Journal Articles, Multidisciplinary Digital Publishing Institute (MDPI)

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The Alternaria alternata Mycotoxin Alternariol Suppresses Lipopolysaccharide-Induced Inflammation
Grover, Shivani; Lawrence, Christopher B. (MDPI, 2017-07-20)
The Alternaria mycotoxins alternariol (AOH) and alternariol monomethyl ether (AME) have been shown to possess genotoxic and cytotoxic properties. In this study, the ability of AOH and AME to modulate innate immunity in the human bronchial epithelial cell line (BEAS-2B) and mouse macrophage cell line (RAW264.7) were investigated. During these studies, it was discovered that AOH and to a lesser extent AME potently suppressed lipopolysaccharide (LPS)-induced innate immune responses in a dose-dependent manner. Treatment of BEAS-2B cells with AOH resulted in morphological changes including a detached pattern of growth as well as elongated arms. AOH/AME-related immune suppression and morphological changes were linked to the ability of these mycotoxins to cause cell cycle arrest at the G2/M phase. This model was also used to investigate the AOH/AME mechanism of immune suppression in relation to aryl hydrocarbon receptor (AhR). AhR was not found to be important for the immunosuppressive properties of AOH/AME, but appeared important for the low levels of cell death observed in BEAS-2B cells.
Association of RERG Expression with Female Survival Advantage in Malignant Pleural Mesothelioma
De Rienzo, Assunta; Coleman, Melissa H.; Yeap, Beow Y.; Severson, David T.; Wadowski, Benjamin; Gustafson, Corinne E.; Jensen, Roderick V.; Chirieac, Lucian R.; Richards, William G.; Bueno, Raphael (MDPI, 2021-02-02)
Sex differences in incidence, prognosis, and treatment response have been described for many cancers. In malignant pleural mesothelioma (MPM), a lethal disease associated with asbestos exposure, men outnumber women 4 to 1, but women consistently live longer than men following surgery-based therapy. This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences. Two microarray datasets of MPM tumors were analyzed to discover estrogen-related genes associated with survival. A validation cohort of MPM tumors was selected to balance the numbers of men and women and control for competing prognostic influences. The RAS like estrogen regulated growth inhibitor (RERG) gene was identified as the most differentially-expressed estrogen-related gene in these tumors and predicted prognosis in discovery datasets. In the sex-matched validation cohort, low RERG expression was significantly associated with increased risk of death among women. No association between RERG expression and survival was found among men, and no relationship between estrogen receptor protein or gene expression and survival was found for either sex. Additional investigations are needed to elucidate the molecular mechanisms underlying this association and its sex specificity.
The Cannabis Proteome Draft Map Project
Jenkins, Conor; Orsburn, Benjamin (MDPI, 2020-01-31)
Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources.
Common Features of Opportunistic Premise Plumbing Pathogens
Falkinham, Joseph O. III (MDPI, 2015-04-24)
Recently it has been estimated that the annual cost of diseases caused by the waterborne pathogens Legionella pneumonia, Mycobacterium avium, and Pseudomonas aeruginosa is $500 million. For the period 2001–2012, the estimated cost of hospital admissions for nontuberculous mycobacterial pulmonary disease, the majority caused by M. avium, was almost $1 billion. These three waterborne opportunistic pathogens are normal inhabitants of drinking water—not contaminants—that share a number of key characteristics that predispose them to survival, persistence, and growth in drinking water distribution systems and premise plumbing. Herein, I list and describe these shared characteristics that include: disinfectant-resistance, biofilm-formation, growth in amoebae, growth at low organic carbon concentrations (oligotrophic), and growth under conditions of stagnation. This review is intended to increase awareness of OPPPs, identify emerging OPPPs, and challenge the drinking water industry to develop novel approaches toward their control.
