Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of TDP-43 and hnRNP proteins in the regulation of different RNA targets

Heteregeneous ribonucleoproteins (hnRNPs) are a family of RNA-binding proteins (RBPs) implicated in several steps of RNA metabolism, including transcription, pre-mRNA splicing, mRNA transport and turnover. Therefore, alteration of their physiological levels may lead to many pathological disorders, such as neurodegeneration and cancer. In this thesis, we focused the attention on three hnRNP proteins, namely DAZAP1, hnRNP Q and hnRNP R, that we previously identified in Drosophila melanogaster as strong modulators of TAR DNA-binding Protein 43 kDa (TDP-43) activity, an RBP involved in Amyotrophyc Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD). First of all, we evaluated the effects of their depletion on TDP-43-controlled mRNAs within human neuroblastoma SH-SY5Y cells and in a cellular model of TDP-43 loss-of- function. We found that DAZAP1 and, to a lesser extent, hnRNP Q were the most consistent modifiers of TDP-43 activity. Therefore, to examine the connection between DAZAP1 and TDP-43, we initially characterized the interaction between these two proteins by immunoprecipitation analysis, demonstrating that DAZAP1 does not bind TDP-43 but can bind TDP-43 controlled mRNAs. Next, we decided to identify all the potentially targets regulated by TDP-43 and DAZAP1, by looking at the transcriptome status of cells silenced for these two hnRNPs and we found differently expressed genes associated with neurodegeneration (ELAVL3 NOVA2, CELF5) and inflammation (TNF, TNFRSF9, ICAM1). Finaly, we extended our analysis to the characterization of hnRNP Q and hnRNPR, since the functional rescue of TDP-43 alterations was described only for hnRNP Q, but not for hnRNPR. We investigated the subcellular distribution and profiled differentially expressed genes analysis from RNA-seq after their knockdown. Interestingly, despite their high sequence similarity, these two proteins show different cellular distribution and affect different cellular pathways, tipically associated with neurodegeneration (PENK, NGR3, RAB26, JAG1) and inflammatory response (TNF, ICAM1, TNFRSF9, ICAM5). In conclusion, our work provides insights on the involvement of the hnRNP family in controlling neuronal and inflammatory pathways, and suggests that the differential expression of these proteins could play an essential role in modulating the onset as well as the progression of neurodegenerative disorders, in particular when related to the TDP-43 proteinopathies.
Elemental Chemical Composition of Forest Biomass at Different Ages for Energy Purposes

This work aimed to evaluate the elemental composition of different biomass components of the forest species Acacia mearnsii De Wild, Eucalyptus grandis W. Hill ex Maiden, Mimosa scabrella Benth and Ateleia glazioviana Baill, at their first, third and fifth year after planting, aiming at bioenergetic use. The biomass elemental composition was determined by quantifying the levels of carbon, hydrogen, nitrogen, sulfur and oxygen. The three ages, the four species, and the four compartments differ in relation to the elementary constituents. The use of trees at any age allows for energy use. The fifth year presents the best carbon and hydrogen values, being the best age for using the biomass energy of the different species. A. mearnsii presents the highest carbon values for the leaf and A. glazioviana presents the highest hydrogen values for all compartments. The leaf is the best compartment for energetic use.
Change in fatty acid composition and evaluation of lipids and protein oxidation in the commercial cooked clams (Ruditapes decussatus)

This study aimed to provide information about the changes in fatty acid composition and quality in Ruditapes decussatus tissue after four culinary treatments (steamed, baked, grilled and fried). All treated samples showed a significant decrease in moisture and protein. In contrast, a significant increase in fat content resulted from the grilled and fried treatments. Saturated fatty acid was significantly higher in fresh clams than all cooking processes, except in fried ones. Monounsaturated fatty acid and polyunsaturated fatty acid varied significantly between fresh and cooked clams with high values recorded for fried clams. The n-3/n-6 ratio, peroxide index, EPA+DHA and atherogenicity index decreased significantly after the cooking processes particularly in fried clams. The mineral levels (Mg, Ca and Mn) of cooked clams decreased considerably with grilled and fried treatments. The impacts of cooking on the fatty acid composition and protein content in clam tissue was evaluated by lipid peroxidation (TBARS, PV, FFA, TOR) and protein oxidation (AOPP and PCO), which varied statistically in fried, steamed, grilled and baked samples; indicating alterations in cooked clam tissues structure. Based on our results, steaming is recommended for the preparation of clams because it preserves the most nutritional tissue quality.
Diversity of avocado (Persea americana Mill.) cultivars from Antioquia (Northeast Colombia) and comparison with a worldwide germplasm collection

