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Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective

Levitis, Elizabeth ; van Praag, Cassandra D Gould ; Gau, Rémi ; [et al.]

Oxford University Press (OUP) ; 2021

In: GigaScience Vol. 10, No. 8 ( 2021-08-20)

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In: GigaScience, Oxford University Press (OUP), Vol. 10, No. 8 ( 2021-08-20)

Abstract: As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

Type of Medium: Online Resource

ISSN: 2047-217X

URL: Article

DOI: 10.1093/gigascience/giab051

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2021

detail.hit.zdb_id: 2708999-X

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An intrinsically disordered proteins community for ELIXIR

Davey, Norman E. ; Babu, M. Madan ; Blackledge, Martin ; [et al.]

F1000 Research Ltd ; 2019

In: F1000Research Vol. 8 ( 2019-10-15), p. 1753-

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In: F1000Research, F1000 Research Ltd, Vol. 8 ( 2019-10-15), p. 1753-

Type of Medium: Online Resource

ISSN: 2046-1402

URL: Journal

URL: Article

DOI: 10.12688/f1000research

DOI: 10.12688/f1000research.20136.1

Language: English

Publisher: F1000 Research Ltd

Publication Date: 2019

detail.hit.zdb_id: 2699932-8

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morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring

Wagner, Ines ; Volkmer, Michael ; Sharan, Malvika ; [et al.]

Springer Science and Business Media LLC ; 2014

In: BMC Bioinformatics Vol. 15, No. 1 ( 2014-12)

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In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 15, No. 1 ( 2014-12)

Type of Medium: Online Resource

ISSN: 1471-2105

URL: Article

DOI: 10.1186/1471-2105-15-263

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2014

detail.hit.zdb_id: 2041484-5

SSG: 12

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A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins

Tawk, Caroline ; Sharan, Malvika ; Eulalio, Ana ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Scientific Reports Vol. 7, No. 1 ( 2017-08-24)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-08-24)

Abstract: Many pathogenic bacteria utilize specialized secretion systems to deliver proteins called effectors into eukaryotic cells for manipulation of host pathways. The vast majority of known effector targets are host proteins, whereas a potential targeting of host nucleic acids remains little explored. There is only one family of effectors known to target DNA directly, and effectors binding host RNA are unknown. Here, we take a two-pronged approach to search for RNA-binding effectors, combining biocomputational prediction of RNA-binding domains (RBDs) in a newly assembled comprehensive dataset of bacterial secreted proteins, and experimental screening for RNA binding in mammalian cells. Only a small subset of effectors were predicted to carry an RBD, indicating that if RNA targeting was common, it would likely involve new types of RBDs. Our experimental evaluation of effectors with predicted RBDs further argues for a general paucity of RNA binding activities amongst bacterial effectors. We obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities. Our study presenting the first systematic evaluation of the RNA-targeting potential of bacterial effectors offers a basis for discussion of whether or not host RNA is a prominent target of secreted bacterial proteins.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-017-09527-0

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2615211-3

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Ten Simple Rules for Organizing an Unconference

Budd, Aidan ; Dinkel, Holger ; Corpas, Manuel ; [et al.]

Public Library of Science (PLoS) ; 2015

In: PLOS Computational Biology Vol. 11, No. 1 ( 2015-1-29), p. e1003905-

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In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 11, No. 1 ( 2015-1-29), p. e1003905-

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1003905

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2015

detail.hit.zdb_id: 2193340-6

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Ten simple rules for establishing a mentorship programme

Treasure, Anne M. ; Hall, Siobhan Mackenzie ; Lesko, Igor ; [et al.]