Diversity Patterns Associated with Varying Dispersal Capabilities as a Function of Spatial and Local Environmental Variables in Small Wetlands in Forested Ecosystems
Tornwall, Brett M.; Pitt, Amber L.; Brown, Bryan L.; Hawley-Howard, Joanna; Baldwin, Robert F. (MDPI, 2020-10-29)
The diversity of species on a landscape is a function of the relative contribution of diversity at local sites and species turnover between sites. Diversity partitioning refers to the relative contributions of alpha (local) and beta (species turnover) diversity to gamma (regional/landscape) diversity and can be influenced by the relationship between dispersal capability as well as spatial and local environmental variables. Ecological theory predicts that variation in the distribution of organisms that are strong dispersers will be less influenced by spatial properties such as topography and connectivity of a region and more associated with the local environment. In contrast, the distribution of organisms with limited dispersal capabilities is often dictated by their limited dispersal capabilities. Small and ephemeral wetlands are centers of biodiversity in forested ecosystems. We sampled 41 small and ephemeral wetlands in forested ecosystems six times over a two-year period to determine if three different taxonomic groups differ in patterns of biodiversity on the landscape and/or demonstrate contrasting relationships with local environmental and spatial variables. We focused on aquatic macroinvertebrates (aerial active dispersers consisting predominantly of the class Insecta), amphibians (terrestrial active dispersers), and zooplankton (passive dispersers). We hypothesized that increasing active dispersal capabilities would lead to decreased beta diversity and more influence of local environmental variables on community structure with less influence of spatial variables. Our results revealed that amphibians had very high beta diversity and low alpha diversity when compared to the other two groups. Additionally, aquatic macroinvertebrate community variation was best explained by local environmental variables, whereas amphibian community variation was best explained by spatial variables. Zooplankton did not display any significant relationships to the spatial or local environmental variables that we measured. Our results suggest that amphibians may be particularly vulnerable to losses of wetland habitat in forested ecosystems as they have high beta diversity. Consequently, the loss of individual small wetlands potentially results in local extirpations of amphibian species in forested ecosystems.
DNA Double-Strand Breaks Are a Critical Regulator of Fear Memory Reconsolidation
Navabpour, Shaghayegh; Rogers, Jessie; McFadden, Taylor; Jarome, Timothy J. (MDPI, 2020-11-26)
Numerous studies have shown that following retrieval, a previously consolidated memory requires increased transcriptional regulation in order to be reconsolidated. Previously, it was reported that histone H3 lysine-4 trimethylation (H3K4me3), a marker of active transcription, is increased in the hippocampus after the retrieval of contextual fear memory. However, it is currently unknown how this epigenetic mark is regulated during the reconsolidation process. Furthermore, though recent evidence suggests that neuronal activity triggers DNA double-strand breaks (DSBs) in some early-response genes, it is currently unknown if DSBs contribute to the reconsolidation of a memory following retrieval. Here, using chromatin immunoprecipitation (ChIP) analyses, we report a significant overlap between DSBs and H3K4me3 in area CA1 of the hippocampus during the reconsolidation process. We found an increase in phosphorylation of histone H2A.X at serine 139 (H2A.XpS139), a marker of DSB, in the Npas4, but not c-fos, promoter region 5 min after retrieval, which correlated with increased H3K4me3 levels, suggesting that the two epigenetic marks may work in concert during the reconsolidation process. Consistent with this, in vivo siRNA-mediated knockdown of topoisomerase II β, the enzyme responsible for DSB, prior to retrieval, reduced Npas4 promoter-specific H2A.XpS139 and H3K4me3 levels and impaired long-term memory, indicating an indispensable role of DSBs in the memory reconsolidation process. Collectively, our data propose a novel mechanism for memory reconsolidation through increases in epigenetic-mediated transcriptional control via DNA double-strand breaks.
Does Stream Size Really Explain Biodiversity Patterns in Lotic Systems? A Call for Mechanistic Explanations
Vander Vorste, Ross; McElmurray, Philip; Bell, Spencer; Eliason, Kevin M.; Brown, Bryan L. (MDPI, 2017-07-08)
Understanding drivers of biodiversity is a long-standing goal of basic and applied ecological research. In riverine systems, there remains a critical need to identify these drivers as efforts to manage and protect rivers grow increasingly desperate in the face of global change. We explored one commonly cited potential driver of riverine biodiversity, stream size (e.g., stream order, watershed area, width), using a systematic literature review paired with an analysis of broad-scale macroinvertebrate and fish communities. Of the 165 papers reviewed, we found mostly positive, but no universal, relationship between biodiversity and stream size despite inconsistent use of over 30 measures of stream size. One-third of studies failed to report explanatory mechanisms driving biodiversity–stream size relationships. Across over 4000 macroinvertebrate and fish samples from 1st–8th order streams in the contiguous USA, our analysis showed biodiversity (Shannon diversity, functional diversity, beta diversity) generally increased with measures of stream size. However, because of inconsistent and generally weak relationships between biodiversity and stream size across organismal groups, we emphasize the need to look beyond simple physical stream size measures to understand and predict riverine biodiversity, and strongly suggest that studies search for more mechanistic explanations of biodiversity patterns in lotic systems.
