bluuebunny/crossref_metadata_2025 huggingface dataset:
Imaging Giant Vesicle Membrane Domains with a Luminescent Europium Tetracycline Complex
Authors: Cawley Jennie L. , Berger Brett A. , Odudimu Adeyemi T. , Singh Aarshi N. , Santa Dane E. , McDarby Ariana I. , Honerkamp-Smith Aurelia R. , Wittenberg Nathan J.
Published: July 2022

Microdomains in lipid bilayer membranes are routinely imaged using organic fluorophores that preferentially partition into one of the lipid phases, resulting in fluorescence contrast. Here we show that membrane microdomains in giant unilamellar vesicles (GUVs) can be visualized with europium luminescence using a complex of europium (III) and tetracycline (EuTc). EuTc is unlike typical organic lipid probes in that it is a coordination complex with a unique excitation/emission wavelength combination (396/617 nm), a very large Stokes shift (221 nm), and a very narrow emission bandwidth (8 nm). The probe preferentially interacts with liquid disordered domains in GUVs, which results in intensity contrast across the surface of phase-separated GUVs. Interestingly, EuTc also alters GM1 ganglioside partitioning. GM1 typically partitions into liquid ordered domains, but after labeling phase-separated GUVs with EuTc, cholera toxin B-subunit (CTxB), which binds GM1, labels liquid disordered domains. We also demonstrate that EuTc, but not free Eu3+or Tc, significantly reduces lipid diffusion coefficients. Finally, we show that EuTc can be used to label cellular membranes similar to a traditional membrane probe. EuTc may find utility as a membrane imaging probe where its large Stokes shift and sharp emission band would enable multicolor imaging.
Helping can be driven by non-affective cues in rat
Authors: Sugano Y. Vieira , Shan H.Z. , Molasky N.M.R. , Mason P.
Published: July 2022

Helping another in distress can be motivated by either affective or cognitive empathy, with the latter commonly believed to be restricted to humans and possibly other apes. Here, we found evidence for rodent helping that occurs in the absence of affective cues. We employed a paradigm in which a free rat can open the door to a restrainer containing a trapped rat. When the trapped rat was treated with the anxiolytic midazolam, the helping behavior exhibited by the free rat was diminished but did not extinguish. Correspondingly, midazolam-treated trapped rats still released themselves when given the opportunity, albeit at longer latencies than controls, evidence that midazolam only partially reduced the distress experienced by trapped rats. To test whether helping could occur for a rat who exhibited no affect, trapped rats were immobilized by general anesthesia or heavy sedation. Surprisingly, rats opened the door to restrainers containing these immobilized rats and pulled the incapacitated rats out of the restrainer, pushing them away from the arena center. The same solicitous behavior was observed when an anesthetized rat was simply placed in the center of the arena, without being confined within a restrainer. We speculate that the cognitive dissonance of immobile rats, at odds with predictive expectations of rat behavior built up over a lifetime, motivated solicitous behavior including helping. To block affective behavioral displays without associated dissonant cues of immobility, metyrapone, a drug that selectively blocks corticosterone synthesis, was administered to trapped rats. Under such circumstances, little helping behavior occurred. In sum, rats may be motivated either by affect or by cognitive dissonance, the latter comprising a rudimentary form of cognitive empathy.
Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common
Authors: Martinez Julien , Ant Thomas H. , Murdochy Shivan M. , Tong Lily , da Silva Filipe Ana , Sinkins Steven P.
Published: July 2022

Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host’s reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
Humanized NBSGW PDX Models of Disseminated Ovarian Cancer Recapitulate Key Aspects of the Tumor Immune Environment within the Peritoneal Cavity
Authors: Steinkamp Mara P. , Lagutina Irina , Brayer Kathryn J. , Schultz Fred , Burke Danielle , Pankratz Vernon S. , Adams Sarah F. , Hudson Laurie G. , Ness Scott A. , Wandinger-Ness Angela
Published: July 2022

The importance of the immune microenvironment in ovarian cancer progression, metastasis, and response to therapies has become increasingly clear, especially with the new emphasis on immunotherapies. In order to leverage the power of patient-derived xenograft (PDX) models within a humanized immune microenvironment, three ovarian cancer PDX were grown in humanized NBSGW mice engrafted with human CD34+ cord blood-derived hematopoietic stem cells. Analysis of cytokine levels in the ascites fluid and infiltrating immune cells in the tumors demonstrated that these humanized PDX (huPDX) established an immune tumor microenvironment similar to what has been reported for ovarian cancer patients. The lack of human myeloid cell differentiation has been a major setback for humanized mouse models, but our analysis shows that PDX engraftment increases the human myeloid population in the peripheral blood. Analysis of cytokines within the ascites fluid of huPDX revealed high levels of human M-CSF, a key myeloid differentiation factor as well as other elevated cytokines that have previously been identified in ovarian cancer patient ascites fluid including those involved in immune cell differentiation and recruitment. Human tumor-associated macrophages and tumor-infiltrating lymphocytes were detected within the tumors of humanized mice, demonstrating immune cell recruitment to tumors. Comparison of the three huPDX revealed certain differences in cytokine signatures and in the extent of immune cell recruitment. Our studies show that huNBSGW PDX models reconstitute important aspects of the ovarian cancer immune tumor microenvironment making this a superior approach for therapeutic trials.
Single cell carbon and nitrogen incorporation and remineralization profiles are uncoupled from phylogenetic groupings of diatom-associated bacteria
Authors: Mayali Xavier , Samo Ty , Kimbrel Jeff , Stuart Rhona K. , Morris Megan , Rolison Kristina , Ramon Christina , Kim Young-Mo , Munoz-Munoz Nathalie , Nicora Carrie , Purvine Sam , Lipton Mary , Weber Peter K.
Published: July 2022

