Miracle-dz/UniFAR-FTUs huggingface dataset:
The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and insights into Kex2 protease processing of fungal effectors

Plant pathogens cause disease through secreted effector proteins, which act to modulate host physiology and promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilised a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination. We show this approach can be successfully applied to effectors from other pathogenic fungi. Complementing this, an in-silico study uncovered the prevalence of an expanded subclass of effectors from fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. We demonstrate that SnTox3 is a pre-pro-protein and that the protease Kex2 removes the pro-domain. Our in-silico studies suggest that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi, and we demonstrate this experimentally for effectors from Fusarium oxysporum f sp. lycopersici. We propose that K2PP effectors are highly prevalent among fungal effectors. The identification and classification of K2PP effectors has broad implications for the approaches used to study their function in fungal virulence.
A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.
Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, periphyton scraping, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional microhabitat periphyton scraping and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton scraping and kick-net methodologies, but there was significant difference between diatom communities depending on site quality (P = 0.029). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms and macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes.
Single-dose replicating RNA vaccine induces neutralizing antibodies against SARS-CoV-2 in nonhuman primates

The ongoing COVID-19 pandemic, caused by infection with SARS-CoV-2, is having a dramatic and deleterious impact on health services and the global economy. Grim public health statistics highlight the need for vaccines that can rapidly confer protection after a single dose and be manufactured using components suitable for scale-up and efficient distribution. In response, we have rapidly developed repRNA-CoV2S, a stable and highly immunogenic vaccine candidate comprised of an RNA replicon formulated with a novel Lipid InOrganic Nanoparticle (LION) designed to enhance vaccine stability, delivery and immunogenicity. We show that intramuscular injection of LION/repRNA-CoV2S elicits robust anti-SARS-CoV-2 spike protein IgG antibody isotypes indicative of a Type 1 T helper response as well as potent T cell responses in mice. Importantly, a single-dose administration in nonhuman primates elicited antibody responses that potently neutralized SARS-CoV-2. These data support further development of LION/repRNA-CoV2S as a vaccine candidate for prophylactic protection from SARS-CoV-2 infection.
Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli

Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an engineered E. coli strain. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth depending on CCM components. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, laying the groundwork for deeper study and engineering of mechanisms enhancing CO2 assimilation. One Sentence Summary A bacterial CO2 concentrating mechanism enables E. coli to fix CO2 from ambient air.
Evaluation of a novel aminopeptidase N inhibitor, in vitro, using two assay systems

The activities of the novel aminopeptidase N inhibitor (APNI), β-Amino-α-Hydroxyl-Phenyl butanic acid-Valine (AHPA-Val), were compared with APNI (amastatin). AHPA-Val and amastatin produced competitive inhibition of the hydrolysis of Tyr-Gly in the guinea-pig striatal membrane preparation, with Ki equal to 14.06 μM and 12.48 μM respectively. Met-enkephalin-induced twitch inhibition of the guinea-pig ileum preparation was enhanced by AHPA-Val and amastatin with pA1/2 values (the negative logarithm concentration of APNI that decreased the IC50 of Met-enkephalin by half), of 7.08 and 7.79 respectively. These results suggest that AHPA-Val has good activity as an APNI and that these two assay systems are useful for evaluating the potency of novel APNIs.
A new PCR-based linkage map in pearl millet.

Pearl millet [Pennisetum glaucum (L.) R. Br. ] is a multipurpose cereal grown for grain, stover, and green fodder. Relative to other cereal species, it ranks sixth in annual world production. Use of molecular marker technology for pearl millet genetic improvement has been limited because of an insufficiently developed linkage map. The majority of the pearl millet molecular markers (RFLP and SSR) mapped to date are clustered around the seven pearl millet chromosome centromeres, and only a few marker loci are mapped to more distal regions. There is a need for more evenly distributed markers throughout the linkage map and greater marker coverage of the gaps in earlier established maps. The objective of this research was to develop a PCR-based molecular marker linkage map for pearl millet on the basis of a recombinant inbred line (RIL) population resulting from a cross between Tift 23DB and PI 536400. This mapping effort involved 152 RILs and 196 PCR-based DNA markers (66 SRAPs, 63 RAPDs, 27 ISSRs, 31 pearl millet, 6 sorghum, and 3 maize SSRs). The average genetic distance between markers was 9.2 cM, varying from 0 to 25.6 cM. The number of markers in each linkage group (LG) ranged from 6 to 35. The resulting map consisted of nine linkage groups that spanned about 1796 cM. The majority of the markers used in this study to construct the genetic linkage map were randomly distributed in each LG, which makes it useful in pearl millet mapping and breeding.
Cloning and sequence analysis of the mouse smooth muscle γ-enteric actin gene

