Prostate-specific antigen level, stage or Gleason score: which is best for predicting outcomes after radical prostatectomy, and does it vary by the outcome being measured? Results from Shared Equal Access Regional Cancer Hospital database
OBJECTIVES: To assess the ability of preoperative prostate-specific antigen level, Gleason score and stage to predict prostate cancer outcomes beyond biochemical recurrence, specifically castration-resistant prostate cancer, metastases and prostate cancer-specific mortality in radical prostatectomy patients.
METHODS: We carried out a retrospective study of 2735 men in the Shared Equal Access Regional Cancer Hospital database treated by radical prostatectomy from 1988 to 2011 with data available on pathological stage, grade and preoperative prostate-specific antigen. We used Cox hazards analyses to examine the predictive accuracy (c-index) of the preoperative prostate-specific antigen (log-transformed), path Gleason score ( < /= 7, 3 + 4, 4 + 3 and 8-10) and path stage grouping (pT2 negative margins; pT2 positive margins; pT3a negative margins; pT3a positive margins; pT3b; vs positive nodes) to predict biochemical recurrence, castration-resistant prostate cancer, metastases and prostate cancer-specific mortality.
RESULTS: Median follow up was 8.7 years, during which, 937 (34%) had biochemical recurrence, 108 (4%) castration-resistant prostate cancer, 127 (5%) metastases and 68 (2%) prostate cancer-specific mortality. For the outcomes of biochemical recurrence, castration-resistant prostate cancer, metastases and prostate cancer-specific mortality, the c-indices were, respectively: prostate-specific antigen 0.65, 0.66, 0.64 and 0.69; Gleason score 0.66, 0.83, 0.76 and 0.85; and pathological stage group 0.69, 0.76, 0.72 and 0.80.
CONCLUSIONS: Gleason score can predict with very high accuracy prostate cancer-specific mortality in patients undergoing radical prostatectomy. Thus, Gleason score should be given more weight in nomograms to predict prostate cancer-specific mortality. Furthermore, men with a high Gleason score should be given special consideration for adjuvant treatment or referral to clinical trials because of a higher risk of prostate cancer-specific mortality.
OBJECTIVES: To determine whether PTEN status in prostate biopsy represents a predictor of intermediate and long-term oncological outcomes after radical prostatectomy, and whether PTEN status predicts response to androgen deprivation therapy.
METHODS: In a retrospective analysis of 77 men treated by radical prostatectomy who underwent diagnostic biopsy between 1992-2006, biopsy samples were stained for PTEN expression by the PREZEON assay with > 10% staining reported as positive. Cox proportional hazards and log-rank models were used to assess the correlation between PTEN loss and clinical outcomes.
RESULTS: During a median follow-up period after radical prostatectomy of 8.8 years, 39 men (51%) developed biochemical recurrence, four (5%) had castration-resistant prostate cancer, two (3%) had metastasis and two (3%) died from prostate cancer. PTEN loss was not significantly associated with biochemical recurrence (hazard ratio 2.1, 95% confidence interval 0.9-5.1, P = 0.10), but significantly predicted increased risk of castration-resistant prostate cancer, metastasis and prostate cancer-specific mortality (all log-rank, P < 0.0001), and time from androgen deprivation therapy to castration-resistant prostate cancer (log-rank, P = 0.003). No patient without PTEN loss developed metastases or died from prostate cancer.
CONCLUSIONS: PTEN loss at the time of biopsy seems to predict time to development of metastasis, prostate cancer-specific mortality and, for the first time, castration-resistant prostate cancer and response to androgen deprivation therapy after radical prostatectomy. If confirmed by larger studies, this would support the use of PTEN loss as an early marker of aggressive prostate cancer.
