Sarvenaz Sarabipour's research while affiliated with Johns Hopkins University and other places

Publications (60)

Preprint
Full-text available
Mentorship is vital for early career researchers in training positions, allowing them to navigate the challenges of work and life in research environments. However, the quality of mentorship received by trainees can vary by investigator and by institution. One challenge faced by those hoping to improve trainee mentorship is that the extent to which...
Preprint
Full-text available
Faculty at research institutions play a central role in advancing knowledge and careers, as well as promoting the well-being of students and colleagues in research environments. Faculty members must balance a host of activities - such as performing research, teaching, sourcing funds, administrative and service duties - with their roles as educators...
Preprint
Full-text available
The vascular endothelial growth factor (VEGF) family of cytokines are key drivers of blood vessel growth and remodeling. These ligands act via multiple VEGF receptors (VEGFR) and co-receptors such as Neuropilin (NRP) expressed on endothelial cells. These membrane-associated receptors are not solely expressed on the cell surface, they move between t...
Article
Full-text available
The SARS‐CoV‐2 pandemic has significantly impacted global health. Research on viral mechanisms, highly effective vaccines, and other therapies is in progress. Neuropilins have recently been identified as host cell receptors enabling viral fusion. Here, we provide context to Neuropilin’s tissue‐specific role in infection and the potential impact of...
Article
Mentorship is experience and/or knowledge‐based guidance. Mentors support, sponsor and advocate for mentees. Having one or more mentors when you seek advice can significantly influence and improve your research endeavours, well‐being and career development. Positive mentee–mentor relationships are vital for maintaining work–life balance and success...
Article
Full-text available
Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We syste...
Article
Full-text available
Securing research funding is a challenge faced by most scientists in academic institutions worldwide. Funding success rates for all career stages are low, but the burden falls most heavily on early career researchers (ECRs). These are young investigators in training and new principal investigators who have a shorter track record. ECRs are dependent...
Article
Full-text available
Conferences are a pivotal part of the scientific enterprise, but large in-person meetings have several disadvantages. As the pandemic experience has shown, online meetings are a viable alternative. Accelerating efforts to improve conferences in virtual formats can lead to a more equitable and sustainable conference culture.
Article
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Writing recommendation letters on behalf of students and other early-career researchers is an important mentoring task within academia. An effective recommendation letter describes key candidate qualities such as academic achievements, extracurricular activities, outstanding personality traits, participation in and dedication to a particular discip...
Article
Full-text available
Scientific conferences have an important role in the exchange of ideas and knowledge within the scientific community. Conferences also provide early-career researchers with opportunities to make themselves known within their field of research. Although the COVID-19 pandemic has brought traditional in-person conferences to a halt for the foreseeable...
Preprint
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Reproducibility is a cornerstone of the scientific method and sets apart science from pseudoscience. Unfortunately, a majority of scientists have experienced difficulties in reproducing their own or someone else’s results. This inability to confirm scientific findings negatively impacts individual scientists, funding bodies, academic journals, phar...
Preprint
Full-text available
Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We syste...
Preprint
Securing research funding is a challenge faced by most scientists in academic institutions worldwide. Funding success rates for all career stages are low, but the burden falls most heavily on early career researchers (ECRs) - young investigators in training and new principal investigators - who have a shorter track record and are dependent on fundi...
Article
Full-text available
Many postdoctoral researchers apply for faculty positions knowing relatively little about the hiring process or what is needed to secure a job offer. To address this lack of knowledge about the hiring process we conducted a survey of applicants for faculty positions: the survey ran between May 2018 and May 2019, and received 317 responses. We analy...
Article
Full-text available
Many postdoctoral researchers apply for faculty positions knowing relatively little about the hiring process or what is needed to secure a job offer. To address this lack of knowledge about the hiring process we conducted a survey of applicants for faculty positions: the survey ran between May 2018 and May 2019, and received 317 responses. We analy...
Article
Full-text available
Many postdoctoral researchers apply for faculty positions knowing relatively little about the hiring process or what is needed to secure a job offer. To address this lack of knowledge about the hiring process we conducted a survey of applicants for faculty positions: the survey ran between May 2018 and May 2019, and received 317 responses. We analy...
Preprint
Full-text available
Scientific conferences provide valuable opportunities for researchers across career stages and disciplines to present their latest work and to network with their peers. The advent of the internet has opened new possibilities for interaction, collaboration and networking, yet the uptake of tools enabling remote participation at scientific meetings h...
