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81.
Division within the North American boreal forest: Ecological niche divergence between the Bicknell's Thrush (Catharus bicknelli) and Gray‐cheeked Thrush (C. minimus) 下载免费PDF全文
Alyssa M. FitzGerald 《Ecology and evolution》2017,7(14):5285-5295
Sister species that diverged in allopatry in similar environments are expected to exhibit niche conservatism. Using ecological niche modeling and a multivariate analysis of climate and habitat data, I test the hypothesis that the Bicknell's Thrush (Catharus bicknelli) and Gray‐cheeked Thrush (C. mimimus), sister species that breed in the North American boreal forest, show niche conservatism. Three tree species that are important components of breeding territories of both thrush species were combined with climatic variables to create niche models consisting of abiotic and biotic components. Abiotic‐only, abiotic+biotic, and biotic‐only models were evaluated using the area under the curve (AUC) criterion. Abiotic+biotic models had higher AUC scores and did not over‐project thrush distributions compared to abiotic‐only or biotic‐only models. From the abiotic+biotic models, I tested for niche conservatism or divergence by accounting for the differences in the availability of niche components by calculating (1) niche overlap from ecological niche models and (2) mean niche differences of environmental values at occurrence points. Niche background similarity tests revealed significant niche divergence in 10 of 12 comparisons, and multivariate tests revealed niche divergence along 2 of 3 niche axes. The Bicknell's Thrush breeds in warmer and wetter regions with a high abundance of balsam fir (Abies balsamea), whereas Gray‐cheeked Thrush often co‐occurs with black spruce (Picea mariana). Niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in the speciation of the Bicknell's Thrush and Gray‐cheeked Thrush. Furthermore, because niche models were improved by the incorporation of biotic variables, this study validates the inclusion of relevant biotic factors in ecological niche modeling to increase model accuracy. 相似文献
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Shannen L. Cravens Joseph D. Schonhoft Meng M. Rowland Alyssa A. Rodriguez Breeana G. Anderson James T. Stivers 《Nucleic acids research》2015,43(8):4087-4097
Intracellular space is at a premium due to the high concentrations of biomolecules and is expected to have a fundamental effect on how large macromolecules move in the cell. Here, we report that crowded solutions promote intramolecular DNA translocation by two human DNA repair glycosylases. The crowding effect increases both the efficiency and average distance of DNA chain translocation by hindering escape of the enzymes to bulk solution. The increased contact time with the DNA chain provides for redundant damage patrolling within individual DNA chains at the expense of slowing the overall rate of damaged base removal from a population of molecules. The significant biological implication is that a crowded cellular environment could influence the mechanism of damage recognition as much as any property of the enzyme or DNA.A significant triumph in biochemistry over the last 20 years was the ability to isolate human DNA repair enzymes and study their in vitro properties using defined DNA substrates containing damaged sites. Typically, these studies have been performed using dilute conditions, where the concentration of the enzyme, DNA and buffer components were low compared to the concentration of water. Although a wealth of insights into the thermodynamic, kinetic and structural properties of enzymes have resulted from such approaches (1–7), DNA repair enzymes act in a crowded cellular environment with quite different physical properties (8,9). Thus, an open question is how the complex intracellular milieu affects the ability of enzymes to locate and repair damage sites embedded in a large polymeric DNA substrate.The human intracellular environment has numerous physical properties that could dramatically affect enzyme activity. These include high inorganic ion and metabolite concentrations (10,11), lower dielectric properties (12–14), higher bulk viscosity (15,16), and the presence of high concentrations of macromolecules which consume available volume (‘molecular crowding’) (17,18). Indeed, the concentration of macromolecules in human cells is an astounding ∼100–300 mg/ml (9,19), which means that 10–40% of the total cellular volume is consumed by large molecules (often called the excluded volume). Taken together, these parameters could affect association of an enzyme with its target in complex ways. For instance, high ion concentrations are expected to shield electrostatic interactions between an enzyme and its highly charged DNA substrate (10,20,21), while a lower dielectric constant could have an opposite effect. Increases in macroscopic viscosity will slow the translational movement of macromolecules and due to entropic effects, crowded environments will push macromolecular association when the complex consumes a smaller volume than the free component species (9,22,23).Although volume exclusion largely explains the effects of crowded environments on binding equilibria, crowding has been reported to have a surprisingly small effect on the diffusion-controlled association kinetics of macromolecules (24). Indeed, it has been observed that some diffusion-controlled association reactions occur at nearly the same rates in crowded solutions and in cells as they do in dilute solution (24,25). These kinetic effects