Inspiring careers in STEM and healthcare fields through medical simulation embedded in high school science education
The most effective ways to promote learning and inspire careers related to science, technology, engineering, and mathematics (STEM) remain elusive. To address this gap, we reviewed the literature and designed and implemented a high-fidelity, medical simulation-based Harvard Medical School MEDscience course, which was integrated into high school science classes through collaboration between medical school and K-12 faculty. The design was based largely on the literature on concepts and mechanisms of self-efficacy. A structured telephone survey was conducted with 30 program alumni from the inaugural school who were no longer in high school. Near-term effects, enduring effects, contextual considerations, and diffusion and dissemination were queried. Students reported high incoming attitudes toward STEM education and careers, and these attitudes showed before versus after gains (P < .05). Students in this modest sample overwhelmingly attributed elevated and enduring levels of impact on their interest and confidence in pursuing a science or healthcare-related career to the program. Additionally, 63% subsequently took additional science or health courses, 73% participated in a job or educational experience that was science related during high school, and 97% went on to college. Four of every five program graduates cited a health-related college major, and 83% offered their strongest recommendation of the program to others. Further study and evaluation of simulation-based experiences that capitalize on informal, naturalistic learning and promote self-efficacy are warranted.
The increasing volume of office-based medical and surgical procedures has fostered the emergence of office-based anesthesia (OBA), a subspecialty within ambulatory anesthesia. The growth of OBA has been facilitated by numerous trends, including innovations in medical and surgical procedures and anesthetic drugs, as well as improved provider reimbursement and greater convenience for patients. There is a lack of randomized controlled trials to determine how office-based procedures and anesthesia affect patient morbidity and mortality. As a result, studies on this topic are retrospective in nature. Some of the early literature broaches concerns about the safety of office-based procedures and anesthesia. However, more recent data have shown that care in ambulatory settings is comparable to hospitals and ambulatory surgery centers, especially when offices are accredited and their proceduralists are board-certified. Office-based suites can continue to enhance the quality of care that they deliver to patients by engaging in proper procedure and patient selection, provider credentialing, facility accreditation, and incorporating patient safety checklists and professional society guidelines into practice. These strategies aiming at patient morbidity and mortality in the office setting will be increasingly important as more states, and possibly the federal government, exercise regulatory authority over the ambulatory setting. We explore these trends, their implications for patient safety, strategies for minimizing patient complications and mortality in OBA, and future developments that could impact the field.
The novel organic arsenical darinaparsin induces MAPK-mediated and SHP1-dependent cell death in T-cell lymphoma and Hodgkin lymphoma cells and human xenograft models
PURPOSE: Darinaparsin (Zio-101) is a novel organic arsenical compound with encouraging clinical activity in relapsed/refractory T-cell lymphoma (TCL) and Hodgkin lymphoma (HL); however, little is known about its mechanism of action.
EXPERIMENTAL DESIGN: TCL cell lines (Jurkat, Hut78, and HH) and HL cell lines (L428, L540, and L1236) were examined for in vitro cell death by MTT assay and Annexin V-based flow cytometry. Jurkat and L540-derived xenografts in SCID mice were examined for in vivo tumor inhibition and survival. Biologic effects of darinaparsin on the MAPK pathway were investigated using pharmacologic inhibitors, RNAi and transient transfection for overexpression for SHP1 and MEK.
RESULTS: Darinaparsin treatment resulted in time- and dose-dependent cytotoxicity and apoptosis in all TCL and HL cell lines. In addition, darinaparsin had more rapid, higher, and sustained intracellular arsenic levels compared with arsenic trioxide via mass spectrometry. In vivo experiments with Jurkat (TCL) and L540 (HL)-derived lymphoma xenografts showed significant inhibition of tumor growth and improved survival in darinaparsin-treated SCID mice. Biologically, darinaparsin caused phosphorylation of ERK (and relevant downstream substrates) primarily by decreasing the inhibitory SHP1 phosphatase and coimmunoprecipitation showed significant ERK/SHP1 interaction. Furthermore, ERK shRNA knockdown or constitutive overexpression of SHP1 resulted in increased apoptosis, whereas cotreatment with pharmacologic MEK inhibitors resulted in synergistic cell death. Conversely, SHP1 blockade (via pharmacologic inhibition or RNAi) and MEK constitutive activation decreased darinaparsin-related cell death.
