Phylogenetic estimates of diversification rate are affected by molecular rate variation

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies.

Patterns of Multivitamin Use after Colorectal Cancer Diagnosis in Association with Long-term Survival

Multivitamin use has been related to a modest reduced risk of colorectal cancer (CRC), but evidence on its use after diagnosis in relation to survival has been limited. Incident, invasive CRC cases were identified through cancer registries from 1997–2008 and enrolled in four population-based sites of the Colon Cancer Family Registry (Fred Hutchinson Cancer Research Center, Cancer Care Ontario, Mayo Clinic, and the Universities of Queensland and Melbourne). At enrollment, a standardized interview ascertained multivitamin use in the year prior to diagnosis. A follow-up questionnaire was administered approximately 5 years after baseline, with 2,586 participants providing information on their multivitamin use at both time points. Survival outcomes were identified through linkage to national death registries. Delayed-entry Cox regression was used to estimate the association between patterns of multivitamin use and overall or CRC-specific survival (Hazard Ratio (HR) and 95% Confidence Interval (CI)), with survival time beginning at the 5-year follow-up survey. Models were adjusted for age at diagnosis, sex, body mass index, smoking history, stage, study center, and number of days from diagnosis to baseline survey. Over a median 4.8 years after the follow-up survey, 397 participants died (103 from CRC). Multivitamin use was common: at the 5-year follow-up, 37% reported continued use since before diagnosis, 12% had initiated use, 17% had discontinued use, and only 34% participants reported never using multivitamins. Compared to never use of multivitamins, continued use was significantly associated with increased subsequent overall survival (HR = 0.71, 95% CI: 0.55–0.91). However, this association did not reach statistical significance for CRC-specific survival (HR = 0.76, 95% CI: 0.47–1.24). No significant association was observed for discontinuing (HR = 0.92, 95% CI: 0.68–1.25) or initiating (HR = 0.80, 95% CI: 0.55–1.13) multivitamin use from baseline to follow-up, compared to never users, though initiating use trended towards increased survival. These findings suggest that continuing multivitamin use after a CRC diagnosis may increase survival; replication and details on the specific micronutrients included are needed.

Zfp462 deficiency causes anxiety-like behaviors with excessive self-grooming in mice

Zfp462 is a newly identified vertebrate-specific zinc finger protein that contains nearly 2500 amino acids and 23 putative C2H2-type zinc finger domains. So far, the functions of Zfp462 remain unclear. In our study, we showed that Zfp462 is expressed predominantly in the developing brain, especially in the cerebral cortex and hippocampus regions from embryonic day 7.5 to early postnatal stage. By using a piggyBac transposon-generated Zfp462 knockout (KO) mouse model, we found that Zfp462 KO mice exhibited prenatal lethality with normal neural tube patterning, whereas heterozygous (Het) Zfp462 KO (Zfp462^+/- ) mice showed developmental delay with low body weight and brain weight. Behavioral studies showed that Zfp462^+/- mice presented anxiety-like behaviors with excessive self-grooming and hair loss, which were similar to the pathological grooming behaviors in Hoxb8 KO mice. Further analysis of grooming microstructure showed the impairment of grooming patterning in Zfp462^+/- mice. In addition, the mRNA levels of Pbx1 (pre-B-cell leukemia homeobox 1, an interacting protein of Zfp462) and Hoxb8 decreased in the brains of Zfp462^+/- mice, which may be the cause of anxiety-like behaviors. Finally, imipramine, a widely used and effective anti-anxiety medicine, rescued anxiety-like behaviors and excessive self-grooming in Zfp462^+/- mice. In conclusion, Zfp462 deficiency causes anxiety-like behaviors with excessive self-grooming in mice. This provides a novel genetic mouse model for anxiety disorders and a useful tool to determine potential therapeutic targets for anxiety disorders and screen anti-anxiety drugs.

