Miracle-dz/UniFAR-FTUs huggingface dataset:
Misfolded proteins affect synaptic plasticity and network activity

Although misfolded and aggregated a-synuclein (a-syn) is recognized in the disease progression of synucleinopathies, its role in the impairment of cortical circuitries and synaptic plasticity remains incompletely understood. We investigated how a-synuclein accumulation affects synaptic plasticity in the mouse somatosensory cortex using two distinct approaches. Long-term in vivo imaging of apical dendrites was performed in mice overexpressing wild-type human a-synuclein. Additionally, intracranial injection of preformed a-synuclein fibrils was performed to induce cortical a-syn pathology. We find that a-synuclein overexpressing mice show decreased spine density and abnormalities in spine dynamics in an age-dependent manner. We also provide evidence for the detrimental effects of seeded a-synuclein aggregates on dendritic architecture. We observed spine loss as well as dystrophic deformation of dendritic shafts in layer V pyramidal neurons. Our results provide a link to the pathophysiology underlying dementia associated with synucleinopathies and may enable the evaluation of potential drug candidates on dendritic spine pathology in vivo.
Notes on the genus Calisto, with descriptions of the immature stages (Part 2) (Lepidoptera: Nymphalidae: Satyrinae).

The biology of Calisto crypto Gali, C. nubila Lathy, and C. tasajera Gonzalez, Schwartz & Wetherbee is described for the first time and the taxonomic implications of these data for the genus are discussed. Characters supporting relatedness of these species to each other and to other species complexes of Calisto are found in immature stages and in the structures of male and female genitalia. The latter are illustrated for the members of the lyceia species complex and relationships between these species are suggested. C. hendersoni Gali is suggested to be a synonym of C. franciscoi. A little known species, C. raburni Gali is found to be the most distinct member of the complex, and an additional locality for it (Dominican Republic: Polo, Barahona Prov.) is provided. New collecting data for the recently discovered C. tasajera add to the knowledge of this species' natural history. Finally, a theory of diversification is proposed for the lyceia complex.
Resistance to Direct-Acting Antiviral Agents in Treatment of Hepatitis C Virus Infections

Compounds targeting nonstructural (NS) proteins of hepatitis C virus (HCV) demonstrate clinical promise, suggesting that NS3/NS4a, NS5A, or NS5B inhibitors are potential components in direct-acting antiviral (DAA) combination therapies. In vitro studies revealed dramatic inhibition of viral replication or alteration in subcellular localization of NS proteins. DAAs bind either to catalytic sites (NS3 and NS5B) or to domain-1 of NS5A. Although >90% of the patients clear HCV RNA from their sera, a significant portion of cirrhotic patients suffer from resistance or virological relapse. Mutations in specific residues (Q80K) in NS3 (M28, A30, L31, and Y93 in genotypes 1a and 1b or L28, L30, M31, and Y93 in genotype 4) in NS5A and A282T in NS5B are associated with resistance to DAA [resistance-associated variants (RAVs)]. Current knowledge on the NS functions, mode of action of DAAs, and impacts of RAVs on treatment response are discussed. Not only mutations affecting the binding of DAAs to target proteins but also substitutions affecting the replication fitness of mutant quasispecies are major determinants of treatment failures. These resistance-associated substitutions (RASs) are now considered the major viral mutants that influence the virological outcome after DAA treatment.
Identification and characterization of brown stem rot resistance in soybean

