bluuebunny/crossref_metadata_2025 huggingface dataset:
JADE1 and HBO1/KAT7 proteins in the cytokinesis of epithelial cells. The role of PHD zinc fingers
Authors: Shao Bo , Panchenko Maria V.
Published: October 2022

Members of the conserved subfamily, JADE1S and JADE1L isoforms, are expressed in epithelial cells, fibroblasts, and epithelial cell lining in vivo. JADE1 proteins interact with histone acetyl transferase HBO1 complex. The two consecutive PHD zinc fingers of JADE1 bind chromatin. We recently reported novel effects of JADE1S on cytokinesis progression. JADE1S depletion facilitated G2/M-to-G1 transition and increased polyploidy and aneuploidy. JADE1S over-expression arrested cells in late cytokinesis, an effect reversed by AURKB inhibitor. In late cytokinesis cells JADE1S protein localized to the midbody. Results suggested a JADE1S role in final abscission delay. Here we investigated the expression of JADE1 in the central spindle, interactions with HBO1, and the role of PHD fingers in late cytokinesis arrest.

The midzone begins to assemble in anaphase and forms into a midbody in cytokinesis. The midbody structure connects two daughter cells and is thought to bear factors controlling the final abscission. We questioned whether, similar to established factors, JADE1S is targeted to the central spindle structures in anaphase. Indeed, in cells transitioning from mitosis to cytokinesis, JADE1S was sequentially targeted to early midzone, midbody flanking zone, and midbody. The step-wise increase of JADE1S expression in midzone and midbody of synchronously dividing cells suggested protein recruitment. The increase of late cytokinesis arrest caused by recombinant JADE1S correlated with increased expression in midbody. Spatial analysis of the members of the chromatin passenger complex, microtubule associated proteins, and centralspindlin, revealed transient co-localization with JADE1S and mapped JADE1S within the cytokinesis bridge.

Deletion of the two PHD zinc fingers inactivated JADE1S ability to arrest cells in late cytokinesis but did not affect its midbody localization. Thus, PHD zinc fingers are required for JADE1S cytokinesis delay but not for midbody targeting. Recombinant HBO1 protein decreased the proportion of late cytokinesis cells, prevented late cytokinesis arrest by JADE1S as well as its midbody localization. Enzyme inactive HBO1 mutant recapitulated the wild type phenotype. The results demonstrate antagonistic relationship and suggest HBO1-mediated midbody dislocation of JADE1S. Our study supports the role of JADE1S in cytokinesis delay and implicates protein partners.
Mycobacterium tuberculosisinfection elevates SLIT2 expression to modulate oxidative stress responses in macrophages
Authors: Borbora Salik Miskat , Bhatt Sneha , Balaji Kithiganahalli Narayanaswamy
Published: October 2022

Mycobacterium tuberculosis (Mtb), the causative agent of the pulmonary ailment, tuberculosis (TB), continues to thrive owing to a disorganized immune response against it by the host. Among other factors, the rewiring of distinct host signaling pathways is effectuated by the intracellular bacterium, resulting in pathogen-favorable outcomes. Oxidative stress build-up is a key cellular manifestation that occurs during mycobacterial infection. Enhanced oxidative stress is brought about by the cumulative effect of elevated reactive oxygen species generation as well as the inept ability of the cell to mitigate ROS levels. Here, we report the increased expression of the neuronal ligand, SLIT2, during mycobacterial infection in macrophages. By employing loss of function analysis using specific inhibitors, we attribute the heightened expression of SLIT2 to the Mtb-mediated phosphorylation of the p38/JNK pathways. Also, using chromatin immunoprecipitation (ChIP) analysis, we found reduced levels of the repressive H3K27me3 signature on the Slit2 promoter during mycobacterial infection. Furthermore, SLIT2 was found to promote the expression of cellular pantetheinase, Vanin1 (VNN1), that contributed to copious levels of ROS within the macrophage cellular milieu. Thus, we dissect essential molecular details leading to the robust expression of SLIT2 during Mtb infection while outlining the potential consequences of SLIT2 upregulation in infected macrophages.

Graphical abstract
TPL2 kinase activity regulates microglial inflammatory responses and promotes neurodegeneration in tauopathy mice
Authors: Wang Yuanyuan , Wu Tiffany , Tsai Ming-Chi , Rezzonico Mitchell G , Abdel-Haleem Alyaa M , Xie Luke , Gandham Vineela D , Ngu Hai , Stark Kimberly , Glock Caspar , Xu Daqi , Foreman Oded , Friedman Brad A , Sheng Morgan , Hanson Jesse E
Published: October 2022