Effect of Cetylpyridinium Chloride (CPC) on Colony Formation of Common Nontuberculous Mycobacteria
Williams, Myra D.; Falkinham, Joseph O. III (MDPI, 2018-10-05)
Cetylpyridinium chloride (CPC) is widely used to decontaminate water samples for the cultivation of nontuberculous mycobacteria (NTM). The rationale for using CPC is that it kills more non mycobacteria than NTM and thereby prevents the outgrowth and detection of mycobacterial colonies on solid media. The few CPC-susceptibility measurements that have been published, suggest that CPC-decontamination does kill significant numbers of NTM. We confirm that observation here and further demonstrate that CPC-susceptibility varied significantly by one log between representative NTM species and between strains of the same species. CPC-susceptibility was the same for cells collected from cultures or water-acclimated (P = 0.6485, T-test) and CPC-susceptibility was relatively similar over the range of commonly employed CPC dosages. We conclude that use of CPC as decontaminating agent may lead to failure to recover an NTM isolate and considerable underestimates of NTM numbers.
Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple
Abdelfattah, Ahmed; Whitehead, Susan R.; Macarisin, Dumitru; Liu, Jia; Burchard, Erik; Freilich, Shiri; Dardick, Christopher; Droby, Samir; Wisniewski, Michael (MDPI, 2020-06-23)
There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washing, waxing, and low-temperature storage at 2 °C for six months on the bacterial and fungal communities of apple calyx-end, stem-end, and peel tissues. The results of the present work reveal that tissue-type is the main factor defining fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a strong impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. The greatest impact was attributed to sanitation practices with major differences among unwashed, washed and washed-waxed apples. The magnitude of the differences, however, was tissue-specific, with the greatest impact occurring on peel tissues. Temporally, the largest shift occurred during the first two months of low-temperature storage, although fungi were more affected by storage time than bacteria. In general, fungi and bacteria were impacted equally by sanitation practices, especially the epiphytic microflora of peel tissues. This research provides a foundation for understanding the impact of postharvest management practices on the microbiome of apple and its potential subsequent effects on postharvest disease management and food safety.
Exogenous Auxin Elicits Changes in the Arabidopsis thaliana Root Proteome in a Time-Dependent Manner
Slade, William O.; Ray, W. Keith; Hildreth, Sherry B.; Winkel, Brenda S. J.; Helm, Richard F. (MDPI, 2017-07-10)
Auxin is involved in many aspects of root development and physiology, including the formation of lateral roots. Improving our understanding of how the auxin response is mediated at the protein level over time can aid in developing a more complete molecular framework of the process. This study evaluates the effects of exogenous auxin treatment on the Arabidopsis root proteome after exposure of young seedlings to auxin for 8, 12, and 24 h, a timeframe permitting the initiation and full maturation of individual lateral roots. Root protein extracts were processed to peptides, fractionated using off-line strong-cation exchange, and analyzed using ultra-performance liquid chromatography and data independent acquisition-based mass spectrometry. Protein abundances were then tabulated using label-free techniques and evaluated for significant changes. Approximately 2000 proteins were identified during the time course experiment, with the number of differences between the treated and control roots increasing over the 24 h time period, with more proteins found at higher abundance with exposure to auxin than at reduced abundance. Although the proteins identified and changing in levels at each time point represented similar biological processes, each time point represented a distinct snapshot of the response. Auxin coordinately regulates many physiological events in roots and does so by influencing the accumulation and loss of distinct proteins in a time-dependent manner. Data are available via ProteomeXchange with the identifier PXD001400.