In this study, the genetic diversity of 90 avocado (Persea americana Mill) cultivars from Antioquia (Colombia) was compared to 67 germplasm collection accessions using 14 microsatellites. An average of 4.32 ± 2.0 alleles per locus was found, as observed in previous studies. The expected and observed heterozygosity ranges were 0.384-0.724 and 0.393-0.686, respectively. The Antioquian avocados were genetically structured according to an analysis of molecular variance test (fixation index (FST) = 0.054, P < 0.00001). An unweighted pair group method with arithmetic mean (UPGMA) dendrogram with FST paired data produced 2 clusters: one composed by Antioquian avocados and the other by the germplasm collection. Another UPGMA dendrogram with individual Nei-Li distances and additional STRUCTURE analysis separated the Antioquian avocados into 3 clusters (K = 3). Combining samples from the Colombian and germplasm collections produced K = 2. Genetic differentiations between the Antioquian and worldwide avocado germplasm collection could be due to crosses within the Antioquian avocados having been enhanced by insect pollinators, whereas avocados stored in the germplasm collection were constituted by cultivars with known genetic origins. Findings from this study demonstrated that criollo avocado genetics are unique in Antioquia, since the species has been naturally crossed in the field and its closest accession is from Guatemala. Nevertheless, it is important to continue genotyping this species in other locations in Colombia from Sylvester and cultivar populations of this crop to determine its origin.
Megathyrsus Maximus cv. Massai at different cutting frequencies

We evaluated the growth dynamics and forage production of Massai grass subjected to different cutting frequencies during the rainy season, with the aim to determine the most suitable cutting frequency to increase grass productivity. A randomized block design with four treatments (four cutting frequencies, 24, 32, 48, and 96 days) was used. The morphological characteristics were evaluated weekly in seven random tillers. Leaf appearance rate, phyllochron value, foliar elongation rate, leaf senescence rate, and stem elongation rate were influenced (p < 0.05) by the cutting frequency, while no effect was found for leaf life span. The number of live leaves per tiller, mean length of leaf blades, population density of tillers (DPP), and sheath length were influenced by the cutting frequency, along with plant height, dry mass of harvested leaf blade, dry mass of harvested stem, dry mass of harvested dead material, and leaf/stem ratio, while there was no effect on dry mass of forage harvested. The rates of leaf blade accumulation, stem accumulation, forage loss, and forage production were not affected by cutting frequency. A cutting frequency of 24 days resulted in the highest productivity values of Massai grass during the rainy season.
SirT7 auto-ADP-ribosylation regulates glucose starvation response through macroH2A1.1

Sirtuins are key players in the response to oxidative, metabolic and genotoxic stress, and are involved in genome stability, metabolic homeostasis and aging. Originally described as NAD+-dependent deacetylases, some sirtuins are also characterized by a poorly understood mono-ADP-ribosyltransferase (mADPRT) activity. Here we report that the deacetylase SirT7 is a dual sirtuin as it also features auto-mADPRT activity. Molecular and structural evidence suggests that this novel activity occurs at a second previously undefined active site that is physically separated in another domain. Specific abrogation of this activity alters SirT7 chromatin distribution, suggesting a role for this modification in SirT7 chromatin binding specificity. We uncover an epigenetic pathway by which ADP-ribosyl-SirT7 is recognized by the ADP-ribose reader macroH2A1.1, a histone variant involved in chromatin organization, metabolism and differentiation. Glucose starvation (GS) boosts this interaction and promotes SirT7 relocalization to intergenic regions in a macroH2A1-dependent manner. Both SirT7 activities are in turn required to promote GS-dependent enrichment of macroH2A1 in a subset of nearby genes, which results in their specific up- or downregulation. Consistently, the expression changes of these genes associated to calorie restriction (CR) or aging are abrogated in SirT7-/- mice, reinforcing the link between Sirtuins, CR and aging. Our work provides a novel perspective about sirtuin duality and suggests a key role for SirT7/macroH2A1.1 axis in mammalian glucose homeostasis, calorie restriction signaling and aging.
Trends in food and nutrient intakes by children in the United States

Monitoring dietary trends can make it easier to target dietary guidance. Trends in intakes among children age 6 to 11 years were examined by using data from the Continuing Survey of Food Intakes by Individuals (CSFII) 1994-96, 1998; the CSFII 1989-91; and the Nationwide Food Consumption Survey 1977-78. Increases were seen in intakes of soft drinks, total grain products, grain mixtures, crackers/popcorn/pretzels/corn chips, fried potatoes, noncitrus juices/nectars, lowfat milk, skim milk, cheese, candy, and fruit drinks/ades. Decreases in intake were observed in whole milk and total milk, yeast breads/rolls, green beans, corn/green peas/lima beans, beef, pork, and eggs. Lower percentages of calories from fat were partly due to increased carbohydrate intakes. Children had decreases in vitamin B12 and increases in thiamin and iron. Servings per day from the food groups of the Food Guide Pyramid were used to discuss diet quality during 1994-96, 1998. For any given Pyramid group, less than one-half of the children consumed the recommended number of servings, and their intakes of discretionary fat and added sugars were much higher than recommended. Guidance should continue to encourage increases in intakes of whole grains, fruits, dark-green and deep-yellow vegetables, legumes, nonfat or lowfat dairy products, and lean meats; decreases in fats and added sugars; and increases in activity. Effective nutrition education efforts for children should be supported at every level.
Security Considerations for VLSI-Based Symmetric Encryption Devices

