JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION, December 2016, p. 495-498 Copyright © 2016 American Society for Microbiology
JOURNAL WATCH
DOI: http://dx.doi.org/10.1128/jmbe.v17i3.1237 In this section, I provide articles on recent developments and new technology used in microbiology and related fields. I also post articles that may help you bring new information or techniques into your laboratory or classroom via case studies or lab exercises. I hope you find this information useful, and I encourage you to send suggestions, questions or comments to me at [email protected]. I look forward to hearing from you! Jennifer A. Herzog Herkimer County Community College Herkimer, NY [email protected] Research Articles Matsunami, H., et al. 2016. Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica. Sci. Rep. 6:27399. (doi: 10.1038/srep27399). (Disrupting flagellar organization and motility in order to treat bacterial infections.) Ladner, J. T., et al. 2016. A multicomponent animal virus isolated from mosquitoes. Cell Host Microbe 20(3):357–367. (doi: 10.1016/j.chom.2016.07.011). (Discovery of a novel virus that requires multiple subunits for active infection.) David, C. N., et al. 2016. GLT-1-dependent disruption of CNS glutamate homeostasis and neuronal function by the protozoan parasite Toxoplasma gondii. PLOS Pathog. 12(6):e1005643 (doi: 10.1371/journal.ppat.1005643). (Glutamate dysregulation linked to pathogenesis of toxoplasmosis.) Villa, R., et al. 2016. PionX sites mark the X chromosome for dosage compensation. Nature 537(7619):244 –248 (doi:10.1038/nature19338). (Elucidation of the enzymatic activity of DCC in the regulation of sex chromosome activity.) Pedagogy Articles Please find material presented at both the Profession of Microbiology track at Microbe 2016 and the ASM’s Conference for Undergraduate Educators (ASMCUE): Microbe: http://www.asm.org/index.php/asm-events/ post-meeting-materials ASMCUE: ht tp://w w w.asmcue.org /index.php/past- meeting-resources Volume 17, Number 3
Reviews
Darwiche, H., et al. 2016. Ebola epidemic: using current events to teach authentic inquiry science. Am. Biol. Teach. 78(3):190–197. (Active learning tool for use in upper high school-level courses/lower undergraduate science courses, whose assessment is linked to the Next Generation Science Standards.) Johnson, W. R. 2016. Why engaging in the practices of science is not enough to achieve scientific literacy. Am. Biol. Teach. 78(5):370–374. (A critical analysis of a major component of the Next Generation Science Standards in regards to the need for reflection.)
WEBSITE Editor’s Note: Many instructors use the current newsfeed to provide timely and relatable material to engage students with application-based instruction. Most printed textbooks lag behind the current news cycle. In this review, Narveen Jandu, PhD, spotlights the Center for Disease Control and Prevention’s database for foodborne outbreaks as one resource instructors and students can access for current, case-based instruction. Microbiology Instruction Using Current Foodborne Outbreak Resources DOI: http://dx.doi.org/10.1128/jmbe.v17i3.1213 Review of: Center for Disease Control and Prevention (CDC) Foodborne Outbreak Online Database (FOOD), wwwn.cdc.gov/foodborneoutbreaks/, CDC Outbreaks, www.cdc.gov/outbreaks/index.html, and Multistate Foodborne Outbreaks, www.cdc.gov/foodsafety/outbreaks/ multistate-outbreaks/outbreaks-list.html. Every season brings a newsworthy outbreak of foodborne infectious diseases such as the 2015 Escherichia coli O26 outbreak associated with Chipotle restaurants. Amid such a nationwide foodborne outbreak, numerous resources can provide students and faculty with timely, accurate, and credible information. While the Centers for Disease Control and Prevention (CDC) website (www.cdc.gov) is a useful starting place, the wealth of information on this website can be overwhelming for new users, such as students. Two specific resources for understanding foodborne outbreaks include the FOOD (Foodborne Outbreak Online Database) Tool and the Multistate Foodborne Outbreaks webpage. Both allow users to gain focus when retrieving information on foodborne infectious outbreaks. The FOOD tool has been available from the CDC since 2009, but its redesign in 2015 provides a much more user-friendly interface (1). There are multiple entry points into the FOOD tool from the CDC website, the most direct being through wwwn.cdc.gov/foodborneoutbreaks/. This is a searchable database of US foodborne outbreaks
Journal of Microbiology & Biology Education
495
REVIEWS
