Miracle-dz/UniFAR-FTUs huggingface dataset:
The Interaction of Munc18-1 Helix 11 and 12 with the Central Region of the VAMP2 SNARE Motif Is Essential for SNARE Templating and Synaptic Transmission

Abstract Sec1/Munc18 proteins play a key role in initiating the assembly of N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes, the molecular fusion machinery. Employing comparative structure modeling, site specific crosslinking by single amino acid substitutions with the photoactivatable unnatural amino acid p-Benzoyl-phenylalanine (Bpa) and reconstituted vesicle docking/fusion assays, we mapped the binding interface between Munc18-1 and the neuronal v-SNARE VAMP2 with single amino acid resolution. Our results show that helices 11 and 12 of domain 3a in Munc18-1 interact with the VAMP2 SNARE motif covering the region from layers −4 to +5. Residue Q301 in helix 11 plays a pivotal role in VAMP2 binding and template complex formation. A VAMP2 binding deficient mutant, Munc18-1 Q301D, does not stimulate lipid mixing in a reconstituted fusion assay. The neuronal SNARE-organizer Munc13-1, which also binds VAMP2, does not bypass the requirement for the Munc18-1·VAMP2 interaction. Importantly, Munc18-1 Q301D expression in Munc18-1 deficient neurons severely reduces synaptic transmission, demonstrating the physiological significance of the Munc18-1·VAMP2 interaction.
Performance of Japanese quails fed diets with low-protein and isoleucine

Aiming to assess isoleucine levels in low protein diets for laying Japanese quails, 648 quails of 182 days of age were distributed in experimental block design with six treatments and six replicates of 18 birds each. Treatments consisted of a basal level corresponding to 0.672% isoleucine and supplemented with isoleucine to the levels of 0.816, 0.960; 1.104; 1.248%. The experimental diets were compared to a control diet containing 20% CP. The parameters studied were: performance, egg quality, total solids and nitrogen in the excreta. There was a linear increase only for isoleucine intake with increasing levels of isoleucine in the diets. The comparison of mean values of each combination of isoleucine levels for diets with 16% CP with the control with 20% CP showed that the intake of CP and isoleucine, egg weight, nitrogen excretion and yolk color were significantly affected. For Japanese quail fed diets with 16% CP, with isoleucine level at 0.672%, meets the requirements for obtaining satisfactory performance and egg quality and promoted a reduction in nitrogen excretion.
Age-related changes and circadian variations in peripheral levels of thyroid hormones in Murrah buffaloes

Abstract The aim of this study was to investigate the variations in plasma triiodothyronine (T3) and thyroxine (T4) with the advancement of age and to determine their circadian patterns in prepubertal and pubertal Murrah buffaloes. The variations in plasma T3 and T4 with the advancement of age were observed from day 1 to 24 months of age. Significant higher levels of T3 and T4 were observed after birth and a gradual decrease in their concentrations occurred until 15 days of age. The mean plasma T3 and T4 ranged between 1.26–3.79 and 60.7–166 ng/ml, respectively, during 1–30 days of age. During 1–24 months of age, the variations in plasma T3 did not differ (p > 0.05) with the advancement of age, whereas significant (p < 0.0001) changes were observed in plasma T4. The circadian patterns of T3 and T4 were evaluated in prepubertal Murrah buffaloes (n = 8) aged between 14 and 16 months. The mean plasma T3 and T4 ranged between 1.04–1.85 and 43.0–76.1 ng/ml, respectively. Significant (p > 0.0001) changes in the secretory pattern of T3 were observed, whereas the secretory pattern of T4 did not differ significantly (p > 0.05). In addition, the circadian patterns of T3 and T4 in pubertal buffaloes (n = 4) aged between 28 and 30 months were observed and compared to that of prepubertal group (n = 4). The prepubertal group showed significant (p < 0.001) higher plasma T3 concentrations over 24 h than the pubertal group.
DESENVOLVIMENTO DE ÁRVORES NATIVAS EM ENSAIOS DE ESPÉCIES. 4. CASTANHA-DO-BRASIL (Bertholletia excelsa Η. B. K.), DEZ ANOS APÓS O PLANTIO

