Search

The Caribbean & Mesoamerica Biogeochemical Isotope Overview (CAMBIO) is an archaeological data community designed to integrate published biogeochemical data from the Caribbean, Mesoamerica, and southern Central America to address questions about dynamic interactions among humans, animals, and the environment in the region over the past 10,000 years. Here we present the CAMBIO human dataset, which consists of more than 16,000 isotopic measurements from human skeletal tissue samples (δ 13 C, δ 15 N, δ 34 S, δ 18 O, 87 Sr/ 86 Sr, 206/204 Pb, 207/204 Pb, 208/204 Pb, 207/206 Pb) from 290 archaeological sites dating between 7000 BC to modern times. The open-access dataset also includes detailed chronological, contextual, and laboratory/sample preparation information for each measurement. The collated data are deposited on the open-access CAMBIO data community via the Pandora Initiative data platform ( https://pandoradata.earth/organization/cambio )., (© 2024. The Author(s).)

During the examination of trace evidence, often a realignment along the edges of known and questioned items are made to determine if a physical fit is present and if those objects were once one continuous piece or object. Duct tape is an evidence type in which the evaluation of physical fits is often conducted and is regarded as conclusive evidence of an association between the items. The examination and conclusion of a physical fit between edges relies heavily on examiner discretion to identify distinctive features across the edges since there are no statistical approaches or objective methodologies for the comparison. This study developed an automated image processing and comparison method to quantify tape end matches using cross-correlation scores and an empirical approach to the assessment. Characterization of 150 hand torn duct tape end pair physical fits were also conducted where matching and non-matching sample distributions were created. This study also evaluated partial duct tape edges and the influence this has on a comparison. Given the strength associated with a physical fit and the presence of stretching or deformation along the fractured edge, an understanding of the value these samples have is paramount. Furthermore, random match probabilities were calculated based on the correlation scores from the inter-comparisons to model the weight of evidence or strength of association between the edges. Finally, the study demonstrated that not every true match holds the same association strength through score distributions, but the approach is able to distinguish matching and non-matching samples at edge widths greater than 27 %., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. Aminobacter sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. Pseudomonas mendocina MET completely metabolized metformin and utilized all the nitrogen atoms for growth. Pseudomonas mendocina MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in Aminobacter sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in Pseudomonas mendocina MET, purified, and characterized. The Aminobacter and Pseudomonas each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Martinez-Vaz, Dodge, Lucero, Stockbridge, Robinson, Tassoulas and Wackett.)

The implementation of course-based undergraduate research experiences (CUREs) has made it possible to expose large undergraduate populations to research experiences. For these research experiences to be authentic, they should reflect the increasingly collaborative nature of research. While some CUREs have expanded, involving multiple schools across the nation, it is still unclear how a structured extramural collaboration between students and faculty from an outside institution affects student outcomes. In this study, we established three cohorts of students: 1) no-CURE, 2) single-institution CURE (CURE), and 3) external collaborative CURE (ec-CURE), and assessed academic and attitudinal outcomes. The ec-CURE differs from a regular CURE in that students work with faculty member from an external institution to refine their hypotheses and discuss their data. The sharing of ideas, data, and materials with an external faculty member allowed students to experience a level of collaboration not typically found in an undergraduate setting. Students in the ec-CURE had the greatest gains in experimental design; self-reported course benefits; scientific skills; and science, technology, engineering, and mathematics (STEM) importance. Importantly this study occurred in a diverse community of STEM disciplinary faculty from 2- and 4-year institutions, illustrating that exposing students to structured external collaboration is both feasible and beneficial to student learning.

Premise: Reproductive fitness of individual plants depends on the timing of flowering, especially in mate-limited populations, such as those in fragmented habitats. When flowering time traits are associated with differential reproductive success, the narrow-sense heritability (h 2 ) of traits will determine how rapidly trait means evolve in response to selection. Heritability of flowering time is documented in many annual plants. However, estimating h 2 of flowering time in perennials presents additional methodological challenges, often including paternity assignment and trait expression over multiple years., Methods: We evaluated the h 2 of onset and duration of flowering using offspring-midparent regressions and restricted maximum likelihood methods in an experimental population of an iterocarpic, perennial, herbaceous plant, Echinacea angustifolia, growing in natural conditions. We assessed the flowering time of the parental cohort in 2005 and 2006; the offspring in 2014 through 2017. We also examined the effects of the paternity assignment from Cervus and MasterBayes on estimates of h 2 ., Results: We found substantial h 2 for onset and duration of flowering. We also observed variation in estimates among years. The most reliable estimates for both traits fell in the range of 0.1-0.17. We found evidence of a genotype by year interaction for onset of flowering and strong evidence that genotypes are consistent in their duration of flowering across years., Conclusions: Substantial heritabilities in this population imply the capacity for a response to natural selection, while also suggesting the potential for differential contributions to adaptive evolution among seasons., (© 2022 Botanical Society of America.)

