ScLi-2 Identify research and review articles What kind of article is this? Click here to open link (access by selecting FIU as the institution and log in with your FIU credentials) Click here to download PDF

Before starting your exam and proceeding to question 2, please complete a thorough environment check.   This includes recording: (1) your clutter-free workspace (desk, table, etc.) that is free of any papers, books, devices etc., (2) showing underneath your workspace, (3) showing a full 360-degree view of the room, (4) you must record yourself turning off your cell phone, show the screen to confirm it is off and place it behind you, out of reach.   If any part of this environment check is missing or incomplete, it will result in a zero for the exam grade, as outlined in the syllabus.   Type your full name indicating that you completed the scan of your environment, did not manipulate anything in your environment, and that you understand that skipping this will result in a zero for the exam.

ScLi-3 Perform a successful literature search   A new research lab-mate has asked you for advice about how to perform a literature search about epigenetic regulation of flowering time in plants. They are proposing to use the following keywords for their search. Which ones would produce the best results?  

ScLi10- Identify study variables in research articles A real study aimed to test whether the pattern of resource distribution in an environment affected how many individuals of the same species could be maintained by such environment. Researchers used single-strain populations of budding yeast (microorganism that you use to raise dough) in plates with the amino acid tryptophan (Trp) as the exploited, renewable resource. Researchers set 96 plates with Trp . Each plate was divided in 12 sections.  Each plate had either a heterogeneous or homogeneous distribution of resources (Trp). A heterogeneous environment was designed by alternating high and low Trp concentrations. A homogeneous environment was designed as having a uniform amount of Trp in all 12 sections. Yeast population in each well was quantified every 24 h as the optical density (OD600) until an asymptote was observed.

ScLi14- Interpret graphs, charts and statistics in results of research studies The following figure is from the study Sediment associated with algal turfs inhibits the settlement of two endangered coral species  coauthored by Dr. Alain Duran (professor in our bio department) The objective of the study was to determine if algal turfs or a mix of algal turfs and their sediments affected the presence of juvenile corals and settlement of new corals of two important coral species in South Florida     Which of the following statements are true?

ScLi-2 Identify research and review articles What kind of article is this? Click here to open link (select FIU as your institution and log in with your FIU credentials) Click here to download PDF

ScLi-3 Perform a successful literature search A lab-mate has given you the following 5 papers for you to decide which to present to your research mentor. Your mentor has asked you both to bring two papers with information about mosquito borne diseases in the Everglades.  Here are titles and excerpts of each paper. Choose the ones you should bring: Article 1 Emergence potential of mosquito-borne arboviruses from the Florida Everglades “In this study, we obtained baseline data on the distribution and abundance of both mosquitos and arboviruses occurring in the southern Everglades region during the summer months of 2013, when water levels were high, and in 2014, when water levels were low. ”   Article 2 Mosquito-borne diseases “Despite centuries of control efforts, mosquito-borne diseases are flourishing worldwide. With a disproportionate effect on children and adolescents, these conditions are responsible for substantial global morbidity and mortality. Malaria kills more than 1 million children annually, chiefly in sub-Saharan Africa. Dengue virus has expanded its range over the past several decades, following its principal vector, Aedes aegypti, back into regions from which it was eliminated in the mid-20th century and causing widespread epidemics of hemorrhagic fever.”   Article 3 The effect of global change on Mosquito-borne disease “Here, we show, through a review of contemporary modelling studies, that no consensus on how future changes in climatic conditions will impact mosquito-borne diseases exists, possibly due to interacting effects of other global change processes, which are often excluded from analyses. We conclude that research should not focus solely on the role of climate change but instead consider growing evidence for additional factors that modulate disease risk.” Article 4 Seasonal Dynamics of Mosquito-Borne Viruses in the Southwestern Florida Everglades, 2016, 2017 “Mosquitoes were collected for 12 consecutive months beginning June 2016, from 11 locations in the Florida Everglades […] Seven species of virus were identified from 110 isolations. […] Everglades, West Nile, Tensaw, and Mahogany Hammock viruses were most frequently isolated. […] Viruses were isolated from mangrove, cypress swamp, hardwood hammock, and sawgrass habitats.”   Article 5 Mammal decline, linked to invasive Burmese python, shifts host use of vector mosquito towards reservoir host of a zoonotic disease “We used historic and current data to investigate potential impacts of these community effects on contact between the reservoir hosts (certain rodents) and vectors of Everglades virus, a zoonotic mosquito-borne pathogen that circulates in southern Florida. The percentage of blood meals taken from the primary reservoir host, the hispid cotton rat, Sigmodon hispidus Say and Ord, increased dramatically (422.2%) from 1979 (14.7%) to 2016 (76.8%), while blood meals from deer, raccoons and opossums decreased by 98.2%, reflecting precipitous declines in relative abundance of these larger mammals”

