Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-scale movements of juvenile blacktip reef sharks Carcharhinus melanopterus in a shallow nearshore nursery

Limited information is available on the fine-scale movements and habitat use of juvenile sharks in very shallow (<1 m) nearshore areas and the factors that drive these behaviours. Active acoustic tracking was used to investigate movements and habitat use of juvenile (683 +/- 58 mm total length; mean +/- SD) blacktip reef sharks Carcharhinus melanopterus at Orpheus Island, Australia. Six juveniles were tracked by foot and boat for over 62 h. Juveniles moved in synchrony with tidal cycles, always remaining within very shallow (<1 m) sandy reef flat or reef crest waters during outgoing, low and incoming tides, and using inundated mangrove habitat during higher tides, indicating that tidal fluctuations were a major driver of movement and habitat use. Individuals never left the bay where they were captured or entered deep water beyond the fringing reef, restricting their movements within water <60 cm deep. In general, linearity and rate of movement were significantly higher during incoming or outgoing tides, whereas these measures were significantly lower during higher tide heights when juveniles were occupying mangrove habitats. The observed behaviour was most likely a predator-avoidance strategy, highlighting the importance of mangrove root habitat use by juvenile blacktip reef sharks in coastal nursery areas and indicating that this may be an essential habitat for the young of this species.
Cornichon Homolog-3 (CNIH3) Modulates Spatial Memory in Female Mice

Cornichon homolog-3 (CNIH3) is an AMPA receptor (AMPAR) auxiliary protein that traffics AMPARs to the postsynaptic membrane and potentiates AMPAR signaling. AMPARs are key components of hippocampal synaptic plasticity and memory formation, however the role of CNIH3 in memory has yet to be elucidated. To study the role of CNIH3 on mouse behavior, we bred and characterized a line of Cnih3-/- mice from C57BL/6 Cnih3tm1a(KOMP)Wtsi mice obtained from the Knockout Mouse Project (KOMP). In agreement with previous studies of CNIH3 in the brain, we observed concentrated expression of Cnih3 in the dorsal hippocampus, a region associated with spatial learning and memory. Therefore, we tested Cnih3+/+, Cnih3+/-, and Cnih3-/- mice in the Barnes maze paradigm to measure spatial memory. We observed no change in spatial memory in male Cnih3+/- and Cnih3-/- mice compared to male Cnih3+/+ controls, however, Cnih3-/- female mice made significantly more primary errors, had a higher primary latency, and took less efficient routes to the target in the maze compared to Cnih3+/+ female mice. Next, to investigate an enhancement of spatial memory by Cnih3 overexpression, specifically in the dorsal hippocampus, we developed an AAV5 viral construct to express wild-type Cnih3 in excitatory neurons. Female mice overexpressing Cnih3 made significantly fewer errors, had a lower primary latency to the target, and took more efficient routes to the maze target compared to YFP expressing control females. No change in spatial memory was observed in male Cnih3 overexpression mice. This study, the first to identify sex-specific effects of the AMPAR auxiliary protein CNIH3 on spatial memory, provides the groundwork for future studies investigating the role of CNIH3 on sexually dimorphic AMPAR-dependent behavior and hippocampal synaptic plasticity.
Globally Harmonized Carbon Storage Data

This paper presents methods and results that combine multiple carbon storage and above-ground biomass datasets using a simple decision tree approach. The resulting dataset combines the positive attributes of the multiple input datasets in order to have global, high-resolution extent while utilizing the best statistical methods where possible. Visual inspection shows very different spatial configurations of carbon storage between the results and the input data, suggesting that combination of methods can improve estimates. The summation of the decision tree result was 336.55 petagrams while the summation of a dataset based on the IPCC Tier 1 method was 502.38 petagrams (49.27% higher than the results from the decision tree).
LRRK2 regulates innate immune responses and neuroinflammation during Mycobacterium tuberculosis infection