Importance: Understanding the motivation of a mass shooter's intent to do harm can help practitioners and policy makers develop more effective intervention strategies., Objective: To examine the prevalence of communication of intent to do harm, known as leakage, in a sample of 170 mass public shooters from 1966 to 2019; the characteristics of perpetrators who do and do not leak their plans; and whether leakage is a form of fame-seeking behavior or a cry for help among individuals who are in crisis or suicidal., Design, Setting, and Participants: This cross-sectional study included perpetrators who killed 4 or more people in a public space from 1996 to 2019 and were included in a comprehensive database of US mass shootings. That database was built from August 2017 to December 2019, and analysis took place from January to May 2021., Main Outcomes and Measures: Leakage was identified and coded using publicly available records. Any communication to a third party of an intent to do harm prior to the shooting was coded as leakage. Logistic regression models were used to examine the risk factors associated with leakage. Models estimating leakage were examined to assess the 2 hypothesized pathways to leakage (the cry-for-help model and the fame-seeking model)., Results: The 170 participants in this sample included 166 (97.7%) male perpetrators and 3 (2.3%) female perpetrators, with a mean (SD) age of 34 (12) years. Overall, 161 participants had known race and ethnicity: 11 (6.8%) Asian individuals, 35 (21.7%) Black individuals, 14 (8.7%) Latinx individuals, 7 (4.4%) Middle Eastern individuals, 3 (1.9%) Native American individuals, 89 (55.3%) White individuals, and 2 (1.2%) individuals with other race and ethnicity. Overall, 79 mass shooters (46.5%) leaked their plans. Of perpetrators who leaked their plans, 35 (44.3%) leaked specific plans about a mass shooting, and 44 (55.1%) leaked nonspecific plans about generalized violence. The study findings indicate that leakage was associated with receiving counseling (odds ratio, 7.0; 95% CI, 2.0-24.8) and suicidality (odds ratio, 3.7; 95% CI, 1.0-13.6), suggesting that leakage may best be characterized as a cry for help from perpetrators prior to their act., Conclusions and Relevance: In this study, nearly half of the perpetrators of mass shootings leaked their plans. Leakage was associated with receiving counseling and suicidality. Leakage is a critical moment for mental health intervention to prevent gun violence. Opportunities to report threats of violence need to be increased. Traditional threat assessment models focused on specific threats of violence may miss critical opportunities for intervention.

A melt-salt-assisted method is utilized to construct an onion-like hybrid with Co/CoO nanoparticles embedded in graphitic Fe-N-doped carbon shells (Co/CoO@FeNC) as a bifunctional electrocatalyst. The iron-polypyrrole (Fe-PPy) is firstly prepared with a reverse emulsion. Direct pyrolysis of Fe-PPy yields turbostratic Fe-N-doped carbon (FeNC) with excellent oxygen reduction reaction (ORR) electrocatalysis, while the melt salt (CoCl 2 ) mediated pyrolysis of Fe-PPy obtains onion-like Co/CoO@FeNC with a reversible overvoltage value of 0.695 V, largely superior to Pt/C and IrO 2 (0.771 V) and other Co-based catalysts reported so far. The ORR activity is mainly due to the graphitic FeNC and further enhanced by CoN x bonds, whereas the oxygen evolution reaction (OER) activity is principally due to the Co/CoO composite. Concurrently, Co/CoO@FeNC as cathode catalyst enables Zn-air battery with a high open circuit voltage of 1.42 V, a peak power density of 132.8 mW cm -2 , a specific capacity of 813 mAh g Zn -1 , and long-term stability., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Maize is a cold sensitive crop that exhibits severe retardation of growth and development when exposed to cold spells during and right after germination, including the slowdown in development of new leaves and in formation of the photosynthetic apparatus. Improving cold tolerance in maize would allow early sowing to improve crop yield by prolonging a growing season and by decreasing the negative effects of summer drought, diseases, and pests. Two maize inbreds widely incorporated into American maize germplasm, B73 and Mo17, exhibit different levels of tolerance to low temperature exposure at seedling stage. In addition, thirty seven diverse inbred maize lines showed large variation for seedling response to low temperature exposure with lines with extremely low tolerance to seedling exposure to low temperatures falling into stiff stalk, non-stiff stalk, and tropical clades. We employed the maize intermated B73×Mo17 (IBM) recombinant inbred line population (IBM Syn4 RIL) to investigate the genetic architecture of cold stress tolerance at a young seedling stage and to identify quantitative trait loci (QTLs) controlling this variation. A panel of 97 recombinant inbred lines of IBM Syn4 were used to measure, and score based on several traits related to chlorophyll concentration, leaf color, and tissue damage. Our analysis resulted in detection of two QTLs with high additive impact, one on chromosome 1 (bin 1.02) and second on chromosome 5 (bin 5.05). Further investigation of the QTL regions using gene expression data provided a list of the candidate genes likely contributing to the variation in cold stress response. Among the genes located within QTL regions identified in this study and differentially expressed in response to low temperature exposure are the genes with putative functions related to auxin and gibberellin response, as well as general abiotic stress response, and genes coding for proteins with broad regulatory functions., Competing Interests: The authors have declared that no competing interests exist.

