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1.  Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption 
mBio  2015;6(2):e00231-15.
A mechanistic understanding of the purported health benefits conferred by consumption of probiotic bacteria has been limited by our knowledge of the resident gut microbiota and its interaction with the host. Here, we detail the impact of a single-organism probiotic, Lactobacillus rhamnosus GG ATCC 53103 (LGG), on the structure and functional dynamics (gene expression) of the gut microbiota in a study of 12 healthy individuals, 65 to 80 years old. The analysis revealed that while the overall community composition was stable as assessed by 16S rRNA profiling, the transcriptional response of the gut microbiota was modulated by probiotic treatment. Comparison of transcriptional profiles based on taxonomic composition yielded three distinct transcriptome groups that displayed considerable differences in functional dynamics. The transcriptional profile of LGG in vivo was remarkably concordant across study subjects despite the considerable interindividual nature of the gut microbiota. However, we identified genes involved in flagellar motility, chemotaxis, and adhesion from Bifidobacterium and the dominant butyrate producers Roseburia and Eubacterium whose expression was increased during probiotic consumption, suggesting that LGG may promote interactions between key constituents of the microbiota and the host epithelium. These results provide evidence for the discrete functional effects imparted by a specific single-organism probiotic and challenge the prevailing notion that probiotics substantially modify the resident microbiota within nondiseased individuals in an appreciable fashion.
Probiotic bacteria have been used for over a century to promote digestive health. Many individuals report that probiotics alleviate a number of digestive issues, yet little evidence links how probiotic microbes influence human health. Here, we show how the resident microbes that inhabit the healthy human gut respond to a probiotic. The well-studied probiotic Lactobacillus rhamnosus GG ATCC 53103 (LGG) was administered in a clinical trial, and a suite of measurements of the resident microbes were taken to evaluate potential changes over the course of probiotic consumption. We found that LGG transiently enriches for functions to potentially promote anti-inflammatory pathways in the resident microbes.
PMCID: PMC4453556  PMID: 25873374
2.  Multi-Site Clinical Evaluation of DW-MRI as a Treatment Response Metric for Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy 
PLoS ONE  2015;10(3):e0122151.
To evaluate diffusion weighted MRI (DW-MR) as a response metric for assessment of neoadjuvant chemotherapy (NAC) in patients with primary breast cancer using prospective multi-center trials which provided MR scans along with clinical outcome information.
Materials and Methods
A total of 39 patients with locally advanced breast cancer accrued from three different prospective clinical trials underwent DW-MR examination prior to and at 3–7 days (Hull University), 8–11 days (University of Michigan) and 35 days (NeoCOMICE) post-treatment initiation. Thirteen patients, 12 of which participated in treatment response study, from UM underwent short interval (<1hr) MRI examinations, referred to as “test-retest” for examination of repeatability. To further evaluate stability in ADC measurements, a thermally controlled diffusion phantom was used to assess repeatability of diffusion measurements. MRI sequences included contrast-enhanced T1-weighted, when appropriate, and DW images acquired at b-values of 0 and 800 s/mm2. Histogram analysis and a voxel-based analytical technique, the Parametric Response Map (PRM), were used to derive diffusion response metrics for assessment of treatment response prediction.
Mean tumor apparent diffusion coefficient (ADC) values generated from patient test-retest examinations were found to be very reproducible (|ΔADC|<0.1x10-3mm2/s). This data was used to calculate the 95% CI from the linear fit of tumor voxel ADC pairs of co-registered examinations (±0.45x10-3mm2/s) for PRM analysis of treatment response. Receiver operating characteristic analysis identified the PRM metric to be predictive of outcome at the 8–11 (AUC = 0.964, p = 0.01) and 35 day (AUC = 0.770, p = 0.05) time points (p<.05) while whole-tumor ADC changes where significant at the later 35 day time interval (AUC = 0.825, p = 0.02).
This study demonstrates the feasibility of performing a prospective analysis of DW-MRI as a predictive biomarker of NAC in breast cancer patients. In addition, we provide experimental evidence supporting the use of sensitive analytical tools, such as PRM, for evaluating ADC measurements.
PMCID: PMC4376686  PMID: 25816249
3.  Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota 
Pathogens and Disease  2015;73(4):ftv019.
