Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenomic Synteny Network Analysis Reveals an Ancient MADS-Box Transcription Factor Tandem Duplication and Lineage-Specific Transpositions

Conserved genomic context (or synteny) provides critical information for comparative evolutionary analysis, such as the inference of ancient polyploidy events, recurrent genomic rearrangements across species and gene ancestry. With the increase of sequenced and assembled plant genomes, we now have the opportunity to use synteny to analyze the dynamics of gene family expansion and contraction across broad phylogenetic groups. Here we present an integrated approach to organize plant kingdom-wide gene synteny networks using k-clique percolation. As an example, we analyzed the gene synteny network of the MADS-box transcription factor family based on fifty-one completed plant genomes. We conclude from two massive gene clusters that one of the two Type II MADS-box gene clades evolved from an ancient tandem gene duplication likely predating the radiation of seed plants, which then expanded by polyploidy events and sub-functionalization. This gene clade now contains key regulators of major phenotypes of angiosperms including flower development. Moreover, we find lineage-specific gene clusters derived from transposition events. For example, lineage-specific clusters in the Brassicales containing genes that are well-known for their function in controlling flower morphology (AP3 and PI). Our phylogenomic synteny network approach can be applied to any group of species to gain new insights into the evolution and dynamics of any set of genes.
Distribution of Bryophytes in South-Eastern Brazil: An Approach on Floristic Similarity and Environmental Filtering

Abstract The south-eastern Brazil comprises the Atlantic forest (a region mainly characterized by tropical evergreen forest), subtropical forest, mangroves, and scrub sandbanks. Sandy areas are found at sea level, and high altitude grassland spots and rocky outcrops occur above 2000 m. This region is important because the richness, diversity, and endemism of species, including bryophytes. The similarity of bryophytes occurring on these different areas has not been evaluated yet. This study aimed to analyse the bryofloristic similarity between 12 different areas in south-eastern Brazil, assessing the environmental factors that influence their distribution. Floristic similarity was analysed under cluster and Detrended Correspondence Analysis; multi-response permutation procedures were employed to test the groups' significance. In order to test whether the geographical distance between the areas is a relevant factor to test the similarity of the species, Spearman correlation analysis was performed, and to determine the relationship between the floristic composition and the environmental variables (altitude, temperature, annual rainfall and distance from the ocean), canonical correspondence analysis was applied. A low similarity between the 12 studied areas was observed, but two groups were revealed, the so-called inland areas and coastal areas. The annual precipitation and annual temperature influenced floristic similarity in the coastal areas and, the distance from the ocean and altitude were the variables that most influenced inland areas.
Experience of mGluR1 gene therapy in transgenic models of sca1 mice

Spinocerebellar ataxia type 1 (SCA1) is a progressive neurodegenerative disease that presents with cerebellar ataxia and motor learning defects. Previously, we examined a mouse model of SCA1 and found a progressive functional impairment of metabotropic glutamate receptor (mGluR) signaling including dendritic Ca2+ signals and a consequent loss of shortand long-term synaptic plasticity at parallel fiber-Purkinje cell synapses in the early disease stage (12 postnatal weeks) prior to Purkinje cell death. According to this findings we suspected that enhancement of mGluR signaling by virus expression of mGluR1 selectively in Purkinje cells should lead to an improvement of motor performance in SCA1 mice. For this aim we construct viruses in a head of adeno-associated virus and murine stem cell virus promoters expressing mGluR1 and green fluorescent protein. Unfortunately, overexpression of this gene constructs gives the opposite effect. Examination of this phenomena leads to understanding of mGluR1 dependent mechanisms of dendritic arborization, synaptogenesis and synaptic plasticity in Purkinje cells. Thus, we found that mGluR1 signaling is a critical but not unique molecular in SCA1 pathogenesis. Also this negative result shows the complicity and ambiguousness of virus therapy benefit.
Rearing conditions have long-term sex-specific fitness consequences in the collared flycatcher