Rational construction of advanced bifunctional catalysts with dual-active-sites is still challenging for both oxygen reduction (ORR) and oxygen evolution reactions (OER). Herein, metal-doped dicyandiamide formaldehyde resin is innovatively exploited to synthesize N/Co/Fe/Ni multi-doped carbon nanotubes (denoted as CoFeNi@CNT) with metal-nitrogen-carbon (MNC) and CoFeNi nanoparticles as the ORR and OER active sites, respectively. Abundant active sites and high degree of graphitization enable CoFeNi@CNT with a high ORR half-wave potential of 0.82 V and a low OER overpotential of 440 mV at 10 mA cm -2 , which are comparable or superior to noble-metal catalysts. Particularly, the CoFeNi@CNT air electrode of rechargeable Zn-air batteries shows remarkable open circuit potential (1.46 V), discharge power density (152.3 mW cm -2 ), specific capacity (814 mAh g -1 ), and cycling stability for more than 250 h. It is worth emphasizing that this synthesis strategy is rather simple, low-cost, high yield, and the proportion and amount of doped metal ions can be easily adjusted according to the needs for different applications., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

The lysine methyltransferase NSD3 is required for the expression of key neural crest transcription factors and the migration of neural crest cells. Nevertheless, a complete view of the genes dependent upon NSD3 for expression and the developmental processes impacted by NSD3 in the neural crest was lacking. We used RNA sequencing (RNA-seq) to profile transcripts differentially expressed after NSD3 knockdown in chick premigratory neural crest cells, identifying 674 genes. Gene Ontology and gene set enrichment analyses further support a requirement for NSD3 during neural crest development and show that NSD3 knockdown also upregulates ribosome biogenesis. To validate our results, we selected three genes not previously associated with neural crest development, Astrotactin 1 (Astn1), Dispatched 3 (Disp3), and Tropomyosin 1 (Tpm1). Using whole mount in situ hybridization, we show that premigratory neural crest cells express these genes and that NSD3 knockdown downregulates (Astn1 and Disp3) and upregulates (Tpm1) their expression, consistent with RNA-seq results. Altogether, this study identifies novel putative regulators of neural crest development and provides insight into the transcriptional consequences of NSD3 in the neural crest, with implications for cancer., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Physical distancing and inaccessibility to laboratory facilities created an opportunity to transition undergraduate research experiences to remote, digital platforms, adding another level of pedagogy to their training. Basic bioinformatics skills together with critical analysis of scientific literature are essential for addressing research questions in modern biology. The work presented here describes a fully online, collaborative research experience created to allow undergraduate students to learn those skills. The research experience was focused on the development and implementation of the Organonitrogen Biodegradation Database (ONDB, z.umn.edu/ondb). The ONDB was developed to catalog information about the cost, chemical properties, and biodegradation potential of commonly used organonitrogen compounds. A cross-institutional team of undergraduate researchers worked in collaboration with two faculty members and a postdoctoral fellow to develop the database. Students carried out extensive online literature searches and used a biodegradation prediction website to research and represent the microbial catabolism of different organonitrogen compounds. Participants employed computational tools such as R, Shiny, and flexdashboard to construct the database pages and interactive web interface for the ONDB. Worksheets and forms were created to encourage other students and researchers to gather information about organonitrogen compounds and expand the database. Student progress was evaluated through biweekly project meetings, presentations, and a final reflection. The ONDB undergraduate research experience provided a platform for students to learn bioinformatics skills while simultaneously developing a teaching and research tool for others., (©2021 Author(s). Published by the American Society for Microbiology.)

The world faces two seemingly unrelated challenges-a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery., (Copyright © 2021 Hurley et al.)

