Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated –omics approaches to explore tomato interaction with the leafminer Tuta absoluta

Tuta absoluta is one of the most destructive pest affecting tomato crops, causing considerable field and greenhouse yield losses. Despite its economic importance, little is known about the molecular basis of the interaction between this leafminer and tomato plants. To investigate the tomato response to T. absoluta challenge , a multi-omic approach was carried out. Tolerant and Susceptible cultivated tomato genotypes as well as the derived F1 hybrid were employed to shed light on the plant response to the herbivore feeding. A RNA-Seq experiment was performed to analyze the transcriptional reprogramming of three tomato genotypes infested by T. absoluta. Metabolome fingerprinting analysis was carried out both to analyze differences in metabolites production among infested and not infested genotypes and to validate gene expression findings. Furthermore, a structural genomic-based analysis allowed us to identify polymorphisms such as SNPs and InDels affecting genes putatively involved in tomato-T. absoluta interaction. In the Tolerant genotype, the reprogramming driven by both direct and indirect defenses is based on an antixenosis mechanism. This is characterized by the lower utilization of the host by the herbivore due to chemicals, physical and morphological barriers. The RNA-Seq gene expression analysis allowed us to assess an active recognition of the insect that leads to a signaling cascade mediated by the systemin/jasmonic acid complex and, subsequently, the activation of genes involved in the growth of trichomes (physical barriers) together with the activation of genes coding for production of volatile terpenes and phenylpropanoids. A direct defense has been well elucidated by the metabolome analysis, revealing an involvement of compounds such as chlorogenic and neo-chlorogenic acids, GABA and, pyridinc alkaloid trigonelline. The susceptible line demonstrates to be less capable of deploying with the defense arsenal. The key genes identified in JA, terpenes and phenylpropanoids pathways resulted down-regulated and affected by deleterious variants that could lead to important changes in the final protein synthesis. The F1 derived from the cross between the Tolerant and Susceptible lines expresses, even if at less extent, the key genes identified in the tolerant line, and is affected by the same structural polymorphisms. Results obtained in this thesis suggest that the tolerance to the leafminer T. absoluta is modulated both by structural variations and by the expression regulation of such genes. The findings gathered in this study could be very useful for better direct future tomato breeding for T. absoluta tolerance.
Huanglongbing (HLB) incidence on 2-3 years old tangerine trees (Citrus reticulata) grown from disease-free nursery stock.

Huanglongbing (HLB) previously referred to as greening disease is a bacterial disease of citrus trees, and a major problem worldwide. HLB affects citrus trees by blocking the phloem or the vascular system of the tree, limiting its ability to uptake nutrients. Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae) is the vector, transmitting Candidatus Liberibacter asiaticus (Las). In this study in 2012-2014, occurrence of HLB disease after infection was monitored in an experimental planting of 589 tangerine trees (Citrus reticulata) grown from disease-free seedlings in a nursery in Chiang Mai, Thailand. An early symptom of HLB on tangerine is the yellowing of leaves on an individual limb or in one sector of a tree's canopy. Field trees can be identified with suspected HLB infection by their foliar but verification requires DNA detection methods. Las can be detected in DNA extracted from infected plants and psyllids by polymerase chain reaction (PCR). An efficient method for DNA extraction from infected plants and psyllids was studied. Polymerase chain reaction (PCR) was performed by using Las606/LSS primer to detect symptomatic leaves. Specific primers, forward primer Las606 (5’GGA GAG GTG AGT GGA ATT CCG A-3’) and reverseprimer LSS (5’ACC CAA CAT CTA GGT AAA AAC C -3’) were used for amplification of the16S rDNA of Candidatus Liberibacter asiaticus (Las), producing specific bands of 500 bp. The study area showed an increasing percentage of disease incidence, from 0.84% in 2012 to 4.41% in 2013 and 11.54% in 2014. It appears that there is a high incidence of HLB-infected trees at the edges of the plantation. One of potential HLB pathways is infected Asian citrus psyllids from natural movement. The Asian citrus psyllid vector of HLB has a wide host range, can achieve high populations at citrus vegetative flush, can be spread over long distances, and its control demands both continuous inspection and regular insecticide applications.
Genetic overlap between in-scanner head motion and the default network connectivity

