Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating and exploiting fungal natural products in Aspergillus spp.

Gliotoxin (GT) is a redox-active natural product produced by some fungal species that contributes to the virulence of the human pathogen Aspergillus fumigatus. It contains a characteristic disulphide bridge responsible for the deleterious effects of this molecule. GT also displays antifungal properties, however the mechanisms of cytotoxicity behind it has not been fully characterised. The work presented here investigates A. niger as a model organism to understand GT cytotoxicity and reveal new metabolic systems, as it does not produce GT. Comparative proteomics revealed that exposure of A. niger to exogenous GT resulted in a significant (p < 0.05) dysregulation of hundreds of proteins involved in several cellular processes, especially metabolism. Two putative S-adenosylmethionine (SAM)-dependent methyltransferases showed de novo abundance under GT conditions. In addition an increase in abundance of proteins involved in the methionine cycle was also observed. Analysis of methionine-related metabolites revealed significant increases in the levels of methionine and adenosine, in correlation with proteomic data. Moreover, proteomic data revealed a significant increase in the abundance of hydrolytic enzymes, including glycoside hydrolases (n = 22) and peptidases (n = 16) which have important applications in the biotechnology industry. A significant dysregulation of proteins involved in amino acid metabolism coupled to an increase in the levels of selected amino acids appeared to occur in A. niger under GT conditions. Furthermore this thesis reveals a novel protection mechanism in A. niger against GT which is mediated by one the methyltransferases (MTases) identified on the proteomic data. This MTase (referred as MT-II) is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation and deletion of MT-II led to increased GT sensitivity in A. niger. The applications of other fungal natural products like siderophores (Fusarinine C), are also evaluated herein. The development and validation of a Fusarinine C based enzyme-linked immunosorbent assay (ELISA) was carried out. Results showed the potential applications of this ELISA in the diagnosis of aspergillus related diseases. Overall, this work highlights the different roles and applications fungal natural products have.
Differentiation of Human Embryonic Stem Cells into Cone Photoreceptors

[Abstract] Photoreceptors are specialized retinal neurons able to respond to light in order to generate visual information. Among photoreceptors, cones are involved in colors discrimination and high-resolution central vision and are selectively depleted in macular degenerations and cone dystrophies. A possible therapeutic solution for these disorders is to replace degenerating cells with functional cones. Here, we describe a simple protocol for the rapid production of large amount of cone photoreceptors from human pluripotent stem cells. The differentiation protocol is based on the “default pathway” of neural induction using the BMP, TGFβ and WNT antagonist COCO.
Production and characterization of VP6-specific monoclonal antibodies against bovine group C rotavirus

dehydrating diarrhea in humans and animals. The importance of group C rotavirus (GpC-RV) infections has not been established as the studies on the GpC-RV have been hampered by the lack of an in vitro culture system. However, diarrheal diseases associated with GpC-RV have been gradually increasing worldwide. In this study, VP6 gene of bovine GpC-RV Korean isolate was expressed, and monoclonal antibodies (mAbs) against VP6 were produced and characterized. The VP6 gene was cloned and expressed based on a baculovirus expression system. Indirect fluorescence antibody (IFA), polymer chain reaction (PCR), and Western blot assays were used to confirm expression of VP6 gene synthesized by the recombinant baculovirus. Eleven mAbs against VP6 were produced using expressed VP6. Cross-reactivity of the mAbs was assessed with recombinant VP6 proteins from porcine GpC-RV and human GpARV, or different serotypes of group A rotavirus strains by IFA test. Some mAbs reacted with intact porcine GpC-RV Cowden strain as well as bovine GpC-RV VP6 recombinant baculoviruses, but not with human and animal GpA-RV strains. The VP6-specific mAbs might be useful to develop immunodiagnostic tests such as rapid diagnostic kit, IFA and enzyme-linked immunosorbent assay (ELISA) for detection of GpC-RV.
Mega-trap-plots: a novel method of Sirex woodwasp management on Pinus radiata plantations in Chile

Sirex noctilio is one of the most important invasive pests that affect Pinus radiata plantations in Chile. Its management is based on a biological control complex, the most important component of which is the nematode, Deladenus siricidicola. However, in some areas, S. noctilio populations attain epidemic levels and no effective control methods exist to reduce large populations in a short period. In this study, we evaluated a novel method called mega-trap-plots (MTPs), which consist of an area of 1 ha with trap trees, which were debilitated in four different months (from November to February) with the purpose of reducing the Sirex wasp population through harvesting of trees attacked. The main objective was to reduce the potential population of S. noctilio, by evaluating four periods or months of MTP installation to maximise the colonisation of trap trees by wood wasps. The results showed that the MTPs that were installed from November to January had the highest wood wasp infestation, which was coincident with the flight period of the insect. The trap trees were clearly attractive to S. noctilio females up to 90 d following their establishment. The MTPs that were established in November concentrated a potential population of 57 901 females of S. noctilio, which represents a population 5.4 times greater than that in the control, with 10 701 females. The population of S. noctilio attracted between November and January shows that the use of MTPs is an effective system for the management of wood wasps on plantations with a high level of infestation and thereby can reduce their spread and the attack of new trees within the same forest compartments.
Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis

Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800–500 cm−1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC–LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA + HET, DMBA versus DMBA + HETNPs and DMBA + HET versus DMBA + HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the antitumor response of drugs.
Structural and functional brain changes following four weeks of unimanual motor training: evidence from behaviour, neural stimulation, cortical thickness and functional MRI

Although different aspects of neuroplasticity can be quantified with behavioural probes, brain stimulation, and brain imaging assessments, no study to date has combined all these approaches into one comprehensive assessment of brain plasticity. Here, 24 healthy right-handed participants practised a sequence of finger-thumb opposition movements for 10 minutes each day with their left hand. After four weeks, performance for the practised sequence improved significantly (p < 0.05 FWE) relative to a matched control sequence, with both the left (mean increase: 53.0% practised, 6.5% control) and right (21.0%; 15.8%) hands. Training also induced significant (cluster p-FWE < 0.001) reductions in functional MRI activation for execution of the learned sequence, relative to the control sequence. These changes were observed as clusters in the premotor and supplementary motor cortices (right hemisphere, 301 voxel cluster; left hemisphere 700 voxel cluster), as well as sensorimotor cortices and superior parietal lobules (right hemisphere 864 voxel cluster; left hemisphere, 1947 voxel cluster). Transcranial magnetic stimulation over the right (‘trained’) primary motor cortex yielded a 58.6% mean increase in a measure of motor evoked potential amplitude, as recorded at the left abductor pollicis brevis muscle. Cortical thickness analyses based on structural MRI suggested changes in the right precentral gyrus, right post central gyrus, right dorsolateral prefrontal cortex and potentially the right supplementary motor area. Such findings are consistent with LTP-like neuroplastic changes in areas that were already responsible for finger sequence execution, rather than improved recruitment of previously non-utilised tissue.
Search for sub-threshold photoproduction of J/ψ [J/psi] mesons

A search was made for sub-threshold J/ψ production from a carbon target using a mixed real and quasi-real Bremsstrahlung photon beam with an endpoint energy of 5.76 GeV. No events were observed, which is consistent with predictions assuming quasi-free production. The results place limits on exotic mechanisms that strongly enhance quasi-free production. PACS numbers: 13.60. Le,14.40. Gx,25.20. Lj
Ecological, Taphonomic, and Paleoecological Dynamics of an Ostracode Metacommunity

Paleobiological archives are essential for understanding long term and large scale diversity patterns. However, prior to using any taxa in these types of studies, the taphonomic processes by which they enter the fossil record should be well documented and understood. This study focuses on the precision and accuracy of the fossil record of Ostracoda (Phylum: Arthropoda) on San Salvador Island, Bahamas. Ostracodes (microcrustaceans) are an important proxy for reconstructing climate change and sea level fluctuations, but their taphonomy is not well known. We test the accuracy of the ostracode record on San Salvador by examining the correlations between rank-abundance and taxonomic composition of sixteen living communities and death assemblages in seven lakes on San Salvador Island. We also test the precision of this record by comparing the taxonomic composition and species abundances of sixteen death assemblages from each of the same seven lakes. In six out of seven of these lakes, the accuracy by which death assemblages record the taxonomic composition and rank-
Fine-scale genetic structuring, divergent selection, and conservation prospects for the overexploited crab (Cardisoma guanhumi) in tropical mangroves from North-eastern Brazil

Popularly known as blue land crab, Cardisoma guanhumi is heavily exploited as food and considered as an important economic resource in Brazil. In recent decades, the species has experienced a sharp population decline by the loss and/or degradation of its natural habitat and overfishing. The present study aimed to investigate the genetic variation and connectivity among 154 specimens of C. guanhumi sampled along the coast of Pernambuco in five different levels of tropical mangroves conservation. Nine ISSR primers were used for assessing the genetic variation of the species. The genetic diversity observed in C. guanhumi was high reinforcing the condition of a resilient species, indicating a good conservation status of this resource in Pernambuco. The hypothesis of panmixia was rejected in favour of a heterogeneous distribution of the genotypes of C. guanhumi (ФST = 0.19) despite the high gene flow observed in the study region. Such difference could be attributed to the candidate loci being under positive selection and differentially distributed between the geographic regions assessed. The genetic structure showed a pattern of fine-scale genetic structuring better fitted to a model of selection-mediated geographic cline. Cluster analysis and candidate loci under positive selection suggested that the populations of C. guanhumi in the North-central and South coasts of Pernambuco might be different management units and must be managed independently. In conclusion, exhaustion of natural stocks upon which fishing is totally dependent will lead to serious ecological and sociocultural impacts.
First Report of Metacordyceps chlamydosporia (Cordyceps chlamydosporia) Isolated from Soil in Korea