Background: An analysis of the position statements of secular US medical and surgical professional societies on physician-assisted suicide (PAS) and euthanasia have not been published recently. Available statements were evaluated for position, content, and sentiment., Methods: In order to create a comprehensive list of secular medical and surgical societies, the results of a systematic search using Google were cross-referenced with a list of societies that have a seat on the American Medical Association House of Delegates. Societies with position statements were identified. These statements were divided into 5 categories: opposed to PAS and/or euthanasia, studied neutrality, supportive, acknowledgement without statement, and no statement. Linguistic analysis was performed using RapidMinder in order to determine word frequency and sentiment respective to individual statements. To ensure accuracy, only statements with word counts > 100 were analyzed. A 2-tailed independent t test was used to test for variance among sentiment scores of opposing and studied neutrality statements., Results: Of 150 societies, only 12 (8%) have position statements on PAS and euthanasia: 11 for PAS (5 opposing and 4 studied neutrality) and 9 for euthanasia (6 opposing and 2 studied neutrality). Although the most popular words used in opposing and studied neutrality statements are similar, notable exceptions exist (suicide, medicine, and treatment appear frequently in opposing statements, but not in studied neutrality statements, whereas psychologists, law, and individuals appear frequently in studied neutrality statements, but not in opposing statements). Sentiment scores for opposing and studied neutrality statements do not differ (mean, 0.094 vs. 0.104; P = 0.90)., Conclusions: Few US medical and surgical societies have position statements on PAS and euthanasia. Among them, opposing and studied neutrality statements share similar linguistic sentiment. Opposing and studied neutrality statements have clear differences, but share recommendations. Both opposing and studied neutrality statements cite potential risks of PAS legalization and suggest that good palliative care might diminish a patient's desire for PAS.

Bioinformatics skills are increasingly relevant to research in most areas of the life sciences. The availability of genome sequences and large data sets provide unique opportunities to incorporate bioinformatics exercises into undergraduate microbiology courses. The goal of this project was to develop a teaching module to investigate the abundance and phylogenetic relationships amongst bacteriophages using a set of freely available bioinformatics tools. Computational identification and examination of bacteriophage genomes, followed by phylogenetic analyses, provides opportunities to incorporate core bioinformatics competencies in microbiology courses and enhance students' bioinformatics skills. The first activity consisted of using PHASTER (PHAge Search Tool Enhanced Release), a bioinformatics tool that identifies bacteriophage sequences within bacterial chromosomes. Further computational analyses were conducted to align bacteriophage proteins, genomes, and determine phylogenetic relationships amongst these viruses. This part of the project was carried out using the Clustal omega, MAFFT (Multiple Alignment using Fast Fourier Transform), and Interactive Tree of Life (iTOL) programs for sequence alignments and phylogenetic analyses. The laboratory activities were field tested in undergraduate directed research, and microbiology classes. The learning objectives were assessed by comparing the scores of pre and post-tests and grading final presentations. Post-tests were higher than pre-test scores at or below p = 0.002. The data suggest in silico phage hunting improves students' ability to search databases, interpret phylogenetic trees, and use bioinformatics tools to examine genome structure. This activity allows instructors to integrate key bioinformatic concepts in their curriculums and gives students the opportunity to participate in a research-directed learning environment in the classroom., (Copyright © 2020 Martinez-Vaz and Mickelson.)

The goal of our study was to measure the kinetics of human colorectal cancer (CRC) development in order to identify aberrant mechanisms in tissue dynamics and processes that contribute to colon tumorigenesis. The kinetics of tumor development were investigated using age-at-tumor diagnosis (adenomas and CRCs) of familial adenomatous coli (FAP) patients and sporadic CRC patients. Plots of age-at-tumor diagnosis data as a function of age showed a distinct sigmoidal-shaped curve that is characteristic of an autocatalytic reaction. Consequently, we performed logistics function analysis and found an excellent fit ( p < 0.05) of the logistic equation to the curves for age-at-tumor diagnoses. These findings indicate that the tissue mechanism that becomes altered in CRC development and growth involves an autocatalytic reaction. We conjecture that colonic epithelium normally functions as a polymer of cells which dynamically maintains itself in a steady state through an autocatalytic polymerization mechanism. Further, in FAP and sporadic CRC patients, mutation in the adenomatous polyposis coli ( APC ) gene increases autocatalytic tissue polymerization and induces tumor tissues to autocatalyze their own progressive growth, which drives tumor development in the colon.