In humans, the vaginal microbiota is thought to be the first line of defense again pathogens including Chlamydia trachomatis. The guinea pig has been extensively used as a model to study chlamydial infection because it shares anatomical and physiological similarities with humans, such as a squamous vaginal epithelium as well as some of the long-term outcomes caused by chlamydial infection. In this study, we aimed to evaluate the guinea pig-C. caviae model of genital infection as a surrogate for studying the role of the vaginal microbiota in the early steps of C. trachomatis infection in humans. We used culture-independent molecular methods to characterize the relative and absolute abundance of bacterial phylotypes in the guinea pig vaginal microbiota in animals non-infected, mock-infected or infected by C. caviae. We showed that the guinea pig and human vaginal microbiotas are of different bacterial composition and abundance. Chlamydia caviae infection had a profound effect on the absolute abundance of bacterial phylotypes but not on the composition of the guinea pig vaginal microbiota. Our findings compromise the validity of the guinea pig-C. caviae model to study the role of the vaginal microbiota during the early steps of sexually transmitted infection.
The vaginal microbiota of the guinea pig differs from that of humans and cannot prevent chlamydial infections efficiently.
Graphical Abstract Figure.The vaginal microbiota of the guinea pig differs from that of humans and cannot prevent chlamydial infections efficiently.
PMCID: PMC4445005  PMID: 25761873
microbiome; model organism; Chlamydia trachomatis; Lactobacillus; vagina
4.  Mussel inspired protein-mediated surface functionalization of electrospun nanofibers for pH-responsive drug delivery 
Acta biomaterialia  2013;10(3):1324-1332.
pH-responsive drug delivery systems could mediate drug releasing rate by changing pH values at specific time as per the pathophysiological need of the disease. Herein, we demonstrated a mussel inspired protein polydopamine coating can tune the loading and releasing rate of charged molecules from electrospun poly (ε-caprolactone) (PCL) nanofibers in solutions with different pH values. In vitro release profiles showed that the positive charged molecules released significantly faster in acidic than those in neutral and basic environments within the same incubation time. The results of fluorescein diacetate staining and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays showed the viability of cancer cells after treatment with doxorubicin released media at different pH values qualitatively and quantitatively, indicating the media contained doxorubicin which was released in solutions at low pH values could kill significantly higher number of cells than that released in solutions at high pH values. Together, the pH-responsive drug delivery systems based on polydopamine-coated PCL nanofibers could have potential applications in oral delivery of anticancer drugs for treating gastric cancer and vaginal delivery of anti-viral drugs or anti-inflammatory drugs, which could raise their efficacy, deliver them to the specific target, and minimize their toxic side effects.
PMCID: PMC3946753  PMID: 24287161
pH-sensitive; Drug delivery; Polydopamine coating; Poly (ε-caprolactone); Electrospun fibers
5.  Sandwich-type Fiber Scaffolds with Square Arrayed Microwells and Nanostructured Cues as Microskin Grafts for Skin Regeneration 
Biomaterials  2013;35(2):10.1016/j.biomaterials.2013.09.111.
The paper reports the fabrication of sandwich-type scaffolds consisting of radially-aligned nanofibers at the bottom, nanofiber membranes with square arrayed microwells and nanostructured cues at the top, and microskin tissues in between as microskin grafts for use in skin regeneration. This class of nanofiber scaffolds was able to confine the microskin tissues in the square arrayed wells and simultaneously present nanotopographic cues to the cultured NIH 3T3 fibroblasts and primary rat skin cells, guiding and facilitating their migration in vitro. More importantly, we demonstrated that the sandwich-type transplants exhibited an even distribution of microskin grafts, greatly improved the ‘take’ rate of microskin tissues, and promoted re-epithelialization on wound in vivo. In addition, the void area in the scaffolds was well suitable for exudate drainage in wound. The sandwich-type scaffolds show great potential as microskin grafts for repairing extensive burn injuries and may provide a good solution for the treatment of acute skin defects and chronic wounds including diabetic ulcer, pressure ulcer, and venous stasis ulcer.
PMCID: PMC3855253  PMID: 24144904
sandwich-type; nanofiber scaffolds; arrayed microwells; nanotopographic cue; skin regeneration
6.  Chitinase 3-like 1 Regulates Cellular and Tissue Responses via IL-13 Receptor α2 
Cell reports  2013;4(4):830-841.
