Differential predation drives the geographical divergence in multiple traits in aposematic frogs

AbstractCurcumin, a potent phytochemical derived from the spice element turmeric, has been identified as a herbal remedy decades ago and has displayed promise in the field of medicinal chemistry. However, multiple traits associated with curcumin, such as poor bioavailability and instability, limit its effectiveness to be accepted as a lead drug-like entity. Different reactive sites in its chemical structure have been identified to incorporate modifications as attempts to improving its efficacy. The diketo group present in the center of the structural scaffold has been touted as the group responsible for the instability of curcumin, and substituting it with a heterocyclic ring contributes to improved stability. In this study, four heterocyclic curcumin analogues, representing some broad groups of heterocyclic curcuminoids (isoxazole-, pyrazole-, N-phenyl pyrazole- and N-amido-pyrazole-based), have been synthesized by a simple one-pot synthesis and have been characterized by FTIR, 1H-NMR, 13C-NMR, DSC and LC–MS. To predict its potential anticancer efficacy, the compounds have been analyzed by computational studies via molecular docking for their regulatory role against three key proteins, namely GSK-3β—of which abnormal regulation and expression is associated with cancer; Bcl-2—an apoptosis regulator; and PR which is a key nuclear receptor involved in breast cancer development. One of the compounds, isoxazole-curcumin, has consistently indicated a better docking score than the other tested compounds as well as curcumin. Apart from docking, the compounds have also been profiled for their ADME properties as well as free energy binding calculations. Further, the in vitro cytotoxic evaluation of the analogues was carried out by SRB assay in breast cancer cell line (MCF7), out of which isoxazole-curcumin (IC50–3.97 µM) has displayed a sevenfold superior activity than curcumin (IC50–21.89 µM). In the collation of results, it can be suggested that isoxazole-curcumin behaves as a potential lead owing to its ability to be involved in a regulatory role with multiple significant cancer proteins and hence deserves further investigations in the development of small molecule-based anti-breast cancer agents. Graphic abstract

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Penalized partial least squares for pleiotropy

BMC Bioinformatics ◽

10.1186/s12859-021-03968-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Camilo Broc ◽

Therese Truong ◽

Benoit Liquet

Keyword(s):

Least Squares ◽

Partial Least Squares ◽

Association Studies ◽

A Priori ◽

Simulated Data ◽

Real Data ◽

Genome Wide Association Studies ◽

Genetic Associations ◽

Multiple Traits ◽

Application Fields

Abstract Background The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting these cross-phenotype genetic associations could help to identify and understand common biological mechanisms underlying some diseases. Common approaches test the association between genetic variants and multiple traits at the SNP level. In this paper, we propose a novel gene- and a pathway-level approach in the case where several independent GWAS on independent traits are available. The method is based on a generalization of the sparse group Partial Least Squares (sgPLS) to take into account groups of variables, and a Lasso penalization that links all independent data sets. This method, called joint-sgPLS, is able to convincingly detect signal at the variable level and at the group level. Results Our method has the advantage to propose a global readable model while coping with the architecture of data. It can outperform traditional methods and provides a wider insight in terms of a priori information. We compared the performance of the proposed method to other benchmark methods on simulated data and gave an example of application on real data with the aim to highlight common susceptibility variants to breast and thyroid cancers. Conclusion The joint-sgPLS shows interesting properties for detecting a signal. As an extension of the PLS, the method is suited for data with a large number of variables. The choice of Lasso penalization copes with architectures of groups of variables and observations sets. Furthermore, although the method has been applied to a genetic study, its formulation is adapted to any data with high number of variables and an exposed a priori architecture in other application fields.

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Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data

Genes ◽

10.3390/genes12060824 ◽

2021 ◽

Vol 12 (6) ◽

pp. 824

Author(s):

Sunghyun Cho ◽

Prabuddha Manjula ◽

Minjun Kim ◽

Eunjin Cho ◽

Dooho Lee ◽

...

