Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: Correlation with its unique phenotypes.

Mealybugs are aggressive pests with world-wide distribution and are suitable for the study of different phenomena like genomic imprinting and epigenetics. Genomic approaches facilitate these studies in absence of robust genetics in this system. We sequenced, de novo assembled, annotated Maconellicoccus hirsutus genome. We carried out comparative genomics it with four mealybug and eight other insect species, to identify expanded, specific and contracted gene classes that relate to pesticide and desiccation resistance. We identified horizontally transferred genes adding to the mutualism between the mealybug and its endosymbionts. Male and female transcriptome analysis indicates differential expression of metabolic pathway genes correlating with their physiology and the genes for sexual dimorphism. The significantly lower expression of endosymbiont genes in males relates to the depletion of endosymbionts in males during development.

Assessment of Vedolizumab Disease-Drug-Drug Interaction Potential in Patients With Inflammatory Bowel Diseases.

Disease-drug-drug interactions (DDDIs) have been identified in some inflammatory diseases in which elevated proinflammatory cytokines can downregulate the expression of cytochrome P450 (CYP) enzymes, potentially increasing systemic exposure to drugs metabolized by CYPs. Following anti-inflammatory treatments, CYP expression may return to normal, resulting in reduced drug exposure and diminished clinical efficacy. Vedolizumab has a well-established positive benefit-risk profile in patients with ulcerative colitis (UC) or Crohn's disease (CD) and has no known systemic immunosuppressive activity. A stepwise assessment was conducted to evaluate the DDDI potential of vedolizumab to impact exposure to drugs metabolized by CYP3A through cytokine modulation. First, a review of published data revealed that patients with UC or CD have elevated cytokine concentrations relative to healthy subjects; however, these concentrations remained below those reported to impact CYP expression. Exposure to drugs metabolized via CYP3A also appeared comparable between patients and healthy subjects. Second, serum samples from patients with UC or CD who received vedolizumab for 52 weeks were analyzed and compared with healthy subjects. Cytokine concentrations and the 4ß-hydroxycholesterol-to-cholesterol ratio, an endogenous CYP3A4 biomarker, were comparable between healthy subjects and patients both before and during vedolizumab treatment. Finally, a medical review of postmarketing DDDI cases related to vedolizumab from the past 6 years was conducted and did not show evidence of any true DDDIs. Our study demonstrated the lack of clinically meaningful effects of disease or vedolizumab treatment on the exposure to drugs metabolized via CYP3A through cytokine modulation in patients with UC or CD.

Mining histone methyltransferases and demethylases from whole genome sequence.

Epigenetic regulation through post-translational modification of histones, especially methylation, is well conserved in evolution. Although there are several insect genomes sequenced, an analysis with a focus on their epigenetic repertoire is limited. We have utilized a novel work-flow to identify one or more domains as highpriority domain (HPD), if present in at least 50% of the genes of a given functional class in the reference genome, namely, that of Drosophila melanogaster. Based on this approach, we have mined histone methyltransferases and demethylases from the whole genome sequence of Aedes aegypti (Diptera), the pea aphid Acyrthosiphon pisum, the triatomid bug Rhodnius prolixus (Hemiptera), the honeybee Apis mellifera (Hymenoptera), the silkworm Bombyx mori (Lepidoptera) and the red flour beetle Tribolium castaneum (Coleoptera). We identified 38 clusters consisting of arginine methyltransferases, lysine methyltransferases and demethylases using OrthoFinder, and the presence of HPD was queried in these sequences using InterProScan. This approach led us to identify putative novel members and currently inaccurate ones. Other than the highpriority domains, these proteins contain shared and unique domains that can mediate protein-protein interaction. Phylogenetic analysis indicates that there is different extent of protein sequence similarity; average similarity between histone lysine methyltransferases varies from 41% (for active mark) to 48% (for repressive mark), arginine methyltransferases is 51%, and demethylases is 52%. The method utilized here facilitates reliable identification of desired functional class in newly sequenced genomes.

Monoclonal antibody targeting BDCA2 ameliorates skin lesions in systemic lupus erythematosus.

