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Q&A with Nonia Pariente, Editor-in-Chief, PLOS Biology
Speaking with Nonia Pariente, Editor-in-Chief, PLOS Biology about open science, new initiatives, and the future of the journal
published: 05 Jun 2020
-
PLOS Biology authors and protocols.io
PLOS has partnered with protocols.io. This video short includes Lenny Teytelman introducing protocols.io and we hear from the authors of two PLOS Biology research articles about their experience using protocols.io.
Credits:
Lenny Teytelman, Cofounder protocols.io
Zita Carvalho-Santos, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Ana Patrícia Francisco, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Carlos Ribeiro, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Zoya Ignatova, University of Hamburg, Germany
Speakers:
All speakers volunteered their participation. None were paid by PLOS.
Production:
João Gonçalo Camilo (Science Communication Office, Champalimaud Centre for the Unknown), Cam...
published: 04 May 2017
-
A Conversation with the Eisen Brothers - PLOS Biology Tenth Anniversary
In honor of PLOS Biology's 10th anniversary, PLOS Co-Founder Michael Eisen and PLOS Biology Advisory Board Chief Jonathan Eisen discuss the history and future of the journal and Open Access.
published: 22 Oct 2013
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PLoS Biology : Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic...
Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic Component of the Type III Secretion Injectisome. Andreas Diepold et al. (2015), PLoS Biology, http://dx.doi.org/10.1371/journal.pbio.1002039
Many gram-negative pathogens employ a type III secretion injectisome to translocate effector proteins into eukaryotic host cells. While the structure of the distal “needle complex” is well documented, the composition and role of the functionally important cytosolic complex remain less well understood. Using functional fluorescent fusions, we found that the C-ring, an essential and conserved cytosolic component of the system, is composed of ~22 copies of SctQ (YscQ in Yersinia enterocolitica), which require the presence of YscQC, the product of an internal translation initiation...
published: 24 Jan 2015
-
Video for PLoS Biology
Pathway modelling
published: 08 Jul 2016
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PLoS Biology : Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules...
Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules Accelerates Viral Adaptation at the Cell and Tissue Levels. Shuhei Miyashita et al (2015), PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1002094
Recent studies on evolutionarily distant viral groups have shown that the number of viral genomes that establish cell infection after cell-to-cell transmission is unexpectedly small (1–20 genomes). This aspect of viral infection appears to be important for the adaptation and survival of viruses. To clarify how the number of viral genomes that establish cell infection is determined, we developed a simulation model of cell infection for tomato mosaic virus (ToMV), a positive-strand RNA virus. The model showed that stochastic processes that govern the replication or degra...
published: 17 Mar 2015
-
Discovery report + update articles - PLOS Biology
PLOS Biology Discover Reports and subsequent Update Articles let researchers communicate scientific advances in a faster, more dynamic way that more naturally mirrors the research process.
published: 01 Mar 2021
-
PLoS Biology : Conformational Changes during Pore Formation by the Perforin-Related Protein...
Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin. Natalya Lukoyanova et al (2015), PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1002049
Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80...
published: 06 Feb 2015
-
PLoS Biology : A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using...
A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using an Interdisciplinary, Biophysical Approach. Karishma S. Kaushik et al. (2015), PLoS Biology, http://dx.doi.org/10.1371/journal.pbio.1002044
We have developed a hands-on experimental module that combines biology experiments with a physics-based analytical model in order to characterize antimicrobial compounds. To understand antibiotic resistance, participants perform a disc diffusion assay to test the antimicrobial activity of different compounds and then apply a diffusion-based analytical model to gain insights into the behavior of the active antimicrobial component. In our experience, this module was robust, reproducible, and cost-effective, suggesting that it could be implemented in diverse settings such as underg...
published: 21 Jan 2015
1:25
Q&A with Nonia Pariente, Editor-in-Chief, PLOS Biology
Speaking with Nonia Pariente, Editor-in-Chief, PLOS Biology about open science, new initiatives, and the future of the journal
Speaking with Nonia Pariente, Editor-in-Chief, PLOS Biology about open science, new initiatives, and the future of the journal
https://wn.com/Q_A_With_Nonia_Pariente,_Editor_In_Chief,_Plos_Biology
Speaking with Nonia Pariente, Editor-in-Chief, PLOS Biology about open science, new initiatives, and the future of the journal
- published: 05 Jun 2020
- views: 1789
3:57
PLOS Biology authors and protocols.io
PLOS has partnered with protocols.io. This video short includes Lenny Teytelman introducing protocols.io and we hear from the authors of two PLOS Biology resear...
