Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of the Involvement of O-GlcNAc-modified Human RNA Polymerase II CTD in Transcription in Vitro and in Vivo*

Background: Modifications of the RNA polymerase II CTD are necessary for transcriptional regulation. Results: Perturbation of O-GlcNAc addition and removal showed transcription defects in vitro and in vivo. Conclusion: O-GlcNAc modification of the CTD functions in transcription initiation. Significance: These data provide an additional modification of the CTD that acts before the initiation of transcription. The RNA polymerase II C-terminal domain (CTD), which serves as a scaffold to recruit machinery involved in transcription, is modified post-translationally. Although the O-GlcNAc modification of RNA polymerase II CTD was documented in 1993, its functional significance remained obscure. We show that O-GlcNAc transferase (OGT) modified CTD serine residues 5 and 7. Drug inhibition of OGT and OGA (N-acetylglucosaminidase) blocked transcription during preinitiation complex assembly. Polymerase II and OGT co-immunoprecipitated, and OGT is a component of the preinitiation complex. OGT shRNA experiments showed that reduction of OGT causes a reduction in transcription and RNA polymerase II occupancy at several B-cell promoters. These data suggest that the cycling of O-GlcNAc on and off of polymerase II occurs during assembly of the preinitiation complex. Our results define unexpected roles for both the CTD and O-GlcNAc in the regulation of transcription initiation in higher eukaryotes.
Amyloid β (Aβ) Peptide Directly Activates Amylin-3 Receptor Subtype by Triggering Multiple Intracellular Signaling Pathways*

Background: Aβ and human amylin peptides share similar biophysical and neurotoxic properties. Results: Aβ directly activates amylin-3 receptor (AMY3) isoform and triggers multiple signaling pathways. Conclusion: Aβ actions are expressed via AMY3 receptors. Significance: AMY3 could serve as a therapeutic target for attenuating Aβ toxicity. The two age-prevalent diseases Alzheimer disease and type 2 diabetes mellitus share many common features including the deposition of amyloidogenic proteins, amyloid β protein (Aβ) and amylin (islet amyloid polypeptide), respectively. Recent evidence suggests that both Aβ and amylin may express their effects through the amylin receptor, although the precise mechanisms for this interaction at a cellular level are unknown. Here, we studied this by generating HEK293 cells with stable expression of an isoform of the amylin receptor family, amylin receptor-3 (AMY3). Aβ1–42 and human amylin (hAmylin) increase cytosolic cAMP and Ca2+, trigger multiple pathways involving the signal transduction mediators protein kinase A, MAPK, Akt, and cFos. Aβ1–42 and hAmylin also induce cell death during exposure for 24–48 h at low micromolar concentrations. In the presence of hAmylin, Aβ1–42 effects on HEK293-AMY3-expressing cells are occluded, suggesting a shared mechanism of action between the two peptides. Amylin receptor antagonist AC253 blocks increases in intracellular Ca2+, activation of protein kinase A, MAPK, Akt, cFos, and cell death, which occur upon AMY3 activation with hAmylin, Aβ1–42, or their co-application. Our data suggest that AMY3 plays an important role by serving as a receptor target for actions Aβ and thus may represent a novel therapeutic target for development of compounds to treat neurodegenerative conditions such as Alzheimer disease.
Whole genome sequencing identifies a novel occludin mutation in microcephaly with band‐like calcification and polymicrogyria that extends the phenotypic spectrum

Whole Genome Sequencing Identifies a Novel Occludin Mutation in Microcephaly With Band-Like Calcification and Polymicrogyria That Extends the Phenotypic Spectrum Mahmoud F. Elsaid, Hussein Kamel, Nader Chalhoub, Nahla Abdel Aziz, Khalid Ibrahim, Tawfeg Ben-Omran, Binu George, Eman Al-Dous, Yasmin Mohamoud, Joel A. Malek, M. Elizabeth Ross, and Alice Abdel Aleem* Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar Weill Cornell Medical College, Qatar Department of Radiology, Hamad Medical Corporation, Doha, Qatar Laboratories Neurogenetics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar Center for Neurogenetics, Brain & Mind Research Institute, Weill Cornell Medical College, New York National Research Center, Cairo, Egypt Genomics Core, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar Department of Neurology, Brain & Mind Research Institute, Weill Cornell Medical College, New York
GTP-binding Protein-like Domain of AGAP1 Is Protein Binding Site That Allosterically Regulates ArfGAP Protein Catalytic Activity*