from 1998 through to 2014, providing at least 16 years of foodborne disease data as of the date of this review (1). On the entry page of FOOD, the dashboard view provides search option tabs on the left of the page with the remainder of the page displaying a large interactive map, a chart of outbreaks by year, and a chart of outbreaks by month, as well as some brief statistics and other links. The search option tabs are also very useful. These tabs are for Year, State, Location of Preparation, Food/Ingredient, and Etiology or causative agent of illness. Fields can be selected within these search options, and the interactive map, charts and quick stats are automatically updated in real time without delay as search option criteria are selected, added, or removed. These rapidly generated graphics provide a quick and easy way to understand the quantitative data of any outbreak, which can then be readily communicated to students. In the same way, students searching for information on a foodborne outbreak can just as rapidly find the information they are looking for. The raw data from any searchable outbreak can be very easily downloaded as an Excel data file. The link for this embedded tool is clearly displayed with the recognizable Excel icon. This data file contains columns with information on the year, month, state, genus, species, serotype or genotype, etiology status, location of preparation, illnesses, hospitalizations, deaths, food vehicle, and contaminated ingredient. While some of these data columns mirror the search option tabs, the additional data columns of Serotype or Genotype, Illnesses, Hospitalizations, and Deaths provide a more comprehensive assessment of the outbreak. In addition, access to this raw data allows users to generate their own tables, graphs, charts and figures. This is a very helpful teaching tool when generating figures for a lecture but even more so for undergraduate students in introductory microbiology courses who are learning how to access public data, use spreadsheets, generate charts, interpret results, and conduct their own analyses. One of the limitations of the FOOD tool is that users are only able to download raw data as Excel files. There are no direct options to download other file formats such as .csv or .txt, but these file formats can be easily generated from the Excel file. Unfortunately, an image of the large interactive map cannot be downloaded for repurposing. There are related minor concerns that are similar, including limited image resolution, the need to create your own state labels, and the inability to change color schemes. Most importantly, the FOOD database only provides data up to 2014. With the regular occurrence of foodborne outbreaks, it is expected that this database will be continually updated. Information on more recent foodborne outbreaks can be found on the Outbreaks webpage of the CDC’s website (www.cdc.gov/outbreaks/index.html). Conveniently, a link to this webpage is prominently provided on the CDC’s homepage. This link navigates to an informational webpage with a list of current and ongoing “US-based outbreaks.” Each of the listed outbreaks is then hyperlinked to more detailed informational pages. The “US-based Outbreaks” 496
homepage provides a direct link to the “Multistate Foodborne Outbreaks” webpage, discussed below. Other helpful links provided on the “US-based Outbreaks” homepage but not discussed in this review include “Morbidity and Mortality Weekly Reports” and a widget on “Food Safety Recalls” from www.foodsafety.org. The “Multistate Foodborne Outbreaks” webpage (www.cdc.gov/foodsafety/outbreaks/multistate-outbreaks/ outbreaks-list.html) displays information on the most recent 10 years of outbreaks including the two most recent years, which were not included in the FOOD tool. The information is presented in user-friendly lists and tabs. There are two sets of lists and tabs: the first set organizes all of the outbreaks by year, while the second set organizes all of the outbreaks by commonly implicated pathogens, such as Escherichia coli, Salmonella, and Listeria. These lists and tabs make it extremely easy to find information on an outbreak. For example, by clicking on 2015 and then Chipotle Mexican Grill, users are linked directly to a complete informational webpage on the outbreak. Key statistics on the cases, states involved, hospitalizations, and deaths are quickly gleaned from the ‘At a Glance’ box. As well, a clickable map on case counts and a clickable epidemiological curve provide additional details in an easy-to-understand visual format. Detailed text communicating the ‘highlights’ of the outbreak and an ‘outbreak summary’ provide complementary information. Mid-page clickable tabs with dates provide a timeline of the events that unfolded as the outbreak occurred. Multiple additional links to general information are also provided. This Multistate Foodborne Outbreaks resource can facilitate instruction on foodborne outbreaks while complementing content on transmission and pathogenesis. Faculty, instructors, and students can consult these resources to discuss outbreaks in real time using applied lecture content coupled with accurate information.
REFERENCES 1. Centers for Disease Control and Prevention (CDC). 2016. Foodborne Outbreak Online Database (FOOD Tool) [Online.] http://www.cdc.gov/foodsafety/fdoss/data/food. html. Accessed July 2016.
Narveen Jandu Gannon University Erie, PA [email protected]
BOOK “It’s a Microbial World; We Just Live in It”: Microbial Symbionts Profiled Masterfully by Yong DOI: http://dx.doi.org/10.1128/jmbe.v17i3.1217 Review of: I Contain Multitudes: The Microbes Within Us and A Grander View of Life; Ed Yong; (2016). Ecco Publishers, New York, NY, 368 p.