PLOS has partnered with protocols.io. This video short includes Lenny Teytelman introducing protocols.io and we hear from the authors of two PLOS Biology research articles about their experience using protocols.io.
Credits:
Lenny Teytelman, Cofounder protocols.io
Zita Carvalho-Santos, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Ana Patrícia Francisco, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Carlos Ribeiro, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Zoya Ignatova, University of Hamburg, Germany
Speakers:
All speakers volunteered their participation. None were paid by PLOS.
Production:
João Gonçalo Camilo (Science Communication Office, Champalimaud Centre for the Unknown), Camera
Christine Polte (University of Hamburg), Camera
Alexei Stoliartchouk (Protocols.io), Camera and Production
Will Jackson (PLOS), Audio
https://wn.com/Plos_Biology_Authors_And_Protocols.Io
PLOS has partnered with protocols.io. This video short includes Lenny Teytelman introducing protocols.io and we hear from the authors of two PLOS Biology research articles about their experience using protocols.io.
Credits:
Lenny Teytelman, Cofounder protocols.io
Zita Carvalho-Santos, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Ana Patrícia Francisco, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Carlos Ribeiro, Behavior and metabolism laboratory, Champalimaud Centre for the Unknown, Lisbon
Zoya Ignatova, University of Hamburg, Germany
Speakers:
All speakers volunteered their participation. None were paid by PLOS.
Production:
João Gonçalo Camilo (Science Communication Office, Champalimaud Centre for the Unknown), Camera
Christine Polte (University of Hamburg), Camera
Alexei Stoliartchouk (Protocols.io), Camera and Production
Will Jackson (PLOS), Audio
- published: 04 May 2017
- views: 530
16:53
A Conversation with the Eisen Brothers - PLOS Biology Tenth Anniversary
In honor of PLOS Biology's 10th anniversary, PLOS Co-Founder Michael Eisen and PLOS Biology Advisory Board Chief Jonathan Eisen discuss the history and future o...
In honor of PLOS Biology's 10th anniversary, PLOS Co-Founder Michael Eisen and PLOS Biology Advisory Board Chief Jonathan Eisen discuss the history and future of the journal and Open Access.
https://wn.com/A_Conversation_With_The_Eisen_Brothers_Plos_Biology_Tenth_Anniversary
In honor of PLOS Biology's 10th anniversary, PLOS Co-Founder Michael Eisen and PLOS Biology Advisory Board Chief Jonathan Eisen discuss the history and future of the journal and Open Access.
- published: 22 Oct 2013
- views: 2138
0:59
PLoS Biology : Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic...
Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic Component of the Type III Secretion Injectisome. Andreas Diepold et al. (2015), PLoS B...
Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic Component of the Type III Secretion Injectisome. Andreas Diepold et al. (2015), PLoS Biology, http://dx.doi.org/10.1371/journal.pbio.1002039
Many gram-negative pathogens employ a type III secretion injectisome to translocate effector proteins into eukaryotic host cells. While the structure of the distal “needle complex” is well documented, the composition and role of the functionally important cytosolic complex remain less well understood. Using functional fluorescent fusions, we found that the C-ring, an essential and conserved cytosolic component of the system, is composed of ~22 copies of SctQ (YscQ in Yersinia enterocolitica), which require the presence of YscQC, the product of an internal translation initiation site in yscQ, for their cooperative assembly. Photoactivated localization microscopy (PALM) reveals that in vivo, YscQ is present in both a free-moving cytosolic and a stable injectisome-bound state. Notably, fluorescence recovery after photobleaching (FRAP) shows that YscQ exchanges between the injectisome and the cytosol, with a t½ of 68 ± 8 seconds when injectisomes are secreting. In contrast, the secretin SctC (YscC) and the major export apparatus component SctV (YscV) display minimal exchange. Under non-secreting conditions, the exchange rate of YscQ is reduced to t½ = 134 ± 16 seconds, revealing a correlation between C-ring exchange and injectisome activity, which indicates a possible role for C-ring stability in regulation of type III secretion. The stabilization of the C-ring depends on the presence of the functional ATPase SctN (YscN). These data provide new insights into the formation and composition of the injectisome and present a novel aspect of type III secretion, the exchange of C-ring subunits, which is regulated with respect to secretion.
Good channel: https://www.youtube.com/Dlium
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https://wn.com/Plos_Biology_Composition,_Formation,_And_Regulation_Of_The_Cytosolic_C_Ring,_A_Dynamic...
