Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 gag-pol mRNA localization regulates the site of virion assembly

HIV-1 full-length, unspliced genomic RNAs (gRNAs) serve both as mRNAs encoding the Gag and Gag-Pol capsid proteins as well as the genetic material packaged by Gag into virions that assemble at the plasma membrane (PM). Whether localized Gag synthesis contributes to assembly at the PM is unknown. Here we show that artificially tethering gRNAs or surrogate gag-pol mRNAs to non-PM membranes or the actin cytoskeleton can markedly affect Gag’s distribution in the cytoplasm, causing aberrant subcellular sites of assembly and severe reductions to virus particle output. Only gag-pol mRNAs competent for translation were capable of altering Gag’s distribution within the cell, and the activity mapped to two cis-acting RNA regulatory elements; the 5’ packaging signal (Psi) bound by Gag and, unexpectedly, the Rev response element (RRE) that regulates the nuclear export of gRNAs and other intron-retaining viral RNAs. Taken together, our results suggest a model wherein localized translation of gRNAs at the PM helps to compartmentalize Gag-gRNA interactions, thereby promoting efficient genome encapsidation. AUTHOR SUMMARY The spatial distribution of messenger RNAs (mRNAs) within the cytoplasm can be a crucial determinant of gene expression. Here we provide evidence that a devastating viral pathogen, human immunodeficiency virus type 1 (HIV-1), exploits localized translation to favor the formation of infectious, transmissible virions at the surface of infected cells. Artificially tethering viral mRNAs encoding the Gag and Gag-Pol capsid proteins (gag-pol mRNAs) to alternative regions of the cell such as cytoplasmic vesicles or the actin cytoskeletion markedly alters Gag subcellular distribution, perturbs sites of assembly, and reduces virus particle production. These and additional findings suggest a model for HIV-1 assembly wherein localized Gag/Gag-Pol translation coupled to confined interactions between Gag and viral genomes ensures infectious virion production at the right place and the right time. Perturbing HIV-1 mRNA subcellular localization could represent a novel antiviral strategy.
Ecological speciation in Neochlamisus bebbianae leaf beetles: The role of postmating isolation and the genetic basis of host use traits

Ecological speciation is the promotion of reproductive isolation via the divergent adaptation of populations to alternative environments. A prediction peculiar to ecological speciation is that hybrids between such populations should be poorly adapted to parental environments, yielding reduced fitness and postmating isolation. However, F1 analyses alone cannot demonstrate that ecological (“extrinsic”) factors contribute to such isolation. Rather, this requires documenting a ‘switch’ in the relative fitnesses of reciprocal backcrosses between environments. Specifically, each backcross should exhibit higher fitness in the environment of its pure parent, with which it shares the most genes – including environment-specific ones. By contrast, because genetic proportions are expected to be similar for all backcrosses (~3⁄4 from one parental type, ~1⁄4 from the other), the more general genetic incompatibilities responsible for “intrinsic” isolation predict no such environment-specific fitness-switches. Thus, although intrinsic isolation may contribute to the fitness reduction and variation underlying such patterns, it offers an insufficient explanation for them. Here, we present a 1 Previously published research article: Egan, S.P. & D.J. Funk. 2009. Ecologically dependent postmating isolation between sympatric host forms of Neochlamisus bebbianae leaf beetles. Proceedings of the National Academy of Sciences 106:19426-19431.
Functional Context Affects Scene Processing

