NeuRiPP : neural network identification of RiPP precursor peptides

Significant progress has been made in the past few years on the computational identification of biosynthetic gene clusters (BGCs) that encode ribosomally synthesized and post-translationally modified peptides (RiPPs). This is done by identifying both RiPP tailoring enzymes (RTEs) and RiPP precursor peptides (PPs). However, identification of PPs, particularly for novel RiPP classes remains challenging. To address this, machine learning has been used to accurately identify PP sequences. Current machine learning tools have limitations, since they are specific to the RiPPclass they are trained for and are context-dependent, requiring information about the surrounding genetic environment of the putative PP sequences. NeuRiPP overcomes these limitations. It does this by leveraging the rich data set of high-confidence putative PP sequences from existing programs, along with experimentally verified PPs from RiPP databases. NeuRiPP uses neural network archictectures that are suitable for peptide classification with weights trained on PP datasets. It is able to identify known PP sequences, and sequences that are likely PPs. When tested on existing RiPP BGC datasets, NeuRiPP was able to identify PP sequences in significantly more putative RiPP clusters than current tools while maintaining the same HMM hit accuracy. Finally, NeuRiPP was able to successfully identify PP sequences from novel RiPP classes that were recently characterized experimentally, highlighting its utility in complementing existing bioinformatics tools

Finite size effects in nonequilibrium wetting

Models with a nonequilibrium wetting transition display a transition also in finite systems. This is different from nonequilibrium phase transitions into an absorbing state, where the stationary state is the absorbing one for any value of the control parameter in a finite system. In this paper, we study what kind of transition takes place in finite systems of nonequilibrium wetting models. By solving exactly a microscopic model with three and four sites and performing numerical simulations we show that the phase transition taking place in a finite system is characterized by the average interface height performing a random walk at criticality and does not discriminate between the bounded-KPZ classes and the bounded-EW class. We also study the finite size scaling of the bKPZ universality classes, showing that it presents peculiar features in comparison with other universality classes of nonequilibrium phase transitions.Comment: 14 pages, 6figures, major change

Carbon and nitrogen stocks and burial rates in intertidal vegetated habitats of a Mesotidal coastal lagoon

Coastal vegetated ecosystems such as saltmarshes and seagrasses are important sinks of organic carbon (OC) and total nitrogen (TN), with large global and local variability, driven by the confluence of many physical and ecological factors. Here we show that sedimentary OC and TN stocks of intertidal saltmarsh (Sporobolus maritimus) and seagrass (Zostera noltei) habitats increased between two- and fourfold along a decreasing flow velocity gradient in Ria Formosa lagoon (south Portugal). A similar twofold increase was also observed for OC and TN burial rates of S. maritimus and of almost one order of magnitude for Z. noltei. Stable isotope mixing models identify allochthonous particulate organic matter as the main source to the sedimentary pools in both habitats (39–68%). This is the second estimate of OC stocks and the first of OC burial rates in Z. noltei, a small, fast-growing species that is widely distributed in Europe (41,000 ha) and which area is presently expanding (8600 ha in 2000s). Its wide range of OC stocks (29–99 Mg ha-1 ) and burial rates (15–122 g m2 y-1 ) observed in Ria Formosa highlight the importance of investigating the drivers of such variability to develop global blue carbon models. The TN stocks (7–11 Mg ha-1 ) and burial rates (2–4 g m-2 y-1 ) of Z. noltei were generally higher than seagrasses elsewhere. The OC and TN stocks (29–101 and 3–11 Mg ha-1 , respectively) and burial rates (19–39 and 3–5 g m-2 y-1 ) in S. maritimus saltmarshes are generally lower than those located in estuaries subjected to larger accumulation of terrestrial organic matter.DL57/2016/CP1361/CT0002; MinECo, MDM2015-0552info:eu-repo/semantics/publishedVersio

First report of charcoal rot, caused by macrophomina phaseolina, on Blueberry in Southwestern Spain

