Miracle-dz/UniFAR-FTUs huggingface dataset:
MECHANISMS OF VESICULAR MONOAMINE TRANSPORTER-2 DEGRADATION

The vesicular monoamine transporter-2 (VMAT2) packages monoamines into synaptic vesicles in the central nervous system. Not only vital for monoaminergic neurotransmission, VMAT2 protects neurons from cytosolic dopamine-related toxicity by sequestering dopamine into vesicles. This dissertation research is focused on determining the basic mechanisms of VMAT2 degradation—an unexplored aspect of VMAT2 regulation. The processes of protein synthesis and degradation balance to maintain proteostasis. As VMAT2 availability and function directly impact monoamine neurotransmission, its degradation is an important aspect of VMAT2 maintenance to study. While it has been proposed that VMAT2 is degraded by the lysosome, an acidic membrane-bound organelle, there is no direct evidence demonstrating this. In a PC12 cell model system stably expressing VMAT2-GFP, pharmacological tools were used to determine the impact of inhibiting pieces of cellular degradation machinery (the lysosome or the 26S proteasome) on VMAT2. Both mature and immature forms of VMAT2 accumulated following inhibition of the proteasome, but not the lysosome. In addition, at least a portion of the accumulated VMAT2 following proteasomal inhibition appears to be K48-linked polyubiquitinated—a post-translational modification associated with proteasomal degradation. Immature VMAT2 also accumulated following inhibition of endoplasmic reticulum-associated degradation (ERAD), a proteasome-dependent quality control mechanism for misfolded or damaged proteins undergoing processing in the ER. Demonstrated with immunocytochemistry and confocal imaging, the proportion of VMAT2 overlapping with an ER marker increased following proteasomal inhibition. These results indicate that immature VMAT2 is likely subject to ERAD as it undergoes processing in the ER. Unexpectedly, mature VMAT2 accumulated following proteasomal, but not lysosomal inhibition. While this result could be due to secondary effects of proteasomal inhibition or changes in VMAT2 synthesis, it is also possible that mature VMAT2 can be degraded by the proteasome. This would be a unique finding, as glycosylated, transmembrane proteins, such as VMAT2, must overcome a large energy barrier for retrotranslocation from a membrane. As these experiments were done under basal conditions, the results don’t exclude a role for lysosomal degradation under other circumstances. For example, there may be multiple pathways of VMAT2 degradation: proteasomal-dependent under basal conditions and lysosomal-dependent under conditions of synaptic activity.
Efecto de la distancia de siembra en variables morfoagronómicas de moringa (Moringa oleifera).

The aim of this study was to determine the effect of ve planting distances in morphoagronomic variables of Moringa oleifera Lam. The work was conducted in areas of the Agricultural Research Institute “Jorge Dimitrov”, the municipality Bayamo, Granma province, Cuba, on the period from November to February of 2014-2015, respectively. A design of randomized blocks with three replications was used. Five treatments were evaluated with consistent planting distances; the cut was made at 10 cm above the oor every fortnight. Signi cant effects (p<0.05) between treatments, plant height and number of shoots/plants where planting distances signi cantly increased the number of bolters/plants (p<0.05) were found with averages of ve and three in the major and minor planting distance respectively. Planting distances used in uenced the morphoagronomic indicators of Moringa oleifera vc. Super Genium. Biomass yield decreased signi cantly (p<0.05) with increasing distance from planting 7 t/ha with the 10 cm x 10 cm, up to 2 t/ha with 20 cm x 20 cm treatment.
mlh3 separation of function and endonuclease defective mutants display an unexpected effect on meiotic recombination outcomes

Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in baker’s yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each separation of function class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+) displayed wild-type endonuclease activities in vitro. Msh2-Msh3, an MSH complex that acts with Mlh1-Mlh3 in MMR, stimulated the endonuclease activity of Mlh1-mlh3-32 but not Mlh1-mlh3-45, suggesting that Mlh1-mlh3-45 is defective in MSH interactions. Whole genome recombination maps were constructed for two mlh3 mutants with opposite separation of function phenotypes, and an endonuclease defective mutant. Unexpectedly, all three showed increases in the number of non-crossover events that were not observed in mlh3Δ. Our observations provide a structure-function map for Mlh3 that reveals the importance of protein-protein interactions in regulating Mlh1-Mlh3’s enzymatic activity. They also illustrate how defective meiotic components can alter the fate of meiotic recombination intermediates, providing new insights for how meiotic recombination pathways are regulated. Author Summary During meiosis, diploid germ cells that become eggs or sperm undergo a single round of DNA replication followed by two consecutive chromosomal divisions. The segregation of chromosomes at the first meiotic division is dependent in most organisms on at least one genetic exchange, or crossover event, between chromosome homologs. Homologs that do not receive a crossover frequently undergo non-disjunction at the first meiotic division, yielding gametes that lack chromosomes or contain additional copies. Such events have been linked to human disease and infertility. Recent studies suggest that the Mlh1-Mlh3 complex is an endonuclease that resolves recombination intermediates into crossovers. Interestingly, this complex also acts as a matchmaker in DNA mismatch repair (MMR) to remove DNA replication errors. How does one complex act in two different processes? We investigated this question by performing a mutational analysis of the baker’s yeast Mlh3 protein. Five mutations were identified that disrupted MMR but not crossing over, and one mutation disrupted crossing over while maintaining MMR. Using a combination of biochemical and genetic analyses to further characterize these mutants we illustrate the importance of protein-protein interactions for Mlh1-Mlh3’s activity. Importantly, we illustrate how defective meiotic components can alter the outcome of meiotic recombination events. They also provide new insights in our understanding of the basis of infertility syndromes.
Phylogenetic measures of biodiversity uncover pteridophyte centres of diversity and hotspots in Tuscany

Abstract Biodiversity studies traditionally use species as their analysis unit. However, observed biodiversity is not necessarily an indicator of significant biodiversity and therefore, should not be used alone, particularly when the results will be employed for conservation planning. Here, we examine pteridophyte diversity in Tuscany using 4668 geo-referenced pteridophyte records stored in Wikiplantbase #Toscana and calculating standard richness measures and phylogenetic indices; in addition, we assessed the environmental predictors of each diversity metric. Finally, we identified which areas hosting significantly high diversity are not adequately covered by protected areas or intersected by human activities. Although considerable diversity is distributed along Tuscany within areas traditionally recognised as biodiversity hotspots, important areas of diversity are identified only after the application of randomisation tests and through the phylogenetic metrics. Topographic ruggedness resulted the single most important variable predicting high value of all indices; temperature seasonality and temperature continentality resulted the secondary explanatory variables with a significant negative effect on most diversity indices.
Combining ability studies in maize (Zea mays L.) for yield and its attributing traits using Griffing's diallel approach

Studies on combining ability and heterosis were carried out at Agricultural Research Farm, PAJANCOA & RI, Karaikal, during kharif 2013 for thirteen agronomic yield traits viz . , 100 grain weight, grain yield for 30 single cross hybrids developed using 6 x 6 full diallel method. The combining ability analysis revealed the presence of higher magnitude of SCA than GCA variance for all characters under study. The ratio of additive to dominance variance was lower than unity for all traits, indicating higher non additive variance than additive variance. Among the 6 parents, inbred line namely UMI 213 was found to be the best parent for grain yield, however, The estimates of sca effects has resulted in the identification of the following hybrids viz . , UMI 66 x UMI 112, UMI 112 x UMI 213 and UMI 122 x UMI 133 as best ones, since these above hybrids registered significant and favourable sca effects for majority of the traits including grain yield per plant.
A taxonomic reassessment of Ichthyosaurus communis and I. intermedius and a revised diagnosis for the genus

