Miracle-dz/UniFAR-FTUs huggingface dataset:
The manifold actions of signaling peptides on subcellular dynamics of a receptor specify stomatal cell fate

Receptor endocytosis is important for signal activation and transduction. However, how a receptor interprets conflicting signals to adjust cellular output is not clearly understood. During plant development, the family of EPIDERMAL PATTERNING FACTOR (EPF) peptides fine-tunes stomatal patterning through ERECTA-family receptor kinases. Using genetic, cell biological, and pharmacological approaches, we report here that ERECTA-LIKE1 (ERL1), the major receptor restricting stomatal differentiation, undergoes dynamic subcellular behaviors in response to different signal inputs. ERL1 is constitutively recycled, whereas its activation by EPF1 peptide induces rapid internalization to multivesicular bodies (MVB). In contrast, dominant-negative ERL1 resides predominantly in plasma membrane. The co-receptor, TOO MANY MOUTHS (TMM), is essential for EPF1-induced ERL1 internalization but dispensable for EPFL6-induced ERL1 internalization. The peptide antagonist of EPF1, Stomagen/EPFL9, triggers retention of ERL1 in the endoplasmic reticulum. Our study elucidates that multiple related yet unique peptides specify cell fate by deploying the differential subcellular dynamics of a single receptor.
Effects of Changing Vegetation Composition on Community Structure, Ecosystem Functioning, and Predator–Prey Interactions at the Saltmarsh-Mangrove Ecotone

Decreasing frequency of freeze events due to climate change is enabling the poleward range expansion of mangroves. As these tropical trees expand poleward, they are replacing herbaceous saltmarsh vegetation. Mangroves and saltmarsh vegetation are ecosystem engineers that are typically viewed as having similar ecosystem functions. However, few studies have investigated whether predation regimes, community structure, and ecosystem functions are shifting at the saltmarsh-mangrove ecotone. In this study, we manipulated predator access to marsh and mangrove creekside habitats to test their role in mediating vegetation and invertebrate structure and stability in a two-year experiment. We also conducted a survey to evaluate how shifting vegetation is modifying structural complexity, invertebrate communities, and ecosystem functioning at the ecotone. Excluding larger (> 2 cm diameter) predators did not affect vegetation or invertebrate structure or stability in either saltmarsh or mangrove habitats. The survey revealed that the two habitat types consistently differ in structural metrics, including vegetation height, inter-stem distance, and density, yet they support similar invertebrate and algal communities, soil properties, and predation rates. We conclude that although mangrove range expansion immediately modifies habitat structural properties, it is not altering larger predator consumptive effects, community stability, community composition, or some other ecosystem functions and properties at the ecotone.
GeDex: A consensus Gene-disease Event Extraction System based on frequency patterns and supervised learning

Motivation The genetic mechanisms involved in human diseases are fundamental in biomedical research. Several databases with curated associations between genes and diseases have emerged in the last decades. Although, due to the demanding and time consuming nature of manual curation of literature, they still lack large amounts of information. Current automatic approaches extract associations by considering each abstract or sentence independently. This approach could potentially lead to contradictions between individual cases. Therefore, there is a current need for automatic strategies that can provide a literature consensus of gene-disease associations, and are not prone to making contradictory predictions. Results Here, we present GeDex, an effective and freely available automatic approach to extract consensus gene-disease associations from biomedical literature based on a predictive model trained with four simple features. As far as we know, it is the only system that reports a single consensus prediction from multiple sentences supporting the same association. We tested our approach on the curated fraction of DisGeNet (f-score 0.77) and validated it on a manually curated dataset, obtaining a competitive performance when compared to pre-existing methods (f-score 0.74). In addition, we effectively recovered associations from an article collection of chronic pulmonary diseases, and discovered that a large proportion is not reported in current databases. Our results demonstrate that GeDex, despite its simplicity, is a competitive tool that can successfully assist the curation of existing databases. Availability GeDex is available at https://bitbucket.org/laigen/gedex/src/master/ and can be used as a docker image https://hub.docker. com/r/laigen/gedex Contact cmendezc@ccg.unam. mx Supplementary information Supplementary material are available at bioRxiv online.
Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance

We used molecular tools and a multilocus approach to investigate the phylogeography of Lepidothrix coronata across most of its ample range. We sequenced six DNA fragments to produce phylogenies, molecular dating estimates, analyses of the dynamics of the demographic history of the species and a biogeographic analysis to estimate the events and changes in the ancestral distribution of the species. The results indicated the presence of four well‐established lineages, with high levels of divergence. These lineages are delineated by well‐defined geographic barriers, with one lineage, restricted to the west of the Andes, being the first to diverge from the complex. The other three lineages are exclusive to the Amazonian distribution of the species, with two being found north of the Amazon River, and the third, south of the Amazon. Some of the relationships found between these lineages were distinct from those described in previous studies. Important disagreements were found between the mtDNA phylogeny and that of the multilocus analysis, in relation to the lineages located to the west of the Andes. We propose that past introgression events may have influenced shifts in the relationships between lineages, despite the fact that the groups were well defined in both the phylogenies. The biogeographic analysis indicates that the lineages arose through successive vicariance events, which had a primary role in the diversification of the group. Two or three genetically structured subclades were also found within each Amazonian lineage, although these subclades are not isolated by an obvious geographic barrier.
Chloroplast genome of critically endangered Cotoneaster wilsonii (Rosaceae) endemic to Ulleung Island, Korea

Abstract Cotoneaster wilsonii Nakai is an endangered species endemic to Ulleung Island, Korea. Here we reported the first complete chloroplast gnome sequences of C. wilsonii, which is 159,999 bp in total length with the large single copy (LSC) region of 87,868 bp, the small single copy (SSC) region of 19,335 bp, and two inverted repeat (IR) regions of 26,399 bp. The plastome contains 131 genes, including 84 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content is 42.6% and those in the LSC, SSC, and IR regions are 34.2, 30.3, and 42.6%, respectively. Phylogenetic analysis of 21 representative plastomes within the family Rosaceae suggests strongly the monophyly of Cotoneaster and C. wilsonii being sister to the clade of Cotoneaster franchetii and Cotoneaster horizontalis.
Enhanced Immunogenicity of Mitochondrial-Localized Proteins in Cancer Cells

Compared to cytosolic antigens, mitochondrial tumor antigens prime a stronger antitumor immune response, instigated by enhanced cross-presentation and involvement of the STING pathway. Thus, cellular location of tumor antigens is relevant to improved cancer vaccine development. Epitopes derived from mutated cancer proteins elicit strong antitumor T-cell responses that correlate with clinical efficacy in a proportion of patients. However, it remains unclear whether the subcellular localization of mutated proteins influences the efficiency of T-cell priming. To address this question, we compared the immunogenicity of NY-ESO-1 and OVA localized either in the cytosol or in mitochondria. We showed that tumors expressing mitochondrial-localized NY-ESO-1 and OVA proteins elicit significantdly higher frequencies of antigen-specific CD8+ T cells in vivo. We also demonstrated that this stronger immune response is dependent on the mitochondrial location of the antigenic proteins, which contributes to their higher steady-state amount, compared with cytosolic localized proteins. Consistent with these findings, we showed that injection of mitochondria purified from B16 melanoma cells can protect mice from a challenge with B16 cells, but not with irrelevant tumors. Finally, we extended these findings to cancer patients by demonstrating the presence of T-cell responses specific for mutated mitochondrial-localized proteins. These findings highlight the utility of prioritizing epitopes derived from mitochondrial-localized mutated proteins as targets for cancer vaccination strategies.
Proteasome subunit PSMC3 variants cause neurosensory syndrome combining deafness and cataract due to proteotoxic stress

Whole-genome sequencing was performed on patients with severe deafness and early-onset cataracts as part of a neurological, sensorial and cutaneous novel syndrome. A unique deep intronic homozygous variant in the PSMC3 gene (c.1127+337A>G, p.Ser376Argfs15*), encoding the 26S proteasome ATPase ring subunit 5 (Rpt5) was identified leading to the transcription of a cryptic exon. Patient’s fibroblasts exhibited impaired protein homeostasis characterized by accumulation of ubiquitinated proteins suggesting severe proteotoxic stress. Indeed, the TCF11/Nrf1 transcriptional pathway allowing proteasome recovery after proteasome inhibition is permanently activated in the patient’s fibroblasts. Upon chemical proteasome inhibition this pathway is however impaired. These cells were unable to compensate for proteotoxic stress although a higher proteasome content. Two different zebrafish studies led to inner ear development anomalies as well as cataracts. PSMC3 proteasome subunit dysfunction leads to various neurological manifestations, early onset cataracts and deafness and suggest that Rpt5 plays a major role in inner ear, lens and central nervous system development.
Application of Semi-Empirical Ventilation Models in A Mediterranean Greenhouse with Opposing Thermal and Wind Effects. Use of Non-Constant Cd (Pressure Drop Coefficient Through the Vents) and Cw (Wind Effect Coefficient)