The association between in-scanner head motion and intrinsic functional connectivity (iFC) may confound explanations for individual differences in functional connectomics. However, the etiology of the correlation between head motion and iFC has not been established. This study aimed to investigate genetic and environmental contributions on the association between head motion and iFC using a twin dataset (175 same-sex twin pairs, aged 14-23 years, 48% females). After establishing that both head motion and default network iFC are moderately heritable, we found large genetic correlations (-0.52 to -0.73) between head motion and the default network iFCs. Common genes can explain 48% - 61% of the negative phenotypic correlation between the two phenotypes. These results advance our understanding of the relationship between head motion and iFC, and may have profound implications for interpreting individual differences in default network connectivity in clinical research and brain-behavior association.
Hydrolysis of a fungicide, buprimate by indigenousAchromobacter species

A soil bacterium (CMG500) capable of degrading a fungicide buprimate (Nimrod), was isolated from vegetable fields and identified as Achromobacter species. It harbors a catabolic plasmid pNS3. The isolate was resistant to streptomycin, penicillin, and ceferozone. The structure of the degraded product was elucidated using mass spectra, U. V. and N. M. R. It was found that the fungicide bupirimate (5-Butyl – 2-ethyl amino 6-methyl-4pyrimidyl dimethyl sulfamate was converted into 5Butyl-2 ethyl amino 6-methyl –4 –pyrimidinol by Achromobacter species. Hydrolysis of buprimate fungicide resulted in the removal of dimethyl sulfamate group. The degrading genes for buprimate were present on a conjugative plasmid pNS3. Key-words: Achromobacter, buprimate, fngicidal hydrolysis,
LACTOBACILLUS SALIVARIUS BACTERIOCIN AND SUPERNATANT ACTIVITY AGAINST ENTAMOEBA HISTOLYTICA IN VITRO AND IN VIVO

Lactobacillus salivarius is a probiotic bacteria species found in the gastrointestinal tract and breaks and exert a range of therapeutic properties, so antiamoebic activity of Lactobacillus salivarius supernatant and bacteriocin were tested in vitro and in vivo on Entamoeba histolytica and using metronidazole as a reference amoebicidal agent. In vivo supernatant have a clear impact more than bacteriocin and metronidazole where led to the disappearance of parasite in the feces of infected mice after 9th day while bacteriocin and metronidazole were the 12th, 11th day respectively, the disappearance of the parasite after dosing while the results were expected to reverse invitro as it was observed that the effect was more of bacteriocin it leads to lower growth rate to (35 - 30.25×104 cell ∕ ml) after 24 and 48hr while the supernatant and metronidazole were lower growth rate after 24 and 48hr (50 - 42×104 cell ∕ ml), (44.5 - 40×104 cell ∕ ml) respectively, compared to control group whose results were (55.5 - 60.75×104 cell ∕ ml). Histological changes also explained that bacteriocin effects were clearly on intestinal tissue while the supernatant was safly and harmless.
First Report of Meloidogyne ethiopica Parasitizing Sugarcane in Brazil

Galling to field, and the reproduction (final population/initial population) was 16.6. The noninoculated plants did not exhibit galls and their development was not affected. These results confirmed the pathogenicity of M. ethiopica on sugarcane. This is the first report of M. ethiopica parasitizing sugarcane roots worldwide, and this finding has great importance for Brazilian agriculture, considering this nematode may damage sugarcane plants and become an additional problem for this crop.
Effects of elevated seawater temperature and phosphate enrichment on the crustose coralline alga Porolithon onkodes (Rhodophyta)

Both global and local environmental changes threaten coral reef ecosystems. To evaluate the effects of high seawater temperature and phosphate enrichment on reef‐building crustose coralline algae, fragments of Porolithon onkodes were cultured for 1 month under laboratory conditions. The calcification rate of the coralline algae was not affected at 30°C, but it decreased to the negatives at 32°C in comparison to the control treatment of 27°C, indicating that the temperature threshold for maintaining positive production of calcium carbonate lies between 30 and 32°C. Phosphate enrichment of 1–2 μmol L −1 did not affect the calcification rate. The net oxygen production rate was enhanced by phosphate enrichment, suggesting that the photosynthetic rate was limited by the availability of phosphate. It was concluded that moderate phosphate enrichment does not directly deteriorate algal calcification but instead ameliorates the negative effects of high seawater temperature on algal photosynthesis.
Genetic diversity within and among gelada (Theropithecus gelada) populations based on mitochondrial DNA analysis

