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Journal articles on the topic 'Alpha and beta diversity'
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1
Hautmann, Michael. "Diversification and diversity partitioning." Paleobiology 40, no. 2 (2014): 162–76. http://dx.doi.org/10.1666/13041.
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Model calculations predict that pathways of alpha- and beta-diversity in diversifying ecosystems notably differ depending on the relative role of competition, predation, positive effects of species' interactions, and environmental parameters. Four scenarios are discussed, in which alpha- and beta-diversity are modeled as a function of increasing gamma-diversity. The graphic illustration of this approach is herein called α-β-γ plot, in which the x-axis indicates increasing diversification rather than absolute time. In purely environmentally controlled systems, beta-diversity maintains near-maximum values throughout the diversification interval, whereas mean alpha-diversity increases linearly, with a slope being reciprocal to beta-diversity. A second scenario is based on the assumption that increasing richness will have predominantly positive effects on the addition of further species; here, alpha- and beta-diversity increase simultaneously (though not necessarily at the same rates) and without reaching a predictable upper limit. In ecosystems that are characterized by low competition between species, mean alpha-diversity asymptotically approaches a saturation level, whereas the increase in beta-diversity accelerates until alpha-diversity stagnates, and then continues to rise linearly. If competition is high, addition of species first increases beta-diversity until no further habitat contraction is possible, followed by a period in which alpha-diversity increase through adaptive divergence becomes the principal drive of diversification. Because there is a continuous transition between the late stage of the low-competition model and the early stage of the high-competition scenario, both can be combined in a single model of diversity partitioning under the premise of a diversity-dependent increase of competition. This summary model predicts three phases of diversity accumulation: (1) a niche overlap phase, (2) a habitat contraction phase, and (3) a niche differentiation phase. The models herein discussed provide a potential tool to assess the question which factors primary controlled the diversification of life over geological times.
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Kulkarni, Narendra, and Leela J. Bhosale. "Alpha - Beta Diversity Assessment of the Mangroves of Two Districts along the Coast of Maharashtra State." Plantae Scientia 4, no. 3 (2021): 168–73. http://dx.doi.org/10.32439/ps.v4i3.168-173.
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Alpha-Beta Diversity (? and ?): During the present study the alpha and beta diversity of mangrove in the study area has been analyzed. Twenty nine estuaries from Ratnagiri and Sindhudurg districts of Maharashtra State are studied and data analyzed for calculating alpha and beta diversity.
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Patel, Pinkal, and Ratna Trivedi. "Alpha and Beta Diversity Indices of Mushrooms from Different Localities." Journal of Pure and Applied Microbiology 11, no. 3 (2017): 1577–81. http://dx.doi.org/10.22207/jpam.11.3.44.
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Garcia, A., H. Solano-Rodríguez, and O. Flores-Villela. "Patterns of alpha, beta and gamma diversity of the herpetofauna in Mexico's Pacific lowlands and adjacent interior valleys." Animal Biodiversity and Conservation 30, no. 2 (2007): 169–77. http://dx.doi.org/10.32800/abc.2007.30.0169.
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The latitudinal distribution patterns of alpha, beta and gamma diversity of reptiles, amphibians and herpetofauna were analyzed using individual binary models of potential distribution for 301 species predicted by ecological modelling for a grid of 9,932 quadrants of ~25 km2 each. We arranged quadrants in 312 latitudinal bands in which alpha, beta and gamma values were determined. Latitudinal trends of all scales of diversity were similar in all groups. Alpha and gamma responded inversely to latitude whereas beta showed a high latitudinal fluctuation due to the high number of endemic species. Alpha and gamma showed a strong correlation in all groups. Beta diversity is an important component of the herpetofauna distribution patterns as a continuous source of species diversity throughout the region.
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Fontanilla, Alyssa M., Akihiro Nakamura, Zhenghui Xu, et al. "Taxonomic and Functional Ant Diversity Along tropical, Subtropical, and Subalpine Elevational Transects in Southwest China." Insects 10, no. 5 (2019): 128. http://dx.doi.org/10.3390/insects10050128.
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Although elevational gradients of biodiversity have long been the topic of scientific research, information on patterns of, and processes that shape insect community structure across elevation is still lacking. Addressing this gap requires the use of both taxonomic and functional approaches when studying diversity across elevational gradients. In this study, we examined taxonomic and functional alpha and beta diversity of ant assemblages sampled along tropical, subtropical, and subalpine elevational transects in Yunnan Province, southwest China. Species richness was used to quantify taxonomic alpha diversity, and two indices (FD and FRic) were calculated using morphological measurements to quantify functional alpha diversity. Taxonomic and functional beta diversity were partitioned into their turnover- and nestedness-resultant components. Though temperature and functional alpha diversity decreased linearly with increasing elevation, taxonomic alpha diversity showed a significant logarithmic decrease, with few species present at elevations greater than 3000 m a.s.l. The turnover-resultant component of taxonomic beta diversity increased with increasing elevational distance, while the nestedness-resultant component of functional beta diversity increased with increasing elevational distance in the subtropical transect. The observed patterns of taxonomic and functional diversity reflected ants’ thermophilic nature, implying functional adaptations (i.e., nested functional diversity) at higher elevations where environmental conditions were unfavorable.
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Sepkoski, J. John. "Alpha, beta, or gamma: where does all the diversity go?" Paleobiology 14, no. 3 (1988): 221–34. http://dx.doi.org/10.1017/s0094837300011969.
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Global taxonomic richness is affected by variation in three components: within-community, or alpha, diversity; between-community, or beta, diversity; and between-region, or gamma, diversity. A data set consisting of 505 faunal lists distributed among 40 stratigraphic intervals and six environmental zones was used to investigate how variation in alpha and beta diversity influenced global diversity through the Paleozoic, and especially during the Ordovician radiations. As first shown by Bambach (1977), alpha diversity increased by 50 to 70 percent in offshore marine environments during the Ordovician and then remained essentially constant for the remainder of the Paleozoic. The increase is insufficient, however, to account for the 300 percent rise observed in global generic diversity. It is shown that beta diversity among level, soft-bottom communities also increased significantly during the early Paleozoic. This change is related to enhanced habitat selection, and presumably increased overall specialization, among diversifying taxa during the Ordovician radiations. Combined with alpha diversity, the measured change in beta diversity still accounts for only about half of the increase in global diversity. Other sources of increase are probably not related to variation in gamma diversity but rather to appearance and/or expansion of organic reefs, hardground communities, bryozoan thickets, and crinoid gardens during the Ordovician.
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Wang, Jianming, Chen Chen, Jingwen Li, Yiming Feng, and Qi Lu. "Different ecological processes determined the alpha and beta components of taxonomic, functional, and phylogenetic diversity for plant communities in dryland regions of Northwest China." PeerJ 6 (January 10, 2019): e6220. http://dx.doi.org/10.7717/peerj.6220.
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Drylands account for more than 30% of China’s terrestrial area, while the ecological drivers of taxonomic (TD), functional (FD) and phylogenetic (PD) diversity in dryland regions have not been explored simultaneously. Therefore, we selected 36 plots of desert and 32 plots of grassland (10 × 10 m) from a typical dryland region of northwest China. We calculated the alpha and beta components of TD, FD and PD for 68 dryland plant communities using Rao quadratic entropy index, which included 233 plant species. Redundancy analyses and variation partitioning analyses were used to explore the relative influence of environmental and spatial factors on the above three facets of diversity, at the alpha and beta scales. We found that soil, climate, topography and spatial structures (principal coordinates of neighbor matrices) were significantly correlated with TD, FD and PD at both alpha and beta scales, implying that these diversity patterns are shaped by contemporary environment and spatial processes together. However, we also found that alpha diversity was predominantly regulated by spatial structure, whereas beta diversity was largely determined by environmental variables. Among environmental factors, TD was most strongly correlated with climatic factors at the alpha scale, while with soil factors at the beta scale. FD was only significantly correlated with soil factors at the alpha scale, but with altitude, soil and climatic factors at the beta scale. In contrast, PD was more strongly correlated with altitude at the alpha scale, but with soil factors at the beta scale. Environment and space explained a smaller portion of variance in PD than in TD and FD. These results provide robust evidence that the ecological drivers of biodiversity differ among different scales and facets of diversity. Future research that focuses on the comparisons among TD, FD and PD would likely provide new insights into elucidating the underlying community assembly.
