Miracle-dz/UniFAR-FTUs huggingface dataset:
12 Gutierrez_final.indd

In this chapter we present an atomic level study of nano-particle impact using molecular dynamics simulation. Two cases have been considered. First, we simulate the bouncing of a ball over a surface due to a constant force (which mimic the gravity force), modeling the inter-atomic interaction by a modified Lennard-Jones potential, where the ball-surface atom interaction is represented by a purely repulsive term. The analysis of the results makes it possible, among other aspects, to determine the restitution coefficient in each bounce as well as to understand the processes of energy loss in inelastic collisions, which are actually not a loss, but a transfer to thermal and vibrational energy. The second simulation describes the impact mechanisms of a solid projectile hitting a target at high velocity. Both the projectile and the target are made of copper, which is modeled by a realistic many-body tight-binding potential. The projectile velocity is kept constant during all the simulation, representing an extreme condition, where the momentum and hardness of the projectile is much higher than the momentum and hardness of the target. In this regime, we identify two different behavior in dependence of the projectile velocity: at low velocities (less than 4 km/s) the target basically recover its structure after the passage of the projectile, but at higher velocities, the projectile left a permanent hole in the target.
Advanced Sampling Methods for Quantum Free Energy Calculations

In this thesis, we address the problem of formulating an accurate and efficient scheme to compute quantum free energies. The inclusion of quantum effects in free energy calculations is important in systems that, presenting the problem of thermally activated events, also contain light atoms and/or are at low temperatures. Therefore, this topic is crucial in several branches of physics, chemistry and biochemistry. This work is divided in two parts. In the first part, a detailed review of two advanced computational methods is made. The first approach is the Quantum Single Sweep method [Bonella and Vuilleumier, (in press)], which is based on the path integral formalism. Though very precise in the reconstruction of quantum free energy profiles, this scheme is computationally expensive. The second technique that is revised here is the Quantum Thermal Bath [Dammak et al., Phys. Rev. Lett. , 103:190601, (2009)], an approach that uses a generalized Langevin equation to effectively include quantum effects in the form a random force and a dissipative term. This technique has the advantage that is less costly than pathintegral-based methods; however, it only gives exact results for harmonic systems. Furthermore, the method’s applicability for free energy calculations has never been tested systematically. The second part of the present project studies precisely a route to combine the former two methodologies in a way that keeps the best elements of them, with the goal to generate an algorithm that is less computationally demanding than the quantum single sweep method but without the problems of the quantum thermal bath. While carrying out this program, we found that a direct use of the quantum thermal bath in the dynamical equations of the quantum single sweep does not yield the correct free energy landscape. Instead, the classical result is obtained for one-dimensional systems. These problems are carefully analysed and explained in this thesis. A second outcome of the present work is a novel scheme that is proposed to overcome the issues mentioned above. This new method combines some steps of the quantum single sweep with a hybrid Monte Carlo calculation in which the trial moves are proposed by evolving a molecular dynamics trajectory based on the quantum thermal bath. Although the performance of this novel technique is not numerically tested here, we present its theoretical formulation and the main points to push forward in its implementation, a task that we believe would be very interesting to follow, since to our knowledge it has not yet been done elsewhere.
Metabolomic analyses of the haemolymph of the Asian citrus psyllid Diaphorina citri, the vector of huanglongbing

The Asian citrus psyllid Diaphorina citri Kuwayama is currently threatening the citrus industry by transmitting the causative agent Candidatus Liberibacter asiaticus (CLas) of huanglongbing. Multiplication of CLas in haemolymph of D. citri indicates that it contains the necessary nutrients for CLas. Although many studies examine D. citri, the haemolymph composition of this dangerous pest remains to be investigated. In the present study, the haemolymph of D. citri is collected using a nanolitre syringe after the removal of one of its forelegs. The haemolymph is either derivatized with methyl chloroformate (MCF) or trimethylsilyl (TMS) derivatizing reagent and analyzed with gas chromatography–mass spectrometry. Nineteen amino acids, two organic acids and seven fatty acids are detected in the haemolymph after MCF derivatization. More metabolites are detected after TMS derivatization. Sugars are the most abundant metabolites in the haemolymph. Glucose and fructose are the main monosaccharides. Trehalose and sucrose are the major disaccharides. Furthermore, three inositol isomers (myo‐inositol, scyllo‐inositol and chiro‐inositol) are detected in the haemolymph. Organic acids are found in low amounts, whereas phosphoric acid is found at a higher concentration. Twenty‐four nucleotides and sugar nucleotides, including ATP, ADP and AMP, are detected using high‐performance anion‐exchange chromatography. Adenine nucleotides are the most abundant nucleotides followed by uridine and guanosine. The adenylate energy charge for the haemolymph is 0.77. Our results show that many metabolites found in the citrus phloem sap are also found in the haemolymph of D. citri.
Differential Responses of Bird Species to Habitat Condition in a Coastal Kenyan Forest Reserve