Experimental plots of Bertholletia excelsa Η. Β. K. were implanted in 1980 at INPA's Experimental Station for Tropical Silviculture to study growth rates in terms of wood and nut production. The plantation was done on a clear-curted area, with 3.0 by 3 0 m spacing. Ten years later we have observed the following averages: dbh 13.9 cm and total heigth 15.41 m; maximum observed dbh and heigth were 21.7 cm and 23.0 m, respectively: basal area average per hectare and mean volume per hectare were 11.7098 m2 and 117.291 m3; mean survival of 69.44%; cylinder-shaped stem and complete absence of disease or pests. According to dbh average increment rate (t%) it was found a low increment at the age of six years, showing the necessity of thinning, not carryied out because it was just a case of growth trial plots. Up to now B. excelsa trees have showed very good natural pruning and adaptation for red-yellowish latossols.
Vegetation analysis of restored and natural mangrove forest in Sagar island, Sundarbans, east coast of India

Ecological conditions were similar in the restored and natural mangrove forests, though they differed in age and elevation. The restored forest experienced total diurnal inundation, but the natural forest was not fully inundated. Thus the former was dominated by Avicennia alba, Avicennia marina and Porteresia coarctata, while the latter was dominated by Excoecaria agallocha, Ceriops decandra, Acanthus ilicifolius and Derris trifoliata. Similarity and diversity for tree and shrub layers were low and the dominance-diversity curves approached geometric series.
IMMATURE LEBIA VIRIDIS SAY (COLEOPTERA: CARABIDAE): BIONOMICS, DESCRIPTIONS, AND COMPARISONS TO OTHER LEBIA SPECIES

In northern Florida, Lebia viridis Say is found in association with the chrysomelid, Alticafoliacea LeConte, larvae and adults of which feed on Evening Primrose (Oenothera spp.). Field observations from September 1987 through July 1988 indicate that L. viridis is a spring breeder and that the larvae are ectoparasitoids of A. foliacea pupae. Rearing of L. viridis in the laboratory on A. foliacea reveals three instars (two larval, one pupal) which are similar to the three instars of previously described Lebia spp. All instars of L. viridis are described and illustrated. Laboratory reared teneral adults are metallic blue in color and gradually change color to metallic green as they mature. Differences in structure and development distinguish larvae of L. (Lebia) viridis from those of L. (Lebia) scapularis Fourcroy larvae. Though carabid beetles are major predators in agricultural ecosystems (Thompson 1979), their larvae are difficult to observe, as most are subterranean and/or secretive, and are laborious to rear (Goulet 1979). Yet, because carabids make up a major component of agricultural ecosystems (Thompson 1979:209), it is paramount these difficulties be overcome to gain a better understanding of these larvae. As of 1979, only 258 of ca. 2,500 North American carabid species had described larvae (Thompson 1979). There is a particular paucity of knowledge of the larval life histories of the members of the genus Lebia Latreille, in which only larvae of one North American species have been described previously. The cosmopolitan genus Lebia is composed of ca. 450 species worldwide. This is the most diverse genus of the tribe Lebiini, which is composed of ca. 60 genera worldwide (Erwin and Sims 1984). The majority of adult Lebia are semiarboreal predators. The larvae, at least the ones known in this stage, are ectoparasitoids of the pupae of chrysomelid beetles. Of the 47 species in North America recognized by Madge (1967), only Lebia grandis Hentz, a parasitoid of the Colorado potato beetle (Leptinotarsa decemlineata Say), has a described larval development (Chaboussou 1939). Larval development has been described for two other Lebia spp. , both from Europe: L. scapularis Fourcroy feeding on Galerucella luteola Mull. (Silvestri 1904) and L. chlorocephala Hoffman on Chrysolina varians Schall. (Lindroth 1954). These three Lebia spp. are not closely related and have been placed in three separate subgenera via adult characteristics: L. (Loxopeza) grandis, L. (Lebia) scapularis, and L. (Lamprias)
Probing the Multiphase Interstellar Medium of the Dwarf Starbust Galaxy NGC 625 with FUSE Spectroscopy