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Saito, T., J. L. Sussman, J. D. Ashwell, and R. N. Germain. "Marked differences in the efficiency of expression of distinct alpha beta T cell receptor heterodimers." Journal of Immunology 143, no. 10 (1989): 3379–84. http://dx.doi.org/10.4049/jimmunol.143.10.3379.
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Abstract Ag recognition by most T lymphocytes is mediated by clonally distributed alpha beta heterodimeric receptors. A major fraction of TCR diversity is believed to be due to the random coexpression in individual T cells of the products of independently rearranging alpha- and beta-genes (combinatorial diversity). However, analysis of cell surface receptors on transfected T hybridoma cells synthesizing various sets of alpha- and beta-chains revealed marked differences in the efficiency of expression of certain alpha beta-pairs. Specifically, using the functionally rearranged gene products of the 2B4 cytochrome c specific T hybridoma (V beta 3, V alpha 11.2) and BW5147 parent lymphoma (V beta 1, V alpha BW), a hierarchy of expression efficiency relative to indirectly measured precursor chain levels in the cell was shown to be 2B4 alpha-BW beta greater than 2B4 alpha - 2B4 beta greater than BW alpha - BW beta greater than BW alpha - 2B4 beta. The estimated difference between the best expressed and worst expressed pairs is on the order of 50-fold. For the beta-chain, the primary determinant of expression efficiency with a given alpha-chain appears to be the V segment, as a second V beta 1-chain with distinct D and J regions from BW beta was expressed with the same pattern. These data imply that alpha- and beta-chains do not form well-expressed TCR in a random manner and that limitations on the useful combinatorial association of these chains may significantly affect the functional T cell repertoire.
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Jones, Gavin M., Berry Brosi, Jason M. Evans, et al. "Conserving alpha and beta diversity in wood‐production landscapes." Conservation Biology 36, no. 3 (2022): e13872. https://doi.org/10.5281/zenodo.14822136.
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(Uploaded by Plazi for the Bat Literature Project) International demand for wood and other forest products continues to grow rapidly, and uncertainties remain about how animal communities will respond to intensifying resource extraction associated with woody bioenergy production. We examined changes in alpha and beta diversity of bats, bees, birds, and reptiles across wood production landscapes in the southeastern United States, a biodiversity hotspot that is one of the principal sources of woody biomass globally. We sampled across a spatial gradient of paired forest landuses (representing pre and postharvest) that allowed us to evaluate biological community changes resulting from several types of biomass harvest. Short-rotation practices and residue removal following clearcuts were associated with reduced alpha diversity (−14.1 and −13.9 species, respectively) and lower beta diversity (i.e., Jaccard dissimilarity) between land-use pairs (0.46 and 0.50, respectively), whereas midrotation thinning increased alpha (+3.5 species) and beta diversity (0.59). Over the course of a stand rotation in a single location, biomass harvesting generally led to less biodiversity. Cross-taxa responses to resource extraction were poorly predicted by alpha diversity: correlations in responses between taxonomic groups were highly variable (−0.2 to 0.4) with large uncertainties. In contrast, beta diversity patterns were highly consistent and predictable across taxa, where correlations in responses between taxonomic groups were all positive (0.05–0.4) with more narrow uncertainties. Beta diversity may, therefore, be a more reliable and information-rich indicator than alpha diversity in understanding animal community response to landscape change. Patterns in beta diversity were primarily driven by turnover instead of species loss or gain, indicating that wood extraction generates habitats that support different biological communities.
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Bartha, Sándor, Roberto Canullo, Stefano Chelli, and Giandiego Campetella. "Unimodal Relationships of Understory Alpha and Beta Diversity along Chronosequence in Coppiced and Unmanaged Beech Forests." Diversity 12, no. 3 (2020): 101. http://dx.doi.org/10.3390/d12030101.
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Patterns of diversity across spatial scales in forest successions are being overlooked, despite their importance for developing sustainable management practices. Here, we tested the recently proposed U-shaped biodiversity model of forest succession. A chronosequence of 11 stands spanning from 5 to 400 years since the last disturbance was used. Understory species presence was recorded along 200 m long transects of 20 × 20 cm quadrates. Alpha diversity (species richness, Shannon and Simpson diversity indices) and three types of beta diversity indices were assessed at multiple scales. Beta diversity was expressed by a) spatial compositional variability (number and diversity of species combinations), b) pairwise spatial turnover (between plots Sorensen, Jaccard, and Bray–Curtis dissimilarity), and c) spatial variability coefficients (CV% of alpha diversity measures). Our results supported the U-shaped model for both alpha and beta diversity. The strongest differences appeared between active and abandoned coppices. The maximum beta diversity emerged at characteristic scales of 2 m in young coppices and 10 m in later successional stages. We conclude that traditional coppice management maintains high structural diversity and heterogeneity in the understory. The similarly high beta diversities in active coppices and old-growth forests suggest the presence of microhabitats for specialist species of high conservation value.
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Johnston, S. L., and P. J. Wettstein. "T cell receptor diversity in CTLs specific for the CTT-1 and CTT-2 minor histocompatibility antigens." Journal of Immunology 159, no. 6 (1997): 2606–15. http://dx.doi.org/10.4049/jimmunol.159.6.2606.
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Abstract Minor histocompatibility Ags (HA) and their associated immunogenic peptides provide a formidable barrier for successful transplantation, but there is virtually no information regarding the diversity of minor HA-specific TCRs. We have investigated the diversity of alpha- and beta-chains in TCRs specific for the CTT-1 and CTT-2 peptides that are immunodominant in CTL responses to multiple minor HA. CTLs were cloned after in vitro stimulation, and alpha- and beta-chain transcripts were amplified and sequenced to identify utilized V genes, complementarity-determining regions 3 (CDR3s), and joining region genes. Twenty-one unique CTT-2-specific TCRs were identified in 31 clones, and 22 CTT-1-specific TCRs were identified in 29 clones. A relatively limited number of V beta subfamilies were represented in these panels of TCRs, with Vbeta 5 and V beta8 genes expressed in multiple TCRs in each panel. Similar diversity was observed with V alpha usage, and V alpha4 subfamily usage was more prominent in CTT-2-specific TCRs than in CTT-1-specific TCRs. Neither alpha nor beta CDR3 regions exhibited prominent motifs or length restriction. However, CTT-1- and CTT-2-specific beta CDR3 regions included an excess of negatively over positively charged residues that were bimodally distributed among CDR3 positions. In fact, 50% of CTT-1-specific CDR3 regions included two negative charges separated by three to five amino acids. Despite the similarities in net charge of beta CDR3 regions, TCRs specific for these two minor HA peptides are relatively diverse and would expectedly withstand attempts at anti-TCR Ab-mediated immunosuppression.
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Kwok, W. W., P. Thurtle, and G. T. Nepom. "A genetically controlled pairing anomaly between HLA-DQ alpha and HLA-DQ beta chains." Journal of Immunology 143, no. 11 (1989): 3598–601. http://dx.doi.org/10.4049/jimmunol.143.11.3598.
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Abstract The HLA-DQ region contains highly polymorphic alpha and beta loci, so that a diverse set of cis- and trans-associated class II alpha/beta dimers are potentially generated in heterozygous individuals. To evaluate the extent of this predicted diversity, DQ2 beta or DQ3.2 beta cDNA were introduced into a panel of homozygous B cell lines that expressed different DQ alpha alleles. Restricted patterns of alpha/beta pairing were observed in which DQ2 beta and DQ3 beta molecules were unable to pair efficiently with DQ1 alpha chains. This pairing anomaly may contribute to altered class II phenotypes in heterozygous individuals, and is reflected in the absence of either DQ1 alpha, DQ2 beta or DQ1 alpha, DQ3 beta haplotypes in the known human gene pool.
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Na, Lin, and Wolfgang Kiessling. "Diversity partitioning during the Cambrian radiation." Proceedings of the National Academy of Sciences 112, no. 15 (2015): 4702–6. http://dx.doi.org/10.1073/pnas.1424985112.