BACKGROUND: Plasmacytoid DCs (pDC) produce large amounts of type I IFN (IFN-I), cytokines convincingly linked to systemic lupus erythematosus (SLE) pathogenesis. BIIB059 is a humanized mAb that binds blood DC antigen 2 (BDCA2), a pDC-specific receptor that inhibits the production of IFN-I and other inflammatory mediators when ligated. A first-in-human study was conducted to assess safety, tolerability, and pharmacokinetic (PK) and pharmacodynamic (PD) effects of single BIIB059 doses in healthy volunteers (HV) and patients with SLE with active cutaneous disease as well as proof of biological activity and preliminary clinical response in the SLE cohort. METHODS: A randomized, double-blind, placebo-controlled clinical trial was conducted in HV (n = 54) and patients with SLE (n = 12). All subjects were monitored for adverse events. Serum BIIB059 concentrations, BDCA2 levels on pDCs, and IFN-responsive biomarkers in whole blood and skin biopsies were measured. Skin disease activity was determined using the Cutaneous Lupus Erythematosus Disease Area and Severity Index Activity (CLASI-A). RESULTS: Single doses of BIIB059 were associated with favorable safety and PK profiles. BIIB059 administration led to BDCA2 internalization on pDCs, which correlated with circulating BIIB059 levels. BIIB059 administration in patients with SLE decreased expression of IFN response genes in blood, normalized MxA expression, reduced immune infiltrates in skin lesions, and decreased CLASI-A score. CONCLUSIONS: Single doses of BIIB059 were associated with favorable safety and PK/PD profiles and robust target engagement and biological activity, supporting further development of BIIB059 in SLE. The data suggest that targeting pDCs may be beneficial for patients with SLE, especially those with cutaneous manifestations. TRIAL REGISTRATION: ClinicalTrials.gov NCT02106897. FUNDING: Biogen Inc.

In praise of mealybugs.

The fascinating chromosomal cycle leading to facultative heterochromatization in the mealybugs has been a challenging system for mechanistic understanding of the phenomenon of genomic imprinting and epigenetics. The elegant cytological dissection of the various processes reported in the literature is equally fascinating for the researchers of current molecular age. Presently, a two way approach is being pursued; continued efforts of utilizing elegant cytology, in combination with the molecular probes to decipher molecular correlates on one hand and on the other, the de novo biochemical/molecular analysis for the identification of the molecular players using genomic tools. The hope is to uncover novel players in genomic imprinting and epigenetic regulation in the mealybug system which shows differential regulation of the entire genome, with 50% of its genome being transcriptionally inactivated in a parental-origin-specific and sex specific manner. In addition to being a model for epigenetic regulation, the mealybugs are being utilized for the analysis of radiation resistance as well as metabolic interactions between the microbiome and the host. The overview presented here is an attempt to bring out some of the work carried out in these directions. We also discuss the areas that remain poorly explored in this system, such as the role/involvement of noncoding RNA in male-specific inactivation and the molecular dissection of heterochromatin, the cytological manifestation of the inactive state of genes and chromosome.

Biofilm forming ability of Sphingomonas paucimobilis isolated from community drinking water systems on plumbing materials used in water distribution.

Sphingomonas paucimobilis, an oligotroph, is well recognized for its potential for biofilm formation. The present study explored the biofilm forming ability of a strain isolated from municipal drinking water on plumbing materials. The intensity of biofilm formation of this strain on different plumbing materials was examined by using 1 × 1 cm2 pieces of six different pipe materials, i.e. polyvinyl chloride (PVC), polypropylene (PP), polyethylene (PE), aluminium (Al), copper (Cu) and rubber (R) and observing by staining with the chemical chromophore, Calcofluor. To understand whether biofilm formation occurs under flow through conditions, a laboratory-scale simulated distribution system, comprised of the above materials was fabricated. Biofilm samples were collected from the designed system at different biofilm ages (10, 40 and 90 hours old) and enumerated. The results indicated that the biofilm formation occurred on all plumbing materials with Cu and R as exceptions. The intensity of biofilm formation was found to be maximum on PVC followed by PP and PE. We also demonstrated the chemical chromophore (Calcofluor) successfully for rapid and easy visual detection of biofilms, validated by scanning electron microscope (SEM) analysis of the plumbing materials. Chlorination has little effect in preventing biofilm development.