Members of the 18 glycosyl hydrolase (GH 18) gene family have been conserved over species and time and are dysregulated in inflammatory, infectious, remodeling, and neoplastic disorders. This is particularly striking for the prototypic chitinase-like protein chitinase 3-like 1 (Chi3l1), which plays a critical role in antipathogen responses where it augments bacterial killing while stimulating disease tolerance by controlling cell death, inflammation, and remodeling. However, receptors that mediate the effects of GH 18 moieties have not been defined. Here, we demonstrate that Chi3l1 binds to interleukin-13 receptor α2 (IL-13Rα2) and that Chi3l1, IL-13Rα2, and IL-13 are in a multimeric complex. We also demonstrate that Chi3l1 activates macrophage mitogen-activated protein kinase, protein kinase B/AKT, and Wnt/β-catenin signaling and regulates oxidant injury, apoptosis, pyroptosis, inflammasome activation, antibacterial responses, melanoma metastasis, and TGF-β1 production via IL-13Rα2-dependent mechanisms. Thus, IL-13Rα2 is a GH 18 receptor that plays a critical role in Chi3l1 effector responses.
PMCID: PMC3988532  PMID: 23972995
7.  Challenges in accurate registration of 3D medical imaging and histopathology in primary prostate cancer 
Due to poor correlation of slice thickness and orientation, verification of medical imaging results with histology is difficult. Often validation of imaging findings of lesions suspicious for prostate cancer is driven by a subjective, visual approach to correlate in vivo images with histopathology. This manuscript describes fallacious assumptions for correlation of imaging findings with pathology and identifies the lack of accurate registration as a major obstacle in the validation of PET and PET/CT imaging in primary prostate cancer. Specific registration techniques that facilitate the most difficult part of the registration process—the mapping of pathology onto high-resolution imaging, preferably aided by the ex vivo prostate specimen—are discussed.
PMCID: PMC3689866  PMID: 23503575
Primary prostate cancer; registration of 3D medical imaging onto pathology; mutual information; computer-aided design
8.  Rational design of nanofiber scaffolds for orthopedic tissue repair and regeneration 
Nanomedicine (London, England)  2013;8(9):10.2217/nnm.13.132.
This article reviews recent significant advances in the design of nanofiber scaffolds for orthopedic tissue repair and regeneration. It begins with a brief introduction on the limitations of current approaches for orthopedic tissue repair and regeneration. It then illustrates that rationally designed scaffolds made up of electrospun nanofibers could be a promising solution to overcome the problems that current approaches encounter. The article also discusses the intriguing properties of electrospun nanofibers, including control of composition, structures, orders, alignments and mechanical properties, use as carriers for topical drug and/or gene sustained delivery, and serving as substrates for the regulation of cell behaviors, which could benefit musculoskeletal tissue repair and regeneration. It further highlights a few of the many recent applications of electrospun nanofiber scaffolds in repairing and regenerating various orthopedic tissues. Finally, the article concludes with perspectives on the challenges and future directions for better design, fabrication and utilization of nanofiber scaffolds for orthopedic tissue engineering.
PMCID: PMC3875778  PMID: 23987110
design; electrospinning; nanofiber scaffold; orthopedic tissue; regeneration; repair; tissue engineering
9.  Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning 
BMC Genomics  2014;15(1):508.
A wealth of genome sequences has provided thousands of genes of unknown function, but identification of functions for the large numbers of hypothetical genes in phytopathogens remains a challenge that impacts all research on plant-microbe interactions. Decades of research on the molecular basis of pathogenesis focused on a limited number of factors associated with long-known host-microbe interaction systems, providing limited direction into this challenge. Computational approaches to identify virulence genes often rely on two strategies: searching for sequence similarity to known host-microbe interaction factors from other organisms, and identifying islands of genes that discriminate between pathogens of one type and closely related non-pathogens or pathogens of a different type. The former is limited to known genes, excluding vast collections of genes of unknown function found in every genome. The latter lacks specificity, since many genes in genomic islands have little to do with host-interaction.
