Miracle-dz/UniFAR-FTUs huggingface dataset:
mir-71 mediates age-dependent opposing contributions of the stress activated kinase KGB-1 in Caenorhabditis elegans

Studying the evolutionary processes that shaped aging offers a path for understanding the causes of aging. The Antagonistic Pleiotropy theory for the evolution of aging proposes that the inverse correlation between natural selection strength and aging allows positive selection of gene variants with early-life beneficial contributions to fitness in spite of detrimental late-life consequences. However, mechanistic understanding of how this principle manifests in aging is still lacking. We previously identified antagonistic pleiotropy in the function of the Caenorhabditis elegans JNK homolog KGB-1, which provided stress protection in developing larvae, but sensitized adults to stress and shortened their lifespan. To a large extent, KGB-1’s contributions depended on age-dependent and opposing regulation of the stress transcription factor DAF-16, but the underlying mechanisms remained unknown. Here we describe a role for the microRNA mir-71 in mediating effects of KGB-1 on DAF-16 and on downstream phenotypes. Fluorescent imaging along with genetic and survival analyses revealed age-dependent regulation of mir-71 expression by KGB-1 – upregulation in larvae, but downregulation in adults, and showed that mir-71 was required both for late-life effects of KGB-1 (infection sensitivity and shortened lifespan), as well as for early life resistance to cadmium. While mir-71 disruption did not compromise development under protein folding stress (known to depend on KGB-1), disruption of the argonaute gene alg-1, a central component of the microRNA machinery, did. These results suggest that microRNAs play a role in mediating age-dependent antagonistic contributions of KGB-1 to survival, with mir-71 playing a central role and additional microRNAs contributing redundantly.
Trait divergence of woody species in relation to affinity for termite mounds in Upper Katanga (DR Congo)

Increasing evidence indicates that edaphic heterogeneity contrib‐ utes to plant community diversity in the tropics (John et al., 2007; Mori, Schietti, Poorter, & Piedade, 2019). In dry tropical woodlands and savannahs of Africa, dramatic edaphic heterogeneity is driven by the activity of termites, with a remarkably general pattern of higher concentrations in base cations and clay in termite mounds (Erpenbach & Wittig, 2016; Jouquet, Traore, Choosai, Hartmann, & Bignell, 2011; Muvengwi, Ndagurwa, Nyenda, & Mbiba, 2016; Sileshi, Arshad, Konaté, & Nkunika, 2010). Termite mound soil also has larger stores of available water compared to surrounding soil Received: 3 June 2019 | Revised: 29 September 2019 | Accepted: 6 October 2019 DOI: 10.1111/jvs.12827
Hybrid zone genomics supports candidate species in Iberian Alytes obstetricans

While estimates of genetic divergence are increasingly used in molecular taxonomy, hybrid zone analyses can provide decisive evidence for evaluating candidate species. Applying a population genomic approach (RAD-sequencing) to a fine-scale transect sampling, we analyzed the transition between two Iberian subspecies of the common midwife toad (Alytes obstetricans almogavarii and A. o. pertinax) in Catalonia (northeastern Spain), which putatively diverged since the Plio-Pleistocene. Their hybrid zone was remarkably narrow, with extensive admixture restricted to a single locality (close to Tarragona), and congruent allele frequency clines for the mitochondrial (13 km wide) and the average nuclear genomes (16 km wide). We also fitted clines independently for 89 taxon-diagnostic SNPs: most of them behave like the nuclear background, but a subset (13%) is completely impermeable to gene flow and might be linked to barrier loci involved in hybrid incompatibilities. Assuming that midwife toads are able to disperse in the area of contact, we conclude that these taxa experience partial reproductive isolation and represent incipient species, i.e. Alytes almogavarii and Alytes obstetricans. Interestingly, their evolutionary age and mitochondrial divergence fall below the thresholds proposed in molecular systematics studies, emphasizing the difficulty of predicting the outcome of secondary contacts between young lineages entering the grey zone of speciation.
A novel pathway linking plasma membrane and chloroplasts is co-opted by pathogens to suppress salicylic acid-dependent defences

Chloroplasts are crucial players in the activation of defensive hormonal responses during plant-pathogen interactions. Here, we show that a plant virus-encoded protein re-localizes from the plasma membrane to chloroplasts upon triggering plant defence, interfering with the chloroplast-dependent activation of anti-viral salicylic acid (SA) biosynthesis. Strikingly, we have found that plant pathogens from different kingdoms seem to have convergently evolved to target chloroplasts and impair SA-dependent defences following an association with membranes, which is based on the co-existence of two subcellular targeting signals, an N-myristoylation site and a chloroplast transit peptide. This pattern is also present in plant proteins, at least one of which conversely activates SA defences from the chloroplast. Taken together, our results suggest that a pathway linking plasma membrane to chloroplasts and activating defence exists in plants, and that such pathway has been co-opted by plant pathogens during host-pathogen co-evolution to promote virulence through suppression of SA responses.
Pre-Harvest Foliar Application of Mineral Nutrients to Retard Chlorophyll Degradation and Preserve Bio-Active Compounds in Broccoli

Foliar application of micronutrients has become a common farm management practice to increase the overall yield of various crops. However, the effects of foliar fertilization on shelf life and postharvest quality of the crops are rather under-researched. The aim of this field experiment was to evaluate the effect of foliar application of individual mineral nutrients (calcium (Ca), zinc (Zn), manganese (Mn), and iron (Fe) on pre and postharvest quality of broccoli. The broccoli plants were subjected to single foliar sprays of either Ca, Fe, Zn, or Mn, which was repeated four times during plant growth at a 1 g/kg concentration. Once harvested, the broccoli heads were refrigerated at 4 °C for 28 days. Our results indicated that foliar application of Ca, Zn, Mn, and Fe did not have a significant effect on plant growth parameters, apart from enhancing Soil Plant Analysis Development (SPAD) chlorophyll meter values. However, during postharvest, foliar application treatment showed a positive response on weight loss during storage and reduction in yellowing of the broccoli heads. Foliar treatments increased the concentration of Nitrogen (N), Phosphorus (P), Ca, Zn, Mn and Fe significantly in the broccoli head tissue. Total chlorophyll content, total phenolic compound, ascorbic acid, peroxidase activity, glucoraphanin and glucobrassicin and flavonoids were significantly increased by all foliar treatments. Crude protein content and sulforaphane were enhanced by Ca and Mn treatments. Overall, foliar application of the investigated mineral nutrients may prove beneficial in improving the shelf-life and nutrient content of broccoli during postharvest handling and storage.
Extremely Widespread Parthenogenesis and a Trade-Off Between Alternative Forms of Reproduction in Mayflies (Ephemeroptera)

Studying alternative forms of reproduction in natural populations is of fundamental importance for understanding the costs and benefits of sex. Mayflies are one of the few animal groups where sexual reproduction co-occurs with different types of parthenogenesis, providing ideal conditions for identifying benefits of sex in natural populations. Here, we establish a catalogue of all known mayfly species capable of reproducing by parthenogenesis, as well as mayfly species unable to do so. Overall, 1.8% of the described species reproduce parthenogenetically, which is an order of magnitude higher than reported in other animal groups. This frequency even reaches 47.8% if estimates are based on the number of studied rather than described mayfly species. In terms of egg-hatching success, sex is a more successful strategy than parthenogenesis, and we found a trade-off between the efficiency of sexual and parthenogenetic reproduction across species. This means that improving the capacity for parthenogenesis may come at the cost of being less able to reproduce sexually, even in facultative parthenogens. Such a trade-off can help explain why facultative parthenogenesis is extremely rare among animals despite its potential to combine the benefits of sexual and parthenogenetic reproduction. We argue that parthenogenesis is frequently selected in mayflies in spite of this probable trade-off because their typically low dispersal ability and short and fragile adult life may frequently generate situations of mate limitation in females. Mayflies are currently clearly underappreciated for understanding the benefits of sex under natural conditions.
A Low-Cost, Efficient, and Precise Technique to Quantify Key Life Cycle Events in Nests of Oviparous Reptiles

Abstract. Phenological timing is of central interest to evolutionary ecologists because it is associated with fitness, but there has been limited study in animal groups with relatively secretive habits such as reptiles. This is especially true for the timing of hatchling behavior in wild reptile nests, likely attributable to few noninvasive methods for estimating parameters associated with egg hatching. We show that tri-axial accelerometers, small data loggers that measure rotation and inclination, can accurately quantify hatchling movement in wild reptile nests. In June 2018, we deployed an accelerometer in each of five freshly laid Snapping Turtle (Chelydra serpentina) nests in Algonquin Provincial Park, Ontario, Canada. In September 2018, nests were visited once daily to quantify the timing of hatchling emergence. The accelerometers worked as expected: there was statistically significant correspondence between the timing of accelerometer rotation in the nest (caused by movement of the hatchlings) and the timing of hatchling emergence. Furthermore, the number of hatchlings emerging from a nest was strongly and significantly correlated with the extent of accelerometer displacement. Our new technique allows new types of phenological data to be collected. It requires minimal effort and financial investment and thus is accessible to a broad range of research programs.
Type-2 diabetes with low LDL-C: genetic insights into a unique phenotype

Although hyperlipidemia is traditionally considered a risk factor for type-2 diabetes (T2D), evidence has emerged from statin trials and candidate gene investigations suggesting that lower LDL-C increases T2D risk. We thus sought to comprehensively examine the phenotypic and genotypic relationships of LDL-C with T2D. Using data from the UK Biobank, we found that LDL-C was negatively associated with T2D (OR=0.43[0.41, 0.45] per mmol/L unit of LDL-C), despite positive associations of LDL-C with HbA1c and BMI. We then performed the first genome-wide exploration of variants simultaneously associated with lower LDL-C and increased T2D risk, using data on LDL-C from the UK Biobank (n=431,167) and the GLGC consortium (n=188,577), and T2D from the DIAGRAM consortium (n=898,130). We identified 31 loci associated with lower LDL-C and increased T2D, capturing several potential mechanisms. Seven of these loci have previously been identified for this phenotype, and 9 have previously been implicated in non-alcoholic fatty liver disease. Finally, two-sample Mendelian randomization analyses suggest that low LDL-C causes T2D, although causal interpretations are challenging due to pleiotropy. Our findings extend our current understanding of the higher T2D risk among individuals with low LDL-C, and of the underlying mechanisms, including those underlying the diabetogenic effect of LDL-C-lowering medications.
Intake and utilization of energy of rations with pelleted forages by dairy cows

A survey of the literature showed that forage processing, that is grinding and pelleting, increased feed intake of ruminants. This increase, due to reduction in particle size distribution of the forage, depends mainly on forage quality, proportion of concentrates in the diet and nutrient requirement of the cow. Pellets could replace part of the concentrates; complete substitution for long forage caused digestive disorders and reduced fat content of the milk. Eating rate, microbial breakdown and production of volatile fatty acids often increased too. Processed forages offered to sheep and beef cattle depressed digestibility, which was compensated by slightly lower losses of methane and less heat production. Data from energy balance trials at Wageningen from 1967 to 1973, mostly with 4-6 lactating Dutch Friesian cows per trial, were examined by multiple factor analysis for effects of processing. Rations in which processed forages replaced part of the long forages or the concentrates were tested in 130 trials. Processing decreased digestibility of energy in the forage by about 9 percentage units, 15%, and its metabolizability by 7 percentage units, 13%. Utilization of metabolizable energy increased, roughly compensating the decrease in metabolizability. Regressions were calculated for the prediction of digestibility and net energy of processed forage in a feed evaluation system for dairy cows, to be introduced in the Netherlands in 1977.
Effects of condition and sperm competition risk on sperm allocation and storage in neriid flies

Ejaculate traits can be sexually selected and often exhibit heightened condition-dependence. However, the influence of sperm competition risk in tandem with condition-dependent ejaculate allocation strategies is relatively unstudied. Because ejaculates are costly to produce, high-condition males may be expected to invest more in ejaculates when sperm competition risk is greater. We examined the condition-dependence of ejaculate size by manipulating nutrient concentration in the juvenile (larval) diet of the neriid fly Telostylinus angusticollis. Using a fully factorial design we also examined the effects of perceived sperm competition risk (manipulated by allowing males to mate first or second) on the quantity of ejaculate transferred and stored in the three spermathecae of the female reproductive tract. To differentiate male ejaculates, we fed males nontoxic rhodamine fluorophores (which bind to proteins in the body) prior to mating, labeling their sperm red or green. We found that high-condition males initiated mating more quickly and, when mating second, transferred more ejaculate to both of the female’s posterior spermathecae. This suggests that males allocate ejaculates strategically, with high-condition males elevating their ejaculate investment only when facing sperm competition. More broadly, our findings suggest that ejaculate allocation strategies can incorporate variation in both condition and perceived risk of sperm competition.
Mapping the micro-proteome of the nuclear lamina and lamin associated domains

The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, so-called lamin associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.
АНАЛИЗ МИКОБИОТЫ В ПОРАЖЕННЫХ ЛИСТЬЯХ КАРТОФЕЛЯ (Solanum tuberosum L.) С ИСПОЛЬЗОВАНИЕМ МЕТАГЕНОМНЫХ ПОДХОДОВ

The problem of potato diseases caused by fungi and fungi-like organisms is relevant for all regions of the world cultivating this crop, since it is mycoses that cause the most significant damage to plants (A. Bernreiter, 2017). The traditional approaches for identification of potato pathogens are aimed at identifying a specific pathogen and do not take into account neither other, often unknown pathogens, nor the other most important component — the beneficial microbiota of the phyllosphere community whose alterations can also become one of the causes of diseases. The novelty of this work lies in the fact that the high-throughput sequencing methods we used here is free of this disadvantages and makes it possible to identify virtually all plant microorganisms, including the phyllosphere and endosphere. The purpose of this study was to use metagenomic approaches to analyze the total fungal and fungi-like community in potato leaves that have morphological markers of damage by pathogens of the genus Alternaria and Phytophthora which are the causative agents of early blight and late blight. For fungal and fungi-like communities analysis, DNA samples was extracted from leaves of potato (Solanum tuberosum L.) cultivar Nikulinsky, affected by “alternaria” and “phytophthora” diseases types, which were later used to create amplicon libraries of ITS1 and ITS2 fragments and high-throughput sequencing on the Illumina MiSeq platform (Illumina, Inc., USA). During the bioinformatic data processing with the Illumina software and the PIPITS software package (H.S. Gweon et al, 2015), 187 OTE, 113 phylotypes for the ITS1 library and 249 OTE, 127 phylotypes for ITS2 were identified. Subsequent annotation of OTE and taxonomic analysis of the resulting communities were carried out with the QIIME program (J.G. Caporaso et al., 2010), the diversity coefficients within the community were calculated using the PAST software package (Ø. Hammer et al., 2001). Comparison of the fungal communities obtained for both types of lesion using different universal primers for the ITS1 regions (M. Usyk et al., 2017) and ITS2 (T.J. White et al., 1990) showed that only the first pair is suitable for the detection of phytophthora, and in general gives a more even community structure. The tools of automatic annotation turned out to be insufficient for objective identification of alternaria in samples, as a result we had to use the methods of manual search with the BLASTn program (S.F. Altschul et al., 1990). Since the primer pair ITS2 does not allow identification of Phytophthora in the samples, the further comparative analysis of the fungal communities of the two types of lesion was carried out using data only from the ITS1 library. The data of taxonomic analysis showed that in the affected areas for both types of mycoses a rich fungal community is formed, and, in the case of “late blight”, the fraction of the pathogen is about 30 % in the community, and in the variant with “early blight”, only 2.07 % with a significant part (about 15 %) accounted
The complete chloroplast genome sequence of Horsfieldia amygdalina (Myristicaceae)

Abstract Horsfieldia amygdalina is a member of Myristicaceae. The H. amygdalina chloroplast genome is found to be 155,683 bp in length and has a base composition of A (29.99%), G (19.32%), C (19.92%), and T (30.77%). The genome contained two short inverted repeat (IRa and IRb) regions (37,754 bp) which were separated by a large single copy (LSC) region (86,931 bp) and a small single copy (SSC) region (30,998 bp). The genome encodes 121 unique genes, including 86 protein-coding genes, 27 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Further, complete chloroplast sequence of H. amygdalina was aligned together with Horsfieldia pandurifolia, Myristica yunnanensis and other Magnoliales and basal angiosperms species which have reported the complete chloroplast sequence. This complete chloroplast genome will provide valuable information for the development of DNA markers for future species resource development and phylogenetic analysis of H. amygdalina.
Assessing the effectiveness of foraging radius models for seabird distributions using biotelemetry and survey data

The design and funding for aerial surveys were provided by Ireland's Dept of Communication, Climate Action and Environment and the Dept of Culture, Heritage and the Gaeltacht, under the ObSERVE Programme established in 2014. We are grateful for the support and assistance of both Depts in undertaking this work. Funding for development of projected distributions was provided by the Petroleum Infrastructure Program (IS013/08), and funding for telemetry work was provided by the Zoological Society of London (Good gifts programme), Petroleum Infrastructure Programme (IS013/08) and the Irish Research Council (GOIPD/2015/81) Ireland's Dept of Agriculture, Fisheries and the Marine.
Pericyte-Like Cells Undergo Transcriptional Reprogramming and Distinct Functional Adaptations in Acute Lung Injury

Background We previously reported on the role of pericyte-like cells as functional sentinel immune cells in lung injury. However, much about the biological role of pericytes in lung injury remains unknown. Lung pericyte-like cells are well-positioned to sense disruption to the epithelial barrier and coordinate local inflammatory responses due to their anatomic niche within the alveoli. In this report, we characterized transcriptional responses and functional changes in pericyte-like cells following activation by alveolar components from injured and uninjured lungs in a mouse model of acute lung injury (ALI). Methods We purified pericyte-like cells from lung digests using PDGFRβ as a selection marker and expanded them in culture as previously described (1). We induced sterile acute lung injury in mice with recombinant human Fas ligand (rhFasL) instillation followed by mechanical ventilation (1). We then collected bronchoalveolar lavage fluid (BALF) from injured and uninjured mice. Purified pericyte-like cells in culture were exposed to growth media only (control), BALF from uninjured mice, and BALF from injured mice for 6 and 24 h. RNA collected from these treatment conditions were processed for RNAseq. Targets of interest identified by pathway analysis were validated using in vitro and in vivo assays. Results We observed robust global transcriptional changes in pericyte-like cells following treatment with uninjured and injured BALF at 6 h, but this response persisted for 24 h only after exposure to injured BALF. Functional enrichment analysis of pericytes treated with injured BALF revealed activation of immuno-inflammatory, cell migration and angiogenesis-related pathways, whereas processes associated with tissue development and remodeling were down-regulated. We validated select targets in the inflammatory, angiogenesis-related, and cell migratory pathways using functional biological assays in vitro and in vivo. Conclusion Lung pericyte-like cells are highly responsive to alveolar compartment content from both uninjured and injured lungs, but injured BALF elicits a more sustained response. The inflammatory, angiogenic, and migratory changes exhibited by activated pericyte-like cells underscore the phenotypic plasticity of these specialized stromal cells in the setting of acute lung injury.