are counterintuitive, but can be understood by considering that macromolecular crowders alter the macroscopic viscosity and available volume in crowded solutions, but do not change the microscopic viscosity (26,27). Thus, over short nanometer distances, the rotational and translational diffusion of proteins is not greatly affected by crowding because the protein only feels the microscopic viscosity of the solvent that is present in the spaces between the larger crowding molecules (28). Over larger distances, hard sphere repulsion between the protein and crowding molecules increases the effective viscosity and slows translational diffusion (8,28,29). When two binding partners approach one another, they are captured within a low viscosity (high mobility) cage created by the larger crowding molecules, which increases the probability for a productive encounter event. Surprisingly, the capture of two binding partners within a high mobility cage can in some cases offset all of the negative effects of high viscosity on the overall association rate (29).The above considerations raise the interesting question of what effect molecular crowding has on enzyme association with DNA, and in particular, the property of facilitated diffusion along a DNA chain? Facilitated diffusion on the DNA chain (‘translocation’) is a distinct process that involves transient states of an enzyme and DNA that are not directly observable in equilibrium binding, steady-state or rapid kinetic measurements (1–4,30). Here, we measure the effect of inert crowding agents on the probability that the DNA repair enzymes uracil and 8-oxguanine DNA repair glycosylase will successfully translocate between two damaged sites in a DNA chain. We find that crowding increases the likelihood that each enzyme will successfully translocate between their respective target sites without dissociation to bulk solution and also increases the average translocation distance. For both enzymes, crowding biases the damage search process toward a chain tracking search mode rather than a 3D search mode. Such a crowder-induced transition in the search mode could significantly impact the effectiveness of the damage search in a crowded nuclear environment. These enzymes represent two of the largest superfamilies of glycosylases and their similar behavior in these studies suggests that the findings will be general for other related glycosylases. 相似文献
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Students targeted by homophobic discrimination are at risk for poor academic outcomes, yet few studies have examined how witnessing discrimination affects students. This study examined the impact of direct and indirect experiences of heterosexism on feelings of safety, belongingness, and connectedness among a sample of 1,702 students at a public university in the Western United States. Sexual minority students were more likely to be a target of and witness to discrimination, and they reported significantly lower levels of safety and belongingness. Hierarchical multiple regression analyses revealed that witnessing discriminatory acts contributed significantly to lower levels of safety, belongingness, and connectedness among heterosexual students, even after accounting for personal experiences with discrimination. For sexual minority students, witnessing discrimination was not associated with school outcomes, but hearing peers intervene against slurs was associated with increased belongingness. Perceptions of the campus climate were robustly associated with student outcomes, regardless of sexual orientation. 相似文献
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Dustin A. Deming Molly E. Maher Alyssa A. Leystra Joseph P. Grudzinski Linda Clipson Dawn M. Albrecht Mary Kay Washington Kristina A. Matkowskyj Lance T. Hall Sam J. Lubner Jamey P. Weichert Richard B. Halberg 《PloS one》2014,9(10)
The treatment of localized colorectal cancer (CRC) depends on resection of the primary tumor with adequate margins and sufficient lymph node sampling. A novel imaging agent that accumulates in CRCs and the associated lymph nodes is needed. Cellectar Biosciences has developed a phospholipid ether analog platform that is both diagnostic and therapeutic. CLR1502 is a near-infrared fluorescent molecule, whereas 124/131I-CLR1404 is under clinical investigation as a PET tracer/therapeutic agent imaged by SPECT. We investigated the use of CLR1502 for the detection of intestinal cancers in a murine model and 131I-CLR1404 in a patient with metastatic CRC. Mice that develop multiple intestinal tumors ranging from adenomas to locally advanced adenocarcinomas were utilized. After 96 hours post CLR1502 injection, the intestinal tumors were analyzed using a Spectrum IVIS (Perkin Elmer) and a Fluobeam (Fluoptics). The intensity of the fluorescent signal was correlated with the histological characteristics for each tumor. Colon adenocarcinomas demonstrated increased accumulation of CLR1502 compared to non-invasive lesions (total radiant efficiency: 1.76×1010 vs 3.27×109 respectively, p = 0.006). Metastatic mesenteric tumors and uninvolved lymph nodes were detected with CLR1502. In addition, SPECT imaging with 131I-CLR1404 was performed as part of a clinical trial in patients with advanced solid tumors. 131I-CLR1404 was shown to accumulate in metastatic tumors in a patient with colorectal adenocarcinoma. Together, these compounds might enhance our ability to properly resect CRCs through better localization of the primary tumor and improved lymph node identification as well as detect distant disease. 相似文献
88.