Breeding for pathogen resistance is an important objective to improve and protect soybean yields. In 2010, 14.4% of total soybean yield was suppressed by diseases. Brown stem rot (BSR), caused by the fungus Phialophora gregata, reduces yield by as much as 38%. To date, three dominant BSR resistance genes have been identified: Rbs1, Rbs2, and Rbs3. The objectives of my research were 1) to determine if plant introductions contained novel BSR resistance genes, 2) to determine the correlation between P. gregata hyphae growth and foliar symptoms as well as characterize the response of the three BSR resistance genes to P. gregata infection, and 3) to identify and characterize the gene networks regulating defense responses to BSR using RNA-Seq and Virus Induced Gene Silencing (VIGS). To identify novel sources of resistance, four plant introductions with unknown sources of resistance (PI 594637, PI 594638B, PI 594650A, and PI 594858B) were each crossed to three genotypes with the three known BSR resistance genes, developing 12 populations for allelism studies. BSR symptoms were assessed under growth chamber conditions five weeks after inoculation by measuring foliar and stem severities, and recovery of P. gregata from stem sections. Allelism tests of plants from the crosses PI 594638B, PI 594858B, and PI 594650A with each of the resistant sources fit a 15:1 ratio, indicating that the resistant gene possessed by each of the PIs was non-allelic to Rbs1, Rbs2, and Rbs3. The three PIs contain at least one novel BSR-resistance gene, and have the potential to serve as donors to elite germplasm increasing stability of host resistance to P. gregata. To understand the relationship between P. gregata hyphae growth and foliar symptom development, BSR severity was recorded for individual leaves on infected plants of five
Modification of feeding strategies of grey herons (Ardea cinerea L.) in response to a major decline in the preyed fish community's biomass

Like other piscivorous birds, the diet of herons is well-known but relatively few studies have compared diet and fish stock, because both bird and fish populations must be studied at the same time (DRAULANS 1988, MARION 1990, MARQUISS & CARSS 1994). Most of the studies have concerned the impact of grey heron on fish cultures, for which the predation rate is relatively small (review in MAruoN 1997). There are very few data regarding the natural habitats of the grey heron (GEIGER 1984, fEUNTEUN & MARION 1994), with a predation rate of 0.3-6%. These studies, except for the last one (2 years), were carried out over one, or less, limited season. In the present paper, we compared the annual variation in fish populations over a relatively long period (5 years), and predation adaptation of the grey heron in the same area, by simultaneously studying the heron diet in the largest European colony (600-1300 breeding pairs) at Grand-Lieu Lake and the fish stock in their main feeding area, Bourgneuf Marsh.
Overexpression of Chrysanthemum morifolium SVP gene delays blossoming and regulates inflorescence architecture in transgenic Arabidopsis

Abstract: Short vegetative phase (SVP) like genes play a key role in floral transition and floral meristem identity. Although SVP-like genes have been isolated from various plant species, their orthologs have not been characterized in the important day-neutral ornamental plant Chrysanthemum morifolium Ramat. Here, a MADS-box gene was cloned from C. morifolium ‘Jinbudiao’ and designated as CmSVP. The open reading frame of CmSVP comprises 672 bp encoding a putative protein of 223 amino acids. Bioinformatics analyses showed that the gene was a member of the SVP gene family with homology to MADS-box transcription factors. Real-time polymerase chain reaction results showed that CmSVP is preferentially expressed in the shoot apex and leaves and its expression is decreased in both flower buds and flowers. Transcription of CmSVP in Arabidopsis plants showed overexpression of CmSVP delayed blossoming for up to 30 d. It also inhibited development of apical flower in the main stem, which resulted in an abortive bud or inflorescence. Additionally, the transgenic Arabidopsis plants contained increased basal inflorescences and branches, whorled leaves, opposite leaves in branches, and absence of main stem cauline leaves. These findings suggest that CmSVP is not only involved in flower timing and floral meristem identity, but also regulates inflorescence architecture.
Effects of Temperature and Moisture on Growth of Common Bean and Its Resistance Reaction against Common Bacterial Blight (Xanthomonas axonopodis pv. phaseoli strains)

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli Smith (Xap) and Xanthomonas axonopodis pv. phaseoli var. fuscan Burkholder (Xapf) is the most serious biotic constraint of common bean (Phaseolus vulgaris L.) production. Variables temperature and moisture are dominant climate factors that affect common bean growth as well as the development of CBB epidemics. Two sets of experiments were conducted in the Plant Pathology Laboratory of Haramaya University) to assess the effect of temperature and moisture on the resistance level of common bean in 2014 and 2015. In the first experiment, two common bean varieties (Gofta and Mexican 142) were inoculated with two bacterial strains (Xap and Xapf) and a control were incubated at four temperature levels (28°C, 30°C, 32°C and 34°C) in growth chambers. In the second experiment, three-soil moisture levels (100%, 75% and 50%) were employed to that of experiment one. The treatment combinations were arranged in factorial completely randomized design (CRD) in the growth chambers for both series of experiments. The disease rating was significantly (P
Taxonomic revision of the ant genus Linepithema (Hymenoptera: Formicidae).