CONCLUSIONS: Altogether, these data show that darinaparsin is highly active in HL and TCL and its activity is dependent primarily on MAPK mechanisms.
We compared (a) the effectiveness of print versus digital educational media for communicating information about Chlamydia trachomatis to adolescents and young adults and (b) the influence of media type on readiness for Chlamydia screening. Young men and women (n = 103), aged 15 to 24 years, were recruited from a youth center and university campus and randomized to receive the print or digital Chlamydia educational intervention. Participant mean knowledge score improved postintervention, but there was no association with type of intervention medium. Nearly two-thirds (61%) of sexually active participants endorsed an increased postintervention stage of readiness for screening; however, there was no association with type of intervention medium. Learning about Chlamydia infection may have positive effects on willingness to be screened. Further study is needed to evaluate the efficacy of educational interventions for increasing actual screening rates.
High glucose-induced downregulation of connexin 30.2 promotes retinal vascular lesions: implications for diabetic retinopathy
PURPOSE: To investigate whether high glucose (HG) alters expression of connexin 30.2 (Cx30.2) and influences gap junction intercellular communication (GJIC) in retinal endothelial cells and promotes vascular lesions characteristic of diabetic retinopathy (DR).
METHODS: Western blot analysis and immunostaining were performed to determine Cx30.2 protein expression and localization in rat retinal endothelial cells (RRECs) grown in normal (N; 5 mM) or HG (30 mM) medium for 7 days. Concurrently, GJIC was assessed in cells grown in N or HG medium and in cells transfected with Cx30.2 siRNA. Similarly, retinal Cx30.2 expression was assessed in nondiabetic and diabetic rats. Additionally, the effect of reduced Cx30.2 on development of acellular capillaries (ACs) and pericyte loss (PL) was studied in retinas of Cx30.2 knockout mice.
RESULTS: Cx30.2 was identified in RRECs in vitro and in vascular cells of retinal capillaries. RRECs grown in HG exhibited significantly reduced Cx30.2 protein levels consistent with decreased Cx30.2 immunostaining compared with those grown in N medium. Cells grown in HG and cells transfected with Cx30.2 siRNA exhibited significantly diminished dye transfer compared with N or nontransfected cells. Importantly, Cx30.2 protein level and immunostaining were decreased in diabetic retinas compared with nondiabetic retinas. Retinal capillaries of Cx30.2 knockout mice exhibited increased numbers of ACs and PL compared with those of wild-type mice.
CONCLUSIONS: These results indicate that HG- or diabetes-induced downregulation of Cx30.2 expression and decrease in GJIC activity play a critical role in the development of retinal vascular lesions in early DR.
Regional Consortium of Community-Engaged Researchers: Brainstorming for Gerontology Research Opportunities
Moderators: A. James Lee, PhD, Karen Devereaux Melillo, PhD, A-GNP-C, FAANP, FGSA, Co-Directors, UMass Lowell Center for Gerontology Research and Partnership; Deborah D’Avolio, Ph.D., BC-ACNP, ANP, Associate Professor, School of Nursing, Center for Gerontology Research and Partnership, Member
A.James Lee, PhD
Karen Devereaux Melillo
Center for Gerontology Research and Partnership Members
The Regional Consortium of Community-Engaged Gerontology Researchers was founded to expand opportunities for collaborative research, publication, and research funding. It was launched by the UMass Lowell Center for Gerontology Research and Partnerships in collaboration with the UMass CCTS Community Engagement and Research Section in 2013. Since then, the Regional Consortium has met annually at the UMCCTS Community Engagement and Research Symposium, and key recommendations and partnerships have resulted in sharing of resources and potential collaborations.