Cyanuric acid is an industrial chemical produced during the biodegradation of s -triazine pesticides. The biodegradation of cyanuric acid has been elucidated using a single model system, Pseudomonas sp. strain ADP, in which cyanuric acid hydrolase (AtzD) opens the s -triazine ring and AtzEG deaminates the ring-opened product. A significant question remains as to whether the metabolic pathway found in Pseudomonas sp. ADP is the exception or the rule in bacterial genomes globally. Here, we show that most bacteria utilize a different pathway, metabolizing cyanuric acid via biuret. The new pathway was determined by reconstituting the pathway in vitro with purified enzymes and by mining more than 250,000 genomes and metagenomes. We isolated soil bacteria that grow on cyanuric acid as a sole nitrogen source and showed that the genome from a Herbaspirillum strain had a canonical cyanuric acid hydrolase gene but different flanking genes. The flanking gene trtB encoded an enzyme that we show catalyzed the decarboxylation of the cyanuric acid hydrolase product, carboxybiuret. The reaction generated biuret, a pathway intermediate further transformed by biuret hydrolase (BiuH). The prevalence of the newly defined pathway was determined by cooccurrence analysis of cyanuric acid hydrolase genes and flanking genes. Here, we show the biuret pathway was more than 1 order of magnitude more prevalent than the original Pseudomonas sp. ADP pathway. Mining a database of over 40,000 bacterial isolates with precise geospatial metadata showed that bacteria with concurrent cyanuric acid and biuret hydrolase genes were distributed throughout the United States. IMPORTANCE Cyanuric acid is produced naturally as a contaminant in urea fertilizer, and it is used as a chlorine stabilizer in swimming pools. Cyanuric acid-degrading bacteria are used commercially in removing cyanuric acid from pool water when it exceeds desired levels. The total volume of cyanuric acid produced annually exceeds 200 million kilograms, most of which enters the natural environment. In this context, it is important to have a global understanding of cyanuric acid biodegradation by microbial communities in natural and engineered systems. Current knowledge of cyanuric acid metabolism largely derives from studies on the enzymes from a single model organism, Pseudomonas sp. ADP. In this study, we obtained and studied new microbes and discovered a previously unknown cyanuric acid degradation pathway. The new pathway identified here was found to be much more prevalent than the pathway previously established for Pseudomonas sp. ADP. In addition, the types of environment, taxonomic prevalences, and geospatial distributions of the different cyanuric acid degradation pathways are described here., (Copyright © 2020 American Society for Microbiology.)

Purpose: This article explores the results of community-engaged PhotoVoice research with the Family Tree Clinic (FTC) in St. Paul, MN. FTC has >45 years of experience providing sexual, reproductive, and primary health care, with a central mission of overcoming issues for their patients including those of poverty, oppression, lack of access, and discrimination in meeting health care needs. Methods: This research presents the findings of social justice-inspired PhotoVoice focus groups with patients of the clinic that asked two central questions: "Why do you choose Family Tree Clinic" and "What stands in the way of achieving your goals for your health?" Results: When health equity is a central priority and evident in clinic culture, practices, and policies, patients articulate positive experiences despite real structural and systemic barriers outside the clinic. Conclusion: We offer suggestions for a health equity-oriented approach to clinic care., Competing Interests: No competing financial interests exist., (© Susi L. Keefe et al. 2019; Published by Mary Ann Liebert, Inc.)

We concretely report feasible synthesis procedures of colloidal Cu 2 ZnSn(S 1- x ,Se x ) 4 -Au (CZTSSe-Au) nano-heterostructured composites, and creatively employ them as the counter electrodes (CEs) of all-solid-state solar cells with inorganic CsSnI 2.95 F 0.05 perovskite hole conductor. Acquired optical characterization indicates that integration of noble metal nanoparticles with cuprum-chalcogenide could heighten light absorption within visible-band due to localized surface plasmon resonance (LSPR) generated by Au, and the forbidden gap of nanocomposites gets adjustment accordingly. It is demonstrated that this novel photocathode alternative with favorable conductivity can not only match the energy level within the device band structure construction, but also restrain recombination so that accelerate charge transfer and extraction occurring on the photocathode. The photocurrent and photoelectric conversion efficiency (PCE) of cells conjugating CZTS-Au photocathodes turn to be respectively 43% and 25% higher than those using pure CZTS. Moreover, it has been demonstrated that CZTS-Au, coupling very well with inorganic perovskite, owns comparable electrocatalytic performance and even higher output photocurrent with respect to platinum CEs, which portends a potential substitution for conventional costly photocathodes. A comprehensive analysis on impedance spectroscopy data is subsequently carried out for the sake of deep understanding charge accumulation and transfer response at CsSnI 2.95 F 0.05 /CE interface, attempting to orient further optimization of device performance., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The present study examined the influence of maternal and child characteristics on parenting behaviors in a genetically informative study. The participants were 976 twins and their mothers from the Colorado Longitudinal Twin Study and the Twin Infant Project. Indicators of positive parenting were coded during parent-child interactions when twins were 7-36 months old. Child cognitive abilities and affection were independent correlates of positive parenting. There were significant gender differences in the magnitude of genetic and environmental influences on positive parenting, with shared environmental influences on parenting of girls and additive genetic influences on parenting of boys. Girls received significantly more positive parenting than boys. Differences in etiology of positive parenting may be explained by developmental gender differences in child cognitive abilities and affection, such that girls may have more rewarding interactions with parents, evoking more positive parenting.