Olivo Miotto Makoto Sekihara Shin-Ichiro Tachibana Masato Yamauchi Richard D. Pearson Roberto Amato Sonia Gonalves Somya Mehra Rintis Noviyanti Jutta Marfurt Sarah Auburn Ric N. Price Ivo Mueller Mie Ikeda Toshiyuki Mori Makoto Hirai Livingstone Tavul Manuel W. Hetzel Moses Laman Alyssa E. Barry Pascal Ringwald Jun Ohashi Francis Hombhanje Dominic P. Kwiatkowski Toshihiro Mita 《PLoS pathogens》2020,16(12)
The rapid and aggressive spread of artemisinin-resistant Plasmodium falciparum carrying the C580Y mutation in the kelch13 gene is a growing threat to malaria elimination in Southeast Asia, but there is no evidence of their spread to other regions. We conducted cross-sectional surveys in 2016 and 2017 at two clinics in Wewak, Papua New Guinea (PNG) where we identified three infections caused by C580Y mutants among 239 genotyped clinical samples. One of these mutants exhibited the highest survival rate (6.8%) among all parasites surveyed in ring-stage survival assays (RSA) for artemisinin. Analyses of kelch13 flanking regions, and comparisons of deep sequencing data from 389 clinical samples from PNG, Indonesian Papua and Western Cambodia, suggested an independent origin of the Wewak C580Y mutation, showing that the mutants possess several distinctive genetic features. Identity by descent (IBD) showed that multiple portions of the mutants’ genomes share a common origin with parasites found in Indonesian Papua, comprising several mutations within genes previously associated with drug resistance, such as mdr1, ferredoxin, atg18 and pnp. These findings suggest that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites’ drug sensitivity. This worrying development reinforces the need for increased surveillance of the evolving parasite populations on the island, to contain the spread of resistance. 相似文献
89.
Phenotypic plasticity is an important driver of species resilience. Often mediated by epigenetic changes, phenotypic plasticity enables individual genotypes to express variable phenotypes in response to environmental change. Barramundi (Lates calcarifer) are a protandrous (male‐first) sequential hermaphrodite that exhibits plasticity in length‐at‐sex change between geographic regions. This plasticity is likely to be mediated by changes in DNA methylation (DNAm), a well‐studied epigenetic modification. To investigate the relationships between length, sex, and DNAm in a sequential hermaphrodite, here, we compare DNAm in four conserved vertebrate sex‐determining genes in male and female barramundi of differing lengths from three geographic regions of northern Australia. Barramundi first mature as male and later sex change to female upon the attainment of a larger body size; however, a general pattern of increasing female‐specific DNAm markers with increasing length was not observed. Significant differences in DNAm between males and females of similar lengths suggest that female‐specific DNAm arises rapidly during sex change, rather than gradually with fish growth. The findings also reveal that region‐specific differences in length‐at‐sex change are accompanied by differences in DNAm and are consistent with variability in remotely sensed sea temperature and salinity. Together, these findings provide the first in situ evidence for epigenetically and environmentally mediated sex change in a protandrous hermaphrodite and offer significant insight into the molecular and ecological processes governing the marked and unique plasticity of sex in fish. 相似文献
90.
Ashley J. Russo Alyssa J. Mathiowetz Steven Hong Matthew D. Welch Kenneth G. Campellone 《Molecular biology of the cell》2016,27(6):967-978
Small G-proteins are key regulatory molecules that activate the actin nucleation machinery to drive cytoskeletal rearrangements during plasma membrane remodeling. However, the ability of small G-proteins to interact with nucleation factors on internal membranes to control trafficking processes has not been well characterized. Here we investigated roles for members of the Rho, Arf, and Rab G-protein families in regulating WASP homologue associated with actin, membranes, and microtubules (WHAMM), an activator of Arp2/3 complex–mediated actin nucleation. We found that Rab1 stimulated the formation and elongation of WHAMM-associated membrane tubules in cells. Active Rab1 recruited WHAMM to dynamic tubulovesicular structures in fibroblasts, and an active prenylated version of Rab1 bound directly to an N-terminal domain of WHAMM in vitro. In contrast to other G-protein–nucleation factor interactions, Rab1 binding inhibited WHAMM-mediated actin assembly. This ability of Rab1 to regulate WHAMM and the Arp2/3 complex represents a distinct strategy for membrane remodeling in which a Rab G-protein recruits the actin nucleation machinery but dampens its activity. 相似文献