scholarly journals Patterning bacteria on agar for understanding distance mediated cell to cell signaling and metabolic exchanges

2017 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Microbial Interactions ◽  
Bacterial Cells ◽  
Microbial Species ◽  
Coarse Surface ◽  
Patterning Technique ◽  
Agar Surface

Microbes, while living in close proximity in biofilms, may in other cases not be closely localized in the environment. In the latter case, their interactions and communications are dependent on myriad factors such as existence of direct connections (e.g., web of hyphae from fungi) or pools of water where they could migrate. Hence, disparate groups of microbes could subsist on nutrients in their local microhabitat while maintaining weak communication links and metabolic exchanges with groups farther afield. But, how do we probe such distance dependent communications links between groups of microbes of the same or different species in the laboratory? Using a purple pigment producing bacterium for “writing” on agar, a surface patterning technique was demonstrated to be a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates, which may find use in understanding possible interactions between different microbial species. Although a coarse surface patterning technique compared to more refined robot assisted patterning methods, simple spread plate deposition of different microbial species, in defined patterns, on separate areas of the agar surface, constituted a useful way forward in allowing us to delve deeper into understanding microbial interactions such as those in spatially resolved synthetic microbial community. Taking into account bacterial motility patterns, pigment diffusivity, and contrast of pigment with agar background color, deposition of patterns of bacterial cells through spread plate technique is an affordable method for lending a lens to spatially defined microbial interactions for microbial brethren unable to undergo migration on the agar surface. A synopsis of the work can be found in the accompanying PDF file, while the original article, “Bacterial calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article. URL: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414

scholarly journals Patterning bacteria on agar for understanding distance mediated cell to cell signaling and metabolic exchanges

2017 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Microbial Interactions ◽  
Bacterial Cells ◽  
Microbial Species ◽  
Coarse Surface ◽  
Patterning Technique ◽  
Agar Surface

Microbes, while living in close proximity in biofilms, may in other cases not be closely localized in the environment. In the latter case, their interactions and communications are dependent on myriad factors such as existence of direct connections (e.g., web of hyphae from fungi) or pools of water where they could migrate. Hence, disparate groups of microbes could subsist on nutrients in their local microhabitat while maintaining weak communication links and metabolic exchanges with groups farther afield. But, how do we probe such distance dependent communications links between groups of microbes of the same or different species in the laboratory? Using a purple pigment producing bacterium for “writing” on agar, a surface patterning technique was demonstrated to be a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates, which may find use in understanding possible interactions between different microbial species. Although a coarse surface patterning technique compared to more refined robot assisted patterning methods, simple spread plate deposition of different microbial species, in defined patterns, on separate areas of the agar surface, constituted a useful way forward in allowing us to delve deeper into understanding microbial interactions such as those in spatially resolved synthetic microbial community. Taking into account bacterial motility patterns, pigment diffusivity, and contrast of pigment with agar background color, deposition of patterns of bacterial cells through spread plate technique is an affordable method for lending a lens to spatially defined microbial interactions for microbial brethren unable to undergo migration on the agar surface. A synopsis of the work can be found in the accompanying PDF file, while the original article, “Bacterial calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article. URL: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414

scholarly journals Bacteria as “ink” for writing the initials of names on agar

2017 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Microbial Interactions ◽  
Bacterial Cells ◽  
Coarse Surface ◽  
Patterning Technique ◽  
Agar Surface ◽  
Research Students

Microbes, while living in close proximity in biofilms, may in other cases not be closely localized in the environment. In the latter case, their interactions and communications are dependent on myriad factors such as existence of direct connections (e.g., web of hyphae from fungi) or pools of water where they could migrate. Hence, disparate groups of microbes could subsist on nutrients in their local microhabitat while maintaining weak communication links and metabolic exchanges with groups farther afield. But, how do we probe such distance dependent communications links between groups of microbes of the same or different species in the laboratory? Using a purple pigment producing bacterium as “ink” for writing on agar, a surface patterning technique was demonstrated to be a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates, which may find use in understanding possible interactions between different microbial species.Although a coarse surface patterning technique compared to more refined robot assisted patterning methods, simple spread plate deposition of different microbial species, in defined patterns, on separate areas of the agar surface, constituted a useful way forward in allowing us to delve deeper into the realmof understanding microbial interactions such as those in spatially resolved synthetic microbial community. Taking into account bacterial motility patterns, pigment diffusivity, and contrast of pigment with agar background color, inscription of patterns of bacterial cells through spread plate technique is an affordablemethod for lending a lens to spatially defined microbial interactions for microbial brethren unable to undergo migration on the agar surface. A synopsis of the work can be found in the accompanying PDF file, while the original article, “Bacterial calligraphy: A Memento for Undergraduate Research Students”, isavailable in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article. URL: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414

scholarly journals Bacteria as “ink” for writing the initials of names on agar

2016 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Research Projects ◽  
Purple Pigment ◽  
Patterning Technique ◽  
Research Students ◽  
Planar Substrates ◽  
Open Access Article

