Data Processing & Analysis for Atomic Force Microscopy (AFM)

Scanning Probe Microscopy (SPM) has become a critical tool for characterization of materials in fields such as physics, material science, chemistry, and biology. Atomic Force Microscopy (AFM) is an increasingly useful technique because of its high resolution in three dimensions, the sample does not need to be conductive, and the technique does not need to take place in vacuum. AFM can image a wide variety of topographies and many different types of materials. AFM can deliver 3D topography information from the angstrom level to the micron scale with high resolution. One of the most important aspects of Atomic Force Microscopy that is not often discussed is data processing and analysis. The goal of this report is to demonstrate various data processing and analysis techniques such as studying the coating process, grain analysis, texture analysis and surface roughness

A Regression-Based Differential Expression Detection Algorithm for Microarray Studies with Ultra-Low Sample Size

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED). Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality

Coping Strategies to Promote Mental Wellness

Coping Strategies to Promote Mental Wellness Over eight weeks, our nursing school leadership team collaborated with a Seattle non- profit agency whose mission is to provide resources, planning, and housing to families with children experiencing homelessness. Our team’s overarching goal by the end of this project, based on the needs expressed by the agency, was to create a tool that provides resources and coping skills to families experiencing homelessness to improve mental health and promote wellness. Background The population that is served by the agency includes families with at least one child under the age of eighteen, children with medical needs, and pregnant women, all of whom are experiencing homelessness (Agency, personal communication, Sep 20, 2023). Outreach for these families is conducted on the phone by appointment, in the community, or by walk-in appointments; guests often don’t return after assistance and resources are provided. According to the agency liaison, there is a high level of stressors seen in this population, including gun violence, theft and other violent crime, past trauma, prevalence of past drug use that causes temptations, and additional personal stressors for the individuals in this community (Agency, personal communication, Sep 20, 2023). The agency serves the unhoused population in South Seattle and collaborates with a secondary agency that provides temporary housing. When our team completed a windshield survey of the area, we observed cracked sidewalks, abandoned buildings, and a large encampment for unhoused individuals across the street. The team also observed environmental stressors such as, loud construction sites, an abundance of liquor stores, convenience stores, abandoned vehicles, and a lack of grocery and retail stores. According to Seattle statistics, “11,751 people [were] experiencing homelessness on one night in January, with 53% sheltered and 43% unsheltered... [which] reflects a 5% increase compared to 2019 count” (City of Seattle, 2023). Despite the continued efforts of the City of Seattle to create more affordable housing with a widespread movement to bring people indoors, the number of individuals who are unhoused continues to increase, and available city resources struggle to keep up with the growing population that is unhoused. According to the Seattle Police Department, crime in the area has increased significantly since 2019. The violent crimes reached a 15-year high in 2022, which is a 4% increase compared to 2021 (Seattle Police Department, 2023). People who are unhoused are already at an increased risk of suffering from mental health disorders, with crime being a significant contributor of stress among individuals who are unhoused, especially for families with children (Lippert & Lee, 2015). Various stressors such as crime, commonly seen in individuals who are unhoused, can exacerbate existing mental health problems by undermining economic stability, safety, and social integration (Lippert & Lee, 2015). The increased stressors exacerbating mental illness prompted a need for education on coping strategies. We established the nursing diagnosis for this population as a knowledge deficit related to healthy coping strategies, as evidenced by the agency liaison reporting the need for resources that promote mental wellness and provide healthy coping mechanisms. Activities/Rationale The priority coping strategies we chose are box breathing, guided imagery, and muscle relaxation (Norelli, 2018). These coping skills are clinically shown to reduce tension, anxiety, physical and psychological challenges. As pictured above, increased mental distress, mental health issues, and associated stress related to homelessness are extremely prevalent among the population the agency serves. The following coping skills can be used anywhere, without the need for equipment, materials, or internet access. The box breathing exercise involves breathing in through