The management of assemblages of species across many taxa is a common concern in conservation. Consequently, the use of one or a few surrogate or indicator species to represent an entire assemblage has become an increasingly important tool in conservation science. However, conservation schemes based on the needs of one or two focal species often fail to account for individualistic responses of larger assemblages of species. Data from bird point counts along with vegetation characteristics from a coastal tropical dry forest in Kenya that is subject to elephant disturbance were used to explore the differential responses of bird species to environmental conditions in a forest reserve where wildlife management includes both endangered birds and mammals. Results revealed that even birds with similar foraging habits had idiosyncratic responses to both environmental traits and elephant disturbance. While overall species responded to important characteristics such as percent canopy cover and leaf litter depth, individualistic responses of different species trait diversity defied easy characterization of optimal forest management schemes. Taken together, our analyses highlight the difficulty in basing the development of management plans for entire assemblages of species on the response of a single or a few species. Implications for wildlife conservation in Arabuko-Sokoke Forest and similar forest reserves are discussed, emphasizing the need for a better understanding of individual species’ responses to forest conditions.
Investigating the effects of organic pollutants on amphibian populations in the UK

Amphibians are undergoing dramatic population declines, with environmental pollution reported as a significant factor in such declines. Technologies are required that are able to monitor populations at risk of deteriorating environmental quality in a rapid, high-throughput and low-cost manner. The application of biospectroscopy in environmental monitoring represents such a scenario. Biospectroscopy is based on the vibrations of functional groups within biological samples and may be used to signature effects induced by chemicals in cells and tissues. Here, attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy in conjunction with multivariate analysis was implemented in order to distinguish between embryos, whole tadpoles at an early stage of development and individual tissues of late-stage tadpoles of the common frog collected from ponds in the UK with varying levels of water quality, due to contamination from both urban and agricultural sources. In addition, a Xenopus laevis cell line was exposed to low-levels of fungicides used in agriculture and assessed with ATR-FTIR spectroscopy. Embryos, in general did not represent a sensitive life stage for discriminating between ponds based on their infrared spectra. In contrast, tadpoles exposed to agricultural and urban pollutants, both at early and late stages of development were readily distinguished on the basis of their infrared spectra. ATR-FTIR spectroscopy also readily detected fungicideinduced changes in X.laevis cells, both as single-agent and binary mixture effects. Data reported in this study confirm the use of ATR-FTIR spectroscopy as a sensitive technique capable of detecting small changes in cellular groups, and as such represents a valuable starting point for its use in the monitoring of amphibian populations. However further research is needed in order to overcome confounding factors existent in natural populations of complex organisms.
Begomoviruses infecting common beans (Phaseolus vulgaris L.) in production areas in Cuba

Viral diseases caused by begomoviruses are economically important for their depressing impact on common bean production in Cuba. Mayabeque is a Cuban province where this crop is significantly grown and affectations by Bean golden yellow mosaic virus (BGYMV) have been detected in the last 30 years. Integrated pest management (IPM) programs in this crop have allowed controlling the disease for a long time. However, in prospections of the last years, an increase of the incidence of various yellowing symptoms typical of begomoviruses has been observed in common bean production areas. DNA was extracted from leaf samples taken from symptomatic plants. Non-radioactive nucleic acid hybridization and a specific PCR assay were used to detect BGYMV, Common bean severe mosaic virus, Common bean mottle virus, and Tobacco leaf curl Cuba virus. Of the 218 bean plants sampled, 89.5 % was positive to BGYMV; the presence of the rest of the begomovirus species was between 3 and 4% (3.08% of CBMoV, 3.08% of TbLCCuV and 4.32% of CBSMV). The viral DNA from some samples was analyzed by rolling circle amplification (RCA), by restriction fragment length polymorphism analysis using restriction enzymes, and by cloning and sequencing of the viral components. The DNA sequences from BGYMV isolates showed 98% of identity with the isolates reported in Cuba in 2003. The infection by Tobacco leaf curl Cuba virus (TbLCCuV) was confirmed also in fields in the Cuban western region. This is the first work where the DNA-B of TbLCCuV is identified. These studies will help to strengthen phytosanitary surveillance and management programs implemented in the country to control the whitefly-begomovirus complex in this economically important crop.
Maintenance of soil ecotypes of Solidago virgaurea in close parapatry via divergent flowering time and selection against immigrants

