Reordering hierarchical tree based on bilateral symmetric distance

Background

In microarray data analysis, hierarchical clustering (HC) is often used to group samples or genes according to their gene expression profiles to study their associations. In a typical HC, nested clustering structures can be quickly identified in a tree. The relationship between objects is lost, however, because clusters rather than individual objects are compared. This results in a tree that is hard to interpret.

Methodology/Principal Findings

This study proposes an ordering method, HC-SYM, which minimizes bilateral symmetric distance of two adjacent clusters in a tree so that similar objects in the clusters are located in the cluster boundaries. The performance of HC-SYM was evaluated by both supervised and unsupervised approaches and compared favourably with other ordering methods.

Conclusions/Significance

The intuitive relationship between objects and flexibility of the HC-SYM method can be very helpful in the exploratory analysis of not only microarray data but also similar high-dimensional data.     

Biosynthesis and characterization of poly(d-lactate-co-glycolate-co-4-hydroxybutyrate)

Poly(d -lactate-co-glycolate-co-4-hydroxybutyrate) [poly(d -LA-co-GA-co-4HB)] and poly(d -lactate-co-glycolate-co-4-hydroxybutyrate-co-d -2-hydroxybutyrate) [poly(d -LA-co-GA-co-4HB-co-d -2HB)] are of interest for their potential applications as new biomedical polymers. Here we report their enhanced production by metabolically engineered Escherichia coli. To examine the polymer properties, poly(d -LA-co-GA-co-4HB) polymers having various monomer compositions (3.4–41.0mol% of 4HB) were produced by culturing the engineered E. coli strain expressing xylBC from Caulobacter crescentus, evolved phaC1 from Pseudomonas sp. MBEL 6-19 (phaC1437), and evolved pct from Clostridium propionicum (pct540) in a medium supplemented with sodium 4HB at various concentrations. To produce these polymers without 4HB feeding, the 4HB biosynthetic pathway was additionally constructed by expressing Clostridium kluyveri sucD and 4hbD. The engineered E. coli expressing xylBC, phaC1437, pct540, sucD, and 4hbD successfully produced poly(d -LA-co-GA-co-4HB-co-d -2HB) and poly(d -LA-co-GA-co-4HB) from glucose and xylose. Through modulating the expression levels of the heterologous genes and performing fed-batch cultures, the polymer content and titer could be increased to 65.76wt% and 6.19g/L, respectively, while the monomer fractions in the polymers could be altered as desired. The polymers produced, in particular, the 4HB-rich polymers showed viscous and sticky properties suggesting that they might be used as medical adhesives.     

Extra domain A-containing fibronectin expression in Spin90-deficient fibroblasts mediates cancer-stroma interaction and promotes breast cancer progression

Cancer-associated fibroblasts (CAFs) in the tumor microenvironment play major roles in supporting cancer progression. A previous report showed that SPIN90 downregulation is correlated with CAF activation and that SPIN90-deficient CAFs promote breast cancer progression. However, the mechanisms that mediate cancer-stroma interaction and how such interactions regulate cancer progression are not well understood. Here, we show that extra domain A (EDA)-containing fibronectin (FN), FN(+)EDA, produced by mouse embryonic fibroblasts (MEFs) derived from Spin90-knockout (KO) mice increases their own myofibroblast differentiation, which facilitates breast cancer progression. Increased FN(+)EDA in Spin90-KO MEFs promoted fibril formation in the extracellular matrix (ECM) and specifically interacted with integrin α4β1 as the mediating receptor. Moreover, FN(+)EDA expression by Spin90-KO MEFs increased proliferation, migration, and invasion of breast cancer cells. Irigenin, a specific inhibitor of the interaction between integrin α4β1 and FN(+)EDA, significantly blocked the effects of FN(+)EDA, such as fibril formation by Spin90-KO MEFs and proliferation, migration, and invasion of breast cancer cells. In orthotopic breast cancer mouse models, irigenin injection remarkably reduced tumor growth and lung metastases. It was supported by that FN(+)EDA in assembled fibrils was accumulated in cancer stroma of human breast cancer patients in which SPIN90 expression was downregulated. Our data suggest that SPIN90 downregulation increases FN(+)EDA and promotes ECM stiffening in breast cancer stroma through an assembly of long FN(+)EDA-rich fibrils; moreover, engagement of the Integrin α4β1 receptor facilitates breast cancer progression. Inhibitory effects of irigenin on tumor growth and metastasis suggest the potential of this agent as an anticancer therapeutic.     