A previously unrecorded species, Metacordyceps chlamydosporia KNU14-22, was isolated from soil in Korea. Identification of the fungal species was based on morphological and molecular characteristics. This species has not been previously reported in Korea and herein we present data with detailed descriptions and figures.
Energy, water vapor and carbon fluxes in Andean agroecosystems: conceptualization and methodological standardization

This paper presents the conceptualization, methodological adjustment and experimental application of the micrometeorological technique eddy covariance - EC, to measure energy, water vapor and CO2 fluxes in two coffee agroecosystems: the first under full sunlight, and the second under shade, both with equatorial Andean hillslope conditions. With a footprint and fetch calculation, the required distance from the edge of the field in the prevailing wind direction to the EC tower is three times higher under shade than full sun. The shaded agroecosystem reached maximum average carbon fixation rates of 21.26 ± 2.469 μmolCO2. m-2s-1 ( = 0.05) (61% higher than under 100% sunlight) which gives a high carbon sink capacity to the association of coffee plants with shading Pigeon peas ( Cajanus cajan L). The average evapotranspiration rate was 2.33 ± 0.0102 mm.d-1 ( = 0.05) and 2.08 ± 0.00732 mm.d-1 under shade and 100% sunlight, respectively. The proportion of net radiation that reached the soil was 2% under shade and 4% under 100% sunlight. Likewise, the soil energy loss during the night was lower under shade, indicating less day-night temperature range in the latter agroecosystem. The methodological adjustment and the results of this first work using EC in Colombian coffee plantations, contribute to the development of reliable research regarding gas and energy exchanges between the atmosphere and ecosystems in conditions of the equatorial Andean hillslope.
Fundamentals of the Host-Virus Evolutionary Arms Race

The immune system has been battling viral infections over the course of millions of years in primate evolution. The constant evolution of hosts and viruses to defeat the other has led to a high stakes genetic arms race. Here I present a detailed study of three antiviral proteins locked in antagonistic viral conflict called Tetherin, Viperin and SAMHD1. Using a combined approach of virology and evolutionary biology, I have reconstructed their evolutionary arms race between primates and lentiviruses, including HIV-1, HIV-2 and related SIVs. The broad themes that emerge from my research are two-fold. First, lentiviruses are able to evolve new functions within existing gene repertoires to counteract rapidly evolving host antiviral genes. Second, hosts escape from viral pressure either by single amino acid changes or by deletions of a ‘susceptibility domain'. Thus, my thesis research has helped define the rules by which host-virus arms races ensue. Based on my findings, we contend that the host evolutionary framework is a fundamental pillar of antiviral restriction.
Behavioural aspects of the departure of waders before long-distance flights flocking vocalizations flight paths and diurnal timing

The departure behaviour of waders was studied on the Bane d'Arguin in Mauritania in spring, and in The Netherlands in both spring and autumn. Most flocks consisted of 10-60 individuals, with the larger species occurring in larger flocks. When conspecifics were best 'available' (during peak migration and at high tides) starting flocks were largest. During departure flocks sometimes joined others or split up, 'stabilizing' between 30-60 birds. Starting flocks usually assembled from clusters into V-formations or echelons. About 4% of the flocks contained more than one species. In more than 90% of the departing flocks birds vocalized intensely. With an optical range-finder we were able to follow flocks leaving the Bane d' Arguin to heights of 1.5 km, with no signs of flocks levelling off. During this ascent birds usually headed into the wind with climb rates ofO.55-0.69 m s·l. Except under the rare condition of tail winds, departing flocks showed no compensation for wind drift. A fixed orientation would make it easier for the birds to calculate wind drift effects between successive geographical fixes on which to base subsequent orientational adjustments. All species headed towards NNW, instead of NNE where the next stopover areas are found. This westerly orientation might represent an adaptation to correct for a continuous easterly drift at high altitude. Most flocks left before sunset, the departures showing a variable relationship to tide height. In the Dutch Wadden Sea, where cloud conditions vary, all 277 witnessed departures occurred with a visible sun. The diurnal timing of departures and the patterns of flocking can be understood as a result of the interactions between orientational and energetic advantages. IZoological Laboratory, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands; 2Netherlands Institute for Sea Research (NIOZ); 3Poundation Working Group for International Wader and Waterfowl Research (WIWO); 4Rijkswaterstaat Plevoland, Lelystad; 5Department of Marine Biology, University of Groningen.
Population Characteristics of Human-Commensal Rodents Present in Households from Mérida, Yucatán, México