Background: The AGAPs are a subtype of ArfGAPs with a G-protein like domain (GLD) postulated to function as an allosteric binding site. Results: The C terminus of RhoA binds to AGAP1 and stimulates GAP activity specifically for Arf1 and dependent on the GLD. Conclusion: AGAP1 is allosterically regulated by specific proteins that bind to the GLD. Significance: These results are the first example of protein-dependent allosteric regulation of an ArfGAP. AGAPs are a subtype of Arf GTPase-activating proteins (GAPs) with 11 members in humans. In addition to the Arf GAP domain, the proteins contain a G-protein-like domain (GLD) with homology to Ras superfamily proteins and a PH domain. AGAPs bind to clathrin adaptors, function in post Golgi membrane traffic, and have been implicated in glioblastoma. The regulation of AGAPs is largely unexplored. Other enzymes containing GTP binding domains are regulated by nucleotide binding. However, nucleotide binding to AGAPs has not been detected. Here, we found that neither nucleotides nor deleting the GLD of AGAP1 affected catalysis, which led us to hypothesize that the GLD is a protein binding site that regulates GAP activity. Two-hybrid screens identified RhoA, Rac1, and Cdc42 as potential binding partners. Coimmunoprecipitation confirmed that AGAP1 and AGAP2 can bind to RhoA. Binding was mediated by the C terminus of RhoA and was independent of nucleotide. RhoA and the C-terminal peptide from RhoA increased GAP activity specifically for the substrate Arf1. In contrast, a C-terminal peptide from Cdc42 neither bound nor activated AGAP1. Based on these results, we propose that AGAPs are allosterically regulated through protein binding to the GLD domain.
A model-driven approach to quantify migration patterns: individual, regional and yearly differences.

1. Animal migration has long intrigued scientists and wildlife managers alike, yet migratory species face increasing challenges because of habitat fragmentation, climate change and over-exploitation. Central to the understanding migratory species is the objective discrimination between migratory and nonmigratory individuals in a given population, quantifying the timing, duration and distance of migration and the ability to predict migratory movements. 2. Here, we propose a uniform statistical framework to (i) separate migration from other movement behaviours, (ii) quantify migration parameters without the need for arbitrary cut-off criteria and (iii) test predictability across individuals, time and space. 3. We first validated our novel approach by simulating data based on established theoretical movement patterns. We then formulated the expected shapes of squared displacement patterns as nonlinear models for a suite of movement behaviours to test the ability of our method to distinguish between migratory movement and other movement types. 4. We then tested our approached empirically using 108 wild Global Positioning System (GPS)-collared moose Alces alces in Scandinavia as a study system because they exhibit a wide range of movement behaviours, including resident, migrating and dispersing individuals, within the same population. Applying our approach showed that 87% and 67% of our Swedish and Norwegian subpopulations, respectively, can be classified as migratory. 5. Using nonlinear mixed effects models for all migratory individuals we showed that the distance, timing and duration of migration differed between the sexes and between years, with additional individual differences accounting for a large part of the variation in the distance of migration but not in the timing or duration. Overall, the model explained most of the variation (92%) and also had high predictive power for the same individuals over time (69%) as well as between study populations (74%). 6. The high predictive ability of the approach suggests that it can help increase our understanding of the drivers of migration and could provide key quantitative information for understanding and managing a broad range of migratory species.
Growth and reproductive costs of larval defence in the aposematic lepidopteran Pieris brassicae.

1. Utilization of plant secondary compounds for antipredator defence is common in immature herbivorous insects. Such defences may incur a cost to the animal, either in terms of survival, growth rate or in the reproductive success. 2. A common defence in lepidopterans is the regurgitation of semi-digested material containing the defensive compounds of the food plant, a defence which has led to gut specialization in this order. Regurgitation is often swift in response to cuticular stimulation and deters predators from consuming or parasitizing the larva. The loss of food and other gut material seems likely to impact on fitness, but evidence is lacking. 3. Here, we raised larvae of the common crop pest Pieris brassicae on commercial cabbage leaves, simulated predator attacks throughout the larval period, and measured life-history responses. 4. We found that the probability of survival to pupation decreased with increasing frequency of attacks, but this was because of regurgitation rather than the stimulation itself. There was a growth cost to the defence such that the more regurgitant that individuals produced over the growth period, the smaller they were at pupation. 5. The number of mature eggs in adult females was positively related to pupal mass, but this relationship was only found when individuals were not subjected to a high frequency of predator simulation. This suggests that there might be cryptic fitness costs to common defensive responses that are paid despite apparent growth rate being maintained. 6. Our results demonstrate a clear life-history cost of an antipredator defence in a model pest species and show that under certain conditions, such as high predation threat, the expected relationship between female body size and potential fecundity can be disrupted.
On observation distributions for state space models of population survey data.