This dataset contains the digitized treatments in Plazi based on the original journal article Wild, A. L. (2007): Taxonomic revision of the ant genus Linepithema (Hymenoptera: Formicidae). University of California Publications in Entomology 126: 1-159, URL: http://antbase.org/ants/publications/21156/21156.pdf
Transcriptomic approaches to study the effects of xenobiotics in ruminants

This thesis is concerned with the study and characterization of the xenobiotics-induced transcriptomic signature in some ruminants. Based on the different studies presented in this thesis, the microarray-based transcriptomics approach was able to provide a holistic view on the global gene expression in diverse types of tissues – namely, skeletal muscle, liver, whole blood, primary hepatocytes- and kidney-derived cell lines. The pre-designed commercial bovine microarray enabled the discovery of many biomarkers with which the differentiation between illicitly-treated and untreated veal calves was possible. It also demonstrated the transcriptomic signature dissimilarity between 2 tissues (i.e. skeletal muscle and liver) exposed to the same treatment (i.e. anabolic steroids). Also, the same approach revealed the presence of some transcriptomic landscape convergence between the hepatocytes primary cultures and the Madin-Darby bovine kidney (MDBK) cell line, which in turn spots the light on the MDBK cells as a possible surrogate in vitro tool for some liver-based functional studies. Finally, a custom-designed whole-transcriptome sheep (Ovis aries) microarray revealed the immune-system-induction and the transcriptional-modulation capacity of organic selenium in sheep. Collectively, the transcriptomics approach overcame the shortcoming of focusing on changes in expression of a priori list of selected genes – instead, it looks at the bigger picture within the protein-coding part of the genome. It is important to mention that using an alternative functional analysis tools [i.e. Gene set enrichment analysis (GSEA)] was useful to cross-validate the output of the conventional overrepresentation tools like the Database for Annotation, Visualization and Integrated Discovery (DAVID). The collective body of work represented here shows the adequacy of using microarray, commercial and custom-designed, to depict a holistic picture about the global gene expression profile of a given tissue. Still, there are some challenges in data analysis, interpretation and integration with the output of other alternative omic techniques – those challenges are highlighted and discussed across the different chapters of this thesis.
Occurrence of different Cacopsylla species in apple orchards in South Tyrol (Italy) and detection of apple proliferation phytoplasma in Cacopsylla melanoneura and Cacopsylla picta (Hemiptera: Psylloidea)

Preventing the diffusion of phytoplasma associated diseases until now is based mainly on indirect control measurements against the transmitting insect vectors. Apple proliferation, one of the economically most important pests in European apple cultivation is caused by the apple proliferation (AP) phytoplasma (‘ Candidatus Phytoplasma mali’), which is spread by the psyllids Cacopsylla (C.) picta (Foerster, 1848) and C. melanoneura (Foerster, 1848). Current control measures primarily comprise treatments against these AP phytoplasma transmitting vectors. The surveillance of C. picta and C. melanoneura population dynamics, as well as the determination of their infection rate in the field are crucial prerequisites to develop suitable and appropriate strategies to limit further spread of AP phytoplasma. Furthermore, the analysis of the species composition of the genus Cacopsylla present in apple orchards provides important information about the presence of other insect vectors potentially involved in spreading AP or other diseases. During an intensive monitoring program realized in the valleys of Val Venosta and Burggraviato (South Tyrol, Italy), the hotspots of apple proliferation epidemics, over 13,000 Cacopsylla individuals were captured and the occurrence of 16 species of the genus Cacopsylla was confirmed. The presence of C. picta was recorded in more than 50% of the investigated apple orchards and the natural infection rate of this vector was about 21% in a three-year average. Conversely, C. melanoneura was confirmed in more than 90% of the investigated sites but its low infection rate of about 1 % further supports that it plays a rather secondary role in spreading AP phytoplasma in South Tyrol.
NEW THIOPHENE BEARING DIMETHYL-5-HYDROXY ISOPHTALATE ESTERS AND THEIR ANTIMICROBIAL ACTIVITIES