Rapid visual perception is often viewed as a bottom-up process. Category-preferred neural regions are often characterized as automatic, default processing mechanisms for visual inputs of their categorical preference. To explore the sensitivity of such regions to top-down information, we examined three scene-preferring brain regions, the occipital place area (OPA), the parahippocampal place area (PPA), and the retrosplenial complex (RSC), and tested whether the processing of outdoor scenes is influenced by the functional contexts in which they are seen. Context was manipulated by presenting real-world landscape images as if being viewed through a window or within a picture frame; manipulations that do not affect scene content but do affect one’s functional knowledge regarding the scene. This manipulation influences neural scene processing (as measured by fMRI): the OPA and PPA exhibited greater neural activity when participants viewed images as if through a window as compared to within a picture frame, while the RSC did not show this difference. In a separate behavioral experiment, functional context affected scene memory in predictable directions (boundary extension). Our interpretation is that the window context denotes three-dimensionality, therefore rendering the perceptual experience of viewing landscapes as more realistic. Conversely, the frame context denotes a two-dimensional image. As such, more spatially-biased scene representations in the OPA and the PPA are influenced by differences in top-down, perceptual expectations generated from context. In contrast, more semantically-biased scene representations in the RSC are likely to be less affected by top-down signals that carry information about the physical layout of a scene.
Kidney research

Kidney research has been one major focus of publications of recent articles published in Acta physiologica. A number of articles deal with the elucidation of kidney disease models 1-12 and the role of oxygen regulation in the kidney 13-16 . This contribution focusses on articles that deal with kidney disease models and in the second part on articles that are related to the topic hypoxia and oxygen regulation.
AN ANALYSIS OF THE COMPONENTS OF CHAOBORUS

We formulated a model for Chaoborus predation on zooplankton and analyzed its various components for fourth-instar Chaoborus americanus and three prey species (Daphnia pulex, Bosmina longirostris, and Diaptomus pallidus). This model is based upon the encounter rates between predator and prey, the probability of a first strike by Chaoborus, and the probability of ingestion given a first strike. This latter probability is a function of the strike efficiency, contact efficiency, and second- strike probability of the predator with each prey. The strike volume of Chaoborus was variable in both size and shape for the different prey species. In each case, however, it could be closely approximated by a cylinder. This strike volume was largest for Daphnia and smallest for Bosmina. The strike efficiency of Chaoborus (probability that a strike will result in a contact) was not significantly different for the three prey types, indicating that the different evasion behaviors of the prey do not influence this parameter. The contact efficiency (prob- ability that a contact will result in a capture) on Daphnia was significantly lower than for the other prey; this is a function of the differing sizes and shapes of the prey. Second-strike probability (probability that if a prey is initially missed by a Chaoborus strike, it will remain in the strike volume and be attacked again) was significantly different for each of the three prey species tested, with Bosmina > Daphnia > Diaptomus. This is mainly the result of the different evasion behaviors of the prey. Our model predicts that Chaoborus is equally efficient at capturing each prey once a first strike occurs. Differential vulnerabilities of these prey to Chaoborus predation are therefore the result of differing encounter rates, which are influenced by both the swimming speeds of the prey and the strike volume of the predator.
Characterisation of biofilm associated with bacterial vaginosis

Bacterial vaginosis, a condition defined by increased vaginal discharge without significant inflammation, is characterised by a change in the bacterial composition of the vagina. Lactobacillus spp. , associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which A. vaginae is part of a G. vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. Adapted from: Hardy L, Jespers V, Dahchour N, Mwambarangwe L, Musengamana V, Vaneechoutte M and Crucitti T. Unravelling the Bacterial Vaginosis-Associated Biofilm: a Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes. PLoS ONE 10(8): e0136658 (authentic paper in appendix).
Grassland invasion by non-native grass species: Ecological issues of multiple species at multiple trophic levels