Keyword(s):

Snp Array ◽

Initial Step ◽

Reproductive Organs ◽

High Linkage Disequilibrium ◽

Primary Data ◽

Multiple Traits ◽

Indigenous Chicken ◽

Primary Data Analysis ◽

The Government ◽

Commercial Chickens

Korean native chickens (KNCs) comprise an indigenous chicken breed of South Korea that was restored through a government project in the 1990s. The KNC population has not been developed well and has mostly been used to maintain purebred populations in the government research institution. We investigated the genetic features of the KNC population in a selection signal study for the efficient improvement of this breed. We used 600K single nucleotide polymorphism data sampled from 191 KNCs (NG, 38; NL, 29; NR, 52; NW, 39; and NY, 33) and 54 commercial chickens (Hy-line Brown, 10; Lohmann Brown, 10; Arbor Acres, 10; Cobb, 12; and Ross, 12). Haplotype phasing was performed using EAGLE software as the initial step for the primary data analysis. Pre-processed data were analyzed to detect selection signals using the ‘rehh’ package in R software. A few common signatures of selection were identified in KNCs. Most quantitative trait locus regions identified as candidate regions were associated with traits related to reproductive organs, eggshell characteristics, immunity, and organ development. Block patterns with high linkage disequilibrium values were observed for LPP, IGF11, LMNB2, ERBB4, GABRB2, NTM, APOO, PLOA1, CNTN1, NTSR1, DEF3, CELF1, and MEF2D genes, among regions with confirmed selection signals. NL and NW lines contained a considerable number of selective sweep regions related to broilers and layers, respectively. We recommend focusing on improving the egg and meat traits of KNC NL and NW lines, respectively, while improving multiple traits for the other lines.

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Constraints on the ecomorphological convergence of zooplanktivorous butterflyfishes

Integrative Organismal Biology ◽

10.1093/iob/obab014 ◽

2021 ◽

Author(s):

Jennifer R Hodge ◽

Yutong Song ◽

Molly A Wightman ◽

Analisa Milkey ◽

Binh Tran ◽

...

Keyword(s):

Evolutionary History ◽

Swimming Performance ◽

Morphological Evolution ◽

Distinct Type ◽

Ancestral State ◽

Multiple Traits ◽

Visual Identification ◽

Form Function ◽

Morphological Distinction ◽

Foraging Modes

Abstract Whether distantly related organisms evolve similar strategies to meet the demands of a shared ecological niche depends on their evolutionary history and the nature of form-function relationships. In fishes, the visual identification and consumption of microscopic zooplankters, selective zooplanktivory, is a distinct type of foraging often associated with a suite of morphological specialisations. Previous work has identified inconsistencies in the trajectory and magnitude of morphological change following transitions to selective zooplanktivory, alluding to the diversity and importance of ancestral effects. Here we investigate whether transitions to selective zooplanktivory have influenced the morphological evolution of marine butterflyfishes (family Chaetodontidae), a group of small-prey specialists well known for several types of high-precision benthivory. Using Bayesian ancestral state estimation, we inferred the recent evolution of zooplanktivory among benthivorous ancestors that hunted small invertebrates and browsed by picking or scraping coral polyps. Traits related to the capture of prey appear to be functionally versatile with little morphological distinction between species with benthivorous and planktivorous foraging modes. In contrast, multiple traits related to prey detection or swimming performance are evolving toward novel, zooplanktivore-specific optima. Despite a relatively short evolutionary history, general morphological indistinctiveness, and evidence of constraint on the evolution of body size, convergent evolution has closed a near significant amount of the morphological distance between zooplanktivorous species. Overall, our findings describe the extent to which the functional demands associated with selective zooplanktivory have led to generalisable morphological features among butterflyfishes and highlight the importance of ancestral effects in shaping patterns of morphological convergence.