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The fossil record offers unique insights into the environmental and geographic partitioning of biodiversity during global diversifications. We explored biodiversity patterns during the Cambrian radiation, the most dramatic radiation in Earth history. We assessed how the overall increase in global diversity was partitioned between within-community (alpha) and between-community (beta) components and how beta diversity was partitioned among environments and geographic regions. Changes in gamma diversity in the Cambrian were chiefly driven by changes in beta diversity. The combined trajectories of alpha and beta diversity during the initial diversification suggest low competition and high predation within communities. Beta diversity has similar trajectories both among environments and geographic regions, but turnover between adjacent paleocontinents was probably the main driver of diversification. Our study elucidates that global biodiversity during the Cambrian radiation was driven by niche contraction at local scales and vicariance at continental scales. The latter supports previous arguments for the importance of plate tectonics in the Cambrian radiation, namely the breakup of Pannotia.
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Xiang, Zhenlong, Haiyu Niu, Quehui Tang, and Ren Hu. "Non-Linear Response of Alpha and Beta Diversity of Taxonomic and Functional Groups of Phytoplankton to Environmental Factors in Subtropical Reservoirs." Microorganisms 12, no. 8 (2024): 1547. http://dx.doi.org/10.3390/microorganisms12081547.
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Exploring the response of the diversity of phytoplankton species and functional groups to environmental variables is extremely important in maintaining biodiversity in aquatic ecosystems. Although there were more taxonomic units at the species level than at the functional group level, it remained unclear whether species diversity was more sensitive than functional group diversity to environmental variables. In this study, taxonomic composition and alpha–beta diversity of phytoplankton were investigated in 23 subtropical reservoirs located in the Han River Basin in South China during wet and dry seasons. Structural Equation Modelling (SEM) and Generalized Dissimilarity Modelling (GDM) were employed to validate the response of phytoplankton species and functional group alpha–beta diversities to environmental variables. The results indicated that the community compositions of phytoplankton in eutrophic reservoirs were similar between wet and dry seasons, while there were distinct differences for community composition in oligotrophic–mesotrophic reservoirs between the two seasons. Across all reservoirs, there were no significant differences in alpha and beta diversities of species and functional groups between wet and dry seasons. The SEM and GDM results revealed that total phosphorus was the primary driving factor influencing alpha and beta diversities of species and functional groups in the 23 reservoirs. Meanwhile, the non-linear results of species beta diversity were stronger than the non-linear results of functional group beta diversity, indicating that phytoplankton species exhibited a higher explanatory power in responding to environmental changes compared to that of functional groups. Compared to that of species beta diversity, the response of functional group beta diversity to environmental variables was significantly lower in the dry season. These research findings lead to re-evaluating the common practice relating to the use of phytoplankton functional groups to assess environmental conditions, which may overlook the explanatory power of subtle changes at the species level, especially during periods of habitat diversification in the dry season.
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Jin, Yu-Song, Yu-Kun Hu, Jing Wang, et al. "Diversity of Understory Communities in Boreal Forests: Influences of Forest Type, Latitude, and Spatial Scale." Forests 10, no. 11 (2019): 1003. http://dx.doi.org/10.3390/f10111003.
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Understory vegetation hosts high biodiversity and plays a critical role in the ecosystem processes of boreal forests. However, the drivers of understory plant diversity in this high-latitude ecosystem remain uncertain. To investigate the influences of forest type and latitude on understory beta diversity at different scales, we quantified the species composition of Vaccinium uliginosum Linnaeus communities under broadleaf and coniferous forests at two latitudes at the quadrat (2 × 2 m) and plot (10 × 10 m) scales in the Greater Xing’an Mountains, NE China. At the quadrat scale, species alpha diversity of V. uliginosum communities was higher in broadleaf forests than that in coniferous forests at both latitudes. The differences in species beta diversity (the Sørensen’s dissimilarity) in two forest types depended on the latitude: beta diversity in broadleaf forests was higher than that in coniferous forests at the higher latitude, while beta diversity in coniferous forests was higher at the lower latitude. At the plot scale, alpha and beta diversity of V. uliginosum communities decreased from broadleaf forests to coniferous forests at the higher latitude, and they did not show significant differences between forest types at the lower latitude. These results indicate the interactive effects of forest type and latitude on beta diversity of understory vegetation. Moreover, the influences of forest type and latitude on species alpha and beta diversity were different across the two spatial scales, suggesting that the assembly mechanisms underlying species diversity may be different at different scales. Understanding the maintenance of understory vegetation diversity will benefit the conservation and management of boreal forests.
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Schupfer, Emily, Soo Liang Ooi, Thomas C. Jeffries, Shaoyu Wang, Peter S. Micalos, and Sok Cheon Pak. "Changes in the Human Gut Microbiome during Dietary Supplementation with Modified Rice Bran Arabinoxylan Compound." Molecules 28, no. 14 (2023): 5400. http://dx.doi.org/10.3390/molecules28145400.
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This study investigated the effects of a modified rice bran arabinoxylan compound (RBAC) as a dietary supplement on the gut microbiota of healthy adults. Ten volunteers supplemented their diet with 1 g of RBAC for six weeks and 3 g of RBAC for another six weeks, with a three-week washout period. Faecal samples were collected every 3 weeks over 21 weeks. Microbiota from faecal samples were profiled using 16S rRNA sequencing. Assessment of alpha and beta microbiota diversity was performed using the QIIME2 platform. The results revealed that alpha and beta diversity were not associated with the experimental phase, interventional period, RBAC dosage, or time. However, the statistical significance of the participant was detected in alpha (p < 0.002) and beta (weighted unifrac, p = 0.001) diversity. Explanatory factors, including diet and lifestyle, were significantly associated with alpha (p < 0.05) and beta (p < 0.01) diversity. The individual beta diversity of six participants significantly changed (p < 0.05) during the interventional period. Seven participants showed statistically significant taxonomic changes (ANCOM W ≥ 5). These results classified four participants as responders to RBAC supplementation, with a further two participants as likely responders. In conclusion, the gut microbiome is highly individualised and modulated by RBAC as a dietary supplement, dependent on lifestyle and dietary intake.
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Jost, Lou. "PARTITIONING DIVERSITY INTO INDEPENDENT ALPHA AND BETA COMPONENTS." Ecology 88, no. 10 (2007): 2427–39. http://dx.doi.org/10.1890/06-1736.1.
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Li, Shudan, Xingzhong Wang, Lu Tan, and Qinghua Cai. "Exploring the Drivers Influencing Multidimensional Alpha and Beta Diversity of Macroinvertebrates in Mountain Streams." Water 16, no. 20 (2024): 2915. http://dx.doi.org/10.3390/w16202915.
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Understanding the driving mechanisms of diversity across multiple dimensions is a fundamental task in biodiversity conservation. Here, we examined the alpha and beta diversity of macroinvertebrates in the taxonomic, functional, and phylogenetic dimensions in mountain streams of northwestern Hubei Province, China. We also assessed how much local environmental, land use, climatic, and spatial variables affected these diversities. We found that (1) there were generally weak or no correlations of alpha and beta diversity between taxonomic, functional, and phylogenetic dimensions; (2) compared to both functional and phylogenetic beta diversity, which was mainly determined by nestedness, taxonomic beta diversity was mostly molded by turnover and was much higher; and (3) local environmental variables predominantly influenced taxonomic and functional dimensions of alpha and beta diversity, while spatial factors primarily drove phylogenetic dimension. These results suggest that regulating local habitats is crucial for lotic biodiversity conservation efforts, though spatial processes cannot be overlooked. Furthermore, our findings verify the supplemental role of functional and phylogenetic data in enriching insights provided by taxonomic data alone. This underscores the importance of a multidimensional approach for a more nuanced understanding of community assembly mechanisms, which is crucial for efficient ecosystem management and biodiversity conservation.
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Cardoso, Pedro, François Rigal, José C. Carvalho, and Steven Kembel. "BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity." Methods in Ecology and Evolution 6, no. 2 (2015): 232–36. https://doi.org/10.5281/zenodo.13438547.