We present new Far Ultraviolet Spectroscopic Explorer (FUSE ) spectroscopy of the dwarf starburst galaxy NGC 625. These observations probe multiple phases of the interstellar medium (ISM), including the coronal, ionized, neutral, and molecular gas. This nearby (D 1⁄4 3:9 0:2Mpc) system shows a clear detection of outflowing coronal gas as traced by O vi k1032 absorption. The centroid of the O vi profile is blueshifted with respect to the galaxy systemic velocity by 30 km s , suggesting a low-velocity outflow. The implied O vi velocity extent is found to be 100 20 km s , which is fully consistent with the detectedH i outflowvelocity found in radio synthesis observations. We detect multiple lines of diffuse H2 absorption from the ISM of NGC 625; this is one of only a few extragalactic systems with FUSE detections of H2 lines in the Lyman and Werner bands. We find a potential abundance offset between the neutral and nebular gas that exceeds the errors on the derived column densities. Since such an offset has been found in multiple dwarf galaxies, we discuss the implications of a lower-metallicity halo surrounding the central star-forming regions of dwarf galaxies. The apparent offset may be due to saturation of the observed O i line, and higher signal-to-noise ratio (S/N) observations are required to resolve this issue. Subject headinggs: galaxies: abundances — galaxies: dwarf — galaxies: individual (NGC 625) — galaxies: kinematics and dynamics — galaxies: starburst
Comparative tolerance and sensitive response of Indian mustard (Brassica juncea L. Czern and Coss) genotypes to high temperature stress.

Indian mustard (Brassica juncea L. Czern & Coss) is an important source of edible oil in India. This crop experiences substantial yield loss due to high temperature, especially at the seedling stage. Therefore, improving seedling stage heat tolerance in Indian mustard is an important breeding objective. In this study, 53 genotypes, including two checks (BPR-543-2 and RH-30), were evaluated for heat tolerance under heat stress (maximum temperature 40.1 °C at 0-10 cm depths on seeding date on September 26, 2012) and normal (maximum temperature 31.0 °C at 0-10 cm depth on seeding date on October 23, 2012) conditions at the research farm of ICARDirectorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan, India. Results indicate that most Indian mustard genotypes respond differently for eight physiological traits under normal and high temperature stress conditions. Among the 53 genotypes used for the study, BPR-349-9, Urvashi, BPR-541-2, BPR-605-40, Pusa Tarak (EJ9912-13), RGN-48, BPR-549-2, DRMR-729 and DRMR-1918 were identified as heat-tolerant at seedling stage with heat susceptibility index (S) and yield stability ratio (YS), ≤ 0.5 and > 80%, respectively. The relative water content showed significant negative correlation with excised-leaf water loss (r = -0.385**) under heat stress condition. The higher membrane stability index and high population survival might also have provided high temperature stress tolerance in genotypes DRMR-541-44 and RGN-48. The heat tolerant genotypes identified in this study could be included in future breeding programmes.
ANTIBACTERIAL ACTIVITY TESTING OF N-HEXANE FRACTION OF RED DRAGON (Hylocereus polyrhizus Britton & Rose) FRUIT PEEL ON Staphylococcus aureus ATCC 25923

Inappropiate antibiotic use was one of the main reason that caused pathogenic microorganism resistance, leads to ineffective treatment. One of those resistance bacteria is Staphylococcus aureus. The research for discovering new antibiotics can help with this issue. The peel of red dragon fruit (Hylocereus polyrhizus) is one of the plants that has antibacterial compounds. The aim of this research is to prove and determine the clear zone value of n-hexane fraction of red dragon fruit’s peel againts Staphylococcus aureus ATCC 2593. The peel was maserated with chloroform, then fractinated by n-hexane. Futhermore, the antibacterial properties of the fraction was tested using Disc Diffusion (Kirby-Bauer) methode with 20 and 40 mg/mL concentrations. Ampicillin used as control positive, and Dymetil sulfoxida (DMSO) used as control negative . Based on the phytochemical screening of the fraction, the n-hexane fraction of the dragon fruit’s peel contain terpenoid and alkaloid. Clear zones produced by 40 mg/mL is 12.80±1,69 mm and for 20 mg/mL is 11.17±1,11 mm.
The Effect of Different Doses of Blue Light on the Biometric Traits and Photosynthesis of Dill Plants

The supplementation of blue light to red light enhanced plant growth compared with the use of red alone. The aim of the study was to determine the effect of different doses of blue light on the biometric traits and photosynthesis of dill plants. The plants were grown in pots in a growth chamber. They were grown in red light (100 μmol m-2 s-1) and blue light (from 10 to 50 μmol m-2 s-1) in five combinations. Light emitting diode modules were the source of light. The plants were evaluated every 7 days during vegetation, for the first time - seven days after germination and later on the 14th, 21st and 28th day after germination. The share of blue light in the spectrum significantly influenced the biometric traits of the dill plants. It significantly inhibited the elongation growth of the plants and negatively affected the increase in fresh weight. A small dose of blue light (20%) had positive effect on the plants’ area. The research did not reveal a simple relationship between the amount of blue light and dry weight yield. The value of physiological indexes depended both on the combination and measurement time. The plants from the combination with 30% blue light were characterised by the greatest photosynthesis intensity. An effective share of blue light in the spectrum may range from 10 to 30% in relation to red light and depends on the plant’s development phase and on the result we want to achieve in the cultivation of plants.
Water-extractable organic compounds in different components of the litter layer of boreal coniferous forest soils along a climatic gradient