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Genome-wide fine-mapping identifies pleiotropic and functional variants that predict many traits across global cattle populations

Nature Communications ◽

10.1038/s41467-021-21001-0 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Ruidong Xiang ◽

Iona M. MacLeod ◽

Hans D. Daetwyler ◽

Gerben de Jong ◽

Erin O’Connor ◽

...

Keyword(s):

Dairy Cattle ◽

Chromosome Segment ◽

Multiple Traits ◽

Functional Variants ◽

Genome Wide ◽

The Usa ◽

Pleiotropic Qtl ◽

Causal Variants ◽

Genetic Value ◽

Bayesian Mixture Models

AbstractThe difficulty in finding causative mutations has hampered their use in genomic prediction. Here, we present a methodology to fine-map potentially causal variants genome-wide by integrating the functional, evolutionary and pleiotropic information of variants using GWAS, variant clustering and Bayesian mixture models. Our analysis of 17 million sequence variants in 44,000+ Australian dairy cattle for 34 traits suggests, on average, one pleiotropic QTL existing in each 50 kb chromosome-segment. We selected a set of 80k variants representing potentially causal variants within each chromosome segment to develop a bovine XT-50K genotyping array. The custom array contains many pleiotropic variants with biological functions, including splicing QTLs and variants at conserved sites across 100 vertebrate species. This biology-informed custom array outperformed the standard array in predicting genetic value of multiple traits across populations in independent datasets of 90,000+ dairy cattle from the USA, Australia and New Zealand.

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Does differential predation explain the replacement of zebra by quagga mussels?

Freshwater Science ◽

10.1086/676658 ◽

2014 ◽

Vol 33 (3) ◽

pp. 895-903 ◽

Cited By ~ 9

Author(s):

Rahmat Naddafi ◽

Lars G. Rudstam

Keyword(s):

Quagga Mussels ◽

Differential Predation

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Evaluation of locations for testing dry bean cultivars in western Canada using statistical procedures, biological interpretation and multiple traits

Canadian Journal of Plant Science ◽

10.4141/cjps93-129 ◽

1993 ◽

Vol 73 (4) ◽

pp. 985-994 ◽

Cited By ~ 4

Author(s):

G. Saindon ◽

G. B. Schaalje

Keyword(s):

Cluster Analysis ◽

Seed Yield ◽

Seed Weight ◽

Visual Assessment ◽

Western Canada ◽

Multiple Traits ◽

Dry Bean ◽

Biological Interpretation ◽

Environmental Events ◽

High Level

Genotype × environment (GE) effects in regional registration trials for dry beans in western Canada were studied to determine whether geographic distribution of sites could be rationalized. The structure of the GE effects on the maturity, seed weight and seed yield of seven dry bean check cultivars grown at eight locations during 4 yr was investigated using GE mean squares decomposition, cluster analysis and the additive main effect and multiplicative interaction (AMMI) method. The analyses revealed a high level of redundancy in the locations which suggested that most GE effects can be captured with fewer testing sites. The partition of the GE mean squares demonstrated the possibility of reproducing the GE structure of the entire data sets with as few as three sites; however, more locations may be needed to compensate for unpredictable environmental effects. Based on biological interpretation of groupings and visual assessment of the AMMI displays, a five-location set fully represented the GE effects on maturity, seed weight and seed yield and accounted for the inconsistent clustering of the Brooks site for the three traits. Also, the set should allow for site losses due to unpredictable environmental events. The dry bean industry in western Canada is expanding to non-traditional growing areas and the establishment of trials in these areas should be considered as they may create GE effects not considered to date. Key words: Phaseolus vulgaris L., genotype × environment interactions, cluster analysis, AMMI analysis

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Morph-specific correlations between floral traits in a distylous Ophiorrhiza napoensis (Rubiaceae) population in southern China

Journal of Tropical Ecology ◽

10.1017/s0266467401001535 ◽

2001 ◽

Vol 17 (5) ◽

pp. 719-728 ◽

Cited By ~ 17

Author(s):