Composition, Formation, and Regulation of the Cytosolic C-ring, a Dynamic Component of the Type III Secretion Injectisome. Andreas Diepold et al. (2015), PLoS Biology, http://dx.doi.org/10.1371/journal.pbio.1002039
Many gram-negative pathogens employ a type III secretion injectisome to translocate effector proteins into eukaryotic host cells. While the structure of the distal “needle complex” is well documented, the composition and role of the functionally important cytosolic complex remain less well understood. Using functional fluorescent fusions, we found that the C-ring, an essential and conserved cytosolic component of the system, is composed of ~22 copies of SctQ (YscQ in Yersinia enterocolitica), which require the presence of YscQC, the product of an internal translation initiation site in yscQ, for their cooperative assembly. Photoactivated localization microscopy (PALM) reveals that in vivo, YscQ is present in both a free-moving cytosolic and a stable injectisome-bound state. Notably, fluorescence recovery after photobleaching (FRAP) shows that YscQ exchanges between the injectisome and the cytosol, with a t½ of 68 ± 8 seconds when injectisomes are secreting. In contrast, the secretin SctC (YscC) and the major export apparatus component SctV (YscV) display minimal exchange. Under non-secreting conditions, the exchange rate of YscQ is reduced to t½ = 134 ± 16 seconds, revealing a correlation between C-ring exchange and injectisome activity, which indicates a possible role for C-ring stability in regulation of type III secretion. The stabilization of the C-ring depends on the presence of the functional ATPase SctN (YscN). These data provide new insights into the formation and composition of the injectisome and present a novel aspect of type III secretion, the exchange of C-ring subunits, which is regulated with respect to secretion.
Good channel: https://www.youtube.com/Dlium
Subscribe, like and comment.
Good website: https://www.dlium.com
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- published: 24 Jan 2015
- views: 192
1:12
PLoS Biology : Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules...
Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules Accelerates Viral Adaptation at the Cell and Tissue Levels. Shuhei Miyashita et al (201...
Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules Accelerates Viral Adaptation at the Cell and Tissue Levels. Shuhei Miyashita et al (2015), PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1002094
Recent studies on evolutionarily distant viral groups have shown that the number of viral genomes that establish cell infection after cell-to-cell transmission is unexpectedly small (1–20 genomes). This aspect of viral infection appears to be important for the adaptation and survival of viruses. To clarify how the number of viral genomes that establish cell infection is determined, we developed a simulation model of cell infection for tomato mosaic virus (ToMV), a positive-strand RNA virus. The model showed that stochastic processes that govern the replication or degradation of individual genomes result in the infection by a small number of genomes, while a large number of infectious genomes are introduced in the cell. It also predicted two interesting characteristics regarding cell infection patterns: stochastic variation among cells in the number of viral genomes that establish infection and stochastic inequality in the accumulation of their progenies in each cell. Both characteristics were validated experimentally by inoculating tobacco cells with a library of nucleotide sequence–tagged ToMV and analyzing the viral genomes that accumulated in each cell using a high-throughput sequencer. An additional simulation model revealed that these two characteristics enhance selection during tissue infection. The cell infection model also predicted a mechanism that enhances selection at the cellular level: a small difference in the replication abilities of coinfected variants results in a large difference in individual accumulation via the multiple-round formation of the replication complex (i.e., the replication machinery). Importantly, this predicted effect was observed in vivo. The cell infection model was robust to changes in the parameter values, suggesting that other viruses could adopt similar adaptation mechanisms. Taken together, these data reveal a comprehensive picture of viral infection processes including replication, cell-to-cell transmission, and evolution, which are based on the stochastic behavior of the viral genome molecules in each cell.
Good channel: https://www.youtube.com/Dlium
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Good website: https://www.dlium.com
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https://wn.com/Plos_Biology_Viruses_Roll_The_Dice_The_Stochastic_Behavior_Of_Viral_Genome_Molecules...