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(Uploaded by Plazi for the Bat Literature Project) Summary Novel algorithms have been recently developed to estimate alpha and partition beta diversity in all their dimensions (taxon, phylogenetic and functional diversity – TD , PD and FD ), whether communities are completely sampled or not. The R package BAT – Biodiversity Assessment Tools – performs a number of analyses based on either species identities ( TD ) or trees depicting species relationships ( PD and FD ). Functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components. All functions allow the rarefaction of communities. Estimation methods include curve‐fitting and nonparametric algorithms. Beta diversity indices include the Jaccard and Sørensen families of measures and deal with both incidence and abundance data. Two auxiliary functions that allow judging the efficiency of the algorithms are also included. Several examples are shown using the data included in the package, which demonstrate the usefulness of the different methods. The BAT package constitutes an open platform for further development of new biodiversity assessment tools.
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Cardoso, Pedro, François Rigal, José C. Carvalho, and Steven Kembel. "BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity." Methods in Ecology and Evolution 6, no. 2 (2015): 232–36. https://doi.org/10.5281/zenodo.13438547.
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(Uploaded by Plazi for the Bat Literature Project) Summary Novel algorithms have been recently developed to estimate alpha and partition beta diversity in all their dimensions (taxon, phylogenetic and functional diversity – TD , PD and FD ), whether communities are completely sampled or not. The R package BAT – Biodiversity Assessment Tools – performs a number of analyses based on either species identities ( TD ) or trees depicting species relationships ( PD and FD ). Functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components. All functions allow the rarefaction of communities. Estimation methods include curve‐fitting and nonparametric algorithms. Beta diversity indices include the Jaccard and Sørensen families of measures and deal with both incidence and abundance data. Two auxiliary functions that allow judging the efficiency of the algorithms are also included. Several examples are shown using the data included in the package, which demonstrate the usefulness of the different methods. The BAT package constitutes an open platform for further development of new biodiversity assessment tools.
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Donson, D., H. Borrero, M. Rutman, R. Pergolizzi, N. Malhado, and S. Macphail. "Gene transfer directly demonstrates a role for TCR V alpha elements in superantigen recognition." Journal of Immunology 158, no. 11 (1997): 5229–36. http://dx.doi.org/10.4049/jimmunol.158.11.5229.
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Abstract Recent structure-function studies of ours and others indicating that regions of the TCR other than V beta are involved in the TCR-superantigen (SAg)-MHC class II trimolecular interaction were correlative; thus, while the conclusions were persuasive, they were not unequivocal. The transfection experiments described in this report show that 1) responsiveness to staphylococcal enterotoxin B in V beta6 T cells was transferred by a V alpha4- but not by V alpha8- and V alpha10-containing alpha-chain cDNA constructs, 2) responsiveness was not transferred by a chimeric alpha-chain construct containing the N and J regions from a responsive T hybrid clone and the V alpha10 V alpha region from a nonresponsive clone, and 3) responsiveness was transferred by a chimeric alpha-chain construct in which most of the V alpha region (from the N terminus to the C-terminal end of the complementarity-determining region 2) was derived from the V alpha4 alpha-chain of a responsive T hybrid and the rest (framework 3, N, and J) from the V alpha8 alpha-chain of a nonresponsive T hybrid. Thus, these data provide the first direct evidence for a specific SAg response facilitating activity in a defined V alpha segment and map this activity N-terminal of framework region 3. Furthermore, the diversity in the alpha- and beta-chain junctional regions of a panel of staphylococcal enterotoxin B-responsive V beta6 T hybrid clones excludes a stringent corequirement for a particular junctional region for the V alpha4 segment to mediate its facilitating activity. Finally, a model postulating a universal role for V alpha elements in TCR recognition of SAg is presented.
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Erős, Tibor, Andrea Funk, Didier Pont, et al. "eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities." PLOS ONE 19, no. 1 (2024): e0296310. http://dx.doi.org/10.1371/journal.pone.0296310.
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Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined the role of habitat specialist vs. generalist species, and the spatial configuration, connectivity, and different environmental characteristics of river-floodplain habitats to get a more mechanistic understanding of alpha and beta diversity of fish metacommunities. We used environmental DNA metabarcoding to characterize species (taxa) richness and composition in two separate floodplains of the river Danube (Austria and Hungary) during two different hydrological conditions. Results showed that differences in the number of generalist and specialist species and their responses to connectivity and environmental gradients influenced patterns in alpha and beta diversity. Of the components of beta diversity, richness difference (nestedness) showed consistently higher values than replacement (turnover), mainly due to the decrease of specialist species along the connectivity gradient (i.e., from the mainstem to the most isolated oxbows). Variance in both alpha and beta diversity could be well predicted by a set of local and regional variables, despite high environmental variability, which characterizes river-floodplain ecosystems. Of these, the joint or shared variance fractions proved to be the most important, which indicates that the effects of local and regional processes cannot be unambiguously separated in these river-floodplain systems. Local scale environmental variables were more important determinants of both alpha and beta diversity in the low water period than in the high water period. These results indicate the differential role of local and regional processes in community organization during different hydrological conditions. Maintenance of both local and regional scale processes are thus important in the preservation of alpha and beta diversity of floodplain fish metacommunities, which should be considered by environmental management.
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Dubreuil, R. R., T. J. Byers, C. T. Stewart, and D. P. Kiehart. "A beta-spectrin isoform from Drosophila (beta H) is similar in size to vertebrate dystrophin." Journal of Cell Biology 111, no. 5 (1990): 1849–58. http://dx.doi.org/10.1083/jcb.111.5.1849.
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Spectrins are a major component of the membrane skeleton in many cell types where they are thought to contribute to cell form and membrane organization. Diversity among spectrin isoforms, especially their beta subunits, is associated with diversity in cell shape and membrane architecture. Here we describe a spectrin isoform from Drosophila that consists of a conventional alpha spectrin subunit complexed with a novel high molecular weight beta subunit (430 kD) that we term beta H. The native alpha beta H molecule binds actin filaments with high affinity and has a typical spectrin morphology except that it is longer than most other spectrin isoforms and includes two knoblike structures that are attributed to a unique domain of the beta H subunit. Beta H is encoded by a different gene than the previously described Drosophila beta-spectrin subunit but shows sequence similarity to beta-spectrin as well as vertebrate dystrophin, a component of the membrane skeleton in muscle. By size and sequence similarity, dystrophin is more similar to this newly described beta-spectrin isoform (beta H) than to other members of the spectrin gene family such as alpha-spectrin and alpha-actinin.
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Laurencio, David, and Lee A. Fitzgerald. "Environmental correlates of herpetofaunal diversity in Costa Rica." Journal of Tropical Ecology 26, no. 5 (2010): 521–31. http://dx.doi.org/10.1017/s0266467410000222.
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Abstract:Disentangling local and historical factors that determine species diversity patterns at multiple spatial scales is fundamental to elucidating processes that govern ecological communities. Here we investigated how environmental correlates may influence diversity at local and regional scales. Primarily utilizing published species lists, amphibian and reptile alpha and beta diversity were assessed at 17 well-surveyed sites distributed among ecoregions throughout Costa Rica. The degree to which regional species diversity patterns were related to environmental variables and geographic distance was determined using Canonical Correspondence Analysis and Mantel tests. Amphibian alpha diversity was highest in lowland Pacific sites (mean = 43.3 species) and lowest at the high elevation site (9 species). Reptile alpha diversity values were high for both lowland Atlantic (mean = 69.5 species) and lowland Pacific (mean = 67 species) sites and lowest for the high elevation site (8 species). We found high species turnover between local sites and ecoregions, demonstrating the importance of beta diversity in the determination of regional diversity. For both amphibians and reptiles, beta diversity was highest between the high-elevation site and all others, and lowest among lowland sites within the same ecoregion. The effect of geographic distance on beta diversity was minor. Ecologically significant climatic variables related to rain, temperature, sunshine and insolation were found to be important determinants of local and regional diversity for both amphibians and reptiles in Costa Rica.
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Cano, Ortiz Ana. "Teaching about biodiversity from phytosociology: evaluation and conservation." Plant Sociology 60 (November 17, 2023): 25–37. https://doi.org/10.3897/pls2023602/02.
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In order to transform the previous erroneous ideas acquired by many of the students, a teaching outside the classroom is proposed, making the students themselves the ones who build their own knowledge from practice. Analyzing alpha, beta and gamma diversity, intrinsic alpha diversity must be measured through the characteristic species, gamma through the companion species, and beta through the gamma/alpha relationship, taking into account this relationship the lower the beta. The higher the conservation status of the community, if beta = 1 it means that there is a balance between characteristic species and companions, if beta is < 1 it means that there is a predominance of characteristic species over companions. As a result to be taken into consideration, it is observed in the inventory analysis that anthropic action is the cause of the changes in diversity, which translates into an instability of the association, being able to change one community for another. For this reason, we consider it is necessary to teach about the meaning of characteristic and companion species, since the student must know how to discern between both types of species, which leads us to learn the ecological niche of the species.