Monitoring of biofilm aging in a Sphingomonas sp. strain from public drinking water sites through changes in capacitance.

This study reports the applicability of a capacitance-based technique for evaluating the biofilm progression of Sphingomonas sp. One hundred and forty isolates of Sphingomonas were screened from public drinking water sites, and one potential strain with biofilm-forming ability was used for the study. The biofilm production by this strain was established in microtiter plates and aluminum coupons. The standard biofilm-forming strain Sphingomonas terrae MTCC 7766 was used for comparison. Changes in biofilm were analyzed by energy-dispersive X-ray spectroscopy (EDX) and scanning electron microscope (SEM). Capacitance values were measured at 1, 100 and 200 kHz frequency; however, 1 kHz was selected since resulted in reproducible values, which could be correlated to biofilm age measured as dry weight over a time of 96 h (4 days) depicting the biofilm growth/progression over time. The EDX, SEM and capacitance values obtained in parallel indicated the related physiological profile usually displayed by biofilms upon growth, suggesting authenticity to the observed capacitance profile. The results of this study demonstrated the feasibility of a capacitance-based method for analyzing biofilm development/progression by Sphingomonas sp. and suggested a simple approach for developing an online system to detect biofilms by this opportunistic pathogen of concern in drinking water.

First-in-human multicenter phase I study of BMS-936561 (MDX-1203), an antibody-drug conjugate targeting CD70.

PURPOSE: The study evaluated the safety, tolerability, and pharmacokinetics of BMS-936561, a fully human monoclonal antibody-drug conjugate targeting CD70 cell-surface protein. METHODS: Eligible patients had ECOG performance status 0-2 and received ≤3 prior chemotherapy regimens. An initial accelerated titration design enrolling one patient per dose level was followed by 3 + 3 dose escalation with the first observation of a grade ≥2 adverse event (AE). We tested escalating doses of BMS-936561 (0.5, 1, 2, 4, 8, 15 mg/kg) administered every 21 days in a 42 day cycle for a maximum of 17 cycles. Pharmacokinetic samples were collected in cycle 1. RESULTS: A total of 26 patients enrolled; 16 and 10 for the escalation and expansion cohorts, respectively. Median age was 63 years (48-74); 18 males and 25 Caucasians. There was no defined MTD per protocol, but a DLT of grade 3 hypersensitivity was recorded in 2 of 16 (13%) subjects at the highest dose of 15 mg/kg. The most frequent AEs were: fatigue (85%), nausea (54%), and decreased appetite (39%). Delayed toxicities (facial edema and pleural/pericardial effusions) occurred in 6 of 16 (38%) subjects at the 15 mg/kg dose. PK analysis showed a dose-proportional increase in active drug levels with increasing doses. There was disease stabilization in 18 of 26 patients (69%) without correlation with received dose. CONCLUSIONS: BMS-936561 is well tolerated over a wide range of doses in patients with advanced ccRCC and B-NHL. The 8 mg/kg dose was the highest best tolerated dose and the recommended dose for future studies.

AU-rich elements in the 3'-UTR regulate the stability of the 141 amino acid isoform of parathyroid hormone-related protein mRNA.

We demonstrated previously that parathyroid hormone-related protein (PTHrP) 1-141 mRNA is the least stable of three isoforms and is the only isoform that is stabilized by TGF-ß. In order to understand how PTHrP mRNA is stabilized by TGF-ß, we first sought to elucidate the mechanism(s) that are responsible for the instability of PTHrP isoform 1-141 mRNA. The 3'-UTR of isoform 1-141 contains four AU-rich elements (AREs), which are known to mediate mRNA degradation. We utilized a luciferase reporter system to test whether these four AREs are responsible for the short half-life of PTHrP 1-141 mRNA. Our results demonstrated that ARE elements in the 3'-UTR of PTHrP 1-141 mRNA play a significant role in regulation of the stability of the mRNA. It is known that AREs mediate their effects on mRNA stability through a number of ARE-binding proteins that recruit the exosome, a complex of exonucleases that degrades the mRNA. We identified tristetraproline (TTP) as an RNA-binding protein that may be involved in ARE-mediated degradation of PTHrP 1-141 mRNA.