Fox Hunting in Wild Apples: Searching for Novel Genes in Malus Sieversii
Wisniewski, Michael; Artlip, Timothy; Liu, Jia; Ma, Jing; Burchard, Erik; Norelli, John; Dardick, Christopher (MDPI, 2020-12-14)
Malus sieversii is considered the progenitor of modern apple (Malus pumila) cultivars and to represent a valuable source of genetic diversity. Despite the importance of M. sieversii as a source of disease resistance, stress tolerance, and novel fruit traits, little is known about gene function and diversity in M. sieversii. Notably, a publicly annotated genome sequence for this species is not available. In the current study, the FOX (Full-length cDNA OvereXpressing) gene hunting system was used to construct a library of transgenic lines of Arabidopsis in which each transgenic line overexpresses a full-length gene obtained from a cDNA library of the PI619283 accession of M. sieversii. The cDNA library was constructed from mRNA obtained from bark tissues collected in late fall–early winter, a time at which many abiotic stress-adaptative genes are expressed. Over 4000 apple FOX Arabidopsis lines have been established from the pool of transgenic seeds and cDNA inserts corresponding to various Gene Ontology (GO) categories have been identified. A total of 160 inserts appear to be novel, with no or limited homology to M. pumila, Arabidopsis, or poplar. Over 1300 lines have also been screened for freezing resistance. The constructed library of transgenic lines provides a valuable genetic resource for exploring gene function and diversity in Malus sieversii. Notably, no such library of t-DNA lines currently exists for any Malus species.
Growth Temperature, Trehalose, and Susceptibility to Heat in Mycobacterium avium
Guenette, Simonne; Williams, Myra D.; Falkinham, Joseph O. III (MDPI, 2020-08-15)
Mycobacterium avium is capable of an adaptive, reversible response to high-temperature survival depending on its growth temperature. Trehalose concentrations of M. avium cells grown at 42 °C were significantly higher compared to those of cells grown at 25 °C. Further, the survival of cells of M. avium grown at 42 °C and exposed to 65 °C were significantly higher than the survival of cells grown at 25 °C. This adaptive response to growth temperature may play a role in the persistence of M. avium in premise plumbing.
Hypolimnetic Hypoxia Increases the Biomass Variability and Compositional Variability of Crustacean Zooplankton Communities
Doubek, Jonathan P.; Campbell, Kylie L.; Lofton, Mary E.; McClure, Ryan P.; Carey, Cayelan C. (MDPI, 2019-10-19)
In freshwater lakes and reservoirs, climate change and eutrophication are increasing the occurrence of low-dissolved oxygen concentrations (hypoxia), which has the potential to alter the variability of zooplankton seasonal dynamics. We sampled zooplankton and physical, chemical and biological variables (e.g., temperature, dissolved oxygen, and chlorophyll a) in four reservoirs during the summer stratified period for three consecutive years. The hypolimnion (bottom waters) of two reservoirs remained oxic throughout the entire stratified period, whereas the hypolimnion of the other two reservoirs became hypoxic during the stratified period. Biomass variability (measured as the coefficient of the variation of zooplankton biomass) and compositional variability (measured as the community composition of zooplankton) of crustacean zooplankton communities were similar throughout the summer in the oxic reservoirs; however, biomass variability and compositional variability significantly increased after the onset of hypoxia in the two seasonally-hypoxic reservoirs. The increase in biomass variability in the seasonally-hypoxic reservoirs was driven largely by an increase in the variability of copepod biomass, while the increase in compositional variability was driven by increased variability in the dominance (proportion of total crustacean zooplankton biomass) of copepod taxa. Our results suggest that hypoxia may increase the seasonal variability of crustacean zooplankton communities.
Identification of Receptor Binding Proteins in Flagellotropic Agrobacterium Phage 7-7-1
Gonzalez, Floricel; Scharf, Birgit E. (MDPI, 2021-06-29)
The rapid discovery of new and diverse bacteriophages has driven the innovation of approaches aimed at detailing interactions with their bacterial hosts. Previous studies on receptor binding proteins (RBPs) mainly relied on their identification in silico and are based on similarities to well-characterized systems. Thus, novel phage RBPs unlike those currently annotated in genomic and proteomic databases remain largely undiscovered. In this study, we employed a screen to identify RBPs in flagellotropic Agrobacterium phage 7-7-1. Flagellotropic phages utilize bacterial flagella as receptors. The screen identified three candidate RBPs, Gp4, Gp102, and Gp44. Homology modelling predicted that Gp4 is a trimeric, tail associated protein with a central β-barrel, while the structure and function of Gp102 and Gp44 are less obvious. Studies with purified Gp4_1-247 confirmed its ability to bind and interact with host cells, highlighting the robustness of the RBP screen. We also discovered that Gp4_1-247 inhibits the growth of host cells in a motility and lipopolysaccharide (LPS) dependent fashion. Hence, our results suggest interactions between Gp4_1-247, rotating flagellar filaments and host glycans to inhibit host cell growth, which presents an impactful and intriguing focus for future studies.