In this study, we developed a supervised machine learning approach that was designed to recognize patterns from large and disparate data types, in order to identify candidate host-microbe interaction factors. The soft rot Enterobacteriaceae strains Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 were used for development of this tool, because these pathogens are important on multiple high value crops in agriculture worldwide and more genomic and functional data is available for the Enterobacteriaceae than any other microbial family. Our approach achieved greater than 90% precision and a recall rate over 80% in 10-fold cross validation tests.
Application of the learning scheme to the complete genome of these two organisms generated a list of roughly 200 candidates, many of which were previously not implicated in plant-microbe interaction and many of which are of completely unknown function. These lists provide new targets for experimental validation and further characterization, and our approach presents a promising pattern-learning scheme that can be generalized to create a resource to study host-microbe interactions in other bacterial phytopathogens.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-508) contains supplementary material, which is available to authorized users.
PMCID: PMC4079955  PMID: 24952641
Pattern recognition; Data mining; Plant pathogen; Genome scale analysis; Enterobacteria
10.  An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform 
Microbiome  2014;2:6.
To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical limitations inherent to the sequencing platforms. Sequencing low sequence diversity libraries such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform and often generates sequences of suboptimal quality.
Here we present an improved dual-indexing amplification and sequencing approach to assess the composition of microbial communities from clinical samples using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform. We introduced a 0 to 7 bp “heterogeneity spacer” to the index sequence that allows an equal proportion of samples to be sequenced out of phase.
Our approach yields high quality sequence data from 16S rRNA gene amplicons using both 250 bp and 300 bp paired-end MiSeq protocols and provides a flexible and cost-effective sequencing option.
PMCID: PMC3940169  PMID: 24558975
11.  Efficacy and Safety of Therapies for Acute Ischemic Stroke in China: A Network Meta-Analysis of 13289 Patients from 145 Randomized Controlled Trials 
PLoS ONE  2014;9(2):e88440.
Many of these therapies have been compared against placebos, but have not been directly compared against each other. To evaluate the efficacy and safety of several commonly used drugs for AIS directly or indirectly.
A systematic literature review was performed to identify randomized controlled trials (RCTs) published prior to April 2013 for AIS therapies. The primary outcome measures were the National Institutes of Health Stroke Scale (NIHSS) scores and the clinical effective rate. A fixed-effects meta-analysis and meta-regression are performed; lastly, performed a mixed treatment comparison was performed through the Bayesian methods.
Outcome of Efficacy of therapies for acute ischemic stroke are as followed: All of the therapies mentioned above yielded results a more effective result than placebo, Sodium ozagrel (RR 3.86, 95%CI 3.18–4.61); Sodium ozagrel + edaravone (RR 9.60, 95%CI 7.04–13.06); Edaravone (RR 4.07, 95%CI 3.30–5.01); Edaravone + Kininogenase (RR 15.33, 95%CI 10.03–23.05). The significant difference in efficacy between edaravone monotherapy and Sodium ozagrel + edaravone was evident (RR 0.43, 95%CI 0.08–0.61) and was also significant between efficacy of edaravone + Kininogenase and Sodium ozagrel (RR 4.00, 95%CI 2.47–6.24). The differences between the risk and benefit were not significant when comparing Sodium ozagrel and edaravone or edaravone + Kininogenase and Sodium ozagrel + Edaravone for AIS. Outcome of the defect of neurological function: Placebo served a significant difference in treating the defects of neurological function compared with Sodium ozagrel (WMD = −3.11, 95%CI −4.43 to −1.79), Sodium ozagrel + edaravone (WMD = −6.25, 95%CI −7.96 to −4.54) and Edaravone + Kininogenase (WMD =  −3.47, 95%CI −5.73 to −1.21).
It provides that the efficacy of edaravone monotherapy in treatment was not more effective than Sodium ozagrel + edaravone.The efficacy of edaravone + Kininogenase monotherapy in treatment was more effective than Sodium ozagrel. Edaravone + Kininogenase and Sodium ozagrel + Edaravone appeared the most effective treatments. And Sodium ozagrel, Sodium ozagrel + edaravone, Edaravone + Kininogenase can improve the nerve dysfunction.
PMCID: PMC3923787  PMID: 24551100
12.  Role of Chitin and Chitinase/Chitinase-Like Proteins in Inflammation, Tissue Remodeling, and Injury 
Annual review of physiology  2011;73:10.1146/annurev-physiol-012110-142250.