Bacterial remineralization of algal organic matter is thought to fuel algal growth, but this has not been quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others, nor whether this is linked their incorporation. We quantified bacterial incorporation of algal-derived complex dissolved organic C (DOC) and N (DON) and net algal incorporation of remineralized C and N at the single cell level using isotope tracing and NanoSIMS for fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum. We found unexpected variability in the net C and N fluxes between algae and bacteria, including non-ubiquitous complex DON utilization and remineralization. We identified three distinct functional categories of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional categories were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics. Using comparative proteogenomic analyses, we show that a complex DON incorporating strain expressed proteins related to growth and peptide transport, and a non-incorporator prioritized reactive oxygen species scavenging and inorganic nutrient uptake. Our analysis suggests that phylogeny does not predict the extent of algae-bacteria metabolite exchange, and activity-based measurements are indispensable to classify the high diversity of microbes into functional groups. These categorizations are useful for conceptual understanding and mechanistic numerical modeling to ultimately predict the fate of elemental cycles in response to environmental change.
Early Electrophysiological Aberrations in the Hippocampus of the TgF344-AD Rat Model as a Potential Biomarker for Alzheimer’s Disease Prognosis
Authors: Moradi Faraz , van den Berg Monica , Mirjebreili Morteza , Kosten Lauren , Verhoye Marleen , Amiri Mahmood , Keliris Georgios A.
Published: July 2022

The hippocampus is thought to guide navigation and has an essential contribution to learning and memory. Hippocampus is one of the brain regions impaired in Alzheimer’s disease (AD), a neurodegenerative disease with progressive memory impairments and cognitive decline. Although successful treatments for AD are still not available, developing new strategies to detect AD at early stages before clinical manifestation is crucial for timely interventions. Here, we investigated in the TgF344-AD rat model the classification of AD-transgenic rats versus Wild-type littermates (WT) from electrophysiological activity recorded in the hippocampus of freely moving subjects at an early, pre-symptomatic stage of the disease (6 months old). To this end, recorded signals were filtered in two separate frequency regimes namely low frequency LFP signals and high frequency spiking activity and passed to machine learning (ML) classifiers to identify the genotype of the rats (TG vs. WT). For the low frequency analysis, we first filtered the signals and extracted the power spectra in different frequency bands known to carry differential information in the hippocampus (delta, theta, slow- and fast-gamma) while for the high frequency analysis, we extracted spike-trains of neurons and calculated different distance metrics between them, including Van Rossum (VR), Inter Spike Interval (ISI), and Event Synchronization (ES). These measures were then used as features for classification with different ML classifiers. We found that both low and high frequency signals were able to classify the rat genotype with a high accuracy with specific signals such as the gamma band power, providing an important fraction of information. In addition, when we combined information from both low and high frequency the classification was boosted indicating that independent information is present across the two bands. The results of this study offer a better insight into how different regions of the hippocampus are affected in earlier stages of AD.
α1 adrenergic receptor - PKC - Pyk2 - Src signaling boosts L-type Ca2+ channel Cav1.2 activity and long-term potentiation in rodents
Authors: Man Kwun Nok Mimi , Henderson Peter B. , Kim Karam , Shi Mei , Zhang Mingxu , Nieves-Cintron Madeline , Navedo Manuel F. , Horne Mary C. , Hell Johannes W.
Published: July 2022

The cellular mechanisms mediating norepinephrine functions in brain to result in behaviors are unknown. We identified the L-type Ca2+ channel (LTCC) CaV1.2 as a principal target for Gq- coupled α1-adrenergic receptors (ARs). α1AR signaling increased LTCC activity in hippocampal neurons. This regulation required PKC-mediated activation of the tyrosine kinases Pyk2 and, downstream, Src. Pyk2 and Src were associated with CaV1.2. In model neuroendocrine PC12 cells, stimulation of PKC induced tyrosine phosphorylation of CaV1.2, a modification abrogated by inhibition of Pyk2 and Src. Upregulation of LTCC activity by α1AR and formation of a signaling complex with PKC, Pyk2, and Src suggests that CaV1.2 is a central conduit for signaling by norepinephrine. Indeed, a form of hippocampal LTP in young mice requires both the LTCC and α1AR stimulation. Inhibition of Pyk2 and Src blocked this LTP, indicating that enhancement of CaV1.2 activity via α1AR - Pyk2 - Src signaling regulates synaptic strength.
MINI-EX: Integrative inference of single-cell gene regulatory networks in plants
Authors: Ferrari Camilla , Manosalva Pérez Nicolás , Vandepoele Klaas
Published: July 2022