Anthropocommensal rodents live in close proximity to humans in many habitats around the world. They are a threat to public health because of the pathogens they carry. Recent studies in Merida, Yucatan, Mexico, have shown that commensal rodents harbor potential zoonotic pathogens such as bacteria, helminths, and viruses. In this study, we describe reproductive and demographic parameters of house mice and black rats present in households from Merida, Yucatan, Mexico, a municipality located in a tropical region in southern Mexico. Rodents were trapped in 142 households within the municipality of Merida from 2011 to 2014. A total of 832 rodents were trapped, constituting 556 (66.8%) house mice (Mus musculus) and 276 (33.2%) black rats (Rattus rattus). The sex ratio in mice was different than parity, while in rats it was 1:1. Mice in the weight class 8.1–12 g were most abundant in both females (52.9%) and males (57.2%). On the other hand, rats weighing ≤ 40 g (25% of females and 28.6% of males) were most abundant. The percentage of pregnancy in mice was 46.7%, whereas in rats it was 21.3%. The mean number of embryos was 4.7 and 5.8 in mice and rats, respectively. This study provides relevant demographic information on the ecology of commensal rodents from a tropical region of Latin America. We consider that our findings could be useful as a first step toward understanding the ecological behavior of rodent populations in tropical regions.
The female reproductive cycle of the european common carp, Cyprinus carpio , at a Transvaal fish farm: Gonadal morphometric development

The annual reproductive cycle of Cyprinus carpio was investigated using morphometric parameters of the body and gonads, including fecundity estimations, gonadosomatic indexes as well as histological evaluation and classification of oocyte developmental stages. It was concluded the C. carpio has an extended spawning season under temperate conditions, from early spring (September) to late summer (February). Results further suggest that by manipulating temperature and daylight period during late winter (August) it would be possible to induce spawning during this period.
Basal area increment series of dominant trees of Pseudotsuga menziesii (Mirb.) Franco show periodicity according to global climate patterns

Las especies forestales como Pseudotsuga menziesii (Mirb.) Franco son sensibles al clima y muestran anillos de crecimiento claramente definidos. La seleccion cuidadosa de arboles dominantes con fuste circular permite el analisis de tendencias de crecimiento arboreo. En este estudio se utilizaron mediciones directas del incremento del area basal (IAB) para explicar las periodicidades biologicas y elaborar predicciones del crecimiento en el abeto Douglas-fir que crece en el oeste de Mexico. Para eliminar el efecto de la edad en el crecimiento de los arboles se hizo un analisis en terminos de la edad del cambium. Los resultados mostraron correlacion significativa (P < 0.05) entre IAB y la precipitacion de enero a julio. Ademas, se encontraron periodicidades de 7, 21, 27 y 60 anos en el crecimiento de los arboles; el periodo de 60 anos fue determinante para la construccion de un modelo ARIMA (0,1,1) para realizar predicciones del IAB en las proximas decadas. Las proyecciones del crecimiento proponen una reduccion del IAB en arboles maduros dominantes en las proximas decadas. Dicha reduccion es un resultado inesperado, debido a que el IAB en arboles dominantes permanece constante hasta una edad biologica de senescencia. Los resultados concuerdan con una tendencia general de reduccion en el crecimiento en otros bosques del mundo debido a estres hidrico, lo cual sugiere que la variabilidad climatica futura puede empeorar la condicion de salud del abeto Douglas-fir de los bosques del norte de Mexico.
Ontogeny of the articulated yiliangellinine trilobite Zhangshania typica from the lower Cambrian (Series 2, Stage 3) of southern China

Abstract. New discoveries of the early Cambrian yiliangellinine trilobite Zhangshania typica Li and Zhang in Kunming preserve almost all instars from early postembryonic (protaspid) to mature (holaspid) phases in articulated state, in addition to mature specimens with antennae bearing paired spines on the basal articles. The ontogenetic series shows protarthrous development with some, but likely not all, early holaspid instars expressing additional pygidial segments, gradual rearward migration of the location of the longest pleural spines on the trunk segments, and striking positive allometry of the genal spines. It also reveals Parazhangshania sichuanensis Li and Zhang, 1990 to be the holaspid stage 3 of Z. typica, and therefore its junior synonym. This new find in the Hongjingshao Formation provides species-based regional correlation across the South China block and Z. typica may provide an important biostratigraphic marker for the base of the traditional Tsanglangpuan Stage.