HIROSHI KUDOH ◽

TAKASHI SUGAWARA ◽

SUGONG WU ◽

JIN MURATA

Keyword(s):

Southern China ◽

Principal Component ◽

Corolla Tube ◽

Floral Traits ◽

Evergreen Forest ◽

Tube Length ◽

Multiple Traits ◽

Floral Trait ◽

Subtropical Evergreen Forest ◽

Positive Correlations

Floral trait correlations were compared between the two flower morphs of a distylous Ophiorrhiza napoensis population in a subtropical evergreen forest at the Defu Natural Animal Preserve, Guangxi, China. Common principal component analyses indicated that overall patterns in correlations among floral traits were morph specific in the study population. Strong positive correlations (r > 0.9) between anther height and corolla-tube length were found in both morphs. Stigma height correlated positively with corolla-tube length in the long-styled morph (r = 0.843), but not in the short-styled morph (r = −0.018). Flower-morph-specific correlation suggests that natural selection by pollinators has moulded trait covariance among floral traits. Because morph-specific correlations are expressed as the patterns of within-morph variation among multiple traits, putative genes responsible for the stigma-corolla tube correlation should not link to the supergene for sex-organ reciprocity between the morphs, but their expression is limited in the long-styled morph.

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Sugar Beet Performance with Curly Top Is Related to Virus Accumulation and Age at Infection

Plant Disease ◽

10.1094/pd-90-0657 ◽

2006 ◽

Vol 90 (5) ◽

pp. 657-662 ◽

Cited By ~ 15

Author(s):

William M. Wintermantel ◽

Stephen R. Kaffka

Keyword(s):

Sugar Beet ◽

Management Practices ◽

Effective Means ◽

Field Trials ◽

Virus Concentration ◽

Multiple Traits ◽

Higher Plant ◽

Plant Weight ◽

Virus Accumulation ◽

Greenhouse Assay

Resistance to curly top disease caused by Beet curly top virus (BCTV) and related curtoviruses has been important to sustainable sugar beet (Beta vulgaris) production in the western United States for most of the last century. Recent advances in sugar beet genetics have led to the development of high-yielding cultivars, but these cultivars have little resistance to curly top disease. These cultivars are highly effective when disease management practices or environmental factors minimize curly top incidence, but can result in significant losses in years with early infection or abundant curly top. A greenhouse assay has been developed to rapidly test cultivars for a broad array of factors affecting performance in the presence of curly top. Previous studies have shown that sugar beet plants were more susceptible and losses more severe when seedlings were infected by BCTV, but less severe when plants were larger at the time of infection. To evaluate more precisely the relationship between age at infection, disease severity, virus accumulation, and yield loss in modern cultivars that were not bred for curly top resistance, individual sugar beet plants varying in degree of resistance and susceptibility to curly top were inoculated by viruliferous beet leafhoppers (Circulifer tenellus) when plants had two, four, or six true leaves, and maintained in a greenhouse for 6 weeks. When plants were inoculated at the two-leaf stage, all cultivars became severely stunted, with high disease ratings and similar rates of symptom development, regardless of resistance or susceptibility of the cultivar. Plants inoculated at four-and six-leaf stages exhibited increasing separation between resistant and susceptible phenotypes, with highly resistant cultivars performing well with low disease ratings and increased plant weights relative to susceptible cultivars. High-yielding cultivars performed only slightly better than the susceptible control cultivar. Results from greenhouse trials matched those from field trials conducted under heavy curly top pressure. Importantly, low virus concentration was directly correlated with lower disease ratings and higher plant weight, while elevated virus concentrations corresponded to higher disease ratings and lower weights. This demonstrates that a rapid greenhouse assay involving multiple traits can provide a rapid and effective means of selecting cultivars with improved curly top control, and could lead to more rapid incorporation of resistance into high-yielding sugar beet.

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