Many invasive species of the southern and central Great Plains native grasslands were introduced to reduce soil erosion or increase forage production on marginal grasslands. Recent studies have indicated arbuscular mycorrhizal (AM) fungi play an important role in restoration success following invasive plant species eradication. We conducted two greenhouse studies: the first assessed mycorrhizal dependence of three warm-season invasive grasses, the second examined 1) mycorrhizal dependence of four native grasses; 2) native seedlings growth in soil collected from areas dominated by native grasses (‘home’) compared to soil collected from areas dominated by invasive grasses (‘away’); 3) the influence of native microbial communities added to ‘away’ soil; and 4) native seedling growth in steam-pasteurized “home’ and ‘away’ soils with native soil amendments. Our results indicate that both invasive and native species varied in mycorrhizal dependency along a continuum from obligately to facultatively dependent. Native species biomass production was consistently reduced when planted into ‘away’ soil, as compared to ‘home’ soil. Increased biomass production of native grasses was consistently observed following additions of native prairie soil to steamed soil from the invaded sites, indicating invasive feedbacks occur through alterations in biotic communities. However, our data also indicate
Reproductive costs are associated with both the male and female functions in Alnus viridis ssp. crispa

Abstract An organism has a finite amount of resources which must be allocated to different functions such as maintenance, growth and reproduction. In cosexual plants, allocation to reproduction is in both male and female structures; there is thus an opportunity for these two functions to compete for the limited resources available for reproduction. Male and female reproductive effort was experimentally manipulated over a three-year period on shoots of Alnus viridis ssp. crispa to detect the presence of trade-offs (i) between the male and female reproductive functions, and (ii) among reproduction, growth and future reproduction. The results show that there is no detectable trade-off between the male and female functions. In fact, the number of male and of female reproductive structures co-vary through time. However, combined male and female reproductive effort reduces current growth and future reproduction. There are thus costs to reproduction in this species, but these are associated with the combined effect of both the male and female functions. To my knowledge, this is the first experimental study on the cost of reproduction in a long-lived woody species showing clear trade-offs.
N1c colon cancer and the use of adjuvant chemotherapy: a current audit of the National Cancer Database

Colorectal cancer staging has evolved to define N1c as the presence of tumour deposits without concurrent positive lymph nodes. Work to date reports poor prognosis in N1c colon cancer, with Stage III categorization and adjuvant chemotherapy (AC) recommended. No study has yet evaluated the prevalence, treatment compliance or treatment‐related outcomes on a national scale. We aimed to evaluate the prevalence of N1c colon cancer, use, outcomes and factors associated with AC in the USA.
Physiological response of duckweed (Lemna minor L.)on herbicide norflurazon

Background and Purpose: Carotenoids deficiency caused by norflurazon (NF) leads to photooxidation of chlorophyll and reduced photosynthesis. Higher level of toxic active oxygen species (AOS) present under high oxidative stress could cause inactivation and degradation of plant proteins. Phytotoxicity of NF on duckweed was evaluated by growth and photosynthetic pigment content. The activity and isoenzyme pattern of peroxidase as well as total protein content and pattern were studied to evaluate the effect of oxidative stress caused by NF on proteins. Material and Methods: Duckweed Lemna minor was grown in axenic and controlled conditions on media with 1.0 and 0.2 μM of NF. Relative plant growth was estimated during 14 days of cultivation. Plant pigments were separated and measured spectrophotometrically after seven days of treatment. Total guaiacol peroxidase activity and protein content was determined every two days during two weeks. Anodic guaiacol peroxidase isoenzymes and soluble proteins were separated through native and SDS polyacrylamid gel electrophoresis, respectively. Results and Conclusion: NF did not significantly influence plant growth but the chlorophyll a, chlorophyll b, β-carotene and lutein content was significantly reduced. NF in concentration 1.0 μM generally inhibited the peroxidase activity but there was no difference in isoperoxidase pattern between control and treated plants. Higher concentration of NF (1.0 μM) caused continuous decrease of large and small subunits amount of Rubisco. Obtained results confirmed presence of higher level of AOS in plants treated with NF that caused modification and degradation of proteins - the effect that cannot be efficiently prevented in treated plants due to decreased amount of carotenoids.
Carcass Yield and Composition of Supplementing Hararghe Highland sheep with Ficus sur (cv. Forssk.) Fruits to a Basal Diet of Natural Pasture Hay