Despite many connections between mutations in leucine-rich repeat kinase 2 (LRRK2) and susceptibility to mycobacterial infection, we know little about its function outside of the brain, where it is studied in the context of Parkinson’s Disease (PD). Here, we report that LRRK2 controls peripheral macrophages and brain-resident glial cells’ ability to respond to and express inflammatory molecules. LRRK2 KO macrophages express elevated basal levels of type I interferons, resulting from defective purine metabolism, mitochondrial damage, and engagement of mitochondrial DNA with the cGAS DNA sensing pathway. While LRRK2 KO mice can control Mycobacterium tuberculosis (Mtb) infection, they exhibit exacerbated lung inflammation and altered activation of glial cells in PD-relevant regions of the brain. These results directly implicate LRRK2 in peripheral immunity and support the “multiple-hit hypothesis” of neurodegenerative disease, whereby infection coupled with genetic defects in LRRK2 create an immune milieu that alters activation of glial cells and may trigger PD.
Modular transcriptional programs separately define axon and dendrite connectivity

Patterns of synaptic connectivity are remarkably precise and complex. Single-cell RNA sequencing has revealed a vast transcriptional diversity of neurons. Nevertheless, a clear logic underlying the transcriptional control of neuronal connectivity has yet to emerge. Here, we focused on Drosophila T4/T5 neurons, a class of closely related neuronal subtypes with different wiring patterns. Eight subtypes of T4/T5 neurons are defined by combinations of two patterns of dendritic inputs and four patterns of axonal outputs. Single-cell profiling during development revealed distinct transcriptional programs defining each dendrite and axon wiring pattern. These programs were defined by the expression of a few transcription factors and different combinations of cell surface proteins. Gain and loss of function studies provide evidence for independent control of different wiring features. We propose that modular transcriptional programs for distinct wiring features are assembled in different combinations to generate diverse patterns of neuronal connectivity.
The Nitrification Inhibitor Vizura® Reduces N2O Emissions When Added to Digestate before Injection under Irrigated Maize in the Po Valley (Northern Italy)

The agricultural area in the Po Valley is prone to high nitrous oxide (N2O) emissions as it is characterized by irrigated maize-based cropping systems, high amounts of nitrogen supplied, and elevated air temperature in summer. Here, two monitoring campaigns were carried out in maize fertilized with raw digestate in a randomized block design in 2016 and 2017 to test the effectiveness of the 3, 4 DMPP inhibitor Vizura® on reducing N2O-N emissions. Digestate was injected into 0.15 m soil depth at side-dressing (2016) and before sowing (2017). Non-steady state chambers were used to collect N2O-N air samples under zero N fertilization (N0), digestate (D), and digestate + Vizura® (V). Overall, emissions were significantly higher in the D treatment than in the V treatment in both 2016 and 2017. The emission factor (EF, %) of V was two and four times lower than the EF in D in 2016 and 2017, respectively. Peaks of NO3-N generally resulted in N2O-N emissions peaks, especially during rainfall or irrigation events. The water-filled pore space (WFPS, %) did not differ between treatments and was generally below 60%, suggesting that N2O-N emissions were mainly due to nitrification rather than denitrification.
In Vitro Propagation of Endangered Orchid, Vanda pumila Hook.f. through Protocorms Culture

The Vanda pumila is a monopodial orchid with beautiful flowers that are native to Thailand but now found across South Asia. The immature seeds of Vanda pumila were used for in vitro culture and then the protocorms developed were used as explants for seedling development and mass propagation. Protocorms were cultured on 1/2 MS (Murashige and Skoog, 1962) medium fortified separately with Kinetin (Kn), 6-Benzyl amino purine (BAP) and Gibberellic Acid (GA3) each in different concentrations as (0.5 mg/L, 1.0 mg/L and 2.0 mg/L) well as each on each concentrations of each medium supplemented with 5% and 10% coconut water (CW) respectively. The greatest number of shoots (9.50 ± 0.29 shoots per culture) was developed on 1/2 MS medium fortified with 1.0 mg/L Kn plus 10% CW and the longest shoots (0.78 ± 0.07 cm per culture) developed on 1/2 MS medium fortified with 2.0 mg/L BAP plus 10% CW. The shoots derived from protocorms were then developed on 1/2 MS medium fortified with three different rooting hormones viz. Indole-3-acetic acid (IAA), Indole-3-butyric acid (IBA) and α-Naphthalene acetic acid (NAA), each in four concentrations (0.5 mg/L, 1.0 mg/L, 1.5 mg/L and 2.0 mg/L) as well as 1.0 mg/L of each hormone supplemented with 10% CW. The 1/2 MS medium fortified with 0.5 mg/L IAA was found to be the most effective condition for the development of maximum number of root (5 ± 0.0 roots per culture) and root length (0.93 ± 0.07 cm). Hence, the present study could be useful for standardizing the protocol for mass propagation of the endangered orchid V. pumila.
The RAS-MAPK pathway in neuroblastoma