The purpose of this interactive breakout session is to expand the gerontology researcher network and brainstorm research ideas around community-engaged research opportunities. Utilizing a group facilitator, attendees will engage in dialogue about action steps, potential research collaborations, and funding opportunities.
Moderator: Robin A. Robinson, University of Massachusetts Dartmouth
The purpose of this interdisciplinary breakout session is to present several different approaches to the perception, creation, and implementation of community engaged research partnerships, and the range of funding sources that support them. Panelists will present brief descriptions of their projects and funding, followed by the UMass Dartmouth Research Development Manager’s insights and suggestions concerning the funding of successful matches of academic researchers and community research partners.
Session Presenters, Titles and Descriptions
Caitlin M. Stover, PhD, RN, PHCNS-BC, CNE, College of Nursing, Department of Community Nursing
Community Based Participatory Research with Community Health Workers of the Southcoast Region
My community partner and I had several ideas and projects that we wanted to work on together. To help organize our thoughts and deliverables, we applied for a spot in the first cohort of the Community Based Participatory Research Academy, a grant funded week-long course presented by the University Of Michigan School Of Public Health and the Detroit Urban Research Center. Spending a week with community engaged researchers and community leaders focused the academic-community partnership of UMass Dartmouth College of Nursing Assistant Professor Caitlin Stover and Community Leader Kathleen Murphy to promote the health of Southcoast region by mobilizing and building the capacity of Community Health Workers in the region. Monthly guided video conferences/workshops/virtual communications conducted by our assigned mentors (one community based mentor and one academic mentor) and the core of community engaged researchers assisted us in receiving a non-competitive Community Partnership Building Grant, creating and accomplishing short and long term goals, all while providing expert mentorship in applying the CBPR tenets to our work.
Andrea Klimt, PhD, College of Arts and Sciences, Department of Sociology & Anthropology
Pride of Place: The Potential of Collaborative Photography
The Fall River Portraits project brought together university sociology and anthropology students, local high school students, and senior citizens to photographically document the complex social realities of a small economically-struggling Massachusetts city. Project photographers documented the impact of decades of economic decline on the social fabric and built environment of this urban space as well as evidence of cultural vibrancy and resilience in the city’s various neighborhoods. The resulting visual narratives fostered a pride of place and hopeful sense of self-recognition amongst local residents and encouraged the thoughtful engagement with local realities of participating college students. This project was funded by the UMass President's Office, Creative Economy Award.
Christina Cipriano, PhD, College of Arts and Sciences, Department of Psychology
Class Interrupted: Improving Under-studied Classroom Environments
Funded by the William T. Grant Foundation and recently, the University of Massachusetts Dartmouth, the RELATE Project has been conducting systematic investigations of self-contained classrooms over the past four years across the Northeast. Towards the end of improving outcomes for students and educators in self-contained special education classrooms, we are advancing the science of classroom observation and improving the quality of educational experiences, one classroom at a time. To date, our work has resulted in a new psychometrically validated tool for evaluating effective interactions in these classrooms and an ecologically valid team-based professional development approach for teacher-paraeducator teams.
Robin A. Robinson, PhD, PsyD, College of Arts and Sciences, Department of Sociology & Anthropology
Psychological Foundations of Power and Relational Abuse Amongst Rural and Small-Town Teens
Initially funded by a pilot grant from the UMass Medical School CTSA-CER Pilot Program, and in community partnership with the Cape Cod Justice for Youth Collaborative and other member agencies of the Barnstable County Council for Children, Youth, and Families, this multi-stage project addressed the question: What are the conscious and unconscious psychological processes and power dynamics that explain behaviors associated with “teen dating violence”? The strong collaborative, and integrated, relationship that already existed between the PI and community partners contributed to the success of this pilot study, and facilitated new alliances amongst ancillary agencies. Collaborations has included regional organization of focus groups across Barnstable County (Cape Cod) to produce a data pool of first-person perspectives of teen relationships and violence in contexts of community challenges and supports. The work has considered diverse social and economic contexts as variable forces that affect psychological processes, to explore the psychology of teen relational abuse.