Article
Full-text available
The need to protect public health during the current COVID-19 pandemic has necessitated conference cancellations on an unprecedented scale. As the scientific community adapts to new working conditions, it is important to recognize that some of our actions may disproportionately affect early-career researchers and scientists from countries with limi...
Preprint
Full-text available
Many postdoctoral fellows in the STEM fields enter the academic job market with little knowledge of the process and expectations, and without any means to assess their qualifications relative to the general applicant pool. Demystifying this process is critical, as there is little information publicly available. In this work, we provide insight into...
Article
Full-text available
Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays...
Preprint
Full-text available
Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent, public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays...
Preprint
Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent, public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays...
Article
Many cellular signaling pathways are initiated by cell‐surface ligand‐sensing complexes that incorporate not just one but multiple receptors. Most studies focus on receptors co‐expressed on a single cell (cis interactions), but complexes containing receptors on adjacent cells (trans interactions) are also possible. Recent work by Morin et al publis...
Article
Full-text available
We disagree with Tom Sheldon’s contention that the preprint ecosystem can present a challenge to accurate and timely journalism (Nature 559, 445; 2018). Restricting when or how preprints are released risks suppressing science communication without any clear advantage to the public. When scientists and journalists follow fundamental principles for r...
Preprint
Full-text available
The timely and accurate dissemination of scientific discoveries is of utmost importance so that scientific knowledge can be advanced and applied to benefit the public. Scientists communicate amongst themselves at conferences, via journal articles, and, increasingly in the life sciences, in preprint manuscripts which have not been subject to peer re...
Preprint
Full-text available
The timely and accurate dissemination of scientific discoveries is of utmost importance so that scientific knowledge can be advanced and applied to benefit the public. Scientists communicate amongst themselves at conferences, via journal articles, and, increasingly in the life sciences, in preprint manuscripts which have not been subject to peer re...
Article
Full-text available
All known splice isoforms of vascular endothelial growth factor A (VEGF-A) can bind to the receptor tyrosine kinases VEGFR-1 and VEGFR-2. We focus here on VEGF-A121a and VEGF-A165a, two of the most abundant VEGF-A splice isoforms in human tissue¹ Kut C, Mac Gabhann F, Popel AS. Where is VEGF in the body? A meta-analysis of VEGF distribution in canc...
Article
Receptor tyrosine kinase (RTK) signal transduction is essential in human skeletal, nervous, and vascular development, in homeostasis, and in disease. RTKs are activated by dimerization in the plasma membrane. The mechanisms of receptor dimerization and activation are multifaceted and complex, and unraveling them remains challenging. Most studies of...
Article
Epithelial cadherin (Ecadherin) is responsible for the intercellular cohesion of epithelial tissues. It forms lateral clusters within adherens cell–cell junctions, but its association state outside these clusters is unknown. Here we use a quantitative FRET approach to show that Ecadherin forms constitutive dimers, and that these dimers exist indepe...
Article
Full-text available
The activity of receptor tyrosine kinases (RTKs) is controlled through their lateral dimerization in the plasma membrane. RTKs are believed to form both homodimers and heterodimers, and the different dimers are believed to play unique roles in cell signaling. However, RTK heterodimers remain poorly characterized, as compared to homodimers, due to l...
Article
Missense mutations which introduce or remove cysteine residues in receptor tyrosine kinases (RTKs) are believed to cause pathologies by stabilizing the active RTK dimers. However, the magnitude of this stabilizing effect has not been measured for full-length receptors. Here, we characterize the dimer stabilities of three full-length fibroblast grow...
Article
ELife digest New blood vessels form by growing out from existing vessels. A signaling molecule called VEGF is crucial for this process and binds to a receptor protein known as VEGFR-2. This binding activates signaling events within the cells that line the blood vessels to promote the growth of new vessels. VEGFR-2 belongs to a family of proteins ca...
Article
The G380R mutation in the transmembrane domain of FGFR3 is a germline mutation responsible for most cases of Achondroplasia, a common form of human dwarfism. Here we use quantitative Fӧster Resonance Energy Transfer (FRET) and osmotically derived plasma membrane vesicles to study the effect of the Achondroplasia mutation on the early stages of FGFR...
Article
Receptor tyrosine kinase (RTK) heterodimers are necessary for proper cell function and have properties unique from those of the better-studied homodimer. However, the heterodimer species’ propensity for formation and physicochemical properties remain largely unknown, because traditional methods struggle to distinguish between hetero- and homo-dimer...
Data
Supplementary Figures 1-11, Supplementary Table 1 and Supplementary References
Article
Full-text available
Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increa...