Journal of Microbiology & Biology Education
Volume 17, Number 3
JOURNAL WATCH
DOI: http://dx.doi.org/10.1128/jmbe.v17i3.1237 In this section, I provide articles on recent developments and new technology used in microbiology and related fields. I also post articles that may help you bring new information or techniques into your laboratory or classroom via case studies or lab exercises. I hope you find this information useful, and I encourage you to send suggestions, questions or comments to me at [email protected]. I look forward to hearing from you! Jennifer A. Herzog Herkimer County Community College Herkimer, NY [email protected] Research Articles Matsunami, H., et al. 2016. Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica. Sci. Rep. 6:27399. (doi: 10.1038/srep27399). (Disrupting flagellar organization and motility in order to treat bacterial infections.) Ladner, J. T., et al. 2016. A multicomponent animal virus isolated from mosquitoes. Cell Host Microbe 20(3):357–367. (doi: 10.1016/j.chom.2016.07.011). (Discovery of a novel virus that requires multiple subunits for active infection.) David, C. N., et al. 2016. GLT-1-dependent disruption of CNS glutamate homeostasis and neuronal function by the protozoan parasite Toxoplasma gondii. PLOS Pathog. 12(6):e1005643 (doi: 10.1371/journal.ppat.1005643). (Glutamate dysregulation linked to pathogenesis of toxoplasmosis.) Villa, R., et al. 2016. PionX sites mark the X chromosome for dosage compensation. Nature 537(7619):244 –248 (doi:10.1038/nature19338). (Elucidation of the enzymatic activity of DCC in the regulation of sex chromosome activity.) Pedagogy Articles Please find material presented at both the Profession of Microbiology track at Microbe 2016 and the ASM’s Conference for Undergraduate Educators (ASMCUE): Microbe: http://www.asm.org/index.php/asm-events/ post-meeting-materials ASMCUE: ht tp://w w w.asmcue.org /index.php/past- meeting-resources Volume 17, Number 3
Reviews
Darwiche, H., et al. 2016. Ebola epidemic: using current events to teach authentic inquiry science. Am. Biol. Teach. 78(3):190–197. (Active learning tool for use in upper high school-level courses/lower undergraduate science courses, whose assessment is linked to the Next Generation Science Standards.) Johnson, W. R. 2016. Why engaging in the practices of science is not enough to achieve scientific literacy. Am. Biol. Teach. 78(5):370–374. (A critical analysis of a major component of the Next Generation Science Standards in regards to the need for reflection.)
WEBSITE Editor’s Note: Many instructors use the current newsfeed to provide timely and relatable material to engage students with application-based instruction. Most printed textbooks lag behind the current news cycle. In this review, Narveen Jandu, PhD, spotlights the Center for Disease Control and Prevention’s database for foodborne outbreaks as one resource instructors and students can access for current, case-based instruction. Microbiology Instruction Using Current Foodborne Outbreak Resources DOI: http://dx.doi.org/10.1128/jmbe.v17i3.1213 Review of: Center for Disease Control and Prevention (CDC) Foodborne Outbreak Online Database (FOOD), wwwn.cdc.gov/foodborneoutbreaks/, CDC Outbreaks, www.cdc.gov/outbreaks/index.html, and Multistate Foodborne Outbreaks, www.cdc.gov/foodsafety/outbreaks/ multistate-outbreaks/outbreaks-list.html. Every season brings a newsworthy outbreak of foodborne infectious diseases such as the 2015 Escherichia coli O26 outbreak associated with Chipotle restaurants. Amid such a nationwide foodborne outbreak, numerous resources can provide students and faculty with timely, accurate, and credible information. While the Centers for Disease Control and Prevention (CDC) website (www.cdc.gov) is a useful starting place, the wealth of information on this website can be overwhelming for new users, such as students. Two specific resources for understanding foodborne outbreaks include the FOOD (Foodborne Outbreak Online Database) Tool and the Multistate Foodborne Outbreaks webpage. Both allow users to gain focus when retrieving information on foodborne infectious outbreaks. The FOOD tool has been available from the CDC since 2009, but its redesign in 2015 provides a much more user-friendly interface (1). There are multiple entry points into the FOOD tool from the CDC website, the most direct being through wwwn.cdc.gov/foodborneoutbreaks/. This is a searchable database of US foodborne outbreaks
Journal of Microbiology & Biology Education
495
REVIEWS