Abstract Actin represents one of the most highly conserved families of proteins in evolution. The work presented here describes the molecular characterization of the mouse smooth muscle (enteric) γ-actin gene (SMGA). It represents the largest isoactin gene characterized to date, measuring aver 23,000 bp from the transcription start site to the polyadenylation signal. The gene is divided into nine exons and encodes a mature actin protein of 374 amino acids. Putative regulatory elements are noted as well as regions of the gene that have the potential to form non-B DNA conformations that may influence gene expression.
Osteoconductive material of a newly developed resin modified glass ionomer cement containing bioactive glasses for biomedical purposes

Hybridization of resin modified- glass ionomer cement (RMGIC) and bioactive glass (BAG) may result higher mechanical strength and resistance to disintegration, while less contain of polyacrylic acid would lead to bioactivity of the cement. In the present study we investigated the effect of BAG from the CaSiO3-Ca3(PO4)2 system addition to the bioactivity of RMGIC. The BAG containing 10, 15, and 20% of P2O5 (denoted as CSP10, 15, and 20) were used in the study to modify the powder of RMGIC, with apatite wollastonite (AWG) was chosen for a comparison. The surface bioactivity was assessed using XRD, FT-IR, and SEM analysis after specimen immersion in the simulated body fluid (SBF). Measurement of Ca, P, F, Sr, and Al was conducted for the remaining SBF. Cells studies were done to evaluate cell attachment, proliferation, and differentiation on the RMGIC containing BAG compared to the one without BAG. Results of Sr and Al analysis lead to the conclusion that addition of BAG may not influence stability of the matrix of the cement. It was also confirmed that addition of bioactive glass was positive factor indicating excellent ions exchange in SBF and spontaneous growth of apatite by consuming the Ca and P ions in the surrounding fluid. The ability of osteoblasts differentiation on the four types of bioactive cements were higher than that of RMGIC without BAG. These results might provide novel insights into the development of a new generation of osteoconductive biomedical materials.
Application du thermohumectographe KIT‐INRA. Etude des risques de tavelure du pommier à l‘échelle du Maine‐et‐Loire (France)

La region d'Angers (Maine-et-Loire), zone importante de production de pommes, est particulierement exposee aux degâts causes par Venturia inaequalis, agent de la tavelure. L'equipement de stations avec un thermohumectographe KIT-INRA et un pluviometre a permis une etude prealable a l'etablissement d'un reseau d'avertissements. Les donnees collectees a partir des appareils sont interpretees selon les courbes de Mills (avec une modification liee aux risques eleves en Val de Loire). L'interpretation en 1980 et 1981 a ete realisee localement. L'epidemie particulierement grave en 1981 a permis de preciser la valeur de la methode d'interpretation et de determiner l'heterogeneite des contaminations a l'echelle du departement (120 × 80 km). A partir des donnees obtenues, il est possible de mieux definir les mailles du reseau et de « regionaliser » les informations en vue d'une extension en 1982, prevoyant une centralisation des donnees et la diffusion par repondeur telephonique d'un message d'avertissement. Les resultats attendus portent avant tout sur une amelioration de la qualite de la lutte chimique, sur une reduction du nombre des interventions et sur une meilleure utilisation des possibilites offertes par les applications curatives.
Monitoring of Excavation Works Using Modern Measuring Technology

