Browse Articles

  • Article
    | Open Access

    Ben Harvey et al. use the gradient provided by a natural CO2 seep off Shikine Island, Japan and lab microcosm experiments to determine how ocean acidification promotes turf algal habitat conditions that create stabilizing feedback loops and hysteresis capable of locking turf systems in place. These results further our understanding of feedback loops initiated by ocean acidification, and can assist in the management of coastal habitats.

    • Ben P. Harvey
    • , Ro Allen
    •  & Jason M. Hall-Spencer
  • Article
    | Open Access

    Li et al. generate chromosome-scale genome assemblies of the three nuclear types of the basidiomycetous fungi Rhizoctonia isolates. Genomic comparisons implicate that uninucleate genomes were hybrids derived potentially from binucleate ancestors, suggesting evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.

    • Cheng Li
    • , Zejian Guo
    •  & Xujun Chen
  • Article
    | Open Access

    Salman Sohrabi et al. develop an automated, high-throughput assay to study spasm-like curling behavior in C. elegans, which is related to motor control symptoms in Parkinson’s disease. They apply this screening approach to identify four candidate drugs for potential late-in-life interventions for Parkinson’s disease.

    • Salman Sohrabi
    • , Danielle E. Mor
    •  & Coleen T. Murphy
  • Article
    | Open Access

    Insulin-like 3 (Insl3) belongs to a class of peptide hormones that are expressed in the Leydig cells and, in zebrafish, under the control of folliclestimulating hormone (Fsh) in the pituitary. Using insl3 knockout zebrafish, the authors found that Insl3 regulates spermatogonia differentiation and apoptosis via the Pparg and retinoic acid pathways.

    • Diego Crespo
    • , Luiz H. C. Assis
    •  & Rüdiger W. Schulz
  • Article
    | Open Access

    Tom Shlesinger and Yossi Loya use ex-situ and in-situ experiments with coral larvae of three brooding species from contrasting shallow- and deep-water habitats and show that larvae originating from deep-water corals have narrower tolerances and higher habitat-specificity in simulated parental-habitat conditions. They also show that survival of juvenile corals experimentally translocated to the sea was significantly lower when not at parental depths. Together these results demonstrate that local adaptations and parental effects interact with larval selectivity and phenotype-environment mismatches to create semipermeable barriers to coral dispersal and connectivity.

    • Tom Shlesinger
    •  & Yossi Loya
  • Article
    | Open Access

    Salmas and Borysik develop HDXmodeller, an online webserver for high-resolution HDX-MS analysis. Their method returns high-resolution exchange rates quantified per residue as well as statistics that validate the exchange rate models with high accuracy. Their method will be very useful for users as it facilitates the evaluation of different data optimisations with high confidence.

    • Ramin Ekhteiari Salmas
    •  & Antoni James Borysik
  • Article
    | Open Access

    George, Assaiya et al. develop a deep learning tool, CASSPER, that automates the detection of protein particles in transmission microscope images. This algorithm uses semantic segmentation and visually prepared training samples to capture the differences in the transmission intensities of microscope images, enabling automation of data processing.

    • Blesson George
    • , Anshul Assaiya
    •  & Ninan S. Philip
  • Article
    | Open Access

    Rui Wang et al. report a comprehensive analysis of nearly 13,000 SARS-CoV-2 genome sequences isolated from patients in the United States, comprising more than 7000 single mutations. They show that SARS-CoV-2 genomes cluster into four distinct groups and that two of these groups are potentially more infectious, underlining the urgent need for viral control strategies in the US.

    • Rui Wang
    • , Jiahui Chen
    •  & Guo-Wei Wei
  • Article
    | Open Access

    Lee et al. construct a cell-penetrating peptides (CPP) library and identify CPPs that can penetrate bacterial cells with minimum or no impact on cell viability. For the identified top CPP candidates, their abilities to deliver macromolecules such as I-SceI and Cre recombinase proteins to bacteria are evaluated as proof-of-concept studies for potential applications.

    • Hyang-Mi Lee
    • , Jun Ren
    •  & Dokyun Na
  • Article
    | Open Access

    Ye et al demonstrate a simple and precise method to simultaneously generate iPSC lines with different gene dosages using paired Cas9 nickases. As proof-of-concept they apply this method to examining amyloid precursor protein gene dosage effects in an Alzheimer’s disease patient-derived iPSC line. Their method could potentially advance what we know about disease mechanisms and assist with gene therapy development.

    • Tao Ye
    • , Yangyang Duan
    •  & Nancy Y. Ip
  • Article
    | Open Access

    Karoyan et al. present a method to inhibit SARS-CoV-2 by means of a peptide-mimic approach. They design a series of peptides mimicking the N-terminal helix of hACE2 protein and their best peptide-mimic blocks SARS-CoV-2 human pulmonary cell infection with an IC50 in nanomolar range.

    • Philippe Karoyan
    • , Vincent Vieillard
    •  & Olivier Lequin
  • Article
    | Open Access

    Mishra, Huang et al. identify 29 linear SARS-CoV-2 epitopes that are immunoreactive with the plasma from individuals who had asymptomatic, mild, or severe SARS-CoV-2 infections. This study suggests the possibility of using these peptides to discriminate the exposure to SARS-CoV-2 and other human coronaviruses.

    • Nischay Mishra
    • , Xi Huang
    •  & W. Ian Lipkin
  • Article
    | Open Access

    Takeda et al. investigate the role of mitochondrial ubiquitin ligase (MITOL) in Alzheimer’s disease progression. They demonstrate that MITOL has a direct effect on mitochondrial dynamics and functioning and its ablation can enhance the seeding effect of Aβ-plaques, leading to cognitive decline in the transgenic mice model of Alzheimer’s disease.

    • Keisuke Takeda
    • , Aoi Uda
    •  & Shigeru Yanagi
  • Article
    | Open Access

    Blumenfeld and Eyer et al. retrace the invasion history of the termite Coptotermes formosansus from eastern Asia to the US using approximate Bayesian computation. They find a complex invasion history, with multiple introductions originating from eastern Asia, as well as a bridgehead introduction originating from Hawaii, which appears to have mitigated the loss of genetic diversity within the invasive US range.

    • Alexander J. Blumenfeld
    • , Pierre-André Eyer
    •  & Edward L. Vargo
  • Article
    | Open Access

    Zhang et al. identify Cystatin C as a new heparan sulfate (HS) binding protein, however only at acidic pH (≤6.5). They further identify two isolated HS binding motifs on Cystatin C that are required to come together to form a complete HS-binding site, which is a unique property among known HS binding proteins.

    • Xiaoxiao Zhang
    • , Xinyue Liu
    •  & Ding Xu
  • Article
    | Open Access

    By analyzing tissue from non-human primates with or without heart failure and in vitro methods, Liu et al. demonstrate that amylin deposition in heart failure contributes to cardiac dysfunction via activation of HIF1α and PFKFB3 signaling. Their study demonstrates the pathological role of amylin and establishes it as a target for heart disease patients.

    • Miao Liu
    • , Nan Li
    •  & Liangbiao George Hu
  • Article
    | Open Access

    Anastasiya Börsch, Daniel Ham, and colleagues generated a time series of phenotypic measurements and RNA-Seq data from mouse skeletal muscle and comparatively analyzed these along comparable rat and human data, to assess the relevance of rodent models for human muscle aging. This study draws attention to the utility of phenotypic measurements in analyzing aging-related molecular data, as several measurements such as muscle mass, were better indicators of muscle health than chronological age.

    • Anastasiya Börsch
    • , Daniel J. Ham
    •  & Mihaela Zavolan
  • Article
    | Open Access

    Using microcomputed tomography, Ginzel, Martynov et al. provide a modernized exploration of the developing midgut in rat embryos. This study enables three-dimensional, spatial interpretations of key structures throughout development, including the umbilicus and umbilical coelom.

    • Marco Ginzel
    • , Illya Martynov
    •  & Dietrich Kluth