Neuroblastoma is a pediatric tumor of the peripheral sympathetic nervous system. It occurs mainly in young children, with a median age of 17 months and has an estimated incidence of 1,1:100.000. Primary neuroblastoma tumors generally respond quite well to chemotherapy. However, a significant part of these, about 25%, relapse and subsequently show resistance to treatment. In this thesis we describe the results of Whole Genome Sequencing of relapse neuroblastoma tumors. We show that these tumors are derived from the corresponding primary tumors and that clonal selection occurs between the primary and the relapse tumor. We also show that mutations affecting the RAS-MAPK pathway occur at a very high frequency (78%) in these relapses and that the presence of these mutations is associated with sensitivity to MEK inhibitors, both in vitro and in vivo. The role of this pathway in neuroblastoma is further explored throughout this thesis. Firstly, we show through a gene signature that activation of this pathway is associated with poor prognosis and the presence of known and novel mutations. Moreover, activation of this pathway causes a significant growth increase in neuroblastoma xenograft tumors. Secondly, we discover through high-throughput screening that combining MEK inhibitors with Bcl2 family inhibitors shows promising results in RAS-MAPK mutated neuroblastoma cell lines. Finally, we use our gene signature to gain some more insight into the role of this pathway in neuroblastoma and review preclinical data on the RAS-MAPK pathway as a target for therapy in pediatric solid tumors.
EVALUATION OF PRODUCTIVE PERFORMANCE IN TWO PLUMAGE-COLOR TYPES OF JAPANESE QUAIL USING MICROSATELLITE MARKERS.

Two plumage-color types of Japanese quail were used to compare the meat production potentialities using five selective microsatellite markers. A total number of birds was 189 for the two plumage-colors of quail [(Brown 114; 49 males, and 65 females), and (Golden 75; 42 males, and 33 females)], were used. Phenotypic data were live body weight at day1 (BW0) and measured weekly till the end of six' weeks of age (BW6). The weight gain was calculated for intervals. The analysis of variance for live body weight at different age’s data revealed that there was a highly significant difference on BW between plumage-color types (Br, and Gd) at the day1 of age (P≥0.001). At the 6 week of age (BW6), there was an interaction effect between the plumage-color type and sex where the females of the Br were highest weight (226.92± 3.75) compared to others (P≥0.05). Considering the weight gain trait, the results revealed that the plumage-color type had significant effect (P≥0.05) on weight gain at the early age (from day1 to the end of the 1 week, WG0-1), and WG1-2. On molecular technique basis, a total of twenty alleles were discovered across the two types of quails. The average of alleles per locus over loci and plumage-color types was 3.30 ±0.15 alleles. Only one private allele at 170bp with allele frequency 0.06 was present in Br for the locus GUJ0029. The polymorphic information content (PIC) average is 0.46 with the values ranging from 0.34 at locus GUJ0063 to 0.61 at locus GUJ0023. In addition, the inter-population genetic differentiation coefficient (GST) ranged from 0.0 of locus GUJ0077 to 0.077 of locus GUJ0029, and the inter-population genetic variation accounted for 3.6% of the total genetic variation. The variance among, and within individuals was observed as 93% and 7% of respectively by using AMOVA. Moreover, the Hardy-Weinberg equilibrium among the five loci was assessed. In spite of the fact that GUJ0077 locus was an exceptionally significant (P≥0.001) for Gd, it was not for Br. In like manner, the GUJ0059 locus was significant (P≥0.05) in Gd yet not in Br. Nevertheless, the general linear model analysis showed significant association in Gd between the locus GUJ0063 not only with live body weight at BW0 (P≥ 0.05), but with gain weight at W2, and W4 also (P≥ 0.05). Whereas, in Br type, the locus GUJ0029 was associated with BW5 (P≥ 0.01) and BW6 (P≥ 0.05). In addition, the same locus associated with weight gain at W1 (P≥ 0.05), and W2 (P≥ 0.01). Which exposed that both of GUJ0029, and GUJ0063 loci linked with the gene(s) that responsible regulator for quails' live body weight. In conclusion, these findings of this study confirm that the association between plumage-color and productive traits have prevailed and sanctioned by using the molecular markers.
The diatom Chaetoceros socialis: spore formation and preservation