Article
Here we describe an experimental tool, termed quantitative imaging Förster resonance energy transfer (QI-FRET), that enables the quantitative characterization of membrane protein interactions. The QI-FRET methodology allows us to acquire binding curves and calculate association constants for complex membrane proteins in the native plasma membrane e...
Article
Plasma membrane-derived vesicles are being used in biophysical and biochemical research as a simple, yet native-like model of the cellular membranes. Here we report on the characterization of vesicles produced via two different vesiculation methods from CHO and A431 cell lines. The first method is a recently developed method which utilizes chloride...
Data
Representative curves of steady-state kinetic analyses for each IGF1R protein characterized.Each data point was performed in duplicate and is shown separately.DOI: http://dx.doi.org/10.7554/eLife.03772.022
Data
Full-text available
Enzyme behavior is linear with respect to enzyme concentration.Velocity (nM of product/min) plotted vs enzyme concentration (nM) for each IGF1R protein investigated.DOI: http://dx.doi.org/10.7554/eLife.03772.024
Data
Full-text available
Enzyme behavior is linear with respect to time.Product/Enzyme plotted vs time (minutes) for each IGF1R protein investigated.DOI: http://dx.doi.org/10.7554/eLife.03772.023
Article
Full-text available
Förster resonance energy transfer (FRET) experiments are often used to study interactions between integral membrane proteins in cellular membranes. However, in addition to the FRET of sequence-specific interactions, these experiments invariably record a contribution due to proximity FRET, which occurs when a donor and an acceptor approach each othe...
Article
Fö rster resonance energy transfer (FRET) experiments are often used to study interactions between integral membrane proteins in cellular membranes. However, in addition to the FRET of sequence-specific interactions, these experiments invariably record a contribution due to proximity FRET, which occurs when a donor and an acceptor approach each oth...
Article
Fibroblast growth factor receptor 3 (FGFR3) is a receptor tyrosine kinase which resides in the plasma membrane and regulates cell survival, differentiation and angiogenesis. Fibroblast growth factors (fgfs) are a family of secreted protein ligands which bind to FGFRs to potentiate signaling. FGFR3 functions via lateral dimerization in the cellular...
Article
Isolated receptor tyrosine kinase transmembrane (TM) domains have been shown to form sequence-specific dimers in membranes. Yet, it is not clear whether studies of isolated TM domains yield knowledge that is relevant to full-length receptors or whether the large glycosylated extracellular domains alter the interactions between the TM helices. Here,...
Article
Membrane protein interactions, which underlie biological function, take place in the complex cellular membrane environment. Plasma membrane derived vesicles are a model system which allows the interactions between membrane proteins to be studied without the need for their extraction, purification, and reconstitution into lipid bilayers. Plasma memb...
Article
There are no direct quantitative measurements of hydrogen bond strengths in membrane proteins residing in their native cellular environment. To address this knowledge gap, here we use fluorescence resonance energy transfer (FRET) to measure the impact of hydrogen bonds on the stability of a membrane protein dimer in vesicles derived from eukaryotic...
Data
Western Blot band intensities as a function of FGFR3 loading. (A): anti-FGFR3 antibodies. (B): anti-P-Y653/4 antibodies. (TIF)
Article
Full-text available
The A391E mutation in fibroblast growth factor receptor 3 (FGFR3) is the genetic cause for Crouzon syndrome with Acanthosis Nigricans. Here we investigate the effect of this mutation on FGFR3 activation in HEK 293 T cells over a wide range of fibroblast growth factor 1 concentrations using a physical-chemical approach that deconvolutes the effects...
Article
Guidelines for submitting commentsPolicy: Comments that contribute to the discussion of the article will be posted within approximately three business days. We do not accept anonymous comments. Please include your email address; the address will not be displayed in the posted comment. Cell Press Editors will screen the comments to ensure that they...
Article
Receptor Tyrosine kinases (RTKs) are family of single-pass cell membrane receptors with extracellular ligand-binding domains and intracellular kinase domains, which conduct biochemical signals via lateral dimerization in the plasma membrane. Mutations in the transmembrane (TM) domains of these receptors are known to promote unregulated signaling. A...

Citations

... It It is worth noting that, prior to the pandemic, concerns about the mental well-being of researchers were already evident. This community operates within a culture that places a premium on productivity at the potential expense of well-being, and it seems to have normalized a pattern of chronic stress and an imbalanced work-life equilibrium (Bartlett et al., 2021;Bekkouche et al., 2021;Guthrie et al., 2018). Their work hours consistently exceed the norm, encompassing increasingly diversified roles and responsibilities within a hypercompetitive job security landscape. ...