The 18 glycosyl hydrolase family of chitinases is an ancient gene family that is widely expressed from prokaryotes to eukaryotes. In mammals, despite the absence of endogenous chitin, a number of chitinases and chitinase-like proteins (C/CLPs) have been identified. However, their roles have only recently begun to be elucidated. Acidic mammalian chitinase (AMCase) inhibits chitin-induced innate inflammation; augments chitin-free, allergen-induced Th2 inflammation; and mediates effector functions of IL-13. The CLPs BRP-39/YKL-40 (also termed chitinase 3-like 1) inhibit oxidant-induced lung injury, augments adaptive Th2 immunity, regulates apoptosis, stimulates alternative macrophage activation, and contributes to fibrosis and wound healing. In accord with these findings, levels of YKL-40 in the lung and serum are increased in asthma and other inflammatory and remodeling disorders and often correlate with disease severity. Our understanding of the roles of C/CLPs in inflammation, tissue remodeling, and tissue injury in health and disease is reviewed below.
PMCID: PMC3864643  PMID: 21054166
asthma; fibrosis; BRP-39/YKL-40; AMCase; chitotriosidase
13.  Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis 
Microbiome  2013;1:29.
Bacterial vaginosis (BV) is a common gynecologic diagnosis characterized by dysbiosis of the vaginal microbiota. It is often accompanied by vaginal symptoms such as odor and discharge, but can be asymptomatic. Despite over 50 years of research, the etiology of BV is not well understood, which is a major impediment to treatment and prevention of BV.
Here we report on the temporal dynamics of 25 vaginal communities over a 10 week period using samples collected daily from women who were diagnosed with symptomatic BV (15 women), asymptomatic BV (6 women), and women who did not have BV (4 women).
This unique resource of samples and data will contribute to a better understanding of the role that the vaginal microbes have in the natural history of BV and lead to improved diagnosis and treatment.
PMCID: PMC3968321  PMID: 24451163
14.  The Risk of Metabolic Syndrome in Patients with Rheumatoid Arthritis: A Meta-Analysis of Observational Studies 
PLoS ONE  2013;8(10):e78151.
Observational studies suggest an association between the incidence of rheumatoid arthritis (RA) and the prevalence of metabolic syndrome (MetS). However, the relationship between RA and MetS is controversial and research in this area is currently lacking.
The aim of this study was to assess whether the prevalence of MetS was higher in a group of RA patients compared to subjects without RA.
A PubMed database search was conducted during April 2013 to identify observational studies of RA and risk of MetS. Reference lists of retrieved articles were also reviewed. Two authors independently extracted information on the study design, the characteristics of the study participants, exposure and outcome assessments, and the method used to control for potential confounding factors. A random-effects model was used for the risk estimates.
Our meta-analysis of four cross-sectional controlled studies plus eight case-control studies involving a total of 2283 cases and 4403 controls identified a significant association between RA and risk of MetS, with an overall OR of 1.24 (95% CI, 1.03-1.50).
This meta-analysis provides further evidence supporting patients with RA have a higher prevalence of MetS than subjects without RA. In addition, the geographic region of the population and the criteria used for MetS diagnosis could influence the association. However, these observations would need to be evaluated using prospective, randomized studies.
PMCID: PMC3808281  PMID: 24205134
15.  Complete Genome Sequence of a Nephropathogenic Infectious Bronchitis Virus Strain Isolated in China 
Genome Announcements  2013;1(5):e00815-13.
Infectious bronchitis virus (IBV) causes tremendous economic losses to the poultry industry. Here, we report the complete genome analysis results for a new natural recombination nephropathogenic IBV strain named SAIBK, which was isolated in the Sichuan province of China in 2005.
PMCID: PMC3795213  PMID: 24115543
16.  Fabrication of Nanofiber Scaffolds with Gradations in Fiber Organization and Their Potential Applications 
Macromolecular bioscience  2012;12(10):1336-1341.