TPL2 (MAP3K8) is a central signaling node in the inflammatory response of peripheral immune cells. We find that TPL2 kinase activity modulates microglial cytokine release and is required for microglia-mediated neuron deathin vitro. In acutein vivoneuroinflammation settings, TPL2 kinase activity regulates microglia activation states and brain cytokine levels. In a tauopathy model of chronic neurodegeneration, loss of TPL2 kinase activity reduces neuroinflammation and rescues synapse loss, brain volume loss, and behavioral deficits. Single-cell RNAseq analysis indicates protection in the tauopathy model was associated with reductions in activated microglia subpopulations as well as infiltrating peripheral immune cells. Overall, using various models, we find that TPL2 kinase activity can promote multiple harmful consequences of microglial activation in the brain including cytokine release, iNOS induction, astrocyte activation, and immune cell infiltration. Consequently, inhibiting TPL2 kinase activity could represent a potential therapeutic strategy in neurodegenerative conditions.
Natural alleles at theDoalocus underpin evolutionary changes inDrosophilalifespan and fecundity
Authors: Hoedjes Katja M. , Kostic Hristina , Keller Laurent , Flatt Thomas
Published: October 2022

‘Evolve and resequence’ (E&R) studies inDrosophila melanogasterhave identified many candidate loci underlying the evolution of ageing and life history, but experiments that validate the effects of such candidates remain rare. In a recent E&R study we have identified several alleles of the LAMMER kinaseDarkener of apricot(Doa) as candidates for evolutionary changes in lifespan and fecundity. Here, we use two complementary approaches to confirm a functional role ofDoain life-history evolution. First, we used transgenic RNAi to study the effects ofDoaat the whole-gene level. Ubiquitous silencing of expression in adult flies reduced both lifespan and fecundity, indicating pleiotropic effects. Second, to characterize segregating variation atDoa, we examined four candidate single nucleotide polymorphisms (SNPs;Doa-1, −2, −3, −4) using a genetic association approach. Three candidate SNPs had effects that were qualitatively consistent with expectations based on our E&R study:Doa-2pleiotropically affected both lifespan and late-life fecundity;Doa-1affected lifespan (but not fecundity); andDoa-4affected late-life fecundity (but not lifespan). Finally, the last candidate allele (Doa-3) also affected lifespan, but in the opposite direction than predicted.
Computational Prediction of Binding Affinities of Human Angiotensin Converting Enzyme-2 with SARS-CoV-2 Spike Protein Variants: Omicron Variants and Potentially Deleterious Mutations
Authors: Williams Alexander H. , Zhan Chang-Guo
Published: October 2022

The Omicron variant (BA.1) and its sub-variants of the SARS-CoV-2 virus which causes the COVID-19 disease continues to spread across the United States and the World at large. As new sub-variants of SARS-CoV-2 continue to proliferate, a reliable computational method of quickly determining the potential infectivity of these new variants is needed to assess their potential threat. In the present study, we have tested and validated an efficient computational protocol, which includes an efficient energy minimization and subsequent molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) calculation of the binding free energy between the SARS-CoV-2 spike protein and human angiotensin converting enzyme-2 (ACE2), to predict the binding affinities of these spike/ACE2 complexes based upon the calculated binding free energies and a previously calibrated linear correlation relationship. The predicted binding affinities are in good agreement with available experimental data including those for Omicron variants, suggesting that the predictions based on this protocol should be reasonable. Further, we have investigated several hundred potential mutations of both the wildtype and Omicron variants of the SARS-CoV-2 spike protein. Based on the predicted binding affinity data, we have identified several mutations that have the potential to vastly increase the binding affinity of the spike protein to ACE2 within both the wildtype and Omicron variants.

Author Summary

As well known, the coronavirus responsible for COVID-19 disease enters human cells through its spike protein binding with a human receptor protein known as angiotensin converting enzyme-2. So, the binding affinity between the spike protein and angiotensin converting enzyme-2 contributes to the infectivity of the coronavirus and its variants. In this study, we demonstrated that a generally applicable, fast and easy-to-use computational protocol was able to accurately predict the binding affinity of angiotensin converting enzyme-2 with spike protein of the currently known variants of the coronavirus. Hence, we believe that this computational protocol may be used to reliably predict the binding affinity of angiotensin converting enzyme-2 with spike protein of new variants to be identified in the future. Using this computational protocol, we have further examined a number of possible single mutations on the spike protein of both the wildtype and Omicron variants and predicted their binding affinity with angiotensin converting enzyme-2, demonstrating that several mutations have the potential to vastly increase the binding affinity of the spike protein to angiotensin converting enzyme-2.
Atf3 defines a population of pulmonary endothelial cells essential for lung regeneration
Authors: Niethamer Terren K. , Levin Lillian I. , Morley Michael P. , Babu Apoorva , Zhou Su , Morrisey Edward E.
Published: October 2022