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created to help them recollect, in future, the strong friendships that they fostered during their final year research projects. Besides the fun activity of “Bacterial calligraphy”, the surface patterning technique can also serve as a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates may find use in understanding possible interactions between different microorganism species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174 as an open access article, URL http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414 .

scholarly journals Bacteria as “ink” for writing the initials of names on agar

2014 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Research Projects ◽  
Purple Pigment ◽  
Patterning Technique ◽  
Research Students ◽  
Planar Substrates ◽  
Open Access Article

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created, to help them remember the strong friendships that they had fostered with their fellow course-mates during their final year research projects. Besides the fun activity of “Bacterial Calligraphy,” the surface patterning technique can also serve as a simple and relatively low-cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates for investigating possible interactions between different microbial species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students,” has been published in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, and is available at http://jmbe.asm.org/index.php/jmbe/article/view/414 as an open-access article.

scholarly journals Bacteria as “ink” for writing the initials of names on agar

2016 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Research Projects ◽  
Purple Pigment ◽  
Patterning Technique ◽  
Research Students ◽  
Planar Substrates ◽  
Open Access Article

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created to help them remember the strong friendships fostered during their final year research projects. Besides the fun activity of “Bacterial calligraphy”, the surface patterning technique can also serve as a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates for investigating possible interactions between different microorganism species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414

scholarly journals Bacteria as “ink” for writing the initials of names on agar

2016 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Undergraduate Research ◽  
Low Cost ◽  
Biology Education ◽  
Surface Patterning ◽  
Research Projects ◽  
Purple Pigment ◽  
Patterning Technique ◽  
Research Students ◽  
Planar Substrates ◽  
Open Access Article

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created to help them remember the strong friendships they fostered with their fellow course mates during their final year research projects. Besides the fun activity of “Bacterial calligraphy”, the surface patterning technique can also serve as a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates for investigating possible interactions between different microbe species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, at http://jmbe.asm.org/index.php/jmbe/article/view/414 as an open access article.

scholarly journals Assessment of Course-Based Undergraduate Research Experiences: A Meeting Report

2014 ◽  
Vol 13 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Lisa Corwin Auchincloss ◽  
Sandra L. Laursen ◽  
Janet L. Branchaw ◽  
Kevin Eagan ◽  
Mark Graham ◽  
...  
Keyword(s):  
Undergraduate Research ◽  
Biology Education ◽  
Operational Definition ◽  
Future Research ◽  
Meeting Report ◽  
Research Experience ◽  
Research Experiences ◽  
Undergraduate Research Experiences ◽  
Foundation Program ◽  
Definition Of

The Course-Based Undergraduate Research Experiences Network (CUREnet) was initiated in 2012 with funding from the National Science Foundation program for Research Coordination Networks in Undergraduate Biology Education. CUREnet aims to address topics, problems, and opportunities inherent to integrating research experiences into undergraduate courses. During CUREnet meetings and discussions, it became apparent that there is need for a clear definition of what constitutes a CURE and systematic exploration of what makes CUREs meaningful in terms of student learning. Thus, we assembled a small working group of people with expertise in CURE instruction and assessment to: 1) draft an operational definition of a CURE, with the aim of defining what makes a laboratory course or project a “research experience”; 2) summarize research on CUREs, as well as findings from studies of undergraduate research internships that would be useful for thinking about how students are influenced by participating in CUREs; and 3) identify areas of greatest need with respect to CURE assessment, and directions for future research on and evaluation of CUREs. This report summarizes the outcomes and recommendations of this meeting.

scholarly journals Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

2019 ◽  
Author(s):  
Sydney B. Blattman ◽  
Wenyan Jiang ◽  
Panos Oikonomou ◽  
Saeed Tavazoie
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Low Cost ◽  
Bacterial Cells ◽  
Single Experiment ◽  
Bacterial Populations ◽  
Single Cell Rna Sequencing ◽  
Gene Expression Heterogeneity ◽  
Mrna Polyadenylation

