Miracle-dz/UniFAR-FTUs huggingface dataset:
Dopamine, Alpha-Synuclein, and Mitochondrial Dysfunctions in Parkinsonian Eyes

Parkinson’s disease (PD) is characterized by motor dysfunctions including bradykinesia, tremor at rest and motor instability. These symptoms are associated with the progressive degeneration of dopaminergic neurons originating in the substantia nigra pars compacta and projecting to the corpus striatum, and by accumulation of cytoplasmic inclusions mainly consisting of aggregated alpha-synuclein, called Lewy bodies. PD is a complex, multifactorial disorder and its pathogenesis involves multiple pathways and mechanisms such as α-synuclein proteostasis, mitochondrial function, oxidative stress, calcium homeostasis, axonal transport, and neuroinflammation. Motor symptoms manifest when there is already an extensive dopamine denervation. There is therefore an urgent need for early biomarkers to apply disease-modifying therapeutic strategies. Visual defects and retinal abnormalities, including decreased visual acuity, abnormal spatial contrast sensitivity, color vision defects, or deficits in more complex visual tasks are present in the majority of PD patients. They are being considered for early diagnosis together with retinal imaging techniques are being considered as non-invasive biomarkers for PD. Dopaminergic cells can be found in the retina in a subpopulation of amacrine cells; however, the molecular mechanisms leading to visual deficits observed in PD patients are still largely unknown. This review provides a comprehensive analysis of the retinal abnormalities observed in PD patients and animal models and of the molecular mechanisms underlying neurodegeneration in parkinsonian eyes. We will review the role of α-synuclein aggregates in the retina pathology and/or in the onset of visual symptoms in PD suggesting that α-synuclein aggregates are harmful for the retina as well as for the brain. Moreover, we will summarize experimental evidence suggesting that the optic nerve pathology observed in PD resembles that seen in mitochondrial optic neuropathies highlighting the possible involvement of mitochondrial abnormalities in the development of PD visual defects. We finally propose that the eye may be considered as a complementary experimental model to identify possible novel disease’ pathways or to test novel therapeutic approaches for PD.
A Ten Million SPH Particle Simulation of the Origin of Obliquity of Uranus

uity of Uranus Luı́s F.A. Teodoro, Donald G. Korycansky, Michael S. Warren, Christopher Fryer, Gabriel Rockefeller, Kevin Zahnle 1 BAER, NASA Ames Research Center, Moffett Field, CA 94935-1000 USA (luis.f.teodoro@nasa.gov), 2 CODEP, Dept. of Earth Sciences, University of California, Santa Cruz, CA 95064, USA, 3 Los Alamos National Laboratory, Los Alamos, NM 87585, USA, 5 NASA Ames Research Center, Moffett Field, CA 94935-1000 USA.
Biodiversity - functioning studies in grasslands: their design, analysis and the importance of realized diversity.

Current and expected decline in biodiversity have motivated a number of experiments studying how biodiversity affects ecosystem functioning. The positive relationship is usually found in experiments where species pool is manipulated; the relationship between productivity and realized species richness does not show any single trend. We constructed a simple competition model for a plant community based on the classical Lotkae Volterra equations, with randomly generated parameters. We varied the species pool size and intensity of competition (range of competition coefficients). Then, we compared two measures of diversity used as predictors of productivity: (1) the size of the species pool and (2) the realized species richness, i.e. the number of species that remained in the system after competitive exclusion. Simulation results showed that productivity was always positively affected by the size of the species pool. With increasing species pool, both the selection effect and complementarity increase. The relationship between realized species richness and productivity was extremely weak within a set of simulations with a fixed species pool (i.e. where the diversity gradient was caused only by differences in the randomly generated parameters). The relationship between realized species richness and productivity was slightly positive for small species pool sizes and slightly negative for larger species pools. A species with high carrying capacity within the generated set of species usually decreases the chance of other species to survive but increases the productivity of the mixture, leading to negative diversity productivity relationship. On the contrary, presence of highly complementary species (i.e. species with low mutual competition coefficients) increases both, the realized species richness and productivity, leading to positive diversity productivity relationship. These two effects mostly counterbalance each other. These trends are not affected by the competition intensity. 2010 Elsevier Masson SAS. All rights reserved.
Evidence for Root Kin Recognition in the Clonal Plant Species Glechoma hederacea