The often patchy distribution of serpentine geology can lead to abrupt changes in soil and microclimates. Thus, serpentine areas provide an ideal natural setting to understand how divergent selection drives the process of local adaptation in edaphically specialized plants. When the serpentine ecotype is surrounded by a related nonserpentine ecotype, a balance of natural selection and potential gene flow should maintain the different ecotypes over very short distances. We aimed to reveal the mechanisms allowing soil ecotypes of a goldenrod species to co‐occur sympatrically in Japan. We performed field surveys to characterize microenvironments and flowering phenology of each ecotype, common garden and reciprocal transplant experiments and artificial crossing, and population genetic analysis to investigate the levels of genetic differentiation between ecotypes. Growth chamber experiments show that serpentine plants showed lower specific leaf area (SLA) and greater resource allocation to their root systems than did their nonserpentine counterparts, a potential adaptation to drier and less fertile soil condition in serpentine habitats. Reciprocal transplant studies demonstrated a clear pattern of local adaptation in the plant growth rate. Importantly, serpentine populations completed flowering by midsummer versus late summer in nonserpentine plants. This pattern is consistent with the hypothesis that early flowering ensures reproductive success, before the microclimatic conditions becomes severe in open habitats. Although prezygotic isolation was a strong barrier to gene flow, genetic differentiation was very low, indicating a recent origin for the serpentine ecotypes and/or gene flow at low frequencies. Synthesis. The findings indicate that the early flowering times of serpentine ecotypes, which would have been selected for by microclimates in serpentine areas, can play roles in local adaptation, but also population isolation via a by‐product of diverged reproductive timings. This study contributes to general understanding of the initial stages of plant ecological speciation under potential gene flow in very small geographic scales.
Cohesin dependent compaction of mitotic chromosomes

Structural Maintenance of Chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply-conserved SMC complexes, organize chromosomes in budding yeast. The canonical role of cohesins is to co-align sister chromatids whilst condensins generally compact mitotic chromosomes. We find strikingly different roles in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosomes arms, independent of and in addition to its role in sister-chromatid cohesion. Cohesin dependent mitotic chromosome compaction can be fully accounted for through cis-looping of chromatin by loop extrusion. Second, condensin is dispensable for compaction along chromosomal arms and instead plays a specialized role, structuring rDNA and peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that SMC-dependent looping is readily deployed in a range of contexts to functionally organize chromosomes. Highlights Cohesin compacts mitotic chromosomes independently of sister chromatid cohesion. Formation of cis-loops by loop extrusion fully accounts for cohesin-mediated compaction. Condensin is not required for mitotic chromosome compaction of yeast chromosome arms Condensin has a focused pre-anaphase role at centromeres and rDNA in yeast
Cryophilic Isotomidae (Collembola) of the Northwestern Rocky Mountains, U.S.A.

Descriptions of Collembola from glaciers, snowfields and cold water seeps in Alaska, British Columbia, Alberta, Washington and Oregon are presented. Myopia alaskana Christiansen and Bellinger, and Desoria uniens Christiansen and Bellinger are redescribed. The following new species are described: Desoria albicornis sp. n. , Desoria triangularis sp. n. , Desoria ater sp. n. , Desoria garibaldii sp. n. , Desoria pilifrons sp. n. , Desoria cryophila sp. n. , Desoria rosea sp. n. , Desoria olympica sp. n. , Desoria capra sp. n. and Gnathisotoma spinolabris sp. n. One new genus, Mucronia gen. n. and its type species Mucronia enigmatica sp. n. are described from Alaska. The new genus possesses some characters of both the Isotomidae and Tomoceridae having a lobed post antennal organ and a mucro with two setae.
Genetic Variation Assessment of Some Prunus Species Using Srap Markers

Genetic variation at molecular level was evaluated among three species of Prunus genus and a wild species, (P. arabica (wild), P. argentea (wild), P. dulcis (local), and P. dulcis (wild ). The genetic variation assessment was carried out using SRAP molecular markers. The genetic similarity coefficient revealed the genetic relationship among the samples tested in which the highest genetic distance was between P. dulcis (local), and P. dulcis (wild), and lowest genetic distance was between P. arabica (wild), P. argentea (wild). The phylogenetic tree was obtained using UPGMA method depending on the total number of SRAP bands. There were two main groups in the dendrogram: the first one consists of two subgroup: P. arabica and P. argentea cluster together in one Subgroup and P. dulcis (wild) appear alone in this subgroup. P. dulcis (Local variety) appear in the second group alone.
The freshwater alga Mucidosphaerium sphagnale (Chlorellaceae: Chlorophyta) in New Zealand: the first record outside Europe