Impact of aprotinin and renal function on mortality: a retrospective single center analysis.

BACKGROUND: An estimated up to 7% of high-risk cardiac surgery patients return to the operating room for bleeding. Aprotinin was used extensively as an antifibrinolytic agent in cardiac surgery patients for over 15 years and it showed efficacy in reducing bleeding. Aprotinin was removed from the market by the U.S. Food and Drug Administration after a large prospective, randomized clinical trial documented an increased mortality risk associated with the drug. Further debate arose when a meta-analysis of 211 randomized controlled trials showed no risk of renal failure or death associated with aprotinin. However, only patients with normal kidney function have been studied. METHODS: In this study, we look at a single center clinical trial using patients with varying degrees of baseline kidney function to answer the question: Does aprotinin increase odds of death given varying levels of preoperative kidney dysfunction? RESULTS: Based on our model, aprotinin use was associated with a 3.8-fold increase in odds of death one year later compared to no aprotinin use with p-value = 0.0018, regardless of level of preoperative kidney dysfunction after adjusting for other perioperative variables. CONCLUSIONS: Lessons learned from our experience using aprotinin in the perioperative setting as an antifibrinolytic during open cardiac surgery should guide us in testing future antifibrinolytic drugs for not only efficacy of preventing bleeding, but for overall safety to the whole organism using long-term clinical outcome studies, including those with varying degree of baseline kidney function.

Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition.

A majority of the studies examining the molecular regulation of human labor have been conducted using single gene approaches. While the technology to produce multi-dimensional datasets is readily available, the means for facile analysis of such data are limited. The objective of this study was to develop a systems approach to infer regulatory mechanisms governing global gene expression in cytokine-challenged cells in vitro, and to apply these methods to predict gene regulatory networks (GRNs) in intrauterine tissues during term parturition. To this end, microarray analysis was applied to human amnion mesenchymal cells (AMCs) stimulated with interleukin-1ß, and differentially expressed transcripts were subjected to hierarchical clustering, temporal expression profiling, and motif enrichment analysis, from which a GRN was constructed. These methods were then applied to fetal membrane specimens collected in the absence or presence of spontaneous term labor. Analysis of cytokine-responsive genes in AMCs revealed a sterile immune response signature, with promoters enriched in response elements for several inflammation-associated transcription factors. In comparison to the fetal membrane dataset, there were 34 genes commonly upregulated, many of which were part of an acute inflammation gene expression signature. Binding motifs for nuclear factor-κB were prominent in the gene interaction and regulatory networks for both datasets; however, we found little evidence to support the utilization of pathogen-associated molecular pattern (PAMP) signaling. The tissue specimens were also enriched for transcripts governed by hypoxia-inducible factor. The approach presented here provides an uncomplicated means to infer global relationships among gene clusters involved in cellular responses to labor-associated signals.

Fully moderated T-statistic for small sample size gene expression arrays.

Gene expression microarray experiments with few replications lead to great variability in estimates of gene variances. Several Bayesian methods have been developed to reduce this variability and to increase power. Thus far, moderated t methods assumed a constant coefficient of variation (CV) for the gene variances. We provide evidence against this assumption, and extend the method by allowing the CV to vary with gene expression. Our CV varying method, which we refer to as the fully moderated t-statistic, was compared to three other methods (ordinary t, and two moderated t predecessors). A simulation study and a familiar spike-in data set were used to assess the performance of the testing methods. The results showed that our CV varying method had higher power than the other three methods, identified a greater number of true positives in spike-in data, fit simulated data under varying assumptions very well, and in a real data set better identified higher expressing genes that were consistent with functional pathways associated with the experiments.

Docosahexaenoic Acid and Amino Acid Contents in Pasteurized Donor Milk are Low for Preterm Infants.