Thiophene belongs to a class of heterocyclic compounds. In this study, three new dimethyl-5-hydroxy isophtalate derived thiophene esters were successfully synthesized and characterized by FT-IR, elemental analysis, 1 H-NMR, 13 C-NMR and HR-Mass techniques. Synthesized compounds antimicrobial effects were tested on Staphylococcus aureus (ATCC 25923); Enterococcus faecalis (ATCC 29212); Enterococcus faecalis (ATCC 51922); Klebsiella pneumoniae (ATCC 700603); Pseudomonas aeruginosa (ATCC 27853); Escherichia coli (ATCC 35218); Escherichia coli (ATCC 25922) and Candida albicans (ATCC 90028); Candida glabrata (ATCC 90030); Candida krusei (ATCC 6258); Candida parapsilosis (ATCC 22019). Compound C 1 showed the highest antimicrobial activity, possessing the same potential as chloramphenicol against, P. aeruginosa ATCC 27853. According to MTT assays, this compound was identified as non-toxic.
Estimation of 305-day milk yield from test-day records of Chinese Holstein cattle

ABSTRACT This study compared six models, namely the Gaines, Sikka, Nelder, Wood, Dhanoa and Hayashi models, for the estimation of 305 days milk yield in Chinese Holstein cattle. We compared their ability to reliably predict 305-day lactation yield from incomplete (3 or 6 test-day (TD)) records. Our findings revealed that the accuracies (ACC) were 0.6655–0.9948, 0.8652–0.9977 and 0.9169–0.9968, whereas the mean square errors (MSE) were 0.0121–2.4807, 0.0139–1.0716 and 0.0170–0.5528 when 3 TD records were used in the first, second and higher lactations, respectively; when 6 TD records were used, the ACC were 0.8800–0.9992, 0.8742–0.9998 and 0.7950–0.9996, whereas the MSE values were 0.0017–0.3348, 0.0011– 0.8605 and 0.0021–1.4869 in the first, second and higher lactations, respectively. All the models were fitted more accurately with 6 TD than 3 TD records. Further analysis revealed that the curves made by the Nelder, Wood and Dhanoa models were close to the actual curves. These three models can be used to predict the 305-day yield for management decisions in farms and for the genetic evaluation of Chinese Holstein cattle.
Straw yield and quality: An extra motivation for the introduction of triticale in mixed farming systems**

Straw is a valuable by-product from cereal production. It is used for agricultural purposes as feed and bedding material for livestock. Additionally, cereal straw is a resource for the production of sustainable biomaterials and bio-energy. To meet the demands of these sectors substantial amounts of straw, with specific properties (e.g. water-holding capacity), are necessary. Since wheat breeding has mainly focused on grain yield rather than on straw yield other cereal species, such as triticale, can be of interest. Therefore, in this research the straw yield and water-holding capacity of four winter wheat and four winter triticale varieties were studied during two growing seasons. For both wheat and triticale there were differences in dry matter yield and percentage dry matter between growing seasons. Furthermore, depending on the growing season, there were significant differences in straw yield between the different wheat and triticale varieties. However, during both growing seasons, the straw yield obtained from the triticale varieties was significantly higher compared to the straw yield obtained from the wheat varieties. Concerning the water-holding capacity, it was concluded that the water absorption potential of triticale straw was higher compared to the water absorption potential of wheat straw. However, only in 2014 a significant difference between wheat and triticale was noted. So, it can be concluded that, besides the known advantages of triticale (performance on marginal soils, disease resistance, low fertilizer input, etc.), this crop has the potential to deliver high yields of high quality straw.
Dinosaur-associated Poaceae epidermis and phytoliths from the Early Cretaceous of China

Grasses (Poaceae) are humans most important crop plants and among the most important extant clades of vascular plants. However, the origin and early evolution of grasses are controversial, with estimated ages from molecular dating ranging between 59 and 129 Ma (million years ago). Here we report the discovery of basalmost grasses from the late Early Cretaceous (Albian, 113-101 Ma) of China based on microfossils (silicified epidermal pieces and phytoliths) extracted from a special structure along the dentition of a basal hadrosauroid (duck-billed dinosaur). Thus, this discovery represents the earliest known grass fossils, and is congruent with previous estimations on grass origin and early evolution calibrated by oldest known fossil grasses, highlighting the role of fossils in molecular dating. This discovery also indicates deep-diverging grasses probably gained broad distribution across both Laurasian and Gondwanan continents during the Barremian (129-125 Ma).
공기괴 역궤적 모델의 통계 분석을 통한 이산화탄소 배출 지역 추정