Mary Hensel, Research Development Manager, University of Massachusetts Dartmouth
Research Development Strategies for Community Engaged Research Partnerships
Chronic Pain Case Management in Opioid Patients: Improving Risk Management and Shifting Prescriber Behavior in a Rural Community Health Center
Andy Lowe, Director of Program Management Resources, Outer Cape Health Services
- Barbara K. Prazak, MD, Internal Medicine, Medical Director, Director of Clinical Quality Outer Cape Health Services
- Ellen Dennehy, PA-C, Physician Assistant, Family Medicine, Outer Cape Health Services
- Tina Rauch, RN, Registered Nurse, Family Medicine, Outer Cape Health Services
- Jennifer Eldredge, Medical Assistant, Family Medicine, Outer Cape Health Services
Outer Cape Health Services (OCHS) is an independent, federally-qualified health center with three locations in the outermost towns of Cape Cod, an area hit hard by the opiate epidemic of recent years. After years of updates to the OCHS Controlled Substance Policy and Procedure, Medical Director Dr. Barbara Prazak worked with the Director of Nursing to develop the Chronic Pain Case Management (CPCM) Program, to be implemented March 1, 2016. The CPCM program uses a team-based case management approach to monitoring patients on opioid prescriptions, with systematic tracking of patient data such as PEG scales, MEQ dosing, concurrent use of benzodiazepines, annual agreements, UDS and PMP checks and visit compliance, and regular provider-to-provider case reviews. While the CPCM program supports the primary care prescriber with consistent, data-based risk management and evaluation, it also aims to shift provider behavior and practices in opiate prescribing, towards an approach that is more collaborative, individualized to patients’ needs, and integrated with primary care. Through this breakout session, we will engage with other prescriber teams to learn about other team-based approaches to chronic pain case management, discuss best practices, and begin formulating issues that warrant research.
The post-translational modification of arginine residues represents a key mechanism for the epigenetic control of gene expression. Aberrant levels of histone arginine modifications have been linked to the development of several diseases including cancer. In recent years, great progress has been made in understanding the physiological role of individual arginine modifications and their effects on chromatin function. The present review aims to summarize the structural and functional aspects of histone arginine modifying enzymes and their impact on gene transcription. We will discuss the potential for targeting these proteins with small molecules in a variety of disease states.
Peptidylarginine Deiminase 3 (PAD3) Is Upregulated by Prolactin Stimulation of CID-9 Cells and Expressed in the Lactating Mouse Mammary Gland
Peptidylarginine deiminases (PADs) post-translationally convert arginine into neutral citrulline residues. Our past work shows that PADs are expressed in the canine and murine mammary glands; however, the mechanisms regulating PAD expression and the function of citrullination in the normal mammary gland are unclear. Therefore, the first objective herein was to investigate regulation of PAD expression in mammary epithelial cells. We first examined PAD levels in CID-9 cells, which were derived from the mammary gland of mid-pregnant mice. PAD3 expression is significantly higher than all other PAD isoforms and mediates protein citrullination in CID-9 cells. We next hypothesized that prolactin regulates PAD3 expression. To test this, CID-9 cells were stimulated with 5 mug/mL of prolactin for 48 hours which significantly increases PAD3 mRNA and protein expression. Use of a JAK2 inhibitor and a dominant negative (DN)-STAT5 adenovirus indicate that prolactin stimulation of PAD3 expression is mediated by the JAK2/STAT5 signaling pathway in CID-9 cells. In addition, the human PAD3 gene promoter is prolactin responsive in CID-9 cells. Our second objective was to investigate the expression and activity of PAD3 in the lactating mouse mammary gland. PAD3 expression in the mammary gland is highest on lactation day 9 and coincident with citrullinated proteins such as histones. Use of the PAD3 specific inhibitor, Cl4-amidine, indicates that PAD3, in part, can citrullinate proteins in L9 mammary glands. Collectively, our results show that upregulation of PAD3 is mediated by prolactin induction of the JAK2/STAT5 signaling pathway, and that PAD3 appears to citrullinate proteins during lactation.