Sinorhiozbium bacteriophage HMSP1-Susan has a genome of 51,963 bp in size, with a GC content of 52.5%. It contains 97 putative coding sequences; 83% of these coding sequences (CDS) encode proteins classified as hypothetical or having unknown functions. HMSP1 has limited homology to previously reported viruses and likely represents a new phage that infects this nitrogen-fixing bacterium., (Copyright © 2018 Fleagle et al.)

Objective: Mesenchymal stem cells (MSCs) are multipotent stromal cells that can differentiate into a variety of cell types. They control the process of hematopoiesis by secreting regulatory cytokines and growth factors and by the expression of important cell adhesion molecules for cell-to-cell interactions. This investigation was intended to examine the effect of bone marrow (BM)-derived MSCs on the differentiation of HL-60 cells according to morphological evaluation, flow cytometry analysis, and gene expression profile., Materials and Methods: The BM-MSCs were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (FBS). After the third passage, the BM-MSCs were irradiated at 30 Gy. To compare how the HL-60 cells differentiated in groups treated differently, HL-60 cells were cultured in RPMI-1640 and supplemented with 10% FBS. The HL-60 cells were seeded into six-well culture plates and treated with all-trans-retinoic acid (ATRA), BM-MSCs, or BM-MSCs in combination with ATRA, while one well remained as untreated HL-60 cells. The expression levels of the granulocyte subset-specific genes in the HL-60 cells were assayed by real-time polymerase chain reaction., Results: Our results revealed that BM-MSCs support the granulocytic differentiation of the human promyelocytic leukemia cell line HL-60., Conclusion: Based on the results of this study, we concluded that BM-MSCs may be an effective resource in reducing or even preventing ATRA's side effects and may promote differentiation for short medication periods. Though BM-MSCs are effective resources, more complementary studies are necessary to improve this differentiation mechanism in clinical cases.

Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both cis- and trans-regulatory features. In order to study the variability in transcriptome response to abiotic stress, RNA sequencing was performed using 14-day-old maize seedlings of inbreds B73, Mo17, Oh43, PH207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified. RNA sequencing was also performed on similar tissues of the F 1 hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele-specific transcript abundance in the F 1 hybrids, we were able to measure the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Although examples of trans-regulatory variation were observed, cis-regulatory variation was more common for both steady-state and stress-responsive expression differences. The genes with cis-allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

Plants are ideal systems to teach core biology concepts due to their unique physiological and developmental features. Advances in DNA sequencing technology and genomics have allowed scientists to generate genome sequences and transcriptomics data for numerous model plant species. This information is publicly available and presents a valuable tool to introduce undergraduate students to the fundamental concepts of gene expression in the context of modern quantitative biology and bioinformatics. Modern biology classrooms must provide authentic research experiences to allow developing core competencies such as scientific inquiry, critical interpretation of experimental results, and quantitative analyses of large dataset using computational approaches. Recent educational research has shown that undergraduate students struggle when connecting gene expression concepts to classic genetics, phenotypic analyses, and overall flow of biological information in living organisms, suggesting that novel approaches are necessary to enhance learning of gene expression and regulation. This review describes different strategies and resources available to instructors willing to incorporate authentic research experiences, genomic tools, and bioinformatics analyses when teaching transcriptional regulation and gene expression in undergraduate courses. A variety of laboratory exercises and pedagogy materials developed to teach gene expression using plants are discussed. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer., (Copyright © 2016 Elsevier B.V. All rights reserved.)

The sheer amount of terminology and conceptual knowledge required for anatomy and physiology can be overwhelming for students. Educational games are one approach to reinforce such knowledge. In this activity, students worked collaboratively to review anatomy and physiology concepts by creating arrays of descriptive tiles to define a term. Once guessed, students located the structure or process within diagrams of the body. The game challenged students to think about course vocabulary in novel ways and to use their collective knowledge to get their classmates to guess the terms. Comparison of pretest/posttest/delayed posttest data revealed that students achieved statistically significant learning gains for each unit after playing the game, and a survey of student perceptions demonstrated that the game was helpful for learning vocabulary as well as fun to play. The game is easily adaptable for a variety of lower- and upper-division courses., (Copyright © 2016 The American Physiological Society.)