Following acute injury, the capillary vascular bed in the lung must be repaired to reestablish gas exchange with the external environment. Little is known about the transcriptional and signaling factors that drive pulmonary endothelial cell (EC) proliferation and subsequent regeneration of pulmonary capillaries, as well as their response to stress. Here, we show that the transcription factor Atf3 is essential for the regenerative response of the mouse pulmonary endothelium after influenza infection.Atf3expression defines a subpopulation of capillary ECs enriched in genes involved in endothelial development, differentiation, and migration. During lung alveolar regeneration, this EC population expands and increases expression of genes involved in angiogenesis, blood vessel development, and cellular response to stress. Importantly, endothelial cell-specific loss of Atf3 results in defective alveolar regeneration, in part through increased apoptosis and decreased proliferation in the endothelium. This leads to the general loss of alveolar endothelium and persistent morphological changes to the alveolar niche, including an emphysema-like phenotype with enlarged alveolar airspaces lined with regions that lack vascular investment. Taken together, these data implicate Atf3 as an essential component of the vascular response to acute lung injury that is required for successful lung alveolar regeneration.
Structural analysis shows that the BIR2 domain of E3 ligase XIAP binds across the RIP2 kinase dimer interface
Authors: Lethier Mathilde , Hons Michael , Favier Adrien , Brutscher Bernhard , Erba Elisabetta Boeri , Cusack Stephen , Pellegrini Erika
Published: October 2022

NOD1 and NOD2 are innate immune system pattern recognition receptors that play a key role in the protection from bacterial infections and in the maintenance of gastro-intestinal homeostasis. Dysregulation of NOD signalling pathways promotes chronic inflammatory diseases such as inflammatory bowel disease. RIP2, which contains a kinase domain (RIP2K) and a CARD domain, is the immediate downstream signalling partner in the NOD pathway and inhibition of its kinase activity and ubiquitination are promising strategies to address these inflammatory diseases. However, recent work indicates that the phosphorylation activity of RIP2K is dispensable for signalling and that inhibitors of both RIP2K activity and RIP2 ubiquitination prevent the essential interaction between RIP2K and the BIR2 domain of XIAP, the key RIP2 ubiquitin E3 ligase. Moreover, XIAP BIR2 antagonists also block this interaction. To reveal the molecular mechanisms involved, we combined Native mass spectrometry, NMR, cryo-electron microscopy and Alphafold2 predictions to determine the structure of the RIP2K-XIAP BIR2 complex with 2:1 stoichiometry. The structure shows that complex formation requires that the kinase is in an active-like (i.e. αC-helix IN) and dimeric conformation and explains both inhibitory mechanisms. It also shows why phosphorylation of the kinase activation loop is dispensable for signalling and reveals the structural role of RIP2K-K209 residue in the RIP2K-XIAP BIR2 interaction. Importantly, our results clarify the features of the RIP2K conformation essential for its role as a scaffold protein for ubiquitination.
Phylogenomics reveals the relationships of butterflies and moths (Lepidoptera): providing the potential landscape using universal single copy orthologues
Authors: Chen Qi , Deng Min , Wang Wei , Wang Xing , Chen Liu-Sheng , Huang Guo-Hua
Published: October 2022

Background

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order following by Diptera and Coleoptera in the world, lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as the indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly unresolved.

Results

we increased taxon sampling among Lepidoptera (40 superfamilies and 76 families contained 286 taxa) and filtered the unqualified samples, then acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling on tree topology by considering a series of systematic errors using ML and BI methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias given rise to topologies divergence of ditrysia in phylogenomic reconstruction. Phylogenetic inference showed a most comprehensive framework by far to reveal the relationships among lepidopteran superfamilies, but limited by taxon sampling, it could only represent the current understanding of the lepidopteran tree of life. The relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly unresolved, which need to increase taxon sampling and adopt lineage-specific genes for further phylogenomic reconstruction.

Conclusions

The present study further expands the taxon sampling of lepidopteran phylogeny and provides a potential phylogenomic foundation for further understanding its current higher-level relationships.
The soluble N-termini of mechanosensitive ion channels MSL8, MSL9, and MSL10 are environmentally sensitive intrinsically disordered regions with distinct biophysical characteristics
Authors: Flynn Aidan J. , Miller Kari , Codjoe Jennette M. , King Matthew R. , Posey Ammon E. , Haswell Elizabeth S.
Published: October 2022