Modern technology plays a fundamental role in the engineering activities undertaken in day-to-day operations, in order to obtain the necessary material for construction or to obtain certain useful materials that are found near the surface. A special contribution of this branch of terrestrial measurements, of the topography, using modern technology, is materialized by specific studies carried out from a preliminary phase of design of the operation and up to the phase in which the perimeter is ecologized. The present article aims to test and evaluate the accuracy of the data for volumetric measurements of exploited material, using modern technology and specialized software based on topographic altitude, with which we will be able to realize the three-dimensional model of the operating perimeter. For this purpose, an exploitation has been chosen on the appropriate surface, materialized through a case study, with reference to the Doman Quarry, Caras Severin, in which we determined the volumes exploited during the activity period.
Biochemical Characteristics of Spontaneous Mutants of Acetobacter aceti Deficient in Ethanol Oxidation

It has frequently been observed that acetic acid bacteria showconsiderable genetic instability which causes spontaneous mutations leading to deficiencies in various physiological properties including taxonomically crucial ones.1)2) Amongthese mutants there were strains which had lost their ethanol oxidizing ability.3~5) We isolated a thermophilic strain, No. 1023, of Acetobacter aceti which exhibited elevated resistance to acetic acid which was probably responsible for its thermophilic characteristics.6) Prolonged cultivation of the strain led to the appearance of acetic acid sensitive mutants which were deficient in ethanol oxidizing ability with high frequency.7)
Site Quality Evaluation Models for Aspen (Populustremuloides Michx.) in Wisconsin

Soil and site relationships were studied in 32 mature quaking aspen (Populustremuloides Michx.) communities in north central Wisconsin. Multiple linear regression techniques indicated that soil texture, available water-holding capacity, water-table depth, and stand exposure were the most important factors controlling site index. Two models developed from combinations of these factors accounted for 62% of the variation in site index. Values for soil calcium, magnesium, potassium, and phosphorus were corrected for bulk density and summed to 12-, 24-, 36-, and 60-in. depths. When included in additional models, only magnesium to a 60-in. depth was found to have additional effect on aspen growth over and above that implicit in available water-holding capacity. The models were validated using 10 additional mature aspen stands and then applied to data from 10 stands in early stages of deterioration.
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis

Bacillus thuringiensis (Bt) which is a spore-forming gram-positive bacterium, has been used as the most successful microbial pesticide for decades. Its toxin genes (cry) have been successfully used for the development of GM crops against pests. We have previously developed a web-based insecticidal gene mining tool BtToxin_scanner, which has been proved to be the most important method for mining cry genes from Bt genome sequences. To facilitate efficiently mining major toxin genes and novel virulence factors from large-scale Bt genomic data, we re-design this tool with a new workflow. Here we present BtToxin_Digger, a comprehensive, high-throughput, and easy-to-use Bt toxin mining tool. It runs fast and can get rich, accurate, and useful results for downstream analysis and experiment designs. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the addition of other query sequences. Availability and Implementation The BtToxin_Digger codes and instructions are freely available at https://github.com/BMBGenomics/BtToxin_Digger. A web server of BtToxin_Digger can be found at http://bcam.hzau. edu.cn/BtToxin_Digger. Contact jszheng@mail.hzau. edu.cn; m98sun@mail.hzau. edu.cn.
Reproduction of Pimelodus maculatus(Siluriformes: Pimelodidae) in three section of Grande River basin, downstream Porto Colombia dam, south-eastern Brazil

The alterations to the hydrologic regime downstream from hydroelectric dams may cause an impact on the reproductive success of fishes. This study aimed to analyse the influence of the physical and chemical parameters of the water of the Grande and Pardo Rivers on gonadal maturation, oocyte diameter, follicular atresia and biological indices of Pimelodus maculatus collected from three river sections: Grande River, downstream from the Porto Colombia dam (S1), Grande River, downstream from the confluence with the Pardo River (S2) and in the Pardo River channel (S3). Males and females captured in S1 presented significantly higher average values for total length and body weight than those captured in S2 and S3. The gonadosomatic index values were significantly higher in fish collected in S3 and the Fulton condition factor did not show significant differences in fish collected from the three sections. The oocyte diameter, the follicular cells height and the zona pellucida thickness did not show any statistical differences between the sections. Conductivity presented a significant difference between S1 and S3 and during the reproductive period, water transparency presented similar values in the two sampling sections of the Grande River, but a much lower value in the Pardo River. A low frequency of fish with reproductive activity was registered in S1, whereas in S2 and S3 higher frequencies were recorded, emphasising the need of preserving the tributaries for the reproductive success of P. maculatus of the Grande River in south-eastern Brazil.
The Global Trade in Live Cetaceans: Implications for Conservation

