Communications Biology turns five!

We reflect on how far we have come while looking forward to the next phase of our journey.

Arabidopsis plants were seeded onto lunar soil samples taken directly from the Apollo 11, 12, and 17 missions. Transcriptomic analyses reveal that plants grown in lunar soil differentially express genes associated with salt, metal, and ROS stress.

Based on genomic data, the Galapagos giant tortoise species native to Fernandina Island appears to be alive and well, survived by at least one female after being considered extinct since 1906.

Deng et al. report a new species of giant rhino, Paraceratherium linxiaense, from specimens of the upper Oligocene Jiaozigou Formation in China with an age of 26.5 Ma. Morphological analysis of the completely preserved skull with articulated mandible and atlas reveals a high level of specialization and the formation of a clade with P. lepidum with close ties to P. bugtiense.

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.

The bones of the archosaur eye socket evolve different shapes dependent on feeding habits and body size.

An analysis of the structural complexity of vocal sequences in chimpanzees in the Taï National Park reveal that single vocal units are combined into numerous structured sequences with adjacency dependencies between units.

George Roff et al. report a 74–92% decline in the catch per unit effort and concurrent declines in body size of large coastal apex sharks near Australia over the past five decades. This study highlights shifting baselines of shark populations in coastal shark assemblages, and indicates that shark populations are highly vulnerable to exploitation.

Data Deficient species are more likely to be at extinction risk than previously thought across multiple taxonomic groups.

Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.

Yohey Suzuki, Seiya Yamashita et al. discover the presence of bacterial cells in the iron-rich smectite on aged subseafloor basaltic rock using nanoscale solid characterizations. Analysis of their lipid profiles and DNA sequences reveals the dominance of heterotrophic bacteria, suggesting the presence of organic matter resources in the subsea basalt.

Cheryl L Ames, Anna Klompen et al. describe cassiosomes, stinging cell structures in the mucus of the upside-down jellyfish Cassiopea xamachana. They show that these motile cell masses consist of an outer epithelial layer largely composed of nematocytes surrounding centralized clusters of endosymbiotic dinoflagellates.

Remaining with the family group may reduce long-term stress effects in orphaned African elephants.

Trade in arachnids includes millions of individuals and over 1264 species, with over 70% of individuals coming from the wild.

Major dams are found to disrupt platypus gene flow and dispersal, with higher genetic differentiation found across dams than along similar stretches of undammed rivers, indicating that they act as significant barriers to platypus movement.

Wolf behavioural, spatial, and serological data over 26 years show that wolf territory overlap with areas of high cougar density is a significant predictor of T. gondii infection. Further, infection increases the likelihood that wolves make high-risk decisions such as dispersing and becoming a pack leader.

Presenting Natovenator polydontus, a non-avian dinosaur from the Upper Cretaceous of Mongolia displaying morphology indicative of swimming behaviour.

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.

C-terminal truncation of a-syn results in a more extended and exposed conformation, providing further insight into the pathological role of this truncation event in the progression of Parkinson’s disease.

Using experimental data, the authors assess the quality and discuss the limitations of AlphaFold2 predictions of protein structures and protein-protein interactions essential for centrosome and centriole biogenesis.

Melanie Bahlo and colleagues report a genome-wide association study on the retinal degenerative disease Macular Telangiectasia Type 2, identifying 8 new genome-wide significant loci. Further analyses suggest key roles for genes that transport and synthesize the amino acids serine, glycine and alanine, providing a more accurate genomic tool for identifying people at risk of the disease.

PLASTER is a broadly-applicable data processing pipeline that enables robust allele typing of SMRT-sequenced amplicons, as evidenced by allele typing of the CYP2D6 gene in a cohort from the Solomon Islands.

Jemilat Salami et al. develop a proteolysis targeting chimera ARCC-4, which inhibits prostate tumor cell proliferation via degradation of the androgen receptor. They show in cells that ARCC-4 is more effective than the prostate cancer drug enzalutamide and can degrade androgen receptor variants resistant to enzalutamide.

A biomimetic inducible model of pulmonary arterial hypertension (PAH) is presented, combining natural and induced BMPR2 dysfunction with hypoxia in lung endothelial cells and blood-derived PAH cells to induce smooth muscle activation & proliferation.

Shimpei Kubota et al. describe a pipeline for quantitative whole-organ analysis that that combines tissue clearing, 3D imaging, and machine learning for analysis of the tumour microenvironment. The authors apply this in a mouse model of lung tumour and reveal the role of TGF-β in remodelling the cellular microenvironment favouring metastatic invasion.

Grinnell et. al report a new mechanism of antibiotic tolerance in rod-shaped bacteria that is dependent on cell density and which specifically targets the cell wall elongation system. Their findings suggest that simultaneous disruption of both the elongasome and the divisome may be an efficient way of overcoming density-dependent growth resistance.

Voltage imaging and machine learning reveal that human breast cancer cells exhibit voltage fluctuations absent in non-tumorigenic breast cells, beginning to shed light on the bioelectric properties of cancer processes.

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.

Wijerathne et al develop an approach to quantify mRNA amounts in extracellular vesicles (EVs) from plasma using a microfluidics device to enrich EVs. They show this method allows for the correlation of specific mRNAs with acute ischemic stroke pointing towards potential clinical use.

Using in silico modeling, Li et al. identify a selective inhibitor for aldehyde dehydrogenase isoform ALDH1A3, which is highly expressed in mesenchymal glioma stem cells and therefore a potential drug target. They solve the structure of the ALDH1A3/MCI-INI-3 inhibitor complex and find that the inhibitor is as efficient as ALDH1A3 depletion in preventing retinoic acid biosynthesis.

Tsai, Zhang, Scholten et al. develop a surfactant- assisted one-pot sample preparation coupled with mass spectrometry method (SOP-MS) for label-free global single-cell proteomics. This method allows researchers to measure hundreds of proteins from single human cells, suggesting its utility for quantitative single-cell proteomics.

Carianopol et al. construct a detailed protein interaction network for the SnRK1 kinase complex to investigate the interaction of SnRK1 and ABA during stress response. They identify 125 proteins that interact with SnRK1, which can be used further to characterise the role of SnRK1 in plant survival under stress.

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.

Vacheron et al. visualize the dynamics of production, cellular transport and release of phage tail-like devices called R-tailocins by Pseudomonas bacteria and demonstrate their kin killing activity at single-cell level. The study offers insights into microbial competition mechanisms.

Benjamin Liffner and Miguel Balbin et al. report that the Plasmodium falciparum protein, PfCERLI2, localises to the cytosolic face of the parasite’s rhoptry bulb and is essential for invasion and growth within human red blood cells.

A Boolean network explorer (BoNE) computational algorithm was used to identify a dual agonist of the nuclear receptors PPARα and PPARγ that may be therapeutic in treating inflammatory bowel disease.

Parashkev Nachev et al. investigate the neural basis of meta-volition, the ability to choose to suspend volition. Using diffusion tensor imaging, they find that less optimized right frontal white matter was correlated with improved meta-volition abilities, suggesting meta-volition is controlled by a parallel rather than hierarchical neural organization.

Combined high-field MRI and DTI analyses in post-mortem mouse, marmoset, and human samples provide insight into the neural connections between nasal cavities and olfactory bulbs.

Comparisons of frontoparietal connectivity between marmosets, rats and grey squirrels suggest the formation of a common frontoparietal network architecture among arboreal species (grey squirrels and marmosets) that might reflect convergent evolution.

Kenji Yamada et al. describe a single-cell chemical defense strategy in Brassicaceae plants that requires formation of endoplasmic reticulum-derived organelles for the accumulation of β-glucosidases. They find that seedlings lacking a specific β-glucosidase lose their resistance to predation by woodlice.

Characterizing mice lacking Inositol Polyphosphate-4-Phosphatase Type II B (INPP4B), Zhang et al. discovered that SREBP1 signaling is activated in livers of Inpp4b^−/− males leading to development of NAFLD and insulin resistance. When fed high fat diet, Inpp4b^−/− males develop type II diabetes, inflammation of adipose tissue, and prostate neoplasia. These findings provide insights into INPP4B protective role from metabolic syndrome.

Ito et al. demonstrate that murine gastric parietal cells produce estrogen using fatty acids as an energy source, and secrete estrogen in response to the blood triglyceride levels. The authors propose that the stomach is involved in the monitoring and the regulation of blood triglyceride levels.

Kelly Chacón et al. report insights into the mechanism of copper transfer between CusF and CusB, which are involved in heavy metal export as a part of bacterial host-defense strategies. Their results indicate fast formation of a complex involving a shared metallosite with ligands derived from each partner, followed by slower intra-complex metal transfer.

Myanmar amber collection and study in palaeontology is clouded with ethical and legal issues. Here, the history and legality of Myanmar amber use in the literature is reviewed.

Navajosphenodon sani, a new sphenodontian species from Early Jurassic North America, is the oldest and most complete tuatara-lineage fossil. This suggests many features of the modern morphology including growth and skeletal architecture were established at least 190 million years ago.

Siddall, Byrnes, Full, and Jusufi observe the function of the Asian flat-tailed gecko tail in gliding and landing on tree trunks in the field, complemented with mathematical and robotic models made of soft active materials. Altogether, their models show how geckos use an active tail reflex to brace the impact and reduce the risk of falling from landings on tree trunks.

Thorsten Wagner et al. present SPHIRE-crYOLO, a particle picking software for selecting particles from digital micrographs in cryoEM data. After training, the method automatically recognizes particles with high recall and precision, simplifying data pre-processing.

Lukas Weber et al. present diffcyt, an open-source computational framework for differential analysis of high-dimensional flow and mass cytometry data. The diffcyt framework uses high-resolution clustering and empirical Bayes moderated tests to provide improved statistical performance, flexible experimental designs, and fast runtimes.

Digital reconstruction of honey bee combs using X-ray micro-computed tomography provides a computational tool to analyze comb geometry and material distribution. Ranging from the individual-cell scale to the whole hive, this tool allows investigation of the relationship between comb architecture, the environment, and social behavior.

Thibault Viennet and colleagues gain structural insight into amyloid fibril formation from their innovative use of lipid bilayer nanodiscs. This study connects α-Synuclein membrane binding modes to its aggregation properties, furthering our understanding of the cause of neurodegerative diseases.

Rational engineering of human spermine oxidase yields crystallizable structures and the design of an allosteric inhibitor.

Interaction of the outer membrane protein (OMP) chaperone SurA and the OMP folding catalyst BAM results in changes in the conformational ensembles of both species, suggesting a mechanism for delivery of OMPs to BAM in Gram-negative bacteria.

Kimura et al. demonstrate that footpad hair formation of Drosophila involves elongation of hair cells and assembly of actin filaments, followed by cuticular deposition. They then use this mechanism to design an artificial highly adhesive device with easy attachment and detachment properties.

Here, the authors develop an in vivo insulin delivery system which consists of a glucose responsive gel combined with hemodialysis hollow fibers. This system is electronics-free, temperature independent, and can stably sustain acute glucose-responsiveness in rats.

Palanikumar et al. prepare pH-responsive nanoparticles with drug-loaded PLGA core, cross-linked BSA corona to avoid opsonisation, and functionalised with ATRAM peptide that binds the cell membrane at low pH such as tumour microenvironment. The nanoparticles display both in vitro and in vivo efficacy while evading recognition by macrophages.

Injured endothelial cells are shown to induce an A1 phenotype in astrocytes, characterized by a genetic signature associated with extracellular matrix remodeling factors (e.g. decorin and vascular Aß deposits).

Here the authors analyze the Alzheimer’s Disease Neuroimaging Initiative dataset using random forest machine learning methods and determine that Aβ and tau biomarkers are better predictors of early dementia status, while glucose hypometabolism is a better predictor of later dementia status. These results suggest the need for stage-oriented Alzheimer’s disease treatments.

Jansson et al. design a high content screening system to target inflammation in human brain cells of the blood–brain barrier (pericytes and endothelial cells) to identify inflammatory modifiers. They identify cardiac glycosides as powerful regulators of neuroinflammatory pathways in brain barrier tissues such as vasculature, meninges and choroid plexus.

Miguel Angrick et al. develop an intracranial EEG-based method to decode imagined speech from a human patient and translate it into audible speech in real-time. This report presents an important proof of concept that acoustic output can be reconstructed on the basis of neural signals, and serves as a valuable step in the development of neuroprostheses to help nonverbal patients interact with their environment.

Multimodal PET-fMRI imaging of Alzheimer’s disease patients and healthy controls suggests that microglia activation in the posterior cingulate cortex is associated with increased brain activity in Alzheimer’s disease, and independent of amyloid accumulation.

Ke Zheng and colleagues repurposed a nickase Cas9-cytidine deaminase fusion protein to effectively direct the conversion of cytosine to thymine on bacterial genome. This study suggests that CRISPR/Cas9-guided base-editing can be used to generate viable mutant bacterial strains.

Li et al. provide insights on the color patterning process during flower development. They identify pigment components of the perianths and the lip segments in the Orchidaceae flowers and use transcriptome profiling and functional assays to identify genes involved in pigment biosynthesis and spatiotemporal specificity.

Kelly et al. show that Arabidopsis hexokinase1 (HXK1) expressed in guard-cells is sufficient to drive hypocotyl elongation through increasing the activity of PIF4 and auxin level, and competing with the effects of HY5. This study provides insights into how light and sucrose antagonistically coordinate the effort to achieve the height necessary for efficient photosynthetic, autotrophic sugar production.

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.

Robert R. Fitak et al. investigate the genetic basis for domestication in camels. They found that the positive selection of candidate domestication genes is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Their work provides insights to the evolutionary history of camels and genetics of domestication.

Belser, Baurens et al. report a chromosome-scale assembly of a banana genome (Musa acuminata) with five out of eleven chromosomes entirely reconstructed in a single contig from telomere to telomere. This work sheds light on the content of complex regions like centromeres or clusters of paralogous genes in the banana genome.

Gen Sobue, Masao Nagasaki and colleagues report a genome-wide association study for amyotrophic lateral sclerosis (ALS) in a large, multi-ethnic cohort comprising Japanese, Chinese, and European ancestry populations. They find a significant association to variants within the ACSL5 gene and identify novel associations with 4 additional genes using a gene-based approach.

Vallianatos et al. study the functional interactions of KMT2A and KDM5C, H3K4me enzymes known to be involved in neurodevelopmental disorders. Using genetic mouse models, neuronal structure analysis, neurobehavior, and epigenomic profiling, they demonstrate a mutually suppressive relationship between KMT2A and KDM5C during neurodevelopment.

Blaskovich et al. demonstrate the antimicrobial applications of cannabidiol and cannabidiol analogs against a range of pathogenic bacteria, including the capacity to kill MRSA and the Gram-negative bacteria Neisseria gonorrhoeae. This article highlights the potential for cannabidiol in the age of antimicrobial resistance.

Qi, Li, Yun, Zhang et al.show that lactobacilli promote the generation of gut mucosa by facilitating the conversion of arginine to L-Ornithine. This study highlights the importance of a crosstalk between arginine metabolism in Lactobacilli and tryptophan metabolism in gut epithelial cells in maintaining a healthy gut barrier.

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.

Dimple Chakravarty et al. review the rapidly emerging data indicating a higher rate of SARS-CoV-2 infection in men. They note that men in the age group most at risk of infection are also at high risk of prostate cancer, and explore the potential links between these diseases and implications for COVID-19 treatment in prostate cancer patients.

Stamatia Rontogianni et al. show that the proteomic profiles of extracellular vesicles secreted by different classes of breast cancer cell lines can be used as biomarkers of their respective subtype. They show these provide molecular evidence for subtype-specific biological processes and pathways.

Yetsko, Farrell, Duffy, and colleagues conduct transcriptomic and immunohistological profiling of tumors from sea turtles with fibropapillomatosis. Internal tumors are distinct from more common external tumors, but share some oncogenic signaling pathways that may serve as treatment targets in future.

Using mice with disrupted neuropeptide signaling, Hughes et al. show that daily scheduled voluntary exercise (SVE) promotes suprachiasmatic nuclei (SCN) clock cell synchrony and robust 24 h rhythms in behavior. This study suggests the potential utility of regular exercise as a non-invasive intervention for the elderly or mentally ill, where circadian rhythms can be poorly aligned to the external world.

Zamprogno et al. report a lung-on-a-chip of the second generation that mimics an array of alveoli with in vivo-like dimensions, based on a thin, stretchable collagen-elastin membrane used to reproduce the air-blood barrier functions. The membrane is stable, can be cultured on both sides for weeks, is biodegradable and its elastic properties allow mimicking respiratory motions by mechanically stretching the cells.

Massen, Hartlieb, Martin et al. study the duration of yawns across mammals and birds to test the brain cooling hypothesis. Consistent with this hypothesis, their findings indicate that brain mass and neuron numbers influence yawn duration, and that mammals yawn longer than birds with similar brain and body masses.

Kim, Hwang et al. use in vitro and in vivo models of autophagy disorder/metabolic dysfunction to show that in this context, the natural compound kaempferide is an autophagy enhancer and reveal that one of the underlying mechanisms governing this is mediated by the mitochondrial elongation factor TUFM. This insight may have therapeutic value in the treatment of metabolic disorders.

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.

Kening Zhao et al. show that yeast extracellular vesicles are depleted of ESCRT proteins but enriched with Fks1 and Chs3. The toxic effect of antifungal agents can be diminished by exposure to the Fks1- and Chs3- rich extracellular vesicles, suggesting a role for yeast extracellular vesicles in cell wall remodelling.

Giovanni Quinones-Valdez et al. examined the role of over 200 RNA-binding proteins in mediating A-to-I RNA editing. They identified several RNA-binding proteins that regulate ADAR1 expression, interaction, or binding with Alu elements in a cell type-specific manner.

Bengi Turegun et al. report an interaction of the highly-conserved pHSA and P1 domains of Sth1, the catalytic subunit of the SWI/SNF-family chromatin remodeler RSC. This interaction is released when ATP-bound Rtt102-Arp7/9 binds to the HSA domain, modulating DNA and nucleosome binding by Sth.

Melanie Das et al. demonstrate that transplantation of young bone marrow preserves the cognitive function of old recipient mice. This study suggests that microglial rejuvenation via peripheral manipulation of the hematopoietic system may be sufficient to delay a cognitive decline during aging.

Investigating signalling induced by the cytokine CCL2 as a therapeutic target, Tu et al demonstrate that blockade of the CCL2 receptor, CCR2 enhances CD8+ T cell recruitment and activation and the therapeutic efficacy of PD-1 inhibition in tumours.

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.

Tahmasian et al. report that associations between sleep duration, intelligence, BMI, and depression are attributed to a shared macroscale brain-anatomy. They apply a comprehensive multivariate approach on two independent neuroimaging datasets and study shared heritability effects driving phenotypic associations in a twin-based sample.

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.