gut microbiota data from 46 Japanese subjects collected according to the same protocol (Matsuki et al., Appl. Environ. Microbiol. 70, 167-173, 2004). The population size and prevalence of Bifidobacterium catenulatum group were significantly lower in the Belgian gut microbiota than in the Japanese gut microbiota (P < 0.001); however, the population size and prevalence of g-Bifid did not differ. This species-level qPCR analysis will be helpful for investigating the diversity of gut microbiota among ethnic groups.

Optical bending sensor using distributed feedback solid state dye lasers on optical fiber

Novel type of optical fiber sensor was proposed and demonstrated. The print-like fabrication technique fabricates multiple distributed feedback solid state dye lasers on a polymeric optical fiber (POF) with tapered coupling. This multi-active-sidecore structure was easily fabricated and provides multiple functions. Mounting the lasers on the same point of a multimode POF demonstrated a bending radius sensitivity of 20 m without any supports. Two axis directional sensing without cross talk was also confirmed. A more complicated mounting formation can demonstrate a twisted POF. The temperature property of the sensor was also studied, and elimination of the temperature influence was experimentally attained.

Development of a sensitive rRNA-targeted reverse transcription-quantitative polymerase chain reaction for detection of Vibrio cholerae/mimicus, V. parahaemolyticus/alginolyticus and Campylobacter jejuni/coli

A sensitive rRNA-targeted reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method was developed for detection of Vibrio cholerae/mimicus, V. parahaemolyticus/alginolyticus and Campylobacter jejuni/coli by using specific primers. Counts of the enteric pathogens spiked in human stools were quantified at the lower detection limit of 10(3) cells/g stool by RT-qPCR, in marked contrast with conventional quantitative polymerase chain reaction (qPCR) at the detection limit of 10(5) to 10(6) cells/g stool. The bacterial counts determined by RT-qPCR were almost equivalent to those determined by the culture method and fluorescence in situ hybridization (FISH) during the course of in vitro culture. Bacterial rRNA in the stools was stable for at least 4 weeks when the stools were kept as the suspensions in RNA-stabilizing agent, RNAlater®, even at 37(o) C. These data suggested that the rapid and high sensitive rRNA-targeted RT-qPCR was applicable for the accurate quantification of viable enteric pathogens, such as V. cholerae/mimicus, V. parahaemolyticus/alginolyticus and C. jejuni/coli.

Temporal coding of insulin action through multiplexing of the AKT pathway

One of the unique characteristics of cellular signaling pathways is that a common signaling pathway can selectively regulate multiple cellular functions of a hormone; however, this selective downstream control through a common signaling pathway is poorly understood. Here we show that the insulin-dependent AKT pathway uses temporal patterns multiplexing for selective regulation of downstream molecules. Pulse and sustained insulin stimulations were simultaneously encoded into transient and sustained AKT phosphorylation, respectively. The downstream molecules, including ribosomal protein S6 kinase (S6K), glucose-6-phosphatase (G6Pase), and glycogen synthase kinase-3β (GSK3β) selectively decoded transient, sustained, and both transient and sustained AKT phosphorylation, respectively. Selective downstream decoding is mediated by the molecules' network structures and kinetics. Our results demonstrate that the AKT pathway can multiplex distinct patterns of blood insulin, such as pulse-like additional and sustained-like basal secretions, and the downstream molecules selectively decode secretion patterns of insulin.

Safe esophageal reconstruction by ileocolic interposition

Many techniques have been proposed for esophageal reconstruction after esophagectomy when a gastric tube cannot be employed. There are two essential criteria for such a substitute: substitute length and sufficient blood supply. We propose ileocolic interposition as an easy and safe option. Two technical aspects contributing to the high success rate of this method are the preservation of an intact arterial network allowing normal blood flow to the ileocolic area, and the ability to quantify blood flow using a Doppler pulse flow meter in six cases. These are enabled by a long (up to 20cm) ileocolic segment. The preservation of the right colic artery is important, because its interruption would reduce blood supply to the long ileum segment. Between July 2003 and October 2008, we used this method in six patients in whom a gastric tube was not an option. We assessed perioperative morbidity and swallowing difficulties in each patient, quantifying dysphagia on scale of 0 to 4. There was no mortality and no anastomotic leak. There was one wound infection, and in one patient, recurrent nerve paralysis was observed. The postoperative hospital stay was 29.5 ± 10.8 days. The average dysphagia score for the six patients was 0.17 ± 0.41 after the operation. All patients can eat normally, without any dietary limitations. Ileocolonic interposition after esophagectomy requires careful assessment of the vascular supply. In this small series, morbidity was low and there was no perioperative mortality. We believe that this is an easy and safe method of reconstruction after esophagectomy in cases in whom a gastric tube cannot be used as a substitute.

