bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupled Positive and Negative Feedbacks Produce Diverse Gene Expression Patterns in Colonies
Authors: Mitarai Namiko , Jensen Mogens Høgh , Semsey Szabolcs 
Published: April 2015

ABSTRACT

Formation of patterns is a common feature in the development of multicellular organism as well as of microbial communities. To investigate the formation of gene expression patterns in colonies, we build a mathematical model of two-dimensional colony growth, where cells carry a coupled positive-and-negative-feedback circuit. We demonstrate that the model can produce sectored, target (concentric), uniform, and scattered expression patterns of regulators, depending on gene expression dynamics and nutrient diffusion. We reconstructed the same regulatory structure in
Escherichia coli
cells and found gene expression patterns on the surface of colonies similar to the ones produced by the computer simulations. By comparing computer simulations and experimental results, we observed that very simple rules of gene expression can yield a spectrum of well-defined patterns in a growing colony. Our results suggest that variations of the protein content among cells lead to a high level of heterogeneity in colonies.

IMPORTANCE
Formation of patterns is a common feature in the development of microbial communities. In this work, we show that a simple genetic circuit composed of a positive-feedback loop and a negative-feedback loop can produce diverse expression patterns in colonies. We obtained similar sets of gene expression patterns in the simulations and in the experiments. Because the combination of positive feedback and negative feedback is common in intracellular molecular networks, our results suggest that the protein content of cells is highly diversified in colonies.
Genetic Basis of Persister Tolerance to Aminoglycosides in Escherichia coli
Authors: Shan Yue , Lazinski David , Rowe Sarah , Camilli Andrew , Lewis Kim 
Published: April 2015

ABSTRACT

Persisters are dormant variants that form a subpopulation of drug-tolerant cells largely responsible for the recalcitrance of chronic infections. However, our understanding of the genetic basis of antibiotic tolerance remains incomplete. In this study, we applied transposon sequencing (Tn-Seq) to systematically investigate the mechanism of aminoglycoside tolerance in
Escherichia coli
. We constructed a highly saturated transposon library that covered the majority of
E. coli
genes and promoter regions and exposed a stationary-phase culture to a lethal dose of gentamicin. Tn-Seq was performed to evaluate the survival of each mutant to gentamicin exposure. We found that the disruption of several distinct pathways affected gentamicin tolerance. We identified 105 disrupted gene/promoter regions with a more than 5-fold reduction in gentamicin tolerance and 37 genes with a more than 5-fold increased tolerance. Functional cluster analysis suggests that deficiency in motility and amino acid synthesis significantly diminished persisters tolerant to gentamicin, without changing the MIC. Amino acid auxotrophs, including serine, threonine, glutamine, and tryptophan auxotrophs, exhibit strongly decreased tolerance to gentamicin, which cannot be restored by supplying the corresponding amino acids to the culture. Interestingly, supplying these amino acids to wild-type
E. coli
sensitizes stationary-phase cells to gentamicin, possibly through the inhibition of amino acid synthesis. In addition, we found that the deletion of amino acid synthesis genes significantly increases gentamicin uptake in stationary phase, while the deletion of flagellar genes does not affect gentamicin uptake. We conclude that activation of motility and amino acid biosynthesis contributes to the formation of persisters tolerant to gentamicin.

IMPORTANCE
Persisters are responsible for the recalcitrance of chronic infections to antibiotics. The pathways of persister formation in
E. coli
are redundant, and our understanding of the mechanism of persister formation is incomplete. Using a highly saturated transposon insertion library, we systematically analyzed the contribution of different cellular processes to the formation of persisters tolerant to aminoglycosides. Unexpectedly, we found that activation of amino acid synthesis and motility strongly contributes to persister formation. The approach used in this study leads to an understanding of aminoglycoside tolerance and provides a general method to identify genes affecting persister formation.
Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity
Authors: Liang Yuting , Wu Liyou , Clark Ian M. , Xue Kai , Yang Yunfeng , Van Nostrand Joy D. , Deng Ye , He Zhili , McGrath Steve , Storkey Jonathan , Hirsch Penny R. , Sun Bo , Zhou Jizhong 
Published: April 2015

ABSTRACT

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receiving nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e.,
z
values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (
P
< 0.0001). The
z
values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (
P
< 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity.