... The participation of transmembrane proteins as independent docking sites with virus fragments served to explain the tissue tropism of SARS-CoV-2: selective ligands of the host cell molecules act as infection cofactors, including membrane-bound serine protease TMPRSS2, furin, cathepsin L, basigin, and neuropilin-1 (NRP-1) (Coutard et al., 2020;Daly et al., 2020). One of the new players in the pathogenesis of COVID-19 is the neuropilin protein (Sarabipour and Mac Gabhann, 2021). ...
... Discussion of significant attributes of exemplary mentors from young research mentees with inclusion of a self-assessment for reflection [84] Discussion of ten important practices of award-winning mentors based in literature research [85] Curricula and training resources for entering mentorship for various research disciplines denoted by career stage of the mentee [86] Workshop recording from the NIH Becoming a Resilient Scientist series discussing various aspects to participating in a mentoring relationship, including running meetings, solving conflicts between members, work style differences, expansion of the mentorship network, and managing up [87] Self-assessment to evaluate six competencies of mentorship, including effective communication, aligning expectations, assessing understanding, addressing diversity, fostering independence, and promoting professional development [88] Provides guidance about conflict resolution in a mentored relationship with examples of how to manage interactions and suggestions for mentees to proactively promote beneficial dynamics [89] Creating protocols Details the format, structure, components, and considerations to include for a detailed research protocol with examples [59,90] Teaching R A step-by-step resource of how to teach R in a workshop style with common issues of first-time students, code examples and exercises, and teaching schedule [91] Teaching scientific writing & manuscript preparation Discussion of barriers of undergraduate publication and 5 best practices to successfully mentor students to first authorship [92] Article detailing the "Results Formula Approach" to teach students to write an effective Results section [93] Teaching resource that discusses the value of undergraduates publishing with decision trees to determine whether publishing is an attainable goal for the project, whether the student has earned authorship, and whether they should serve as first author. Also included are recommended strategies for publishing with undergraduates. ...
... Many pre-existing examples of this format are open access (e.g. repro4everyone; Auer et al., 2021;Boyle et al., 2023); therefore, we encourage readers to search for examples that are relevant to the course formats and topics that interest them. ...
... The actions highlighted here do not aim to privilege minoritized groups over others, rather, they aim to provide an equitable platform, which allows everyone to fully participate in and lead marine research. There was discussion among the author group as to whether to advocate for positive discrimination, a position, which has been favoured in much of the literature and by a number of the author team (Manfredi, 2017;Gibson et al., 2020;de Winde et al., 2021;Llorens et al., 2021;Maas et al., 2021;Mori, 2021). Positive discrimination involves the use of "positive measures" or "special measures" to foster greater equality by supporting women and other minoritized groups who face, or have faced, entrenched discrimination, to ensure they have similar access to opportunities as others in the community (Australian Human Rights Commission, 2022). ...
... Re-assessing preparation for conferences is timely, given that in-person events are rapidly re-emerging. Innovations established due to COVID restrictions and now the climate challenges additionally spurred innovations in conferences formats, including new forms of poster sessions (Tao et al., 2021;Skiles et al., 2022) and as equity and inclusivity of traditional conference formats are being debated (Sarabipour et al., 2021), more innovations can be expected. Posters are now often presented both in-person and in virtual spaces, accompanied by poster-flash talks, or short recorded talks. ...
... Even if there is no page limit, aim for a concise letter of no more than two pages using 11-or 12-point Times New Roman or sans serif font. Long letters requiring the selection committee to search for the candidate's qualifications can be off-putting (Sarabipour et al., 2022). ...
... The audience was also quite diverse from new demographics, allowing participants to connect across borders and disciplines, noting that research and science are inherently transnational cross-border activities. Virtual conferences allow inclusive, accessible, and equitable meetings (Sarabipour, 2020). However, some challenges driven by systemic inequalities persisted, reducing the participation of under-represented communities (Olzmann, 2020). ...
... We expect a mentoring scheme within the CODECHECK community (experienced codecheckers will provide on-the-job training or serve as fall-back advisors). Codecheckers may also be found by collaborating with reproducible research initiatives such as ReproHack, ReproducibiliTea, 115 , and Repro4Everyone, 116 . ...
... For instance, OA uptake in business, management, and accounting fields is only 6% (Laakso & Björk, 2021), showing a low OA uptake in the Social Sciences (Piwowar et al., 2018). This may be a result of enduring opposition to OA by authors and publishers, lack of awareness, disciplinary norm or limited funding opportunities (de Winde et al., 2020;Eve, 2015). To analyze this further, a closer look at researchers' OA publishing practices in different stages of their careers is warranted. ...