AbstractDespite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotes has been hindered by their extremely low mRNA abundance, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a low-cost, high-throughput, prokaryotic scRNA-seq pipeline that overcomes these technical obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. PETRI-seq captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and low bias, with median capture rates >200 mRNAs/cell for exponentially growing E. coli. These characteristics enable robust discrimination of cell-states corresponding to different phases of growth. When applied to wild-type S. aureus, PETRI-seq revealed a rare sub-population of cells undergoing prophage induction. We anticipate broad utility of PETRI-seq in defining single-cell states and their dynamics in complex microbial communities.

scholarly journals The Oleaginous Yeast Metschnikowia pulcherrima Displays Killer Activity against Avian-Derived Pathogenic Bacteria

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1227
Author(s):  
Robert H. Hicks ◽  
Mauro Moreno-Beltrán ◽  
Deborah Gore-Lloyd ◽  
Christopher J. Chuck ◽  
Daniel A. Henk
Keyword(s):  
Pathogenic Bacteria ◽  
Low Cost ◽  
Industrial Applications ◽  
Microbial Interactions ◽  
Bacterial Strains ◽  
Bacterial Killing ◽  
Killer Activity ◽  
Metschnikowia Pulcherrima ◽  
Livestock Health ◽  
Yeast Interactions

Metschnikowia pulcherrima is a non-conventional yeast with potential to be used in biotechnological processes, especially those involving low-cost feedstock exploitation and biocontrol applications. The combination of traits that supports these industrial applications in M. pulcherrima also makes it an attractive option to study in the context of livestock health. In this study, we examined the specific interactions between M. pulcherrima and multiple avian pathogenic bacteria. We tested individual bacteria–yeast interactions and bacterial combinations in both solid and liquid media and in variable nutrient environments. Across multiple isolates of M. pulcherrima, we observed different levels of antimicrobial activity, varying from supporting the growth of competing bacteria through suppression and bacterial killing, and we found that these responses varied depending on the bacterial strains and media. We identified multiple molecular routes, including proteins produced by M. pulcherrima strains, that acted to control these microbial interactions. Furthermore, protein screening revealed that M. pulcherrima strains were induced to produce proteins specifically when exposed to bacterial strains, suggesting that fine-tuned mechanisms allow M. pulcherrima to function as a potential lynchpin in a microbial community.

scholarly journals LOW ENERGY BACTERIA PRESERVATION OF EXTREMELY HALOPHILIC ARCHAEA HALOFERAX LUCENTENSE AND HALOFERAX CHUDINOVII IMMOBILIZED USING NATURAL ZEOLITE

2019 ◽  
Vol 10 (2) ◽  
pp. 16-28
Author(s):  
Rizal Awaludin Malik ◽  
Nilawati Nilawati ◽  
Novarina Irnaning Handayani ◽  
Rame Rame ◽  
Silvy Djayanti ◽  
...  
Keyword(s):  
Surface Area ◽  
Pore Volume ◽  
Low Cost ◽  
Halophilic Archaea ◽  
High Energy ◽  
Slight Reduction ◽  
Bacterial Cells ◽  
Preservation Method ◽  
Chemical Content ◽  
Physical And Chemical

The methods of microbial cells preservation were already known by liquid drying, freeze-drying, and freezing. Those methods could preserve bacteria cells in a long period of time but its survivability was relatively low and used relatively high energy during preservation. Immobilization was known as entrapping, attaching or encapsulating bacterial cells in a suitable matrix. This research was conducted to know the suitability of zeolite as immobilization carrier and also as preservation matrix of two halophilic archaea Haloferax chudinovii and Haloferax lucentense. Variable of this research was the type of the carrier which was raw zeolite, 110oC and 300oC heat-activated zeolite carrier, parameters measured in this study was physical and chemical of zeolite such as chemical content, Si/Al ratio, surface area and pore volume, and biochemical assay, bacterial cells numbers after immobilization and bacterial cells after preservation as bacterial response to the immobilization and preservation. Heat activation was significantly affecting the chemical composition, carrier surface area, and pore volume. Highest surface area, pore volume, and Si/Al ratio were obtained in 110oC pretreated zeolite followed by 300oC pretreated zeolite. The bacterial cells obtained after immobilization process was 1,8x107 cfu/g, 3,0 x 107 cfu/g, and 2,1x107 for raw zeolite, 110oC pretreated zeolite and 300oC zeolite respectively. After 4 months preservation, the slight reduction of the bacterial cells was observed. Immobilization halophilic archaeae using zeolite as carrier was proven as low cost and effective preservation method due to relatively simple process and unspecific preservation temperature requirements.

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