Genomic Release Research Articles

Cadmium activates the innate immune system through the AIM2 inflammasome

Cadmium (Cd) is a widely used heavy metal and has recently been recognized as a possible source of human toxicity due to its ability to accumulate in organs. Accumulation of heavy metals has several adverse effects, including inducing inflammation, in multiple organs, such as the testis. However, how Cd ions are sensed by host cells and how tissue inflammation eventually occurs remains unclear. Here, we show that Cd activates the AIM2 inflammasome by mediating genomic DNA release into the cytoplasm after DNA damage via oxidative stress, to trigger IL-1β secretion and pyroptosis. Specifically, the toxicity effects induced by Cd in cells were prevented by melatonin, which served as an antagonist of oxidative stress. Accordingly, in a mouse model, Cd-induced inflammation in the testis and consequential male reproductive dysfunction were effectively reversed by melatonin. Thus, our results suggest a function of AIM2 in Cd-mediated testis inflammation and identify AIM2 as a major pattern recognition receptor in response to heavy metal Cd ions.

The Ubiquitin-Proteasome System Facilitates Membrane Fusion and Uncoating during Coronavirus Entry.

Although the involvement of the ubiquitin-proteasome system (UPS) in several coronavirus-productive infections has been reported, whether the UPS is required for infectious bronchitis virus (IBV) and porcine epidemic diarrhea virus (PEDV) infections is unclear. In this study, the role of UPS in the IBV and PEDV life cycles was investigated. When the UPS was suppressed by pharmacological inhibition at the early infection stage, IBV and PEDV infectivity were severely impaired. Further study showed that inhibition of UPS did not change the internalization of virus particles; however, by using R18 and DiOC-labeled virus particles, we found that inhibition of UPS prevented the IBV and PEDV membrane fusion with late endosomes or lysosomes. In addition, proteasome inhibitors blocked the degradation of the incoming viral protein N, suggesting the uncoating process and genomic RNA release were suppressed. Subsequently, the initial translation of genomic RNA was blocked. Thus, UPS may target the virus-cellular membrane fusion to facilitate the release of incoming viruses from late endosomes or lysosomes, subsequently blocking the following virus uncoating, initial translation, and replication events. Similar to the observation of proteasome inhibitors, ubiquitin-activating enzyme E1 inhibitor PYR-41 also impaired the entry of IBV, enhanced the accumulation of ubiquitinated proteins, and depleted mono-ubiquitin. In all, this study reveals an important role of UPS in coronavirus entry by preventing membrane fusion and identifies UPS as a potential target for developing antiviral therapies for coronavirus.

Performance of ImproGene cfDNA blood collection tubes for mutation analysis in cancer patients

With the widely application of liquid biopsy and the development of detection technology, the standardization of pre-analysis procedures is necessary. For controlling pre-analysis variation of circulating tumor DNA (ctDNA) in blood samples, the blood collection tubes for ctDNA preservation particularly contribute a lot. The objective of this study was to investigate whether ImproGene® Cell Free DNA Tube (ImproGene tube) can be used in sample collection, preservation and NGS based mutation detection for ctDNA. We investigated hemolysis and cell free DNA (cfDNA) concentration of blood samples stored in ImproGene tubes and detected β-actin, LINE1 and exogenous gene level by qPCR. We compared cfDNA and RNA quantity between samples in ImproGene tube and Streck Cell-Free DNA BCT® (Streck tube). And 10 gene mutations and three fusion mutations analysis were compared by sequencing. When stored at room temperature within 7 days in ImproGene tubes, blood samples had no visible hemolysis and the cfDNA concentration, levels of β-actin, LINE1 and exogenous gene remained stable which means no genomic DNA release and cfDNA was protected. There was no significant difference in cfDNA and RNA quantity between ImproGene tubes and Streck tubes. Furthermore, based on this limited data set, ImproGene tubes showed increased detection rates of low-level mutations. Therefore, ImproGene Cell Free DNA Tubes may have promising applications in sample collection, preservation and NGS based mutation detection for ctDNA by its good preservation performance.

Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri.

Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.

U.S. Federal Genomic Data Release and Access Policies

Researchers today have access to a vast aggregation of human and nonhuman genomic data, largely on an open access basis. According to the Joint Genome Institute’s Genomes OnLine Database (GOLD), data from more than 40,000 sequencing projects around the world, representing more than 375,000 different organisms, were publicly available to researchers as of July 2020. The availability of this tremendous public resource is due, in large part, to the data release policies developed a quarter century ago, toward the beginning of the Human Genome Project (HGP), which have been carried forward, in modified form, to the present. These policies impose requirements on both the generators of data (typically the sequencing centers and other laboratories conducting genetic experiments) and the users of that data (i.e., researchers who download and/or use it). This chapter, briefly outlines the history of such data release policies, particularly in the U.S. and with respect to human genomic data, and provides an overview of the obligations imposed on both data generators and data users.

Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region.

Influenza A viruses (IAVs) enter into cells by receptor-dependent endocytosis. Subsequently, conformational changes of haemagglutinin are triggered by low environmental pH and the N terminus of HA2 glycoprotein (gp) is inserted into the endosomal membrane, resulting in fusion pore formation and genomic vRNA release into the cytoplasm. However, the pH optimum of membrane fusion is host- and virus-specific and can have an impact on virus pathogenicity. We prepared mutants of neurotropic IAV A/WSN/33 (H1N1) with aa substitutions in HA2 gp at the site of HA1/HA2 interaction, namely T642H (HA2 numbering position 64, H1 numbering position HA407; referred to as mutant '64'), V662H ('66') (HA409); and a double mutant ('D') with two aa substitutions (T642H, V662H). These substitutions were hypothesized to influence the pH optimum of fusion. The pH optimum of fusion activity was measured by a luciferase assay and biological properties of viruses were monitored. The in vitro and in vivo replication ability and pathogenicity of mutants were comparable (64) or lower (66, D) than those of the wild-type virus. However, the HA2 mutation V662H and double mutation T642H, V662H shifted the fusion pH maximum to lower values (ranging from 5.1 to 5.3) compared to pH from 5.4 to 5.6 for the wild-type and 64 mutant. The decreased replication ability and pathogenicity of 66 and D mutants was accompanied by higher titres in late intervals post-infection in lungs, and viral RNA in brains compared to wild-type virus-infected mice. These results have implications for understanding the pathogenicity of influenza viruses.

Abstract 2758: Comparison of cell-free DNA blood collection tubes

Abstract Critical biomarkers such as cell-free DNA (cfDNA) derived from tumors and circulating tumor cells (CTCs) can be detected and analyzed from a simple blood draw. These analytes are fragile, prone to degradation, and present in extremely low quantities. Therefore, proper preservation of these analytes is necessary to ensure accuracy of test results. Several blood collection tubes are commercially available for cfDNA applications, and selecting the ideal blood collection tube for cfDNA impacts test results, sample collection logistics and costs. However, no comprehensive and systematic evaluation of performance among these tubes is available. This study evaluates five commercial blood collection tubes: LBgard™ Blood Tube (Biomatrica), Streck cfDNA BCT® (Streck), PAXgene Blood ccfDNA Tube (PreAnalytiX), Cell-Free DNA Collection Tube (Roche), and EDTA (BD). Healthy donor blood samples were collected in each tube type and incubated over several days at different temperatures. Total plasma DNA was subsequently isolated, and the yield, fold increase versus time 0 and quality of purified DNA were compared. cfDNA controls were also spiked into blood samples collected in each tube type and measured by droplet digital PCR to determine the mutant allele frequencies over time. Finally, the yield and quality of cfDNA isolated from stage IV colorectal cancer blood collected in LBgard Blood Tube, Streck cfDNA BCT and EDTA were compared. Additionally, the inhibition of hemolysis and CTC stabilization were also assessed. Our results show that LBgard Blood Tube, Streck cfDNA BCT, PAXgene ccfDNA Tube and Cell-Free DNA Collection Tube are superior to EDTA tubes in maintaining cfDNA yield and quality over 7 days at ambient temperature. LBgard Blood Tube out-performs all tested blood tubes in inhibiting genomic DNA release for the longest duration (14 days) and across the widest temperature range (4°C, 25°C and 37°C). LBgard Blood Tube shows equivalent inhibition of genomic DNA release to Streck cfDNA BCT for clinical samples, and both tubes out-perform EDTA blood tubes. LBgard Blood Tube also consistently shows better CTC stabilization and inhibition of hemolysis over Streck cfDNA BCT. This comprehensive and systematic study of blood collection tube performance provides a quantitative and exhaustive assessment of blood sample stability, allowing researchers to make informed decisions based on their sample stabilization needs. Citation Format: Cecille D. Browne, Margrith E. Mattmann, Marc J. Wycoco, Sheila N. Chen, Rajeswari Ravichandran, Joel Desharnais, Laura J. Varela, Jonathan D. Browne, Vasco Liberal, Florence Lee. Comparison of cell-free DNA blood collection tubes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2758. doi:10.1158/1538-7445.AM2017-2758

Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation.

The histone 3 lysine 9 methyltransferase Setdb1 is essential for both stem cell pluripotency and terminal differentiation of different cell types. To shed light on the roles of Setdb1 in these mutually exclusive processes, we used mouse skeletal myoblasts as a model of terminal differentiation. Ex vivo studies on isolated single myofibres showed that Setdb1 is required for adult muscle stem cells expansion following activation. In vitro studies in skeletal myoblasts confirmed that Setdb1 suppresses terminal differentiation. Genomic binding analyses showed a release of Setdb1 from selected target genes upon myoblast terminal differentiation, concomitant to a nuclear export of Setdb1 to the cytoplasm. Both genomic release and cytoplasmic Setdb1 relocalisation during differentiation were dependent on canonical Wnt signalling. Transcriptomic assays in myoblasts unravelled a significant overlap between Setdb1 and Wnt3a regulated genetic programmes. Together, our findings revealed Wnt-dependent subcellular relocalisation of Setdb1 as a novel mechanism regulating Setdb1 functions and myogenesis.

Cell-free DNA in maternal plasma and serum: A comparison of quantity, quality and tissue origin using genomic and epigenomic approaches

ObjectivesThe objectives of this study were to compare the concentrations, size profiles and major tissue contributors of cell-free DNA (cfDNA) in plasma and in serum. Design and methodsThirteen pregnant women in the third trimester were recruited for this study. We collected EDTA-plasma and serum samples using various collection tubes. We determined their cfDNA concentrations and fetal cfDNA fractions using a zinc-finger X (ZFX)/zinc-finger Y (ZFY) droplet digital polymerase chain reaction (ZFX/ZFY ddPCR) assay. We used paired-end massively parallel sequencing (MPS) to measure plasma and serum cfDNA sizes at single-base resolution. We deconvoluted the genome-wide bisulfite sequencing data with reference to the methylation profiles of different tissues. ResultsThe concentrations of cfDNA collected in Sarstedt Serum Z tubes were found to be significantly higher than those in Greiner Bio-One Vacuette® Z Serum Separator Clot Activator tubes or Vacuette® Z Serum Clot Activator tubes. The concentrations of fetal cfDNA were significantly reduced in samples collected in the Vacuette® serum collection tubes. Fetal cfDNA fractions were significantly reduced in all sera compared to plasma. MPS of serum cfDNA revealed a right shift of the size distributions compared to plasma. Methylation-based tissue mapping of serum cfDNA revealed an increase of cfDNA from neutrophils and B cells but not T cells. ConclusionsThe use of different serum collection tubes has a significant impact on serum cfDNA concentrations. This effect is likely mediated through the combined effect of genomic DNA release from white blood cells and DNA degradation or removal.

The synergy of berberine chloride and totarol against Staphylococcus aureus grown in planktonic and biofilm cultures.