Abrp, a new gene, confers reduced susceptibility to tetracycline, glycylcine, chloramphenicol and fosfomycin classes in Acinetobacter baumannii

Acinetobacter baumannii, a non-fermenting gram-negative coccobacillus, is a major pathogen responsible for a variety of healthcare-associated infections, including pneumonia, urinary tract and bloodstream infections. Moreover, A. baumannii is associated with alarming increases in drug resistance rates to almost all available antibiotics leaving limited treatment options. Here, we characterize the biological functions of a novel gene, abrp, which encodes a peptidase C13 family. We demonstrate that the abrp is associated with decreased susceptibility to tetracycline, minocycline, doxycycline, tigecycline, chloramphenicol and fosfomycin. Deletion of abrp was able to increase cell membrane permeability and display slower cell growth rate. Results from the present study show that abrp plays an important role in conferring reduced susceptibility to different classes of antibiotics and cell growth in A. baumannii. The change of antibiotic sensitivities may result from modifications to the cell membrane permeability of A. baumannii.

Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

An outbreak of carbapenem-resistant Klebsiella pneumoniae strains emerged at a hospital, and was tracked in order to understand the spread of these infectious pathogens. A total of 66 K. pneumoniae strains were collected from sterile samples in 2012. The MICs of 20 antimicrobial agents were determined for all strains. Molecular typing was performed with pulsed-field gel electrophoresis (PFGE). Twelve blaKPC-producing K. pneumoniae strains isolated from ten patients were selected for whole genome sequencing. Phylogenetic reconstruction of these 12 strains was performed by the use of single-nucleotide polymorphism (SNP) row sequences of each draft genome sequence. Plasmids from the 12 strains were separated by S1 digestion and PFGE. The 12 K. pneumoniae strains isolated from the ten patients were deemed to be representative of the hospital outbreak, owing to their similar PFGE patterns. These 12 blaKPC-producing strains conferred multidrug resistance, which contrasted with the remaining 54, more susceptible, strains in the hospital. Differences in SNPs between each draft genome of the blaKPC-producing strains partitioned the 12 outbreak strains into three separate clades. The patients with each clade shared close hospital units. All 12 strains harboured at least one multidrug resistance plasmid. Strains showing high-level resistance may facilitate nosocomial dissemination and result in an infectious pathogen outbreak. Although the 12 blaKPC-producing K. pneumoniae strains possessed similar PFGE patterns, SNP variations throughout the genome allowed the strains to be divided into three clades. These results suggest that three independent transmission events led to hospital-wide dissemination of the outbreak strains.

The role of 3D computed tomography (CT) imaging in the diagnosis of foreign body aspiration in children

OBJECTIVE

The aim of this study was to improve the understanding of FBA in children and to decrease the rate of misdiagnosis, missed diagnosis and morbidity.

PATIENTS AND METHODS

We analyzed the clinical features and the three-dimensional reconstructed CT images of 590 children with foreign body aspiration (FBA) in the Xuzhou area of the Jiangsu province.

RESULTS

CT imaging revealed common complications of FBA including emphysema (n = 379), pneumonia (n = 174), and atelectasis (n = 26). The remaining 120 patients had no visible complications on the three-dimensional reconstructed CT images. Serious complications including pneumothorax, pneumomediastinum, subcutaneous emphysema, pneumatorrhachis could also be observed. The types of foreign bodies were diverse: the most common were peanuts and sunflower seeds. The diagnostic accuracy of the three-dimensional CT imaging was high, with a sensitivity and specificity of 99.83% and 99.89%, respectively.

CONCLUSIONS

3D CT imaging is an accurate, non-invasive technique to evaluate children with suspected FBA that can help decrease the rate of misdiagnosis and eliminate a delay in treatment for this potentially life-threatening condition.

Obesity, hypertension and diabetes mellitus affect complication rate of different nephrectomy techniques

INTRODUCTION

To investigate whether obesity, hypertension, and diabetes mellitus (DM) would increase post-nephrectomy complication rates using standardized classification method.

METHODS

We retrospectively included 843 patients from March 2006 to November 2012, of whom 613 underwent radical nephrectomy (RN) and 229 had partial nephrectomy (PN). Modified Clavien classification system was applied to quantify complication severity of nephrectomy. Fisher's exact or chi-square test was used to assess the relationship between complication rates and obesity, hypertension, as well as DM.