The experiment was conducted to evaluate the supplementary value of dried and ground Ficus sur fruits (FSF) mixed at different proportions with oats grain (OG) on carcass yield, carcass composition, and pH concentration. Thirty Hararghe highland lambs with initial live weights of 14.32±0.25kg (mean±SEM) were used for the experiment. The experimental sheep were grouped into 5 based on their initial body weight. Thus, the experiment was laid out in a randomized complete block design (RCBD) consisting of 5 treatments and 6 replications. The treatments were: ad libitum natural pasture hay (control); 100%FSF:0%OG [100FSF]; 67%FSF:33%OG [67FSF]; 33%FSF:67%OG [33FSF]; 0%FSF:100%OG [0FSF], which were randomly assigned to the sheep in each block. Noug seed ( Gizotia abysinica ) cake (NSC) was supplemented at isonitrogenous levels to all treatments and control diets. No significant (P>0.05) effect of the dietary treatments was observed on carcass parameters and most of the edible and non-edible offal components. The carcass of lambs fed 100FSF diet consist the highest (P<0.001) moisture and crude protein (CP), but the least ether extract (EE) as compared to those consumed 0FSF diet. The pH of the carcass consistently declined from the initial measure taken at 45 minutes post-evisceration to measurement taken at 24 hours. Carcass of lamb fed treatment diets 67FSF aand 100FSF have better maintained pH value within the desirable range. Hence, it can be concluded that feeding FSF to Hararghe highland sheep as a supplement to natural pasture hay based diet with sufficient protein supplement improved carcass yield and pH as compared to oat grains.
Structural properties of high-protein, low glycaemic index (GI) rice flour

Abstract Low glycaemic index (GI) rice flour was prepared by the enzymatic hydrolysis method. The protein content of treated (high-protein, low GI) rice flour was about 3.5 times higher than untreated rice flour, suggesting its use in infant formula or other protein-fortified food products. The GI of untreated and treated rice flour was found to be 88.0 ± 0.2 and 46.1 ± 0.2, respectively. High-protein, low-GI rice flour was studied for thermal and structural properties, which showed significant (p < 0.05) differences from untreated rice flour. The results of thermal properties showed a decrease in transition temperatures and enthalpy of gelatinization. The ratio of peaks at 1045 cm−1 and 1015 cm−1 of treated rice flour was significantly (p<0.05) lower than that of untreated rice flour. This could be ascribed to the loss of crystallinity due to enzymatic degradation. These results further support the decrease in transition temperatures and enthalpy of gelatinization. The results of the rheological studies of high-protein, low-GI rice flour revealed that both untreated and treated rice flour samples exhibited non-Newtonian shear-thinning flow behaviour (n < 1), which is characterized by a decrease in viscosity with an increase in shear rate.
Androgens Accentuate TGF‐β Dependent Erk/Smad Activation During Thoracic Aortic Aneurysm Formation in Marfan Syndrome Male Mice