A new and simple method for fabrication of nanofiber scaffolds with gradations in fiber organization is reported. The nanofiber organization, achieved by deposition of random fibers on the uniaxially-aligned nanofiber mat in a gradient manner, directed morphological changes of applied adipose-derived stem cells. These morphological changes and resultant biochemical changes can help mimic the structural orientation of complex biomechanical structures like the collagen fiber structure at the tendon-to-bone insertion site. In addition, chemical gradients can be established through nanoencapsulation in this novel scaffold allowing for enhanced biomedical applications.
PMCID: PMC3544006  PMID: 22847852
Electrospinning; Gradient; Nanofibers; Organization; Tendon-to-Bone
17.  The vaginal microbiome: rethinking health and diseases 
Annual review of microbiology  2012;66:371-389.
Vaginal microbiota form a mutually beneficial relationship with their host and have major impact on health and disease. In recent years our understanding of vaginal bacterial community composition and structure has significantly broadened as a result of investigators using cultivation-independent methods based on the analysis of 16S ribosomal RNA (rRNA) gene sequences. In asymptomatic, otherwise healthy women, several kinds of vaginal microbiota exist, the majority often dominated by species of Lactobacillus, while others comprise a diverse array of anaerobic microorganisms. Bacterial vaginosis is the most common vaginal conditions and is vaguely characterized as the disruption of the equilibrium of the ‘normal’ vaginal microbiots. A better understanding of ‘normal’ and ‘healthy’ vaginal ecosystems that is based on its ‘true’ function and not simply on its composition would help better define health and further improve disease diagnostics as well as the development of more personalized regimens to promote health and treat diseases.
PMCID: PMC3780402  PMID: 22746335
vaginal microbiota; vaginal ecosystem; bacterial vaginosis; health and disease
18.  Chitinase 3-like-1 Promotes Streptococcus pneumoniae Killing and Augments Host Tolerance to Lung Antibacterial Responses 
Cell host & microbe  2012;12(1):34-46.
Host antibacterial responses include mechanisms that kill bacteria, but also those that protect or tolerize the host to potentially damaging antibacterial effects. We determined that Chitinase 3-like-1 (Chi3l1), a conserved prototypic chitinase-like protein, is induced by Streptococcus pneumoniae and plays central roles in promoting bacterial clearance and mediating host tolerance. S. pneumoniae-infected Chi3l1 null mice exhibit exaggerated lung injury, inflammation and hemorrhage, more frequent bacterial dissemination, decreased bacterial clearance, and enhanced mortality compared to controls. Chi3l1 augments macrophage bacterial killing by inhibiting caspase-1-dependent macrophage pyroptosis and augments host tolerance by controlling inflammasome activation, ATP accumulation, expression of ATP receptor P2×7R, and production of thymic stromal lymphopoietin and type 1, type 2, and type 17 cytokines. These data demonstrate that Chi3l1 is induced during infection, where it promotes bacterial clearance while simultaneously augmenting host tolerance, and that these roles likely contributed to the retention of Chi3l1 over species and evolutionary time.
PMCID: PMC3613130  PMID: 22817986
19.  Renal Protective Role of Xiexin Decoction with Multiple Active Ingredients Involves Inhibition of Inflammation through Downregulation of the Nuclear Factor-κB Pathway in Diabetic Rats 
In Chinese medicine, Xiexin decoction (XXD) has been used for the clinical treatment of diabetes for at least 1700 years. The present study was conducted to investigate the effective ingredients of XXD and their molecular mechanisms of antidiabetic nephropathy in rats. Rats with diabetes induced by high-fat diet and streptozotocin were treated with XXD extract for 12 weeks. XXD significantly improved the glucolipid metabolism disorder, attenuated albuminuria and renal pathological changes, reduced renal advanced glycation end-products, inhibited receptor for advanced glycation end-product and inflammation factors expression, suppressed renal nuclear factor-κB pathway activity, and downregulated renal transforming growth factor-β1. The concentrations of multiple components in plasma from XXD were determined by liquid chromatography and tandem mass spectrometry. Pharmacokinetic/pharmacodynamic analysis using partial least square regression revealed that 8 ingredients of XXD were responsible for renal protective effects via actions on multiple molecular targets. Our study suggests that the renal protective role of XXD with multiple effective ingredients involves inhibition of inflammation through downregulation of the nuclear factor-κB pathway, reducing renal advanced glycation end-products and receptor for advanced glycation end-product in diabetic rats.