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Nasution, Muhammad Arif, Rudi Hermi, Heriansyah Heriansyah, et al. "Seagrass Biodiversity and its Drivers in the Kepulauan Banyak Marine Nature Park, Indonesia." ILMU KELAUTAN: Indonesian Journal of Marine Sciences 29, no. 1 (2024): 156–69. http://dx.doi.org/10.14710/ik.ijms.29.1.156-169.
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Seagrasses are important marine plants that provide a variety of ecosystem services, including food and shelter for marine life, and protection from coastal erosion. This study investigated the biodiversity (alpha and beta diversity) of seagrass in the Kepulauan Banyak Marine Nature Park, Indonesia, with a specific focus on eight sites. Alpha diversity was calculated using Shannon's index, Simpson's index, and Pielou evenness. Beta diversity was determined using Bray-Curtis dissimilarity and Jaccard dissimilarity allowing us to examine the variations in species composition among different sites. Principal coordinate analysis and Partial distance-based redundancy analysis was used to visualize and investigate the impact of constraint variables to the structure of the seagrass communities. Alpha diversity varied among the sites, with the highest alpha diversity found at the Orongan and Matahari site and the lowest at the Ujung Lolok and Balai sites. The dominant substrate type (mud or sand) was found to be a significant (P≤ 0.01) determinant of seagrass alpha diversity, with mud substrates supporting higher diversity than sand substrates. The relationship between alpha diversity and constrain variables was only significant with closest distance to forest lost and longitude variables. The analysis found that water pH, closest distance to forest lost, mean distance to tourism spots, and closest distance to settlement collectively explained a significant (P≤ 0.001) portion (88.48%) of the variation in beta diversity of seagrass across the sites. The results of this study can be used to develop management strategies for the conservation of seagrass meadows in the park.
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Man, S., J. P. Ridge, and V. H. Engelhard. "Diversity and dominance among TCR recognizing HLA-A2.1+ influenza matrix peptide in human MHC class I transgenic mice." Journal of Immunology 153, no. 10 (1994): 4458–67. http://dx.doi.org/10.4049/jimmunol.153.10.4458.
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Abstract The TCR structures of CTL derived from HLA-A2.1 transgenic mice were analyzed to determine features important in the interaction of murine TCR with the HLA-A2.1 + influenza M1(57-68) peptide complex. V beta 8.1 was dominant in 9 of 11 murine CTL lines, although three other V beta segments were also represented. Sequencing of TCR cDNA from a group of six independently derived CTLs that were V beta 8.1-positive demonstrated a restricted set of D-N-J beta sequences and an apparently restricted set of alpha-chains. However, at least five other distinct alpha beta pairs were found among HLA-A2.1 + M1 peptide-specific CTL in the absence of these chains. Consideration of all TCR sequences obtained demonstrated diverse beta-chain CDR3 regions with some restriction in V alpha segment usage and bias in amino acid sequence of alpha-chain CDR3 regions. Nevertheless, the strongest correlation with HLA-A2.1 + M1 specificity was clearly V beta 8.1 usage. Comparison with previously identified human TCR sequences specific for the same Ag-MHC complex revealed that the dominant murine V alpha and V beta segments used were not the homologues of the dominant human V beta and V alpha segments used. These results together with the lack of interspecies conservation in the alpha- and beta-chain CDR3 regions demonstrate that the dominant TCR structures recognizing HLA-A2.1 + M1(57-68) are substantially different between mouse and humans. Different factors may influence Ag-driven selection of the dominant TCRs used in each species.
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Slevin, Morgan C., Jennifer L. Houtz, David J. Bradshaw, and Rindy C. Anderson. "Evidence supporting the microbiota–gut–brain axis in a songbird." Biology Letters 16, no. 11 (2020): 20200430. http://dx.doi.org/10.1098/rsbl.2020.0430.
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Recent research in mammals supports a link between cognitive ability and the gut microbiome, but little is known about this relationship in other taxa. In a captive population of 38 zebra finches ( Taeniopygia guttata ), we quantified performance on cognitive tasks measuring learning and memory. We sampled the gut microbiome via cloacal swab and quantified bacterial alpha and beta diversity. Performance on cognitive tasks related to beta diversity but not alpha diversity. We then identified differentially abundant genera influential in the beta diversity differences among cognitive performance categories. Though correlational, this study provides some of the first evidence of an avian microbiota–gut–brain axis, building foundations for future microbiome research in wild populations and during host development.
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Agiannidou, Christiana. "Effective Intercultural Management of Diversity in Greek Schools." Indiana Journal of Economics and Business Management 5, no. 1 (2025): 15–29. https://doi.org/10.5281/zenodo.14712536.
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The year 2015[1] marked a pivotal moment for migration within the European Union. This cultural diversity is notably mirrored in the student demographic. The establishment of reception or ZEP[2] classes have thus become essential to address the demands of contemporary intercultural education[3] and to advance educational equity for all students. In order to investigate this phenomenon further, teachers' perspectives on managing Ιntercultural education within schools hosting reception classes were examined. Samples' educators emphasized their communication skills towards foreign or refugee students, and less the professional attributes of contemporary educators, in order to manage a multicultural classroom setting. Notably, it appears that the majority of educators perceive the management of multicultural classrooms as significantly more challenging than that of traditional classes. Moreover, educators appear to encounter challenges in effectively managing the linguistic and cultural diversity present among their students. They do not feel interculturally prepared enough to cope with the demands of modern intercultural education, while they consider teacher training seminars essential. [1] Documento, (2019). <em>Πόσοι πρόσφυγες βρίσκονται στην Ελλάδα και πού διαμένουν</em>. Ανακτήθηκε 11 Νοεμβρίου 2021, από: https://www.documentonews.gr/article/posoi-prosfyges-briskontai-sthn-ellada-kai-poy-diamenoyn [2] ZEP classes: Priority Zones of Education [3] LAW 3879/2010 Article 26 (Π.Δ. 163<sup>Α</sup>/21.09.2010) <em>«Ανάπτυξη της Δια Βίου Μάθησης και λοιπές διατάξεις». </em>Available at: https://www.kodiko.gr/nomothesia/document/131747/nomos-3879-2010#google_vignette
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Benone, Naraiana Loureiro, and Luciano Fogaça de Assis Montag. "MÉTODOS QUANTITATIVOS PARA MENSURAR A DIVERSIDADE TAXONÔMICA EM PEIXES DE RIACHO." Oecologia Australis 25, no. 02 (2021): 398–414. http://dx.doi.org/10.4257/oeco.2021.2502.11.
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Species diversity is defined as the variety of species and their relative abundances, and can be decomposed in local (alpha), regional (gamma) and between-communities (beta) diversity. For decades, studies with Brazilian stream fish focused on the relationship between local environmental variables and diversity patterns. However, dispersal gained notoriety for being important to the organization of communities. Besides, large scale variables are increasingly being perceived as good predictors of diversity, complementing the role of habitat variables. We present here a brief review of the methods to obtain alpha and beta taxonomic diversity, considerations regarding their predictors, and their main analysis.
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Partula, S., A. de Guerra, J. S. Fellah, and J. Charlemagne. "Structure and diversity of the TCR alpha-chain in a teleost fish." Journal of Immunology 157, no. 1 (1996): 207–12. http://dx.doi.org/10.4049/jimmunol.157.1.207.