Intrinsically disordered protein regions (IDRs) are highly dynamic sequences that rapidly sample a collection of conformations. In the past several decades, IDRs have emerged as a core component of many proteomes, comprising ∼30% of all eukaryotic protein sequences. IDRs are ubiquitous throughout different biological pathways, with a notable enrichment in responses to environmental stimuli such as abiotic stress. However, the diversity of IDR-based systems that biology has evolved to respond to different stimuli is expansive, warranting the exploration of IDRs present in unique molecular contexts. Here, we identify and characterize intrinsic disorder in the soluble, cytoplasmic N-terminal domains of three members of the MscS-Like (MSL) family of mechanosensitive ion channels, MSL8, MSL9 and MSL10. In plants, MSL channels are proposed to mediate the reactions to cell swelling, pathogenic invasion, and touch. A series of bioinformatic tools unanimously predicted that the cytosolic N-termini of MSLs are intrinsically disordered. We confirmed this prediction for the N-terminus of MSL10 (MSL10N) via circular dichroism spectroscopy. MSL10Nadopted a predominately helical structure when exposed to the helix-inducing compound trifluoroethanol (TFE) and underwent structural changes and alterations to homotypic interaction favorability in the presence of molecular crowding agents. Lastly,in vitroimaging of condensates indicated that MSL8N, MSL9Nand MSL10Nhave sharply differing propensities for condensate formation both inherently and in response to salt, temperature, and molecular crowding. Altogether, these data establish the N-termini of MSL channels as intrinsically disordered regions with distinct biophysical properties and the potential to respond disparately to changes in their physiochemical environment.
Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States
Authors: Vogels Chantal B.F. , Brackney Doug E. , Dupuis Alan P. , Robich Rebecca M. , Fauver Joseph R. , Brito Anderson F. , Williams Scott C. , Anderson John F. , Lubelczyk Charles B. , Lange Rachel E. , Prusinski Melissa A. , Kramer Laura D. , Gangloff-Kaufmann Jody L. , Goodman Laura B. , Baele Guy , Smith Robert P. , Armstrong Philip M. , Ciota Alexander T. , Dellicour Simon , Grubaugh Nathan D.
Published: October 2022

Powassan virus is an emerging tick-borne virus of concern for public health, but very little is known about its transmission patterns and ecology. Here, we expanded the genomic dataset by sequencing 279 Powassan viruses isolated fromIxodes scapularisticks from the northeastern United States. Our phylogeographic reconstructions revealed that Powassan virus lineage II was likely introduced or emerged from a relict population in the Northeast between 1940-1975. Sequences strongly clustered by sampling location, suggesting a highly focal geographical distribution. Our analyses further indicated that Powassan virus lineage II emerged in the northeastern U.S. mostly following a south to north pattern, with a weighted lineage dispersal velocity of ~3 km/year. Since the emergence in the Northeast, we found an overall increase in the effective population size of Powassan virus lineage II, but with growth stagnating during recent years. The cascading effect of population expansion of white-tailed deer andI. scapularispopulations likely facilitated the emergence of Powassan virus in the northeastern U.S.

Significance statement

Our work provides important fundamental insights in the local transmission dynamics of an emerging tick-borne pathogen of public health concern. Without the availability of vaccines or specific treatments, prevention of Powassan virus infection is dependent on education and control. We identified that Powassan virus is maintained in highly localized transmission foci that have been maintained for several years, without introductions of new virus clades. This provides both opportunities for better education about high risk areas and effective targeted control in Powassan virus foci with a long lasting impact.
The tendon interfascicular basement membrane provides a vascular niche for CD146+pericyte cell subpopulations
Authors: Marr Neil , Zamboulis Danae E. , Werling Dirk , Felder Alessandro A. , Dudhia Jayesh , Pitsillides Andrew A. , Thorpe Chavaunne T.
Published: October 2022

The interfascicular matrix (IFM) is critical to the mechanical adaptations and response to load in energy-storing tendons, such as the human Achilles and equine superficial digital flexor tendon (SDFT). We hypothesized that the IFM is a tendon progenitor cell niche housing an exclusive cell subpopulation. Immunolabelling of equine SDFT was used to identify the IFM niche, localising expression patterns of CD31 (endothelial cells), CD146 (IFM cells) and LAMA4 (IFM basement membrane marker). Magnetic-activated cell sorting was employed to isolate and comparein vitroproperties of CD146+and CD146-subpopulations. CD146 demarcated an exclusive interfascicular cell subpopulation that resides in proximity to a basal lamina which forms interconnected vascular networks. Isolated CD146+cells exhibited limited mineralization (osteogenesis) and lipid production (adipogenesis). This study demonstrates that the IFM is a unique tendon cell niche, containing a vascular-rich network of basement membrane, CD31+endothelial cells and CD146+cell populations that are likely essential to tendon structure- and/or function. Interfascicular CD146+subpopulations did not exhibit stem cell-like phenotypes and are more likely to represent a pericyte lineage. Previous work has shown that tendon CD146 cells migrate to sites of injury, therefore mobilisation of endogenous tendon IFM cell populations may promote intrinsic repair.
Discovering cryptic splice mutations in cancers via a deep neural network framework
Authors: Teboul Raphaël , Grabias Michalina , Zucman-Rossi Jessica , Letouzé Eric
Published: October 2022