Plant competition belowground is a crucial factor that determines plant fitness and shapes plant communities. It has been shown that roots possess the ability to recognize between self and non-self individuals and modify their growth patterns accordingly. Roots may also be further able to discriminate between kin and non-kin roots. Competition is stronger with non-kin than kin neighbors, but whether root growth patterns determined by kin interactions are modified in stressful environments is largely unexplored. In this study we used two different experimental set-ups to confirm whether the clonal species Glechoma hederacea exhibits kin recognition between roots, and how water limitation modifies this response. A split-root design was conducted using a focal clonal fragment of G. hederacea placed onto the ridge that separated two adjacent containers: either square petri-dishes boxes with 200 ml of soil or 400 ml clear pots. Focal plants were randomly allocated to either growing alone or in competition with another G. hederacea ramet (of similar size taken from the same stolon as the focal plant) or a non-kin individual (a ramet selected from a different population). A water limitation treatment was applied to both experiments. Five root parameters were measured during the experiment using boxes: the maximum depth and the maximum width of the deepest root, the depth and the maximum width of the widest root, and the total number of roots visible. All plants were harvested after 36 days and several final root measurements were taken and analyzed using GiaRoots. Our results show that G. hederacea roots have kin recognition mechanisms, showing a significant tendency to avoid growing toward a non-kin neighbor but not avoiding the roots of a kin plant, even though the presence of a kin plant modifies root distribution within the soil. As expected, water limitation significantly affected plant growth and root parameters, but this effect was not related to neighbor kin identity. Taken together, our results confirm the existence of root recognition in this species and suggest that the mechanisms of kin recognition are probably related to a root-derived chemical cues, as recognition took place before physical contact occurred.
Functional genetic diversity of chestnut (Castanea sativa Mill.) populations from southern Spain: Short communication

Aim of the study: To evaluate the adaptive genetic variability of chestnut (Castanea sativa Mill.) populations from southern Spain in relation to bud burst and water stress.Area of study: Andalusia (southern Spain) where many chestnut groves were progressively abandoned and have become ‘naturalized’. Material and methods: A total of 126 chestnut trees from eight populations were assessed by means of nine genic microsatellite loci (expressed sequence tag simple sequence repeat markers) related to bud burst and water stress.Main results: Significant differences in genetic diversity were detected within and among populations, not found with neutral microsatellite markers. The structure analysis indicated the presence of two different gene pools.Research highlights: These results could contribute to the development of conservation strategies for this species in southern areas exposed to the effects of climate change. The genetic diversity of these populations could be useful in minimizing this risk and other predictable factors related to global change.
Pengaruh Penggunaan Daun Indigofera Segar Sebagai Suplemen Pakan Terhadap Produksi dan Warna Yolk Itik

ABSTRAK Protein kasar Indigofera cukup tinggi yaitu 27,89 % dan dapat memberikan kontribusi dalam pemenuhan kebutuhan protein itik sehingga tidak akan menurunkan produksi telur. Adanya ? -caroten dan xantophyl daun Indigofera akan memperbaiki angka pigmentasi yolk. Rancangan percobaan yang digunakan ialah Rancangan Acak Lengkap (RAL) dengan 4 perlakuan yaitu tanpa pemberian daun Indigofera segar (0%, kontrol), pemberian daun Indigofera segar 5%, 10%, dan 15% dari BK yang dibutuhkan. Setiap perlakuan terdapat 10 ekor itik siap produksi sebagai ulangan, sehingga ada 40 ekor.Variabel utama yang diamati meliputi konsumsi pakan, produksi telur, berat telur dan warna yolk. Data yang diperoleh dianalisis variansi dan apabila terdapat perbedaan dilakukan uji lanjut dengan Duncan Multiple Range Test (DMRT). Penggunaan daun indigo segar 15% ternyata menurunkan konsumsi pakan, produksi telur dan berat telur hal ini diduga itik membatasi konsumsi indigo yang bersifat bulky. Produksi telur itik rata-rata memberikan perbedaan yang nyata. Penggunaan daun indigo segar sampai dengan 10 % tidak mempengaruhi produksi telur, konsumsi pakan, dan konversi pakan. Konversi pakan terjelek adalah penggunaan 15% indigofera segar. Hal ini disebabkan karena telur yang dihasilkan rendah. Penggunaan daun indigo segar menaikkan warna yolk lebih tinggi daripada tanpa daun indigo segar Kata kunci : Indigofera, telur, yolk
Growing the biphasic framework: Techniques and recommendations for fitting emerging growth models