Microbiology courses often include a laboratory activity on the identification of unknown microbes. This activity consists of providing students with microbial cultures and running biochemical assays to identify the organisms. This approach lacks molecular techniques such as sequencing of genes encoding 16S rRNA, which is currently the method of choice for identification of unknown bacteria. A laboratory activity was developed to teach students how to identify microorganisms using 16S rRNA polymerase chain reaction (PCR) and validate microbial identities using biochemical techniques. We hypothesized that designing an experimental protocol to confirm the identity of a bacterium would improve students' knowledge of microbial identification techniques and the physiological characteristics of bacterial species. Nitrogen-fixing bacteria were isolated from the root nodules of Medicago truncatula and prepared for 16S rRNA PCR analysis. Once DNA sequencing revealed the identity of the organisms, the students designed experimental protocols to verify the identity of rhizobia. An assessment was conducted by analyzing pre- and posttest scores and by grading students' verification protocols and presentations. Posttest scores were higher than pretest scores at or below p = 0.001. Normalized learning gains (G) showed an improvement of students' knowledge of microbial identification methods (LO4, G = 0.46), biochemical properties of nitrogen-fixing bacteria (LO3, G = 0.45), and the events leading to the establishment of nitrogen-fixing symbioses (LO1&2, G = 0.51, G = 0.37). An evaluation of verification protocols also showed significant improvement with a p value of less than 0.001.

The maize genome is relatively large (∼ 2.3 Gb) and has a complex organization of interspersed genes and transposable elements, which necessitates frequent boundaries between different types of chromatin. The examination of maize genes and conserved noncoding sequences revealed that many of these are flanked by regions of elevated asymmetric CHH (where H is A, C, or T) methylation (termed mCHH islands). These mCHH islands are quite short (∼ 100 bp), are enriched near active genes, and often occur at the edge of the transposon that is located nearest to genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications revealed that mCHH islands mark the transition from heterochromatin-associated modifications to euchromatin-associated modifications. The presence of an mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of insertion/deletions in promoters often influences the presence and position of an mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities and are lost in mop1 and mop3 mutants, but the nearby genes rarely exhibit altered expression levels. Instead, loss of an mCHH island is often accompanied by additional loss of DNA methylation in CG and CHG contexts associated with heterochromatin in nearby transposons. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of nearby genes.

Integration of inquiry-based approaches into curriculum is transforming the way science is taught and studied in undergraduate classrooms. Incorporating quantitative reasoning and mathematical skills into authentic biology undergraduate research projects has been shown to benefit students in developing various skills necessary for future scientists and to attract students to science, technology, engineering, and mathematics disciplines. While large-scale data analysis became an essential part of modern biological research, students have few opportunities to engage in analysis of large biological data sets. RNA-seq analysis, a tool that allows precise measurement of the level of gene expression for all genes in a genome, revolutionized molecular biology and provides ample opportunities for engaging students in authentic research. We developed, implemented, and assessed a series of authentic research laboratory exercises incorporating a large data RNA-seq analysis into an introductory undergraduate classroom. Our laboratory series is focused on analyzing gene expression changes in response to abiotic stress in maize seedlings; however, it could be easily adapted to the analysis of any other biological system with available RNA-seq data. Objective and subjective assessment of student learning demonstrated gains in understanding important biological concepts and in skills related to the process of science., (© 2015 I. Makarevitch et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).)

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as "junk" DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

The National Institutes of Health (NIH) are responsible for the largest proportion of biological science funding in the United States. To protect the public interest in access to publicly funded scientific research, the NIH amended terms and conditions in funding agreements after 2009, requiring funded Principal Investigators to deposit published copies of research in PubMed, an Open Access repository. Principal Investigators have partially complied with this depository requirement, and the NIH have signaled an intent to enforce grant agreement terms and conditions by stopping funding deposits and engaging in legal action. The global economic value of accessible knowledge offers a unique opportunity for courts to evaluate the impact of enforcing 'openness' contract terms and conditions within domestic and international economies for public and economic benefit. Through judicial enforcement of Open Access terms and conditions, the United States can increase economic efficiency for university libraries, academic participants, and public consumers, while accelerating global innovation, improving financial returns on science funding investments, and advancing more efficient scientific publishing models.

Aberrant activation of fibroblast growth factor receptors (FGFR) contributes to breast cancer growth, progression, and therapeutic resistance. Because of the complex nature of the FGF/FGFR axis, and the numerous effects of FGFR activation on tumor cells and the surrounding microenvironment, the specific mechanisms through which aberrant FGFR activity contributes to breast cancer are not completely understood. We show here that FGFR activation induces accumulation of hyaluronan within the extracellular matrix and that blocking hyaluronan synthesis decreases proliferation, migration, and therapeutic resistance. Furthermore, FGFR-mediated hyaluronan accumulation requires activation of the STAT3 pathway, which regulates expression of hyaluronan synthase 2 (HAS2) and subsequent hyaluronan synthesis. Using a novel in vivo model of FGFR-dependent tumor growth, we demonstrate that STAT3 inhibition decreases both FGFR-driven tumor growth and hyaluronan levels within the tumor. Finally, our results suggest that combinatorial therapies inhibiting both FGFR activity and hyaluronan synthesis is more effective than targeting either pathway alone and may be a relevant therapeutic approach for breast cancers associated with high levels of FGFR activity. In conclusion, these studies indicate a novel targetable mechanism through which FGFR activation in breast cancer cells induces a protumorigenic microenvironment.