Lay Summary Early-life conditions have stronger effects on the fitness of male than female collared flycatchers. Male nestlings from experimentally enlarged broods had fewer eggs from their mates during their life than male nestlings from reduced broods, which was a consequence of their shorter breeding lifespan. In females, rearing conditions had no effect on fitness. Together with earlier results, we show that although sex differences in growth disappear by fledging, the greater sensitivity of males had lifelong consequences.
Calculating hazard rates of introgression with branching processes

Introgression is the permanent incorporation of genes from the genome of one population into that of another through hybridisation and backcrossing. With the advent of genetically modified crops, the potential that transgenes might introgress from cultivated to wild plants has become a point of scientific scrutiny. This thesis presents a methodology by which the risk of introgression can be quantified in terms of empirically determined quantities. A proposed measure of risk is the hazard rate. The hazard rate of introgression is the probability per time unit that introgression occurs given that it has not previously occurred. Particular attention is drawn to demographic stochasticity, genetical mechanisms and both random and deterministic time-inhomogeneities. A sample chapter also outlines the application of the models with empirical data.
Characterization and Expression Analysis of WRKY Transcription Factors in Groundnut (Arachis hypogaea L.)

Groundnut (Arachis hypogaea L.), is an important subsistence oil yielding crop of the semi-arid tropics and often exposed to several environmental cues (high temperature, drought & heavy metal). The WRKY transcription factor (TF) is one of the master regulator, and play vital role in stress responses. However, far less information is available on functional characterization and tolerance mechanism of stress responsive WRKY genes in groundnut till date. In this study, a comprehensive phylogenetic, protein features, gene structure and motif analysis of WRKY TF gene family was carried out. We conducted expression profiling of 10 WRKY genes under high temperature, drought and heavy metal (CdCl 2 ) in various tissues. Majority of the AhWRKY ( Arachis hypogaea WRKY ) proteins were clustered and share close relationship with Arabidopsis and Glycine max . RT- qPCR analysis of AhWRKY genes revealed differential expression either in their transcript abundance or in their expression patterns in response to at least one abiotic stress. In particular, AhWRKY41 expression level was found to be maximum in all the stress conditions . On the other hand, AhWRKY20 and AhWRKY22 were down regulated. The obtained data demonstrate that AhWRKY41 may act as a positive regulator in drought/ high temperature/ heavy metal and would exhibit stress tolerance mechanism by activation of stress-associated gene expression.
Optimization of high quality total RNA isolation from the microalga, Chlorella sp. (Trebouxiophyceae, Chlorophyta) for next‐generation sequencing

The advent of high‐throughput next‐generation sequencing (NGS) has enabled more comprehensive transcriptome analyses to obtain gene expression data and understand metabolic pathways essential for functional analysis and systems biology. The isolation of high purity and intact RNA of sufficient quality and yield is crucial to the success of NGS sequencing. In green microalgae, extraction of nucleic acids is hindered by high concentration of lipids and polysaccharides that co‐precipitate with nucleic acids thus resulting in reduced yield and poor quality extracts. The present study compared the performance of standard and modified total RNA isolation protocols using different cell disruption techniques combined with TRIzol reagent or a commercially available kit, in meeting the stringent requirements for downstream NGS application of a green freshwater microalga, Chlorella sp. The protocols were evaluated for (i) the yield of RNA, (ii) integrity of RNA as determined by the RNA integrity number and (iii) the purity of RNA as determined by the A260/A280 and A260/A230 ratios. In general, higher yields were obtained by cell disruption via flash freezing and homogenizing with liquid nitrogen followed by lysis with TRIzol reagent. We recommend the incorporation of a salt precipitation step to improve the purity and integrity of RNA isolated. Results of this study served as a simple and low‐cost practical guide for researchers working on isolation of high quality total RNA from microalgae, considering that most relevant publications do not provide a detailed methodology for total RNA isolation or use more expensive methods (e.g. bead‐beater).
Notes on the marine algae of the Bermudas. 15. Dichotomaria huismanii (Galaxauraceae, Rhodophyta), a new species in the D. marginata complex from the western Atlantic