PMCID: PMC3713598  PMID: 23935673
20.  Evaluation of an Automatic Registration-Based Algorithm for Direct Measurement of Volume Change in Tumors 
Assuming that early tumor volume change is a biomarker for response to therapy, accurate quantification of early volume changes could aid in adapting an individual patient’s therapy and lead to shorter clinical trials. We investigated an image registration–based approach for tumor volume change quantification that may more reliably detect smaller changes that occur in shorter intervals than can be detected by existing algorithms.
Methods and Materials
Variance and bias of the registration-based approach were evaluated using retrospective, in vivo, very-short-interval diffusion magnetic resonance imaging scans where true zero tumor volume change is unequivocally known and synthetic data, respectively. The interval scans were nonlinearly registered using two similarity measures: mutual information (MI) and normalized cross-correlation (NCC).
The 95% confidence interval of the percentage volume change error was (−8.93% to 10.49%) for MI-based and (−7.69%, 8.83%) for NCC-based registrations. Linear mixed-effects models demonstrated that error in measuring volume change increased with increase in tumor volume and decreased with the increase in the tumor’s normalized mutual information, even when NCC was the similarity measure being optimized during registration. The 95% confidence interval of the relative volume change error for the synthetic examinations with known changes over ±80% of reference tumor volume was (−3.02% to 3.86%). Statistically significant bias was not demonstrated.
A low-noise, low-bias tumor volume change measurement algorithm using nonlinear registration is described. Errors in change measurement were a function of tumor volume and the normalized mutual information content of the tumor.
PMCID: PMC3401904  PMID: 22172911
Tumor volume change; Image registration; Dual baseline examination; Coffee-break examination; Linear mixed-effects model
21.  Inferring ancient metabolism using ancestral core metabolic models of enterobacteria 
BMC Systems Biology  2013;7:46.
Enterobacteriaceae diversified from an ancestral lineage ~300-500 million years ago (mya) into a wide variety of free-living and host-associated lifestyles. Nutrient availability varies across niches, and evolution of metabolic networks likely played a key role in adaptation.
Here we use a paleo systems biology approach to reconstruct and model metabolic networks of ancestral nodes of the enterobacteria phylogeny to investigate metabolism of ancient microorganisms and evolution of the networks. Specifically, we identified orthologous genes across genomes of 72 free-living enterobacteria (16 genera), and constructed core metabolic networks capturing conserved components for ancestral lineages leading to E. coli/Shigella (~10 mya), E. coli/Shigella/Salmonella (~100 mya), and all enterobacteria (~300-500 mya). Using these models we analyzed the capacity for carbon, nitrogen, phosphorous, sulfur, and iron utilization in aerobic and anaerobic conditions, identified conserved and differentiating catabolic phenotypes, and validated predictions by comparison to experimental data from extant organisms.
This is a novel approach using quantitative ancestral models to study metabolic network evolution and may be useful for identification of new targets to control infectious diseases caused by enterobacteria.
PMCID: PMC3694032  PMID: 23758866
Constraint-based modeling; Enterobacteria; Metabolic network reconstruction; Ancient metabolism; Paleo systems biology; Ancestral core
22.  ent-Kaurane diterpenoids from the plant Wedelia trilobata 
Four new ent-kaurane diterpenoids, namely, 3α-tigloyloxypterokaurene L3 (1), ent-17-hydroxy-kaura-9(11),15-dien-19-oic acid (2), and wedelobatins A (3) and B (4), together with 11 known ent-kaurane diterpenoids (5-15), were isolated from the ethanol extract of Wedelia trilobata. All the structures of 1–15 were elucidated on the basis of spectroscopic studies.
Electronic Supplementary Material
Supplementary material is available for this article at 10.1007/s13659-013-0029-4 and is accessible for authorized users.
PMCID: PMC4131666
ent-kaurane diterpenoids; Wedelia trilobata; phytochemical investigation
23.  Chitinase-like Proteins in Lung Injury, Repair, and Metastasis 
This report explains how our studies of asthma and Th2 inflammation led us to investigate the roles of chitinase-like proteins (CLPs) in lung injury and repair and puts forth an overall hypothesis that can explain the roles that these moieties play in biology and a hypothesis regarding the ways that dysregulated CLP expression may contribute to the pathogenesis of a variety of diseases. We test this hypothesis by assessing the contributions of the CLP breast regression protein (BRP)-39 in the pathogenesis of malignant melanoma metastasis to the lung.