the nose, holding the breath, and slowly breathing out. The duration of each step can be adjusted per individual preferences. The second coping mechanism is guided imagery, which involves visualizing a calm environment by recalling a distant memory or imagining a happy place while using the five senses to visualize the setting. The final coping strategy involves progressive muscle relaxation, a series of tensing and relaxing the different muscles of the body. The chosen delivery method is through a pamphlet, which can be disseminated to the agency\u27s guests either in person or electronically in the form of a PDF. The pamphlet can be folded into a small, pocket-sized piece that can then be inserted into a protective plastic badge holder, attached to a badge reel. The plastic badge holder serves the purpose to ensure that the pamphlet is durable and sustainable even in the target community’s living environments with harsh weather conditions. In addition, we have included a QR code on the back of the pamphlet which can be utilized to keep the information available on personal devices. Outcome This project had two main goals; the first outcome to achieve was to give unhoused families access to mental health coping strategies and tools to manage stress and anxiety. This goal was met, as our group produced and provided a pamphlet to the agency that contains three different coping strategies that can be used to improve mental wellness. While there were many other possible coping strategies available, we strategically narrowed down to three evidenced- based tools that can be easily completed anywhere the families may be. The second goal was to give unhoused families immediate access to mental health resources outside of the provided coping strategies. We provided the crisis line phone number on the front of the pamphlet, as well as in the coping card section. The rationale was to provide a resource for immediate assistance, that connects the guest to a trained crisis interventionist who can then provide additional resources. Overall, both goals were met in terms of the content of the mental wellness pamphlet. The team sought to evaluate the implementation of the mental wellness pamphlet, a three- question qualitative survey was sent to the agency; however, there was inadequate time for agency to disseminate to staff, thus responses beyond our two agency liaisons could not be evaluated. In addition, assessing the effectiveness of the pamphlet is not feasible; firstly, the population will receive the pamphlet upon completion of the project and thus cannot be surveyed after use. Secondly, walk-in guests receive assistance and resources one time and often do not return. Conclusion The wellness pamphlet will provide a convenient and accessible resource for the South Seattle population dealing with stressors that negatively impact their mental health. We’ve accomplished this by creating flexibility and providing a choice between carrying the pamphlet, badge holder, or QR code. This enables the clients to readily execute the coping skills wherever they are. Limitations identified pertain to the inability to directly assess the population and evaluate implementation of coping strategies, and agency being given inadequate time to disseminate and return qualitative evaluation survey prior to the project deadline. Moreover, the goals were met by providing simplified mental health resources through implementation of coping strategies and providing the crisis line phone number. Lastly, future projects could include an outreach program that focuses on teaching coping strategies to the community. References City of Seattle. (2023). Addressing homelessness. https://www.seattle.gov/human- services/reports-and-data/addressing-homelessness City of Seattle. (2023). Homelessness action plan. Office of the Mayor. https://www.seattle.gov/mayor/one-seattle-initiatives/homelessness-action-plan Gibbs, K. D., Jones, J. T., LaMark, W., Abdulmooti, S., Bretz, L., Kearney, K. D., Narendorf, S. C., & Santa Maria, D. M. (2023). Coping during the COVID‐19 pandemic among young adults experiencing homelessness and unstable housing: A qualitative study. Public Health Nursing, 40(1), p. 17-27. https://doi.org/10.1111/phn.13136 Lippert, A., & Lee, B. (2015). Stress, coping, and mental health differences among homeless people. Sociology Inquiry, 85(3), p. 343-374. https://doi.org/10.1111/soin.12080 Mayne, S.L., DiFiore, G., Hannan, C., Virudachalam, S., Glanz, K., & Fiks, A. G. (2022). Association of neighborhood social context and perceived stress among mothers of young children. Academic Pediatrics, 22(8), 1414-1421.https://doi.org/10.1016/j.acap.2022.03.013 Norelli, S., Long, A., & Krepps, J. (2018). Relaxation techniques. StatsPearls Publishing, Treasure Island (FL). https://europepmc.org/article/nbk/nbk513238#__NBK513238_dtls__ Seattle Police Department. (2023). Crime report 2022. https://www.seattle.gov/documents/Departments/Police/Reports/2022_SPD_CRIME_RE PORT_FINAL.pd

Speciation within Bonneted Bats (Genus \u3ci\u3eEumops\u3c/i\u3e): The Complexity of Morphological, Mitochondrial, and Nuclear Data Sets in Systematics