IMPORTANCE
Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.
Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection
Authors: Rogers Matthew B. , Song Timothy , Sebra Robert , Greenbaum Benjamin D. , Hamelin Marie-Eve , Fitch Adam , Twaddle Alan , Cui Lijia , Holmes Edward C. , Boivin Guy , Ghedin Elodie 
Published: April 2015

ABSTRACTResistance following antiviral therapy is commonly observed in human influenza viruses. Although this evolutionary process is initiated within individual hosts, little is known about the pattern, dynamics, and drivers of antiviral resistance at this scale, including the role played by reassortment. In addition, the short duration of human influenza virus infections limits the available time window in which to examine intrahost evolution. Using single-molecule sequencing, we mapped, in detail, the mutational spectrum of an H3N2 influenza A virus population sampled from an immunocompromised patient who shed virus over a 21-month period. In this unique natural experiment, we were able to document the complex dynamics underlying the evolution of antiviral resistance. Individual resistance mutations appeared weeks before they became dominant, evolved independently on cocirculating lineages, led to a genome-wide reduction in genetic diversity through a selective sweep, and were placed into new combinations by reassortment. Notably, despite frequent reassortment, phylogenetic analysis also provided evidence for specific patterns of segment linkage, with a strong association between the hemagglutinin (HA)- and matrix (M)-encoding segments that matches that previously observed at the epidemiological scale. In sum, we were able to reveal, for the first time, the complex interaction between multiple evolutionary processes as they occur within an individual host.IMPORTANCEUnderstanding the evolutionary forces that shape the genetic diversity of influenza virus is crucial for predicting the emergence of drug-resistant strains but remains challenging because multiple processes occur concurrently. We characterized the evolution of antiviral resistance in a single persistent influenza virus infection, representing the first case in which reassortment and the complex patterns of drug resistance emergence and evolution have been determined within an individual host. Deep-sequence data from multiple time points revealed that the evolution of antiviral resistance reflects a combination of frequent mutation, natural selection, and a complex pattern of segment linkage and reassortment. In sum, these data show how immunocompromised hosts may help reveal the drivers of strain emergence.
The Transcription Factor FoxK Participates with Nup98 To Regulate Antiviral Gene Expression
Authors: Panda Debasis , Gold Beth , Tartell Michael A. , Rausch Keiko , Casas-Tinto Sergio , Cherry Sara 
Published: April 2015

ABSTRACT

Upon infection, pathogen recognition leads to a rapidly activated gene expression program that induces antimicrobial effectors to clear the invader. We recently found that Nup98 regulates the expression of a subset of rapidly activated antiviral genes to restrict disparate RNA virus infections in
Drosophila
by promoting RNA polymerase occupancy at the promoters of these antiviral genes. How Nup98 specifically targets these loci was unclear; however, it is known that Nup98 participates with transcription factors to regulate developmental-gene activation. We reasoned that additional transcription factors may facilitate the Nup98-dependent expression of antiviral genes. In a genome-wide RNA interference (RNAi) screen, we identified a relatively understudied forkhead transcription factor, FoxK, as active against Sindbis virus (SINV) in
Drosophila
. Here we find that FoxK is active against the panel of viruses that are restricted by Nup98, including SINV and vesicular stomatitis virus (VSV). Mechanistically, we show that FoxK coordinately regulates the Nup98-dependent expression of antiviral genes. Depletion of FoxK significantly reduces Nup98-dependent induction of antiviral genes and reduces the expression of a forkhead response element-containing luciferase reporter. Together, these data show that FoxK-mediated activation of gene expression is Nup98 dependent. We extended our studies to mammalian cells and found that the mammalian ortholog FOXK1 is antiviral against two disparate RNA viruses, SINV and VSV, in human cells. Interestingly, FOXK1 also plays a role in the expression of antiviral genes in mammals: depletion of FOXK1 attenuates virus-inducible interferon-stimulated response element (ISRE) reporter expression. Overall, our results demonstrate a novel role for FOXK1 in regulating the expression of antiviral genes, from insects to humans.

IMPORTANCE
Innate immunity is characterized by rapid gene expression programs, from insects to mammals. Furthermore, we find that Nup98, known for its roles in the nuclear pore, plays a noncanonical role in binding the promoters and poising a subset of loci for rapid antiviral gene induction. It was unclear how Nup98 accesses these specific genes, and we here demonstrate that Nup98 cooperates with the transcription factor FoxK to regulate this gene expression program. Depletion of FoxK specifically reduces the induction of Nup98-dependent genes. Further, we find that the antiviral function of FoxK is conserved, as the human ortholog FOXK1 is also antiviral and regulates gene expression from virus-induced promoters. Although other forkhead transcription factors have been implicated in immunity, a role for FoxK in antiviral defense was previously unappreciated. Our findings reveal a conserved and novel role for FoxK in coordinating with Nup98 to promote a robust and complex antiviral transcriptional response.
‘You don't know which bits to believe’: qualitative study exploring carers’ experiences of seeking information on the internet about childhood eczema
Authors: Santer Miriam , Muller Ingrid , Yardley Lucy , Burgess Hana , Ersser Steven J , Lewis-Jones Sue , Little Paul 
Published: April 2015