The development and fabrication of secure, trustworthy, and efficient technical devices becomes an increasingly difficult task because of the high complexity of today’s systems. Dedicated hardware solutions based on Application-Specific Integrated Circuits (ASICs) or FieldProgrammable Gate Arrays (FPGAs) are generally preferred over their software counterparts to achieve ambitious throughput, power, or energy goals. Similar to their software equivalents, these hardwareoriented approaches suffer from several vulnerabilities that might be exploited by an attacker during the life cycle of a device. As part of this thesis, we investigate risks and performance aspects, immanent in the development and fabrication of any VLSIbased symmetric encryption device. We consider ASICs and FPGAs as the lowest hierarchy level where an attacker may intrude the system. Therefore, we implant a hardware Trojan into an ASIC just prior to fabrication in a 180 nm CMOS technology by UMC. Both the genuine and the malicious design have actually been manufactured. Subsequently, we apply Trojan detection techniques based on side-channel fingerprinting. Despite the comparatively small size of the Trojan (0.5% of the original design), we successfully distinguish malicious from genuine ASICs. Since FPGAs are of particular interest for high-throughput designs of cryptographic algorithms, we also analyze Trojans on reconfigurable hardware. More specifically, we insert a malicious circuitry into a bitstream after placement and routing. Thereafter, we show how to use electromagnetic radiation as a side-channel to successfully detect the Trojan and experimentally demonstrate a method to actually localize it on the FPGA.
The topologies of N6 -Adenosine methylation (m6 A) in land plant mitochondria and their putative effects on organellar gene-expression.

Mitochondria serve as major sites of ATP production, and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e., mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the posttranscriptional level. Following transcription, the polycistronic pre-RNAs in undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6 -methylation of Adenosine ribonucleotides (m6 A-RNA) in plant mitochondria. m6 A is a prevalent modification in nuclear-encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6 A mediates structural switches which affect RNA stability and/or activity. Using m6 A-pulldown/RNA-seq (m6 A-RIP-seq) assays of Arabidopsis and cauliflower mitochondria, we provide here with information on the m6 A-RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6 A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non-coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6 A modifications, m6 A-modifications within mRNAs seem preferably positioned near start-codons and may modulate their translatability.
Effect of Harvest Time on Phytochemical Profile of Citrus aurantifolia Leaf Essential Oil Grown in North Central, Nigeria

Citrus aurantifolia essential oils are volatile phytochemicals obtained from various part of the plant which has found wide range of domestic, medicinal and industrial applications. The research seeks to investigate the effect of time of harvest on the yield and phytochemical composition of Citrus aurantifolia leaf oil. Pulverized leaves of Citrus aurantifolia harvested in the morning (7a.m) and afternoon (2p.m) on the same day were separately subjected to hydro-distillation which yielded 0.4 and 0.5% (v/w) of the volatile oil respectively. Analyses of the oil harvested in the morning (7am) revealed the predominance of oxygenated terpenes which constituted 58.3% of the oil. The principal constituents were; isolimonene (22.2%), neral (22.2%), citral (21.5%), caryophyllene (4.3%), and α-geranyl acetate (4.1%). Furthermore, the leaf oil from the afternoon (2pm) harvest also showed predominance of oxygenated terpenes which constituted 57.7%. The principal constituents in the oil were; limonene (20.2%), neral (24.5%), citral (10.3%), caryophyllene (5.4%), and α-geranyl acetate (3.3%). This study established that there was compositional variation in the leaf essential oil obtained from the different time of harvests.
A mechanism for how Cdr1/Nim1 kinase promotes mitotic entry by inhibiting Wee1