from 1998 through to 2014, providing at least 16 years of foodborne disease data as of the date of this review (1). On the entry page of FOOD, the dashboard view provides search option tabs on the left of the page with the remainder of the page displaying a large interactive map, a chart of outbreaks by year, and a chart of outbreaks by month, as well as some brief statistics and other links. The search option tabs are also very useful. These tabs are for Year, State, Location of Preparation, Food/Ingredient, and Etiology or causative agent of illness. Fields can be selected within these search options, and the interactive map, charts and quick stats are automatically updated in real time without delay as search option criteria are selected, added, or removed. These rapidly generated graphics provide a quick and easy way to understand the quantitative data of any outbreak, which can then be readily communicated to students. In the same way, students searching for information on a foodborne outbreak can just as rapidly find the information they are looking for. The raw data from any searchable outbreak can be very easily downloaded as an Excel data file. The link for this embedded tool is clearly displayed with the recognizable Excel icon. This data file contains columns with information on the year, month, state, genus, species, serotype or genotype, etiology status, location of preparation, illnesses, hospitalizations, deaths, food vehicle, and contaminated ingredient. While some of these data columns mirror the search option tabs, the additional data columns of Serotype or Genotype, Illnesses, Hospitalizations, and Deaths provide a more comprehensive assessment of the outbreak. In addition, access to this raw data allows users to generate their own tables, graphs, charts and figures. This is a very helpful teaching tool when generating figures for a lecture but even more so for undergraduate students in introductory microbiology courses who are learning how to access public data, use spreadsheets, generate charts, interpret results, and conduct their own analyses. One of the limitations of the FOOD tool is that users are only able to download raw data as Excel files. There are no direct options to download other file formats such as .csv or .txt, but these file formats can be easily generated from the Excel file. Unfortunately, an image of the large interactive map cannot be downloaded for repurposing. There are related minor concerns that are similar, including limited image resolution, the need to create your own state labels, and the inability to change color schemes. Most importantly, the FOOD database only provides data up to 2014. With the regular occurrence of foodborne outbreaks, it is expected that this database will be continually updated. Information on more recent foodborne outbreaks can be found on the Outbreaks webpage of the CDC’s website (www.cdc.gov/outbreaks/index.html). Conveniently, a link to this webpage is prominently provided on the CDC’s homepage. This link navigates to an informational webpage with a list of current and ongoing “US-based outbreaks.” Each of the listed outbreaks is then hyperlinked to more detailed informational pages. The “US-based Outbreaks” 496
homepage provides a direct link to the “Multistate Foodborne Outbreaks” webpage, discussed below. Other helpful links provided on the “US-based Outbreaks” homepage but not discussed in this review include “Morbidity and Mortality Weekly Reports” and a widget on “Food Safety Recalls” from www.foodsafety.org. The “Multistate Foodborne Outbreaks” webpage (www.cdc.gov/foodsafety/outbreaks/multistate-outbreaks/ outbreaks-list.html) displays information on the most recent 10 years of outbreaks including the two most recent years, which were not included in the FOOD tool. The information is presented in user-friendly lists and tabs. There are two sets of lists and tabs: the first set organizes all of the outbreaks by year, while the second set organizes all of the outbreaks by commonly implicated pathogens, such as Escherichia coli, Salmonella, and Listeria. These lists and tabs make it extremely easy to find information on an outbreak. For example, by clicking on 2015 and then Chipotle Mexican Grill, users are linked directly to a complete informational webpage on the outbreak. Key statistics on the cases, states involved, hospitalizations, and deaths are quickly gleaned from the ‘At a Glance’ box. As well, a clickable map on case counts and a clickable epidemiological curve provide additional details in an easy-to-understand visual format. Detailed text communicating the ‘highlights’ of the outbreak and an ‘outbreak summary’ provide complementary information. Mid-page clickable tabs with dates provide a timeline of the events that unfolded as the outbreak occurred. Multiple additional links to general information are also provided. This Multistate Foodborne Outbreaks resource can facilitate instruction on foodborne outbreaks while complementing content on transmission and pathogenesis. Faculty, instructors, and students can consult these resources to discuss outbreaks in real time using applied lecture content coupled with accurate information.
REFERENCES 1. Centers for Disease Control and Prevention (CDC). 2016. Foodborne Outbreak Online Database (FOOD Tool) [Online.] http://www.cdc.gov/foodsafety/fdoss/data/food. html. Accessed July 2016.
Narveen Jandu Gannon University Erie, PA [email protected]
BOOK “It’s a Microbial World; We Just Live in It”: Microbial Symbionts Profiled Masterfully by Yong DOI: http://dx.doi.org/10.1128/jmbe.v17i3.1217 Review of: I Contain Multitudes: The Microbes Within Us and A Grander View of Life; Ed Yong; (2016). Ecco Publishers, New York, NY, 368 p.
Journal of Microbiology & Biology Education
Volume 17, Number 3
