Miracle-dz/UniFAR-FTUs huggingface dataset:
Poplar and Pathogen Interactions: Insights from Populus Genome-Wide Analyses of Resistance and Defense Gene Families and Gene Expression Profiling

Our understanding of the molecular basis of plant-pathogen interactions is derived mostly from studies of model annual plant species, and until recently, few addressed disease resistance and defense responses in long-lived species such as trees. The release of the Populus genome sequence has permitted extensive genome-wide surveys of gene families and comparative analyses of other sequenced plant genomes. These have revealed striking features for gene families that play key roles in the plant defense response. For example, the NBS-LRR resistance ( R )-gene family is expanded compared with other plant genomes, including R -gene subfamilies not previously reported in plants. Some of these genes are clustered on the subtelomeric part of a chromosome that shows segregation distortion in genetic studies. Similar expansion is observed for other genes playing key roles in plant defense such as pathogenesis-related proteins. Among the many pathogens that infect poplar trees, Melampsora spp. fungi, which cause rust diseases in plants, are responsible for considerable damage in poplar plantations. This biotrophic pathogen has attracted recent attention and here we describe molecular insights into the Populusdefense response against rust infection. Transcript profiles derived from compatible (susceptible) and incompatible (specific host -resistance) Populus-Melampsora interactions were leveraged to describe molecular changes occurring during defense responses against rust fungi. This highlighted responses that are similar to defense responses of annual plant species, such as up-regulation of transcripts encoding pathogenesis-related proteins. The molecular evidence gathered for the poplar-rust pathosystem indicates a temporal delay in the activation of defense responses between susceptibility and partial or full resistance that is consistent with the signal conversion model described for Arabidopsis. The genome of Melampsora larici-populina, which infects several species of Populus, was recently sequenced and provides a model pathosystem for forest pathology and offers unprecedented opportunities to understand how tree species cope with disease. Ultimately, understanding the molecular basis of Populus rust resistance will greatly improve our understanding of other major diseases of poplar.
Linking intronic polymorphism on the CHD1-Z gene with fitness correlates in Black-tailed Godwits Limosa l. limosa

We show that variation in an intronic length polymorphism in the CHD1-Z gene in Black-tailed Godwits Limosa l. limosa is associated with fitness correlates. This is the second example of the CHDZ-1 gene being correlated with fitness, a previous study having established that Moorhens Gallinula chloropus carrying the rare Z* allele have reduced survival. In Godwits, however, carriers of the Z* allele (374 bp) fared better than those with the more frequent Z allele (378 bp) with respect to body mass, plumage ornamentation, reproductive parameters and habitat quality. The Z* allele was found in 14% of 251 adult birds from nature reserves, but was absent from 33 birds breeding in intensively managed agricultural lands. Males and females with the Z* allele had less extensive breeding plumage, and females had a higher body mass, bred earlier and had larger eggs. There were no significant differences in annual survival between birds with and without the Z* allele. DNA isolated from museum skins demonstrated that this polymorphism was present at low frequency in 1929. We speculate that strong asymmetrical overdominance may explain the low frequency of the Z* allele and that genetic linkage to causal genes might be an explanation for the phenotypic correlations. Our findings suggest a degree of cryptic genetic population structuring in the Dutch Godwit population.
Creating an Emotion Responsive Dialogue System

The popularity of deep neural networks and vast amounts of readily available multidomain textual data has seen the advent of various domain/task specific and domain agnostic dialogue systems. In our work we present a general dialogue system that can provide a custom response based on the emotion or sentiment label selected. A dialogue system that can vary its response based on different affect labels can be very helpful for designing help-desk or social help assistant systems where the response has to follow a certain affective tone, such as positive, compassionate, etc. To address this task, we design a model that can generate coherent response utterances conditioned on a specified affect label (emotion or sentiment). We use a Sequence-toSequence model with an adversarial objective to remove affect from the learned representation of the input utterance, and generate the response based on this representation and the target affect label. Two models were evaluated: affect embedding and multi-decoder. We hypothesize that removal of the affect from the input utterance is helpful in generating a response conditioned on a different affect label. The models were evaluated on a large Twitter dialogue corpus. The results support our hypothesis.
Comparison of diets of the acouchy, agouti and paca, the three largest terrestrial rodents of French Guianan forests