To enter into mitosis, cells must shut off the cell cycle inhibitor Wee1. SAD family protein kinases regulate Wee1 signaling in yeast and humans. In S. pombe, two SAD kinases (Cdr1/Nim1 and Cdr2) act as upstream inhibitors of Wee1. Previous studies found that S. pombe Cdr1/Nim1 directly phosphorylates and inhibits Wee1 in vitro, but different results were obtained for budding yeast and human SAD kinases. Without a full understanding of Cdr1 action on Wee1, it has been difficult to assess the in vivo relevance and conservation of this mechanism. Here, we show that both Cdr1 and Cdr2 promote Wee1 phosphorylation in cells, but only Cdr1 inhibits Wee1 kinase activity. Inhibition occurs when Cdr1 phosphorylates a cluster of serine residues linking α-helices G and H of the Wee1 kinase domain. This region is highly divergent among different Wee1 proteins, consistent with distinct regulatory mechanisms. A wee(4A) mutant that impairs phosphorylation by Cdr1 delays mitotic entry and causes elongated cells. By disrupting and re-targeting Cdr1 localization, we show that Cdr1 inhibition of Wee1 occurs in cells at cortical nodes formed by Cdr2. Based on our results, we propose a two-step model for inhibition of Wee1 by Cdr1 and Cdr2 at nodes.
The ARRIVE guidelines 2019: updated guidelines for reporting animal research

Reproducible science requires transparent reporting. The ARRIVE guidelines were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here we introduce ARRIVE 2019. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise the items and split the guidelines into two sets, the ARRIVE Essential 10, which constitute the minimum requirement, and the Recommended Set, which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers to verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration document that serves 1) to explain the rationale behind each item in the guidelines, 2) to clarify key concepts and 3) to provide illustrative examples. We aim through these changes to help ensure that researchers, reviewers and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
Accuracy of different modalities of reaction time testing: Implications for online cognitive assessment tools

Reaction time testing is widely used in computerized cognitive assessments, and clinical studies have repeatedly shown it to be a sensitive indicator of cognitive function. Typically, the reaction time test is administered by presenting a subject with a visual stimulus on a computer monitor and prompting the individual to respond (via keypad or computer mouse) as quickly as possible. The individual’s reaction time is calculated as the interval between presentation of the stimulus and the time recorded from the mechanical response. However, there are many inherent latencies and variabilities that may be introduced to the measure by both hardware (computer monitor and mouse) and software (operating system). Because of these delays, we hypothesized that a comparison of hardware protocols (excluding human response) would demonstrate significant differences in the resulting reaction time measures. To simulate the delays of various components of the common systems used to obtain reaction time, we conducted a simple experiment in which either a visual or tactile stimulus evoked a movement from a mechanical transducer to respond to a computer peripheral or a dedicated response device. In the first condition, a simulated visual reaction time test was conducted by flashing a visual stimulus on a computer monitor. The stimulus was detected by a dedicated light sensor, and a linear actuator delivered the mechanical response via computer mouse. The second test condition employed a mobile device as the medium for the visual stimulus, and the mechanical response was delivered to the mobile device’s touchscreen. The third and fourth test conditions simulated tactile reaction time tests in which the stimulus was generated by a dedicated hardware device. The third condition simulated a tactile stimulus, which was detected by a mechanical switch, and again a hardware device delivered the response via computer mouse. The fourth condition also simulated a tactile stimulus, but the response was delivered by a dedicated hardware device designed to store the interval between stimulus delivery and stimulus response. There were significant differences in the range of responses recorded from the four different conditions with the reaction time collected from a visual stimulus on a mobile device being the worst and the device with dedicated hardware designed for the task being the best. The results suggest that some of the commonly used visual tasks on consumer grade computers could be introducing significant errors for reaction time testing and that dedicated hardware designed for the reaction time task is needed to minimize testing errors.
Research Article GA3 and ABI3 gene expression in coffee seeds during maturation

During maturation in seeds, metabolic processes dependent on gene expression are controlled by hormones, including abscisic acid and gibberellin. These hormones determine dormancy or the capacity for germination in seeds and may have different expression levels in the endosperm and embryo of coffee seeds. We quantified gene expression in the biosynthetic pathway of gibberellin and abscisic acid in different parts of Coffea arabica L. seeds in pre and post physiological maturity, in order to better understand the germination mechanisms of this species. Coffee fruits were harvested at green, yellowish-green, cherry, over-ripe and dry stages. For studies of gene expression, intact seeds were used in addition to endosperm and isolated embryos. The RNA from different tissues was extracted and treated with DNAse to synthesize cDNA. Transition levels of CaGA3 (gibberellin) and CaABI3 (abscisic acid) genes were quantified with qRT-PCR, using specific primers for coffee. Intact seeds at each phenological stage were submitted to germination tests, to evaluate the physiological quality of the seeds. Seed harvested at green and dry stages showed lower hysiological quality when compared to the other maturation stages, and germination at the green stage was close to zero. Greatest expression of CaGA3 and CaABI3 occurs in the endosperm of coffee seeds in cherry and over-ripe stages, with better physiological performance. There are differences in CaABI3 and CaGA3 gene expression in embryos and endosperm of the coffee seeds.