Miracle-dz/UniFAR-FTUs huggingface dataset:
Unravelling the genomic basis and evolution of the pea aphid male wing dimorphism

Wing dimorphisms have long served as models for examining the ecological and evolutionary tradeoffs associated with alternative morphologies [1], yet the mechanistic basis of morph determination remains largely unknown. Here we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing dimorphism, wherein males exhibit one of two alternative morphologies that differ dramatically in a set of correlated traits that inclused the presence or absence of wings [2-4]. Unlike the environmentally-induced asexual female aphid wing polyphenism [5], the male wing polymorphism is genetically determined by a single uncharacterized locus on the X chromosome called aphicarus (“aphid” plus “Icarus”, api) [6, 7]. Using recombination and association mapping, we localized api to a 130kb region of the pea aphid genome. No nonsynonymous variation in coding sequences strongly associated with the winged and wingless phenotypes, indicating that api is likely a regulatory change. Gene expression level profiling revealed an aphid-specific gene from the region expressed at higher levels in winged male embryos, coinciding with the expected stage of api action. Comparison of the api region across biotypes (pea aphid populations specialized to different host plants that began diverging ~16,000 years ago [8, 9]) revealed that the two alleles were likely present prior to biotype diversification. Moreover, we find evidence for a recent selective sweep of a wingless allele since the biotypes diversified. In sum, this study provides insight into how adaptive, complex traits evolve within and across natural populations.
Iron (III) induces aggregation of hyperphosphorylated τ and its reduction to iron (II) reverses the aggregation: implications in the formation of neurofibrillary tangles of Alzheimer's disease

Iron as well as aluminum is reported to accumulate in neurons with neurofibrillary tangles (NFTs) of Alzheimer's disease (AD) brain. Previously we demonstrated that aluminum (III) shows phosphate‐dependent binding with hyperphosphorylated τ (PHFτ), the major constituent of NFTs, thereby inducing aggregation of PHFτ. Herein we report that iron (III) can also induce aggregation of soluble PHFτ. Importantly, for the aggregation of PHFτ to occur, iron in the oxidized state (III) is essential since iron in the reduced state (II) lacks such ability. Furthermore, iron (III)‐induced aggregation is reversed by reducing iron (III) to iron (II). Thus the iron‐participating aggregation is mediated not only by τ phosphorylation but also by the transition of iron between reduced (II) and oxidized (III) states. Further incubation of insoluble PHFτ aggregates isolated from AD brain with reducing agents produced liberation of solubilized PHFτ and iron (II), indicating that PHFτ in association with iron (III) constitutes the insoluble pool of PHFτ. These results indicate that iron might play a role in the aggregation of PHFτ leading to the formation of NFTs in AD brain.
Transcriptional regulation following Mycobacterium tuberculosis infection

by Rebecca L. Geister Tumor necrosis factor alpha (TNF-α) and nitric oxide synthase 2 (NOS2) are crucial in the control of Mycobacterium tuberculosis infection. Previous studies have shown that murine macrophages produce lower levels of TNF-α and NOS2 following infection with pathogenic mycobacteria compared to non-pathogenic mycobacteria. Here we compare the virulent (H37Rv) and avirulent (H37Ra) isogenic strains of M. tuberculosis and their ability to activate TNF-α and NOS2 at a transcriptional level. We determined that macrophages infected with H37Rv compared to H37Ra and M. smegmatis showed diminished TNF-α and NOS2 promoter activity. Differences in the ability of the isogenic strains to activate the transcription factors Ets/Elk and NF-κB were also observed. The reduced ability of H37Rv to activate Ets/Elk correlates with diminished TNF-α production by infected cells relative to cells infected with H37Ra. This work demonstrates that virulent M. tuberculosis is capable of modulating the host immune response at a transcriptional level.
Australian freshwater crayfish exploitation by fishing and aquaculture