Ichthyosaurus communis De la Beche & Conybeare, 1821 and I. intermedius Conybeare, 1822 have been considered synonymous by some researchers, but distinct species by others. The distinction between the two species was originally based on tooth morphology, which has been shown to vary ontogenetically as well as within an individual. Subsequent literature of the nineteenth century did not propose adequate diagnostic features to distinguish the two species. In addition, illustrations suggest that both species were confused with I. breviceps, which was defined over 50 years later. The type specimens of both species are missing, making the problem unresolvable. However, a neotype was designated for I. communis to retain the widely used species name and to stabilize the taxonomy. The species can be recognized by a symmetric, triangular maxilla with long processes and a large, broad, triradiate lacrimal, as well as a unique combination of other characters. The neotype shares numerous features with the I. intermedius ‘type figure’, including the morphologies of the maxilla, prefrontal, lacrimal, jugal and postorbital, such that the two are nearly indistinguishable. Thus I. intermedius must be considered a synonym of I. communis. Ichthyosaurus communis can be identified from the Lyme Regis-Charmouth coast, west Dorset; the ? Whitby coast of Yorkshire; and probably from Street, Somerset. The stratigraphical range of I. communis is at least lower Hettangian to lower Sinemurian.
Swimming behaviour can maintain localised jellyfish (Chironex fleckeri: Cubozoa) populations

The potentially lethal Chironex fleckeri (Class Cubozoa) inhabits estuarine and nearshore coastal waters in the western Pacific. The spatial scales of connectivity between C. fleckeri populations are poorly understood. Biophysical modelling of Port Musgrave, a 17 × 21 km shallow bay in tropical Australia, was used to investigate the potential for connections between populations separated by medium (10s of km) to small (100s of m) spatial scales. We measured the swimming speeds and orientations of medusae ranging in size from 4 to 12 cm interpedalial distance (the distance between two adjacent corners on the bell of the medusae). Medusae swam longshore at average speeds (5.3 ± 3.5 cm s-1 SD) that exceeded the local average current speeds (2.7 ± 2.4 cm s-1). These and other ecological data were used to parameterise the biophysical model. No medusae modelled as passive were advected from the bay in 14 d; <2.5% of swimming medusae were lost. When medusae swam directionally, a high percentage aggregated in shallow waters within 10s to 100s of m of the seeding locations. Newly metamorphosed medusae are likely to be retained in the bay through a combination of ‘sticky water’ (i.e. water with reduced current speeds, reduced through diversion around obstacles) in shallow complex habitats and favourable currents. C. fleckeri are vulnerable to low salinities; however, modelling a strong flood revealed higher salinity refugia in shallow water. As there was high retention within the system, we conclude that populations of C. fleckeri inhabiting shallow, semi-enclosed estuarine bays probably represent stocks. Within these stocks, swimming and favourable currents may minimise connectivity and maintain populations at multiple spatial scales.
Investigation of Atypical Binding Behaviours of the SH3 Domain of the Yeast Protein, Fus1p

The yeast Fus1p SH3 domain recognizes non-PXXP motif targets. This is contrary to most SH3 domains, which recognize PXXP-containing sequences. In this thesis, I characterized atypical binding of the Fus1p SH3 domain and provide insight into atypical SH3 domain interactions. I demonstrated that the Fus1p SH3 domain binds R(S/T)(S/T)SL-containing peptides derived from yeast proteins, Bnr1p and Ste5p. Through mutagenesis studies and comparisons to other SH3 domains, I showed that the Fus1p SH3 domain utilizes a portion of the same binding surface as typical SH3 domains. However, the PXXP-binding surface is debilitated in the WT domain by the substitution of unusual residues at three key conserved positions. By replacing these residues, I created a version of the Fus1p SH3 domain that binds a PXXPcontaining peptide with extremely high affinity. Based on my data and analysis, I clearly delineated two distinct surfaces comprising the typical SH3 domain binding interface, and show that one of these surfaces is the primary mediator of almost every “non-canonical” SH3 domain-mediated interaction.
Impairment of zebrafish reproduction upon exposure to TDCPP