1. State space models are starting to replace more simple time series models in analyses of temporal dynamics of populations that are not perfectly censused. By simultaneously modelling both the dynamics and the observations, consistent estimates of population dynamical parameters may be obtained. For many data sets, the distribution of observation errors is unknown and error models typically chosen in an ad-hoc manner. 2. To investigate the influence of the choice of observation error on inferences, we analyse the dynamics of a replicated time series of red kangaroo surveys using a state space model with linear state dynamics. Surveys were performed through aerial counts and Poisson, overdispersed Poisson, normal and log-normal distributions may all be adequate for modelling observation errors for the data. We fit each of these to the data and compare them using AIC. 3. The state space models were fitted with maximum likelihood methods using a recent importance sampling technique that relies on the Kalman filter. The method relaxes the assumption of Gaussian observation errors required by the basic Kalman filter. Matlab code for fitting linear state space models with Poisson observations is provided. 4. The ability of AIC to identify the correct observation model was investigated in a small simulation study. For the parameter values used in the study, without replicated observations, the correct observation distribution could sometimes be identified but model selection was prone to misclassification. On the other hand, when observations were replicated, the correct distribution could typically be identified. 5. Our results illustrate that inferences may differ markedly depending on the observation distributions used, suggesting that choosing an adequate observation model can be critical. Model selection and simulations show that for the models and parameter values in this study, a suitable observation model can typically be identified if observations are replicated. Model selection and replication of observations, therefore, provide a potential solution when the observation distribution is unknown.
Patterns and causes of demographic variation in a harvested moose population: evidence for the effects of climate and density-dependent drivers.

1. Better understanding of the mechanisms affecting demographic variation in ungulate populations is needed to support sustainable management of harvested populations. While studies of moose Alces alces L. populations have previously explored temporal variation in demographic processes, managers responsible for populations that span large heterogeneous landscapes would benefit from an understanding of how demography varies across biogeographical gradients in climate and other population drivers. Evidence of thresholds in population response to manageable and un-manageable drivers could aid resource managers in identifying limits to the magnitude of sustainable change. 2. Generalized additive models (GAMs) were used to evaluate the relative importance of population density, habitat abundance, summer and winter climatic conditions, primary production, and harvest intensity in explaining spatial variation in moose vital rates in Ontario, Canada. Tree regression was used to test for thresholds in the magnitudes of environmental predictor variables that significantly affected population vital rates. 3. Moose population growth rate was negatively related to moose density and positively related to the abundance of mixed deciduous habitat abundant in forage. Calf recruitment was negatively related to a later start of the growing season and calf harvest. The ratio of bulls to cows was related to male harvest and hunter access, and thresholds were evident in predictor variables for all vital rate models. 4. Findings indicate that the contributions of density-dependent and independent factors can vary depending on the scale of population process. The importance of density dependence and habitat supply to low-density ungulate populations was evident, and management strategies for ungulates may be improved by explicitly linking forest management and harvest. Findings emphasize the importance of considering summer climatic influences to ungulate populations, as recruitment in moose was more sensitive to the timing of vegetation green-up than winter severity. The efficacy of management decisions for harvested ungulates may require regional shifts in targets where populations span bioclimatic gradients. The use of GAMs in combination with recursive partitioning was demonstrated to be an informative analytical framework that captured nonlinear relationships common in natural processes and thresholds that are relevant to population management in diverse systems.
Production, purification and characterization of a rabbit recombinant IL-1 receptor antagonist

An in vivo colonic perfusion system in rats was used to examine the mechanism responsible for diarrhea in colitis induced experimentally by dextran sulfate. These rats had the same gross pathological and histopathological features as those in human ulcerative colitis. The rats also had severe hemorrhagic diarrhea and poor nutrition. The water and ion absorption as well as reduced osmolar pressure which were observed throughout the colon of colitis-rats were associated with a significant increase in colonic VIP content. These changes returned to control levels when a specific antagonist of VIP was administered. In control rats, the administration of VIP caused similar water and ion movement which was similar to that seen in colitis-rats
Warming effects on consumption and intraspecific interference competition depend on predator metabolism.

1. Model analyses show that the stability of population dynamics and food web persistence increase with the strength of interference competition. Despite this critical importance for community stability, little is known about how external factors such as the environmental temperature affect intraspecific interference competition. 2. We aimed to fill this void by studying the functional responses of two ground beetle species of different body size, Pterostichus melanarius and Poecilus versicolor. These functional response experiments were replicated across four predator densities and two temperatures to address the impact of temperature on intraspecific interference competition. 3. We generally expected that warming should increase the speed of movement, encounter rates and in consequence interference among predator individuals. In our experiment, this expectation was supported by the results obtained for the larger predator, P. melanarius, whereas the opposite pattern characterized the interference behaviour of the smaller predator P. versicolor. 4. These results suggest potentially nontrivial implications for the effects of environmental temperature on intraspecific interference competition, for which we propose an explanation based on the different sensitivity to warming of metabolic rates of both species. As expected, increasing temperature led to stronger interference competition of the larger species, P. melanarius, which exhibited a weaker increase in metabolic rate with increasing temperature. The stronger increase in the metabolic rate of the smaller predator, P. versicolor, had to be compensated by increasing searching activity for prey, which did not leave time for increasing interference. 5. Together, these results suggest that any generalization how interference competition responds to warming should also take the species' metabolic response to temperature increases into account.
Benefiting from a migratory prey: spatio-temporal patterns in allochthonous subsidization of an Arctic predator.

1. Flows of nutrients and energy across ecosystem boundaries have the potential to subsidize consumer populations and modify the dynamics of food webs, but how spatio-temporal variations in autochthonous and allochthonous resources affect consumers' subsidization remains largely unexplored. 2. We studied spatio-temporal patterns in the allochthonous subsidization of a predator living in a relatively simple ecosystem. We worked on Bylot Island (Nunavut, Canada), where arctic foxes (Vulpes lagopus L.) feed preferentially on lemmings (Lemmus trimucronatus and Dicrostonyx groenlandicus Traill), and alternatively on colonial greater snow geese (Anser caerulescens atlanticus L.). Geese migrate annually from their wintering grounds (where they feed on farmlands and marshes) to the Canadian Arctic, thus generating a strong flow of nutrients and energy across ecosystem boundaries. 3. We examined the influence of spatial variations in availability of geese on the diet of fox cubs (2003-2005) and on fox reproductive output (1996-2005) during different phases of the lemming cycle. 4. Using stable isotope analysis and a simple statistical routine developed to analyse the outputs of a multisource mixing model (SIAR), we showed that the contribution of geese to the diet of arctic fox cubs decreased with distance from the goose colony. 5. The probability that a den was used for reproduction by foxes decreased with distance from the subsidized goose colony and increased with lemming abundance. When lemmings were highly abundant, the effect of distance from the colony disappeared. The goose colony thus generated a spatial patterning of reproduction probability of foxes, while the lemming cycle generated a strong temporal variation of reproduction probability of foxes. 6. This study shows how the input of energy owing to the large-scale migration of prey affects the functional and reproductive responses of an opportunistic consumer, and how this input is spatially and temporally modulated through the foraging behaviour of the consumer. Thus, perspectives of both landscape and foraging ecology are needed to fully resolve the effects of subsidies on animal demographic processes and population dynamics.
Photophysical properties of cinchona organocatalysts in organic solvents

The photophysical properties of cinchona organocatalysts 1 (dehydroquinidine) and 2 (9-benzylcupreidine) in several organic solvents have been studied by means of absorption and fluorescence spectroscopy. In addition to a locally excited (LE) state emission near 360 nm for both compounds, broad emission bands were observed at longer wavelengths. For 1, the long-wavelength emission bands are pronounced in polar solvents, and their appearance is accompanied by a strong reduction of the LE emission. Electron transfer from the quinuclidine amino group to the locally excited quinoline ring is a likely mechanism that accounts for these observations. For 2, on the other hand, the long-wavelength emission is relatively strong even in nonpolar solvents. Protonation of the quinuclidine amino group by a strong acid in acetonitrile solution leads to an increase of the LE emission at the expense of the long wavelength bands, both for 1 and 2. Upon addition of water to 1 and 2 in acetonitrile, however, the emission spe.
Crystal Structure of Elongator Subcomplex Elp4–6*

Background: Elongator is a multiprotein complex that exhibits acetyltransferase activity. Results: In the subcomplex Elp4–6, Elp6 acts as a bridge to assemble Elp4 and Elp5, and each subunit adopts a similar RecA-ATPase-like fold. Conclusion: Subcomplex Elp4–6 forms a hexameric ring-shaped structure that is important for histone H3 binding. Significance: This finding may shed light on holo-Elongator complex assembly and its substrate recognition. Elongator is a multiprotein complex composed of two subcomplexes, Elp1–3 and Elp4–6. Elongator is highly conserved between yeast and humans and plays an important role in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. Here, we determined the crystal structure of the Elp4–6 subcomplex of yeast. The overall structure of Elp4–6 revealed that Elp6 acts as a bridge to assemble Elp4 and Elp5. Detailed structural and sequence analyses revealed that each subunit in the Elp4–6 subcomplex forms a RecA-ATPase-like fold, although it lacks the key sequence signature of ATPases. Site-directed mutagenesis and biochemical analyses indicated that the Elp4–6 subcomplex can assemble into a hexameric ring-shaped structure in vitro and in vivo. Furthermore, GST pulldown assays showed that the ring-shaped assembly of the Elp4–6 subcomplex is important for its specific histone H3 binding. Our results may shed light on the substrate recognition and assembly of the holo-Elongator complex.