The Impact of Protein Acetylation/Deacetylation on Systemic Lupus Erythematosus
Ren, Jingjing; Panther, Eric J.; Liao, Xiaofeng; Grammer, Amrie C.; Lipsky, Peter E.; Reilly, Christopher M. (MDPI, 2018-12-12)
Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease in which the body’s immune system mistakenly attacks healthy cells. Although the exact cause of SLE has not been identified, it is clear that both genetics and environmental factors trigger the disease. Identical twins have a 24% chance of getting lupus disease if the other one is affected. Internal factors such as female gender and sex hormones, the major histocompatibility complex (MHC) locus and other genetic polymorphisms have been shown to affect SLE, as well as external, environmental influences such as sunlight exposure, smoking, vitamin D deficiency, and certain infections. Several studies have reported and proposed multiple associations between the alteration of the epigenome and the pathogenesis of autoimmune disease. Epigenetic factors contributing to SLE include microRNAs, DNA methylation status, and the acetylation/deacetylation of histone proteins. Additionally, the acetylation of non-histone proteins can also influence cellular function. A better understanding of non-genomic factors that regulate SLE will provide insight into the mechanisms that initiate and facilitate disease and also contribute to the development of novel therapeutics that can specifically target pathogenic molecular pathways.
Individual Variability of Nosema ceranae Infections in Apis mellifera Colonies
Mulholland, Grace E.; Traver, Brenna E.; Johnson, Nels G.; Fell, Richard D. (MDPI, 2012-11-01)
Since 2006, beekeepers have reported increased losses of Apis mellifera colonies, and one factor that has been potentially implicated in these losses is the microsporidian Nosema ceranae. Since N. ceranae is a fairly recently discovered parasite, there is little knowledge of the variation in infection levels among individual workers within a colony. In this study we examined the levels of infection in individual bees from five colonies over three seasons using both spore counting and quantitative real-time PCR. The results show considerable intra-colony variation in infection intensity among individual workers with a higher percentage of low-level infections detected by PCR than by spore counting. Colonies generally had the highest percentage of infected bees in early summer (June) and the lowest levels in the fall (September). Nosema apis was detected in only 16/705 bees (2.3%) and always as a low-level co-infection with N. ceranae. The results also indicate that intra-colony variation in infection levels could influence the accuracy of Nosema diagnosis.
Influence of Forest Disturbance on La Crosse Virus Risk in Southwestern Virginia
Hopkins, M. Camille; Zink, Steven D.; Paulson, Sally L.; Hawley, Dana M. (MDPI, 2019-12-30)
Forest disturbance effects on La Crosse virus (LACV) are currently unknown. We determined the abundance of three LACV accessory vectors (Aedes albopictus, Ae. canadensis, and Ae. vexans) and the primary amplifying host (Eastern chipmunk; Tamias striatus), and tested for LACV prevalence in both vectors and chipmunks, across a gradient of experimental forest disturbance treatments in southwest Virginia. Forest disturbance significantly affected the abundance of LACV accessory vectors, with a higher abundance on disturbed sites for Ae. canadensis and Ae. vexans. However, there was no significant disturbance effect on chipmunk abundance. Forest disturbance significantly affected LACV prevalence in mosquito vectors, with most (80%) detections on unlogged control sites, which past work showed harbor the highest abundance of the two most common LACV vectors (the primary vector Aedes triseriatus, and Ae. japonicus). Interestingly, LACV nucleic acid was only detected in Ae. japonicus and Culex pipiens/restuans, with no detections in the primary vector, Ae. triseriatus. In contrast to the vector results, antibodies were only found in chipmunks on logged sites, but this result was not statistically significant. Overall, our results suggest that human LACV risk should generally decline with logging, and reveal the potential importance of accessory vectors in LACV maintenance in Appalachian forests.
Inhibition of Adherence of Mycobacterium avium to Plumbing Surface Biofilms of Methylobacterium spp.