OBJECTIVE: To evaluate whether pasteurized donor human milk meets the nutritional needs of preterm infants in terms of free fatty acid and amino acid contents. STUDY DESIGN: Milk samples were prospectively collected from 39 donors to the Mothers' Milk Bank of Ohio. The fatty acid and amino acid compositions in donor milk samples were measured before and after pasteurization, and values were compared with previously published findings and preterm infant nutrition guidelines. The nutritional adequacy of donor milk for preterm infants was based on estimated daily intake of 150 mL/kg. Statistical significance was adjusted to account for multiple comparisons. RESULTS: Pasteurization did not appreciably affect donor milk composition. Docosahexaenoic acid level (0.1 mol wt %), and concentrations of glycine, aspartate, valine, phenylalanine, proline, lysine, arginine, serine, and histidine in donor milk were all significantly lower than previously reported concentrations in milk. CONCLUSIONS: Donor milk is not substantially affected by pasteurization, but has low concentrations of docosahexaenoic acid and amino acids. Targeted nutritional supplementation of human donor milk for feeding preterm infants might be warranted.

Erk1 and Erk2 regulate endothelial cell proliferation and migration during mouse embryonic angiogenesis.

Angiogenesis is a complex process orchestrated by both growth factors and cell adhesion and is initiated by focal degradation of the vascular basement membrane with subsequent migration and proliferation of endothelial cells. The Ras/Raf/MEK/ERK pathway is required for EC function during angiogenesis. Although in vitro studies implicate ERK1 and ERK2 in endothelial cell survival, their precise role in angiogenesis in vivo remains poorly defined. Cre/loxP technology was used to inactivate Erk1 and Erk2 in endothelial cells during murine development, resulting in embryonic lethality due to severely reduced angiogenesis. Deletion of Erk1 and Erk2 in primary endothelial cells resulted in decreased cell proliferation and migration, but not in increased apoptosis. Expression of key cell cycle regulators was diminished in the double knockout cells, and decreased DNA synthesis could be observed in endothelial cells during embryogenesis. Interestingly, both Paxillin and Focal Adhesion Kinase were expressed at lower levels in endothelial cells lacking Erk1 and Erk2 both in vivo and in vitro, leading to defects in the organization of the cytoskeleton and in cell motility. The regulation of Paxillin and Focal Adhesion Kinase expression occurred post-transcriptionally. These results demonstrate that ERK1 and ERK2 coordinate endothelial cell proliferation and migration during angiogenesis.

Effect of postnatal maturation on the mechanisms of esophageal propulsion in preterm human neonates: primary and secondary peristalsis.

OBJECTIVES: The changes in esophageal propulsive characteristics during maturation are not known. Our aim was to define the effects of postnatal maturation on esophageal peristaltic characteristics in preterm human neonates. We tested the hypotheses that: (i) maturation modifies esophageal bolus propulsion characteristics, and (ii) the mechanistic characteristics differ between primary and secondary peristalsis. METHODS: Esophageal motility in 10 premature neonates (mean 27.5 weeks gestational age) was evaluated twice at 33.8 weeks (time 1, earlier study) and 39.2 weeks (time 2, later study) mean postmenstrual age. Esophageal manometry waveform characteristics (amplitude and duration, peristaltic velocity, and intrabolus pressure domains) were analyzed during spontaneous primary peristalsis and infusion-induced secondary peristalsis. Repeated-measures and unstructured variance-covariance or compound symmetry matrixes were used for statistical comparison. Values stated as least squares means+/-s.e.m. or percent. RESULTS: A total of 200 primary peristalsis and 227 secondary peristalsis events were evaluated. Between time 1 and time 2: (i) proximal esophageal waveform amplitude increased (P<0.02), with primary peristalsis (38+/-6 vs. 48+/-7 mm Hg) and with secondary peristalsis (34+/-6 vs. 46+/-5 mm Hg); (ii) distal esophageal waveform amplitude was similar (P=NS), with primary peristalsis (42+/-4 vs. 43+/-4 mm Hg) and secondary peristalsis (29+/-3 vs. 32+/-4 mm Hg); (iii) proximal esophageal waveform onset to peak duration decreased (P=0.02) with primary (2.6+/-0.3 vs. 1.9+/-0.1 s, P<0.003) and with secondary peristalsis (2.2+/-0.2 vs. 1.8+/-0.1 s); (iv) distal esophageal waveform onset to peak duration decreased (P=0.01) with primary (2.4+/-0.3 vs. 1.8+/-0.1 s) and with secondary peristalsis (1.9+/-0.2 vs. 1.5+/-0.1 s); (v) effects of identical stimulus volume on intrabolus pressure were similar (P=NS); however, greater infusion volumes (2 vs. 1 ml) generated higher intrabolus pressure at both time 1 and time 2 (both Ps<0.05). Between primary and secondary peristalsis (mechanistic variable): (i) no differences were noted at either period, with proximal esophageal waveform amplitudes (P=NS); (ii) differences were noted with distal esophageal waveform amplitudes at each time period (P=0.0002); (iii) no differences were noted with both esophageal waveforms duration at either period (P=NS); (iv) peristaltic velocity was faster with secondary peristalsis than with primary peristalsis at either period (at earlier study, 7.9+/-1.4 vs. 2.5+/-1.4 cm/s and at later study 6.2+/-1.6 vs. 1.2+/-1.5 cm/s, both Ps<0.01). CONCLUSIONS: In preterm neonates, longitudinal maturation modulates the characteristics of primary and secondary peristalsis. Differences in proximal striated muscle and distal smooth muscle activity during peristalsis are evident. Peristaltic velocity is faster with secondary peristalsis. These findings may represent maturation of central and peripheral neuromotor properties of esophageal bolus propulsion in healthy preterm human neonates.