ABSTRACT Planktonic diatoms thrive in the water column, and several species can transform into resting stages – spores or resting cells – that sink to the bottom of the sea. Resting stages are generally produced when environmental conditions are not optimal for growth and can remain viable in sediments for a long time. We tested different aspects related to the formation of spores in Chaetoceros socialis, one of the dominant diatoms in the Gulf of Naples (Mediterranean Sea, Italy). Observations in time lapse and confocal laser scanning microscopy allowed illustration of the formation of endogenous spores, in which valve deposition is accompanied by an acytokinetic nuclear division. The complete transition from vegetative cell to spore takes about 8–10 h and, if exposed to the light, spores can germinate again after a few days. The depletion of nitrogen source in the culture medium induced the formation of spores, with very similar dynamics among different sympatric strains; extremely high percentages of spores (up to >95%) were produced after 4–5 days. Once formed, spores can remain viable for up to nine months, and anoxic conditions favour their preservation. Identical dynamics of spore formation were detected in freshly established cultures and in cultures produced by the germination of spores kept dormant for different lengths of time. Our results suggest that spores of C. socialis can, in principle, rapidly shift between vegetative cells and resting stages that may explain the success of this species in coastal water. Our results also demonstrate that storage of resting spores may represent an alternative to cryopreservation.
Amine variations in faecal content in the first weeks of life of newborns in relation to breast-feeding or infant formulas

Abstract Breast-feeding is the ideal nutrition for a newborn’s integral necessities. It seems crucial therefore to know its composition in order to provide suitable infant formula when required. Of these, polyamines (with lactation and the microbiota being its intestinal source) are involved in the development of gut epithelium and immunity. Safety concerns limit human intervention studies. Therefore, we studied the amounts of polyamines supplied by breast milk (varying among mothers) or infant formula feeding, up to day 30 postpartum, in the faeces of newborns. Independent samples (68) of breast milk from fifty-nine healthy Caucasian woman (day 0, 1, 3, 5, 7, 15 and 30 postpartum) who had natural deliveries after week 38, same-day faeces of newborns when available (eighty-one from breast milk and fifty-five from infant formula fed) and six infant formulas were collected and the polyamine content was determined by HPLC. In breast milk, polyamines and isoamylamine (a primary amine), with inter-individual variations, increased over time (with a higher content of spermidine; no other amines were present). Overall, they were much higher than in infant formula. By the 2nd week after birth, polyamines, cadaverine and tyramine, but not isoamylamine, were higher in the faeces of those fed infant formula compared with those fed breast milk. Cadaverine and tyramine could be used to predict the feeding type used for newborns. The differences in the content may be related to distinct colonisation of amine-producing bacteria, which can be established by polyamines. Further studies are required to determine the clinical utility of these findings.
The impact of genetics and environment on the polar fraction metabolome of commercial Brassica napus seeds: a multi-site study