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Abstract T cell receptor beta-chain genes are well characterized in representatives of most vertebrate phyla, from sharks to mammals, but the molecular structure of complete TCR alpha-chains has not yet been established in cold-blooded vertebrates. We used a PCR approach to isolate cDNAs encoding putative teleost fish (Oncorhynchus mykiss, rainbow trout) TCR alpha-chains. Eight V alpha segments were identified, belonging to six different families, and the best amino acid sequence identity scores for these trout V alpha were all provided by mammalian V alpha or V delta sequences. Twenty-four (60.1 %) of the 39 analyzed V alpha segments belong to the V alpha 2 family, which has limited homology with mammalian V alpha/delta sequences and with the human V pre-B sequence. A total of 32 different J alpha segments were identified from 40 J alpha regions sequenced, suggesting that a large repertoire of J alpha segments is a characteristic of most vertebrates. The structural properties of the TCR alpha-chain complementarity-determining region 3 loop are well conserved between trout and mammals, suggesting that this region has been under continuous selective pressure in jawed vertebrate evolution. The trout C alpha segment has conserved N-terminal and transmembrane domains, but the C alpha intercysteine distance contains only 40 residues, significantly smaller as compared with mammals (49-56 residues). The conserved features of teleost fish TCR beta- and alpha-chains with their mammalian equivalents suggest that TCR-alpha beta receptors were still present in the common Devonian ancestors of modern teleost fish and mammals, about 450 million years ago.
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Leung, Eric T., Roshan Noronha, Ali Mirza, Reva Shenwai, and Asterios Mpatziakas. "ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations." F1000Research 7 (April 20, 2018): 479. http://dx.doi.org/10.12688/f1000research.14217.1.
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In the past few decades, ecologists have developed many diversity indices to describe within and between sample diversity. Consequently, it can be difficult to determine which index to choose and how the distribution of microbial communities affect these indices. We've developed an interactive application, ShinyDiversity, that dynamically visualizes different alpha or beta diversity indices. In enabling users to select and simultaneously visualize different indices, our application aims to facilitate understanding of how the microbial data affects selected indices.
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Sorger, S. B., S. M. Hedrick, P. J. Fink, M. A. Bookman, and L. A. Matis. "Generation of diversity in T cell receptor repertoire specific for pigeon cytochrome c." Journal of Experimental Medicine 165, no. 2 (1987): 279–301. http://dx.doi.org/10.1084/jem.165.2.279.
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17 T cell clones and 3 T cell lines, specific for pigeon cytochrome c, were analyzed for fine specificity and rearranged T cell receptor (TCR) gene elements. Clones of similar fine specificities were grouped into one of four phenotypes, and correlations between phenotype differences and gene usage could be made. All the lines and clones rearranged a member of the V alpha 2B4 gene family to a limited number of J alpha regions. The beta chain was made up of one of three non-cross-hybridizing V beta regions, each rearranging to only one or two J beta s. The use of alternate V beta regions could be correlated with phenotype differences, which were manifested either as MHC- or MHC and antigen-specificity changes. In addition, the presence of alloreactivity, which defined a phenotype difference, could be correlated solely with the use of an alternate J alpha region. These observations were substantiated by prospective analyses of pigeon cytochrome c-specific T cell lines that were selected for alternate MHC specificity or alloreactivity and were found to express the correlated alpha and beta chain rearrangements. Previously, the TCR DNA sequences from two clones, each representing a variant of one phenotype, showed sequence differences only in the N regions of their TCR genes. Since only these two variants, using identical V alpha-J alpha and V beta-J beta gene elements, were repeatedly observed in this study, we would predict that the junctional diversity differences are selectable. In this T cell response, all the gene elements involved in the generation of diversity appear to be selected, and may therefore be important in the determination of TCR specificity. This high degree of receptor gene selection represents a fundamental difference from the diversity seen in several extensively analyzed antibody responses.
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Martínez-Roldán, Hellen, María José Pérez-Crespo, and Carlos Lara. "Unraveling habitat-driven shifts in alpha, beta, and gamma diversity of hummingbirds and their floral resource." PeerJ 12 (July 10, 2024): e17713. http://dx.doi.org/10.7717/peerj.17713.
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Background Biodiversity, crucial for understanding ecosystems, encompasses species richness, composition, and distribution. Ecological and environmental factors, such as habitat type, resource availability, and climate conditions, play pivotal roles in shaping species diversity within and among communities, categorized into alpha (within habitat), beta (between habitats), and gamma (total regional) diversity. Hummingbird communities are influenced by habitat, elevation, and seasonality, making them an ideal system for studying these diversities, shedding light on mutualistic community dynamics and conservation strategies. Methods Over a year-long period, monthly surveys were conducted to record hummingbird species and their visited flowering plants across four habitat types (oak forest, juniper forest, pine forest, and xerophytic shrubland) in Tlaxcala, Mexico. Three locations per habitat type were selected based on conservation status and distance from urban areas. True diversity measures were used to assess alpha, beta, and gamma diversity of hummingbirds and their floral resources. Environmental factors such as altitude and bioclimatic variables were explored for their influence on beta diversity. Results For flowering plants, gamma diversity encompassed 34 species, with oak forests exhibiting the highest richness, while xerophytic shrublands had the highest alpha diversity. In contrast, for hummingbirds, 11 species comprised the gamma diversity, with xerophytic shrublands having the highest richness and alpha diversity. Our data reveal high heterogeneity in species abundance among habitats. Notably, certain floral resources like Loeselia mexicana and Bouvardia ternifolia emerge as key species in multiple habitats, while hummingbirds such as Basilinna leucotis, Selasphorus platycercus, and Calothorax lucifer exhibit varying levels of abundance and habitat preferences. Beta diversity analyses unveil habitat-specific patterns, with species turnover predominantly driving dissimilarity in composition. Moreover, our study explores the relationships between these diversity components and environmental factors such as altitude and climate variables. Climate variables, in particular, emerge as significant contributors to dissimilarity in floral resource and hummingbird communities, highlighting the influence of environmental conditions on species distribution. Conclusions Our results shed light on the complex dynamics of hummingbird-flower mutualistic communities within diverse habitats and underscore the importance of understanding how habitat-driven shifts impact alpha, beta, and gamma diversity. Such insights are crucial for conservation strategies aimed at preserving the delicate ecological relationships that underpin biodiversity in these communities.
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Mammadova, Sh., M. Nasrullayeva, Y. Kalbiyeva, R. Isgandarova, and T. Huseynova. "STUDY OF GENETIC DIVERSITY OF GLOBULIN PROTEINS IN COMMON BEAN (PHASEOLUS VULGARIS L.) GENOTYPES." Znanstvena misel journal, no. 78 (May 29, 2023): 4–9. https://doi.org/10.5281/zenodo.7980516.
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Electrophoretic analysis of globulin storage proteins was performed in the seeds of 15 introduced common bean samples in the study. The goal was identifying, passportizing, and studying the genetic diversity of common bean genotypes. Moreover, the genetic diversity index (H-) was calculated in zones (ω-, ϒ- β- and α-) according to the frequency of occurrence of patterns in the electrophoregrams of globulin storage proteins in the seeds of common bean samples. 16 spectra and 21 patterns were detected in common bean samples, and polymorphism was observed in most of them. 4 spectra and 5 patterns, 4 spectra and 4 patterns, 4 spectra and 5 patterns, and 4 spectra and 7 patterns were observed in the ω, ϒ, β, α zones, respectively. The genetic diversity index was calculated based on Nei's formula for each of the 4 zones - ω, ϒ, β, and α. According to calculations, more genetic diversity was observed in ω-zone (H=0.993), slightly less in β zone (H=0.707), α (H=0.837), and least in ϒ zone (H= 0.580). Genotypes were divided into 4 groups based on cluster analysis. Based on the obtained results, electrophoretic analysis of globulin storage proteins was performed for the first time in polyacrylamide gel (APAGE) and polymorphism was found in common bean genotypes.
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Muschler, J. L., and A. F. Horwitz. "Down-regulation of the chicken alpha 5 beta 1 integrin fibronectin receptor during development." Development 113, no. 1 (1991): 327–37. http://dx.doi.org/10.1242/dev.113.1.327.
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We have characterized the diversity of the chicken beta 1 integrin family and studied the expression of individual receptors during development. The diversity of the beta 1 integrin family was investigated by affinity purifying the beta 1 integrins from a variety of adult and embryonic tissues. These purifications reveal the relative levels of expression and also the differential expression of the alpha subunits in those tissues. Monoclonal antibodies were generated against the prominent ‘band 1’ of the embryonic chicken integrins and used to characterize the expression of this alpha subunit in embryonic and adult tissues. This alpha subunit is shown to be the chicken homologue of human alpha 5 fibronectin receptor. The chicken alpha 5 beta 1 integrin is the most prominent beta 1 integrin in the embryo and is expressed on the majority of cell types through the day 17 stage. The distribution of this receptor in the embryo closely parallels the distribution of its ligand, fibronectin. In adult tissues, expression of this receptor is greatly diminished relative to the expression of other alpha subunits. The cell type distribution is highly restricted: limited primarily to the vasculature and to connective tissue regions. These studies reveal a prominent role for the alpha 5 beta 1 integrin in embryonic cell types and a down-regulation of this receptor on many cell types during development.