TDCPP is one of the most common organophosphate flame retardant, which has been widely used in many products. It has been detected in the environment and biota; however, its potential affect to the wildlife and human health remains largely unknown. In this study, we aimed to investigate the effect of long-term exposure to TDCPP on fish reproduction. Zebrafish eggs were treated with various concentration of TDCPP (0, 1, 10 and 100 μg/L) from 1 day post-fertilization (hpf) to 6 months. The fecundity of female fish was significantly decreased as indicated by reduced embryos production. The egg quality was decreased and the malformation rates were increased in the F1 generation. Taken together, long-term exposure to TDCPP affects the reproduction of zebrafish.
Description and redescription of Transeius species (Acari: Phytoseiidae) from arborescent ferns from Brazilian Mixed Ombrophylus Forest

ABSTRACT One new species of genus Transeius is described from arborescent ferns from Brazilian Mixed Ombrophylus Forest, Rio Grande do Sul State, Brazil. These new species differ from other species by having smaller spermathecae and differences in the setae Z4 Z5 and s4 as well as in the macrosetae. The male of Transeius kroeffis Gonçalves & Ferla is described and the female redescribed to account for a new hypothesis on the j-series setae. A dichotomous key for the Brazilian Transeius species is provided.
Prevalence of Shiga Toxin-Producing Genes in Escherichia Coli Isolated From Patients with Urinary Tract Infections in Khorramabad

Background and Objectives: Shiga toxins (verotoxin) is one of the most important bacterial toxin produced by the Escherichia coli (O157: H7 and nonO157: H7), and is responsible for various diseases in humans and animals. Hemolytic uremic syndrome (HUS) is serious human diseases that occur because of these toxins. There is no comprehensive information in this regard, here will studied the prevalence of these genes among the Ecoli isolated from urine samples in Khorramabad. Material and Method: The study is based on 146 Escherichia coli isolates of Patients with symptoms of urinary tract infection referred to clinical laboratories in Khorramabad during 90-1389. We used we identified the isolates by biochemical tests . The Multiplex PCR Multiplex PCR method were used to presence of genes. Results: A total of 117 (13/80%) of the women and 29 (86/19) of the men and none of them carried both stx1and stx2. Conclusion: Shiga toxin-producing E. coli isn't responsible for urinary tract infection in KhorramabadAlthough the frequency of these genes in urine samples is low, but evaluation of the other human and animal samples in different parts of the country is essential.
Environment, Management, and Genetic Contributions to Maize Kernel Hardness and Grain Yield

Dry milling performance of maize (Zea mays L.) is directly related to kernel hardness. This study assessed the contribution of maize hybrid and crop growing condition on kernel hardness and grain yield. Three hybrids that fully explore the available genetic variability for kernel hardness were planted at different environments across the Argentinean cropping area. At each environment, early and late planting dates and supplemental fertilization were evaluated. Kernel coarse-to-fine ratio was used as an indicator of kernel hardness. Coarse-to-fine ratio ranged from 2.0 to 7.0 g g−1, grain yield ranged from 494 to 1391 g m−2, and both were affected by hybrid and growing conditions. Hybrid ranking was stable across growing conditions; however, differences among hybrids in kernel coarse-to-fine ratio and grain yield increased when growing condition favored kernel hardness and grain yield. Growing condition explained >60% of total variability in coarseto-fine ratio and grain yield. Fertilization management had significant but small influence on assessed variables. In contrast, the interaction between planting date and environment was the major determinant of kernel coarse-to-fine ratio and grain yield. Delayed planting consistently reduced kernel hardness at high-latitude locations. Potential photosynthetic source during maize reproductive period explained 37% of the variation in kernel coarse-to-fine ratio. Environment and agronomic management should be considered together with the hybrid in the design of maize production strategies oriented to end-use quality. A. Cerrudo, D. Martinez, N.G. Izquierdo, and F.H. Andrade, Facultad de Ciencias Agrarias, Univ. Nacional de Mar del Plata (FCA, UNMdP), Argentina; A. Cerrudo, A.G. Cirilo, L. Reinoso, O. Valentinuz, and F.H. Andrade, Instituto Nacional de Tecnología Agropecuaria (INTA), Argentina; N.G. Izquierdo, M.P. Laserna, and F.H. Andrade, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; L. Reinoso, Dep. de Ciencias Exactas, Naturales y de Ingeniería, Univ. Nacional de Río Negro, Argentina; C. Balbi, Facultad de Ciencias Agrarias, Univ. Nacional del Noreste, Corrientes, Argentina. Received 14 Dec. 2016. Accepted 20 June 2017. *Corresponding author (cerrudo. anibal@inta.gob.ar). Assigned to Associate Editor Jeffrey Coulter. Abbreviations: IPAR, incident photosynthetic active radiation; RUE, radiation use efficiency. Published in Crop Sci. 57:2788–2798 (2017). doi: 10.2135/cropsci2016.12.0997 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. Published online August 17, 2017
Preliminary analysis of age, growth, and reproduction of Coney (Cephalopholis fulva) at Bermuda