Public Library of Science (PLoS) ; 2022

In: PLOS Computational Biology Vol. 18, No. 5 ( 2022-5-12), p. e1010015-

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In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 18, No. 5 ( 2022-5-12), p. e1010015-

Abstract: In recent years, a wide variety of mentorship programmes targeting issues that cannot be addressed through traditional teaching and learning methods alone have been developed. Mentoring plays significant roles in the growth and development of both mentors and mentees, and the positive impacts of mentoring have been well documented. Mentorship programmes are therefore increasingly being implemented in a wide variety of fields by organisations, academic institutes, businesses, and governments. While there is a growing body of literature on mentoring and mentorship programmes, gaining a clear overview of the field is often challenging. In this article, we therefore provide a concise summary of recommendations to consider when designing and establishing mentorship programmes. These recommendations are based on the collective knowledge and experiences of 4 different emerging and established mentorship programmes and can be adapted across various mentorship settings or contexts.

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1010015

DOI: 10.1371/journal.pcbi.1010015.g001

DOI: 10.1371/journal.pcbi.1010015.t001

DOI: 10.1371/journal.pcbi.1010015.s001

DOI: 10.1371/journal.pcbi.1010015.s002

DOI: 10.1371/journal.pcbi.1010015.s003

DOI: 10.1371/journal.pcbi.1010015.s004

DOI: 10.1371/journal.pcbi.1010015.s005

DOI: 10.1371/journal.pcbi.1010015.s006

DOI: 10.1371/journal.pcbi.1010015.s007

DOI: 10.1371/journal.pcbi.1010015.s008

DOI: 10.1371/journal.pcbi.1010015.s009

DOI: 10.1371/journal.pcbi.1010015.s010

DOI: 10.1371/journal.pcbi.1010015.s011

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2022

detail.hit.zdb_id: 2193340-6

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Chlamydia preserves the mitochondrial network necessary for replication via microRNA-dependent inhibition of fission

Chowdhury, Suvagata Roy ; Reimer, Anastasija ; Sharan, Malvika ; [et al.]

Rockefeller University Press ; 2017

In: Journal of Cell Biology Vol. 216, No. 4 ( 2017-04-03), p. 1071-1089

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In: Journal of Cell Biology, Rockefeller University Press, Vol. 216, No. 4 ( 2017-04-03), p. 1071-1089

Abstract: Obligate intracellular bacteria such as Chlamydia trachomatis depend on metabolites of the host cell and thus protect their sole replication niche by interfering with the host cells’ stress response. Here, we investigated the involvement of host microRNAs (miRNAs) in maintaining the viability of C. trachomatis–infected primary human cells. We identified miR-30c-5p as a prominently up-regulated miRNA required for the stable down-regulation of p53, a major suppressor of metabolite supply in C. trachomatis–infected cells. Loss of miR-30c-5p led to the up-regulation of Drp1, a mitochondrial fission regulator and a target gene of p53, which, in turn, severely affected chlamydial growth and had a marked effect on the mitochondrial network. Drp1-induced mitochondrial fragmentation prevented replication of C. trachomatis even in p53-deficient cells. Additionally, Chlamydia maintain mitochondrial integrity during reactive oxygen species–induced stress that occurs naturally during infection. We show that C. trachomatis require mitochondrial ATP for normal development and hence postulate that they preserve mitochondrial integrity through a miR-30c-5p–dependent inhibition of Drp1-mediated mitochondrial fission.

Type of Medium: Online Resource

ISSN: 0021-9525 , 1540-8140

URL: Article

DOI: 10.1083/jcb.201608063

RVK:

WA 15000

Language: English

Publisher: Rockefeller University Press

Publication Date: 2017

detail.hit.zdb_id: 1421310-2

SSG: 12

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García-Betancur, Juan-Carlos ; Goñi-Moreno, Angel ; Horger, Thomas ; [et al.]

eLife Sciences Publications, Ltd ; 2017

In: eLife Vol. 6 ( 2017-09-12)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 6 ( 2017-09-12)