We investigated the concentrations and stocks of water-extractable carbon (WEC), nitrogen (WEN), phenolics and sugars in the main litter types (tree, dwarf shrub, moss) in boreal forests on two site types (mesic Norway spruce and sub-xeric Scots pine forests) in the south and north boreal climatic zones. WEC, sugar, and phenolic concentrations in the dwarf shrub and tree litter were higher in the north, whereas WEC and phenolic concentrations in the moss litter were higher in the south. Trees, dwarf shrubs, and mosses contributed to a varying extent to soil WEOM in the north and south boreal forests, the trees accounting for a major part of the WEOM in the south, but the understorey dwarf shrubs in the north. WEOM stocks were not predominantly determined by the concentrations of water-extractable compounds in each litter type, but instead by the quantitative proportions of the individual litter types.
Aging increases lateral but not local inhibition of orientation processing in primary visual cortex

Aging-related declines in vision can decrease well-being of the elder. Concerning early sensory changes as in the primary visual cortex, physiological and behavioral reports seem contradictory. Neurophysiological studies on orientation tuning properties suggested that neuronal changes might come from decreased cortical local inhibition. However, behavioral results either showed no clear deficits in orientation processing in the elder, or proposed stronger surround suppression. Through psychophysical experiments conducted on old and young human subjects combined with computational modeling, we resolved these discrepancies by demonstrating stronger lateral inhibition in the elder while neuronal orientation tuning widths, related to local inhibition, stayed globally intact across age. We confirmed this later finding by re-analyzing published neurophysiological data from rhesus monkeys, which showed no systematic tuning width changes, but instead a higher neuronal noise with aging. These results suggest a stronger lateral inhibition and mixed effects on local inhibition during aging, revealing a more complex picture of age-related effects in the central visual system than previously thought. Significance Statement Visual functions decline during aging, adversely affecting quality of life. Much of this dysfunction is probably mediated by disturbances in the balance between inhibition and excitation in the central visual system. It was proposed that the inhibitory function within the aging visual cortex might be modified, but huge discrepancies exist among different reports. Here we identify the specific inhibitory circuit change, which has not been clearly evaluated, by using behavioral measures, neural modeling and re-analysis of non-human primate electrophysiological data. We provide evidence that a stronger lateral inhibition and mixed effects on local inhibition during aging, revealing a more complex picture of age-related effects in the central visual system than previously thought. Author contributions ZCW and TT designed and analyzed behavioral experiments; ZCW performed experiments; ZCW and TT performed data analysis and neurophysiological re-analysis; YS and FY provided physiological data and discussed its re-analysis; TT performed modeling; ZCW, YFZ and TT provided project supervision and funds; ZCW and TT wrote the paper; all authors discussed and commented on the manuscript.
Effectiveness of curing in controlling fungal-induced storage rot in sweetpotato in Ghana

Fungal pathogens isolated from rotten sweetpotato root tubers were Aspergillus ochraceus, Botryodiplodia theobromae, Fusarium moniliforme, F. oxysporum and Rhizopus stolonifer. The thickness of the wound periderms in tubers cured in an incubator in polyethylene and in the sun were significantly different at 270.5, 232.2 and 17.6 μm respectively. The thickness of the normal periderm was 312.6 μm. Curing prolonged the period for which sweet potatoes can be stored without rotting. Incubator-cured roots stored for at least 18 weeks.
Seed Coat Structure and Histochemistry of Abelmoschus esculentus. Chalazal Region and Water Entry