Somatic mutations can disrupt splicing regulatory elements and have dramatic effects on cancer genes, yet the functional consequences of mutations located in extended splice regions is difficult to predict. Here, we use a deep neural network (SpliceAI) to characterize the landscape of splice-altering mutations in cancer. In our in-house liver cancer series, SpliceAI uncovers many cryptic splice mutations, located outside essential splice sites, that validate at a high rate in matched RNA-seq data. We then extend the analysis to a large pan-cancer cohort of 18,115 tumors, revealing >100,000 cryptic splice mutations. Taking into account these mutations increases the power of driver gene discovery, revealing >100 new candidate driver genes. It also reveals new driver mutations in known cancer genes, doubling the frequency of splice alterations in tumor suppressor genes. Mutational signature analysis reveals the mutational processes that give rise to splice mutations in each cancer type, with an enrichment of signatures related to clock-like processes and DNA repair deficiency. Altogether, this work sheds light on the causes and impact of cryptic splice mutations in cancer, and highlights the power of deep learning approaches to better annotate the functional consequences of mutations in oncology.
Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length
Authors: Ng Sheung Chun , Biswas Abin , Huyton Trevor , Schünemann Jürgen , Reber Simone , Görlich Dirk
Published: October 2022

Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We found that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier, all consistent with a sieve-like phase. Phase separation tolerated mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remained preserved. NTR-entry, however, was sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we found arginines to promote FG-phase-entry apparently also by hydrophobic interactions/ H-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displayed remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations made the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxed this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
Machine-guided cell-fate engineering
Authors: Appleton Evan , Tao Jenhan , Fonseca Greg , Liu Songlei , Glass Christopher , Church George
Published: October 2022

Abstract

The creation of induced pluripotent stem cells (iPSCs) has enabled scientists to explore the derivation of many types of cells. While there are diverse general approaches for cell-fate engineering, one of the fastest and most efficient approaches is transcription factor (TF) over-expression. However, finding the right combination of TFs to over-express to differentiate iPSCs directly into other cell-types is a difficult task. Here were describe a machine-learning (ML) pipeline, calledCellCartographer, for using chromatin accessibility data to design multiplex TF pooled-screens for cell type conversions. We validate this method by differentiating iPSCs into twelve diverse cell types at low efficiency in preliminary screens and then iteratively refining our TF combinations to achieve high efficiency differentiation for six of these cell types in < 6 days. Finally, we functionally characterized engineered iPSC-derived cytotoxic T-cells (iCytoT), regulatory T-cells (iTReg), type II astrocytes (iAstII), and hepatocytes (iHep) to validate functionally accurate differentiation.
Investigating the unique ability ofTrichodesmiumto fix carbon and nitrogen simultaneously using MiMoSA
Authors: Gardner Joseph J. , Hodge Bri-Mathias S. , Boyle Nanette R.
Published: October 2022

The open ocean is an extremely competitive environment, partially due to the dearth of nutrients.Trichodesmium erythraeum, a marine diazotrophic cyanobacterium, is a keystone species in the ocean due to its ability to fix nitrogen and leak 30-50% into the surrounding environment, providing a valuable source of a necessary macronutrient to other species. While there are other diazotrophic cyanobacteria that play an important role in the marine nitrogen cycle,Trichodesmiumis unique in its ability to fix both carbon and nitrogen simultaneously during the day without the use of specialized cells called heterocysts to protect nitrogenase from oxygen. Here, we use the advanced modeling framework calledMultiscaleMultiobjectiveSystemsAnalysis (MiMoSA) to investigate howTrichodesmium erythraeumcan reduce dimolecular nitrogen to ammonium in the presence of oxygen. Our simulations indicate that nitrogenase inhibition is best modeled as Michealis Menten competitive inhibition and that cells along the filament maintain microaerobia using high flux through Mehler’s reactions in order to protect nitrogenase from oxygen. We also examined the effect of location on metabolic flux and found that cells at the end of filaments operate in distinctly different metabolic modes than internal cells despite both operating in a photoautotrophic mode. These results give us important insight into how this species is able to operate photosynthesis and nitrogen fixation simultaneously, giving it a distinct advantage over other diazotrophic cyanobacteria because they can harvest light directly to fuel the energy demand of nitrogen fixation.