Background Male patients with Marfan syndrome have a higher risk of aortic events and root dilatation compared with females. The role androgens play during Marfan syndrome aneurysm development in males remains unknown. We hypothesized that androgens potentiate transforming growth factor beta induced Erk (extracellular‐signal‐regulated kinase)/Smad activation, contributing to aneurysm progression in males. Methods and Results Aortic diameters in Fbn1 C1039G/+ and littermate wild‐type controls were measured at ages 6, 8, 12, and 16 weeks. Fbn1 C1039G/+ males were treated with (1) flutamide (androgen receptor blocker) or (2) vehicle control from age 6 to 16 weeks and then euthanized. p‐Erk1/2, p‐Smad2, and matrix metalloproteinase (MMP) activity were measured in ascending/aortic root and descending aorta specimens. Fbn1 C1039G/+ male and female ascending/aortic root‐derived smooth muscle cells were utilized in vitro to measure Erk/Smad activation and MMP‐2 activity following dihydrotestosterone, flutamide or transforming growth factor beta 1 treatment. Fbn1 C1039G/+ males have increased aneurysm growth. p‐Erk1/2 and p‐Smad2 were elevated in ascending/aortic root specimens at age 16 weeks. Corresponding with enhanced Erk/Smad signaling, MMP‐2 activity was higher in Fbn1 C1039G/+ males. In vitro smooth muscle cell studies revealed that dihydrotestosterone potentiates transforming growth factor beta‐induced Erk/Smad activation and MMP‐2 activity, which is reversed by flutamide treatment. Finally, in vivo flutamide treatment reduced aneurysm growth via p‐Erk1/2 and p‐Smad2 reduction in Fbn1 C1039G/+ males. Conclusions Fbn1 C1039G/+ males have enhanced aneurysm growth compared with females associated with enhanced p‐Erk1/2 and p‐Smad2 activation. Mechanistically, in vitro smooth muscle cell studies suggested that dihydrotestosterone potentiates transforming growth factor beta induced Erk/Smad activation. As biological proof of concept, flutamide treatment attenuated aneurysm growth and p‐Erk1/2 and p‐Smad2 signaling in Fbn1 C1039G/+ males.
Population dynamics of Arabis alpina in the French Alps: evidence for demographic compensation?

Due to its genetic proximity with Arabidopsis thaliana, Arabis alpina (Brassicaceae) is increasingly used as a perennial model species in studies of molecular evolution and adaptation. We studied the demography of A. alpina in six natural sites widely differing in their degree of disturbance, slope and vegetation, and encompassing the full altitudinal range of the species. We estimated three vital rates (growth, reproductive effort and survival) for individually-marked plants, studied for six years (2008-2014). We characterized the thermic conditions of each site with different thermal variables obtained using in situ continuous-time data loggers. Although A. alpina is described as a perennial species, the average life expectancy was only 1.82 years and most plants died before setting seeds. Plant size was a strong predictor of all three vital rates. Mean daily temperature showed a positive effect on growth and a negative effect on survival. Furthermore, reproductive effort covaried negatively with survival, suggesting a mechanism of demographic compensation acting on an elevational gradient. Synthesis. These results are informative of the selective pressures experienced by A. alpina in natural conditions and will help design experimental and molecular studies of local adaptation in this species.
Events and Machine Learning

An important question to understanding events is how they arise from unstructured sensory information. (Baldwin & Kosie, 2019) and (Shin & DuBrow, 2019) point out some problems with the ‘Event Segmentation Theory’ account of how events are formed, and oﬀer plausible extensions or alternatives. We outline one interesting way that ‘events’ might arise in machine learning contexts, where we have some ability to look under the hood of the cognitive machinery, and consider how this relates to the other accounts given in this issue. In exploring some possible conditions for event segmentation, the articles in this special issue invite discussion on several important high-level questions. This commentary focuses on the two articles, (Baldwin & Kosie, 2019) and (Shin & DuBrow, 2019), which give accounts of how cognitive agents might segment event boundaries. These papers highlight the role of organising structure, especially hierarchy and abstraction, in information processing. Our own research engages with these ideas in the context of creating machine learning agents that make sensible decisions in complicated environments, and we see a great deal of value in ﬁelds outside of computer science as we converge on some of the same questions. The
Borojó (borojoa patinoi): fuente de polifenoles con actividad antimicrobiana

of phenolic compounds. The content of polyphenols and their antimicrobial activity against pathogens as Escherichia coli and Staphylococcus aureus were evaluated in this research. Borojó fruit has polyphenol content between 600 and 800 mg gallic acid/100gr, and antimicrobial activity against S. aureus and E. coli with inhibition halos between 12 and 9 mm respectively. These results showed the advantages that have this fruit from the Rubiaceae family as a potential antimicrobial agent in food and cosmetics industries.