The seed coat structure and histochemistry of Abelmoschus esculentus , an important species of the Malvaceae, were studied by bright-field, fluorescence and scanning electron microscopy. Our purpose was to correlate the morphological and histochemical features of the seed coat, mostly in the chalazal region, with the onset of water entry
Magnetic resonance imaging of retinal physiology and anatomy in mice

iii ACKNOWLEDGEMENTS I wish to thank my advisor Dr. Timothy Duong for supervision and guidance of my graduate studies and research; my thesis committee members Drs. Pardue for their time and suggestions with my proposal and defense. In addition I would like to thank Xiaoping Hu for financial support through his institutional training grant, Machelle Pardue for her advisement on fellowship proposals, and Shella Keilholz for acting as a " co-advisor " at Georgia Tech after Dr. Duong moved to the UT Health Science Center. I would also like to thank those who helped in the design and execution of experiments; Dr. Qiang Shen for much help showing how to operate the MR scanners, perform blood flow imaging, and in particular helping test and optimize arterial spin labeling and the cardiac arterial spin labeling method in mice; Dr. René Rentería for providing the diabetic Ins2 Akita mice and db/db mice as well as performing all visual tests on these mice; helpful discussions and help setting up and organizing experiments; Bryan De La Garza and Dr. Machelle Pardue showing me how to acquire and analyze retinal histology; Drs. Govind Nair and Yingxia Li for their suggestions and help with the initial development of retinal imaging in mice; Drs. Swati Rane and Xiaodong Zhang for help with operation of MR scanners and image analysis; and Robbie Champion for help working with and getting mice for the early studies.
Assessment of biodiversity and environmental quality using macrozoobenthos communities in the seagrass meadow (Gulf of Gdańsk, southern Baltic)

Abstract This study shows the macrozoobenthic biodiversity and the quality status of the Zostera marina meadow in the Gulf of Gdansk. To our knowledge, this is the first study focused on the assessment of environmental quality based on macrofauna occurring on such a small and specific habitat as a seagrass meadow. The meadow is dominated by Zostera marina, but also Zanichellia palustris and Potamogeton pectinatus are present. Compared to the soft bottom macrofauna in the southern Baltic, the biodiversity of macrozoobenthos is very high, which is reflected in 33 taxa observed during the whole research, while the mean number of taxa was 12. There were also some taxa found only on the bottom overgrown with vegetation, e.g. Idotea balthica or even taxa that are currently rarely observed in the Gulf of Gdansk, e.g. Gammarus locusta or Gammarus ineaquicauda. Nineteen percent of the stations were classified into the very good quality status and 50% into the good quality status, so the environmental status of this meadow based on the BQI index is assessed as good. Given these results, this is probably one of the best preserved meadows in the southern Baltic.
An investigation into the roles of Talpid3 and primary cilia in the developing brain

The developing brain requires an intricate network of signals to direct proliferation, differentiation and cell fate decisions. Primary cilia are vital organelles with an emerging role regulating several major signalling cascades, in particular the Hedgehog pathway. Talpid3 (Ta3) is 166.7 kD protein found at the distal tip of centrioles. It has been shown to interact with a number of key centriolar proteins and is essential for the formation of primary cilia. A recent mouse model has been designed to conditionally target the highly conserved coiled-coil domain of Ta3 using the Cre/loxP system. This project uncovers the role of Ta3 in the developing brain. It characterises in detail the phenotype of mice with conditional loss of Ta3 in the central nervous system using the Nestin-Cre deleter strain. Morphological and histological analyses demonstrate that significant defects occur postnatally with mice developing severe ataxia and hydrocephaly. Immunohistochemical techniques further characterise the distinct phenotypes of three key brain regions including the cerebellum, cortex and hippocampus. Ta3fl/fl;NesCre mutant mice exhibit defects in the proliferation, organisation, morphology and migration of both neuronal and glial cells. We have shown the mechanistic cause to be the result of widespread loss of primary cilia and a concomitant disruption in the transduction of the Hedgehog signalling pathway. The neural roles of Ta3 are explored further through the optimisation of an in vitro neurosphere system to culture postnatal hippocampal progenitors. The use of a tamoxifen inducible strain allows the timely recombination of Ta3 to study its role in a controlled environment. The cultured cells recapitulate many of the in vivo defects showing loss of primary cilia and reduced migration. Finally, characterisation of the phenotypes seen in the Ta3fl/fl;NesCre mice were shown to resemble neurological traits seen in human conditions with loss of Primary cilia, known as ‘human ciliopathies’. Through clinical collaboration this project demonstrated a human ciliopathy case of Joubert Syndrome with compound heterozygous mutations in TA3. This presents the Ta3fl/fl;NesCre mutant mice as a valuable model system to study a rare but clinically relevant condition.