IMPORTANCE

Trichodesmium erythraeumis a marine cyanobacterium responsible for approximately half of all biologically fixed nitrogen, making it an integral part of the global nitrogen cycle. Interestingly, unlike other nitrogen fixing cyanobacteria,Trichodesmiumdoes not use temporal or spatial separation to protect nitrogenase from oxygen poisoning; instead, it operates photosynthesis and nitrogen fixation reactions simultaneously during the day. Unfortunately, the exact mechanism the cells utilize to operate carbon and nitrogen fixation simultaneously is unknown. Here, we use an advanced metabolic modeling framework to investigate and identify the most likely mechanismsTrichodesmiumuses to protect nitrogenase from oxygen. The model predicts that cells operate in a microaerobic mode, using both respiratory and Mehler reactions to dramatically reduce intracellular oxygen concentrations.
Incorporating knowledge of plates in batch normalization improves generalization of deep learning for microscopy images
Authors: Lin Alexander , Lu Alex X.
Published: October 2022

Data collected by high-throughput microscopy experiments are affected by batch effects, stemming from slight technical differences between experimental batches. Batch effects significantly impede machine learning efforts, as models learn spurious technical variation that do not generalize. We introducebatch effects normalization(BEN), a simple method for correcting batch effects that can be applied to any neural network with batch normalization (BN) layers. BEN aligns the concept of a “batch” in biological experiments with that of a “batch” in deep learning. During each training step, data points forming the deep learning batch are always sampled from the same experimental batch. This small tweak turns the batch normalization layers into an estimate of the shared batch effects between images, allowing for these technical effects to be standardized out during training and inference. We demonstrate that BEN results in dramatic performance boosts in both supervised and unsupervised learning, leading to state-of-the-art performance on the RxRx1-Wilds benchmark.1
Single-gene resolution of diversity-driven community overyielding
Authors: Wuest Samuel E. , Schulz Lukas , Rana Surbhi , Frommelt Julia , Ehmig Merten , Pires Nuno D. , Grossniklaus Ueli , Hardtke Christian S. , Hammes Ulrich , Schmid Bernhard , Niklaus Pascal A.
Published: October 2022

In plant communities, diversity often increases community productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute the positive diversity effects to complementary niches occupied by different species or genotypes. However, the type of niche complementarity often remains unclear, including how complementarity is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to identify differences associated with positive diversity effects in mixtures of naturalArabidopsis thalianagenotypes. Using two orthogonal genetic mapping approaches, we found that between-plant allelic differences at theAtSUC8locus contribute strongly to mixture overyielding. The corresponding gene encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation inAtSUC8affected the biochemical activities of protein variants and resulted in different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying such genes important for ecosystem functioning may ultimately allow the linking of ecological processes to evolutionary drivers, help to identify the traits underlying positive diversity effects, and facilitate the development of high-performing crop variety mixtures in agriculture.
An Associative Memory Hamiltonian Model for DNA and Nucleosomes
Authors: Lu Weiqi , Onuchic José N. , Pierro Michele Di
Published: October 2022

A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), is able to reproduce the complex mechanics of the double helix including its bending persistence length and twisting persistence length, and their respective temperature dependence. The WEChroM Hamiltonian is composed of chain connectivity, steric interactions, and associative memory terms representing all remaining interactions leading to the structure, dynamics, and mechanical characteristics of the B-DNA. Several applications of this model are discussed to demonstrate its applicability. WEChroM is used to investigate the behavior of circular DNA in the presence of positive and negative supercoiling. We show that it recapitulates the formation of plectonemes and of structural defects that relax mechanical stress. The model spontaneously manifests an asymmetric behavior with respect to positive or negative supercoiling, similarly to what was previously observed in experiments. Additionally, we show that the associative memory Hamiltonian is also capable of reproducing the free energy of partial DNA unwrapping from nucleosomes. WEChroM can readily emulate the continuously variable mechanical properties of the 10nm fiber and, by virtue of its simplicity, allows the simulation of molecular systems large enough to study the structural ensembles of genes. WEChroM is implemented in the OpenMM simulation toolkits and is freely available for public use.

Author Summary

The structural ensembles of genes have been so far out of the reach of theoretical and computational investigations because genes are molecular complexes too big to be tackled with even the most efficient computational chemistry approaches and yet too strongly affected by heterogeneous molecular factors to be effectively modeled as a simple polymer. In this work, we develop a computationally efficient, easy-to-use, and widely editable chromatin model to study the principles of DNA folding at the gene scale. Using the framework of Associative Memory Hamiltonians, this model reproduces the structural and mechanical properties of double-stranded DNA and accounts for the effects of nucleosome-forming histone octamers and other proteins bound to DNA. Our results open the path to studying the structural and mechanical ensembles of genetic systems as large as tens of kilobases of chromatin, i.e., the size of mammalian genes.
PIC50: An open source tool for interconversion of PIC50values and IC50for efficient data representation and analysis
Authors: Thakur Aman , Kumar Ajay , Sharma Vivek , Mehta Vineet
Published: October 2022