Protein citrullination is a post-translational modification of arginine that is catalyzed by the Protein Arginine Deiminase (PAD) family of enzymes. Aberrantly increased citrullination is associated with a host of inflammatory diseases and cancer and PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis, lupus, atherosclerosis, and ulcerative colitis. In rheumatoid arthritis, citrullinated proteins serve as key antigens for rheumatoid arthritis-associated autoantibodies. These data suggest that citrullinated proteins may serve more generally as biomarkers of specific disease states, however, the identification of citrullinated residues remains challenging due to the small 1Da mass change that occurs upon citrullination. Herein, we highlight the available techniques to identify citrullinated proteins/residues focusing on advanced MS techniques as well as chemical derivatization strategies that are currently being employed to identify citrullinated proteins as well as the specific residues modified within those proteins.
Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the mechanisms of their formation and how they exert their regulatory effect on embedded genes. Further, similar domains have been detected in other organisms, including flies, worms, fungi and bacteria. Although in all these cases these domains appear similar as detected by 3C-based methods, their biology appears to be quite distinct with differences in the protein complexes involved in their formation and differences in their internal organization. Here we outline our current understanding of such domains in different organisms and their roles in gene regulation.
Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs. Stoichiometric metabolic network modeling integrated with "omics" data has addressed this challenge by generating nonintuitive, testable hypotheses about metabolic flux rewiring. Model organism studies have also yielded novel insight into metabolic networks. This review covers three topics: the feedback loops inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies utilizing Caenorhabditis elegans and various bacterial diets that have revealed novel metabolic paradigms.
Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus
Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation.
Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire
Early B cell development is characterized by large-scale Igh locus contraction prior to V(D)J recombination to facilitate a highly diverse Ig repertoire. However, an understanding of the molecular architecture that mediates locus contraction remains unclear. We have combined high-resolution chromosome conformation capture (3C) techniques with 3D DNA FISH to identify three conserved topological subdomains. Each of these topological folds encompasses a major VH gene family that become juxtaposed in pro-B cells via megabase-scale chromatin looping. The transcription factor Pax5 organizes the subdomain that spans the VHJ558 gene family. In its absence, the J558 VH genes fail to associate with the proximal VH genes, thereby providing a plausible explanation for reduced VHJ558 gene rearrangements in Pax5-deficient pro-B cells. We propose that Igh locus contraction is the cumulative effect of several independently controlled chromatin subdomains that provide the structural infrastructure to coordinate optimal antigen receptor assembly.
Oncogenes are activated through well-known chromosomal alterations, including gene fusion, translocation and focal amplification. Recent evidence that the control of key genes depends on chromosome structures called insulated neighborhoods led us to investigate whether proto-oncogenes occur within these structures and if oncogene activation can occur via disruption of insulated neighborhood boundaries in cancer cells. We mapped insulated neighborhoods in T-cell acute lymphoblastic leukemia (T-ALL), and found that tumor cell genomes contain recurrent microdeletions that eliminate the boundary sites of insulated neighborhoods containing prominent T-ALL proto-oncogenes. Perturbation of such boundaries in non-malignant cells was sufficient to activate proto-oncogenes. Mutations affecting chromosome neighborhood boundaries were found in many types of cancer. Thus, oncogene activation can occur via genetic alterations that disrupt insulated neighborhoods in malignant cells.
The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.
Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin fibers imposes a range of constraints on such communication. The molecular and biophysical mechanisms by which chromosomal communication is established, or prevented, have become a topic of intense study, and important roles for the spatial organization of chromosomes are being discovered. Here we present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other. We propose the existence of topological machines dedicated to set up and to exploit a 3D genome organization to both promote and censor communication along and between chromosomes.