Abstract Using plastid-encoded rbcL and mitochondrial COI-5P sequence data, the species in Bermuda formerly recognized as Dichotomaria marginata was found to be a cryptic species in a wide complex of species all falling under the morphologically broad species concept for this supposed pantropical species. The new species, Dichotomaria huismanii, shows subtle anatomical and morphological differences when compared to D. marginata, and at present is only known from Bermuda. Bermuda specimens were compared with our isolates of D. marginata from St. Croix (Virgin Is.), as well as rbcL sequenced specimens with those from Guadeloupe and Puerto Rico in GenBank as D. marginata. Morphological and molecular characterization of D. marginata is provided along with the new species.
Metabolite Composition of Grapefruit (Citrus paradisi) Grown in Japan Depends on the Growing Environment and Harvest Period

‘Sagan-Ruby’ is the first grapefruit ( Citrus paradisi ) cultivar to be developed in Japan and is used for food, cosmetics, and other purposes owing to its favorable characteristics, such as the absence of harmful pesticides and its long shelf life. The desired qualities of grapefruit depend on the specific use, and these qualities are influenced by the metabolite composition of the fruits. However, little is known about the influence of the growing environment or harvest period on the metabolite composition of the ‘Sagan-Ruby’ grapefruit. Therefore, we harvested fruits that were grown either in a plastic house without artificial heating or outdoors with rain cover from December, 2014 to April, 2015, on a monthly basis, and we investigated the composition of the primary metabolites such as sugars, organic acids, and amino acids, in the juice and peel of the fruit using gas chromatography mass spectrometry (GC/MS). We detected a total of 53 and 68 compounds in the juice and peel, respectively, and the first and second components of the principal component analyses of the detected metabolites of both juice and peel were associated with the growing environment and harvest period, respectively. Since we observed that glucose, fructose, sucrose, and citric acid were more concentrated in the juice of outdoor-grown fruits than in that of the house-grown fruits, especially in March and April, it is likely that the sweetness and acidity of the fruits are dependent on the growing environment. Similarly, the primary metabolite contents, including succinic acid and other organic acids, were higher in peels from outdoor-grown fruits. In addition, we also observed that the contents of proline, phenylalanine, and other amino acids in the juice increased continuously from December to April, and many sugars, including glucose and fructose, gradually decreased in peels from December to February and were lower from February to April. These results indicated that quality of the ‘Sagan-Ruby’ grapefruit varies with the harvest period.
Genetic and demographic investigation of population structure and social system in four delphinid species

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Basidiospores as sources of inoculum in the spread of Ganoderma boninense in oil palm plantations in Papua New Guinea

Basal and upper stem rot of oil palm is caused by the agaricomycete Ganoderma boninense. This study investigated the transmission of basal stem rot from Ganoderma-infected oil palm stumps to young oil palm seedlings. Low seedling mortalities (2.5%) were observed in a field trial after 24 months, but G. boninense could be detected in the rachis, bole and roots of a significant proportion of seedlings that were outwardly healthy. A high level of genetic heterogeneity amongst G. boninense isolates within the trial area was revealed. Furthermore, germinated seedlings growing in close proximity to infected palms in a mature oil palm field contained multiple isolates of G. boninense indicating that colonization of roots by basidiospores and dikaryons, arising from mating between basidiospores, is a common occurrence in oil palm plantations. The probability that basidiospores are a direct source of inoculum in addition to diseased trunk tissue is discussed as a means of explaining the observed heterogeneity in populations of G. boninense on oil palm. Such a scenario presents challenges for the long-term management of basal stem rot.
Shrub encroachment, productivity pulses, and core-transient dynamics of Chihuahuan Desert rodents