PMCID: PMC3359113  PMID: 22550243
BRP-39/YKL-40; inflammation; injury; repair; metastasis
24.  Studies of Vascular Endothelial Growth Factor in Asthma and Chronic Obstructive Pulmonary Disease 
Vascular endothelial growth factor (VEGF) is a potent stimulator of vascular angiogenesis, permeability, and remodeling that also plays important roles in wound healing and tissue cytoprotection. To begin to define the roles of VEGF in diseases like asthma and COPD, we characterized the effects of lung-targeted transgenic VEGF165 and defined the innate immune pathways that regulate VEGF tissue responses. The former studies demonstrated that VEGF plays an important role in Th2 inflammation because, in addition to stimulating angiogenesis and edema, VEGF induced eosinophilic inflammation, mucus metaplasia, subepithelial fibrosis, myocyte hyperplasia, dendritic cell activation, and airways hyperresponsiveness via IL-13–dependent and -independent mechanisms. VEGF was also produced at sites of aeroallergen-induced Th2 inflammation, and VEGF receptor blockade ameliorated adaptive Th2 inflammation and Th2 cytokine elaboration. The latter studies demonstrated that activation of the RIG-like helicase (RLH) innate immune pathway using viral pathogen–associated molecular patterns such as Poly(I:C) or viruses ameliorated VEGF-induced tissue responses. In accord with these findings, Poly(I:C)-induced RLH activation also abrogated aeroallergen-induced Th2 inflammation. When viewed in combination, these studies suggest that VEGF excess can contribute to the pathogenesis of Th2 inflammatory disorders such as asthma and that abrogation of VEGF signaling via RLH activation can contribute to the pathogenesis of viral disorders such as virus-induced COPD exacerbations. They also suggest that RLH activation may be a useful therapeutic strategy in asthma and related disorders.
PMCID: PMC3359071  PMID: 22052929
asthma; chronic obstructive pulmonary disease; virus; RIG-like helicase; mitochondrial antiviral signaling molecule
25.  Mechanisms Decreasing In Vitro Susceptibility to the LpxC Inhibitor CHIR-090 in the Gram-Negative Pathogen Pseudomonas aeruginosa 
Testing P. aeruginosa efflux pump mutants showed that the LpxC inhibitor CHIR-090 is a substrate for MexAB-OprM, MexCD-OprJ, and MexEF-OprN. Utilizing P. aeruginosa PAO1 with a chromosomal mexC::luxCDABE fusion, luminescent mutants arose on medium containing 4 μg/ml CHIR-090, indicating upregulation of MexCD-OprJ. These mutants were less susceptible to CHIR-090 (MIC, 4 μg/ml) and had mutations in the mexCD-oprJ repressor gene nfxB. Nonluminescent mutants (MIC, 4 μg/ml) that had mutations in the mexAB-oprM regulator gene mexR were also observed. Plating the clinical isolate K2153 on 4 μg/ml CHIR-090 selected mutants with alterations in mexS (immediately upstream of mexT), which upregulates MexEF-OprN. A mutant altered in the putative1ribosomal binding site (RBS) upstream of lpxC and overexpressing LpxC was selected on a related LpxC inhibitor and exhibited reduced susceptibility to CHIR-090. Overexpression of LpxC from a plasmid reduced susceptibility to CHIR-090, and introduction of the altered RBS in this construct further increased expression of LpxC and decreased susceptibility to CHIR-090. Using a mutS (hypermutator) strain, a mutant with an altered lpxC target gene (LpxC L18V) was also selected. Purified LpxC L18V had activity similar to that of wild-type LpxC in an in vitro assay but had reduced inhibition by CHIR-090. Finally, an additional class of mutant, typified by an extreme growth defect, was identified. These mutants had mutations in fabG, indicating that alteration in fatty acid synthesis conferred resistance to LpxC inhibitors. Passaging experiments showed progressive decreases in susceptibility to CHIR-090. Therefore, P. aeruginosa can employ several strategies to reduce susceptibility to CHIR-090 in vitro.
PMCID: PMC3256010  PMID: 22024823

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