The Sodium Storage Mechanism in Tunnel‐Type Na0.44MnO2 Cathodes and the Way to Ensure Their Durable Operation

Tunnel‐type sodium manganese oxide is a promising cathode material for aqueous/nonaqueous sodium‐ion batteries, however its storage mechanism is not fully understood, in part due to the complicated sodium intercalation process. In addition, low cyclability due to manganese dissolution has limited its practical application in rechargeable batteries. Here, the intricate sodium intercalation mechanism of Na_0.44MnO₂ is revealed by combination of electrochemical characterization, structure determination from powder X‐ray diffraction data, 3D bond valence difference maps, and barrier‐energy calculations of the sodium diffusion. NaI is proposed as an important electrolyte solution additive. It is shown to form a thin, beneficial, and durable cathode surface film that prevents manganese dissolution. The addition of 0.01 m NaI to electrolyte solutions based on alkyl carbonate solvents and NaClO₄ greatly improves the cycling efficiency, raising the capacity retention from 86% to 96% after 600 cycles. This study determines the core aspects of the sodium intercalation mechanism in tunnel‐type sodium manganese oxide and shows how it can serve as a durable cathode material for rechargeable Na batteries.     

Association between BDNF Gene Polymorphisms and Serotonergic Activity Using Loudness Dependence of Auditory Evoked Potentials in Healthy Subjects

It has been proposed that the loudness dependence of auditory evoked potentials (LDAEP) would be a reliable indicator of central serotonin system activity in humans. Serotonin levels and turnover are also increased by brain-derived neurotrophic factor (BDNF). The aim of the present study was to determine whether there is an association between genetic polymorphisms of BDNF and the LDAEP in healthy Korean young adults. The cohort comprised 211 mentally and physically healthy subjects, all of whom were nonsmokers (111 males, 100 females; age: 20∼32 years). To avoid hormonal effects, the LDAEP was measured during days 2–5 after the beginning of menstruation for female subjects. In addition, BDNF polymorphisms (rs6265, rs2030324, and rs1491850) were genotyped. The strength of the LDAEP differed significantly among the BDNF genotype groups. Furthermore, the distribution of genotypic frequencies differed significantly between subjects with high and low LDAEPs. In particular, subjects with the Val/Met (A/G) genotype for rs6265, the T/T genotype for rs2030324, or the C/C genotype for rs1491850 had a higher LDAEP, indicating lower central serotonergic activity. A low LDAEP was more prevalent than a high LDAEP among those with the C-T haplotype (C genotype for rs2030424 and T genotype for rs1491850). Our results concur with previous findings on BDNF polymorphisms and serotonergic drug responses in psychiatric disorder patients. The present results suggest the possibility that BDNF polymorphisms and LDAEP patterns can predict altered serotonergic activity.     

The Occurrence of Warfarin-Related Nephropathy and Effects on Renal and Patient Outcomes in Korean Patients

Background

Warfarin-related nephropathy (WRN) is a recently described disease entity, in which excessive warfarinization (international normalized ratio (INR) >3.0) causes acute kidney injury. Previous reports regarding WRN included few Asian patients who might have differed from the western WRN patients in terms of genetic and environmental factors.

Methods

During the period of March 2003 to December 2011, the data about a total of 1297 patients who had serum creatinine (sCr) level measured within 1 week after INR >3.0 and within 6 months before INR >3.0 was analyzed through the retrospective review of electronic medical records of a single tertiary hospital in Korea.

Result

WRN developed in 19.3% of patients having excessive warfarinization. The incidence was higher in the chronic kidney disease (CKD) group than the non-CKD group. The risk of WRN increased as the basal serum albumin level decreased and was strongly associated with highest quartile serum AST level at post INR elevation and the presence of congestive heart failure. But the presence of atrial fibrillation was protective against the development of WRN. Neither the presence of CKD nor basal estimated glomerular filtration rate (eGFR) was an independent risk factor for WRN. Despite no difference in the basal sCr level, the sCr level was higher in patients with WRN than those without WRN after follow-up. The mortality rates were also higher in patients with WRN.

Conclusions

WRN developed in 19.3% of patients having excessive warfarinization. A lower basal serum albumin, highest quartile serum AST level at post INR elevation, and congestive heart failure were associated with the occurrence of WRN. The development of WRN adversely affected renal and patient outcomes.