Drylands worldwide are experiencing shrub encroachment into grasslands with potential consequences for biodiversity and ecosystem services. Climate change could increase the rate of shrub encroachment, amplify precipitation variability, and thus alter bottom-up processes for animal communities. Desert rodents are important biodiversity elements of arid grasslands and shrublands that exert strong effects on soil, vegetation, and other animal species. We used long-term data from the Jornada Basin Long Term Ecological Research site in the Chihuahuan Desert of southern New Mexico to ask whether bottomup control of desert rodents changes across shrub encroachment gradients. Our design included spatial blocks with replicated ecological states representing transitions from black grama (Bouteloua eriopoda) to honey mesquite (Prosopis glandulosa). Grassland-to-shrubland transitions did not produce degraded ecosystems, on average, with reduced net primary production or decreased rodent biomass. However, more rodent biomass was supported on unencroached grasslands following droughts whose frequency and severity may increase in southwestern United States. Hence, the observed evenness in rodent biomass across ecological states should be sensitive to climate change. The best predictors of rodent biomass also differed markedly for two trophic groups. This outcome was explained by considering core-transient dynamics. Granivores were mostly core species that regularly occurred on sites and responded to lagged net primary production at local scales, whereas folivores included transient species (especially Sigmodon hispidus) that responded to lagged precipitation at broader scales via spillover dynamics. Bottom-up processes for desert rodents across shrub invasion gradients were understood by integrating lagged responses to productivity pulses with core-transient structuring of communities.
State of the art in rumen lipid protection technologies and emerging interfacial protein cross‐linking methods

Polyunsaturated fatty acids given to ruminants are to a large extent hydrogenated to more saturated forms by microbial metabolism. Numerous protection technologies have been developed to overcome this hydrogenation process in order to increase the amount of unsaturated fatty acids bypassing the rumen and resulting in an effective transfer to the peripheral tissues. This review gives an overview of the current state of the art in rumen lipid bypass technologies, with the focus on both patent-described protection mechanisms, possible advantages or drawbacks of the technologies, and protection results being described in recent scientific literature. Lipid bypass techniques which are dealt with include calcium salts, fatty acyl amides, aldehyde treatment, non-enzymatic browning, lipid composite gels, and encapsulation within lipids. Further, the potential of a novel rumen lipid protection technology, based on interfacial cross-linking of emulsions, is explored. Therefore, an overview is given on current knowledge of different types of enzymatically induced cross-linking of protein at emulsion interfaces, both for existing food and possible ruminal bypass applications. Practical applications: Both from a human and animal health care as well as from a resource-saving and economic perspective, protection of PUFA from ruminal BH is of interest. Protection, release, and absorption principle of a lipophilic rumen bypass product: As polyunsaturated fatty acids (P) are hydrogenated to more saturated fatty acids (S) upon ruminal passage (panel A), P sources administered to ruminants have to be protected against microbial turnover to transfer them to the peripheral tissues (panel B).
EVALUATION AND IMPROVEMENT OF BUFFER‐pH LIME REQUIREMENT METHODS