We studied genetic characteristics within and among gelada (Theropithecus gelada) populations inhabiting the southern and northern plateaus of Ethiopia. Twenty-one mtDNA haplotypes were identified. Geladas on the southern plateau were genetically separated from those on the northern plateau, with a large differentiation as indicated by Fst values of 0.665–0.917. The difference between the subspecies (T. g. gelada and T. g. obscurus) on the northern plateau highlighted a substantial genetic variation. Divergence times were estimated as ~250000 years between subspecies on the northern plateau and ~400000 years between those on the northern and southern plateaus. The genetic differentiation between the geographically distant Simien Mountain and Arsi groups (640 km) was ~2/3 of that between the geographically closer Debra Libanos and Arsi groups (250 km). The difference between subspecies within the northern plateau was similar to that between Papio hamadryas hamadryas and P. h. anubis. The difference between geladas in the north and south was similar to inter-subspecies differences in other mammals, and thus suggested that the Arsi geladas belong to subspecies T. g. arsi (tentative name). Considering the present distribution, geladas appear to have a complicated history of speciation. However, further analyses based on genetics, morphology and ecology are required to confirm these findings.
Genetic and biological factors influencing host response to Porcine Reproductive and Respiratory Syndrome virus in growing pigs

Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major importance in the swine industry due to its economic impact and its negative effects on animal welfare. PRRS has been estimated to cost the US swine industry alone $664 million per year and impacts all stages of swine production. Current efforts to contain PRRS include biosecurity and vaccination strategies but these have not been widely successful, partly due to large genetic and antigenic variation observed between different PRRS virus (PRRSV) strains. The PRRS Host Genetics Consortium was created with the goal of increasing understanding of the host genetic response to PRRSV infection and evaluating the potential of genetic selection of pigs that are more resistant to PRRS. Approximately 200 commercial crossbred pigs in each of 15 trials were experimentally infected with either the NVSL-97-7895 (NVSL) or KS-2006-78109 (KS06) isolate of PRRSV at approximately 28 days of age. Serum was collected at 0, 4, 7, 11, 14, 21, 28, 35 and 42 days post infection (dpi). Weights were collected at 0 dpi and weekly thereafter. Tonsils and ear samples for genotyping were collected at 42 dpi. Serum viremia and tonsil virus levels were measured using a semi-quantitative PCR assay. The levels of serum PRRSV N protein specific immunoglobulin G was quantified at 42 dpi using fluorescent microsphere immunoassay, and measurements were reported as a sample to positive ratio (S:P). Monophasic or biphasic Wood’s curves were fitted to serum viremia records, and the parameters for these curves were used to derive serum curve characteristics for each animal. Additionally, 2 order Legendre polynomials were fitted to weight measurements. Serum viremia and weight curve fittings allowed daily serum viremia and daily weights to be interpolated to
Faculty Opinions recommendation of Effects of an oral ghrelin mimetic on body composition and clinical outcomes in healthy older adults: a randomized trial.

Background: Growth hormone secretion and muscle mass decline from midpuberty throughout life, culminating in sarcopenia, frailty, decreased function, and loss of independence. The decline of growth hormone in the development of sarcopenia is one of many factors, and its etiologic role needs to be demonstrated. Objective: To determine whether MK-677, an oral ghrelin mimetic, increases growth hormone secretion into the young-adult range without serious adverse effects, prevents the decline of fat-free mass, and decreases abdominal visceral fat in healthy older adults. Design: 2-year, double-blind, randomized, placebo-controlled, modified-crossover clinical trial. Measurements: Growth hormone and insulin-like growth factor I levels. Fat-free mass and abdominal visceral fat were the primary end points after 1 year of treatment. Other end points were body weight, fat mass, insulin sensitivity, lipid and cortisol levels, bone mineral density, limb lean and fat mass, isokinetic strength, function, and quality of life. All end points were assessed at baseline and every 6 months. Results: Daily administration of MK-677 significantly increased growth hormone and insulin-like growth factor I levels to those of healthy young adults without serious adverse effects. Mean fat-free mass decreased in the placebo group but increased in the MK-677 group (change, (cid:1)
ACTIVITY OF SOME BRAZILIAN ISOLATES OF ENTOMOPATHOGENIC FUNGI AGAINST THE POULTRY RED MITE DERMANYSSUS GALLINAE DE GEER (ACARI: DERMANYSSIDAE)