Groupers have historically been an important component of the Bermuda fishery. The coney (Cephalopholis fulva) comprised almost 50% of the total landed weight of all grouper species in Bermuda from 1991 – 2003. In light of this significant contribution to fishery landings and because little is known about the fishery biology of the coney, a study was initiated in January 2000. One of the principal components of this study was to examine age and growth. Opaque rings on polished transverse sections of sagittal otoliths were used to estimate age. Fish were collected by hook and line from several locations on the Bermuda reef platform. Fork lengths of conies sampled ranged from 151 mm to 384 mm. Age estimates, determined for 997 specimens, ranged from 2 to 28 years with wide variability in the length-at-age. There was a significant positive correlation between otolith weight (OW) and age estimates which will enable the use of OW as a proxy for age of conies in future stock assessments. The other important aspect of the study was to characterize the sexual pattern and reproductive biology of the coney. Gonads were examined histologically to confirm sex and reproductive condition. The results confirm protogynous hermaphroditism in this species. Of the 998 fish sexed, 46.1% were female, 40.1% were male and 13.8% were transitional fish. There was considerable overlap in the length distributions of males (mean length 256 mm FL ± 28 mm SD), females (mean length 232 mm FL ± 34 mm SD) and transitionals (mean length 241 mm FL ± 30 mm SD) and the overall sex ratio was female biased (1.15F:1M). The reproductive season was from April to July inclusive with peak spawning occurring in June.
A global meta‐analysis of exotic versus native leaf decay in stream ecosystems

Streams are reliant on streamside plants for allochthonous inputs that form the base of the stream food web. The impact of exotic leaves on stream ecosystems has been investigated regionally, but not assessed globally. In this study, we conducted a global meta-analysis contrasting native and exotic aquatic litter decay. We used a linear mixed effects model to identify how the site-specific factors and experimental treatments of latitude, temperature, pH, conductivity and the exclusion of invertebrates (via mesh size) cause relative differences in exotic and native decay rates. Subsequently, we assessed whether differences in native and exotic litter decay rates were driven by the intrinsic factors of leaf litter quality. We found that overall leaf litter decay rates were similar for native and exotic leaves on a global scale. However, we also found that exotic leaves decayed faster than native leaves at higher stream temperatures and in larger mesh sizes (allowing macroinvertebrate access); yet, those differences disappeared at lower temperatures and in finer mesh sizes which excluded macroinvertebrates. Post hoc analysis of leaf quality suggested that differences between higher native and lower exotic leaf C:N ratios might explain differences in decomposition rates observed at high temperature, and differences between lower native and higher exotic leaf C:P ratios associated with differences in decomposition rates observed at coarse mesh sizes. Our study suggests that exotic leaf litter is likely to have the most impact in high-temperature stream ecosystems and that the nature of the impact is potentially related to the C:N ratio differences between native and exotic leaves. This might indicate that higher temperature stream ecosystems are more vulnerable to changes in litter decay rates due to invasion by exotic plant species than lower temperature stream ecosystems, and should be monitored accordingly. We recommend that future leaf litter decay studies include stream discharge measurements and leaf litter quality information so that both intrinsic and extrinsic factors that impact litter decay can be fully accounted for when assessing the factors that drive differences in leaf litter decay rates.