Abstract This study was designed to elucidate the biological variation in expression of many metabolites due to environment, genotype, or both, and to investigate the potential utility of metabolomics to supplement compositional analysis for the design of a new resilient cultivar of Brassica napus that can be steady in phytochemicals in different regions in France. Eight rapeseed varieties, grown in eight regions of France, were compared using a non-targeted metabolomics approach. The statistical analysis highlighted the distance and closeness between the samples in terms of both genotypes and geographical regions. A major environmental impact was observed on the polar metabolome, with different trends, depending on the varieties. Some varieties were very sensitive to the environment, while others were quite resilient. The identified secondary metabolites were mapped into the KEGG pathway database to reveal the most sensitive target proteins susceptible to environmental influences. A glucosyl-transferase encoded by the UGT84A1 gene involved in the biosynthesis of phenylpropanoid was identified. This protein could be rate limiting/promoting in this pathway depending on environmental conditions. The metabolomics approach used in this study demonstrated its efficiency to characterize the environmental influence on various cultivars of Brassica napus seeds and may help identify targets for crop improvement.
Modulation of Yeast-Derived Volatile Aromas by Oleic Acid and Sterols

Unsaturated fatty acids and sterols are essential constituents of the yeast plasma membrane. Recently, their contribution to modulating the production of yeast-derived volatile compounds has received significant attention. The objective of this study was to determine how sterol and lipid supplementation, including ergosterol, plant sterols or oleic acid, differentially influenced yeast growth as well as the production of fermentative aromas when added individually or in combinations. Oleic acid significantly altered the volatile profiles produced and lowered yeast growth. Generally, phytosterol (β-sitosterol) and ergosterol supplementation resulted in similar responses regarding the production of aromas, however, they differed in the magnitude of the response in the case of medium chain fatty acids and acetate esters synthesis. The combinations of sterols with oleic acid resulted in a response more closely associated with the oleic acid control treatment, showing lower levels of acetate ester production.
Classificação filogenética e caracterização patotípica de isolados de Escherichia coli patogênicos e comensais de suínos da região sul do Brasil

MASTER OF SCIENCE Programa de Pós-Graduação em Medicina Veterinária Universidade Federal de Santa Maria PHYLOGENETIC CLASSIFICATION AND PATHOTYPE CHARACTERIZATION OF PATHOGENIC AND COMMENSAL Escherichia coli ISOLATED OF SWINE FROM SOUTHERN BRAZIL AUTORA: LILIAN KOLLING ORIENTADOR: AGUEDA CASTAGNA DE VARGAS Data e Local da Defesa: Santa Maria, 18 de fevereiro de 2009. The aim of the study was to evaluate the presence of different virulence factors in intestinal and extra-intestinal Escherichia coli swine isolates from Southern Brazil by multiplex PCR (mPCR) and classify them in A, B1, B2 and D phylogenetic groups based on three pathogenicity markers: chuA, yjaA and a DNA anonymous fragment designated TSPE4.C2. Were analyzed 152 samples from different origins: urine (70), feces (35), small intestine (35) and tissues (12). The mPCR was carried out to pathotypification of the isolates and a PCR with the pathogenicity markers, to classify in phylogenetic groups. Seventy seven (51%) isolates when tested by mPCR were positive to at least one of the virulence factors, while the phylogenetic characterization of the isolates showed 21 (14%) isolates in A, 65 (42%) in B1, 19 (13%) in B2 and 47 (31%) in D group. Fourteen (20%) urine isolates were characterized as UPEC; nine (12.8%) presented UPEC and ETEC factors simultaneously and four (5.8%) were classified as ETEC. In the phylogenetic classification, the groups of major occurrence were D (45.8%) and B1 (32.8%). Of the analyzed feces samples, 25 (71.4%) demonstrated virulence factors characteristic of pathotype ETEC. Phylogeneticaly, the group of higher incidence was B1 with 21 (60%) samples, followed by B2 with six (17.2%), group A with five (14.2%) and group D with three (8.6%) isolates. For the small intestine samples, 20 (57.2%) were characterized as ETEC. By the phylogeny, 23 (65.6%) isolates were classified in groups A or B1, among them 51.4% belonged to B1 and six (17.2%) were located in equal percentage in groups B2 and D. Six tissue isolates (50%) were qualified as ETEC. In regards to the phylogenetic classification, six (50%) samples were located in group D, followed by A and B1, with three (50%) samples in each group. For the tested isolates, the phylogenetic analysis demonstrated to be efficient, and it may be included in laboratorial routine for epidemiologic studies of the intestinal and extra intestinal swine samples, allowing the differentiation of pathogenic and non-pathogenic isolates, as well as helping in the strains selection for the vaccine production.