Abstract: While in hospital, patients can be unwittingly exposed to bacteria that can cause disease. These hospital-associated bacteria can lead to potentially life-threatening infections that may also complicate the treatment of the patients’ existing medical conditions. Staphylococcus aureus is one such bacterium, and it can cause several types of infection including pneumonia, blood infections and long-term infections of prosthetic devices. It is thought that S. aureus is able to cause so many different types of infection because it is capable of colonizing distinct tissues and organs in various parts of the body. Understanding the biological processes that drive the different infections is crucial to improving how these infections are treated. S. aureus lives either as an independent, free-swimming cell or as part of a community known as a biofilm. These different lifestyles dictate the type of infection the bacterium can cause, with free-swimming cells producing toxins that contribute to intense, usually short-lived, infections and biofilms promoting longer-term infections that are difficult to eradicate. However, it is not clear how a population of S. aureus cells chooses to adopt a particular lifestyle and whether there are any environmental signals that influence this decision. Here, Garcia-Betancur et al. found that S. aureus populations contain small groups of cells that have already specialized into a particular lifestyle. These groups of cells collectively influence the choice made by other cells in the population. While both lifestyles will be represented in the population, environmental factors influence the numbers of cells that initially adopt each type of lifestyle, which ultimately affects the choice made by the rest of the population. For example, if the bacteria colonize a tissue or organ that contains high levels of magnesium ions, the population is more likely to form biofilms. In the future, the findings of Garcia-Betancur et al. may help us to predict how an infection may develop in a particular patient, which may help to diagnose the infection more quickly and allow it to be treated more effectively.

Type of Medium: Online Resource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.28023

DOI: 10.7554/eLife.28023.001

DOI: 10.7554/eLife.28023.002

DOI: 10.7554/eLife.28023.003

DOI: 10.7554/eLife.28023.004

DOI: 10.7554/eLife.28023.005

DOI: 10.7554/eLife.28023.006

DOI: 10.7554/eLife.28023.007

DOI: 10.7554/eLife.28023.008

DOI: 10.7554/eLife.28023.009

DOI: 10.7554/eLife.28023.010

DOI: 10.7554/eLife.28023.011

DOI: 10.7554/eLife.28023.012

DOI: 10.7554/eLife.28023.013

DOI: 10.7554/eLife.28023.016

DOI: 10.7554/eLife.28023.017

DOI: 10.7554/eLife.28023.018

DOI: 10.7554/eLife.28023.019

DOI: 10.7554/eLife.28023.014

DOI: 10.7554/eLife.28023.015

DOI: 10.7554/eLife.28023.020

DOI: 10.7554/eLife.28023.021

DOI: 10.7554/eLife.28023.022

DOI: 10.7554/eLife.28023.023

DOI: 10.7554/eLife.28023.024

DOI: 10.7554/eLife.28023.025

DOI: 10.7554/eLife.28023.026

DOI: 10.7554/eLife.28023.027

DOI: 10.7554/eLife.28023.030

DOI: 10.7554/eLife.28023.031

Language: English

Publisher: eLife Sciences Publications, Ltd

Publication Date: 2017

detail.hit.zdb_id: 2687154-3

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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Wibberg, Daniel ; Batut, Bérénice ; Belmann, Peter ; [et al.]

F1000 Research Ltd ; 2020

In: F1000Research Vol. 8 ( 2020-9-11), p. 1877-

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In: F1000Research, F1000 Research Ltd, Vol. 8 ( 2020-9-11), p. 1877-

Type of Medium: Online Resource

ISSN: 2046-1402

URL: Journal

URL: Article

DOI: 10.12688/f1000research

DOI: 10.12688/f1000research.20244.2

Language: English

Publisher: F1000 Research Ltd

Publication Date: 2020

detail.hit.zdb_id: 2699932-8

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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Wibberg, Daniel ; Batut, Bérénice ; Belmann, Peter ; [et al.]

F1000 Research Ltd ; 2019

In: F1000Research Vol. 8 ( 2019-11-7), p. 1877-

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In: F1000Research, F1000 Research Ltd, Vol. 8 ( 2019-11-7), p. 1877-

Type of Medium: Online Resource

ISSN: 2046-1402

URL: Journal

URL: Article

DOI: 10.12688/f1000research

DOI: 10.12688/f1000research.20244.1

Language: English

Publisher: F1000 Research Ltd

Publication Date: 2019

detail.hit.zdb_id: 2699932-8

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