Browse Articles

  • Article
    | Open Access

    This study focuses on the role of simple sequence repeats (SSRs) in the evolution of the genomes of two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. They observed a significant expansion in SSRs in the genomes of these species (~23%) compared what is seen in other animal genomes (~1%) and suggest a possible mechanistic relationship between SSRs and transposable elements.

    • Jianbo Yuan
    • , Xiaojun Zhang
    •  & Fuhua Li
  • Article
    | Open Access

    Marcin Luzarowski et al. use a new method PROMIS for systematic analysis of protein small molecule interactions in yeast. Their work provides an experimentally-derived catalogue of protein–metabolite complexes in S. cerevisiae and reveals that the Ser-Leu dipeptide activates Pgk1, and alters cellular metabolism.

    • Marcin Luzarowski
    • , Rubén Vicente
    •  & Aleksandra Skirycz
  • Article
    | Open Access

    With DeepACSON, Abdollahzadeh et al. combines existing deep learning-based methods for semantic segmentation and a novel shape decomposition technique for the instance segmentation. The pipeline is used to segment low-resolution 3D-EM datasets allowing quantification of white matter morphology in large fields-of-view.

    • Ali Abdollahzadeh
    • , Ilya Belevich
    •  & Jussi Tohka
  • Article
    | Open Access

    Chisato Kinoshita et al. use a microbubble and ultrasound delivery system to inhibit miR-96-5p in the mouse brain. They demonstrate that miR96-5p regulates glutathione levels through the NOVA1 RNA binding protein, suggesting that this microRNA could be a target for altering glutathione levels in neurodegenerative disease.

    • Chisato Kinoshita
    • , Kazue Kikuchi-Utsumi
    •  & Toshio Nakaki
  • Article
    | Open Access

    Analysing the 3D movement of MKLP1 motors, Maruyama et al. find that dimeric C. elegans MKLP1 drives a left-handed helical motion around the microtubule with minimum protofilament switching to the right side whereas less persistent motions are driven by monomers or by heterotetramers with CYK4. These findings suggest how obstacles along crowded spindle microtubules may be avoided by CYK4 binding to MKLP1.

    • Yohei Maruyama
    • , Mitsuhiro Sugawa
    •  & Junichiro Yajima
  • Article
    | Open Access

    Honggu Choi et al. use biodynamic Doppler imaging to monitor bacterial infection of 3D living tissue and describe changes in the intracellular motions of living host tissue induced by early-stage infection. This work demonstrates the potential for the clinical use of this method to test for antibiotic-resistant infections.

    • Honggu Choi
    • , Zhe Li
    •  & David D. Nolte
  • Article
    | Open Access

    Fatma-Elzahraa Eid et al. illustrate a principled approach for identifying biases that can inflate the performance of biological machine learning models. When applied to three biomedical prediction problems, they identify previously unrecognized biases and ultimately show that models are likely to learn primarily from data biases when there is insufficient learnable signal in the data.

    • Fatma-Elzahraa Eid
    • , Haitham A. Elmarakeby
    •  & Kasper Lage
  • Article
    | Open Access

    Reconstructed floras from southernmost South America during the Middle Eocene Climate Optimum show the impact of this warming event on floral diversity. This reconstructed biota reflects a greenhouse world and offers a climatic and ecological deep time scenario of a sub-Antarctic region in the absence of ice.

    • Damián A. Fernández
    • , Luis Palazzesi
    •  & Viviana D. Barreda
  • Article
    | Open Access

    Yash Sondhi et al. annotate the genomes and transcriptomes of 175 Lepidoptera species and identify 14 independent opsin duplications associated with bright environments. From estimating their rates of evolution, the authors reveal that opsins from diurnal taxa evolve faster, and that high light availability increases opsin diversity and evolution rate in this order.

    • Yash Sondhi
    • , Emily A. Ellis
    •  & Akito Y. Kawahara
  • Article
    | Open Access

    Youngchang Kim, Jacek Wower, and colleagues explore the sequence specificity, metal ion dependence and catalytic mechanism of the Nsp15 endoribonuclease NendoU from SARS-CoV-2. The authors also solve five new crystal structures of the enzyme in complex with 5’UMP, 3’UMP, 5’cGpU, uridine 2′,3′-vanadate (transition state analog) and Tipiracil (uracil mimic), and demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site.

    • Youngchang Kim
    • , Jacek Wower
    •  & Andrzej Joachimiak
  • Article
    | Open Access

    Ivashenka et al. report that galectin-3 (Gal3) binding to lactotransferrin drives its transcytosis in enterocytes. Such trafficking is Gal3- and glycosphingolipid-dependent, and Gal3 is found in clathrin-independent carriers. These findings suggest that polarized trafficking across the intestinal barrier relies on this glycolipid and lectin (GL-Lect)-mediated endocytosis.

    • Alena Ivashenka
    • , Christian Wunder
    •  & Massiullah Shafaq-Zadah
  • Article
    | Open Access

    Carolin Koss et al. show that IL-36 produced from neutrophils is a key amplifier of lung inflammation in mice by activating neutrophils, macrophages and fibroblasts in cooperation with GM-CSF and the viral mimic poly(I:C). This study suggests that targeting IL-36 may improve the treatment of neutrophilic lung diseases.

    • Carolin K. Koss
    • , Christian T. Wohnhaas
    •  & Karim C. El Kasmi
  • Research Highlight
    | Open Access

    While loss-of-function mutations affecting the α2-Na/K ATPase are known to cause familial hemiplegic migraine, it is unclear how reduced protein activity could contribute toward migraine or paralysis observed in patients. A recent study from Sarah Smith and colleagues demonstrates that conditional deletion of the α2-Na/K ATPase in astrocytes can evoke episodic paralysis in mice, potentially due to altered metabolic processing of serine and glycine. By feeding juvenile α2-Na/K ATPase mutant mice a serine- and glycine-free diet, the authors are able to prevent the onset of episodic paralysis. This study suggests that loss of α2-Na/K ATPase in astrocytes may affect amino acid metabolism in the brain, ultimately leading to episodic paralysis.

    • George Andrew S. Inglis
  • Article
    | Open Access

    Simone Rampelli, Silvia Turroni and colleagues report ancient bacterial profiles of fecal sediments from four stratigraphic units of El Salt Middle Paleolithic site in Spain. The results of this study suggest a core human gut microbiome that could have been shared by Neanderthals and modern humans, and would pre-date the split between these two lineages.

    • Simone Rampelli
    • , Silvia Turroni
    •  & Marco Candela
  • Article
    | Open Access

    Kuwaki and Kanno examine courtship behavior in orexin neuron-ablated mice (ORX-AB), which are a model of narcolepsy/cataplexy. They find that ORX-AB mice showed cataplexy-like behavior during both dark and light periods in response to a female encounter, however this behavior was predominantly present during dark periods when exposed to chocolate. Studying cataplexy-like behavior in narcoleptic mice is useful for understanding mechanisms behind positive emotions, such as those associated with chocolate and courtship.

    • Tomoyuki Kuwaki
    •  & Kouta Kanno
  • Article
    | Open Access

    CLN3 disease is characterised by childhood-onset vision loss and premature death. Using patient-derived retinal cells, the authors show that CLN3 is required for retinal pigment epithelium (RPE) cell structure, microvilli and phagocytosis of photoreceptor outer segments that are essential for vision. They further suggest that gene-therapy targeting RPE cells can be effective for CLN3 disease.

    • Cynthia Tang
    • , Jimin Han
    •  & Ruchira Singh