We phylogenetically analyze 705 base pairs of the cytochrome-b gene and 351 amplified fragment length polymorphism (AFLP) bands from populations of the karyotypically variable Wagner’s bonneted bat, Eumops glaucinus, and the Florida bonneted bat, Eumops floridanus (Chiroptera: Molossidae). Three karyotypes have been documented across the range of E. glaucinus, and we report that the karyotype from Cuba is morphologically similar to that from Jamaica. A 4th karyotype is present in specimens from western Ecuador. Three distinct lineages are present in both the cytochrome-b and AFLP trees. One lineage is restricted to western Ecuador and exhibits cytochrome-b divergence values comparable to the values seen between recognized species of Eumops, suggesting that this lineage represents a distinct species. The other 2 lineages are distributed in disjunct areas: Paraguay and Venezuela; and Mexico, the Caribbean, and the United States. Specimens of E. floridanus are morphologically distinct from E. glaucinus, but cannot be distinguished by examination of cytochrome-b or AFLP DNA data. We conclude that there are 4 species in the E. glaucinus complex— E. glaucinus (South America east of the Andes), E. ferox (Caribbean, Mexico, and Central America), E. floridanus in south Florida, and an unnamed taxon in western Ecuador. Speciation is a complex process and no single mechanism, model, concept, or definition is likely to cover all the diverse patterns observed

Speciation within bonneted bats (genus Eumops): The complexity of morphological, mitochondrial, and nuclear datasets in systematics

We phylogenetically analyze cytochrome-b gene sequences and Amplified Fragment Length Polymorphisms (AFLPs) from populations of the karyotypically variable Wagner’s bonneted bat, Eumops glaucinus, and the Florida bonneted bat, Eumops floridanus (Chiroptera: Molossidae). Three karyotypes have been documented previously across the range of E. glaucinus, and we report that the karyotype from Cuba is morphologically similar to that found in specimens from Jamaica. A 4th karyotype (described herein) is present in specimens from western Ecuador. DNA sequence variation within 705 base pairs of the cytochrome-b gene from 47 specimens from Florida, Cuba, Jamaica, Mexico, Venezuela, Ecuador, and Paraguay were examined and analyzed using maximum likelihood and Bayesian analyses. Additionally, 351 AFLP bands from 23 specimens were phylogenetically analyzed. Three distinct lineages are present in both the cytochrome-b and AFLP trees. One clade is restricted to western Ecuador and has a 7-8% cytochrome b sequence divergence from all other haplotypes of the species complex. The other 2 lineages have cytochrome-b divergences > 3–4% and are distributed in disjunct areas: 1) Paraguay and Venezuela; and 2) Mexico, the Caribbean, and the United States. The cytochrome b divergence between populations of E. glaucinus west of the Andes and all other populations of E. glaucinus is comparable to that between recognized species of Eumops, suggesting that the Ecuadorian bonneted bats represent a distinct species. Specimens of E. floridanus are morphologically distinct from E. glaucinus, but cannot be distinguished by cytochrome-b or AFLP DNA data. We conclude that there are 4 species in the Eumops glaucinus complex—Eumops glaucinus (in South America east of the Andes), E. ferox (in the Caribbean, Mexico, and Central America), E. floridanus in south Florida, and an unnamed taxon in western Ecuador. Speciation is a complex process and no single mechanism, model, concept, or definition is likely to cover all the diverse patterns observed

Dissection, Culture, and Analysis of Xenopus laevis Embryonic Retinal Tissue

The process by which the anterior region of the neural plate gives rise to the vertebrate retina continues to be a major focus of both clinical and basic research. In addition to the obvious medical relevance for understanding and treating retinal disease, the development of the vertebrate retina continues to serve as an important and elegant model system for understanding neuronal cell type determination and differentiation(1-16). The neural retina consists of six discrete cell types (ganglion, amacrine, horizontal, photoreceptors, bipolar cells, and Muller glial cells) arranged in stereotypical layers, a pattern that is largely conserved among all vertebrates (12,14-18). While studying the retina in the intact developing embryo is clearly required for understanding how this complex organ develops from a protrusion of the forebrain into a layered structure, there are many questions that benefit from employing approaches using primary cell culture of presumptive retinal cells (7,19-23). For example, analyzing cells from tissues removed and dissociated at different stages allows one to discern the state of specification of individual cells at different developmental stages, that is, the fate of the cells in the absence of interactions with neighboring tissues (8,19-22,24-33). Primary cell culture also allows the investigator to treat the culture with specific reagents and analyze the results on a single cell level (5,8,21,24,27-30,33-39). Xenopus laevis, a classic model system for the study of early neural development (19,27,29,31-32,40-42), serves as a particularly suitable system for retinal primary cell culture (10,38,43-45). Presumptive retinal tissue is accessible from the earliest stages of development, immediately following neural induction (25,38,43). In addition, given that each cell in the embryo contains a supply of yolk, retinal cells can be cultured in a very simple defined media consisting of a buffered salt solution, thus removing the confounding effects of incubation or other sera-based products (10,24,44-45). However, the isolation of the retinal tissue from surrounding tissues and the subsequent processing is challenging. Here, we present a method for the dissection and dissociation of retinal cells in Xenopus laevis that will be used to prepare primary cell cultures that will, in turn, be analyzed for calcium activity and gene expression at the resolution of single cells. While the topic presented in this paper is the analysis of spontaneous calcium transients, the technique is broadly applicable to a wide array of research questions and approaches (Figure 1)