ObjectiveWe sought to explore parents and carers’ experiences of searching for information about childhood eczema on the internet.DesignA qualitative interview study was carried out among carers of children aged 5 years or less with a recorded diagnosis of eczema. The main focus of the study was to explore carers’ beliefs and understandings around eczema and its treatment. As part of this, we explored experiences of formal and informal information seeking about childhood eczema. Transcripts of interviews were analysed thematically.SettingParticipants were recruited from six general practices in South West England.ParticipantsInterviews were carried out with 31 parents from 28 families.ResultsExperiences of searching for eczema information on the internet varied widely. A few interviewees were able to navigate through the internet and find the specific information they were looking for (for instance about treatments their child had been prescribed), but more found searching for eczema information online to be a bewildering experience. Some could find no information of relevance to them, whereas others found the volume of different information sources overwhelming. Some said that they were unsure how to evaluate online information or that they were wary of commercial interests behind some information sources. Interviewees said that they would welcome more signposting towards high quality information from their healthcare providers.ConclusionsWe found very mixed experiences of seeking eczema information on the internet; but many participants in this study found this to be frustrating and confusing. Healthcare professionals and healthcare systems have a role to play in helping people with long-term health conditions and their carers find reliable online information to support them with self-care.
Boundedness of Singular Integrals on Hardy Type Spaces Associated with Schrödinger Operators
Authors: Dong Jianfeng , Huang Jizheng , Liu Heping 
Published: April 2015

LetL=-Δ+Vbe a Schrödinger operator onRn,n≥3, whereV≢0is a nonnegative potential belonging to the reverse Hölder classBn/2. The Hardy type spacesHLp, n/(n+δ) <p≤1,for someδ>0, are defined in terms of the maximal function with respect to the semigroup{e-tL}t>0. In this paper, we investigate the bounded properties of some singular integral operators related toL, such asLiγand∇L-1/2, on spacesHLp. We give the molecular characterization ofHLp, which is used to establish theHLp-boundedness of singular integrals.
An Estimate of the Probability Density Function of the Sum of a Random Number N of Independent Random Variables
Authors: Gifuni Angelo , Sorrentino Antonio , Ferrara Giuseppe , Migliaccio Maurizio 
Published: April 2015

A new estimate of the probability density function (PDF) of the sum of a random number of independent and identically distributed (IID) random variables Xi (i=1, 2, …, N) is shown. The sum PDF is represented as a sum of normal PDFs weighted according to the N PDF. The analytical model is verified by numerical simulations. The comparison is made by the Chi-Square Goodness-of-Fit test.
Phase I Hepatic Immunotherapy for Metastases Study of Intra-Arterial Chimeric Antigen Receptor–Modified T-cell Therapy for CEA+ Liver Metastases
Authors: Katz Steven C. , Burga Rachel A. , McCormack Elise , Wang Li Juan , Mooring Wesley , Point Gary R. , Khare Pranay D. , Thorn Mitchell , Ma Qiangzhong , Stainken Brian F. , Assanah Earle O. , Davies Robin , Espat N. Joseph , Junghans Richard P. 
Published: April 2015

AbstractPurpose: Chimeric antigen receptor–modified T cells (CAR-T) have demonstrated encouraging results in early-phase clinical trials. Successful adaptation of CAR-T technology for CEA-expressing adenocarcinoma liver metastases, a major cause of death in patients with gastrointestinal cancers, has yet to be achieved. We sought to test intrahepatic delivery of anti-CEA CAR-T through percutaneous hepatic artery infusions (HAIs).Experimental Design: We conducted a phase I trial to test HAI of CAR-T in patients with CEA+ liver metastases. Six patients completed the protocol, and 3 received anti-CEA CAR-T HAIs alone in dose-escalation fashion (108, 109, and 1010 cells). We treated an additional 3 patients with the maximum planned CAR-T HAI dose (1010 cells × 3) along with systemic IL2 support.Results: Four patients had more than 10 liver metastases, and patients received a mean of 2.5 lines of conventional systemic therapy before enrollment. No patient suffered a grade 3 or 4 adverse event related to the CAR-T HAIs. One patient remains alive with stable disease at 23 months following CAR-T HAI, and 5 patients died of progressive disease. Among the patients in the cohort that received systemic IL2 support, CEA levels decreased 37% (range, 19%–48%) from baseline. Biopsies demonstrated an increase in liver metastasis necrosis or fibrosis in 4 of 6 patients. Elevated serum IFNγ levels correlated with IL2 administration and CEA decreases.Conclusions: We have demonstrated the safety of anti-CEA CAR-T HAIs with encouraging signals of clinical activity in a heavily pretreated population with large tumor burdens. Further clinical testing of CAR-T HAIs for liver metastases is warranted. Clin Cancer Res; 21(14); 3149–59. ©2015 AACR.
CDKN2A/p16 Loss Implicates CDK4 as a Therapeutic Target in Imatinib-Resistant Dermatofibrosarcoma Protuberans
Authors: Eilers Grant , Czaplinski Jeffrey T. , Mayeda Mark , Bahri Nacef , Tao Derrick , Zhu Meijun , Hornick Jason L. , Lindeman Neal I. , Sicinska Ewa , Wagner Andrew J. , Fletcher Jonathan A. , Mariño-Enriquez Adrian 
Published: April 2015