Leafy green vegetables have been identified as a source of foodborne illnesses worldwide over the past decade. Human enteric pathogens, such as Escherichia coli O157:H7 and Salmonella, have been implicated in numerous food poisoning outbreaks associated with the consumption of fresh produce. An understanding of the mechanisms responsible for the establishment of pathogenic bacteria in or on vegetable plants is critical for understanding and ameliorating this problem as well as ensuring the safety of our food supply. While previous studies have described the growth and survival of enteric pathogens in the environment and also the risk factors associated with the contamination of vegetables, the molecular events involved in the colonization of fresh produce by enteric pathogens are just beginning to be elucidated. This review summarizes recent findings on the interactions of several bacterial pathogens with leafy green vegetables. Changes in gene expression linked to the bacterial attachment and colonization of plant structures are discussed in light of their relevance to plant-microbe interactions. We propose a mechanism for the establishment and association of enteric pathogens with plants and discuss potential strategies to address the problem of foodborne illness linked to the consumption of leafy green vegetables.

Trimethylation of histone H3 Lys-27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize (Zea mays) plants of two genetic backgrounds, B73 and Mo17. There were more substantial differences in the genome-wide profile of H3K27me3 between different tissues than between the two genotypes. The tissue-specific patterns of H3K27me3 were often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. A comparison of the H3K27me3 targets in rice (Oryza sativa), maize, and Arabidopsis thaliana provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole-genome duplication, suggesting the potential for subfunctionalization of chromatin regulation of paralogs. Genomic profiling of H3K27me3 in loss-of-function mutant lines for Maize Enhancer of zeste-like2 (Mez2) and Mez3, two of the three putative H3K27me3 methyltransferases present in the maize genome, suggested partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 required Mez2 and/or Mez3, and there was limited evidence for functional consequences of H3K27me3 at these targets.

The role of brassinosteroids in plant growth and development has been well-characterized in a number of plant species. However, very little is known about the role of brassinosteroids in maize. Map-based cloning of a severe dwarf mutant in maize revealed a nonsense mutation in an ortholog of a brassinosteroid C-6 oxidase, termed brd1, the gene encoding the enzyme that catalyzes the final steps of brassinosteroid synthesis. Homozygous brd1-m1 maize plants have essentially no internode elongation and exhibit no etiolation response when germinated in the dark. These phenotypes could be rescued by exogenous application of brassinolide, confirming the molecular defect in the maize brd1-m1 mutant. The brd1-m1 mutant plants also display alterations in leaf and floral morphology. The meristem is not altered in size but there is evidence for differences in the cellular structure of several tissues. The isolation of a maize mutant defective in brassinosteroid synthesis will provide opportunities for the analysis of the role of brassinosteroids in this important crop system.

In this laboratory exercise, students were taught concepts of microbiology and scientific process through an everyday activity - cosmetic use. The students' goals for the lab were to develop a hypothesis regarding microbial contamination in cosmetics, learn techniques to culture and differentiate microorganisms from cosmetics, and propose best practices in cosmetics use based on their findings. Prior to the lab, students took a pretest to assess their knowledge of scientific hypotheses, microbiology, and cosmetic safety. In the first week, students were introduced to microbiological concepts and methodologies, and cosmetic terminology and safety. Students completed a hypothesis-writing exercise before formulating and testing their own hypotheses regarding cosmetic contamination. Students provided a cosmetic of their own and, in consultation with their lab group, chose one product for testing. Samples were serially diluted and plated on a variety of selective media. In the second week, students analyzed their plates to determine the presence and diversity of microbes and if their hypotheses were supported. Students completed a worksheet of their results and were given a posttest to assess their knowledge. Average test scores improved from 5.2 (pretest) to 7.8 (posttest), with p-values < 0.0001. Seventy-nine percent (79%) of students correctly identified hypotheses that were not falsifiable or lacked variables, and 89% of students improved their scores on questions concerning safe cosmetic use. Ninety-one percent (91%) of students demonstrated increased knowledge of microbial concepts and methods. Based on our results, this lab is an easy, yet effective, way to enhance knowledge of scientific concepts for nonmajors, while maintaining relevance to everyday life.