Staphylococcus aureus (S. aureus) is commonly associated with hospital-acquired infections and is known to form biofilms. Bacteria inside biofilms display an increased resistance to chemotherapeutics and host immune defences. Efficient antibiotics or combination therapy are urgently needed to treat patients with biofilm-associated MRSA infections. The objective of the current study was to evaluate the in vitro antimicrobial activities of totarol alone or in combination with berberine chloride (BBR) against S. aureus grown in planktonic and biofilm cultures. The synergistic antimicrobial effects between BBR and totarol were observed in all tested strains grown in biofilms using a chequerboard microdilution method, with the fractional inhibitory concentration index values ranging from 0.125 to 0.375. No antagonistic activity was observed in any of the strains tested in suspension or biofilm cultures. The synergistic activity against S. aureus biofilms was also corroborated by confocal laser scanning microscopy and adhesion assays. Moreover, the present study demonstrated that combination BBR and totarol treatment effectively decreased the formation of S. aureus biofilms by affecting extracellular genomic DNA release and polysaccharide intercellular adhesin expression. Subsequently, real-time reverse transcriptase PCR analysis revealed that the combination of BBR and totarol effectively inhibited the transcription of the biofilm-related genes sarA, cidA and icaA. These results suggest that the combination of totarol and BBR is momentous for the further development of a therapy protocol against S. aureus biofilms.

Temporal expression ofagrB,cidA, andalsSin the early development ofStaphylococcus aureusUAMS-1 biofilm formation and the structural role of extracellular DNA and carbohydrates

Extracellular DNA (eDNA) is an important component of the extracellular polymeric substance matrix and is important in the establishment and persistence of Staphylococcus aureus UAMS-1 biofilms. The aim of the study was to determine the temporal expression of genes involved in early biofilm formation and eDNA production. We used qPCR to investigate expression of agrB, which is associated with secreted virulence factors and biofilm dispersal, cidA, which is associated with biofilm adherence and genomic DNA release, and alsS, which is associated with cell lysis, eDNA release and acid tolerance. The contribution of eDNA to the stability of the biofilm matrix was assessed by digesting with DNase I (Pulmozyme) and quantifying structure by confocal microscopy and comstat image analysis. AgrB expression initially increased at 24 h but then dramatically decreased at 72 h in an inverse relationship to biomass, supporting its role in regulating biofilm dispersal. cidA and alsS expression steadily increased over 72 h, suggesting that eDNA was an important component of early biofilm development. DNase I had no effect on biomass, but did cause the biofilms to become more heterogeneous. Carbohydrates in the matrix appeared to play an important role in structural stability.

Optimizing blood collection, transport and storage conditions for cell free DNA increases access to prenatal testing

ObjectivesFetal mutations and fetal chromosomal abnormalities can be detected by molecular analysis of circulating cell free fetal DNA (ccffDNA) from maternal plasma. This comprehensive study was aimed to investigate and verify blood collection and blood shipping conditions that enable Noninvasive Prenatal Testing. Specifically, the impact of shipping and storage on the stability and concentration of circulating cell-free DNA (ccfDNA) in Streck® Cell-Free DNA™ Blood Collection Tubes (Streck BCTs, Streck, Omaha NE). These BCTs were designed to minimize cellular degradation, and thus effectively prevent dilution of fetal ccf DNA by maternal genomic DNA, was evaluated. Design and methodsPeripheral venous maternal blood was collected into Streck BCTs to investigate four aspects of handling and processing conditions: (1) time from blood draw to plasma processing; (2) storage temperature; (3) mechanical stress; and (4) lot-to-lot tube variations. ResultsMaternal blood stored in Streck BCTs for up to 7days at ambient temperature provides stable concentrations of ccffDNA. The amount of fetal DNA did not change over a broad range of storage temperatures (4°C, 23°C, 37°C, 40°C), but the amount of total (largely maternal) DNA increased in samples stored at 23°C and above, indicating maternal cell degradation and genomic DNA release at elevated temperatures. Shipping maternal blood in Streck BCTs, did not affect sample quality. ConclusionsMaternal plasma DNA stabilized for 0 to 7days in Streck BCTs can be used for non-invasive prenatal molecular applications, when temperatures are maintained within the broad parameters assessed in this study.