Muñoz Egea, Mari Carmen; Ji, Pan; Pruden, Amy; Falkinham, Joseph O. III (MDPI, 2017-09-14)
Both Mycobacterium spp. and Methylobacterium spp. are opportunistic premise plumbing pathogens that are found on pipe surfaces in households. However, examination of data published in prior microbiological surveys indicates that Methylobacterium spp. and Mycobacterium spp. tend not to coexist in the same household plumbing biofilms. That evidence led us to test the hypothesis that Methylobacterium spp. in biofilms could inhibit the adherence of Mycobacterium avium. Measurements of adherence of M. avium cells to stainless steel coupons using both culture and PCR-based methods showed that the presence of Methylobacterium spp. biofilms substantially reduced M. avium adherence and vice versa. That inhibition of M. avium adherence was not reduced by UV-irradiation, cyanide/azide exposure, or autoclaving of the Methylobacterium spp. biofilms. Further, there was no evidence of the production of anti-mycobacterial compounds by biofilm-grown Methylobacterium spp. cells. The results add to understanding of the role of microbial interactions in biofilms as a driving force in the proliferation or inhibition of opportunistic pathogens in premise plumbing, and provide a potential new avenue by which M. avium exposures may be reduced for at-risk individuals.
Interaction between Ailanthus altissima and Native Robinia pseudoacacia in Early Succession: Implications for Forest Management
Nilsen, Erik T.; Huebner, Cynthia D.; Carr, David E.; Bao, Zhe (MDPI, 2018-04-20)
The goal of this study was to discover the nature and intensity of the interaction between an exotic invader Ailanthus altissima (Mill.) Swingle and its coexisting native Robinia pseudoacacia L. and consider management implications. The study occurred in the Mid-Appalachian region of the eastern United States. Ailanthus altissima can have a strong negative influence on community diversity and succession due to its allelopathic nature while R. pseudoacacia can have a positive effect on community diversity and succession because of its ability to fix nitrogen. How these trees interact and the influence of the interaction on succession will have important implications for forests in many regions of the world. An additive-replacement series common garden experiment was established to identify the type and extent of interactions between these trees over a three-year period. Both A. altissima and R. pseudoacacia grown in monoculture were inhibited by intraspecific competition. In the first year, A. altissima grown with R. pseudoacacia tended to be larger than A. altissima in monoculture, suggesting that R. pseudoacacia may facilitate the growth of A. altissima at the seedling stage. After the second year, R. pseudoacacia growth decreased as the proportion of coexisting A. altissima increased, indicating inhibition of R. pseudoacacia by A. altissima even though the R. pseudoacacia plants were much larger aboveground than the A. altissima plants. In early successional sites A. altissima should be removed, particularly in the presence of R. pseudoacacia in order to promote long-term community succession.
Karyotype Aberrations in Action: The Evolution of Cancer Genomes and the Tumor Microenvironment
Baudoin, Nicolaas C.; Bloomfield, Mathew (MDPI, 2021-04-12)
Cancer is a disease of cellular evolution. For this cellular evolution to take place, a population of cells must contain functional heterogeneity and an assessment of this heterogeneity in the form of natural selection. Cancer cells from advanced malignancies are genomically and functionally very different compared to the healthy cells from which they evolved. Genomic alterations include aneuploidy (numerical and structural changes in chromosome content) and polyploidy (e.g., whole genome doubling), which can have considerable effects on cell physiology and phenotype. Likewise, conditions in the tumor microenvironment are spatially heterogeneous and vastly different than in healthy tissues, resulting in a number of environmental niches that play important roles in driving the evolution of tumor cells. While a number of studies have documented abnormal conditions of the tumor microenvironment and the cellular consequences of aneuploidy and polyploidy, a thorough overview of the interplay between karyotypically abnormal cells and the tissue and tumor microenvironments is not available. Here, we examine the evidence for how this interaction may unfold during tumor evolution. We describe a bidirectional interplay in which aneuploid and polyploid cells alter and shape the microenvironment in which they and their progeny reside; in turn, this microenvironment modulates the rate of genesis for new karyotype aberrations and selects for cells that are most fit under a given condition. We conclude by discussing the importance of this interaction for tumor evolution and the possibility of leveraging our understanding of this interplay for cancer therapy.

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