Alveolar process anabolic activity in C3H/HeJ and C57BL/6J inbred mice.

BACKGROUND: The purpose of this study was to characterize bone activity of the alveolar process in C3H/HeJ (C3H) and C57BL/6J (B6) inbred mice. Based on observations in other animal species, we hypothesized that the bone-formation rate/bone surface (BFR/BS) is greater in the alveolar process compared to the body of the mandible and that the bone anabolic activity is greater in the alveolar process of the mandible than in the maxilla. We also examined the alveolar process of C3H and B6 mice for the presence of secondary osteons. METHODS: Jaws from 17-week-old C3H and B6 female mice (N = 15/group) were harvested. Histomorphometric parameters were evaluated in sections from the alveolar process, each of which included at least one molar root. RESULTS: In C3H and B6 mice, BFR/BS was not significantly different (P >0.05) between the alveolar process and the body of the mandible. In C3H mice, BFR/BS was significantly greater (P = 0.05) in the mandible compared to the maxilla. BFR/bone volume (BV) was not significantly different (P >0.05) between C3H mandible and maxilla. In the B6 inbred mouse, BFR/BS and BFR/bone volume (BV) were not significantly different (P >0.05) between jaws. After analyzing 165 bone sections, we identified 25 secondary osteons. CONCLUSIONS: The surface anabolic activity was not different between the body and the alveolar process of the mandible. The surface activity was greater in the C3H mandible than in the maxilla. Although secondary osteonal bone remodeling existed in the C3H and B6 alveolar bone, this process was not a consistent finding.

Adaptations in the mandible and appendicular skeleton of high and low bone density inbred mice.

The appendicular skeletons of high [C3H/HeJ (C3H)] and low [C57BL/6J (B6)] density inbred mice have been shown to differ in morphology, mechanical properties, and cellular activity. The focus of the current study was to (1) characterize the mandibular bone formation rate (BFR/BS), bone mass, indentation modulus (IM), and hardness of C3H and B6 mice and (2) investigate the relationship of the mechanical properties in three skeletal sites: mandible, femur, and tibia. Specimens from 17-week-old female C3H and B6 (n = 15/group) mice were obtained. Mandibular bone mass was estimated from the lateral-view area (LVA) and transverse cross sections. BFR/BS was measured in the mandibular section distal to the third molar. In addition, bone blocks from the distal surface of the third molar and the femoral and tibial midshaft were obtained for mechanical testing. BFR/BS, cortical area, and LVA were greater (P < 0.001) in C3H mandibles. IM was approximately 2 GPa higher in the C3H mandible (P > 0.05), femur (P < 0.001), and tibia (P < 0.01). Mandibular IM was lower (P < 0.05) than the femoral and tibial IM within each inbred mouse. IM was not significant between C3H and B6 mandibles. However, the magnitude of the difference ( approximately 12%) in the mandible was similar to the difference in the appendicular skeleton. This mandibular bone phenotype is similar to that observed in the appendicular skeleton of these distinct inbred mice.