Multicellular organisms, such as plants, are characterized by highly specialized and tightly regulated cell populations, establishing specific morphological structures and executing distinct functions. Gene regulatory networks (GRNs) describe condition-specific interactions of transcription factor (TF) regulating the expression of target genes, underpinning these specific functions. As efficient and validated methods to identify cell-type specific GRNs from single-cell data in plants are lacking, limiting our understanding of the organization of specific cell-types in both model species and crops, we developed MINI-EX (Motif-Informed Network Inference based on single-cell Expression data), an integrative approach to infer cell-type specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. Next, regulons are assigned to different cell-types, leveraging cell-specific expression, and candidate regulators are prioritized using network centrality measures, functional annotations, and expression specificity. This embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell-types controlling a biological process of interest. We demonstrate MINI-EX’s stability towards input data sets with low number of cells and its robustness towards missing data, and we show it infers state-of-the-art networks with a better performance compared to related single-cell network tools. MINI-EX successfully identifies key regulators controlling root development in Arabidopsis and rice, Arabidopsis leaf development, and governing ear development in maize, enhancing our understanding of cell-type specific regulation and unraveling the role of different regulators controlling the development of specific cell-types in plants.
Context-dependent transcriptional remodeling of TADs during differentiation
Authors: Chahar Sanjay , Zouari Yousra Ben , Salari Hossein , Molitor Anne M , Kobi Dominique , Maroquenne Manon , Erb Cathie , Mossler Audrey , Karasu Nezih , Jost Daniel , Sexton Tom
Published: July 2022

Metazoan chromosomes are organized into discrete domains (TADs), believed to contribute to the regulation of transcriptional programs. Despite extensive correlation between TAD organization and gene activity, a direct mechanistic link is unclear, with perturbation studies often showing little effect. To follow TAD dynamics during development, we used Capture Hi-C to interrogate the TADs around key differentially expressed genes during mouse thymocyte maturation, uncovering specific remodeling events. Notably, one TAD boundary was broadened to accommodate RNA polymerase elongation past the border, and sub-domains were formed around some activated genes without changes in CTCF binding. The ectopic induction of one gene was sufficient to recapitulate microdomain formation in embryonic stem cells, providing strong evidence that transcription can directly remodel chromatin structure. These results suggest that transcriptional processes drive complex, but non-universal, chromosome folding patterns that can be important in certain genomic contexts.
A novel Smg6 mouse model reveals regulation of circadian period and daily CRY2 accumulation through the nonsense-mediated mRNA decay pathway
Authors: Katsioudi Georgia , Dreos René , Arpa Enes S. , Gaspari Sevasti , Liechti Angelica , Sato Miho , Gabriel Christian H. , Kramer Achim , Brown Steven A. , Gatfield David
Published: July 2022

Nonsense-mediated mRNA decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or RNA processing errors. While additional roles in controlling regular mRNA stability have emerged, possible functions in mammalian physiology in vivo have remained unclear. Here, we report a novel conditional mouse allele that allows converting the NMD effector nuclease SMG6 from wild-type to nuclease domain-mutant protein. We analyzed how NMD downregulation affects the function of the circadian clock, a system known to require rapid mRNA turnover. We uncover strong lengthening of free-running circadian periods for liver and fibroblast clocks, and direct NMD regulation of Cry2 mRNA, encoding a key transcriptional repressor within the rhythm-generating feedback loop. In the entrained livers of Smg6 mutant animals we reveal transcriptome-wide alterations in daily mRNA accumulation patterns, altogether expanding the known scope of NMD regulation in mammalian gene expression and physiology.
The human placenta exhibits a unique transcriptomic void
Authors: Gong Sungsam , Gaccioli Francesca , Aye Irving L.M.H. , Avellino Giulia , Cook Emma , Lawson Andrew R.J. , Harvey Luke M.R. , Smith Gordon C.S. , Charnock-Jones D. Stephen
Published: July 2022

We have recently demonstrated that the human placenta exhibits a unique genomic architecture with an unexpectedly high mutation burden(Coorens et al. 2021) and it is also well recognized that the placenta uniquely expresses many genes(Gong et al. 2021). However, the placenta is relatively understudied in systematic comparisons of gene expression in different organs. The aim of the present study was to identify transcripts which were uniquely absent or depleted, comparing the placenta with 46 other human organs. Here we show that 40/46 of the other organs had no transcripts which were selectively depleted and that of the remaining six, the liver had the largest number with 26. In contrast, the term placenta had 762 depleted transcripts. Gene Ontology analysis of this depleted set highlighted multiple pathways reflecting known unique elements of placental physiology. However, analysis of term samples demonstrated massive over representation of genes involved in mitochondrial function (P=5.8×10−10), including PGC-1α - the master regulator of mitochondrial biogenesis, and genes involved in polyamine metabolism (P=2.1×10−4). We conclude that the term placenta exhibits a unique metabolic environment.
Cytotoxic effect of Rotheca serrata on cancer cell lines MCF-7 and Neuroblastoma SH-SY5Y
Authors: Gadade Jayashree Pandurang , Patil Swaroopa Amit
Published: July 2022