Half-maximal inhibitory concentration (IC50) is used to determine the potency of a drug against a variety of enzymes/ biological targets associated with the pathogenesis of multiple disorders. The IC50values can be depicted in multiple ways, which makes it difficult to analyze the results presented in different concentrations. Representing data in the form of PIC50values depicting the IC50values as the negative logarithm of IC50in molar concentration is considered to be a better approach as it not only makes data easily understandable but also eliminates the possibility of errors in data representation and reproducibility. Considering the importance of data representation for a better understanding of data and comparing efficacy and potency of the drugs, besides, the significance of PIC50value in the field of CADD, we found that at present there is no single open-source software available to convert the IC50values to PIC50values and vice versa from millimolar to picomolar range. Therefore, in the present study, we develop a tool that could help researchers to interconvert IC50values and PIC50values in a reliable way to eliminate the possibility of errors. We validated our tool through three case studies where the data generated by our tool was found to be 100% accurate. Moreover, we present a case where data was published in literature with errors in calculated PIC50values and demonstrated the importance and reliability of our tool.
Green leaf volatiles co-opt proteins involved in molecular pattern signaling in plant cells
Authors: Tanarsuwongkul Sasimonthakan , Fisher Kirsten , Mullis B. Todd , Roberts Jamie , Negi Harshita , Wang Qiang , Stratmann Johannes W.
Published: October 2022

The green leaf volatiles (GLVs)Z-3-hexen-1-ol andZ-3-hexenyl acetate are airborne infochemicals released from damaged plant tissues that prime defenses against herbivores and pathogens in receiver plants. They are conceptually similar to well-known damage-associated molecular patterns (DAMPs), but little is known about their mechanism of action. Using tomato cell cultures, we found that rapid responses to the two GLVs and the polypeptide DAMP systemin showed a significant overlap but also GLV-specific patterns. Within five minutes, GLVs induced changes in MAPK activity and proton-fluxes as well as rapid and massive changes in the phosphorylation status of proteins. Many of these proteins are involved in reprogramming the proteome from cellular homeostasis to stress and include pattern recognition receptors, a receptor-like cytoplasmic kinase, MAPK cascade components, calcium signaling proteins, and transcriptional regulators, all of which are also components of DAMP signaling pathways. This phosphoproteome may represent an early priming state that enables plants to respond forcefully to a subsequent stress signal.
WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
Authors: Chao Kuan-Hao , Chen Pei-Wei , Seshia Sanjit A. , Langmead Ben
Published: October 2022

A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome indexes. However, there are no practical tools to visualize or to check graphs that may have the Wheeler properties. Here we presentWheelie, an algorithm that combines arenaming heuristicwith a permutation solver (Wheelie-PR) or a Satisfiability Modulo Theory (SMT) solver (Wheelie-SMT) to check whether a given graph has the Wheeler properties, a problem that is NP complete in general.Wheeliecan check a variety of random and real-world graphs in far less time than any algorithm proposed to date. It can check a graph with 1,000s of nodes in seconds. We implement these algorithms together with complementary visualization tools in the WGT toolkit, available as open source software athttps://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit.
Variability of visual field maps in human early extrastriate cortex challenges the canonical model of organization of V2 and V3
Authors: Ribeiro Fernanda L. , York Ashley , Zavitz Elizabeth , Bollmann Steffen , Rosa Marcello G. P. , Puckett Alexander M.
Published: October 2022

Visual field maps in human early extrastriate areas (V2 and V3) are traditionally thought to form mirror-image representations which surround the primary visual cortex (V1). According to this scheme, V2 and V3 form nearly symmetrical halves with respect to the calcarine sulcus, with the dorsal halves representing lower contralateral quadrants, and the ventral halves representing upper contralateral quadrants. This arrangement is considered to be consistent across individuals, and thus predictable with reasonable accuracy using templates. However, data that deviate from this expected pattern have been observed, but mainly treated as artifactual. Here we systematically investigate individual variability in the visual field maps of human early visual cortex using the 7T Human Connectome Project (HCP) retinotopy dataset. Our results demonstrate substantial and principled inter-individual variability. Visual field representation in the dorsal portions of V2 and V3 was more variable than in their ventral counterparts, including substantial departures from the expected mirror-symmetrical patterns. In addition, left hemisphere retinotopic maps were more variable than those in the right hemisphere. Surprisingly, only one-third of individuals had maps that conformed to the expected pattern in the left hemisphere. Visual field sign analysis further revealed that in many individuals the area conventionally identified as dorsal V3 shows a discontinuity in the mirror-image representation of the retina, associated with a Y-shaped lower vertical representation. Our findings challenge the current view that inter-individual variability in early extrastriate cortex is negligible, and that the dorsal portions of V2 and V3 are roughly mirror images of their ventral counterparts.
TPLATE complex dependent endocytosis is required for shoot apical meristem maintenance by attenuating CLAVATA1 signaling
Authors: Wang Jie , Jiang Qihang , Pleskot Roman , Grones Peter , Denay Grégoire , Galván-Ampudia Carlos , Bahafid Elmehdi , Xu Xiangyu , Vandorpe Michael , Mylle Evelien , De Smet Ive , Vernoux Teva , Simon Rüdiger , Nowack Moritz K. , Van Damme Daniel
Published: October 2022

Endocytosis regulates the turnover of cell surface localized receptors, which are crucial for plants to sense and rapidly respond to both endogenous and environmental stimuli. The evolutionarily ancient TPLATE complex (TPC) plays an essential role in clathrin-mediated endocytosis (CME) in Arabidopsis plants. Knockout or strong knockdown of single TPC subunits causes male sterility and seedling lethality phenotypes, complicating analysis of the roles of TPC during plant development. Partially functional alleles of TPC subunits however only cause very mild developmental deviations. Here, we took advantage of the recently reported partially functional TPLATE allele, WDXM2, to investigate a role for TPC-dependent endocytosis in receptor-mediated signalling. We discovered that reduced TPC-dependent endocytosis confers a hypersensitivity to very low doses of CLAVATA3 (CLV3) peptide signalling. This hypersensitivity correlated with the abundance of the CLV3 receptor protein kinase CLAVATA1 (CLV1) at the plasma membrane. Genetic analysis and live-cell imaging revealed that TPC-dependent regulation of CLV3-dependent internalization of CLV1 from the plasma membrane is required for CLV3 function in the shoot. Our findings provide evidence that clathrin-mediated endocytosis of CLV1 is a mechanism to dampen CLV3-mediated signaling during plant development.
A fast-killing tyrosine amide ((S)-SW228703) with blood and liver-stage antimalarial activity associated with the Cyclic Amine Resistance Locus (PfCARL)
Authors: Imlay Leah S. , Lawong Aloysus K. , Gahalawat Suraksha , Kumar Ashwani , Xing Chao , Mittal Nimisha , Wittlin Sergio , Churchyard Alisje , Niederstrasser Hanspeter , Crespo-Fernandez Benigno , Posner Bruce , Gamo Francisco Javier , Baum Jake , Winzeler Elizabeth A. , Laleu Benoît , Ready Joseph M. , Phillips Margaret A.
Published: October 2022

Current malaria treatments are threatened by drug resistance and new drugs are urgently needed. In a phenotypic screen for new antimalarials, we identified (S)-SW228703 ((S)-SW703), a tyrosine amide with asexual blood and liver stage activity and a fast-killing profile. Resistance to (S)-SW703 is associated with mutations inPlasmodium falciparumcyclic amine resistance locus (PfCARL) andP. falciparumacetyl CoA transporter (PfACT), similarly to several other compounds that share features such as fast activity and liver-stage activity. Compounds with these resistance mechanisms are thought to act in the ER, though their target(s) are unknown. The tyramine of (S)-SW703 is shared with some reportedPfCARL-associated compounds; however, we observed that strict S-stereochemistry was required for activity of (S)-SW703, suggesting differences in mechanism of action or binding mode. (S)-SW703 provides a new chemical series with broad activity on multiple life-cycle stages and a fast-killing mechanism of action, available for lead optimization to generate new treatments for malaria.
CRF neurons of the BNST promote resilience by blunting the internal experience of aversion
Authors: Haynes Sherod E , Mayberg Helen S , Young Larry J. , Han Ming-Hu
Published: October 2022

The Bed Nucleus of the Stria Terminalis (BNST) has been studied extensively for its coordination of opposing adaptive behaviors. Previously, we uncovered a critical role for Corticotropin-Releasing Factor (CRF)-expressing neurons of the oval nucleus of the BNST (BNSTovCRF) in maintaining resilience to social defeat through stress-dependent self-sustaining neuronal activity.1However, as mice develop resilience, it is not well-understood how affect and motivation are altered to achieve adaptive behavior in the face of ongoing threat. Here, we explore how this neuronal population exerts a powerful influence over internal state in various stress contexts to promote adaptive social responding. Using cell-type-selective optogenetics, a suite of behavioral paradigms, and transgenic Crf-ChR2 mice, we show that BNSTovCRFneurons induce resiliency by altering the encoding of psychosocial stress, enhancing the appetitiveness of social interaction, and enhancing tolerability to physical stress. Adaptive responses to stress typically emanate as a response to negative internal states by external stimuli; here, we show that in resilient mice, stressful environments are less aversive than susceptible mice, suggesting a different motivational capacity to endure stress in this group. Thus, we describe a novel role for BNSTovCRFneurons in resisting the emotional effects of cumulative stress by reducing the internal experience of aversion
Selecting 16S rRNA primers for microbiome analysis in a host-microbe system: the case of the jellyfishRhopilema nomadica
Authors: Barak Noga , Fadeev Eduard , Brekhman Vera , Aharonovich Dikla , Lotan Tamar , Sher Daniel
Published: October 2022

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remained a major decision when initiating any new microbiome study. Here, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfishRhopilema nomadicaas a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and composition. Nevertheless, based on our results, we propose that the V3V4 primer set is the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.