RESULTS

The prevalence of obesity, hypertension, and DM was 11.51%, 30.84%, 8.78%, respectively. The overall complication rate was 19.31%, 30.04%, 35.71% and 36.36% for laparoscopic radical nephrectomy (LRN), open-RN, LPN and open-PN respectively. An increasing trend of low grade complication rate as BMI increased was observed in LRN (P=.027) and open-RN (P<.001). Obese patients had greater chance to have low grade complications in LRN (OR=4.471; 95% CI: 1.290-17.422; P=0.031) and open-RN (OR=2.448; 95% CI: 1.703-3.518; P<.001). Patients with hypertension were more likely to have low grade complications, especially grade ii complications in open-RN (OR=1.526; 95% CI: 1.055-2.206; P=.026) and open PN (OR=2.032; 95% CI: 1.199-3.443; P=.009). DM was also associated with higher grade i complication rate in open-RN (OR=2.490; 95% CI: 331-4.657; P=.016) and open-PN (OR=4.425; 95% CI: 1.815-10.791; P=.013). High grade complication rates were similar in comparison.

CONCLUSIONS

Obesity, hypertension, and DM were closely associated with increased post-nephrectomy complication rates, mainly low grade complications.

Tigecycline resistance in Acinetobacter baumannii mediated by frameshift mutation in plsC, encoding 1-acyl-sn-glycerol-3-phosphate acyltransferase

Acinetobacter baumannii is an important pathogen of healthcare-associated infections and shows multidrug resistance. With the increasing application of tigecycline, isolates resistant to this antibiotic are of growing concern clinically. However, the definitive mechanism of tigecycline resistance remains unclear. To explore the mechanism of tigecycline resistance in A. baumannii, a tigecycline-resistant strain was obtained by increasing the concentration of the antimicrobial in liquid culture. Three mutations were identified by the whole genome comparison, including one synonymous substitution in a hypothetical protein and a frameshift mutation in plsC and omp38. The plsC gene was confirmed to cause decreased susceptibility to tigecycline by a complementation experiment and cellular membrane change was detected by flow cytometry. By measuring the relative growth rate, the fitness cost of plsC was estimated to be approximately 8 %. In conclusion, plsC was found to play an important role in tigecycline resistance in A. baumannii. The minor fitness cost of plsC indicates a high risk of the emergence and development of tigecycline resistance in A. baumannii.

Homocysteine induces blood vessel global hypomethylation mediated by LOX-1

Homocysteine (Hcy) is an independent risk factor of atherosclerosis through its involvement with the methionine cycle. In this study, we aimed to determine the blood vessel global methylation rate in Hcy-induced atherosclerosis in apolipoprotein-E-deficient (ApoE-/-) mice, and to explore the possible mechanism of this change in endothelial cells. ApoE-/- mice were divided into a hyperlipidemia (HLP) group, a hyperhomocysteinemia (HHcy) group, and an HHcy + folate + vitamin B12 (HHcy+FA+VB) group. Wild-type C57BL/6J mice were prepared as controls. Total Hcy, lipids, S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH) contents in serum were measured with an automatic biochemistry analyzer and high-performance liquid chromatography. Methylation of B1 repetitive elements in blood vessels was tested using nested methylation-specific-polymerase chain reaction (nMS-PCR). Endothelial cells (ECs) were pretreated with Hcy or by adding FA and VB. Lectin-like oxidized LDL receptor-1 (LOX-1) expressions were determined by quantitative PCR, Western blot, and nMS-PCR. The HHcy group displayed severe HLP and HHcy. SAM and SAH contents were also elevated in the HHcy group compared with other groups. Methylation of B1 repetitive elements was significantly increased in the HHcy group (0.5050 ± 0.0182) compared to the HLP (0.5158 ± 0.0163) and control (0.5589 ± 0.0236) groups. mRNA and protein expressions of LOX-1 increased (0.2877 ± 0.0341, 0.6090 ± 0.0547), whereas methylation expression decreased (0.5527 ± 0.0148) after 100 μM Hcy stimulation in ECs. In conclusion, Hcy-induced atherosclerosis was closely associated with induced hypomethylation status in the blood vessel, and this process was partially mediated by LOX-1 DNA methylation.