The diets of the acouchy Myoprocta exilis, agouti Dasyprocta leporina and paca Agouti paca, the three largest terrestrial rodents of French Guiana forests, were investigated from stomachs collected over several years. These species are primarily frugivores. The percentage of fruit in their diet decreased, and seasonal variation increased from the smallest species, the acouchy, to the largest, the paca (contents in dry mass: respectively, 98.5% ± 0.6%, 87.4% ± 3.5%, and 83.9% ± 7.6%). They differed from each other in the proportions of pulp and secondary foods (leaves, fibre, insects) consumed annually as well as seasonally. Dietary diversity in the acouchy was half that of the two other species. The seasonal variation in consumption of different fruit parts and of secondary foods by these species corresponded well with the fruit production in the forest, and was linked to their reproductive events. Overall, the diets of these three large rodents appeared intermediate between the small rodent species and the artiodactyls (peccaries and brocket deer) inhabiting the same areas, which also concords with their body mass and their place within the guild of terrestrial mammals.
Populations and Local Extinctions of Birds on Barro Colorado Island, Panama

A 1960—71 study of populations of color—banded ant—following antbirds of three species on a tropical—forested lowland reserve, Barro Colorado Island, showed that the small species (Spotted Antbird, Hylophylax naevioides) remained stable at about 20 pairs/km2. A medium—sized species, the Bicolored Antbird (Gymnopithys bicolor), decreased from about 3 pairs to 1.5 pairs/km2. A large species, the Ocellated Antbird (Phaenostictus mcleannani), declined from 1.5 pairs/km2 to near extinction–only one female remained in early 1971. Two of three other species that regularly follow army ants showed relatively stable populations, but a third large species (Barred Woodcreeper, Dendrocolaptes certhia) declined from two pairs to local extinction. Prior to 1960 a very large ground—cuckoo that follows ants had already become extinct there. Thus, the three largest of the seven original species that regularly followed ants were gone or nearly gone by 1970. The decrease in numbers of regular ant—following birds was not made up by increases in occasional followers. Detailed studies of antbirds showed no clear reasons for declines, except that annual mortalities of adults were high in Ocellated Antbirds (about 30%) compared to Spotted Antbirds (15%—17%) and nest losses perhaps higher in the former (96% compared to 91%). Nest mortalities were slightly lower (88%) and adult mortalities intermediate (about 25%) in Bicolored Antbirds. Female Ocellated Antbirds had higher mortalities than males. The antbirds renest repeatedly during long nesting seasons, up to 14 times per year for Ocellated Antbirds. However, to replace females of this species under Barro Colorado conditions 19 nestings per year would be needed. Concurrent listing of all birds of the island showed that 45 species of breeding birds, 22% of the avifauna present when the island was made a reserve, had disappeared by 1970. No new species replaced them. Of the lost species 13 are forest birds, in danger if forests are cut elsewhere. The other species, second—growth and forest—edge birds, have been crowded out by growth of the forest. Loss of species from this tropical reserve, especially the part apparently caused by the small size and isolation of the reserve, poses problems for conservation and ecological studies of tropical biotas. It is suggested that large future reserves have corridor zones to each other, that is, that intensive human use not preempt too much area nor interrupt immigration of animals or plants from one refuge to another.
Nicotinic Receptor Assembly Requires Multiple Regions throughout the γ Subunit

Assembly of ionotropic neurotransmitter receptors typified by acetylcholine receptors (AChRs) is thought to be directed by an N-terminal extracellular domain of a subunit. Consistent with this hypothesis, chimeras with the δ subunit N-terminal domain fused to the rest of the γ subunit can substitute for δ, but not γ, subunits during AChR assembly. However, chimeras with the γ subunit N-terminal domain fused to the rest of the δ subunit cannot substitute for γ or δ subunits during assembly. Furthermore, expression of this chimera with the four wild-type subunits prevents the formation of α-bungarotoxin (Bgt) binding sites. Instead of AChR pentamers, complexes are assembled containing only the chimera and either α or β subunits. Based on the results of additional γ-δ chimeras, there are at least two different regions within the C-terminal half of the chimera required for the dominant-negative effect. Our results indicate that the N-terminal domain of the γ subunit mediates the initial subunit associations, whereas signals in the C-terminal half of the subunit are required for subsequent subunit interactions.
Isolation and characterization of a novel human gene, DRCTNNB1A, the expression of which is down-regulated by β-catenin

β-Catenin plays significant roles in cell-to-cell adhesion and the Wnt/Wg signal transduction pathway. Accumulation of this protein in the cytoplasm and nucleus as a result of mutations of the adenomatous polyposis coli tumor suppressor gene or of the β-catenin gene itself is often seen in a wide variety of tumors including carcinomas of the colon, liver, uterus, and brain. Interaction of accumulated β-catenin with Tcf/Lef transcription factors is known to deregulate expression of some downstream genes, but the precise mechanisms whereby β-catenin contributes to carcinogenesis remain to be disclosed. Here we report isolation of a novel murine gene, Drctnnb1a (down-regulated by Ctnnb1 , a), the expression of which was experimentally down-regulated in response to the activated form of β-catenin. To investigate a possible role of DRCTNNB1A in cancers, we also isolated the human homologue, DRCTNNB1A , the deduced product of which was 91% identical to the murine protein. The transcript was expressed in all human tissues examined, and we assigned the genomic location of DRCTNNB1A to chromosomal band 7p15.3 by in situ hybridization. Expression of DRCTNNB1A in SW480 colon cancer cells was significantly increased in response to reduction of intracellular β-catenin by adenovirus-mediated transfer of the β-catenin-binding domain of the adenomatous polyposis coli gene into the cells. Furthermore, we documented reduced expression of DRCTNNB1A in 12 of 15 primary colorectal cancers examined, compared with corresponding adjacent noncancerous mucosae. Our results implied that DRCTNNB1A is one of the genes involved in theβ -catenin-Tcf/Lef signaling pathway, and that reduced expression of DRCTNNB1A may have some role in colorectal carcinogenesis.
Sperm morphology of two species of Olivancillaria (Gastropoda: Olividae) from the south-western Atlantic

Sperm ultrastructure in two species of the marine snail family Olividae is examined. Euspermatozoa of both species are composed of a conical, membrane-bound acrosomal vesicle; an axial rod and a basal plate similar in both species; a solid and highly electron-dense nucleus; an elongate midpiece consisting of the axoneme sheathed by helical mitochondrial elements; an elongate glycogen piece; a double electron-dense ring at the junction of the midpiece and glycogen piece; and a free tail region. The slight narrowing in the acrosomal vesicle invagination is situated in different levels between Olivancillaria deshayesiana and Olivancillaria carcellesi. This morphology could be considered as a specific character. The length of the nucleus in O. carcellesi and in O. deshayesiana is shorter than that of other neogastropods, and could be diagnostic at family level.
Identification of Bacteria Infecting Seedlings of Mung Bean Used in Rooting Bioassays

Seeds of 'Berken' mung bean (Vigna radiata (L.) R. Wilcz. ) were surface-sterilized with NaOCl and then either aerated 24 hours before sowing (routine procedure), planted immediately after the NaOCl treatment, or treated with hot cupric acetate and antibiotics before planting. Nine- or 10-day-old seedlings were used in rooting bioassays. Up to 10% of the seedlings and 17% of the cuttings had collapsed upper stems or wilted leaves. None of the seed treatments completely eliminated the pathogen, but the combination of hot cupric acetate plus antibiotics reduced the quantity of diseased cuttings to 3.3%. A white and two yellow-pigmented (Y1 and Y2) bacteria were isolated from diseased cuttings and used in subsequent pathogenicity tests. The Y2 strain was nonpathogenic. Stems of plants inoculated with the white strain turned brown and collapsed 2 days after inoculation, whereas leaves of plants inoculated with the Y1 strain wilted after 7 days. Electron microscopy, fatty acid analysis, and standard biochemical and physiological tests were used to identify the white strain as Pseudomonas syringae pv. syringae van Hall and the Y1 strain as Curtobacterium flaccumfaciens ssp. flaccumfaciens (Hedges) Collins and Jones. These results emphasize that seeds of mung bean should be checked for seedborne pathogens to avoid experimental artifacts. Mung bean is used as a model system for physiological stud- ies on plant mitochondria (Musgrave et al., 1988) and adven- titious root initiation and development (Blazich and Heuser, 1979a; Tripepi et al., 1983; Norcini et al., 1985). The mung bean rooting bioassay (Blazich and Heuser, 1979b) is often used to determine the root-promoting ability of growth regulators or plant extracts (Kling and Meyer, 1983; Kling et al., 1988). An important requirement of this bioassay is to limit rooting vari- ability from factors other than experimental treatments (Bassuk and Howard, 1981). Several studies have shown that external factors can affect adventitious root formation in cuttings of mung bean. Water quality (Blazich and Heuser, 1979b; Duvall and Krul, 1985), age of the cuttings (Bassuk and Howard, 1981; Blazich and Heuser, 1979b), cotyledons (Bassuk and Howard, 1981), den- sity of cuttings in the rooting medium, and parental genotype (Duvall and Krul, 1985) can cause rooting variability among cuttings. In our work with the rooting bioassay, seedlings and cuttings of mung bean displayed symptoms of collapsed upper stems, wilted leaves, necrotic spots on leaves, or various combinations of these abnormalities (Fig. 1). Others (Blazich and Heuser, 1979b; J. Norcini, personal communication) have also encoun- tered similar difficulties with seedlings and cuttings of mung bean or reported that cuttings that lacked roots or rooted poorly often had lesions on their leaves. No information is available describing stem or leaf problems of mung beans used for rooting bioassays. Therefore, we document and identify the cause of leaf lesions and stem wilting in mung bean.
Photopigment radiolabelling as a tool for determining in situ growth rates of the toxic dinoflagellate Karenia brevis (Dinophyceae)

Determination of growth rates of harmful algae is critical to understanding bloom dynamics. However, we have few reliable methods of directly determining in situ growth rates on natural populations. One available method is photopigment radiolabelling, where C-specific growth rates are based on synthesis rates of chlorophylls and carotenoids using 14C-bicarbonate as a tracer. Here, we examined radiolabelling of the biomarker pigment gyroxanthin-diester as a tool for determining in situ growth rates of the toxic dinoflagellate Karenia brevis. We also characterized growth responses of K. brevis to various nitrogenous (N) nutrient sources and the presence or absence of a natural plankton community (including grazers) at two irradiances. We found that gyroxanthin radiolabelling may be used successfully to determine C-specific growth rates of K. brevis during monospecific blooms. However, the approach may be of limited use in mixed assemblages when there is low Karenia biomass because low concentrations of gyroxanthin per cell and low turnover rates result in poor signal for the gyroxanthin pigment. Growth rates of K. brevis generally ranged between 0.1 and 0.4 d−1. Cells in batch culture grew equally well on inorganic and organic forms of N, so they may be physiologically capable of using the major N forms present in agricultural run-off, atmospheric deposition, and other anthropogenic inputs. This has implications for the control of K. brevis blooms in nutrient-impacted coastal waters in that organic N inputs should be considered (along with inorganic N) in nutrient management strategies. Our highest C-specific growth rates (0.7 d−1) were measured in the presence of microzooplankton grazers, also indicating that the release of dissolved compounds may play a role in stimulating the growth of K. brevis in nature.
The art of modelling range‐shifting species

1. Species are shifting their ranges at an unprecedented rate through human transportation and environmental change. Correlative species distribution models (SDMs) are frequently applied for predicting potential future distributions of range‐shifting species, despite these models’ assumptions that species are at equilibrium with the environments used to train (fit) the models, and that the training data are representative of conditions to which the models are predicted. Here we explore modelling approaches that aim to minimize extrapolation errors and assess predictions against prior biological knowledge. Our aim was to promote methods appropriate to range‐shifting species.
Effects of Enzyme Combinations on Apparent Metabolizable Energy of Corn-Soybean Meal-Based Diets in Broilers

SUMMARY Corn and soybean meal (SBM) are high-quality feed ingredients for broiler diets. Antinutritive factors in SBM, such as protease inhibitors and lectins, are successfully inactivated by heat treatment. However, the nutritive value of these ingredients also depends on the amount of indigestible carbohydrates, in particular the amount of oligosaccharides and nonstarch polysaccharides (NSP). Despite the fact that such diets are low in indigestible carbohydrates, it has been suggested that the inclusion of exogenous feed enzymes to such diets could improve nutrient availability and, subsequently, improve energy digestibility. Four consecutive AME bioassays were conducted to investigate the effects of three singleactivity enzyme products, two multi-activity enzyme preparations, and a commercially available enzyme product added to a corn–SBM-based broiler diet. None of the evaluated enzyme combinations successfully improved the performance of 3- to 4wk-old broiler chickens. However, in experiments 1 and 2, when enzymes were included in a lowerenergy corn–SBM basal diet, the combination of pectinase, protease, and amylase significantly improved AMEn in comparison to the unsupplemented basal diet. Subsequent experiments with a higher energy and protein basal diet failed to show the same improvement when enzymes were added. Results of this study indicated that although enzyme addition to corn–SBM-based basal diets can significantly improve AMEn, the success of such improvement depended greatly on the raw ingredients available at the time.
Involvement of FgMad2 and FgBub1 in regulating fungal development and carbendazim resistance in Fusarium graminearum

Resistance to carbendazim of Fusarium graminearum is conferred by point mutation in the β2-tubulin gene that plays an important role in spindle assembly. The spindle assembly checkpoint is a cellular surveillance system that is critical for maintaining genomic stability. Predicted protein Mad2- and Bub1-encoding genes in F. graminearum (FgMad2 and FgBub1) were isolated and characterized. There was no difference in FgMad2 and FgBub1 expression levels between carbendazim-sensitive and -resistant strains; however, after carbendazim treatment FgMad2 expression increased while FgBub1 expression stayed the same. Both the FgMad2 and FgBub1 deletion mutants became more sensitive to carbendazim. The FgMad2 deletion mutants grew more slowly, produced fewer conidia and both hyphae and conidia were malformed. Conversely, deletion of FgBub1 had no effect on fungal development other than a reduction in conidia production. FgMad2 deletion mutants exhibited a severe decrease in perithecia production and pathogenicity along with a down-regulation of trichothecene production, whereas FgBub1 deletion mutants exhibited only a slight reduction in perithecia production and was accompanied by a twofold increase in trichothecene production. Overall, the results indicate that both FgMad2 and FgBub1 are involved in carbendazim resistance and trichothecene biosynthesis, and FgMad2 plays an important role in fungal development in F. graminearum.
The ‘debt’ is in the detail: A synthesis of recent temporal forest carbon analyses on woody biomass for energy

The temporal imbalance between the release and sequestration of forest carbon has raised a fundamental concern about the climate mitigation potential of forest biomass for energy. The potential carbon debt caused by harvest and the resulting time spans needed to reach pre‐harvest carbon levels (payback) or those of a reference case (parity) have become important parameters for climate and bioenergy policy developments. The present range of analyses however varies in assumptions, regional scopes, and conclusions. Comparing these modeling efforts, we reveal that they apply different principle modeling frameworks while results are largely affected by the same parameters. The size of the carbon debt is mostly determined by the type and amount of biomass harvested and whether land‐use change emissions need to be accounted for. Payback times are mainly determined by plant growth rates, i.e. the forest biome, tree species, site productivity and management. Parity times are primarily influenced by the choice and construction of the reference scenario and fossil carbon displacement efficiencies. Using small residual biomass (harvesting/processing), deadwood from highly insect‐infected sites, or new plantations on highly productive or marginal land offers (almost) immediate net carbon benefits. Their eventual climate mitigation potential however is determined by the effectiveness of the fossil fuel displacement. We deem it therefore unsuitable to define political guidance by feedstock alone. Current global wood pellet production is predominantly residue based. Production increases based on low‐grade stemwood are expected in regions with a downturn in the local wood product sector, highlighting the importance of accounting for regional forest carbon trends. © 2013 Society of Chemical Industry and John Wiley & Sons, Ltd