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Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity.

We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT--add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide-and-conquer framework to scale its most accurate version, MAFFT-linsi--add, to constraint alignments with many sequences. We show that EMMA has an accuracy advantage over other techniques for adding sequences into alignments under many realistic conditions and can scale to large datasets with high accuracy (hundreds of thousands of sequences). EMMA is available athttps://github.com/c5shen/EMMA.

EMMA is a new tool that provides high accuracy and scalability for adding sequences into an existing alignment.

 

Medicago truncatulais a model legume that has been extensively investigated in diverse subdisciplines of plant science.Medicago littoraliscan interbreed withM. truncatulaandM. italica; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated thatM. truncatulaaccessions are heterogeneous but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverseM. truncatulaaccessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from bothM. truncatulaandM. littoralis.Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material.Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. TwoMedicagoaccessions were placed within aM. italicasubclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within theM. littoralissubclade. Our results suggest that theM. truncatulaaccession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.

 

Abstract Employing renewable materials for fabricating clean energy harvesting devices can further improve sustainability. Microorganisms can be mass produced with renewable feedstocks. Here, we demonstrate that it is possible to engineer microbial biofilms as a cohesive, flexible material for long-term continuous electricity production from evaporating water. Single biofilm sheet (~40 µm thick) serving as the functional component in an electronic device continuously produces power density (~1 μW/cm 2 ) higher than that achieved with thicker engineered materials. The energy output is comparable to that achieved with similar sized biofilms catalyzing current production in microbial fuel cells, without the need for an organic feedstock or maintaining cell viability. The biofilm can be sandwiched between a pair of mesh electrodes for scalable device integration and current production. The devices maintain the energy production in ionic solutions and can be used as skin-patch devices to harvest electricity from sweat and moisture on skin to continuously power wearable devices. Biofilms made from different microbial species show generic current production from water evaporation. These results suggest that we can harness the ubiquity of biofilms in nature as additional sources of biomaterial for evaporation-based electricity generation in diverse aqueous environments. 

The observed magnifications and light curves of the quadruply imaged iPTF16geu supernova (SN) offers a unique opportunity to study a lens system with a variety of independent constraints. The four observed positions can be used to constrain the macrolens model. The magnifications and light curves at the four SN positions are more useful to constrain microlensing models. We define the macrolens model as a combination of a baryonic component that traces the observed light distribution, and a dark matter halo component. We constrained the macrolens model using the positional constraints given by the four observed images, and compared it with the best model obtained when magnification constraints were included. We found that the magnification cannot be explained by a macrolens model alone, and that contributions from substructures such as microlenses are needed to explain the observed magnifications. We considered microlens models based on the inferred stellar mass from the baryonic component of the macrolens model, and used the observed magnification and light curves to constrain the contribution from microlenses. We computed the likelihood of a variety of macro and micro lens models where we varied the dark matter halo, baryonic component, and microlens configurations. We used information about the position, magnification, and, for the first time, the light curves of the four observed SN images. We combined macrolens and microlens models in order to reproduce the observations; the four SN positions, magnifications, and lack of fluctuations in the light curves. After marginalizing over the model parameters, we found that larger stellar surface mass densities are preferred. This result suggests that the mass of the baryonic component is dominated by its stellar component. We conclude that microlensing from the baryonic component suffices to explain the observed flux ratios and light curves. 

Increasing numbers of protein interactions have been identified in high-throughput experiments, but only a small proportion have solved structures. Recently, sequence coevolution-based approaches have led to a breakthrough in predicting monomer protein structures and protein interaction interfaces. Here, we address the challenges of large-scale interaction prediction at residue resolution with a fast alignment concatenation method and a probabilistic score for the interaction of residues. Importantly, this method (EVcomplex2) is able to assess the likelihood of a protein interaction, as we show here applied to large-scale experimental datasets where the pairwise interactions are unknown. We predict 504 interactions de novo in theE. colimembrane proteome, including 243 that are newly discovered. While EVcomplex2 does not require available structures, coevolving residue pairs can be used to produce structural models of protein interactions, as done here for membrane complexes including the Flagellar Hook-Filament Junction and the Tol/Pal complex.

 

We present optical and near-infrared (NIR) observations of the Type Icn supernova (SN Icn) 2022ann, the fifth member of its newly identified class of SNe. Its early optical spectra are dominated by narrow carbon and oxygen P-Cygni features with absorption velocities of ∼800 km s−1; slower than other SNe Icn and indicative of interaction with a dense, H/He-poor circumstellar medium (CSM) that is outflowing slower than typical Wolf–Rayet wind velocities of >1000 km s−1. We identify helium in NIR spectra 2 weeks after maximum and in optical spectra at 3 weeks, demonstrating that the CSM is not fully devoid of helium. Unlike other SNe Icn, the spectra of SN 2022ann never develop broad features from SN ejecta, including in the nebular phase. Compared to other SNe Icn, SN 2022ann has a low luminosity (o-band absolute magnitude of ∼−17.7), and evolves slowly. The bolometric light curve is well-modelled by 4.8 M⊙ of SN ejecta interacting with 1.3 M⊙ of CSM. We place an upper limit of 0.04 M⊙ of 56Ni synthesized in the explosion. The host galaxy is a dwarf galaxy with a stellar mass of 107.34 M⊙ (implied metallicity of log(Z/Z⊙) ≈ 0.10) and integrated star-formation rate of log (SFR) = −2.20 M⊙ yr−1; both lower than 97 per cent of galaxies observed to produce core-collapse supernovae, although consistent with star-forming galaxies on the galaxy Main Sequence. The low CSM velocity, nickel and ejecta masses, and likely low-metallicity environment disfavour a single Wolf–Rayet progenitor star. Instead, a binary companion is likely required to adequately strip the progenitor and produce a low-velocity outflow.

 

We present an observational study of the luminous red nova (LRN) AT 2021biy in the nearby galaxy NGC 4631. The field of the object was routinely imaged during the pre-eruptive stage by synoptic surveys, but the transient was detected only at a few epochs from ∼231 days before maximum brightness. The LRN outburst was monitored with unprecedented cadence both photometrically and spectroscopically. AT 2021biy shows a short-duration blue peak, with a bolometric luminosity of ∼1.6 × 10 41 erg s −1 , followed by the longest plateau among LRNe to date, with a duration of 210 days. A late-time hump in the light curve was also observed, possibly produced by a shell-shell collision. AT 2021biy exhibits the typical spectral evolution of LRNe. Early-time spectra are characterised by a blue continuum and prominent H emission lines. Then, the continuum becomes redder, resembling that of a K-type star with a forest of metal absorption lines during the plateau phase. Finally, late-time spectra show a very red continuum ( T BB  ≈ 2050 K) with molecular features (e.g., TiO) resembling those of M-type stars. Spectropolarimetric analysis indicates that AT 2021biy has local dust properties similar to those of V838 Mon in the Milky Way Galaxy. Inspection of archival Hubble Space Telescope data taken on 2003 August 3 reveals a ∼20 M ⊙ progenitor candidate with log ( L / L ⊙ ) = 5.0 dex and T eff  = 5900 K at solar metallicity. The above luminosity and colour match those of a luminous yellow supergiant. Most likely, this source is a close binary, with a 17–24 M ⊙ primary component. 

Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31Medicagotaxa we detected exceptionally high post‐IGT amplification of mitochondrial (mt) DNA sequences containingrps10in the nuclear genome ofMedicago polymorphaand closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in theM. polymorphanuclear genome. The mtrps10‐like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6–3.0% of total genomic DNA, a value approximately three‐fold greater than the entire mitogenome inM. polymorpha. Compared to a typical mt gene, the mtrps10‐like sequence coverage level was 691.5–7198‐fold higher inM. polymorphaand closely related species. In addition to the post‐IGT amplification, our analysis identified the canonical telomeric repeat and the species‐specific satellite arrays that are likely attributable to an ancestral chromosomal fusion inM. polymorpha. A possible relationship between chromosomal instability and the mtrps10‐like tandem repeat family in theM. polymorphaclade is discussed.