Abstract 2592: Host dependency factors for binding and internalization of oncolytic Seneca Valley Virus

Abstract Background Seneca Valley Virus (SVV-001), an experimental oncolytic picornavirus, is the prototype member of the genus Senecavirus of the family Picornaviridae. SVV-001 is remarkable for its exquisite tumor selectivity for human cancers with neuroendocrine features including small cell lung carcinoma (SCLC) and numerous pediatric cancers while being non-cytotoxic in normal human cells in vitro and in vivo. The mechanism of tropism and neuroendocrine tumor specificity of SVV-001 has not been elucidated previously. Identification of host factors involved in infection would have immediate benefit for ongoing clinical trials by providing potential biomarker candidates to predict efficacy. Here we present data implicating α4 integrin as a key component of SVV-001 infection and demonstrating that the virus is dependent on caveloae for internalization and trafficking. Results Microarray analysis comparing permissive with non-permissive cell lines and membrane sub-proteome analysis of permissive H446 SCLC cells predict α4 integrin is a potential receptor candidate for SVV-001. To test SVV-001 dependency on α4 integrin, stable shRNA knockdown cell lines were generated from the permissive parental SCLC cell line H446. Viral infection was studied by single virus particle tracking, GFP reporter virus infection, and FACS analysis. α4 integrin knockdown cells showed reduced viral internalization and intracellular motility and were resistant to infection. Heterologous expression of human α4 integrin in chinese hamster ovary (CHO) cells significantly increased binding of fluorescently-labeled virus to the cell surface, but did not result in productive infection. Tracking of fluorescently-labeled SVV-001 in permissive cells expressing either clathrin-GFP, caveolin-1-GFP, or flotillin-1-GFP revealed a striking and long-lasting colocalization of internalized viral particles with caveolin-rich vesicles. Dependency on caveolin-1 for internalization was supported by results from pharmacological inhibition experiments. Pre-treatment of cells with nystatin, a cholesterol sequestration drug, resulted in a reduction in virus-induced cytopathic effect when compared to untreated cells. Stable shRNA caveolin-1 knockdown cells showed significantly reduced internalization, reduced infection by recombinant GFP reporter virus and significant impairment in SVV-001 genomic RNA release. Conclusions Defining the mechanism of tropism for SVV-001 is a key factor in successful clinical application. α4 integrin and caveolin-1 represent the first host cell factors identified in the mechanism of tropism of SVV-001 leading to a basic understanding of how the virus binds and enters permissive cells. These findings may have direct relevance for current clinical trials of SVV-001 in adult and pediatric settings and for development of second-generation derivatives of this agent. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2592.

VitisNet: “Omics” Integration through Grapevine Molecular Networks

BackgroundGenomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet).Methodology/Principal FindingsThe sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 “Metabolic”, 15 “Genetic Information Processing”, 12 “Environmental Information Processing”, 3 “Cellular Processes”, 21 “Transport”, and 80 “Transcription Factors”. The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment.Conclusions/SignificanceVitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage) and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome location can be accessed and downloaded from the VitisNet tab at http://vitis-dormancy.sdstate.org.

Modulation of eDNA Release and Degradation Affects Staphylococcus aureus Biofilm Maturation

Recent studies have demonstrated a role for Staphylococcus aureus cidA-mediated cell lysis and genomic DNA release in biofilm adherence. The current study extends these findings by examining both temporal and additional genetic factors involved in the control of genomic DNA release and degradation during biofilm maturation. Cell lysis and DNA release were found to be critical for biofilm attachment during the initial stages of development and the released DNA (eDNA) remained an important matrix component during biofilm maturation. This study also revealed that an lrgAB mutant exhibits increased biofilm adherence and matrix-associated eDNA consistent with its proposed role as an inhibitor of cidA-mediated lysis. In flow-cell assays, both cid and lrg mutations had dramatic effects on biofilm maturation and tower formation. Finally, staphylococcal thermonuclease was shown to be involved in biofilm development as a nuc mutant formed a thicker biofilm containing increased levels of matrix-associated eDNA. Together, these findings suggest a model in which the opposing activities of the cid and lrg gene products control cell lysis and genomic DNA release during biofilm development, while staphylococcal thermonuclease functions to degrade the eDNA, possibly as a means to promote biofilm dispersal.