Several new growth models have been proposed to account for the life‐history trade‐offs that occur when indeterminately growing species allocate energy between somatic growth and reproduction. These models can improve the understanding of lifetime growth and life history, but can be more difficult to fit than conventional growth models. Increased data demands, multiple growth phases and increased parameterization all serve as barriers to the adoption and proper use of these new models. We review and comment on confounding issues during model fitting for several of these models, and provide advice on surmounting such issues. We then simulation‐test an example model, the Lester biphasic growth model, using several common fitting approaches. We highlight the biases and precision of each approach and provide guiding documents using r and jags code. The Bayesian Markov chain Monte Carlo and likelihood profiling approaches generally provided the best fits. Simpler approaches can be unbiased and precise if sampled data are of relatively high quality (e.g. moderate sample sizes for juvenile and adult phases) and model assumptions are met. Bayesian hierarchical approaches can accommodate more complicated data scenarios (e.g. unbalanced design across multiple populations); we provide an example of such an approach by recovering growth trajectories and inferring growth‐associated trait variation and environmental effects across multiple populations. Conventional growth models provide limited inference on life history. Many biphasic growth models can provide direct inference on multiple life‐history traits, but can be difficult to fit. The recommended approaches herein provide a path forward for fitting biphasic growth models in a variety of scenarios, allowing for wider application and tests of life history and ecological theory.
In vivo gene expression analyses provide unique insights on P. vivax gametocytogenesis and chloroquine response

Studies of gene expression have provided insights on the regulation of Plasmodium parasites. However, few studies have targeted P. vivax, the cause of one third of all human malaria cases outside Africa, due to the lack of in vitro culture system and the difficulties associated with studying clinical samples. Here, we describe robust RNA-seq profiles of P. vivax parasites generated directly from infected patient blood. Gene expression deconvolution analysis reveals that most parasite mRNAs derive from trophozoites and that the asynchronicity of P. vivax infections is unlikely to confound gene expression studies. We also show that gametocyte genes form two clusters of co-regulated genes, possibly indicating the independent regulation of male and female gametocytogeneses. Finally, despite a large effect on parasitemia, we find that chloroquine does not alter trophozoite gene expression. Overall, our study highlights the biological knowledge that can be gathered by directly studying P. vivax patient infections. Importance Plasmodium vivax is the second most common cause of human malaria worldwide but, since it cannot be cultured in the laboratory, its biology remains poorly understood. In this study, we describe the analysis of the parasite gene expression profiles generated from 26 patient infections. We show that the proportion of male and female parasites varies greatly among infections, suggesting that they are independently regulated. We also compare the gene expression profiles of the same infections before and after treatment with chloroquine, a common antimalarial, and show that the drug efficiently kills most P. vivax parasites but appears to have little effect on one specific parasite stage, the trophozoites, in contrast with the effect of the drug on P. falciparum. Overall, our study exemplifies the biological insights that can be gained from applying modern genomic tools to study this difficult human pathogen.
Distribution patterns of the fish assemblage in the Mamanguape River Estuary, North-eastern Brazil

ABSTRACT The Mamanguape River Estuary was studied along a continuum ranging from shallow sandstone reefs adjacent to the river mouth up to the limit of influence of seawater, the upper portions of the estuary. Fish samples were gathered using three types of nets along 17 sample sites, grouped in four regions according to salinity range (reefs and low, middle and upper estuaries), to seasonality (dry and rainy seasons) and to habitat usage (marine visitor, marine estuarine-opportunist, marine estuarine-dependent, estuarine resident and estuarine & marine). Differences were found in the fish assemblages along the estuarine-reef gradient, with most species (n = 30) being considered marine, estuarine-opportunists or estuarine-dependent, according to its abundance and distribution. A low number of species (n = 11) were considered estuarine residents. Some species exhibited significant differences in spatial distribution pattern, in which juveniles and adults predominated in different portions of the estuary, suggesting an ontogenetic migration both in relation to the adjacent reef area and across estuarine regions. Several species were newly recorded in the Mamanguape Estuary: Anchoa spinifer, Halichoeres poeyi, Hyporhamphus roberti, Scomberomorus cavalla, Sphyraena barracuda and Ocgocephalus vesperilio.
Secondary structure of proteins on oil release in aqueous enzymatic extraction of rapeseed oil as affected hydrolysis state