In this experiment, we sought to determine the accuracy and useful range of six buffer-pH lime requirement (LR) tests, improve their accurate range, and select the best methods to determine the LR of acid mineral soils by routine analysis. Four single-buffer methods (Woodruff, Shoemaker et al. (SMP-SB), Adams and Evans, and Mehlich) and two double-buffer methods (Yuan and McLean et al. (SMP-DB)) were verified by comparing the estimated to the incubation LR, using correlation and regression techniques. Seventy acid mineral soils requiring from 1.4 to 40 milliequivalents CaCO3/100 grams to achieve pH 6.5 were used in this experiment. The proportion of soil acidity reacting with the LR buffers decreased as the LR of soils increased. Because this proportion is not constant (linear) as is generally assumed, but tends to be slightly exponential (curvilinear), the calibrations of these buffers were found to be more accurate for a particular range of soils. Accordingly, when used as proposed, the Woodruff, SMP-SB, and SMP-DB buffer methods predicted on the average 96, 130, and 102 percent of the actual requirements of soils requiring less than 10 meq CaCO3/100 g to attain pH 6.5, but predicted 69, 98, and 90 percent of the actual requirements for soils requiring between 10 and 40 meq CaCO3/100 g, respectively. The accuracy of these methods can be improved substantially by using two linear or a single curvilinear regression equation to correct for the exponential relationship between the proportion of soil acidity determined by such a buffer and the incubation LR. As these regression equations make the Woodruff and Shoemaker et al. single-buffer methods as accurate as the more involved Yuan and McLean et al. double-buffer methods, these single-buffer methods are recommended for routine LR determination.
First evidence of intersex condition in extensively reared mullets from Sardinian lagoons (central–western Mediterranean, Italy)

Abstract The term intersex describes alterations in gonadal development with the simultaneous presence of male and female reproductive stages in the same gonad of a gonochoristic species. In coastal and estuarine environments, euryhaline fish living in polluted waters such as Mugilidae can frequently show these sexual anomalies. In this work, we analysed adult specimens of three species of euryhaline mullets (Chelon labrosus, Liza aurata and Mugil cephalus) from two Sardinian lagoons (Marceddì and San Teodoro) devoted to extensive aquacultural practices, in order to identify putative alterations in gonads and in gamete development. Overall, 13 of the 158 mullets examined (8.2%) were affected by gonadal disorders: four subjects (one C. labrosus, two L. aurata and one M. cephalus) exhibiting an intersex condition were found in the Marceddì lagoon and the other nine (five C. labrosus, two L. aurata and two M. cephalus) in the San Teodoro lagoon. Twelve of these gonads were classified as testis-ova (TOs) and one, belonging to a C. labrosus specimen, was a mixed gonadal tissue (MGT). Intersex condition was evaluated using an intersex index and all the recorded values showed a mild Ovotestis Severity Index (OSI). However, our findings suggest that fish gonadal disorders may be underestimated in extensive reared fish species, particularly in coastal brackish environments polluted by intensive agriculture and animal husbandry activities.
THE INFLUENCE OF VIRAL STATUS ON POLLEN CHARACTERISTICS OF SOME APRICOT CULTIVARS

Apricot is one of the leading temperate zone fruit-bearing crops and obtaining of its new cultivars with the highest economically-valuable features is an actual problem. The most effective method of new cultivars breeding is the hybridization. Considering the modern ecological situation, it is extremely important to create virus-free forms with high adaptive potential. During the monitoring of the viral diseases spread within apricot collection plots of Nikita Botanical Gardens – National Scientific Center (NBG-NSC)the analysis of mature pollen of 11 apricot cultivars was investigated. It was found out that studied cultivars are characterized by resistance to pathogens and affection by viruses. Two cultivars of NBG-NSC breeding (Krymsky Amur and Krymsky Medunec) and two introduced cultivars (Harcot and Markuleshti) demonstrated the difference to specified parameters. For example, the cultivar Krymsky Medunec is resistant to viral pathogens; its mature pollen has a large percentage of morphologically normal pollen grains characterized by high germination (up to 90% and 32%, respectively). At the same time, cultivars Markuleshti and Harcot are strongly affected by Plum pox virus; their ripe pollen is morphologically normal, but low vital capacity level. On 15% sucrose solution pollen grains of cultivar Harcot did not germinate, and cultivar Markuleshti had only 1% of germinating pollen grains. It should be noticed that complex application of biotechnological methods (chemotherapy and meristem culture), further using and propagation of virus-free explants in vitro let us get healthy plant material. Thus, the results suggest the potential for creating new perspective cultivars of apricot with preset characteristics for further breeding.