Undergraduates as Science Museum Docents: Training Students to Be the Teachers Using Peer Led Team Learning

[ILLUSTRATION OMITTED] * The Genomic Revolution From June 2004 through January of 2005, the Fernbank Museum of Natural History in Atlanta hosted the traveling exhibit, The Genomic Revolution, described as the most comprehensive presentation on the complex subject of genomics. Originally created by the American Museum of Natural History, this exhibit presented cutting edge information on genetic research and how that knowledge is impacting decisions about our health, our food, and our stewardship of the natural world (The Genomic Revolution press release, 2004). In addition to displays featuring hands-on models, interactive stations, and short films, the exhibition also included a working laboratory where attendees could experience firsthand the techniques used in modern genetics research through short exercises in DNA extraction (see cover) and forensic analysis (Figure 1). Electronic polling stations were also placed throughout the exhibit space so visitors could voice their opinions on controversial scientific issues and compare their responses with the accumulated views of other attendees. By examining these scientific breakthroughs and their potential applications in areas like medicine, nutrition, and the legal system, visitors could evaluate their own reactions from scientific, technical, and socio-ethical perspectives. [FIGURE 1 OMITTED] As stated on its Web site, the mission of the Fernbank Museum is to inspire life-long learning of natural history through dynamic programming to encourage a greater appreciation of our planet and its people (http://www.fernbank.edu). The museum is typically self-guided but because of the complexity of the topic and the functional lab within the exhibit, it was decided to staff The Genomic Revolution with a team of paid undergraduate interns. A docent (derived from the latin word docere meaning to teach) serves as a bridge between the museum and the attendees, acting as the face and voice of the collection and interpreting it for the visitors (Chin, 1995). Consequently it's a challenging job requiring a person to act as an educator, a public speaker, and a leader. The museum directors felt that undergraduate science majors would make especially effective candidates for this exhibit because of their backgrounds in the discipline, enthusiasm for the subject matter, and good communication skills. Exhibit interpreters have been shown to promote a more effective learning experience when used in science museums (Stronck, 1983). Additionally, at least one report has described greater student and teacher satisfaction with student docents compared with their adult counterparts, based on their interactions with elementary school groups (Cox-Peterson & Ramirez, 2001). The Fernbank Museum of Natural History partnered with the Center for Behavioral Neuroscience (a consortium of eight colleges and universities focused on neurobiology research and education [http://www.cbn-atl.org]) to enlist and train undergraduate students as docents for The Genomic Revolution. Undergraduate students were recruited from schools in the metropolitan Atlanta area, including the Georgia Institute of Technology, Emory University, and Spellman College. Eight of the nine students in the program were science majors (biology, neuroscience, biomedical engineering), ranging from sophomores to recently-graduated seniors, and all but one had previously taken at least some coursework in genetic fundamentals. Also, students were required to have at least a 3.0 GPA. From this group, two classes of docents were formed to staff the duration of the exhibit: one group of five students covering the summer to early fall, and a second group of four students covering the fall through the winter. * Undergraduate Docent Training Our challenge was to create a docent training program that would cover the genetic principles in the exhibit along with the communication and leadership techniques needed for their interpretation in a museum setting. …

Extracellular DNA Chelates Cations and Induces Antibiotic Resistance in Pseudomonas aeruginosa Biofilms

Biofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of DNA, bacterial polysaccharides and proteins, which are up to 1000-fold more antibiotic resistant than planktonic cultures. To date, extracellular DNA has been shown to function as a structural support to maintain Pseudomonas aeruginosa biofilm architecture. Here we show that DNA is a multifaceted component of P. aeruginosa biofilms. At physiologically relevant concentrations, extracellular DNA has antimicrobial activity, causing cell lysis by chelating cations that stabilize lipopolysaccharide (LPS) and the outer membrane (OM). DNA-mediated killing occurred within minutes, as a result of perturbation of both the outer and inner membrane (IM) and the release of cytoplasmic contents, including genomic DNA. Sub-inhibitory concentrations of DNA created a cation-limited environment that resulted in induction of the PhoPQ- and PmrAB-regulated cationic antimicrobial peptide resistance operon PA3552–PA3559 in P. aeruginosa. Furthermore, DNA-induced expression of this operon resulted in up to 2560-fold increased resistance to cationic antimicrobial peptides and 640-fold increased resistance to aminoglycosides, but had no effect on β-lactam and fluoroquinolone resistance. Thus, the presence of extracellular DNA in the biofilm matrix contributes to cation gradients, genomic DNA release and inducible antibiotic resistance. DNA-rich environments, including biofilms and other infection sites like the CF lung, are likely the in vivo environments where extracellular pathogens such as P. aeruginosa encounter cation limitation.

Estrogen, cognition and female ageing

Starting from fetal life, estrogens are crucial in determining central gender dimorphism, and an estrogen-induced synaptic plasticity is well evident during puberty and seasonal changes as well as during the ovarian cycle. Estrogens act on the central nervous system (CNS) both through genomic mechanisms, modulating synthesis, release and metabolism of neurotransmitters, neuropeptides and neurosteroids, and through non-genomic mechanisms, influencing electrical excitability, synaptic function and morphological features. Therefore, estrogen's neuroactive effects are multifaceted and encompass a system that ranges from the chemical to the biochemical to the genomic mechanisms, protecting against a wide range of neurotoxic insults. Clinical evidences show that, during the climacteric period, estrogen withdrawal in the limbic system gives rise to modifications in mood, behaviour and cognition and that estrogen administration is able to improve mood and cognitive efficiency in post-menopause. Many biological mechanisms support the hypothesis that estrogens might protect against Alzheimer's disease (AD) by influencing neurotransmission, increasing cerebral blood flow, modulating growth proteins associated with axonal elongation and blunting the neurotoxic effects of beta-amyloid. On the contrary, clinical studies of estrogen replacement therapy (ERT) and cognitive function have reported controversial results, indicating a lack of efficacy of estrogens on cognition in post-menopausal women aged >or=65 years. These findings suggest the presence of a critical period for HRT-related neuroprotection and underlie the potential importance of early initiation of therapy for cognitive benefit. In this review, we shall first describe the multiple effects of steroids in the nervous system, which may be significant in the ageing process. A critical update of HRT use in women and a discussion of possible prospectives for steroid use are subsequently proposed.

Endocrinology of Menopausal Transition and Its Brain Implications

The central nervous system is one of the main target tissues for sex steroid hormones, which act on both through genomic mechanisms, modulating synthesis, release, and metabolism of many neuropeptides and neurotransmitters, and through non-genomic mechanisms, influencing electrical excitability, synaptic function, morphological features, and neuron-glia interactions. During the climacteric period, sex steroid deficiency causes many neuroendocrine changes. At the hypothalamic level, estrogen withdrawal gives rise to vasomotor symptoms, to eating behavior disorders, and altered blood pressure control. On the other hand, at the limbic level, the changes in serotoninergic, noradrenergic, and opioidergic tones contribute to the modifications in mood, behavior, and nociception. Hormone replacement therapy (HRT) positively affects climateric depression throughout a direct effect on neural activity and on the modulation of adrenergic and serotoninergic tones and may modulate the decrease in cognitive efficiency observed in climaterium. The identification of the brain as a de novo source of neurosteroids, suggests that the modifications in mood and cognitive performances occurring in postmenopausal women may also be related to a change in the levels of neurosteroids. These findings open new perspectives in the study of the effects of sex steroids on the central nervous system and on the possible use of alternative and/or auxiliary HRT.

Benchmarking the CATMA Microarray. A Novel Tool forArabidopsis Transcriptome Analysis

Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.