Poultry red mite Dermanyssus gallinae is a cosmopolitan and hematophagous species commonly found in layer houses around the world. Poultry mite infestations may cause anemia, stress, low body weight and egg production, and mortality. Mite control is typically based on chemical products, but they are not effective and leave residues in eggs; therefore, alternative control methods, such as entomopathogenic fungi, need to researched. This study aimed at evaluating, in the laboratory, the activity of Brazilian isolates of entomopathogenic fungi against D. gallinae. The mites were collected from a commercial layer house and were sprayed with conidial suspensions (1 × 108 conidia/mL) of five isolates of Beauveria bassiana and Metarhizium anisopliae. All tested isolates were pathogenic for the red mite, with confirmed mortality ranging from 22.9 to 52.4%. This demonstrate the potential of the tested entomopathogenic fungi isolates for mite control, and reinforces the need for further studies with other isolates, application strategies, and with fungal formulations.
First record of the Atlantic blue crab Callinectes sapidus (Crustacea: Brachyura: Portunidae) in the Segura River mouth (Spain, southwestern Mediterranean Sea)

A single male individual of Callinectes sapidus (Crustacea, Decapoda, Portunidae) was collected on 6 December 2014 in the Segura River mouth in southeastern Spain. Information on collection site, DNA barcoding, and its present distribution and dispersal strategies are provided.
The role of thyroid hormone transporters and thyroglobulin processing enzymes in auto-regulation of the mouse thyroid gland

Introduction: Thyroid hormones (TH) are important for almost all organs in the body. TH transport into target cells is crucial for their biological action. The thyroid gland, as the TH producing organ, is also a target of its hormones. Therefore regulation of the processing of the TH precursor molecule thyroglobulin and transport of TH across the plasma membrane of thyroid epithelial cells is vital for thyroid development and function. Objectives and Methods: We hypothesized that the thyroid gland must exhibit TH sensing mechanisms to ensure extra- and intra-thyroidal TH homeostasis and therefore investigated the relationship between thyroglobulin processing enzymes and TH transporters. Thereby, the auto-regulation of the mouse thyroid gland in general and in a TSH-independent manner was addressed. Hence, mouse models were bred combining both, TH transporter- and cysteine cathepsin-deficiency, and a computer-based thyroid phenotyping tool was developed to quantitatively analyse thyroid morphology and functional states. TH transporter expression and localization patterns were analysed in cysteine cathepsin-deficient animals as models of impaired thyroglobulin processing, and in reverse, the protein levels of cathepsins in TH transporter-deficient mice with altered serum TH levels were addressed. Results: The established diagnostic tool offers a non-biased and reproducible thyroid phenotyping system to basic thyroid research. The functional assessment of the angio-follicular unit by our phenotyping tool reveals how the structure-function-relationship contributes to the compensation of functional losses in the mouse thyroid gland. Additionally, thyroid gland tissue of Mct8- and Mct10- double-deficient mice revealed both, increased cathepsin L expression levels and increased thyroglobulin solubilisation and degradation. Interestingly, animals deficient in both, cathepsin K and Mct8, exhibited apical Lat2 signal, whereas the knock-out of Mct10 led to decreased Lat2 levels in thyrocytes. Conclusion: These results indicate that a possible sensing mechanism might involve TH transporter Lat2 as `transceptor´ in a localisation-dependent signalling pathway linking sensing capabilities and lysosomal function in thyrocytes, the latter being disrupted in Mct8- and Mct10- double-deficient mice leading to increased TH liberation potential despite the already toxic intra-thyroidal TH levels. In summary, TSH-independent regulative measures of the thyroid gland were described and point towards a more complex thyroid regulation than described before. Supported by the Deutsche Forschungsgemeinschaft, in the framework of the SPP 1629 “Thyroid Trans Act” project, BR 1308/11-1.
Biosynthesis of amphotericin B