Viruses Roll the Dice: The Stochastic Behavior of Viral Genome Molecules Accelerates Viral Adaptation at the Cell and Tissue Levels. Shuhei Miyashita et al (2015), PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1002094
Recent studies on evolutionarily distant viral groups have shown that the number of viral genomes that establish cell infection after cell-to-cell transmission is unexpectedly small (1–20 genomes). This aspect of viral infection appears to be important for the adaptation and survival of viruses. To clarify how the number of viral genomes that establish cell infection is determined, we developed a simulation model of cell infection for tomato mosaic virus (ToMV), a positive-strand RNA virus. The model showed that stochastic processes that govern the replication or degradation of individual genomes result in the infection by a small number of genomes, while a large number of infectious genomes are introduced in the cell. It also predicted two interesting characteristics regarding cell infection patterns: stochastic variation among cells in the number of viral genomes that establish infection and stochastic inequality in the accumulation of their progenies in each cell. Both characteristics were validated experimentally by inoculating tobacco cells with a library of nucleotide sequence–tagged ToMV and analyzing the viral genomes that accumulated in each cell using a high-throughput sequencer. An additional simulation model revealed that these two characteristics enhance selection during tissue infection. The cell infection model also predicted a mechanism that enhances selection at the cellular level: a small difference in the replication abilities of coinfected variants results in a large difference in individual accumulation via the multiple-round formation of the replication complex (i.e., the replication machinery). Importantly, this predicted effect was observed in vivo. The cell infection model was robust to changes in the parameter values, suggesting that other viruses could adopt similar adaptation mechanisms. Taken together, these data reveal a comprehensive picture of viral infection processes including replication, cell-to-cell transmission, and evolution, which are based on the stochastic behavior of the viral genome molecules in each cell.
Good channel: https://www.youtube.com/Dlium
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Good website: https://www.dlium.com
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- published: 17 Mar 2015
- views: 104
3:15
Discovery report + update articles - PLOS Biology
PLOS Biology Discover Reports and subsequent Update Articles let researchers communicate scientific advances in a faster, more dynamic way that more naturally m...
PLOS Biology Discover Reports and subsequent Update Articles let researchers communicate scientific advances in a faster, more dynamic way that more naturally mirrors the research process.
https://wn.com/Discovery_Report_Update_Articles_Plos_Biology
PLOS Biology Discover Reports and subsequent Update Articles let researchers communicate scientific advances in a faster, more dynamic way that more naturally mirrors the research process.
- published: 01 Mar 2021
- views: 630
0:35
PLoS Biology : Conformational Changes during Pore Formation by the Perforin-Related Protein...
Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin. Natalya Lukoyanova et al (2015), PLoS Biology http://dx.doi.org/10.1...
Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin. Natalya Lukoyanova et al (2015), PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1002049
Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ~70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.
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https://wn.com/Plos_Biology_Conformational_Changes_During_Pore_Formation_By_The_Perforin_Related_Protein...
Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin. Natalya Lukoyanova et al (2015), PLoS Biology http://dx.doi.org/10.1371/journal.pbio.1002049
Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ~70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.
Good channel: https://www.youtube.com/Dlium
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- published: 06 Feb 2015
- views: 718
30:19
PLoS Biology : A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using...
A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using an Interdisciplinary, Biophysical Approach. Karishma S. Kaushik et al. (2015), PLoS Bi...
A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using an Interdisciplinary, Biophysical Approach. Karishma S. Kaushik et al. (2015), PLoS Biology, http://dx.doi.org/10.1371/journal.pbio.1002044
We have developed a hands-on experimental module that combines biology experiments with a physics-based analytical model in order to characterize antimicrobial compounds. To understand antibiotic resistance, participants perform a disc diffusion assay to test the antimicrobial activity of different compounds and then apply a diffusion-based analytical model to gain insights into the behavior of the active antimicrobial component. In our experience, this module was robust, reproducible, and cost-effective, suggesting that it could be implemented in diverse settings such as undergraduate research, STEM (science, technology, engineering, and math) camps, school programs, and laboratory training workshops. By providing valuable interdisciplinary research experience in science outreach and education initiatives, this module addresses the paucity of structured training or education programs that integrate diverse scientific fields. Its low-cost requirements make it especially suitable for use in resource-limited settings.
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https://wn.com/Plos_Biology_A_Low_Cost,_Hands_On_Module_To_Characterize_Antimicrobial_Compounds_Using...
A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using an Interdisciplinary, Biophysical Approach. Karishma S. Kaushik et al. (2015), PLoS Biology, http://dx.doi.org/10.1371/journal.pbio.1002044
We have developed a hands-on experimental module that combines biology experiments with a physics-based analytical model in order to characterize antimicrobial compounds. To understand antibiotic resistance, participants perform a disc diffusion assay to test the antimicrobial activity of different compounds and then apply a diffusion-based analytical model to gain insights into the behavior of the active antimicrobial component. In our experience, this module was robust, reproducible, and cost-effective, suggesting that it could be implemented in diverse settings such as undergraduate research, STEM (science, technology, engineering, and math) camps, school programs, and laboratory training workshops. By providing valuable interdisciplinary research experience in science outreach and education initiatives, this module addresses the paucity of structured training or education programs that integrate diverse scientific fields. Its low-cost requirements make it especially suitable for use in resource-limited settings.
Good channel: https://www.youtube.com/Dlium
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- published: 21 Jan 2015
- views: 135