We do not want to “cure plant blindness” we want to grow plant love

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150580/1/ppp310062_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150580/2/ppp310062.pd

Conservation Status of the Plains Spotted Skunk, Spilogale putorius interrupta, in Texas, with an Assessment of Genetic Variability in the Species

Robert C. Dowler, Department of Biology at Angelo State University is the corresponding author, robert dot dowler at angelo dot eduIn this report, we present results of research on the conservation status of the plains spotted skunk (Spilogale putorius interrupta) in Texas and an assessment of the genetic variability in populations throughout the range of the species. The conservation status portion of the study included (1) mapping the species’ potential habitat in Texas using maximum entropy modeling (Maxent) with historic museum specimen records, (2) field-based surveying of locations in 10 counties to determine occurrence of the plains spotted skunk, (3) seeking additional occurrence records in Texas through crowd sourcing and citizen scientist approaches (4) using all current (2001 – 2017) occurrences to produce a model of probable geographic distribution in Texas and (5) assessing anthropogenic changes in land use, which may threaten the species’ habitats, by mapping current and forecasted oil and gas development and urbanization within the species’ modeled range. The species distribution model, combined with the land-change assessment, was used to select sites in 10 representative counties for field-based surveys in the hopes of revealing patterns of current distribution. Field surveys were carried out using live traps, enclosed track plates, and camera traps. These methods documented detections of plains spotted skunks (n = 12) in 4 of the 10 sites sampled. All methods of detection were successful, but cameras and live traps out-performed track plates. Crowd-sourced approaches and citizen scientist camera trapping revealed an additional 82 occurrences in the state, 79 of which were since 2009. These recent records were used to produce a species distribution model that provides relative probability of occurrence for the plains spotted skunk in the state. Our land-change mapping revealed potential anthropogenic threats to habitats at 2 of the sites (Katy Prairie and Fort Hood), which also had robust populations of plains spotted skunks based on 25 and 51detections, respectively). For our genetic assessment, samples of tissue from three sources (i.e., field surveys, state agencies throughout the distribution of the eastern spotted skunk, and museum tissue collections) allowed a detailed assessment of the genetic variability in the species (S. putorius) using both microsatellite markers and cytochrome b gene sequence. Our analysis of 119 specimens was able to establish that genetic patterns were consistent with currently accepted taxonomy of the 3 recognized subspecies of S. putorius (S. p. putorius, S. p. ambarvalis, and S. p. interrupta). We also determined that there was no evidence for hybridization with the congener, S. gracilis (western spotted skunk), a species co-occurring with the eastern spotted skunk in parts of Texas. The differentiation between S. p. putorius and S. p. ambarvalis was less pronounced (FST = 0.178; cytochrome b sequence divergence = 1.2%) than between these subspecies and the plains spotted skunk (average FST = 0.278; cytochrome b sequence divergence = 2.9%). Overall, genetic variability (observed heterozygosity = 0.474) in the plains spotted skunk was lower than that seen in common carnivores (striped skunks, raccoons), but slightly higher than some endangered carnivores (black-footed ferret). The heterozygosity levels more closely resemble the levels found within the island spotted skunk (S. gracilis amphiala) from the Channel Islands of California and other vertebrates that have a “threatened” conservation status. Key findings of the study include: 1) the current geographic distribution of the plains spotted skunk in Texas is reduced relative to historic records; 2) the species distribution model based on recorded occurrences since 2001 suggests areas of the state that are in need of further survey efforts; 3) genetic variability of plains spotted skunks is lower than more common carnivores, but higher than some recognized endangered species; 4) the subspecies, S. p. interrupta is a distinct genetic subunit of the eastern spotted skunk; and 5) continued energy development and especially future urbanization in some parts of Texas may affect populations of the plains spotted skunk.Texas Comptroller of Public AccountsBureau of Economic Geolog

Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists