Miracle-dz/UniFAR-FTUs huggingface dataset:
Homeostatic control of meiotic G2/prophase checkpoint function by Pch2 and Hop1

Checkpoints cascades coordinate cell cycle progression with essential chromosomal processes. During meiotic G2/prophase, recombination and chromosome synapsis are monitored by what are considered distinct checkpoints [1–3]. In budding yeast, the AAA+ ATPase Pch2 is thought to specifically promote cell cycle delay in response to synapsis defects [4–6]. However, unperturbed pch2Δ cells are delayed in meiotic G2/prophase [6], suggesting paradoxical roles for Pch2 in cell cycle progression. Here, we provide insight into the checkpoint roles of Pch2 and its connection to Hop1, a HORMA domain-containing client protein. Contrary to current understanding, we find that the Pch2-Hop1 module is crucial for checkpoint function in response to both recombination and synapsis defects, thus revealing a shared meiotic checkpoint cascade. Meiotic checkpoint responses are transduced by DNA break-dependent phosphorylation of Hop1 [7, 8]. Based on our data and on the effect of Pch2 on HORMA topology [9–11], we propose that Pch2 promotes checkpoint proficiency by catalyzing the availability of signaling-competent Hop1. Conversely, we demonstrate that Pch2 can act as a checkpoint silencer, also in the face of persistent DNA repair defects. We establish a framework in which Pch2 and Hop1 form a homeostatic module that governs general meiotic checkpoint function. We show that this module can - depending on the cellular context - fuel or extinguish meiotic checkpoint function, which explains the contradictory roles of Pch2 in cell cycle control. Within the meiotic checkpoint, the Pch2-Hop1 module thus operates analogous to the Pch2/TRIP13-Mad2 module in the spindle assembly checkpoint that monitors chromosome segregation [12–16].
The gradient between pre-dawn rhizoplane and bulk soil matric potentials, and its relation to the pre-dawn root and leaf water potentials of four species

Uptake of soil water by plants may result in significant gradients between bulk soil and soil in the vicinity of roots. Few experimental studies of water potential gradients in close proximity to roots, and no studies on the relationship of water potential gradients to the root and leaf water potentials, have been conducted. The occurrence and importance of pre-dawn gradients in the soil and their relation to the pre-dawn root and leaf water potentials were investigated with seedlings of four species. Pre-germinated seeds were grown without watering for 7 and lid in a silt loam soil with initial soil matric potentials of -0.02, -0.1 and -0.22 MPa. Significant gradients, independent of the species, were observed only at pre-dawn soil matric potentials lower than -0.25 MPa; the initial soil matric potentials were -0.1 MPa. At an initial bulk soil matric potential of -0.22 MPa, a steep gradient between bulk and rhizoplane soil was observed after 7 d for maize (Zea mays L. cv. Issa) and sunflower (Helianthus annuus L. cv. Nanus), in contrast to barley (Hordeum vulgare L. cv. Athos) and wheat (Triticum aestivum L. cv. Kolibri). Pre-dawn root water potentials were usually about the same as the bulk soil matric potential and were higher than the rhizoplane soil matric potential. Pre-dawn root and leaf water potentials tended to be much higher than rhizoplane soil matric potentials when the latter were lower than -0.5 MPa. It is concluded that plants tend to become equilibrated overnight with the wetter bulk soil or with wetter zones in the bulk soil. Plants can thus circumvent negative effects of localized steep pre-dawn soil matric potential gradients. This may be of considerable importance for water uptake and growth in drying soil.
Shared neuronal bases of inhibition and economic choice in orbitofrontal cortex

Economic choice and inhibition are two important elements of our cognitive repertoires that may be closely related. We and others have noted that during economic choice, options are typically considered serially; this fact provides important constraints on our understanding of choice. Notably, asynchronous contemplation means that each individual option is subject to an accept-reject decision. We have proposed that these component accept-reject decisions may have some kinship with stopping decisions. One prediction of this idea is that stopping and choice may reflect similar neural processes occurring in overlapping brain circuits. To test the idea, we recorded neuronal activity in orbitofrontal cortex (OFC) Area 13 while macaques performed a stop signal task interleaved with a structurally matched choice task. Using neural network decoders, we find that OFC ensembles have overlapping codes for stopping and choice: the decoder that was only trained to identify accept vs. reject trials performed with higher efficiency even when tested on the stop trials. These results provide tentative support for the idea that mechanisms underlying inhibitory control and choice selection may be subject to theoretical unification.
P2X-GCaMPs as Versatile Tools for Imaging Extracellular ATP Signaling

Abstract ATP is an extracellular signaling molecule involved in numerous physiological and pathologic processes. However, in situ characterization of the spatiotemporal dynamic of extracellular ATP is still challenging because of the lack of sensor with appropriate specificity, sensitivity, and kinetics. Here, we report the development of biosensors based on the fusion of cation permeable ATP receptors (P2X) to genetically encoded calcium sensors [genetically encoded calcium indicator (GECI)]. By combining the features of P2X receptors with the high signal-to-noise ratio of GECIs, we generated ultrasensitive green and red fluorescent sniffers that detect nanomolar ATP concentrations in situ and also enable the tracking of P2X receptor activity. We provide the proof of concept that these sensors can dynamically track ATP release evoked by depolarization in mouse neurons or by extracellular hypotonicity. Targeting these P2X-based biosensors to diverse cell types should advance our knowledge of extracellular ATP dynamics in vivo.
Ecological growth response specificity of two Douglas-fir ecotypes inoculated with coexistent beneficial rhizosphere bacteria

The influence of inoculation with rhizosphere bacteria on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedling emergence in a controlled environment and on survival and growth in the field was investigated. Seed or seedlings of interior and coastal Douglas-fir ecotypes originating from the vicinity of Williams Lake and Chilliwack, British Columbia, Canada, respectively, were inoculated with two strains of rhizosphere bacteria, Arthrobacter oxydans strain N74 and Pseudomonas aureofaciens strain K23. These strains were previously isolated from naturally regenerating Douglas-fir seedlings collected from the Williams Lake and Chilliwack sites, respectively. Seed inoculation with either strain of bacteria, K23 or N74, stimulated the rate of seedling emergence, but these effects were not ecotype specific. While inoculation did not affect germination percentage, ecotype-specific seedling growth responses were detected 13 months after field planting. Arthrobacter oxydans strain N74 significantly stimulated.
Phytoextraction of Zinc by Oat (Avena sativa), Barley (Hordeum vulgare), and Indian Mustard (Brassica juncea)

The success of phytoremediation hinges on the selection of plant species and soil amendments that maximize contaminant removal. Indian mustard (Brassica juncea) has been shown to be effective in phytoextracting Zn, particularly after the synthetic chelate EDTA has been applied to the soil. However, the effectiveness of grass species for phytoremediation has not been addressed in great detail. A hydroponic screening of 22 grass species indicated that oat (Avena sativa) and barley (Hordeum vulgare) tolerated the high Cu, Cd, and Zn concentrations present in the solution and also accumulated elevated concentrations of these metals in the plant shoots. A hydroponic experiment comparing these two grasses to Indian mustard indicated that, although shoot Zn concentrations were greater for Indian mustard, the grasses were considerably more tolerant. A pot experiment conducted using a Zn-contaminated soil showed that the addition of EDTA to the soil significantly increased Zn accumulation by B. juncea but not oat .
On the Robustness of Graph-Based Clustering to Random Network Alterations

Biological functions emerge from complex and dynamic networks of protein-protein interactions. Because these protein-protein interaction networks, or interactomes, represent pairwise connections within a hierarchically organized system, it is often useful to identify higher-order associations embedded within them, such as multi-member protein-complexes. Graph-based clustering techniques are widely used to accomplish this goal, and dozens of field-specific and general clustering algorithms exist. However, interactomes can be prone to errors, especially interactomes that infer interactions using high-throughput biochemical assays. Therefore, robustness to network-level variability is an important criterion for any clustering algorithm that aims to generate robust, reproducible clusters. Here, we tested the robustness of a range of graph-based clustering algorithms in the presence of network-level noise, including algorithms common across domains and those specific to protein networks. We found that the results of all clustering algorithms measured were profoundly sensitive to injected network noise. Randomly rewiring 1% of network edges yielded up to a 57% change in clustering results, indicating that clustering markedly amplified network-level noise. However, the impact of network noise on individual clusters was not uniform. We found that some clusters were consistently robust to injected network noise while others were not. Therefore, we developed the clust.perturb R package and Shiny web application, which measures the reproducibility of clusters by randomly perturbing the network. We show that clust.perturb results are predictive of real-world cluster stability: poorly reproducible clusters as identified by clust.perturb are significantly less likely to be reclustered across experiments. We conclude that quantifying the robustness of a cluster to network noise, as implemented in clust.perturb, provides a powerful tool for ranking the reproducibility of clusters, and separating stable protein complexes from spurious associations.
Tumor-infiltrating nerves create an electro-physiologically active microenvironment and contribute to treatment resistance

Patients with densely innervated tumors do poorly as compared to those with sparsely innervated disease. Why some tumors heavily recruit nerves while others do not, remains unknown as does the functional contribution of tumor-infiltrating nerves to cancer. Moreover, while patients receive chemotherapeutic treatment, whether these drugs affect nerve recruitment has not been tested. Using a murine model of ovarian cancer, we show that tumor-infiltrating sensory nerves potentiate tumor growth, decrease survival, and contribute to treatment resistance. Furthermore, matched patient samples show significantly increased tumor innervation following chemotherapy. In vitro analysis of tumor-released extracellular vesicles (sEVs) shows they harbor neurite outgrowth activity. These data suggest that chemotherapy may alter sEV cargo, endowing it with robust nerve recruiting capacity.
Comparative evaluation of the efficacy of cereal and microbial phytases in growing pigs fed diets with marginal phosphorus supply

Two experiments with a total of 76 growing pigs (average initial body weight 16.6 kg) were conducted to compare the efficacy of cereal phytases (wheat and rye) and supplemented microbial phytase (Natuphos®). Using the slope ratio technique, the dose–response relationship between five levels of phytase (0, 50, 100, 150 and 200 U kg−1) and the apparent absorption of phosphorus (P) within each source of phytase was calculated. Graded phytase levels in the diets were obtained by adding increasing amounts of microbial phytase or phytase-containing wheat (Exp 1) or rye (Exp 2) to phytase-inactivated basal diets at the expense of phytase-inactivated wheat (Exp 1) or rye (Exp 2). Except for wheat phytase, addition of phytase to the basal diets increased (P < 0.05) apparent P absorption, with microbial phytase being more efficient (P < 0.05) than cereal phytase. There were no significant differences in apparent P absorption between the wheat- or rye-based diets when either microbial or cereal phytases were supplemented from 0 to 200 U kg−1. It could be derived from the results of this study, by means of regression analysis, that the efficacy of cereal phytases was 40% compared to microbial phytase. © 2002 Society of Chemical Industry
The polymorphism, mimicry, and host plant relationships of Hypolimnas butterflies

The 30 species of Hypolimnas butterflies recognized are divided amongst six pattern morphism classes: monomorphic, weakly dimorphic, simple dual, unimodal polymorphic, partial 9-limited polymorphic, and multiple ♀ dual polymorphic. Eighty per cent of Hypolimnas species belong to one or other of the first three categories. About 60% of the species show evidence of mimicry, some 40% being mimetic in both sexes. In the Oriental region the great majority of mimetic species within the genus are modelled on Euptoea, whilst those of the Afrotropical region are mostly modelled on Amauris. The host plants recorded for the genus strongly suggest that the Urticaceae are primitive for the group, but eleven other families of flowering plants are recorded as hosts. The apparent non-utilization of Urticaceae by H. misippus (L.), the most widespread species of the group, is discussed in terms of its possible ecological and phylogenetic relationships with H. bolina (L.). A check-list of butterflies feeding on Ipomoea (a host plant for both H. bolina and H. misippus), and on other Convolvulaceae, is included.
Differential growth dependency of normal and habituated sugarbeet cell lines upon endogenous ethylene production and exogenous ethylene application

A fully habituated (auxin- and cytokinin-independent) nonorganogenic (HNO) sugarbeet (Beta vulgaris) callus produces very little ethylene as compared with a normal (N) hormone-requiring callus of the same strain. Both callus types react by growth changes to application of inhibitors of ethylene biosynthesis and ethylene action, of 1-aminocyclopropane-1-carboxylic acid (ACC) as the immediate precursor of ethylene, to transfer from light to darkness, and also to application of exogenous ethylene or an ethylene trapper. This indicates their growth dependency upon their endogenously biosynthesized ethylene and also their sensitivity to exogenous gas. However, the sensitivity was generally higher for the HNO callus producing naturally less ethylene. The weaker reaction of the HNO callus to the exogenous ethylene was attributed to its hyperhydric status (a water layer surrounding the cells). Because low ethylene production appears as a general characteristic of habituated cell lines, the causal and/or consequential relationships of this low ethylene production with other characteristics of habituated tissues (absence of exogenous hormones in the culture media, deficiency of cell differentiation, accumulation of polyamines in neoplastic tissues) are discussed.
Lenalidomide Plus Decitabine Treatment in a Myelodysplastic Syndrome Patient With Deletion 5q and Excess Blasts

This is the first case of decitabine plus lenalidomide treatment for a myelodysplastic syndrome (MDS) patient with 5q deletion (del(5q)) and elevated number of blasts. Upon bone marrow aspiration and biopsy with conventional cytogenetical studies she was diagnosed with MDS with del(5q) and refractory anemia with excess blasts (RAEB-1). Decitabine was started at a daily dose of 20 mg/m2 1 - 5 days and lenalidomide was started at daily doses of 10 mg 6 - 20 days a month. After two cycles, her hemoglobin level increased and transfusion dependency ceased. After four cycles, bone marrow aspiration showed blast ratio of < 5%. Decitabine and lenalidomide were applied for three more cycles. Decitabine was terminated after seven cycles and lenalidomide has been continued for 12 months. Latest blood values (February 2020) were as follows: white blood cells (WBCs) of 8,670/mm3, neutrophil count of 3,470/mm3, hemoglobin (Hb) level of 11.7 g/dL and platelet count of 203,000/mm3, and the patient continues to follow-up without treatment. In conclusion, combination of lenalidomide and decitabine seems to be an effective treatment modality without notable side effects in MDS patients with del(5q) and excess blasts. The efficacy of this combination should be validated with studies including large patient groups and with longer follow-up periods.
Water-promoted interfacial pathways in methane oxidation to methanol on a CeO2-Cu2O catalyst

A water boost for methanol synthesis Model catalysts based on metals and metal oxides can dissociate methane (CH4) at room temperature, converting it directly to methanol (CH3OH). Liu et al. show that for one of these catalysts, an “inverted” CeOx-Cu2O oxide on Cu(111), water tunes the selectivity from forming CO and CO2 to forming surface CH3O groups, as revealed by ambient-pressure x-ray photoelectron spectroscopy. Theoretical modeling showed that adsorbed water blocks O2 dissociation and O2 instead oxidizes the reduced catalyst. Hydroxyl groups from water generate the CH3O species from dissociated CH4, and water then goes on to form and displace CH3OH to the gas phase. Science, this issue p. 513 Water can play a direct role in the heterogeneous partial oxidation of methane to methanol. Highly selective oxidation of methane to methanol has long been challenging in catalysis. Here, we reveal key steps for the promotion of this reaction by water when tuning the selectivity of a well-defined CeO2/Cu2O/Cu(111) catalyst from carbon monoxide and carbon dioxide to methanol under a reaction environment with methane, oxygen, and water. Ambient-pressure x-ray photoelectron spectroscopy showed that water added to methane and oxygen led to surface methoxy groups and accelerated methanol production. These results were consistent with density functional theory calculations and kinetic Monte Carlo simulations, which showed that water preferentially dissociates over the active cerium ions at the CeO2–Cu2O/Cu(111) interface. The adsorbed hydroxyl species blocked O-O bond cleavage that would dehydrogenate methoxy groups to carbon monoxide and carbon dioxide, and it directly converted this species to methanol, while oxygen reoxidized the reduced surface. Water adsorption also displaced the produced methanol into the gas phase.
Interactive effects of larval host and competition on adult fitness: an experimental test with seed beetles (Coleoptera: Bruchidae)

Summary 1Resources and intensity of competition encountered during development can have significant consequences for adult fitness, yet their effects are rarely considered simultaneously. Furthermore, it is often assumed that these factors affect adult fitness only indirectly through their effects on body mass. Here, I examined the direct effects of larval host type and intensity of competition on mass at emergence and fecundity in two species of bruchid beetles (Callosobruchus spp.). 2There was no effect of competition treatments on mass at emergence of C. chinensis females reared in Adzuki or Mung Beans. Controlling for body mass, there was a significant effect of competition treatment on number of eggs laid by C. chinensis females that had been reared on Mung Beans, with those reared with a competitor laying significantly fewer eggs than females that had been reared in the absence of competition. Competition had a highly significant effect on mass at emergence of C. maculatus females reared in Mung Beans. In the absence of a significant effect of competition on mean mass at emergence in Adzuki Beans, females reared with two competitors laid significantly fewer eggs than did females reared with either one or no competitors. 3For certain combinations of bruchid species and resource type, thus, females laid fewer eggs for a given mass at emergence if they had been subject to competition during their larval phase. These results reveal subtle differences in the responses of closely related species with similar life histories to resources and competition during development, calling into question current generalizations about the direct effects of competition on fitness.
The viviparous8 mutation delays vegetative phase change and accelerates the rate of seedling growth in maize

Summary Post-embryonic shoot development in plants can be divided into a juvenile vegetative, an adult vegetative, and a reproductive phase, which are expressed in different domains on the shoot axis. The number and position of the phytomers in each phase are determined by the time at which a plant begins and ceases making phytomers of a particular phase and the rate at which phytomers are made during that phase. The viviparous8 (vp8) mutation of maize increases the number of juvenile vegetative phytomers and decreases the number of adult vegetative phytomers by affecting both of these processes. vp8 increases the number of juvenile vegetative phytomers by increasing the rate of leaf initiation early in shoot development and delaying the juvenile-to-adult transition (vegetative maturation). It reduces the number of adult phytomers because the delay in vegetative maturation is not matched by a corresponding delay in flowering time; vp8 plants produce a tassel at the same time as wild-type plants. Thus, Vp8 normally controls the production of a factor that functions both to repress the rate of growth early in shoot development and to promote vegetative maturation, but which has no major role in floral induction. vp8 dramatically enhances the phenotypes of the dwarf and Teopod mutants and requires a functional Glossy15 gene to prolong the expression of juvenile epidermal traits. Evidence suggesting that vp8 does not affect phase change by reducing the level of abscisic acid is discussed.
A Survey of Intrusion Detection Systems in Wireless Sensor Networks

- Wireless Sensor Networking is a standout amongst the most promising advancements that have applications running from medicinal services to strategic military. Wireless Sensor Networks (WSNs) are made out of sensor center points and sinks. Despite the fact that Wireless Sensor Networks (WSNs) have engaging highlights (e.g., low establishment cost, unattended system task), because of the absence of a physical line of guard (i.e., there are no doors or changes to screen the data stream), the security of such systems is a major concern, particularly for the applications where security has prime significance. For the most part sensor center points are used in such districts where wired frameworks are hard to be passed on. Various security-related responses for WSNs have been proposed, for instance, check, key exchange, and secure coordinating or security frameworks for specific ambushes. These security instruments are prepared for ensuring security at some measurement; at any rate they can't wipe out by far most of the security ambushes An IDS is one possible response for area a broad assortment of security strikes in WSNs. In this article, Intrusion Detection Systems (IDSs) that are proposed for WSNs is given. This is sought after by the examination and relationship of each arrangement alongside their positive conditions and burdens