In Europe, Huelva province in Southwestern Spain is the main berry production area. Blueberry(Vaccinium spp.) was introduced during the early 90?s as an addition to strawberry cultivation.From 2011 to 2018, blueberry acreage increased from 777 ha to 3,000 ha. In May 2015 andSeptember 2017, wilted southern highbush blueberry plants (cvs. "Star", "Ventura", and "Legacy")were collected from three orchards located in the Huelva production area (Gibraleón and Moguer).The diseased plants showed drying of foliage and brown discoloration of stems and roots. Root andstem of symptomatic plants were surface sterilized (2 min,1% sodium hypochlorite), rinsed, dried,and plated on potato dextrose agar (PDA). After 7 days at 30º C in the dark, fungal isolatesproduced numerous black, round to ovoid shaped sclerotia with an average diameter of 98 μm(range: 61 to 128 μm). Genomic DNA from a single sclerotium isolate (TOR-872) was extractedfollowing the technique described by Bekesiova et al. (1999). Four DNA regions were amplifiedand sequenced: the exon region of translation elongation factor 1- α (TEF-1 α), β-tubulin (β-TUB),calmodulin (CAL), and the ITS region. TEF-1 α was amplified with the EF1-728F and EF1-986Rprimers (Carbone and Kohn, 1999), the β-TUB with the T1 and T22 primers (O?Donnell andCigelnik, 1997), the CAL with the CAL-228F and CAL-737R primers (Carbone and Kohn, 1999)and the ITS with the ITS5 and ITS4 primers (White et al., 1990). After BLASTing the 4 sequencesagainst the GenBank database, the top hits corresponded to Macrophomina phaseolina with a 99-100% of sequence identity for all cases. Our sequences were submitted to GenBank underAccession numbers: MK447854 (TEF-1 α), MK447918 (β-TUB), MK447823 (CAL) andMK447886 (ITS). Morphological and molecular results confirmed this isolate as M. phaseolina(Holliday and Punithalingam, 1970). In Gibraleón, in 7.87% of nearly dead plants (cv. Ventura)only M. phaseolina was isolated, whereas in Moguer disease incidence was 30, 7, and 2.27% in cvs."Star", "Ventura", and "Legacy", respectively. Inoculum for pathogenicity testing was produced bygrowing isolates TOR-872 and TOR-862 (both from diseased blueberry plants) on PDA. Inaddition, pathogenicity of a M. phaseolina isolate (TOR-102), from a strawberry soil and confirmedas pathogenic to strawberry, was tested because blueberry is usually cultivated in soils wherestrawberry had grown. Six potted blueberry plants (cv. "Star") per isolate were inoculated bysubstrate irrigation with 50 ml of a sclerotia suspension (104 sclerotia/ml) of each isolate. Sixcontrol plants were irrigated with water. Plants were held at 28°C and 40/70% relative humidity(day/night) in a growth chamber with a 16-h photoperiod. Four months after inoculation, themortality of the inoculated plants was 33, 50 and 50% for isolates TOR-862, TOR-872, and TOR-102, respectively. M. phaseolina was reisolated from all dead plants. No symptoms were observedin control plants. Macrophomina phaseolina has been associated with a blight disease on blueberryin Serbia (Popović et al., 2018) but this is the first report of charcoal rot on blueberry in Spain. Theaggressiveness of the strawberry soil isolate was also confirmed on blueberry. In Spain, chemicalfumigation in soil is banned in blueberry production. Thus, blueberry may be grown on fields with a previous history of strawberry production and carry-over of M. phaseolina causing charcoal rot maysignificantly impact crop production.Fil: de los Santos, B.. Ifapa Centro Las Torres; EspañaFil: Aguado, A.. Ifapa Centro Las Torres; EspañaFil: Borrero, C.. Departamento de Ciencias Agroforestales; EspañaFil: Viejobueno, Josefina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Tucuman-Santiago del Estero. Estación Experimental Agropecuaria Famaillá; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán; ArgentinaFil: Avilés, M.. Departamento de Ciencias Agroforestales; Españ

Variation in flexural, morphological, and biochemical leaf properties of eelgrass (Zostera marina) along the European Atlantic climate regions

Seagrasses need to withstand hydrodynamic forces; therefore, mechanical properties such as flexibility or breaking resistance are beneficial for survival. The co-variation of leaf breaking properties with biochemical traits in seagrasses has been documented, but it is unknown if the same patterns apply to leaf flexural properties. To interpret changes in the ecological function of seagrass ecosystems based on acclimation responses to environmental changes, it is necessary to understand the factors that affect flexural leaf properties. Here, morphological and flexural leaf properties of the perennial type of Zostera marina across different environmental conditions along European Atlantic climate regions are presented together with C:N ratio and neutral detergent fibre content as descriptors of biochemical leaf composition. Eelgrass leaves from cold regions were similar to threefold more elastic and similar to tenfold more flexible, were also narrower (1.7-fold), and contained similar to 1.9-fold higher fibre content than from plants growing in warmer regions. Eelgrass also showed acclimation to local conditions such as seasonality, water depth, and hydrodynamic exposure. Leaves collected from exposed or shallower locations or during winter were more flexible, suggesting an avoidance strategy to hydrodynamic forcing, which is generally higher under those conditions. Flexural rigidity was almost equally controlled by bending modulus (35%) and leaf thickness (37%), indicating functional differences compared to leaf breaking described in the literature. Overall, the findings indicate that Zostera marina has a high flexural plasticity and high acclimation capacity to some climate change effects such as sea level rise and increase in storm frequency and intensity.German Science FoundationGerman Research Foundation (DFG) [PA 2547/1-1]Royal Swedish Academy of Sciences (KVA travel grant)FCT-Foundation for Science and TechnologyPortuguese Foundation for Science and Technology [UID/Multi/04326/2019, SFRH/BPD/119344/2016

Quantum capacitor with discrete charge-anticharge: spectrum and forces

The quantum capacitor with discrete charge is modeled by a Hamiltonian containing an inductive intrinsic term (tunnel effect between plates). The spectrum is obtained using a double Hilbert space. Fluctuations in the charge-anticharge pairs (zero total charge) give rise to an elementary attraction which is compared to the Casimir force. In this case, the field-fluctuations force could be also interpreted as charge-fluctuations force