Communications Biology 2 year anniversary collection

As we celebrate our second year of publishing, we look back on some highlights from 2019 in Communications Biology and consider what it means to study biology.

In light of their recent finding that insertion of a rare endogenous retrovirus, β4, is the cause of the characteristic coat coloring in agouti and piebald mice, Akira Tanave and Tsuyoshi Koide now discuss the origin and expansion of this element as well as potential roles of β4 in the mouse genome.

Following up on their recent study in Communications Biology Sasha Tetu et al discuss how plastic pollution of the oceans may affect marine microbes as well as strategies to identify the substances responsible for leachate toxicity and to further understand their impact.

Wagner and Raunser recently presented a deep learning based particle picking program for Cryo-EM, crYOLO. Here they discuss recent improvements to the program, a graphical user interface and share their thoughts on desired future developments.

Research from Helen Goodridge and Clive Svendsen’s groups published in Communications Biology showed that young bone marrow transplantation slows down cognitive decline in old mice. The authors now discuss subsequent studies examining the relationship between blood components and aging-associated cognitive impairment and rejuvenation as well as their own ongoing work.

Karen Echeverri and her colleagues showed in their recent Communications Biology study that an unconventional Fos/Jun heterodimer regulates axon regeneration in axolotl. In this article, she emphasises the diverse mechanisms of regeneration in other species and discusses future work needed to understand how the nervous system can be regenerated.

Yamamoto and Higashido discuss the possible routes of the hormone oxytocin in the body, and highlight their recent study in Communications Biology where they showed that the RAGE receptor is a transporter for oxytocin across the blood−brain barrier.

Adree Khondker and Maikel Rheinstadter discuss how bacteria escape being killed by polymyxin antibiotics. Touching on their recent Communications Biology paper, they elaborate on the mechanism by which the bacterial membrane becomes resistant and on future directions to take in order to understand this phenomenon.

Akiko Okita et al. demonstrate that heterochromatin suppresses gross chromosomal rearrangements by repressing Tfs1/TFIIS-dependent transcription of repetitive sequences. This study underscores the role of heterochromatin for maintaining chromosome stability.

Andrew Tilker, Jesse F. Abrams et al. assessed habitat degradation and hunting on tropical terrestrial mammals and birds in Southeast Asia. They find higher levels of functional extinction and consistently lower animal occupancy in hunted sites, suggesting that indiscriminate hunting is a more immediate threat for tropical animal communities.

Amy Eacock et al. examine the sensory input mechanism for slow colour change in the twig-mimicking caterpillars of the peppered moth. They find that this camouflage process does not require the use of eyes, relying instead on extraocular colour sensing.

Natalija Kashuba et al. analysed human DNA from ancient chewing gums collected from western Sweden. They provide genomic information for three Scandinavian hunter-gatherers, expanding the range of this genetic group and linking them to eastern lithic technologies.

Liu et al. measured the frequency of DNA rearrangements at the qγ27 locus and linked it to the variation in the maize endosperm texture. Through a series of genetic and RNAi experiments, they were able to identify the mechanism to improve maize’s nutritive value.

Jansen, Trojahn, Saxton, et al. examine the transcriptional changes that occur during the seasonal cycle in grizzly bears. They find that during hibernation, adipose tissue has the largest number of differentially expressed genes of the three tissues examined, revealing potential therapeutic targets for human diseases.

Niels Kerstes et al. report a citizen science effort to record the shell colour and banding patterns of nearly 8000 Cepaea nemoralis snails in the Netherlands to understand the potential evolutionary effect of urban environments on that snail species. They find that snails in urban centres are more likely to be yellow than pink, which may be explained by thermal selection.

Akira Tanave, Yuji Imai, and Tsuyoshi Koide find that nested retrotransposition is the cause of the classical nonagouti mutation. They identify a β4 element that was integrated into an intronic VL30 retrovirus in the agouti gene, leading to abnormal splicing and nonagouti coat color, and show that this allele likely arose in an East Asian mouse lineage.

Sasha Tetu et al. have examined the effects of plastic leachate exposure on the marine bacteria Prochlorococcus, the most abundant photosynthetic organism on Earth. They find plastic leachates impair growth, photosynthetic capacity and cause global changes in transcription.

Lindsay Zanno et al. report the discovery of a new tyrannosaur that helps to fill in a 70 million year gap in the fossil record. This new species reveals that the earliest North American tyrannosaurs relied on speed and small body size to survive and that apex predator status and large body sizes were not reached until much later in their evolutionary history.

Yamaguchi et al. investigated evolutionary pressure of 16 pneumococcal choline-binding cell-surface proteins (Cbp) and identified CbpJ as a virulence factor that contributes to pneumococcal evasion of neutrophil killing. This study highlights the utility of molecular evolutionary analysis in discovering virulence factors.

Fujisawa, Ichinose, and Dobata used simulated robot swarms to study the evolution of pheromone-guided foraging and traffic rules. Interestingly, they showed that in most cases traffic rules evolved before the foraging traits suggesting an important role for regulatory mechanisms in guiding core evolutionary adaptations.

Kathleen Prudic et al. examine the persistence of mimicry in viceroy butterflies in locations with low model abundance. They show that when queen butterflies are less abundant, viceroy butterflies become more abundant, but also increase their chemical defenses to gain protection from predation.

Holly Vincent et al. use species distribution modeling, climate change projections, and geographical analyses of more than 1200 crop wild relatives, identifying 150 key conservation areas most effective in preserving genetic diversity of crop wild relatives.

Fujita et al. demonstrate that a TonB-dependent receptor (TBDR) is involved in the outer membrane transport of lignin-derived biphenyl in a Gram-negative bacterial strain capable of degrading lignin-derived aromatic compounds. They also show that overexpression of corresponding TBDR gene enhances uptake of the compound, providing basis for establishing engineered strains optimized for use in lignin valorization.

Thomas et al. uses ancestral sequence reconstruction (ASR) tool to reconstruct functional ancestors of the Mycobacterial and Nocardial CAR1 orthologues, representing one of the largest reconstructed proteins to date. These ancestral CARs display varied tolerances to solvents, pH and in vivo-like salt concentrations along with high thermostability compared to well-studied extant CARs.

Johanna Michl et al. use real-time pH measurements of cell culture media and intracellular pH data from live-cell culture conditions to explore the effects of commonly-used buffers. Based on these data, they propose guidelines for controlling pH in cell culture systems and improving reproducibility.

Krystofiak et al. combined carbon replicas with phase-contrast electron microscopy to overcome the limited fidelity and resolution of metal replicas. This method reveals a double stranded morphology of the tight junction intramembrane fibrils, demonstrating its superiority over conventional freeze-fracture methods.

Stefan Görlich et al. investigate the role of a highly-conserved diatom gene Sin1 in the biogenesis of the biosilica cell wall. Analyzing Sin1 knockout mutants of the diatom Thalassiosira pseudonana, they find that this gene is necessary for generating mechanically robust cell walls.

David Filman et al. present the cryo-EM structure of an electrically conductive filament from Geobacter sulfurreducens, termed bacterial nanowires. They find that these structures are composed of a bacterial cytochrome, and suggest a possible role in long-range biological electron transport.

Ellefsen et al. monitor Piezo-dependent Calcium signals in live cells by TIRF and super-resolution microscopy and find that Ca²⁺ flickers localize to areas of high traction force. They show that Myosin II activity and MLCK are needed for the generation of Piezo Ca²⁺ signals and that Piezo1 channels are mobile in the plasma membrane.

Lingjun Li et al. show that antibiotic pressure provides a growth advantage to a mutually beneficial bacterial community, in which one strain is a nutrient provider and the other is an antibiotic protector, by changing their spatial distribution. This study presents spatial coordination as a strategy that drives mutually beneficial symbiosis.

Mabanglo, Leung, Vahidi, Seraphim et al. examine the structural changes to ClpP from Neisseria meningitidis and Escherichia coli upon binding to two novel activators. They show that reorganization of the electrostatic interaction networks at the ClpP entrance pores is needed for activation.

Yu Kang T Xu et al. combined nanofiber culture methods, automated imaging, and analytic algorithms to develop a quantitative high-throughput system to measure oligodendrocyte ensheathment. The analytic methods employed include a heuristic approach to model oligodendrocyte ensheathment characteristics and a deep learning neural network to recognize ensheathment by individual oligodendrocytes.

Lane, Simon, Vintu et al. analyze the protein content of small extracellular vesicles produced by different glioblastoma cell lines and patient-derived stem cells. They show that the proteomic cargo of small extracellular vesicles can be used as biomarkers for glioblastoma subtyping.

Mélanie Roch et al. demonstrate that extracellular protein folding factors contribute to MRSA’s resistance to β-lactam antibiotics by influencing PBP2A quality control. This study suggests that targeting chaperones or disrupting partially folded proteins represents an effective strategy to combat the spread of antibiotic resistance.

Lukas Dahlin et al. report the development of Picochlorum renovo, a high-productivity, halophilic, thermotolerant microalga. They report the nuclear and chloroplast genomes, and develop a system for inserting transgenes in both organelles.

Hwang et al. uses NanoLuc Binary Technology to develop a bioluminescent immunoassay for monitoring activation of multiple signaling pathways through specific nodes of phosphorylation. Their method takes less than two hours to complete in a homogeneous “Add and Read” format with no requirement for cell engineering.

Ohtsubo et al. show that mechanically sheared DNA 3’ terminus has 47% phosphate group, 20% hydroxyl group with remaining as abnormal termini, half of which is not repaired with T4 DNA polymerase treatment. They devise a method, scrap and build or SB-repairing, to efficiently repair 3’ DNA ends by combining phosphatase and exonuclease (scrap) followed by T4 DNA polymerase (build) reactions.

Nhan Phan et al. present a high-throughput approach to screen tumor organoids by seeding cells in mini-rings. They apply their method to cell lines and patient-derived tumor organoids representing four different cancers, and identified personalized responses for each organoid within a clinically relevant timeline.

Jaindra Tirpathi et al. report a strategy for inactivating endogenous banana streak virus sequences in the plantain B genome using CRISPR/Cas9. They show that three-quarters of edited plants had no viral symptoms under stress conditions, providing an improved B genome germplasm for plantain and banana breeding.

Leonard Goldstein et al. use high-throughput single-cell B-cell receptor sequencing on thousands of individual B cells from rat, mouse, and human repertoires. They obtained paired full-length heavy- and light-chain variable regions, and show that this approach is a powerful tool for antibody discovery.

Lu, Tang, Liu et al. present a 3D super-resolution fluorescence microscope that uses selective plane illumination and a spontaneously blinking dye for localization-based imaging. They show that their microscope can be used to study complex biological structures.

Karina Nakayama et al. bioengineer endothelialized mouse skeletal muscle using parallel-aligned nanofibrillar scaffolds. They find that muscle produced using the aligned scaffolds developed a spatially patterned structure and showed improved endothelial interaction compared to muscle engineered with randomly-oriented scaffolds.

Govender et al. report that the common African mutation V260E in the podocin protein is associated with autosomal recessive steroid resistant nephrotic syndrome in black South African children with biopsy-proven focal segmental glomerulosclerosis. This variant was absent in children with steroid sensitive nephrotic syndrome, indicating its utility in treatment decisions.

Rocio S. Alcala, J. Martin Caliva et al. quantify and model the effect of social environments and individual dominance on temporal dynamics of behaviour in the Japanese quail. They show that dominance can decrease behavioural complexity due to higher levels of synchronization in locomotion.

Ai et al. report that endogenous formaldehyde bidirectionally modulates cognition via the NMDA-R receptor, with both insufficiency and overabundance resulting in cognitive defects. The target site of formaldehyde enhancing NMDA-currents is cysteine C232 residue in amino terminal domain sequence of the NR2B subunit of NMDA-R and excessive formaldehyde suppresses NMDA-R activity by cross-linking NR1 to NR2B residues.

Marsolier et al. show that a parasite-encoded prolyl-isomerase, TaPin1, stabilizes host pyruvate kinase isoform M2 (PKM2), leading to metabolically transformed phenotypes in parasite-infected cells. This study illustrates how intracellular parasites use prolyl isomerization to manipulate host metabolism to their advantage.

Yamaguchi et al. investigated evolutionary pressure of 16 pneumococcal choline-binding cell-surface proteins (Cbp) and identified CbpJ as a virulence factor that contributes to pneumococcal evasion of neutrophil killing. This study highlights the utility of molecular evolutionary analysis in discovering virulence factors.

Aquilano et al. identify conserved plant miR159a and miR156c in dried nuts and show that these miRNAs target TNF receptor superfamily member 1a to suppress TNF-α-mediated inflammation. This study highlights the potential of plant miR-based oligonucleotides as a therapeutic option to treat metabolic diseases hallmarked by inflammation.

Yasuhiko Yamamoto et al. show that oxytocin is transported into the brain by the receptor for advanced glycation end-products (RAGE) on the blood-brain barrier. This study explains how circulating oxytocin crosses the blood-brain barrier, which is important to manifest oxytocin’s maternal bonding effects.

Pedro Alves et al. use a functional alignment approach to build an improved map of the default-mode network (DMN) from resting state fMRI-based individual DMN maps. They find that thalamus and basal forebrain are central to the DMN and validate these findings through tractography and graph theory analysis of structural connectivity in their DMN model.

Melanie Mark et al demonstrate that RGS2, a protein associated with stress disorders, drives male aggression through the serotonergic system. They show that exogenous expression of RGS2 in serotogenic neurons augments aggression in male mice and rescues the docile phenotype of Rgs2 knockouts but does not affect anxiety.

Balint Kacsoh et al. identify six Drosophila brain regions necessary for flies to learn the ‘dialect’ of another fly species and understand their warnings about the presence of parasitoid wasps. They find that the neural circuits for interspecific dialect learning are much more complicated than those for intra-specific learning, relying on multisensory cues.

Martinello et al. show that the KV7 K⁺ channels, active at rest, diminish action potential-induced Ca²⁺ influx into hippocampal mossy fiber boutons. This reduction alters presynaptic spikes, reduces neurotransmitter release, and decreases short-term synaptic plasticity, highlighting a role for these channels in hippocampal CA3 neuronal excitability.

Guilherme de Oliveira and Jerson Silva combine cryo-electron microscopy and biochemical approaches to characterise the aggregation of alpa-synuclein into fibrils, a feature associated with Parkinson’s disease. They provide direct structural insights into the mechanism of polymerisation of a pathological A53T mutant.

Markus Kern et al. use subdural recordings to understand how the human motor cortex is engaged during orofacial motor behavior such as speech production, laughing, and smiling. They find the motor cortex makes use of sparse and action-specific activation during these behaviors, which are organized in distinct but overlapping subareas.