AbstractDermatofibrosarcoma protuberans (DFSP) is an aggressive PDGFB-dependent cutaneous sarcoma characterized by infiltrative growth and frequent local recurrences. Some DFSP progress to a higher-grade fibrosarcomatous form, with rapid growth and increased risk of metastasis. Imatinib provides clinical benefit in approximately 50% of patients with unresectable or metastatic DFSP. However, efficacious medical therapies have not been developed for imatinib-resistant DFSP. We established a model of imatinib-resistant DFSP and evaluated CDK4/6 inhibition as a genomically credentialed targeted therapy. DFSP105, an imatinib-resistant human cell line, was established from a fibrosarcomatous DFSP (FS-DFSP), and was studied by SNP arrays and sequencing to identify targetable genomic alterations. Findings were validated in vitro and in vivo, and confirmed in a series including 12 DFSP and 6 FS-DFSP. SNP analysis of DFSP105 revealed a homozygous deletion encompassing CDKN2A and CDKN2B. The resultant p16 loss implicated CDK4/6 as a potential therapeutic target in DFSP. We further demonstrated CDKN2A homozygous deletion in 1 of 12 conventional DFSP and 2 of 6 FS-DFSP, whereas p16 expression was lost in 4 of 18 DFSP. In vitro treatment of DFSP105 with two structurally distinct selective CDK4/6 inhibitors, PD-0332991 and LEE011, led to inhibition of RB1 phosphorylation and inhibition of proliferation (GI50 160 nmol/L and 276 nmol/L, respectively). In vivo treatment of DFSP105 with PD-0332991 (150 mg/kg) inhibited xenograft growth in mice, in comparison with imatinib-treated or -untreated tumors. In conclusion, CDKN2A deletion can contribute to DFSP progression. CDK4/6 inhibition is a preclinically effective treatment against p16-negative, imatinib-resistant FS-DFSP, and should be evaluated as a therapeutic strategy in patients with unresectable or metastatic imatinib-resistant DFSP. Mol Cancer Ther; 14(6); 1346–53. ©2015 AACR.
Effective Targeting of Estrogen Receptor–Negative Breast Cancers with the Protein Kinase D Inhibitor CRT0066101
Authors: Borges Sahra , Perez Edith A. , Thompson E. Aubrey , Radisky Derek C. , Geiger Xochiquetzal J. , Storz Peter 
Published: April 2015

AbstractInvasive ductal carcinomas (IDC) of the breast are associated with altered expression of hormone receptors (HR), amplification or overexpression of HER2, or a triple-negative phenotype. The most aggressive cases of IDC are characterized by a high proliferation rate, a great propensity to metastasize, and their ability to resist to standard chemotherapy, hormone therapy, or HER2-targeted therapy. Using progression tissue microarrays, we here demonstrate that the serine/threonine kinase protein kinase D3 (PKD3) is highly upregulated in estrogen receptor (ER)–negative (ER−) tumors. We identify direct binding of the ER to the PRKD3 gene promoter as a mechanism of inhibition of PKD3 expression. Loss of ER results in upregulation of PKD3, leading to all hallmarks of aggressive IDC, including increased cell proliferation, migration, and invasion. This identifies ER− breast cancers as ideal for treatment with the PKD inhibitor CRT0066101. We show that similar to a knockdown of PKD3, treatment with this inhibitor targets all tumorigenic processes in vitro and decreases growth of primary tumors and metastasis in vivo. Our data strongly support the development of PKD inhibitors for clinical use for ER− breast cancers, including the triple-negative phenotype. Mol Cancer Ther; 14(6); 1306–16. ©2015 AACR.