[Extract] The Australian freshwater crayfish fauna includes over 100 species of Parastacidae, a family of freshwater crayfish with Gondwanan distribution. There ae nine genera that cover a wide ecological diversity including burrowing forms, Engaeus, Engaewa, Gramastacus, Parastacoides and Geocherax, genera containing the world’s largest species of freshwater crayfish Astacopsis and Euastacus, and the widely distributed genus Cherax. Freshwater crayfish have been exploited by Aboriginal Australians for thousands of years. In the Murray-Darling Basin, remains (especially gastroliths) of River Murray crayfish Euastacus armatus and yabbies Cherax destructor are common in middens around Aboriginal sites.
A Non-Linear Analogy Procedure for Gene Repair

Interactions between sub-systems and their environment are everywhere. In this paper, logistic map is applied, which felicitously stimulates the chaotic behavior of gene, to make analogy of a health DNA sequence and a mutation DNA sequence. By successfully repairing mutational part of a DNA sequence segment with help of neighbor-compressed method, we propose that compressing the neighbor healthy part to replay the mutational part is an effective way for gene repair. Since information ecosystem also possesses chaotic characteristics, the concept that extracting information from the neighboring environment can amend or complete information of corresponding elements also apply to information ecosystems.
Analysis of microRNA precursors in multiple species by data mining techniques

RNA Sequencing has recently emerged as a breakthrough technology for microRNA (miRNA) discovery. This technology has allowed the discovery of thousands of miRNAs in a large number of species. However, despite the benefits of this technology, it also carries its own limitations, including the need for sequencing read libraries and of the genome. Differently, ab initio computational methods need only the genome as input to search for genonic locus likely to give rise to novel miRNAs. In the core of most of these methods, there are predictive models induced by using data mining techniques able to distinguish between real (positive) and pseudo (negative) miRNA precursors (pre-miRNA). Nevertheless, the applicability of current literature ab initio methods have been compromised by high false detection rates and/or by other computational difficulties. In this work, we investigated how the main aspects involved in the induction of predictive models for pre-miRNA affect the predictive performance. Particularly, we evaluate the discriminant power of feature sets proposed in the literature, whose computational costs and composition vary widely. The computational experiments were carried out using sequence data from 45 species, which covered species from eight phyla. The predictive performance of the classification models induced using large training set sizes (≥ 1, 608) composed of instances extracted from real and pseudo human pre-miRNA sequences did not differ significantly among the feature sets that lead to the maximal accuracies. Moreover, the differences in the predictive performances obtained by these models, due to the learning algorithms, were neglectable. Inspired by these results, we obtained a feature set which can be computed 34 times faster than the less costly among those feature sets, producing the maximal accuracies, albeit the proposed feature set has achieved accuracy within 0.1% of the maximal accuracies. When classification models using the elements previously discussed were induced using small training sets (120) from 45 species, we showed that the feature sets that produced the highest accuracies in the classification of human sequences were also more likely to produce higher accuracies for other species. Nevertheless, we showed that the learning complexity of pre-miRNAs vary strongly among species, even among those from the same phylum. These results showed that the existence of specie specific features indicated in previous studies may be correlated with the learning complexity. As a consequence, the predictive accuracies of models induced with different species and same features and instances spaces vary largely. In our results, we show that the use of training examples from species phylogenetically more complex may increase the predictive performances for less complex species. Finally, by using ensembles of computationally less costly feature sets, we showed alternative ways to increase the predictive performance for many species while keeping the computational costs of the analysis lower than those using the feature sets from the literature.
Use of penetration of zona-free hamster eggs by bovine sperm as an estimation of fertility /

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Breeding potential of Philippine traditional maize varieties.