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Saito, T., F. Hochstenbach, S. Marusic-Galesic, A. M. Kruisbeek, M. Brenner, and R. N. Germain. "Surface expression of only gamma delta and/or alpha beta T cell receptor heterodimers by cells with four (alpha, beta, gamma, delta) functional receptor chains." Journal of Experimental Medicine 168, no. 3 (1988): 1003–20. http://dx.doi.org/10.1084/jem.168.3.1003.
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Surface expression of TCR dimers by cells synthesizing three or four distinct types of receptor chains was analyzed. Cells containing intact gamma, alpha, and beta chains had only gamma delta dimers on the cell surface. In human PEER cells, addition of a functional alpha chain led to the loss of gamma delta dimer expression and expression of only alpha beta dimers. This result was not due to transcriptional down-regulation of the gamma or delta loci. In murine cells expressing all four chains, both gamma delta and alpha beta dimers could be demonstrated on a single cell. No other chain combinations (alpha gamma, alpha delta, beta gamma, or beta delta) were detected. Thus, there is stringent control of assembly and/or transport of TCR heterodimers, such that functional receptors consist only of alpha beta and gamma delta pairs, and no additional repertoire diversity is generated by cross pairing.
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Gebriel, M. Shamia, and Eddin Alshareef Ala. "Segregation concepts and using generalized diversity indices in environmental communities." World Journal of Advanced Research and Reviews 24, no. 2 (2024): 2616–26. https://doi.org/10.5281/zenodo.15142040.
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The concept of segregation has received less attention in ecology. Species diversity is a concept that includes the number of species (the total number of possible species) in the community, their abundance, and the individuals who are divided among the species, for which biodiversity is generally considered in three dimensions: within communities (<em>α</em>-diversity), between or among communities (<em>β</em>-diversity), and in the total dataset (<em>γ</em>-diversity). Recently, Shamia proposed using an improved generalized diversity index, which includes special cases of MacArthur's and Hill’s indices. Such an index is easy to interpret when all species have equal even abundances resulting in an equivalent number to refer to the output in the community. index, when community weights are unequal relative abundances, has been applied to real data for comparing the index's performance under the segregation concept. Such measure for different sites gives meaningful results of multiplicative partitioning.
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Stefanidou, Natassa, Matina Katsiapi, Dimitris Tsianis, Maria Demertzioglou, Evangelia Michaloudi, and Maria Moustaka-Gouni. "Patterns in Alpha and Beta Phytoplankton Diversity along a Conductivity Gradient in Coastal Mediterranean Lagoons." Diversity 12, no. 1 (2020): 38. http://dx.doi.org/10.3390/d12010038.
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Understanding the diversity patterns of phytoplankton assemblages in coastal lagoons is clearly important for water management. In this study, we explored alpha and beta diversity patterns in phytoplankton communities across five Mediterranean lagoons hydrologically connected to Vistonikos Gulf. We examined the phytoplankton community composition and biomass on a monthly basis from November 2018 to October 2019. For this, water samples were collected from seven inshore, brackish and coastal waters, sampling sites covering a wide range of conductivity. We found significant spatial and temporal differences in phytoplankton alpha diversity and in phytoplankton biomass metrics explained by the high variation of conductivity. Evenness remained low throughout the study period, reflecting significant dominance of several phytoplankton blooms. Harmful algal blooms of Prorocentrum minimum, Alexandrium sp., Rhizosolenia setigera and Cylindrotheca closterium occurred. The system’s species pool was characterized by relatively high phytoplankton beta diversity (average ~0.7) resulting from high temporal species turnover (90%). Overall, alpha and beta diversity components were indicative of rather heterogeneous phytoplankton communities which were associated with the high differences in conductivity among the sampling sites.
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Turner, S. J., S. C. Cose, and F. R. Carbone. "TCR alpha-chain usage can determine antigen-selected TCR beta-chain repertoire diversity." Journal of Immunology 157, no. 11 (1996): 4979–85. http://dx.doi.org/10.4049/jimmunol.157.11.4979.
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Abstract There is considerable variation in the TCR repertoire diversity selected by different peptide Ags. Certain responses show limited V region bias with minimal restrictions in the remainder of the sequence while others can be dominated by a single TCR clonotype repeatedly isolated from different individuals. CTL specific for a Kb-restricted determinant from the herpes simplex virus glycoprotein B (gB) preferentially express a dominant TCRBV10 beta-chain subset with extensive conservation located at the V-D junction. However, unlike some biased responses, no single beta-chain V-D-J combination appears to dominate these CTL. Different animals respond with a large array of unique or "private" beta-chain sequences with little J region preference. Here we examine the contribution of the TCR alpha-chain to the gB-specific CTL diversity. The TCR alpha-chains from different TCRBV10-positive gB-specific CTL clones were found to exhibit extensive sequence variation. However, when T cells were forced to use a single alpha-chain in TCR alpha-chain transgenic mice, gB-specific CTL showed limited variation in their beta-chain selection. These T cells retained the TCRBV10 bias but were now dominated by a single beta-chain sequence that could be repeatedly isolated from different transgenic animals. This "public" TCR consisted of the transgenic alpha-chain and a common TCRBV10D2J2S6 beta-chain. These results suggest that preferential use of one TCR subunit can restrict the level of diversity in the other chain due to interchain interactions involving J-derived sequences.
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Veech, Joseph A., and Thomas O. Crist. "Diversity partitioning without statistical independence of alpha and beta." Ecology 91, no. 7 (2010): 1964–69. http://dx.doi.org/10.1890/08-1727.1.
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Feilhauer, Hannes, and Sebastian Schmidtlein. "Mapping continuous fields of forest alpha and beta diversity." Applied Vegetation Science 12, no. 4 (2009): 429–39. http://dx.doi.org/10.1111/j.1654-109x.2009.01037.x.
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Laliberté, Etienne, Anna K. Schweiger, and Pierre Legendre. "Partitioning plant spectral diversity into alpha and beta components." Ecology Letters 23, no. 2 (2019): 370–80. http://dx.doi.org/10.1111/ele.13429.
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Burnham, Robyn J. "Alpha and beta diversity of Lianas in Yasunı́, Ecuador." Forest Ecology and Management 190, no. 1 (2004): 43–55. http://dx.doi.org/10.1016/j.foreco.2003.10.005.
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Ramiro, A. R., C. Trigueros, C. Márquez, J. L. San Millán, and M. L. Toribio. "Regulation of pre-T cell receptor (pT alpha-TCR beta) gene expression during human thymic development." Journal of Experimental Medicine 184, no. 2 (1996): 519–30. http://dx.doi.org/10.1084/jem.184.2.519.
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In murine T cell development, early thymocytes that productively rearrange the T cell receptor (TCR) beta locus are selected to continue maturation, before TCR alpha expression, by means of a pre-TCR alpha- (pT alpha-) TCR beta heterodimer (pre-TCR). The aim of this study was to identify equivalent stages in human thymocyte development. We show here that variable-diversity-joining region TCR beta rearrangement and the expression of full-length TCR beta transcripts have been initiated in some immature thymocytes at the TCR alpha/beta- CD4+CD8- stage, and become common in a downstream subset of TCR alpha/beta- CD4+CD8+ thymocytes that is highly enriched in large cycling cells. TCR beta chain expression was hardly detected in TCR alpha/beta- CD4+CD8- thymocytes, whereas cytoplasmic TCR beta chain was found in virtually all TCR alpha/beta- CD4+CD8+ blasts. In addition, a TCR beta complex distinct from the mature TCR alpha/beta heterodimer was immunoprecipitated only from the latter subset. cDNA derived from TCR alpha/beta- CD4+CD8+ blasts allowed us to identify and clone the gene encoding the human pT alpha chain, and to examine its expression at different stages of thymocyte development. Our results show that high pT alpha transcription occurs only in CD4+CD8- and CD4+CD8+ TCR alpha/beta- thymocytes, whereas it is weaker in earlier and later stages of development. Based on these results, we propose that the transition from TCR alpha/beta- CD4+CD8- to TCR alpha/beta- CD4+CD8+ thymocytes represents a critical developmental stage at which the successful expression of TCR beta promotes the clonal expansion and further maturation of human thymocytes, independent of TCR alpha.