Statistical trajectory analysis has been widely used to identify potential source regions for chemically and radiatively important chemical species in the atmosphere. The most widely used method is a statistical source-receptor model developed by Stohl (1996), of which the underlying principle is that elevated concentrations at an observation site are proportion- ally related to both the average concentrations on a specific grid cell where the observed air mass has been passing over and the residence time staying over that grid cell. Thus, the method can compute a residence-time-weighted mean concentration for each grid cell by superimpos- ing the back trajectory domain on the grid matrix. The concentration on a grid cell could be used as a proxy for potential source strength of corresponding species. This technical note describes the statistical trajectory approach and introduces its application to estimate potential source regions of CO2 enhancements observed at Korean Global Atmosphere Watch Observa- tory in Anmyeon-do. Back trajectories are calculated using HYSPLIT 4 model based on wind fields provided by NCEP GDAS. The identified CO2 potential source regions responsible for the pollution events observed at Anmyeon-do in 2010 were mainly Beijing area and the North- ern China where Haerbin, Shenyang and Changchun mega cities are located. This is consistent with bottom-up emission information. In spite of inherent uncertainties of this method in esti- mating sharp spatial gradients within the vicinity of the emission hot spots, this study suggests that the statistical trajectory analysis can be a useful tool for identifying anthropogenic poten- tial source regions for major GHGs.
Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data

Motivation Tn-seq (transposon mutagenesis and sequencing) and constraint-based metabolic modelling represent highly complementary approaches. They can be used to probe the core genetic and metabolic networks underlying a biological process, revealing invaluable information for synthetic biology engineering of microbial cell factories. However, while algorithms exist for integration of –omics data sets with metabolic models, no method has been explicitly developed for integration of Tn-seq data with metabolic reconstructions. Results We report the development of Tn-Core, a Matlab toolbox designed to generate gene-centric, context-specific core reconstructions consistent with experimental Tn-seq data. Extensions of this algorithm allow: i) the generation of context-specific functional models through integration of both Tn-seq and RNA-seq data; ii) to visualize redundancy in core metabolic processes; and iii) to assist in curation of de novo draft metabolic models. The utility of Tn-Core is demonstrated primarily using a Sinorhizobium meliloti model as a case study. Availability and implementation The software can be downloaded from https://github.com/diCenzo-GC/Tn-Core. All results presented in this work have been obtained with Tn-Core v. 1.0. Contact georgecolin.dicenzo@unifi.it, marco.fondi@unifi.it Supplementary information Supplementary data are available at Bioinformatics online.
Temperature-dependent adverse effects of drifting macroalgae on the survival of Manila clams in a eutrophic coastal lagoon

The proliferation of drifting macroalgae and the accompanying occurrence of the impoverishment of zoobenthic species has become a major problem worldwide. We examined the temperature dependency of the effects of macroalgae on the survival of Manila clams in Nakaumi Lagoon in western Japan. We conducted (i) semi-monthly field surveys to clarify seasonal changes in macroalgal abundance and clam density and (ii) 7-day macroalgal enclosing and excluding experiments in two temperature settings (mean water temperatures: 19 and 29°C) to test temperature-induced differences in algal effects on bottom-water redox conditions and clam survival. Clam density decreased during summer (July–September), when increased coverage and thickness of drifting macroalgae was observed. In contrast, clam density increased from autumn to spring as macroalgal abundance decreased. Further, reducing conditions (Eh<0) were only detected in bottom waters in the presence of macroalgae during summer (water temperature >29°C), suggesting that drifting macroalgae induced hypoxia under summer temperatures and consequently led to clam mortality. The 7-day algal enclosure experiment resulted in reducing bottom water conditions when mean water temperature was 29°C. Further, clam survival decreased in the algal enclosure at 29°C, whereas no such changes were detected at 19°C. These results indicate that the effects of drifting macroalgae on the geochemical environment and clam survival are temperature dependent; therefore, global warming may enhance the likelihood of macroalgae-induced hypoxia with its associated adverse consequences in marine life.