Immunoglobulin (Ig)M antibodies against oxidized cardiolipin but not native cardiolipin are novel biomarkers in haemodialysis patients, associated negatively with mortality

The risk of premature death is high in haemodialysis (HD) patients. Antibodies against cardiolipin (anti-CL) are thrombogenic in diseases such as systemic lupus erythematosus (SLE). CL is easily oxidized (Ox) and plays a role in apoptosis. In this work we studied immunoglobulin (Ig)M anti-CL and anti-OxCL in HD-patients. We conducted an observational study with a prospective follow-up examining the relationship between anti-CL, anti-OxCL and mortality risk in a well-characterized cohort of 221 prevalent HD patients [56% men, median age 66 (interquartile range 51-74) years, vintage time 29 (15-58) months] with a mean follow-up period of 41 (20-48 months). According to the receiver operator characteristic (ROC) analysis, anti-OxCL [area under the curve (AUC) 0·62, P < 0·01], but not anti-CL (AUC 0·52, P = 0·2), is associated with mortality. In crude and adjusted Cox analysis, every log increase in anti-OxCL inversely predicted all-cause [adjusted hazard ratios (HR) 0·62 (0·43-0·89)] and CVD-related [adjusted HR 0·56 (0·32-0·98)] mortality. Patients with anti-OxCL levels below median also had increased all-cause and cardiovascular disease (CVD)-related mortality. Although anti-OxCL and anti-phosphorylcholine (PC) were related positively to each other (ρ = 0·57, P < 0·01), patients with one or two of these autoantibody levels below the median were associated with an incrementally increased death risk. Anti-OxCL were co-factor β2-GPI-independent; anti-CL from patients with anti-phospholipid antibody syndrome were β2-GPI-dependent, while sera from HD-patients less so. Sera from healthy donors was not β2-GPI-dependent. Anti-OxCL IgM is β2-glycoprotein 1 (GPI)-independent and a novel biomarker; low levels are associated with death among HD patients (and high levels with decreased risk). Combination with anti-PC increases this association. Putative therapeutic implications warrant further investigation.

Inhibition of hepatic fibrosis with artificial microRNA using ultrasound and cationic liposome-bearing microbubbles

We sought to investigate the antifibrotic effects of an artificial microRNA (miRNA) targeting connective tissue growth factor (CTGF) using the ultrasound-targeted cationic liposome-bearing microbubble destruction gene delivery system. Cationic liposomes were conjugated with microbubbles using a biotin-avidin system. Plasmids carrying the most effective artificial miRNA sequences were delivered by ultrasound-targeted cationic liposome-bearing microbubble destruction gene delivery system to rats with hepatic fibrosis. The results show that this method of gene delivery effectively transported the plasmids to the rat liver. The artificial miRNA reduced hepatic fibrosis pathological alterations as well as the protein and mRNA expressions of CTGF and transforming growth factor β1. Furthermore, the CTGF gene silencing decreased the levels of type I collagen and α-smooth muscle actin (P<0.01). These data suggest that delivery of an artificial miRNA targeted against CTGF using ultrasound-targeted cationic liposome-bearing microbubble destruction may be an efficacious therapeutic method to ameliorate hepatic fibrosis.

Realization of high performance silicon nanowire based solar cells with large size

We report the realization of high performance silicon nanowire (SiNW) based solar cells with a conversion efficiency of 17.11% and a large size of 125 × 125 mm(2). The key factor for success lies in an efficient approach of dielectric passivation to greatly enhance the electrical properties while keeping the advantage of excellent light trapping of the SiNW structure. The suppression of carrier recombination has been demonstrated through the combination of the SiO2/SiNx stack, which exhibits a good passivation effect on heavily doped SiNWs via reducing both the Shockley-Read-Hall recombination and near surface Auger recombination. We have examined in detail the effects of different passivations and SiNW lengths on the effective minority carrier lifetime, reflectance and carrier recombination characteristics, as well as cell performance. The proposed passivation techniques can be easily adapted to conventional industrial manufacturing processes, providing a potential prospect of SiNW based solar cells in mass production.