[A case of advanced gastric cancer responding to S-1 therapy, leading to pathologically complete response]

Our patient was a 74-year-old man with abdominal pain. A gastrofiberscope revealed type 2 advanced gastric cancer. An abdominal computed tomography(CT)demonstrated liver and lymph node metastases. The No. 8a lymph node was 7 cm in diameter, and it invaded the head of the pancreas. Since a curative operation was deemed impossible, S-1 was administered orally for 28 consecutive days with a 14-day interval. After 2 courses of monotherapy, CT showed that metastatic lymph nodes were reduced and that liver metastases had mostly disappeared. After 8 courses, the primary lesion was scarred and the lymph node metastases were remarkably reduced. Therefore, we conducted distal gastrectomy and lymph node resection (D2). Histological findings revealed that there were no cancer cells in either the primary tumor or the lymph nodes, meaning that the resected lesions were Grade 3 in pathology. This rare case showed that S-1 monotherapy enabled curative surgery of unresectable gastric cancer with pathological CR.

Laparoscopy-assisted spleen-preserving pancreatic resection for epidermoid cyst in an intrapancreatic accessory spleen

A rare case of an epidermoid cyst originating in an intrapancreatic accessory spleen in a 50-year-old Japanese female is reported. A hypoechoic cystic tumor was detected incidentally by abdominal ultrasonography. It appeared to be a single cyst in the pancreatic tail with a contrasted mass lesion beside it. Laparoscopy-assisted spleen-preserving pancreatic tail resection was performed. Microscopic examination revealed that the cyst was surrounded by fibrous tissue and a thin layer of splenic tissue, adjacent to normal pancreatic parenchyma. The inner surface of the cyst was lined with non-keratinizing squamous epithelium. The diagnosis of an epidermoid cyst occurring in an intrapancreatic accessory spleen was confirmed. Laparoscopy-assisted spleen-preserving pancreatic resection is a safe and effective procedure for benign or low-grade malignant cystic diseases in the pancreas.

Left-sided approach for cardiac procedure and thoracoplasty in a patient with Marfan syndrome

We present a case of a 20-year-old female in whom we successfully performed a simultaneous Bentall procedure and thoracoplasty by initially removing only the left side of the costal cartilages. This modified sternal elevation technique offered chest stability and an excellent surgical view, and the postoperative course was satisfactory.

Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics

In cellular signal transduction, the information in an external stimulus is encoded in temporal patterns in the activities of signaling molecules; for example, pulses of a stimulus may produce an increasing response or may produce pulsatile responses in the signaling molecules. Here, we show how the Akt pathway, which is involved in cell growth, specifically transmits temporal information contained in upstream signals to downstream effectors. We modeled the epidermal growth factor (EGF)-dependent Akt pathway in PC12 cells on the basis of experimental results. We obtained counterintuitive results indicating that the sizes of the peak amplitudes of receptor and downstream effector phosphorylation were decoupled; weak, sustained EGF receptor (EGFR) phosphorylation, rather than strong, transient phosphorylation, strongly induced phosphorylation of the ribosomal protein S6, a molecule downstream of Akt. Using frequency response analysis, we found that a three-component Akt pathway exhibited the property of a low-pass filter and that this property could explain decoupling of the peak amplitudes of receptor phosphorylation and that of downstream effectors. Furthermore, we found that lapatinib, an EGFR inhibitor used as an anticancer drug, converted strong, transient Akt phosphorylation into weak, sustained Akt phosphorylation, and, because of the low-pass filter characteristics of the Akt pathway, this led to stronger S6 phosphorylation than occurred in the absence of the inhibitor. Thus, an EGFR inhibitor can potentially act as a downstream activator of some effectors.