Cetaceans—small whales, dolphins and porpoises—have long been popular performers in oceanaria. Captive cetaceans have also been used for research and employed in military operations. In some jurisdictions cetacean display facilities have been phased out or prohibited, and in the US and Hong Kong a high proportion of the whales and dolphins now in captivity have been captive-bred. A large, growing and increasingly opportunistic trade in dolphins and small toothed whales nevertheless exists, its centres of supply having shifted away from North America, Japan, and Iceland to the Russian Federation and developing nations in Latin America, the Caribbean, West Africa, and Southeast Asia. Demand for live captures is being driven by: a new wave of traditional-type oceanaria and dolphin display facilities, as well as travelling shows, in the Middle East, Asia, Latin America, and the Caribbean; increasingly popular programs that offer physical contact with cetaceans, including the opportunity to feed, pet, and swim with them; and the proliferation of facilities that offer ‘dolphin assisted therapy’ to treat human illness or disability. Rigorous assessment of source populations is often lacking, and in some instances live capture is adding to the pressure on stocks already at risk from hunting, fishery bycatch, habitat degradation, and other factors. All too often, entrepreneurs appear to be taking advantage of lax (or non-existent) regulations in small island states or less developed or politically unstable countries to supply the growing global demand for dolphins and small whales. The regulation of trade in live cetaceans under CITES is fraught with problems, not least the poor quality of reporting and the lack of a rigorous mechanism for preparation, review, and evaluation of non-detriment findings. Preparation of this article was supported by WDCS, the Whale and Dolphin Conservation Society. The authors are especially grateful to Cathy Williamson and Philippa Brakes for contributing data, ideas, and helpful critical comments.
Spatial patterns in periphyton biomass after low-magnitude flow spates: geomorphic factors affecting patchiness across gravel–cobble riffles

Abstract The patchy spatial distribution of benthic algae (periphyton) on gravel-bed rivers might be caused by physical disturbances during small frequent flow spates. During such spates, the gravel–cobble river bed is stable, but flows are often strong enough to transport large quantities of sand by a hopping motion called saltation. We tested the hypothesis that a spate-related refuge habitat exists in a transition zone (TZ) between the edge of the varial zone and the thalweg of the river channel where high hydraulic stress and saltating sand reduce biomass. We documented physical disturbance and periphyton biomass across 15 riffles after 3 summer spate periods in an oligomesotrophic river in Quebec. Periphyton perturbation thresholds were identified for near-bed water velocity during prespate growth (0.25 m/s) and for sand transport (64–180 g m−1event−1) and flow shear stress (15 Pa) during spates. Generalized linear models were used to examine cross-riffle trends in these 3 disturbance variables and in postspate periphyton biomass. The highest biomass occurred in the TZ. Periphyton increased away from the thalweg as sand transport rates decreased. Biomass continued to increase toward the edge of this zone unless disturbed by high rates of sand transport that were associated with a small, near-shore secondary peak in sand transport rate. Of the 3 disturbance variables, sand transport patterns controlled the spatial distribution of periphyton biomass after small spates with an average recurrence interval of 7 d. No cross-riffle refuge was found after a higher-magnitude spate (3× mean annual discharge) when disturbance thresholds were typically exceeded across the entire riffle. The intensity and distribution of physical disturbance, particularly sand abrasion, over the streambed dictated size and arrangement of periphyton refuge zones. These zones are crucial to promote stream system resilience to landuse change.
Variation in the outline and distribution of epithelial cell imprints on the surface of polygnathacean conodont elements

The elements of many conodont taxa exhibit a polygonal surface micro-ornamentation. Four main types are recognized (striation, linear texture, regular (idiomorphic) texture and granular texture) and their distribution over the conodont elements of different morphology is considered. The intraspecific (ontogenetic and ecological) and interspecific (phylogenetic) causes of the reticulation texture variations are also considered.