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Ruiz-Cobo, Darío Hernán, Julián Bueno-Villegas, and Alexander Feijoo-Martínez. "Uso de la tierra y diversidades alfa, beta y gamma de diplópodos en la cuenca del río Otún, Colombia." Universitas Scientiarum 15, no. 1 (2010): 59. http://dx.doi.org/10.11144/javeriana.sc15-1.luaa.
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<p><strong></strong> <strong>Objective: </strong>To determine the relationship between changes in ecosystems and agrosystems provoked by human intervention and the alpha, beta and gamma diversity of the Diplopoda in the middle basin of the Otún river. <strong>Materials and methods: </strong>In this research we used a stratified systematic design with seven sampling windows and 16 sampling points. Millipedes were divided into families and morphotypes to calculate the alpha, beta and gamma diversity related to the heterogeneity of land uses. <strong>Results: </strong>We identified 35 morphotypes from 12 families and five orders. Alpha diversity of Diplopoda revealed significant differences between land uses (P &lt;0.05) and a decrease of richness from preserved areas to transformed areas by human activity. A high number of exclusive morphotypes were found in forest relicts and fallow with low species turnover between them, while the pastures, crop fields and plantations presented similar numbers of morphotypes but the species turnover between them was high (complementarity &gt; 85%) in spite of the low diversity in the land uses, which determined the high contribution of the beta diversity to the gamma diversity of the landscape. <strong>Conclusion: </strong>The heterogeneity of land uses showed that the changes modify the structure of diversity in Diplopoda with gradients diverging from the preserved ones to the highly transformed ones.</p> <p><strong>Key words: </strong>alpha, beta, gamma diversity, Colombian Andes, soil Diplopoda.</p><br />
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Porcelli, S., C. E. Yockey, M. B. Brenner, and S. P. Balk. "Analysis of T cell antigen receptor (TCR) expression by human peripheral blood CD4-8- alpha/beta T cells demonstrates preferential use of several V beta genes and an invariant TCR alpha chain." Journal of Experimental Medicine 178, no. 1 (1993): 1–16. http://dx.doi.org/10.1084/jem.178.1.1.
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CD4-CD8- (double negative [DN]) alpha/beta T cells are a largely uncharacterized subpopulation of unknown function. To investigate whether these cells are selected to recognize particular antigens or antigen-presenting molecules, DN alpha/beta T cells were purified from the peripheral blood of five normal donors and their T cell receptor (TCR) alpha and beta chains were examined. Random cloning of TCR alpha chains by single-sided polymerase chain reaction (PCR) amplification identified an invariant rearrangement between V alpha 24 and J alpha Q, with no N region diversity, which was expressed preferentially by DN alpha/beta T cells from all donors. Random cloning also identified a precise V alpha 7.2-J alpha (IGRJa14) rearrangement, with two variable amino acids encoded in the V-J junction, which was enriched in the DN alpha/beta T cell preparations from some, but not all, donors. Analysis of TCR beta chains by quantitative PCR amplification demonstrated that the expression of four V beta gene families, V beta 2, 8, 11, and 13, was markedly increased in these DN alpha/beta T cell preparations. The expression of particular TCRs by DN alpha/beta T cells from multiple donors indicates that these cells, or at least a subpopulation of cells with this phenotype, recognize a limited spectrum of antigens and suggests that they may use nonpolymorphic antigen-presenting molecules.
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Wahidiyat, Pustika Amalia, Djajadiman Gatot, Tenny Tjitrasari, et al. "Phenotypic diversity in beta-HbE thalassemia patients." Paediatrica Indonesiana 46, no. 2 (2016): 82. http://dx.doi.org/10.14238/pi46.2.2006.82-6.
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Background Thalassemia is a monogenic disease, yet the clini-cal manifestations (phenotype) are variable although they havethe same genotype. The clear-cut correlation between genotypeand phenotype in β-thalassaemia/HbE patients remains unex-plained. There are several factors that play a role in the severity ofthe clinical manifestations, i.e. two alpha-gene deletion, homozy-gote Xmn1 polymorphism +/+, -+-++, ++-++ haplotype, and hemo-globin Constant Spring.Objective To understand the clinical diversity of patients with HbE/α thalassemia and to determine whether it is possible to predictphenotypic severity from genetic factors.Methods A descriptive study on clinical presentations and hema-tological data of beta-HbE thalassemia patients. DNA analysis wasperformed to detect β-thalassemia mutations and the amelioratingfactors (alpha-globin genes deletions and Xmn1 restriction site poly-morphism at position –158 upstream of the G γ-globin gene) whichwere already known.Results Thirty patients with HbE/β thalassemia (4 to 29 years old)were recruited. IVS1-nt5 (G>C) severe β + mutation was detectedin 20 patients. Eighteen of 20 patients with positive IVS1-nt5 mu-tation group were heterozygous for Xmn1 restriction site polymor-phism and none of the patients was co-inherited with two á-globingene deletion. Almost all patients (19/20) with positive IVS1-nt5mutation group required regular transfusions, yet the mean age atfirst blood transfusion was older in negative IVS1-nt5 mutation groupthan that of positive IVS1-nt5 mutation group (5.7 vs 4 years). Meanhemoglobin before initial transfusion was higher in negative IVS1-nt5 mutation group than that of positive IVS1-nt5 mutation group(5.88 vs 5.39 g/dl). The mean total transfusion per year was lowerin the negative IVS1-nt5 mutation group than that of positive IVS1-nt5 mutation group (190.6 vs 215.1 ml/year).Conclusions Beta-HbE thalassemia patients with identical betathalassemia mutation (IVS1-nt5) show remarkable clinical diver-sity. Neither two alpha-gene deletion, nor the Xmn1- G γ polymor-phism can explain the phenotypic variation. Other amelioratingdeterminants or genetic modifications responsible for the variableclinical severity remain to be explored.
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Song, Q. L., P. K. Gregersen, R. W. Karr, and J. Silver. "Recombination between DQ alpha and DQ beta genes generates human histocompatibility leukocyte antigen class II haplotype diversity." Journal of Immunology 139, no. 9 (1987): 2993–95. http://dx.doi.org/10.4049/jimmunol.139.9.2993.
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Abstract Two major DR7 haplotypes have been defined on the basis of serologic typing: those that type as DQw2 and others that type as DQw3. In order to define the molecular basis for these serologic differences we have isolated and sequenced DQ alpha, DR beta I, and DQ beta cDNA clones from both representative haplotypes. These studies reveal that although the DQ alpha and DR beta I genes of both haplotypes are identical, the DQ beta genes are very different. These data suggest that the serologic differences of these two DR7 haplotypes are the result of a recombinational event that occurred between the DQ alpha and DQ beta genes. In addition, they emphasize the role of DQ recombination in generating "hybrid" HLA-DQ heterodimers.
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Cano Ortiz, Ana. "Teaching about biodiversity from phytosociology: evaluation and conservation." Plant Sociology 60, no. 2 (2023): 25–37. http://dx.doi.org/10.3897/pls2023602/02.
Full textAbstract:
In order to transform the previous erroneous ideas acquired by many of the students, a teaching outside the classroom is proposed, making the students themselves the ones who build their own knowledge from practice. Analyzing alpha, beta and gamma diversity, intrinsic alpha diversity must be measured through the characteristic species, gamma through the companion species, and beta through the gamma/alpha relationship, taking into account this relationship the lower the beta. The higher the conservation status of the community, if beta = 1 it means that there is a balance between characteristic species and companions, if beta is &lt; 1 it means that there is a predominance of characteristic species over companions. As a result to be taken into consideration, it is observed in the inventory analysis that anthropic action is the cause of the changes in diversity, which translates into an instability of the association, being able to change one community for another. For this reason, we consider it is necessary to teach about the meaning of characteristic and companion species, since the student must know how to discern between both types of species, which leads us to learn the ecological niche of the species.