The high level incorporation of isotopically labelled sodium acetate and sodium propionate into amphotericin B is reported. Double quantum filtered heteronuclear single quantum coherence NMR (DQF-HSQC) is employed to demonstrate coupling between labelled carbons on intact acetate units after biosynthesis. Electrospray mass spectroscopy demonstrates the high level incorporation of label is present in only half the molecules, the other half remaining unlabelled.
Resting state functional coupling between the ascending synchronising system, limbic system and the default mode network via theta oscillations

In order to better understand dysfunction in dementia and psychiatric illnesses, the underlying neuronal systems that give rise to normal memory and cognitive processes need to be better understood. Based on electrophysiological recordings in animals, theta oscillations have been proposed as an intrinsic mechanism for the orchestration of memory functions, especially episodic and autobiographical memory. Theta oscillations are controlled by the ascending synchronising system, a set of nucleui in the pontine tegmentum and basal forebrain. At a network level, the default mode network has been shown to be responsible for episodic and autobiographical. Using resting state fMRI data, we show using an ICA approach, seed based connectivity and dynamic causal modelling that the ascending synchronising system is coupled to the medial temporal lobe nodes including the hippocampus and parahippocampal gyrus and with the default mode network. Our results provide thus support the role of theta oscillations in memory function and coordination at a network level. Highlights Resting state functional coupling between the DMN, MTL and ascending synchronising system. Theta oscillations may be the basis of this coupling given the role of these structures in control of theta. Theta oscillations have been implicated in memory, cognition and predictive coding. DMN, MTL and ASS are implicated in Alzheimer’s disease. Abbreviations MRI Magnetic resonance imaging fMRI functional magnetic resonance imaging rs-fmri resting state functional magnetic resonance imaging PnO Pontine nucleus oralis SuM Supra-mamillary nucleus. MS Medial septum DB Diagonal band of Broca. VTA ventral tegmental area PCC Posterior cingulate cortex HC Hippocampus ARAS Ascending reticular activating system ASS Ascending synchronising system DMN Default Mode Network aMPFC Anterior Medial Prefrontal Cortex pIPL Posterior inferior parietal lobule NBM Nucleus Basalis Mynert DCM Dynamic causal modelling PHG Parahippocampal Gyrus
Size related processes in phytoplankton

Growth, death, respiration, excretion and sedimentation describe the major rate processes of phytoplankton. These rates often scale allometrically (rate=a*mass^b). The allometric coefficient (b) describes the deviation from a linear reltionship. Literature values derived from experiments showed allometric coefficients of -0.48 to -0.1. Experiments with natural phytoplankton communities from the baltic and the subtropical gyre of the North Atlantic ocean showed an allometric coeffcient range of -0.72 to -0.3. The results indicate that size scaling of rate processes in phytoplankton is more pronounced than previously thought.
An evaluation of urine patch simulation methods for nitrous oxide emission measurement

SUMMARY Global nitrous oxide (N2O) inventory estimates for pasture systems are refined based on measurements of N2O loss from simulated urine patches. A variety of methods are used for patch simulation but they frequently use a uniform wetted area (UWA), often smaller than a bovine urine patch. However, natural patches follow non-uniform infiltration patterns expanding naturally from a point of deposit with a non-wetted zone of influence. Using 2 litres of urine the UWA method was compared, using a 0·156 m2 collar, with a naturally expanding effective area (NEEA) method, using a 0·462 m2 collar under high (HL) and low (LL) N2O loss conditions. The method chosen affects urine nitrogen (N) loading to the soil. Under HL the UWA method induced a N2O-N loss of 280·6 mg/patch, significantly less than the 434·8 mg/patch loss for the NEEA method, for the same simulated urination. Under LL there was no method effect. Efforts should be made to employ patch simulation methods, which mimic natural deposits and can be achieved, at least in part, by: (a) Using a urine volume and N content similar to that of the animal of interest. (b) Allowing natural infiltration of the chosen urine volume to permit tapering towards the edges. (c) Measuring from the zone of influence in addition to the wetted area, i.e. the patch effective area.