Rotheca serrata (Lamiaceae), a highly medicinal plant is used as an antidote for snakebite and the plant possesses medicinal properties like hepatoprotective, antitussive, antioxidant, anticancer, neuro-protective, used in rheumatoid arthritis and is also a α-glucoside inhibitor. This work aimed to study the anticancerous effect of Rotheca serrata (root and leaf) on cancer cell lines MCF-7 (breast cancer cell line) and Neuroblastoma SH-SY5Y. The results indicated that the Methanolic extract of Rotheca serrata (root and leaf) showed high anticancer activity. Different concentrations of plant extracts (25, 50, 100, 200, 400 μg/ml) were used to study the anticancerous activity, amongst which the significant results were obtained for 400 μg/ml concentration (both root & leaf). Effective anticancer activity against MCF – 7 breast cancer cells was shown in methanoilc extracts and were expressed as IC 50 values; in root (IC 50 value= 61.8259 ± 7.428 μg/ml) and in leaf (IC 50 value = 78.1497 ± 6.316μg/ml). The MTT assay in case of neuroblastoma (SH-SY5Y) cell lines revealed that 400μg/ml concentration of leaf methanolic extract showed effective inhibition of cancer cells with IC 50 value 37.8462 ± 2.957 μg/ml as compared to IC 50 value of root methanolic extract which was 57.0895 ± 2.351 μg/ml.
Electric Field Responsive Nanotransducers for Glioblastoma
Authors: Jain Akhil , Jobson Isobel , Griffin Michaela , Rahman Ruman , Smith Stuart , Rawson Frankie
Published: July 2022

Electric field therapies such as Tumor Treating Fields (TTFields) have emerged as a bioelectronic treatment for isocitrate dehydrogenase wild-type and IDH mutant grade 4 astrocytoma Glioblastoma (GBM). TTFields rely on alternating current (AC) electric fields (EF) leading to the disruption of dipole alignment and induced dielectrophoresis during cytokinesis. Although TTFields have a favourable side effect profile, particularly compared to cytotoxic chemotherapy, survival benefits remain limited (∼ 4.9 months) after an extensive treatment regime (20 hours/day for 18 months). The cost of the technology also limits its clinical adoption worldwide. Therefore, the discovery of new technology that can enhance survival benefit and improve the cost per added quality of life year per patient, of these TTFields will be of great benefit to cancer treatment and decrease healthcare costs worldwide. In this work, we report the role of electrically conductive gold (GNPs), dielectric silica oxide (SiO2), and semiconductor zinc oxide (ZnO) nanoparticles (NPs) as transducers for enhancing EF mediated anticancer effects on patient derived GBM cells. Physicochemical properties of these NPs were analyzed using spectroscopic, electron microscopy, and light-scattering techniques. In vitro TTFields studies indicated an enhanced reduction in the metabolic activity of patient-derived Glioma INvasive marginal (GIN 28) and Glioma contrast enhanced core (GCE 28) GBM cells in groups treated with NPs vs. control groups, irrespective of NPs dielectric properties. Our results indicate the inorganic NPs used in this work enhance the intracellular EF effects by virtue of bipolar dielectrophoretic and electrophoretic effects. This work presents preliminary evidence which could help to improve future EF applications for bioelectronic medicine. Furthermore, the merits of spherical morphology, excellent colloidal stability, and low toxicity, make these NPs ideal for future studies for elucidating the detailed mechanism and efficacy upon their delivery in GBM preclinical models.
Social and individual learners use different pathways to success in an ant mini-society
Authors: Glaser Simone M , Grüter Christoph
Published: July 2022

Animals can acquire information through individual learning or by copying others. Simulations suggest that social learning is expected to lead to better rewards, but experimental studies confirming this remain scarce. We tested how a well-known form of social learning in ants, tandem running, affects individual foraging success ofTemnothroax nylanderiforagers in controlled laboratory experiments. We manipulated the number and the variability of food sources and assessed the foraging choices of ants searching individually (i.e. scouts) or using social learning (i.e. recruits). We found that social learners indeed discovered better food sources than individual learners, but only in rich environments. However, social learners collected less food (∼60% fewer foraging trips) than scouts during our trials. Interestingly, individual learners improved their success over time by switching food sources more frequently than social learners. These experimental findings highlight that the relative value of social and individual learning in an ant society depend on the foraging environment and show different temporal dynamics. The ability of individual learners to exploit profitable food sources through a strategy of food source switching, while avoiding the opportunity costs of social learning can help explain why many social insects, especially those living in small colonies, do not use communication in foraging.
DBlink: Dynamic localization microscopy in super spatiotemporal resolution via deep learning
Authors: Saguy Alon , Alalouf Onit , Opatovski Nadav , Jang Soohyen , Heilemann Mike , Shechtman Yoav
Published: July 2022