ScLi9- Identify type of research in research articles The following is an excerpt of the study The Diversity of Sulfide Oxidation and Sulfate Reduction Genes Expressed by the Bacterial Communities of the Cariaco Basin, Venezuela performed by Dr. Maria Jose Rodriguez Mora, professor in our bio department.  “The Cariaco Basin, off the coast of Venezuela, is the largest truly marine permanently anoxic basin in the world. […] […]a localized sulfur cycle has been postulated for the redoxcline/anoxic zones of the Cariaco Basin […]: a portion of the carbon fixed by chemoautotrophic microorganisms could be oxidized by sulfate-reducing microorganisms […] The dissimilatory sulfite reductase, encoded by the dsrAB genes [13], is ubiquitous to all known sulfate-reducing prokaryotes. […] The diversity of either sqr or dsrA has not yet been studied in the Cariaco Basin. […] Therefore, in order to build a cloning library for both DNA and mRNA of the sqr and dsrAB genes, a novel sampling devise “Deep-SID” was used and, as a result, the diversity and expression of the two sulfur metabolism genes in the Cariaco Basin redox transition zone were ascertained. […] Bacterioplankton samples were collected during the Car153 cruise on January 13th 2009 at station A (10.30°N, 64.40°W), […] situated in the eastern sub-basin, with a depth of 1400 m. […] The dsrA gene from sulfate-reducing microorganisms was amplified using primers designed to target conserved regions of the gene, based on multiple alignments of cultured and environmental SRB sequences retrieved from GenBank. dsrA1FM […] To perform phylogenetic analyses of the cloned genes, alignments were built that included sequences of respective genes from several representatives of known cultured bacteria as well as sequences from the closest cultured and non-cultured relatives identified by BLASTn. […] What type of study is this?

ScLi9- Identify type of research in research articles The following are excerpts of the study The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition coauthored by Dr. De Etta Mills (professor in our bio department) “The use of microbial community variations of underlying grave soils has not been thoroughly studied for the determination of time and placement of a body […] The objective of this study was to determine changes in eubacterial metagenomic composition of the soil on which bodies had been placed with respect to ‘pristine’ soils using a fast and reliable molecular method commonly used in the ecological field and applying it to potentially identify burial sites. […] Soils were collected within the Anthropology Research Facility, the outdoor laboratory of the Forensic Anthropology Center of the University of Tennessee in Knoxville, Tennessee. Because of the very limited number of ‘new’ cadavers available for study, nine sites were sampled and soil was collected in triplicate from underneath the bodies at a maximumdepth of 2.5 cm at 1, 2, 4, 8, and 16 weeks postplacement. The donated/available cadavers used were placed on the soil between late April and early November of 2007. In addition, four control site soil samples (non grave sites) were collected during May and November of 2007 and February of 2008. The control sites were located at each of four cardinal points within the same enclosed wooded area. (to determine the bacterial community at each site) Two of the nine hypervariable domains of the 16SrRNA genes were amplified using universal eubacterial primers.  The non-overlapping domains assayed were chosen based on the results from a previous study (Moreno et al., 2006) that indicated these two domains in combination provided discrete information that could discriminate between soil microbial communities.” What type of study is this?

ScLi-8 Identify the structure of paragraphs in introductions of research papers The following statements are [1] A study reported that changing to workshop (or studio) models of instruction, which emphasize collaborative group work in class, cut failure rates by 40–60% in introductory physics across a range of institutions. Researchers found that the use of peer instruction with clickers reduced the drop rate in introductory physics at a community college and at a research university by factors of two to three. A study which implemented reading quizzes, in-class active-learning activities and weekly practice exams, showed that the failure rates in an introductory biology course for majors, was lower compared with low-structure course designs that are based on lecturing and a few high-risk assessments.  To produce a simple paragraph we would need [2] The following would be an adequate statement to be included in the paragraph [3] (modified from Eddy, S.L. and Hogan, K.A., 2014. Getting under the hood: How and for whom does increasing course structure work?. CBE—Life Sciences Education, 13(3), pp.453-468. and Freeman, S., Haak, D. and Wenderoth, M.P., 2011. Increased course structure improves performance in introductory biology. CBE—Life Sciences Education, 10(2), pp.175-186.)