ABSTRACT In this study, the relationship between protein hydrolysis and oil release was studied by fluorescence microscopy and Fourier Transform Infrared (FTIR) spectroscopy, respectively. Five commercial proteases (Flavourzyme 1000L, Neutrase 1.5MG, Protamex, Alcalase 2.4L, and Thermolysin) were evaluated for oil extraction from rapeseed, and Alcalase 2.4L was found to be the best enzyme for highest free oil yield (81.81%). When use this enzyme, the results showed that parts of proteins restricted the release of oil, and the oil released almost completely was achieved after hydrolysis for 3.0 h. To further reveal the relationship between oil release and protein hydrolysis, the effects of hydrolysis time on the degree of hydrolysis of protein, and free oil yield were studied. The results showed that the release of oil was only related to the hydrolysis of parts of proteins, and when the degree of hydrolysis of protein was more than 17.05%, the effect of protein hydrolysis on oil release was greatly reduced. The intrinsic relationship between the structural changes of proteins and the release of oil in the hydrolysis process was analyzed by comparing protein secondary structure of different hydrolysis time, and the results showed that the transition of protein structure from order to disorder was an important factor for oil release.
Nest Site Selection in Least Terns (Sterna antillarum) in New Jersey and New York

-East Coast Least Terns (Sterna antillarum) generally nest in relatively barren, homogeneous habitats of broad sandy beaches on barrier islands or on spoil deposition sites. We studied Least Terns at several New York (N=4) and New Jersey colonies. About 300 pairs of Least Terns nested along 2 km of beach on Brigantine Beach, NJ in 1983. The New York colonies contained from 20-300 pairs estimated from single visits in 1971, 1974 and 1977. At most sites choice of nest sites differed from random with respect to position on the beach, elevation and slope, shell cover, vegetation cover, and distance to vegetation. Terns preferred to nest in the middle third of the beach, on areas with shell cover, and on ridges and slopes. On sparsely vegetated beaches, nests were closer to vegetation than were the random points; on heavily vegetated areas, nests were further from vegetation than were the random points. At Brigantine, fox and cats entered the colony from the dunes and preyed heavily on nests closest to the dunes. Terns nesting during the peak of the nesting season fledged the most young and suffered the fewest losses to predators. At Brigantine, disturbance was less at the ends of the colony, resulting in higher reproductive success in these sections. In the Long Island colonies beach vehicles, humans, and cats were the main causes of egg and clutch mortality. Received 28 November 1988, accepted 29 June 1989.
Diversity of Natural Enemies on Different Ornamental Plants at Palampur, Himachal Pradesh, India

Palampur is located at 32.6 0 N, 76.3 0 E, at an elevation of 1290 meters above mean sea level and represents mid hill sub-humid zone of HP (Singh et al, 2016). This region is suitable for growing different types of ornamental plants and trees, which have great aesthetic value and are grown for commercial value as cut flower, loose flowers and seed purpose. Many different kinds of insects and mites feed on ornamental plants which hamper their aesthetic and economic value (Pal and Sarkar, 2009). To combat these pests, usually insecticides are recommended but by keeping in view the harmful effects of the chemicals on environment and non-target organisms, there is a need to develop some alternate control strategies. Various workers have reported different species of natural enemies on ornamental crops from different regions (Nisha and Gupta, 2010; Sood and Kakar, 1990).
Snake fungal disease affects behavior of free-ranging Massasauga rattlesnakes