The present work analyses the natural ventilation of a multi-span greenhouse with one roof vent and two side vents by means of sonic anemometry. Opening the roof vent to windward, one side vent to leeward, and the other side vents to windward (this last vent obstructed by another greenhouse), causes opposing thermal GT (m3 s−1) and wind effects Gw (m3 s−1), as outside air entering the greenhouse through the roof vent circulates downward, contrary to natural convection due to the thermal effect. In our case, the ventilation rate RM (h−1) in a naturally ventilated greenhouse fits a second order polynomial with wind velocity uo (RM = 0.37 uo2 + 0.03 uo + 0.75; R2 = 0.99). The opposing wind and thermal effects mean that ventilation models based on Bernoulli’s equation must be modified in order to add or subtract their effects accordingly—Model 1, in which the flow is driven by the sum of two independent pressure fields GM1=GT2±Gw2, or Model 2, in which the flow is driven by the sum of two independent fluxes GM2=GT±Gw. A linear relationship has been obtained, which allows us to estimate the discharge coefficient of the side vents (CdVS) and roof vent (CdWR) as a function of uo [CdVS = 0.028 uo + 0.028 (R2 = 0.92); CdWR = 0.036 uo + 0.040 (R2 = 0.96)]. The wind effect coefficient Cw was determined by applying models M1 and M2 proved not to remain constant for the different experiments, but varied according to the ratio uo/∆Tio0.5 or δ [CwM1 = exp(-2.693 + 1.160/δ) (R2 = 0.94); CwM2 = exp(−2.128 + 1.264/δ) (R2 = 0.98)].
Rites of Passage: Germination of Vertebrate Dispersed, Regurgitated or Defecated Phoenix canariensis Seeds

Canary Island Date Palms are widely planted as ornamental plants in private and public spaces. As both prolific and long-duration seeders, their drupes provide food for a range of volant and terrestrial vertebrates. This study experimentally examined the germination of vertebrate digested seeds. Whereas seeds in Flying- fox spat did not yield a higher germination rate than undigested controls, seeds that had passed through the gastro-intestinal tract and were deposited in scats, or those that were ingested and regurgitated from the crop, have a significantly better probability of germinating. This establishes Pied Currawongs as effective short-range dispersers and canid frugivores, such as the Red Fox, as major medium- and long-distance vectors of ornamental palms.
The complete mitochondrial genome of oceanic puffer (Lagocephalus lagocephalus) from South China Sea

Abstract Lagocephalus lagocephalus is one of genus Lagocephalus and widely distributed in tropical and temperate oceans. In this study, we described the complete mitochondrial genome of L. lagocephalus. The genome is 166,443 bp in length, encoding the standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding D-loop, with circular organization. The overall base composition of the whole mitochondrial genome was A (27.95%), T (25.07%), G (16.14%), and C (30.83%) with an AT bias of 53.03%. The longest PCG of these species was ND5, whereas the shortest ATP8.
Blueberry consumption and healthy lifestyles in an emerging market

Aim of study: This study focuses on the preference for and consumption habits of blueberries ( Vaccinium corymbosum L. ) in an emerging market. The objective is to analyze the determinants of blueberry consumption in Chile and evaluate to what extent traditional factors, such as income and price, are more determinant than other attitudinal factors and lifestyles. Area of study: The Biobio Region (Chillan City), the second most important region in Chile. Material and methods: A face-to-face survey is applied to a random stratified sample. The survey collected information on adoption of healthy lifestyles, knowledge of blueberries as a natural functional food, some sociodemographic characteristics, and traditional economic factors. A Heckman model is estimated by the Maximum Likelihood. Main results: Results suggest that higher blueberry consumption is positively associated with the adoption of healthy lifestyles, a higher self-perception of healthy habits, and the recognition of blueberries as a natural functional food. The nutritional status reflected that people with a lower body mass index consume fewer blueberries. Finally, traditional factors, such as income and price, are showed to be more influential on blueberry consumption than attitudinal and lifestyle factors. Research highlights: Chilean consumers perceive blueberries as a healthy product, which can contribute to adopt healthier lifestyles. Domestic markets should be supplied with higher quality product taking into account that the demand is price inelastic. Branding and packaging with functional claims could be an efficient strategy to increase domestic consumption.
Bats in urbanising landscapes: habitat selection and recommendations for a sustainable future

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Landscape genomics predicts climate change‐related genetic offset for the widespread Platycladus orientalis (Cupressaceae)

Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome‐wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high‐quality variants from Platycladus orientalis range‐wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature‐related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.
Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome

Somatic transposition in neural tissue could contribute to neuropathology and individuality, but its prevalence is debated. We used single-cell mRNA sequencing to map transposon expression in the Drosophila midbrain. We found that neural transposon expression is driven by cellular genes. Every expressed transposon is resident in at least one cellular gene with a matching expression pattern. A new long-read RNA sequencing approach revealed that coexpression is a physical link in the form of abundant chimeric transposon-gene mRNAs. We identified 148 genes where transposons introduce cryptic splice sites into the nascent transcript and thereby produce many additional mRNAs. Some genes exclusively produce chimeric mRNAs with transposon sequence and on average transposon-gene chimeras account for 20% of the mRNAs produced from a given gene. Transposons therefore significantly expand the neural transcriptome. We propose that chimeric mRNAs produced by splicing into polymorphic transposons may contribute to functional differences between individual cells and animals.
A Survey of Termitomyces (Lyophyllaceae, Agaricales), Including a New Species, from a Subtropical Forest in Xishuangbanna, China

Abstract A survey of mushrooms was conducted in Xishuangbanna, Yunnan Province, China, in the rainy season (May to October) of 2012, 2013, and 2014, during which 16 specimens of Termitomyces were collected. Preliminary macro- and micro-characteristics, together with ITS sequence data, showed that four of the specimens belonged to a new species (Termitomyces fragilis), while the other 12 belonged to T. aurantiacus, T. eurrhizus, T. globules, T. microcarpus, and T. bulborhizus. In this paper, T. fragilis is introduced as a species new to science based on morphological characterization and phylogenetic analyses. Macro- and micro- morphological descriptions, color photographs and line drawings of the new species, and a phylogenetic tree to show the placement of the new species are provided. T. fragilis is then compared with other closely related taxa in the genus Termitomyces.
Genomic landscape of reproductive isolation in Lucania killifish: The role of sex chromosomes and salinity

Understanding how speciation occurs and how reproductive barriers contribute to population structure at a genomic scale requires elucidating the genetic architecture of reproductive isolating barriers. In particular, it is crucial to determine if loci underlying reproductive isolation are genetically linked or if they are located on sex chromosomes, which have unique inheritance and population genetic properties. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are closely related species that have diverged across a salinity gradient and are reproductively isolated by assortative mating, hybrid male infertility, viability of hybrid offspring at high salinities, as well as reduced overall fitness of F2 offspring and backcrosses to L. goodei. We conducted QTL mapping in backcrosses between L. parva and L. goodei to determine the genetic architecture of sex determination, mate attractiveness, fertility, and salinity tolerance. We find that the sex locus appears to be male determining and located on a chromosome that has undergone a Robertsonian fusion in L. parva relative to L. goodei. We find that the sex locus on the fused chromosome is involved in several genomic incompatibilities, which affect the survival of backcrossed offspring. Among the backcrossed offspring that survived to adulthood, we find that one QTL for male attractiveness to L. goodei females is closely linked to this sex locus on chromosome 1. Males homozygous for L. goodei alleles at the sex locus laid more eggs with L. goodei females. QTL associated with salinity tolerance were spread across the genome but did not tend to co-localize with reproductive isolation. Thus, speciation in this system appears to be driven by reinforcement and indirect selection against hybrids rather than direct natural selection for salinity tolerance. Our work adds to growing evidence that sex chromosome evolution may contribute to speciation.
A macro-ecological approach to predators’ functional response

Predation often deviates from the law of mass action: many micro- and meso-scale experiments have shown that consumption saturates with resource abundance, and decreases due to interference between consumers. But does this observation hold at macro-ecological scales, spanning many species and orders of magnitude in biomass? If so, what are its consequences for large-scale ecological patterns and dynamics? We perform a meta-analysis of predator-prey pairs of mammals, birds and reptiles, and show that predation losses appear to increase, not as the product of predator and prey densities following the Lotka-Volterra (mass action) model, but rather as the square root of that product. This suggests a phenomenological power-law expression of the effective cross-ecosystem functional response. We consider the possibility that the same power-law holds dynamically within an ecosystem, and explore its consequences in a simple food chain model. The empirical exponents fall close to the boundary between regimes of donor and consumer limitation. Exponents on this boundary are singular in multiple ways. First, they maximize predator abundance and some stability metrics. Second, they create proportionality relations between biomass and productivity, both within and between trophic levels. These intuitive relations do not hold in general in mass action models, but are widely observed empirically. These results provide evidence of mechanisms limiting predation across multiple ecological scales. Some of this evidence was previously associated with donor control, but we show that it supports a wider range of possibilities, including forms of consumer control. Limiting consumption counter-intuitively allows larger populations. It is worthwhile to reconsider whether the observed functional response arises from microscopic mechanisms and constraints, or could hint at selective pressure at the population level.