ABSTRACT Mucidosphaerium sphagnale, a new record for New Zealand, is reported from Awarua Wetland. The genus Mucidosphaerium has recently been separated from the well-known Dictyosphaerium, a colonial green alga with cells connected by thin, branching stalks, to encompass those forms with near-spherical adult cells. The previous name for this taxon, Dictyosphaerium sphagnale, is not recorded from New Zealand; however, Mucidosphaerium pulchellum (syn. Dictyosphaerium pulchellum), which has been reported here many times and is very difficult to distinguish without DNA sequences, may represent previously misidentified instances of M. sphagnale. The M. sphagnale is reported here from a Sphagnum bog, as is typical of its European range, whereas M. pulchellum in New Zealand appears to have been reported exclusively from lakes and rivers. The organism reported here is therefore quite likely a genuine new occurrence. Co-introduction to New Zealand with foreign Sphagnum is a possibility.
High‐throughput sequencing allowed the completion of the genome of grapevine Red Globe virus and revealed recurring co‐infection with other tymoviruses in grapevine

&NA; Grapevine Red Globe virus (GRGV) is a member of family Tymoviridae tentatively assigned to genus Maculavirus. There is evidence that the distribution of this virus may be widespread. In a recent report, the authors of the present study described the presence of GRGV in Spain. To further estimate its incidence, a survey was carried out that allowed the detection of the virus using RT‐PCR in a germplasm collection in northern Spain. In the present study, three isolates were selected to obtain full‐length genome sequences using high‐throughput sequencing (HTS) of RNA combined with Sanger sequencing. The GRGV complete genome consists of 6850 nucleotides, excluding the polyA tail. Two ORFs could be identified as the putative replicase and coat protein. Although comparison of the complete genomes provided no evidence for the presence of the additional ORF previously described, another ORF was identified within the coat protein ORF, but it probably lacks functional significance. Phylogenetic analysis supported the ascription of GRGV to genus Maculavirus. The profile of vsiRNA (virus‐derived small interfering RNA) distribution along the GRGV genomes suggested the presence of a subgenomic RNA corresponding to the coat protein ORF. To improve detection of GRGV, new primer sets were designed based on consensus sequences. HTS revealed a frequent co‐infection of GRGV and grapevine rupestris vein feathering virus (GRVFV). Biological indexing by grafting two GRGV‐infected vines on indicator plants and the visual inspection of symptoms in other infected plants revealed that the virus has a negligible impact on grapevine.
One-pot conversion of biomass-derived xylose to furfuralcohol by a chemo-enzymatic sequential acid-catalyzed dehydration and bioreduction

One-pot furfuralcohol (FOL) production via dehydration of corncob-derived xylose followed by bioreduction of furfural has been described. The synthesized biocompatible solid acid catalyst SO42−/SnO2-attapulgite has been characterized and used for the dehydration of xylose-rich hydrolysate, and the highest furfural yield of 44% is achieved when employing 3.6 wt% catalyst loading at 170 °C for 20 min. The recombinant Escherichia coli CCZU-A13 harboring a NADH-dependent reductase (SsCR) is found to catalyze the bioreduction of furfural to FOL, the whole-cell catalyst could tolerate as high as 300 mM furfural substrate to give 221 mM FOL after 12 h of reaction under the optimum conditions (1.0 mM glucose per mM furfural, 30 °C, pH 6.5, 0.1 g wet cells per mL). The two processes are successfully combined in a one-pot manner to transform the xylose-rich hydrolysate to furfural, and then to FOL with 44% yield based on the starting material xylose (100% FOL yield for the bioreduction step). Finally, recycling experiments for the carrageenan immobilized whole-cell and solid acid catalyst in one-pot FOL production are conducted; both catalysts show excellent recyclability and no obvious decrease in activity is detected after 5 cycles of reaction. The developed one-pot chemo-enzymatic approach is greatly useful for practical green FOL production from renewable biomass resources.
Genetic diversity within and relationships among Dutch horse populations

1 Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, the Netherlands anouk.schurink@wur.nl (Corresponding Author) 2 Wageningen University & Research, Centre for Genetic Resources, the Netherlands (CGN), P.O. Box 338, 6700 AH Wageningen, the Netherlands 3 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007 Uppsala, Sweden 4 Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112-114, 3584 CM Utrecht, the Netherlands 5 Department of Surgery and Anaesthesiology of Domestic Animals, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium