bluuebunny/crossref_metadata_2025 huggingface dataset:
A realistic benchmark for the identification of differentially abundant taxa in (confounded) human microbiome studies
Authors: Wirbel Jakob , Essex Morgan , Forslund Sofia Kirke , Zeller Georg
Published: May 2022

Background

In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance (DA) testing is lacking, and it remains unexplored how these cope with confounding. Previous DA benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

Results

Here we develop a simulation framework which implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole-metagenome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies to a much greater extent than in previous benchmarks. With extensively parametrized simulations we benchmark the performance of eighteen DA methods and further evaluate the best ones on confounded simulations. Only linear models,limma, fastANCOM, and the Wilcoxon test properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find thatpost hocadjustment can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

Conclusions

For microbiome association studies tight error control is critical. The unsatisfactory performance of many DA methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.
Trapped pore waters in the open proton channel HV1
Authors: Boytsov Danila , Brescia Stefania , Chaves Gustavo , Koefler Sabina , Hannesschlaeger Christof , Siligan Christine , Gössweiner-Mohr Nikolaus , Musset Boris , Pohl Peter
Published: May 2022

The voltage-gated proton channel, HV1, is crucial for innate immune responses. According to alternative hypotheses, protons either hop on top of an uninterrupted water wire or bypass titratable amino acids, interrupting the water wire halfway across the membrane. To distinguish between both hypotheses, we estimate the water mobility for the putative case of an uninterrupted wire. The predicted single-channel water permeability 3×10−12cm3s−1 reflects the permeability-governing number of hydrogen bonds between water molecules in single-file configuration and pore residues. However, the measured unitary water permeability does not confirm the prediction, i.e., it is negligible. Osmotic deflation of reconstituted lipid vesicles reveals trapped water inside the HV1 wild-type channel and D174A mutant open at 0 mV. The conductance of 1400 H+ s−1 per wild-type channel agrees with the calculated diffusion limit for a ~2 Å capture radius for protons. Removal of a charged amino acid (D174) at the pore mouth decreases H+ conductance, conceivably by reducing the capture radius. At least one intervening amino acid contributes to H+ conductance while blocking water flow.
Application of rapid invisible frequency tagging for brain computer interfaces
Authors: Brickwedde Marion , Bezsudnova Yulia , Kowalczyk Anna , Jensen Ole , Zhigalov Alexander
Published: May 2022

Background

Brain-computer interfaces (BCI) based on steady-state visual evoked potentials (SSVEPs/SSVEFs) are among the most commonly used BCI systems. They require participants to covertly attend to visual objects flickering at specified frequencies. The attended location is decoded in real-time by analysing the power of neuronal responses at the flicker frequency.

New method

We implemented a novel rapid invisible frequency-tagging technique, utilizing a state-of-the-art projector with refresh rates of up to 1440 Hz. We flickered the luminance of visual objects at 56 and 60 Hz, which was invisible to participants but produced strong neuronal responses measurable with magnetoencephalography (MEG). The direction of covert attention, decoded from frequency-tagging responses, was used to control a real-time BCI PONG game.

Results

Our results show that seven out of eight participants were able to play the pong game controlled by the frequency-tagging signal, with average accuracies exceeding 60%. Importantly, participants were able to modulate the power of the frequency-tagging response within a 1-second interval, while only seven occipital sensors were required to reliably decode the neuronal response.

Comparison with existing methods

In contrast to existing SSVEP-based BCI systems, rapid frequency-tagging does not produce a visible flicker. This extends the time-period participants can use it without fatigue, by avoiding distracting visual input. Furthermore, higher frequencies increase the temporal resolution of decoding, resulting in higher communication rates.

Conclusion

Using rapid invisible frequency-tagging opens new avenues for fundamental research and practical applications. In combination with novel optically pumped magnetometers (OPMs), it could facilitate the development of high-speed and mobile next-generation BCI systems.
Peptide Avidity for TCR on CD4 Effectors Determines the Extent of Memory Generation
Authors: Jones Michael C. , Castonguay Catherine , Nanaware Padma P. , Weaver Grant C. , Stadinski Brian , Kugler-Umana Olivia A. , Huseby Eric , Stern Lawrence J. , Devarajan Priyadharshini , Swain Susan L.
Published: May 2022

The impact of initial peptide antigen affinity for TCR in driving memory fate has been studied previously, however its contributions when effectors contract to memory is unclear. To become memory, effector CD4 T cells must recognize antigen at 5-8 days post-infection, at what we call the “effector checkpoint.” We examined whether peptide affinity for the TCR of effectors impacts the extent of memory and degree of protection against rechallenge. We made an influenza A virus (IAV) nucleoprotein (NP)-specific TCR transgenic strain, FluNP, and generated NP-peptide variants that bind FluNP TCR with a broad range of avidity. To vary avidityin vivo, we primed naïve donor FluNP in IAV-infected hosts, purified 6d FluNP effectors and co-transferred them with peptide-pulsed APC into uninfected second hosts. Higher affinity peptides yielded higher numbers of FluNP memory cells in the spleen and most dramatically in the lung and dLN, and drove better protection against lethal influenza infection. The major impact of avidity was on memory cell number, not cytokine production, and was already apparent within several days of transfer. We previously showed that autocrine IL-2 production during the effector checkpoint prevented default effector apoptosis and supported memory formation. Here, peptide avidity determined the level of IL-2 produced by effectors. IL-2Rα expression by APC drove more memory cell formation, suggesting that transpresentation of IL-2 by APC at this checkpoint enhanced CD4 memory generation. Secondary memory generation was also avidity-dependent. We propose this pathway selects CD4 effectors of highest affinity to progress to memory.
PeSTo: parameter-free geometric deep learning for accurate prediction of protein interacting interfaces
Authors: Krapp Lucien F. , Abriata Luciano A. , Rodriguez Fabio Cortés , Peraro Matteo Dal
Published: May 2022

Predicting the interactions that a protein can establish with other molecules from its structure remains a major challenge. As shown by recent applications to tertiary structure prediction and opposite to current mainstream methods for interaction interface prediction, low-level, geometry-based, physicochemical-agnostic representations of structures have several advantages over methods that require pre-calculation of surfaces, charges, hydrophobicity, and other kinds of parameterizations. Here we introduce a new geometric transformer that acts directly on protein atoms labelled with nothing more than element names. The resulting model outperforms the state of the art for the prediction of protein-protein interaction interfaces and distinguishes interfaces with nucleic acids, lipids, small molecules and ions with high confidence. The low computational cost of this method (available online at https://pesto.epfl.ch/) enables processing high volumes of structural data, such as molecular dynamics trajectories allowing the discovery of interfaces that remain inconspicuous in static experimentally solved structures.
No branch left behind: tracking terrestrial biodiversity from a phylogenetic completeness perspective
Authors: Pinto-Ledezma Jesús N. , Díaz Sandra , Halpern Benjamin S. , Khoury Colin , Cavender-Bares Jeannine
Published: May 2022

Biodiversity, as we see it today, ultimately is the outcome of millions of years of evolution; however, biodiversity in its multiple dimensions is changing rapidly due to increasing human domination of Earth. Here, we present the “phylogenetic completeness” (PC) a concept and methodology that intends to safeguard Earth’s evolutionary heritage by maintaining all branches of the tree of life. We performed a global evaluation of the PC approach using data from five major terrestrial clades and compared the results to an approach in which species are conserved or lost randomly. We demonstrate that under PC, for a given number of species extinctions, it is possible to maximize the protection of evolutionary innovations in every clade. The PC approach is flexible and can be used to conduct a phylogenetic audit of biodiversity under different conservation scenarios. The PC approach complements existing conservation efforts and is linked to the post-2020 Convention of Biodiversity targets.
Roughening instability of growing 3D bacterial colonies
Authors: Martínez-Calvo Alejandro , Bhattacharjee Tapomoy , Bay R. Kōnane , Luu Hao Nghi , Hancock Anna M. , Wingreen Ned S. , Datta Sujit S.
Published: May 2022

How do growing bacterial colonies get their shapes? While colony morphogenesis is well-studied in 2D, many bacteria grow as large colonies in 3D environments, such as gels and tissues in the body, or soils, sediments, and subsurface porous media. Here, we describe a morphological instability exhibited by large colonies of bacteria growing in 3D. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria—Escherichia coli, Vibrio cholerae, Pseudomonas aeruginosa, andKomagataeibacter sucrofermentans—generically roughen as they consume nutrients and grow beyond a critical size, eventually adopting a characteristic branched, broccoli-like, self-affine morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between 2D and 3D colonies: while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient-limited in its interior, driving a transition to rough growth at its surface. We elucidate the onset of roughening using linear stability analysis and numerical simulations of a continuum model that treats the colony as an ‘active fluid’ whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the growing colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies—as well as other forms of growing active matter, such as tumors and engineered living materials—in 3D environments.
Chronic clinical signs of upper respiratory tract disease shape gut and respiratory microbiomes in cohabitating domestic felines
Authors: Arnold Holly K. , Hanselmann Rhea , Duke Sarah M. , Sharpton Thomas J. , Beechler Brianna R.
Published: May 2022

Feline upper respiratory tract disease (FURTD), often caused by infections etiologies, is a multifactorial syndrome affecting feline populations worldwide. Because of its highly transmissible nature, infectious FURTD is most prevalent anywhere cats are housed in groups such as animal shelters, and is associated with negative consequences such as decreasing adoption rates, intensifying care costs, and increasing euthanasia rates. Understanding the etiology and pathophysiology of FURTD is thus essential to best mitigate the negative consequences of this disease. Clinical signs of FURTD include acute respiratory disease, with a small fraction of cats developing chronic sequelae. It is thought that nasal mucosal microbiome changes play an active role in the development of acute clinical signs, but it remains unknown if the microbiome may play a role in the development and progression of chronic clinical disease. To address the knowledge gap surrounding how microbiomes link to chronic FURTD, we asked if microbial community structure of upper respiratory and gut microbiomes differed between cats with chronic FURTD signs and clinically normal cats. We selected 8 households with at least one cat exhibiting chronic clinical FURTD, and simultaneously collected samples from cohabitating clinically normal cats. Microbial community structure was assessed via 16S rDNA sequencing of both gut and nasal microbiome communities. Using a previously described ecophylogenetic method, we identified 37 and 27 microbial lineages within gut and nasal microbiomes respectively that significantly associated with presence of active FURTD clinical signs in cats with a history of chronic signs. Overall, we find that nasal and gut microbial communities may contribute to the development of chronic clinical course, but more research is needed to confirm our observations.
MPZ-T124M mouse model replicates human axonopathy and suggest alteration in axo-glia communication
Authors: Shackleford Ghjuvan’Ghjacumu , Marziali Leandro N. , Sasaki Yo , Weinstock Nadav I. , Rossor Alexander M. , Silvestri Nicholas J. , Wilson Emma R. , Hurley Edward , Kidd Grahame J. , Manohar Senthilvelan , Ding Dalian , Salvi Richard J. , Laura Feltri M. , D’Antonio Maurizio , Wrabetz Lawrence
Published: May 2022

Myelin is essential for rapid nerve impulse propagation and axon protection. Accordingly, defects in myelination or myelin maintenance lead to secondary axonal damage and subsequent degeneration. Studies utilizing genetic (CNPase-, MAG-, and PLP-null mice) and naturally occurring neuropathy models suggest that myelinating glia also support axons independently from myelin. Myelin protein zero (MPZ or P0), which is expressed only by Schwann cells, is critical for myelin formation and maintenance in the peripheral nervous system. Many mutations in MPZ are associated with demyelinating neuropathies (Charcot-Marie-Tooth disease type 1B [CMT1B]). Surprisingly, the substitution of threonine by methionine at position 124 of P0 (P0T124M) causes axonal neuropathy (CMT2J) with little to no myelin damage. This disease provides an excellent paradigm to understand how myelinating glia support axons independently from myelin. To study this, we generated targeted knock-in P0T124M mutant mice, a genetically authentic model of T124M-CMT2J neuropathy. Similar to patients, these mice develop axonopathy between 2 and 12 months of age, characterized by impaired motor performance, normal nerve conduction velocities but reduced compound motor action potential amplitudes, and axonal damage with only minor compact myelin modifications. Mechanistically, we detected metabolic changes that could lead to axonal degeneration, and prominent alterations in non-compact myelin domains such as paranodes, Schmidt-Lanterman incisures, and gap junctions, implicated in Schwann cell-axon communication and axonal metabolic support. Finally, we document perturbed mitochondrial size and distribution along P0T124M axons suggesting altered axonal transport. Our data suggest that Schwann cells in P0T124M mutant mice cannot provide axons with sufficient trophic support, leading to reduced ATP biosynthesis and axonopathy. In conclusion, the P0T124M mouse model faithfully reproduces the human neuropathy and represents a unique tool for identifying the molecular basis for glial support of axons.
A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture
Authors: Matzko Michelle E. , Sephton-Clark Poppy C. S. , Young Eleanor L. , Jhaveri Tulip A. , Martinsen Melanie A. , Mojica Evan , Boykin Rich , Pierce Virginia M. , Cuomo Christina A. , Bhattacharyya Roby P.
Published: May 2022

Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow.
Single-cell profiling coupled with lineage analysis reveals distinct sacral neural crest contributions to the developing enteric nervous system
Authors: Tang Weiyi , Jacobs-Li Jessica , Li Can , Bronner Marianne E.
Published: May 2022

During development, the enteric nervous system (ENS) arises from neural crest cells that emerge from the neural tube, migrate to and along the gut, and colonize the entire intestinal tract. While much of the ENS arises from vagal neural crest cells that originate from the caudal hindbrain, there is a second contribution from the sacral neural crest that migrates from the caudal end of the spinal cord to populate the post-umbilical gut. By coupling single cell transcriptomics with axial-level specific lineage tracing in avian embryos, we compared the contributions between embryonic vagal and sacral neural crest cells to the ENS. The results show that the two neural crest populations form partially overlapping but also complementary subsets of neurons and glia in distinct ganglionic units. In particular, the sacral neural crest cells appear to be the major source of adrenergic/dopaminergic and serotonergic neurons, melanocytes and Schwann cells in the post-umbilical gut. In addition to neurons and glia, the results also reveal sacral neural crest contributions to connective tissue and mesenchymal cells of the gut. These findings highlight the specific properties of the sacral neural crest population in the hindgut and have potential implications for understanding development of the complex nervous system in the hindgut environment that may influence congenital neuropathies.
Scaled-expansion of the membrane associated cytoskeleton requires conserved kinesin adaptors
Authors: Glomb Oliver , Swaim Grace , LLancao Pablo Munoz , Lovejoy Christopher , Sutradhar Sabyasachi , Park Junhyun , Wu Youjun , Hammarlund Marc , Howard Jonathon , Ferguson Shawn M. , Yogev Shaul
Published: May 2022

A periodic lattice of actin rings and spectrin tetramers scaffolds the axonal membrane. How spectrin is delivered to this structure to scale its size to that of the growing axon is unknown. We found that endogenous spectrin, visualized with singe axon resolution in vivo, is delivered to hotspots in the lattice that support its expansion at rates set by axon stretch-growth. Unlike other cytoskeletal proteins, whose apparent slow movement consists of intermittent bouts of fast movements, spectrin moves slowly and processively. We identified a pair of coiled coil proteins that mediate this slow movement and the expansion of the lattice by linking spectrin to kinesin-1. Thus, processive slow transport and local lattice incorporation support scaled cytoskeletal expansion during axon stretch-growth.

One-Sentence Summary

Kinesin adaptors control spectrin transport and expansion of the membrane periodic skeleton.
A sporulation-independent way of life for Bacillus thuringiensis in the late stages of an infection
Authors: Toukabri Hasna , Lereclus Didier , Slamti Leyla
Published: May 2022

The formation of endospores has been considered as the unique mode of survival and transmission of sporulating Firmicutes due to the exceptional resistance and persistence of this bacterial form. However, the persistence of non-sporulated bacteria (Spo-) was reported during infection in Bacillus thuringiensis, an entomopathogenic sporulating Gram-positive bacterium. In this study, we investigated the behavior of a bacterial population in the late stages of an infection as well as the characteristics of the Spo- bacteria in the B. thuringiensis/Galleria mellonella infection model. Using fluorescent reporters coupled to flow cytometry as well as molecular markers, we demonstrated that the Spo- cells constitute about half of the population two weeks post-infection (pi) and that these bacteria present vitality signs. However, a protein synthesis and a growth recovery assay indicated that they are in a metabolically slowed-down state. Interestingly, they were extremely resistant to the cadaver environment which proved deadly for in vitro-grown vegetative cells and, strikingly, did not support spore germination. A transcriptomic analysis of this subpopulation at 7 days pi revealed a signature profile of this state. The expression analysis of individual genes at the cell level suggests that iron homeostasis is important at all stages of the infection, whereas the oxidative stress response seems of particular importance as the survival time increases. Altogether, these data show that non-sporulated bacteria are able to survive for a prolonged period of time and indicate that they engage in a profound adaptation process that leads to their persistence in the host cadaver.
Ocular and Facial Far-UVC Doses from Ceiling-Mounted 222 nm Far-UVC Fixtures
Authors: Duncan Michael A. , Welch David , Shuryak Igor , Brenner David J.
Published: May 2022

Far-UVC radiation, commonly defined as wavelengths from 200 nm – 235 nm, is a promising tool to help prevent the spread of disease. The unique advantage of far-UVC technology over traditional ultraviolet germicidal irradiation lies in the potential for direct application of far-UVC into occupied spaces since antimicrobial doses of far-UVC are significantly below the recommended daily safe exposure limits. This study used a ceiling-mounted far-UVC fixture emitting at 222 nm to directly irradiate an indoor space and then evaluated the doses received upon a manikin. Radiation sensitive film was affixed to the head, nose, lip, and eyes of the manikin, and the 8-hour equivalent exposure dose was determined. Variables examined included manikin height (sitting or standing position), manikin offset from directly below the fixture, tilt of the manikin, the addition of glasses, the addition of hair, and different anatomical feature sizes. Importantly, at the manikin position with the highest dose to eyes, the average eye dose was only 5.8% of the maximum directly measured dose. These results provide the first experimental analysis of possible exposure doses a human would experience from an indoor far-UVC installation.
Interaction between VPS13A and the XK scramblase is required to prevent VPS13A disease in humans
Authors: Park Jae-Sook , Hu Yiying , Hollingsworth Nancy. M. , Miltenberger-Miltenyi Gabriel , Neiman Aaron M.
Published: May 2022

VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans there are four VPS13 paralogs each of which is required to prevent a different inherited disorder. VPS13 proteins contain multiple conserved domains. The VAB domain binds to adaptor proteins to recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A in preventing VPS13A disease (chorea-acanthocytosis). The Pleckstrin Homology (PH) domain at the C-terminus of VPS13A is required to form a complex with the XK scramblase and for proper localization of VPS13A within the cell. Mutations in the interaction surface between VPS13A and XK predicted by Alphafold modeling disrupt complex formation and colocalization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in XK argue that loss of VPS13A-XK complex is the basis of both diseases.

Summary Statement

VPS13A disease and McLeod syndrome are related disorders caused by mutation of the VPS13A and XK genes, respectively. A pathologic VPS13A mutation disrupts binding of the VPS13A and XK proteins, suggesting a common basis of both diseases.
Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Authors: Ghafari Mahan , Liu Qihan , Dhillon Arushi , Katzourakis Aris , Weissman Daniel B
Published: May 2022

The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, fundamental facts about the evolutionary origins of VOCs remain largely unknown. One major uncertainty is whether the VOCs evolved during transmission chains of many acute infections or during long-term infections within single individuals. We test the consistency of these two possible paths with the observed dynamics, focusing on the clustered emergence of the first three VOCs, Alpha, Beta, and Gamma, in late 2020, following a period of relative evolutionary stasis. We consider a range of possible fitness landscapes, in which the VOC phenotypes could be the result of single mutations, multiple mutations that each contribute additively to increasing viral fitness, or epistatic interactions among multiple mutations that do not individually increase viral fitness—a “fitness plateau”. Our results suggest that the timing and dynamics of the VOC emergence, together with the observed number of mutations in VOC lineages, are in best agreement with the VOC phenotype requiring multiple mutations and VOCs having evolved within single individuals with long-term infections.
CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone processing
Authors: Alahmari Abdulrahman. A. , Chaubey Aditi H. , Tisdale Arwen A. , Schwarz Carla D. , Cornwell Abigail C. , Maraszek Kathryn E. , Paterson Emily J. , Kim Minsuh , Venkat Swati , Gomez Eduardo Cortes , Wang Jianmin , Gurova Katerina V. , Feigin Michael E.
Published: May 2022

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options. This potentiates the importance of uncovering novel drug targets. We have discovered global dysregulation of the gene regulatory process alternative polyadenylation (APA) in PDAC. APA is a pre-mRNA processing mechanism that generates mRNAs with distinct 3’ ends, impacting gene expression and protein function. We revealed that APA dysregulation in PDAC drives oncogenic signatures and predicts poor patient outcome. As APA directs widespread gene expression dysregulation across the PDAC patient population, we hypothesized that inhibition of APA has therapeutic potential. APA is controlled by a complex of proteins, including cleavage and polyadenylation specificity factor 3 (CPSF3). CPSF3 is the endonuclease catalyzing mRNA cleavage, and a potentially druggable target. We now find that CPSF3 is highly expressed and associated with poor prognosis in PDAC patients. CPSF3 knockdown decreases PDAC proliferation and clonogenicity in vitro and tumor growth in vivo. We demonstrate that CPSF3 knockdown induces widespread APA alterations of oncogenes and tumor suppressors, and determine the contribution of one of these events to CPSF3-induced cell proliferation phenotype. Furthermore, we find that PDAC, but not non-transformed pancreatic cells, are sensitive to the CPSF3 small molecule inhibitor JTE-607. Mechanistically, JTE-607 impairs replication-dependent histone processing, disrupting nucleosome assembly and destabilizing chromatin structure. Finally, we determine that JTE-607 attenuates cell proliferation by arresting cells in early S-phase of the cell cycle. Altogether, we identify CPSF3 as a druggable target in PDAC and reveal novel mechanisms by which CPSF3 controls cancer cell growth.

Significance

This work identifies CPSF3 as a potential drug target in pancreatic ductal adenocarcinoma and reveals new mechanisms by which CPSF3 inhibition attenuates PDAC cell proliferation through modulating alternative polyadenylation and histone processing.
Increased sedoheptulose-1,7-bisphosphatase content in the C4 species Setaria viridis does not affect photosynthesis
Authors: Ermakova Maria , Lopez-Calcagno Patricia E. , Furbank Robert T. , Raines Christine A. , von Caemmerer Susanne
Published: May 2022

Sedoheptulose-1,7-bisphosphatase (SBPase) is one of the rate-limiting enzymes of the Calvin cycle, and, in C3 plants, increasing the abundance of SBPase is known to provide higher photosynthetic rates and stimulate biomass and yield. C4 plants usually have higher photosynthetic rates because they operate a biochemical CO2 concentrating mechanism between mesophyll and bundle sheath cells. In the C4 system, SBPase and other enzymes of Calvin cycle are localised to the bundle sheath cells. Here we tested what effect increasing abundance of SBPase would have on C4 photosynthesis. Using Setaria viridis, a model C4 plant of NADP-ME subtype, we created transgenic plants with 1.5 to 3.2-times higher SBPase content, compared to wild type plants. Transcripts of the transgene were found predominantly in the bundle sheaths suggesting the correct cellular localisation of the protein. Abundance of RBCL, the large subunit of Rubisco, was not affected in transgenic plants overexpressing SBPase, and neither was relative chlorophyll content or photosynthetic electron transport parameters. We found no correlation between SBPase content in S. viridis and saturating rates of CO2 assimilation. Moreover, detailed analysis of CO2 assimilation rates at different CO2 partial pressure, irradiance and leaf temperature, showed no improvement of photosynthesis in plants overexpressing SBPase. We discuss potential implications of these results for understanding the regulation of C4 photosynthesis.
Ontogeny of risk assessment and escape-hatching performance by red-eyed treefrog embryos in two threat contexts
Authors: Güell Brandon A. , Jung Julie , Almanzar Adeline , Cuccaro-Díaz Juliana , Warkentin Karen M.
Published: May 2022

Arboreal embryos of red-eyed treefrogs, Agalychnis callidryas, hatch prematurely in response to hypoxia when flooded and mechanosensory cues (MC) in snake attacks, but hatching later improves tadpole survival. We studied ontogenetic changes in risk assessment and hatching performance of embryos in response to flooding and physical disturbance. We hypothesized that risk assessment decreases as hatchling survival improves and hatching performance increases as embryos develop. Because snakes eat faster than embryos asphyxiate, we hypothesized that embryos decide to hatch sooner and hatch faster in response to MC. We video-recorded individual embryos hatching in response to each cue type, then compared the incidence and timing of a series of events and behaviors from cue onset to complete hatching across ages and stimuli. Latency from cue to hatching decreased developmentally in both contexts and was shorter with MC, but the elements contributing to those changes differed. Hypoxia-assessment involved position changes, which decreased developmentally along with assessment time. MC-assessment was passive, faster, and also decreased with age. The first stages of hatching, membrane rupture and head emergence, were surprisingly age-independent but faster with MC, congruent with greater effort under more immediate risk. In contrast, body emergence and compression showed ontogenetic improvement consistent with morphological constraints but no cue effect. Both appropriate timing and effective performance of hatching are necessary for continued development. Different stages of the process vary with development and environmental context, suggesting combinations of adaptive context- and stage-dependent behavior, cue-related constraints on information acquisition, and ontogenetic constraints on elements of performance.

Summary statement

Development reduces risk assessment and improves hatching performance by red-eyed treefrog embryos in both flooding and simulated attacks. Predation cues elicit faster decisions and hatching, congruent with more immediate risk.
Non-Covalently Associated Streptavidin Multi-Arm Nanohubs Exhibit Mechanical and Thermal Stability in Protein-Network Materials
Authors: Knoff David S. , Kim Samuel , Fajardo Cortes Kareen A. , Rivera Jocelyne , Altamirano Dallas , Kim Minkyu
Published: May 2022

Constructing protein-network materials that exhibit physicochemical and mechanical properties of individual protein constituents requires molecular cross-linkers with specificity and stability. A well-known example involves specific chemical fusion of a four-arm polyethylene glycol (tetra-PEG) to desired proteins with secondary cross-linkers. However, it is necessary to investigate tetra-PEG like biomolecular cross-linkers that are genetically fused to the proteins, simplifying synthesis by removing additional conjugation and purification steps. Non-covalently, self-associating, streptavidin homotetramer is a viable, biomolecular alternative to tetra-PEG. Here, a multi-arm streptavidin design is characterized as a protein-network material platform using various secondary, biomolecular cross-linkers, such as high-affinity physical (i.e., non-covalent), transient physical, spontaneous chemical (i.e., covalent), or stimuli-induced chemical cross-linkers. Stimuli-induced, chemical cross-linkers fused to multi-arm streptavidin nanohubs provide sufficient diffusion prior to initiating permanent covalent bonds, allowing proper characterization of streptavidin nanohubs. Surprisingly, non-covalently associated streptavidin nanohubs exhibit extreme stability which translates into material properties that resemble hydrogels formed by chemical bonds even at high temperatures. Therefore, this study not only establishes that the streptavidin nanohub is an ideal multi-arm biopolymer precursor but also provides valuable guidance for designing self-assembling nanostructured molecular networks that can properly harness the extraordinary properties of protein-based building blocks.
Diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, inhibits the growth of Bacillus subtilis but promotes the growth of Escherichia coli
Authors: Tanabe Nozomu , Takasu Rena , Hirose Yuu , Kamei Yasuhiro , Kondo Maki , Nakabachi Atsushi
Published: May 2022

Diaphorin is a polyketide produced by Candidatus Profftella armatura (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). The analyses revealed that diaphorin inhibits the growth of B. subtilis but moderately promotes the growth of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host + symbionts) against some bacterial lineages but is beneficial for others, which potentially include obligate symbionts of D. citri.

Importance

Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of symbiosis between animal hosts and bacteria but may also potentially be exploited to promote the effectiveness of industrial material production by microorganisms.
Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives
Authors: Hejblum Boris P , Ba Kalidou , Thiébaut Rodolphe , Agniel Denis
Published: May 2022

By reproducing differential expression analysis simulation results presented by Li et al, we identified a caveat in the data generation process. Data not truly generated under the null hypothesis led to incorrect comparisons of benchmark methods. We provide corrected simulation results that demonstrate the good performance of dearseq and argue against the superiority of the Wilcoxon rank-sum test as suggested by Li et al. Please see related Research article with DOI 10.1186/s13059-022-02648-4.
Mechanochemical rules for shape-shifting filaments that remodel membranes
Authors: Meadowcroft Billie , Palaia Ivan , Pfitzner Anna-Katharina , Roux Aurélien , Baum Buzz , Šarić Anđela
Published: May 2022

The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how ESCRT-III polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodelling and show this mechanism is efficient because sequential polymer assembly lowers the energetic barrier for membrane deformation.
Inferring future changes in gene flow under climate change in riverscapes
Authors: Nakajima Souta , Suzuki Hiroaki , Nakatsugawa Makoto , Matsuo Ayumi , Hirota Shun K. , Suyama Yoshihisa , Nakamura Futoshi
Published: May 2022

Global climate change poses a significant threat to the habitat connectivity of cold-water-adapted organisms, leading to species extinctions. Because gene flow is itself a functional connectivity among wild populations, if gene flow is modeled by landscape variables, changes in population connectivity could be predicted. In this study, using a model-based riverscape genetics technique and a hydrological model to estimate water temperature, we inferred the determinants of and future changes in gene flow of the fluvial sculpin Cottus nozawae in the upstream section of the Sorachi River, Hokkaido, Japan. As a result of model selection, stream order, water temperature, slope, and distance were detected as landscape variables affecting the strength of gene flow in each stream section. In particular, the trend of greater gene flow in sections with higher stream order and lower temperature fluctuations or summer water temperatures was pronounced. The map from the model showed that gene flow is overall prevented in small tributaries in the southern area, where spring-fed environments are less prevalent. Estimating future changes in gene flow using future water temperature predictions, genetic connectivity was predicted to decrease dramatically until the end of the 21st century under IPCC representative concentration pathway scenario 8.5 (RCP8.5).
Quantifying exposure of bumblebee (Bombus spp.) queens to pesticide residues when hibernating in agricultural soils
Authors: Rondeau Sabrina , Baert Nicolas , McArt Scott , Raine Nigel E.
Published: May 2022

Exposure to pesticides is a major threat to bumblebee (Bombus spp.) health. In temperate regions, queens of many bumblebee species hibernate underground for several months, putting them at potentially high risk of exposure to soil contaminants. The extent to which bumblebees are exposed to residues in agricultural soils during hibernation is currently unknown, which limits our understanding of the full pesticide exposome for bumblebees throughout their lifecycle. To generate field exposure estimates for overwintering bumblebee queens to pesticide residues, we sampled soils from areas corresponding to suitable likely hibernation sites at six apple orchards and 13 diversified farms throughout Southern Ontario (Canada) in fall 2019-2020. Detectable levels of pesticides were found in 65 of 66 soil samples analysed for multi-pesticide residues (UPLC-MS/MS). A total of 53 active ingredients (AIs) were detected in soils, including 27 fungicides, 13 insecticides, and 13 herbicides. Overall, the frequency of detection, residue levels (median = 37.8 vs. 2.2 ng/g), and number of pesticides per sample (mean = 12.3 vs. 4.3 AIs) were highest for orchard soils compared to soils from diversified farms. Ninety-one percent of samples contained multiple residues, including mixtures of insecticides and fungicides that might lead to synergistic effects. Up to 29 different AIs were detected per soil sample. Our results suggest that when hibernating in agricultural areas, bumblebee queens are very likely to be exposed to a wide range of pesticide residues in soil. Our study indicates the importance of empirically testing the potential effects of pesticide residues in soils for hibernating bumblebee queens, using field exposure data such as those generated here. The differences in exposure that we detected between cropping systems can also be used to better inform regulations that govern the use of agricultural pesticides, notably in apple orchards.
The autism-associated gene SYNGAP1 regulates human cortical neurogenesis
Authors: Birtele Marcella , Del Dosso Ashley , Xu Tiantian , Nguyen Tuan , Wilkinson Brent , Hosseini Negar , Nguyen Sarah , Urenda Jean-Paul , Knight Gavin , Rojas Camilo , Flores Ilse , Atamian Alexander , Moore Roger , Sharma Ritin , Pirrotte Patrick , Ashton Randolph S. , Huang Eric J. , Rumbaugh Gavin , Coba Marcelo P. , Quadrato Giorgia
Published: May 2022

Autism spectrum disorder (ASD) is a genetically heterogeneous disorder linked with rare, inherited andde novomutations occurring in two main functional gene categories: gene expression regulation and synaptic function1. Accumulating evidence points to dysregulation in cortical neurogenesis as a convergent mechanism in ASD pathophysiology2-8. While asynchronous development has been identified as a shared feature among ASD-risk genes in the category of gene expression regulation, it remains unknown whether this phenotype is also associated with ASD-risk genes in the synaptic function category. Here we show for the first time the expression of the synaptic Ras GTP-ase activating protein 1 (SYNGAP1), one of the top ASD risk genes9, in human cortical progenitors (hCPs). Interestingly, we found that multiple components of the postsynaptic density (PSD) of excitatory synapses, of which SYNGAP1 is one of the most abundant components10,11, are enriched in the proteome of hCPs. Specifically, we discover that SYNGAP1 is expressed within the apical domain of human radial glia cells (hRGCs) where it lines the wall of the developing cortical ventricular zone colocalizing with the tight junction-associated protein and MAGUK family member TJP1. In a cortical organoid model of SYNGAP1 haploinsufficiency, we show dysregulated cytoskeletal dynamics that impair the scaffolding and division plane of hRGCs, resulting in disrupted lamination of the cortical plate and accelerated maturation of cortical projection neurons. Overall, the discovery of the expression and function of SYNGAP1 in cortical progenitor cells reframes our understanding of the pathophysiology of SYNGAP1-related disorders and, more broadly, underscores the importance of dissecting the role of synaptic genes associated with neurodevelopmental disorders in distinct cell types across developmental stages.
Entorhinal-hippocampal circuit integrity is related to mnemonic discrimination and amyloid-β pathology in older adults
Authors: Adams Jenna N. , Kim Soyun , Rizvi Batool , Sathishkumar Mithra , Taylor Lisa , Harris Alyssa L. , Mikhail Abanoub , Keator David B. , McMillan Liv , Yassa Michael A.
Published: May 2022

Mnemonic discrimination, a cognitive process that relies on hippocampal pattern separation, is one of the first memory domains to decline in aging and preclinical Alzheimer’s disease. We tested if functional connectivity (FC) within the entorhinal-hippocampal circuit, measured with high-resolution resting state fMRI, is associated with mnemonic discrimination and Aβ pathology, measured with PET, in nondemented older adults. Low object mnemonic discrimination performance was specifically associated with increased FC between anterolateral entorhinal cortex (alEC) and dentate gyrus (DG)/CA3, supporting the importance of this connection to object memory. This hyperconnectivity between alEC-DG/CA3 was related to Aβ pathology and decreased entorhinal cortex volume. In contrast, spatial mnemonic discrimination was not associated with altered FC. Aβ was further associated with decreased FC and volume within hippocampal subfields. Our findings suggest that Aβ may indirectly lead to memory impairment through entorhinal-hippocampal circuit dysfunction and neurodegeneration, and provide a mechanism for vulnerability of object mnemonic discrimination.