— Snake fungal disease (SFD) caused by Ophidiomyces ophiodiicola can lead to morbidity and mortality in snakes. However, we know little about the behavior of free-ranging individuals with the disease and the implications this may have for threatened taxa. We discovered Massasaugas (Sistrurus catenatus), a federally protected rattlesnake in eastern USA, with SFD in northern Michigan during a radio-telemetry study we conducted from 2013–2017. We were consequently provided with an opportunity to investigate differences in movement, visibility, thermoregulation, and overwintering site selection between eight infected and 17 uninfected snakes. Across the active season, infected snakes moved distances ≥ 10 m less frequently and were less visible than uninfected snakes. This suggests disease imposed an energetic cost of movement too great for debilitated snakes that was possibly outweighed by other behaviors, such as avoiding predators. Monthly body temperatures of infected snakes differed from uninfected snakes only near the end of the active season, supporting observations of infected snakes surface basking when uninfected snakes had retreated to overwintering refugia. Most infected individuals overwintered in a concentrated area, suggesting environmentally driven hotspots for the fungus could exist within the landscape. Our findings provide a baseline for future studies investigating more consequential behavior for infected snakes. Linking snake behavior with the distribution of the fungus and habitat features at localized scales will ultimately lead to increased epidemiological knowledge of SFD, which could aid management and conservation efforts for imperiled species such as Massasaugas.
DNA barcoding : a practical tool for fundamental and applied biodiversity research

In the last ten years, 14 species of cetaceans and five species of pinnipeds stranded along the Atlantic coast of Brittany in the North West of France. All species included, an average of 150 animals strand each year in this area. Based on reports from the stranding network operating along this coast, the most common stranding events comprise six cetacean species (Delphinus delphis, Tursiops truncatus, Stenella coeruleoalba, Globicephala melas, Grampus griseus, Phocoena phocoena) and one pinniped species (Halichoerus grypus). Rare stranding events include deep-diving or exotic species, such as arctic seals. In this study, our aim was to determine the potential contribution of DNA barcoding to the monitoring of marine mammal biodiversity as performed by the stranding network. We sequenced more than 500 bp of the 5’ end of the mitochondrial COI gene of 89 animals of 15 different species (12 cetaceans, and three pinnipeds). Except for members of the Delphininae, all species were unambiguously discriminated on the basis of their COI sequences. We then applied DNA barcoding to identify some “undetermined” samples. With again the exception of the Delphininae, this was successful using the BOLD identification engine. For samples of the Delphininae, we sequenced a portion of the * These authors contributed equally to this work. ZooKeys 365: 5–24 (2013) doi: 10.3897/zookeys.365. 5873
Variasi Genetik Itik Bayang Berbasis Marka Mikrosatelit Pada Lokus AY287 dan Lokus AY283

West Sumatera Province has poultry genetic resource of local duck that potential in supply eggs and duck meat. Bayang duck was set by Indonesian Agricultural Ministry in 2012 as national livestock breeds in Indonesia. Microsatellite markers are widely used as a genetic identifier because of their abundant existence, co-dominant and high polymorphic. The purpose of this study was to determine the genetic diversity of Bayang ducks based on two microsatellite loci which include AY287 and AY283. DNA substances used in the study were blood samples from 24 Bayang duck in Pesisir Selatan Regency. The isolated DNA genom from 24 blood samples of Bayang duck could be detected by gel electrophoresis. Results showed that AY287 locus has 6 alleles; allele A (108 bp), allele B (142 bp), allele C (183 bp), allele D (227 bp), allele E (272 bp) and allele F (340 bp). Both allele E and F were specific genetic markers of Bayang duck. Alleles frequencies of the AY287 locus were as follow: allele C (26,93%), allele D (19,24%), allele A (15,38%), allele B (15,38%), allele E (15,38%) and allele F (7,69%). The AY283 locus has 6 alleles consisted of allele A (230 bp), allele B (320 bp), allele C (345 bp), allele D (390 bp), allele E (450 bp) and allele F (500 bp). Allele frequencies of this marker were allele B (20,51%), allele D (20,51%), allele E (20,51%), allele A (15,39%), allele C (15,39%), and allele F (7,69%), respectively. Our finding suggest that two microsatellite markers, AY287 and AY283, were polymorphic in Bayang duck population. Key words: Bayang duck, microsatellite, AY283, AY287