Maize in the Philippines has been evolving through natural and human-directed selection for more than 500 years. Forty-eight initially collected Philippine traditional maize varieties or populations were characterized with emphasis on tolerance and/or resistance to biotic and abiotic stresses. The varieties exhibited high variability for 9 qualitative and 15 quantitative traits. Several varieties showed outstanding performance in terms of downy mildew resistance, potential corn borer resistance, lysine content and earliness.
A Novel Approach to Prepare Protein-proanthocyanidins Nano-complexes by the Reversible Assembly of Ferritin Cage

The application of proanthocyanidins (PCs) in food industry is limited because of its instability and vulnerability against oxidative damage. In this work, by taking advantage of the reversible assembly characteristic of ferritin, apo-red bean ferritin (apoRBF)-PCs composites (FPs) were designed, and results showed a ratio of 1/10 of PCs (PCs/ apoRBF, w/w) were encapsulated into a ferritin cage, and the encapsulation ratio was 23.8%. The FPs exhibited a homogeneous form, and maintained a spherical morphology. Further more, the thermal and light stability of PCs in FPs was significantly increased compared to free PCs (p < 0.05). The in vitro digestion indicated that apoRBF could prolong the release of PCs in simulated gastrointestinal tract. Additionally, the antioxidant activity of FPs was partly retained (56.6%) as compared to free PCs. This work offers a novel method to encapsulate and stabilize polyphenols and might be favorable for the application of ferritin in food industry.
Phosphorylation of histone proteins during cell cycle & genomic analyses of the maize shoot apical meristem

This dissertation contains two distinct sections. The first section characterizes the phosphorylation of the maize centromeric histone H3 variant (CENH3) at Ser50. Phosphorylation of histone H3 occurs at Ser10/28 and Thr3/11, and marks chromosome arms or pericentromeres during cell division. Using molecular and cytological methods, we find that maize CENH3 is efficiently phosphorylated at Ser50 in a prophase-telophase pattern that mirrors known H3 phosphorylation events. These data extend the proposed “histone code” to centromeres. We propose that the primary role of histone H3 phosphorylation is to demarcate distinct chromosomal domains (i.e. centromere, pericentromere, chromosome arm) so that chromosomes can align and segregate properly. CENH3 phosphorylation may function as a component of the anaphase checkpoint, and/or mediate kinetochore maturation. The second section describes the meristem-specific transcript profiling analyses of two maize leaf developmental mutants, narrow sheath1 (ns1) and ragged seedling2 (rgd2). ns mutant plants harbor mutations in the duplicate genes ns1 and ns2, and display narrow leaves due to the loss of a mediolateral domain. The ns genes encode duplicate WUSCHEL1-like homeobOX (WOX) transcription factors that function redundantly and non-cell autonomously to direct recruitment of leaf founder cell-initials in a lateral domain of the shoot apex. Our analyses indicated that genes predicted to be involved in hormonal transport and signaling, signal transduction, and growth are especially implicated during NS-mediated leaf founder cell recruitment and mediolateral axis specification. Moreover, potentially conserved WOX gene functions during the regulation of two component response pathways and of jasmonate-induced gene expression are identified. RGD2 is required to coordinate leaf lateral expansion and dorsiventral patterning. rgd2-R mutant plants display narrow to radial leaves that fail to expand laterally, with no reduction of adaxial or abaxial identity. This peculiar phenotype enables the use of the rgd2-R mutant as a genetic tool to re-examine a widely accepted model for dorsiventral and mediolateral patterning in plants. Transcriptome analyses revealed that genes predicted to be involved in transcription regulation, chromatin remodeling, signal transduction, and proteolysis/protein fate are especially misexpressed in the rgd2-R mutant apex. Our data suggest that RGD2 may function through either the ARP (ASYMMETRIC LEAVES 1/ROUGH SHEATH2/PHANTASTICA) pathway or via a previously undescribed proteolytic pathway to coordinate dorsiventral patterning and mediolateral growth during maize leaf development.
Bony traits and genetics drive intraspecific variation in vertebrate elemental composition

Summary Interspecific variation in elemental composition is well known and often leads to predictable differences in ecosystem interactions, but little is known about the extent, causes and importance of intraspecific variation in elemental composition. If intraspecific variation is substantial and has a genetic basis, it may underlie an important mechanism of evolutionary interplay with ecology as individuals compensate for evolutionary changes in elemental demand. To investigate the extent and causes of intraspecific elemental variation in vertebrates, we sampled evolutionary model species Gasterosteus aculeatus (Threespine Stickleback) from 12 locations in British Columbia, Canada. Fish were phenotyped, genotyped for Eda alleles underlying lateral plate variation and assayed for elemental content (C, N, P). We found stickleback vary widely in elemental composition (2.2 – 6.5%P; 3.0 – 9.4:1 N:P). Phenotypic models explained the majority of this variation using bony armour traits (pelvis length, lateral plate count), bone mineralization, body size and condition. Subsequent genetic models found allelic variation at Eda generates a 7-14% change in whole organism N:P. As Eda allele frequencies are commonly changed through strong natural selection in freshwater habitats, we infer that stickleback elemental composition can evolve rapidly. Further, as genetics are known to drive variation in many of the other influential traits, we conclude that genetic variation constitutes a major source of variation in the elemental composition of Gasterosteus aculeatus. As such, we find that elemental composition has a large evolutionary potential which may underlie important evo-eco interactions. This article is protected by copyright. All rights reserved.
BRANCH OCCLUSION AFTER PRUNING IN FOUR CONTRASTING SUB-TROPICAL EUCALYPT SPECIES

SMITH, R. G. B. , DINGLE, J., KEARNEY, D. & MONTAGU, K. 2006. Branch occlusion after pruning in four contrasting sub-tropical eucalypt species. Branch related defects are the major cause of degrade in eucalypts grown for solid wood. The effects of pruning on the growth and branch occlusion in Eucalyptus cloeziana, E. pilularis, E. dunnii and E. grandis were studied. Trees of each species were pruned to remove 30% of the green crown at 3.5 years of age. Diameters and the state of all branches in two 0.5 m sections of trunk were assessed at one, two and four years after pruning. Growth rates were unaffected two years after pruning in all species. In all species, except E. cloeziana, the rate of occlusion of dead branches was not significantly different between pruned and unpruned branches. In contrast, the greatest difference in occlusion rates was between pruned and unpruned live branches. Eucalyptus grandis and E. dunnii showed high early rates of occlusion compared with E. pilularis and E. cloeziana for the first year. The occlusion rates of unpruned branches generally showed a positive correlation between branch size and time to occlusion. Relationships were more complex in species that self-pruned less efficiently. Since occlusion rates in dead branches (pruned and unpruned) were similar, there would be little benefit in pruning dead branches and it may increase susceptibility to decay entry and the occurrence of loose knots. Pruning only green branches may be difficult in efficient self-pruning species.
Understanding the gut transcriptome responses to lactobacillus probiotics and investigating the impact of nutrition and rotavirus infection on the infant gut microbiome

ii Acknowledgments. v Vita . vii Table of contents . xi List of Tables . xvi List of Figures . xvii Chapter 1: Review of Literature . 1 1.1 Infant gut microflora and its significance . 2 1.2 Gut microflora colonization phases in infants.4 1.3 Milk microbiota and milk oriented gut microbiota.7 1.4 Genesis of milk microbiota . 9 1.5 Mechanisms of microflora colonization.10 1.6 Impact of diet, antibiotic, and probiotic on infant gut microbiota.12 1.6. 1 Diet.12 1.6. 1.1 Pre-weaning.12
Impact of Extracellular Osmolality on Saccharomyces Yeast Populations during Brewing Fermentations

Osmotic stress represents one of the major environmental challenges experienced by yeast during industrial fermentations. This stress is particularly associated with high-gravity processes, which utilize concentrated substrates to yield products with elevated concentrations of ethanol. The aims of this work were to quantitatively measure factors affecting extracellular osmotic pressure (osmolality) during brewing fermentations and to determine their effects on yeast at the physiological and molecular level. Osmolality was observed to increase during fermentation owing predominantly to ethanol production, indicating a strong relationship between these environmental parameters. High osmolality was shown to have a negative impact on yeast physiology, viability, and vitality, and although genome integrity was unaffected, cell membrane fluidity became altered. These data not only demonstrate the occurrence of an increase in osmotic pressure during fermentation but also provide an explanation for the decrease in yeast quality typically observed under high-gravity conditions. The results presented here are directly relevant to all brewery fermentations worldwide and have applications within associated industries in which microorganisms are used for ethanol production, including food products, alcoholic beverages, and biofuels.
Wariness of reef fish to passive diver presence with varying dive gear type across a coral reef depth gradient

Both active and passive human interactions with reef fish communities are increasingly recognized to cause fish behavioural changes. However, few studies have considered how these behavioural adaptations impact standard reef survey techniques, particularly across natural gradients of interest to ecologists and reef managers. Here we measure fish abundance, biomass and minimum approach distance using stereo-video surveys to compare the effects of bubble-producing open-circuit scuba vs near-silent closed-circuit rebreathers. Surveys extended across a shallow to upper-mesophotic gradient on the fringing reefs of Utila, Honduras, to explore how the effects of diver gear choice vary with depth. For most fish families we recorded similar abundances and biomass with the two diving techniques, suggesting that open-circuit transects are generally appropriate for surveying western Atlantic reefs similar to Utila with regular tourist diving but no spearfishing. Despite no overall significant difference in fish abundance or biomass, we identified several fish families (Labridae, Pomacentridae, Scaridae) that allowed closed-circuit rebreather divers to approach more closely than open-circuit divers. In addition, smaller fish generally allowed divers to approach more closely than larger fish, and in most cases divers could approach fish more closely on mesophotic than shallow reefs. Despite these significant differences in approach distances, their magnitude suggest they are unlikely to affect reef fish detectability during normal fish surveys for most families. Our findings highlight the importance of considering variation in fish behavioural adaptations along natural gradients such as depth, which otherwise has the potential to cause biases when surveying by traditional monitoring programmes.
Immunological response profiles to salmon lice infections in Atlantic salmon : modulation by nutrition and selective breeding

Atlantic salmon skin tissues with and without scales were taken from two preferred sites of salmon louse (Lepeophtheirus salmonis) attachment, behind the dorsal fin (scaled) and from the top of the head (scaleless), respectively. Tissues were profiled by qPCR of 32 genes to study responses to copepodids, 4 days post infection (dpi), and during the moult of copepodids to the chalimus stage, at 8 dpi. Basal/ constitutive differences were found for many immune-related genes between the two skin sites; e.g., mannose binding protein C was over 100 fold higher expressed in the scaled skin from the back in comparison to the skin without scales from the head. With lice-infection, at 4 dpi most genes in both tissues showed lower values than in the non-infected control. By 8 dpi, the majority of responses increased towards the control levels, including cytokines of Th1, Th17 and Th2 pathways. Immunohistochemistry of three immune factors revealed an even distribution of MHC class II positive cells throughout epidermis, including the top layer of keratinocytes, marked compartmentalization of Mxþ and CD8aþ cells close to stratum basale, and an increase in numbers of CD8aþ cells in response to infection. In conclusion, suppression of immune genes during the copepodid stage likely sets off a beneficial situation for the parasite. At the moult to chalimus stage 8 dpi, only few genes surpassed the non-infected control levels, including CD8a. The gene expression pattern was reflected in the increased number of CD8a expressing cells, thus revealing a relatively minor activation of skin T-cell defenses in Atlantic salmon in response to L. salmonis infection. © 2016 Elsevier Ltd. All rights reserved.
A superfamily of proteins that contain the cold-shock domain

Notall CSPs are induced by cold shock,however; some are involved in other cellular processes.CSPs are defined on the basis of theirsequences, which are conserved, at.45% identity, between Gram-positiveand Gram-negative species. Recently,CSPs were found in the earliest-diverg-ing bacterial branches of