Single molecule localization microscopy (SMLM) has revolutionized biological imaging, improving the spatial resolution of traditional microscopes by an order of magnitude. However, SMLM techniques depend on accumulation of many localizations over thousands of recorded frames to yield a single super-resolved image, which is time consuming. Hence, the capability of SMLM to observe dynamics has always been limited. Typically, a few minutes of data acquisition are needed to reconstruct a single super-resolved frame. In this work, we present DBlink, a novel deep-learning-based algorithm for super spatiotemporal resolution reconstruction from SMLM data. The input to DBlink is a recorded video of single molecule localization microscopy data and the output is a super spatiotemporal resolution video reconstruction. We use bi-directional long short term memory (LSTM) network architecture, designed for capturing long term dependencies between different input frames. We demonstrate DBlink performance on simulated data of random filaments and mitochondria-like structures, on experimental SMLM data in controlled motion conditions, and finally on live cell dynamic SMLM. Our neural network based spatiotemporal interpolation method constitutes a significant advance in super-resolution imaging of dynamic processes in live cells.
An isoform-specific function of Cdc42 in regulating mammalian Exo70 during axon formation
Authors: Ravindran Priyadarshini , Püschel Andreas W.
Published: July 2022

The highly conserved GTPase Cdc42 is an essential regulator of cell polarity and promotes exocytosis through the exocyst complex in budding yeast and Drosophila. In mammals, this function is performed by the closely related GTPase TC10 while mammalian Cdc42 does not interact with the exocyst. Axon formation is facilitated by the exocyst complex that tethers vesicles prior to their fusion to expand the plasma membrane. This function depends on the recruitment of the Exo70 subunit to the plasma membrane. Alternative splicing generates two Cdc42 isoforms that differ in their C-terminal 10 amino acids. Our results identify an isoform-specific function of Cdc42 in neurons. We show that the brain-specific Cdc42b isoform, in contrast to the ubiquitous isoform Cdc42u, can interact with Exo70. Cdc42b regulates exocytosis and axon formation downstream of its activator Arhgef7. Thus, the function of Cdc42 in regulating exocytosis is conserved in mammals but specific to one isoform.
Reproductive fitness is associated with female chronotype in a songbird
Authors: Womack Robyn J. , Capilla-Lasheras Pablo , McGlade Ciara L. O. , Dominoni Davide M. , Helm Barbara
Published: July 2022

Research on biological rhythms has revealed widespread variation in diel timing within populations. Repeatable individual chronotypes have been linked to performance in humans but, in free-living species, benefits of chronotype are poorly understood. To address this gap, we investigated fitness correlates of incubation patterns in female songbirds (great tit, Parus major) at urban and forest sites. We confirm repeatable chronotypes (r ≥ 0.31) and show novel links between chronotype and reproductive success. In both habitats, females that started activity earlier in the day raised more fledglings. We also observed that forest females started their day at a similar time throughout the breeding season, whereas urban females tied their onset of activity closely to sunrise. Our study points to possible mechanisms that underlie chronotype variation and provides sought-after evidence for its relevance to fitness.
MRN and Topoisomerase IIIα-RMI1/2 synchronize DNA resection motor proteins
Authors: Soniat Michael M. , Nguyen Giaochau , Kuo Hung-Che , Finkelstein Ilya J.
Published: July 2022

DNA resection—the nucleolytic processing of broken DNA ends—is the first step of homologous recombination. Resection is catalyzed by the resectosome, a multi-enzyme complex that includes BLM helicase, DNA2 or EXO1 nucleases, and additional DNA-binding proteins. Although the molecular players have been known for over a decade, how the individual proteins work together to regulate DNA resection remain unknown. Using single-molecule imaging, we characterized the roles of MRN and TOP3A-RMI1/2 during long-range DNA resection. BLM partners with TOP3A-RMI1/2 to form the BTRR complex (or BLM dissolvasome). TOP3A-RMI1/2 aids BLM in initiating DNA unwinding, and along with MRN, stimulates DNA2-mediated resection. Furthermore, MRN promotes the association between BTRR and DNA, and synchronizes BLM and DNA2 translocation to prevent BLM from pausing during resection. Together, this work provides direct observation of how MRN and DNA2 harness the BTRR complex to resect DNA efficiently and how TOP3A-RMI1/2 regulates BLM’s helicase activity to promote efficient DNA repair.
Host-symbiont-gene phylogenetic reconciliation
Authors: Menet Hugo , Trung Alexia Nguyen , Daubin Vincent , Tannier Eric
Published: July 2022

Motivation

Biological systems are made of entities organized at different scales (e.g.macro-organisms, symbionts, genes…) which evolve in interaction. These interactions range from independence or conflict to cooperation and coevolution, which results in them having a common history. The evolution of such systems is approached by phylogenetic reconciliation, which describes the common patterns of diversification between two different levels,e.g.genes and species, or hosts and symbionts for example. The limit to two levels hides the multi-level inter-dependencies that characterize complex systems.

Results

We present a probabilistic model of evolution of three nested levels of organization which can account for the codivergence of hosts, symbionts and their genes. This model allows gene transfer as well as host switch, gene duplication as well as symbiont diversification inside a host, gene or symbiont loss. It handles the possibility of ghost lineages as well as temporary free-living symbionts.

Given three phylogenetic trees, we devise a Monte Carlo algorithm which samples evolutionary scenarios of symbionts and genes according to an approximation of their likelihood in the model. We evaluate the capacity of our method on simulated data, notably its capacity to infer horizontal gene transfers, and its ability to detect hostsymbiont co-evolution by comparing host/symbiont/gene and symbiont/gene models based on their estimated likelihoods. Then we show in a aphid enterobacter system that some reliable transfers detected by our method, are invisible to classic 2-level reconciliation. We finally evaluate different hypotheses on human population histories in the light of their coevolvingHelicobacter pylorisymbionts, reconciled together with their genes.

Availability

Implementation is available on GitHubhttps://github.com/hmenet/TALE. Data are available on Zenodohttps://doi.org/10.5281/zenodo.7667342.
Gene symbol recognition with GeneOCR
Authors: Geser Paul , Zhang Jitao David
Published: July 2022

Motivation

Figures in biomedical publications often contain lists of gene symbols. Human intelligence and manual curation is required to recognize, extract, and validate the symbols in order to reuse them. The task is laborious, error prone, and amenable to automation.

Results

We introduce GeneOCR, a web-based software to recognize, extract, and check gene symbols from figures. It features both an interactive user interface and programmatic access. Simulation-based benchmark reveals that GeneOCR recognizes or suggests correct gene symbols in more than 80% cases. The performance qualifies GeneOCR as an enhancement to manual curation.

Availability

The source code of GeneOCR is available with GNU v3 license at https://github.com/bedapub/GeneOCR-UI (frontend) and https://github.com/bedapub/GeneOCR-API (backend). A Docker/Singularity image is available via BioContainers.

Contact

jitao_david.zhang@roche.com
Predicting leaf traits across functional groups using reflectance spectroscopy
Authors: Kothari Shan , Beauchamp-Rioux Rosalie , Blanchard Florence , Crofts Anna L. , Girard Alizée , Guilbeault-Mayers Xavier , Hacker Paul W. , Pardo Juliana , Schweiger Anna K. , Demers-Thibeault Sabrina , Bruneau Anne , Coops Nicholas C. , Kalacska Margaret , Vellend Mark , Laliberté Etienne
Published: July 2022

Plant ecologists use functional traits to describe how plants respond to and influence their environment. Reflectance spectroscopy can provide rapid, non-destructive estimates of leaf traits, but it remains unclear whether general trait-spectra models can yield accurate estimates across functional groups and ecosystems.

We measured leaf spectra and 22 structural and chemical traits for nearly 2000 samples from 104 species. These samples span a large share of known trait variation and represent several functional groups and ecosystems. We used partial least-squares regression (PLSR) to build empirical models for estimating traits from spectra.

Within the dataset, our PLSR models predicted traits like leaf mass per area (LMA) and leaf dry matter content (LDMC) with high accuracy (R2>0.85; %RMSE<10). Models for most chemical traits, including pigments, carbon fractions, and major nutrients, showed intermediate accuracy (R2=0.55-0.85; %RMSE=12.7-19.1). Micronutrients such as Cu and Fe showed the poorest accuracy. In validation on external datasets, models for traits like LMA and LDMC performed relatively well, while carbon fractions showed steep declines in accuracy.

We provide models that produce fast, reliable estimates of several widely used functional traits from leaf reflectance spectra. Our results reinforce the potential uses of spectroscopy in monitoring plant function around the world.
Characterization of DNA replicators of a 75-kb region of Chromosome 2 of fission yeast, Schizosacharomyces pombe
Authors: Yadav Mukesh Pratap , Dubey Dharani Dhar
Published: July 2022

DNA replication origins of a 75-kb region of chromosome 2 of Schizosacharomyces pombe, are well characterized. Here, we have further characterized two origins, ars2-3358 and ars2-3363 on plasmids using an Autonomous Replicating Sequences (ARS) assay. Sequence analysis of the five ARSs located within the 75-kb region revealed several asymmetric AT motifs ≥10 bp in each of these origins. Interestingly, we have also found a 29 bp AT-rich sequence (29W) in ars2-3358, which alone is not sufficient to provide DNA replication origins to plasmid. A genomic search for asymmetric AT motifs ≥10 bp gave a total 2309 near matches to 9 of these motifs in the genome. Majority (>65% to >77%) of six of these AT motifs overlapped with the earlier mapped genome-wide DNA replication origins. Moreover, functional comparison of these AT motifs to the deletion and mutational studies showed strong correlation with DNA replication origins efficiency. Therefore, we hypothesize that these sequences are important redundant core elements of S. pombe origins.
Local adaptation to hosts and parasitoids shapeHamiltonella defensagenotypes across aphid species
Authors: Wu Taoping , Monnin David , Lee Rene A. R. , Henry Lee M.
Published: July 2022

Facultative symbionts are common in insects and are known to provide important adaptations that can drive rapid host evolution. Yet we still have a limited understanding of what shapes their distributions, such as why particular symbiont strains are common in some host species yet absent in other. To address this question, we genotyped the defensive symbiontHamiltonella defensain 26 aphid species that commonly carry this microbe. We found thatHamiltonellastrains were strongly associated with specific aphid species and that strains found in one host species rarely occurred in others. To explain these associations, we reciprocally transferred theHamiltonellastrains of 3 aphid species,Acyrthosiphon pisum, Macrosiphoniella artemisiaeandMacrosiphum euphorbiae, in the other host species, and assessed the impact ofHamiltonellastrain on: the stability of the symbiosis, aphid fecundity, and parasitoid resistance. We demonstrate that theHamiltonellaassociations found in nature are locally adapted both to the aphid host itself, and its ecology, in that aphids tend to carryHamiltonellastrains that provide strong protection against their dominant parasitoid species. Our results suggest thatHamiltonellastrains function as a horizontal gene pool that aphids draw from to rapidly adapt to pressures from different natural enemies.
The Genome of the Mustard Hill Coral,Porites astreoides
Authors: Wong Kevin H. , Putnam Hollie M.
Published: July 2022

Coral reefs are threatened both locally and globally by anthropogenic impacts, which to date have contributed to substantial declines in coral cover worldwide. However, some corals are more resilient to these environmental changes and therefore have increased relative abundance on local scales and may represent prominent members shaping future reef communities. Here, we provide the first draft reference genome for one such reef-building coral, the mustard hill coral,Porites astreoides. This reference genome was generated from a sample collected in Bermuda, with DNA sequenced via Pacific Biosciences HiFi long-read technology to provide an initial draft reference genome assembly. Assembly of the PacBio reads with FALCON UnZip resulted in a 678 Mbp assembly with 3,051 contigs with an N50 of 412,256. The genome BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. Anab initiotranscriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% when compared to the metazoan gene set. The function annotation was obtained through a hierarchical approach of SwissProt, TrEMBL, and NCBI nr database of which 86.6% of proteins were annotated. Through ourab initiogene prediction for structural annotation and generation of a functional annotation for theP. astreoidesdraft genome assembly, we provide valuable resources for improving biological knowledge, which can facilitate comparative genomic analyses for corals, and enhance our capacity to test for the molecular underpinnings of adaptation and acclimatization to support evidence-based restoration and human assisted evolution of corals.

Classifications

Genetics and Genomics; Animal Genetics; Marine Biology
Nucleus of the lateral olfactory tract (NLOT): a hub linking water homeostasis-associated SON-AVP circuit and neocortical regions to promote social behavior under osmotic challenge
Authors: Hernández-Pérez Oscar R. , Hernández Vito S. , Zetter Mario A. , Eiden Lee E. , Zhang Limei
Published: July 2022

Homeostatic challenges increase the drive for social interaction. The neural activity that prompts this motivation remains poorly understood. Here, we identify direct projections from the hypothalamic supraoptic nucleus (SON) to the cortico-amygdalar nucleus of the lateral olfactory tract (NLOT). Dualin situhybridization (DISH) with probes for PACAP, and VGLUT1, VGLUT2, V1a and V1b revealed a population of vasopressin-receptive PACAPergic neurons in NLOT layer 2 (NLOT2). Water deprivation (48 hours, WD48) increased sociability compared to euhydrated subjects, assessed with the three-chamber social interaction test (3CST). Fos expression immunohistochemistry showed NLOT and its main efferent regions had further increases in rats subjected to WD48+3CST. These regions strongly expressed PAC1 mRNA. Microinjections of AVP into NLOT produced similar changes in sociability to water deprivation, and these were reduced by co-injection of V1a or V1b antagonists along with AVP. We conclude that during challenge to water homeostasis, there is a recruitment of a glutamatergic-multi-peptidergic cooperative circuit that promotes social behavior.
Complement receptor C5aR1 signaling in sensory neuron-associated macrophages drives neuropathic pain
Authors: Quadros Andreza U. , Maganin Alexandre G. M. , Silva Conceição E. A. , Damasceno Samara , Cavallini Maria C. M. , Davoli-Ferreira Marcela , Lopes Alexandre H. P. , Sagar Devi R. , Brandolini Laura , Lee Sang Hoon , Alves-Filho Jose C. , Cunha Fernando Q. , Berta Temugin , Köhl Jörg , Allegretti Marcello , Chapman Victoria , Cunha Thiago M.
Published: July 2022

Neuroimmune interactions across the pain pathway play a predominant role in the development of neuropathic pain. Previous reports demonstrated that complement driven effector systems including the C5a/C5aR1 axis contribute to these neuro-immune mechanisms. However, the cellular and molecular mechanisms underlying C5a/C5aR1 signaling-mediated neuropathic pain development remain ill-identified. Here we show that neuropathic pain following peripheral nerve injury was attenuated in C5aR1-deficient male and female mice as well as in wild type mice treated with a selective allosteric C5aR1 antagonist. Using two complementary cell-specific C5aR1 knockout mouse strains, we identified C5a/C5aR1 driven-activation of sensory neuron-associated macrophages (sNAMs) located in the sensory ganglia as the key site of peripheral nerve injury-induced neuropathic pain, whereas activation of macrophages of the local of peripheral nerve injury was not involved. Mechanistically, we uncovered IL-1b the main mediator of pain hypersensitivity in response to C5aR1 signaling in sNAMs. Our findings highlight a crucial role of C5a/C5aR1 axis activation in sNAMs for the development of neuropathic pain and identify this pathway as a promising novel target for neuropathic pain therapy.
Backbone amides are key determinants of Cl− selectivity in CLC ion channels
Authors: Leisle Lilia , Lam Kin , Dehghani-Ghahnaviyeh Sepehr , Fortea Eva , Galpin Jason , Ahern Christopher A. , Tajkhorshid Emad , Accardi Alessio
Published: July 2022

Chloride homeostasis is tightly regulated in cellular compartments by dedicated channels and transporters. Whereas CLC-type channels select for Cl− over other anions, all other ‘chloride’ channels are indiscriminate in their anionic permeability. Pore-lining side chains are thought to determine Cl− selectivity in CLC channels. However, orientation and functional roles of these side chains is not conserved among CLCs. All CLC pores are lined by backbone amides in a conserved structural arrangement, suggesting a role of mainchain groups in selectivity. We replaced pore-lining residues in the CLC-0 and bCLC-k channels with their respective α-hydroxy acid counterparts using nonsense suppression method. This exchanges peptide-bond amides with ester-bond oxygens, incapable of hydrogen-bonding with permeating anions. Backbone substitutions functionally degrade inter-anion discrimination in a site-specific manner. These effects depend on the presence of a glutamate side chain that competes with ions permeating through the pore. Molecular dynamics simulations show that ion energetics within the bCLC-k pore are primarily determined by interactions with backbone amides. Insertion of an α-hydroxy acid significantly alters ion selectivity and global pore hydration. We propose that backbone amides are conserved determinants of Cl− specificity in CLC channels in a mechanism reminiscent of that described for K+ channels.
Reducing chlorophyll level in seed filling stages results in higher seed nitrogen without impacting canopy carbon assimilation
Authors: Cho Young B. , Boyd Ryan A. , Ren Yudong , Lee Moon-Sub , Jones Sarah I. , Ruiz-Vera Ursula M. , McGrath Justin , Masters Michael D. , Ort Donald R.
Published: July 2022

Chlorophyll is the major light absorbing pigment for plant photosynthesis. While evolution has selected for higher chlorophyll content in leaves, previous work suggests that domesticated crops grown in modern agricultural environments overinvest in chlorophyll production thereby lowering light use and nitrogen use efficiency. To investigate the potential benefits of reducing chlorophyll level, we created ethanol inducible RNAi tobacco mutants that suppress Mg-chelatase subunit I (CHLI) with small RNA (sRNA) within 3 hours of induction and reduce chlorophyll within 5 days in field conditions. We initiated chlorophyll reduction later in plant development to avoid the highly sensitive seedling stage, and to allow young plants to have full green leaves to maximize light interception before canopy formation. This study demonstrated that >60% reduction of leaf chlorophyll could be tolerated without penalty on above-ground biomass or canopy photosynthesis in field conditions. Leaf chlorophyll reduction during seed filling stages increased tobacco seed nitrogen concentration as much as 17%, while biomass and seed yields were maintained. These results indicate that time-specific reduction of chlorophyll could be a niche strategy that decouples the inverse relationship between yield and seed nitrogen by utilizing saved nitrogen from the reduction of chlorophyll while maintaining full carbon assimilation capacity.
Frequent sexual reproduction limits adaptation in outcrossed populations of the algaChlamydomonas reinhardtii
Authors: Moerman Felix , Colegrave Nick
Published: July 2022

Sexual reproduction can facilitate adaptation by reshuffling genetic variation. However, sexual reproduction can also bear costs. Such costs come in two forms: direct costs and evolutionary costs. Direct costs are associated with the cost of producing males (twofold cost of sex), the cost of meiosis, and the typically slower cell division during sexual reproduction of single-celled organisms. Evolutionary costs occur when too frequent sexual reproduction would hinder adaptation, by breaking apart adaptive allele combinations. Whereas the direct costs of sexual reproduction have been studied repeatedly in theoretical studies, the evolutionary costs of sex remain less well understood. We investigate here how the frequency of sexual reproduction affects adaptation to a non-stressful and a stressful environment in populations of the green alga Chlamydomonas reinhardtii, while minimizing the direct costs of sexual reproduction. Contrary to several previous studies, we found that an increasing frequency of sexual reproduction hindered adaptation of populations. In populations experiencing the highest frequency of sexual reproduction, adaptation was entirely prevented. These findings suggest that there were strong evolutionary costs associated with too frequent sexual reproduction in our populations. This observation may help to explain why in many facultative sexual species, there is a low frequency of sexual reproduction.