bluuebunny/crossref_metadata_2025 huggingface dataset:
Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination inSaccharomyces cerevisiae
Authors: Shodhan Anura , Xaver Martin , Wheeler David , Lichten Michael
Published: May 2022

The DNA double strand breaks (DSBs) that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in budding yeast contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red are important for DSB formation; DSB levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with DSB levels. How axis protein levels influence DSB formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parSpartition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased DSBs and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in DSBs did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote DSB formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, only a small fraction of crossovers that formed at an insert locus required MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local DSB levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.
Biophysical and functional characterization of K+-Cl-co-transporters fromDrosophila melanogasterandHydra vulgaris
Authors: Fudo Satoshi , Verkhovskaya Marina , Scala Coralie Di , Rivera Claudio , Kajander Tommi
Published: May 2022

The cation-chloride co-transporter (CCC) superfamily includes ion symporters, which co-transport monovalent cations and Cl-. CCCs have crucial roles in shaping signalling and neuronal connectivity in the vertebrate brain. K+-Cl-co-transporters (KCCs) are a subfamily of CCCs and carry out the symport of K+and Cl−ions across the plasma membrane. The KCC proteins are involved in various physiological processes, such as cell volume regulation, transepithelial ion transport, synapse formation and signal transmission, and blood pressure regulation.

Among KCCs, KCC2 has gained attention because of its unique and crucial functions in the central nervous system neuronal network. Loss of activity of this transporter has been associated with several neurological disorders including schizophrenia, epilepsy, and chronic pain.

On the other hand, only a limited number of studies of KCCs have been published for invertebrates. Among invertebrate proteins, theDrosophila melanogasterKCC (DmKCC) has been studied most and suggested critical for neuronal transmission. Also CnidarianHydra vulgarishas been shown to have a functional KCC (HvKCC). Comparative analyses of these transporters with vertebrate ones and understanding functional and biophysical aspects of them as a model system can help understand the KCC mechanism of ion transport and its regulation and evolution broadly.

In this study, we choseDmKCC andHvKCC as model systems and purifiedDmKCC andHvKCC from Sf9 insect cells and characterized their biophysical properties with differential scanning fluorimetry and light scattering techniques. We tested their functionality using a fluorescence assay and developed a method to measure recombinant KCC ion transport activity with flame photometry.
Selective auditory attention modulates cortical responses to sound location change for speech in quiet and in babble
Authors: Ozmeral Erol J. , Palandrani Katherine N.
Published: May 2022

Listeners use the spatial location or change in spatial location of coherent acoustic cues to aid in auditory object formation. From stimulus-evoked onset responses in normal-hearing listeners using electroencephalography (EEG), we have previously shown measurable tuning to stimuli changing location in quiet, revealing a potential window into cortical object formation. These earlier studies used non-fluctuating, spectrally narrow stimuli, so it was still unknown whether previous observations would translate to speech stimuli and whether responses would be preserved for stimuli in the presence of background maskers. To examine the effects that selective auditory attention and interferers have on object formation, we measured cortical responses to speech changing location in the free field with and without background babble (+6 dB SNR) during both passive and active conditions. Active conditions required listeners to respond to the onset of the speech stream when it occurred at a new location, explicitly indicating yes or no to whether the stimulus occurred at a block-specific location either 30 degrees to the left or right of midline. In the aggregate, results show similar evoked responses to speech stimuli changing location in quiet compared to babble background. However, the effect of the two background environments diverges when considering the magnitude and direction of the location change, in which there was a clear influence of change vector in quiet but not in babble. Therefore, consistent with challenges associated with cocktail party listening, directed spatial attention can be shunted in the presence of stimulus noise and likely leads to poorer use of spatial cues in auditory streaming.
Aspects of the glycome of endochondral ossification
Authors: McClure Sheena F , McClure John
Published: May 2022

Comparatively little is known about the glycome (the set of glycans and glycoconjugates made by the cell, tissue or organism) of bone and cartilage. The glycome has a high-density coding capacity and is important in post-translational modification. Lectin histochemistry provides insights into the glycome and we applied this technique to an ectopic ossification site in human bronchial cartilages.

Our results show that cartilage matrix at the site of erosion by chondroclasts has a limited but definite glycoprofile. In contrast, bone matrix does not express many lectin ligands. Chondroclasts have an extensive glycoprofile similar to that of, but not identical to, osteoclasts. N and O glycans are both expressed in the zone of presumptive mineralization and are relevant to that process. Bone trabecular lining cells communicate with osteocytes via intracanalicular processes and some lectin ligands were expressed by these three components.

Mast cells and angiogenesis were prominent. Since cartilage normally resists vascular penetration by the secretion of antiangiogenesis factors it is postulated that the hypertrophic chondrocytes in the mineralization zone produce proteases which inhibit antiangiogenesis and facilitate angiogenesis by mast cells.
Small-molecule inhibitors targeting prokaryotic ClpQ protease in Plasmodium display anti-malarial efficacies against blood and liver stages
Authors: Jain Shaifali , Asad Mohd , Caldelari Reto , Datta Gaurav , Singh Shweta , Rathore Sumit , Stanway Rebecca R. , Heussler Volker T. , Mohmmed Asif
Published: May 2022

The ATP-dependent ClpQY system is a prokaryotic proteasome-like machinery in the mitochondrion of malaria parasite, Plasmodium. This protease system is identified as a validated target for malaria intervention. Here we have identified drug-like small chemical compounds, pyrimidotriazine derivatives, as specific inhibitors of P. falciparum ClpQ (PfClpQ) having effective parasiticidal efficacies on asexual and liver stages. Screening of the ‘Malaria Box’ compound library, using a robust in vitro activity assay, identified a hit compound targeting the PfClpQ protease with IC50 at ~750nM. Further, Structure-Activity Relationship (SAR) analysis, using a small library of derivatives of the hit compound, identified three potential lead compounds, ICGEB-L1, ICGEB-L2 and ICGEB-L3, which inhibited enzyme activity with IC50 in 100-200nM ranges. The three lead compounds effectively inhibited in vitro asexual stage parasite growth in similar concentration ranges with ~100-fold selectivity over mammalian cell line; in addition, these compounds effectively inhibited in vitro growth and maturation of hepatocytic stage parasites with EC50 in low nano-molar ranges. These compounds were found to effectively block the development of trophozoite stages to schizont stage, concurrently arresting development and segregation of parasite mitochondria, in asexual as well as hepatocytic stages of the parasite. These morphological and developmental effects of the drugs on parasites mimic the data from genetic ablation of PfClpQ. Importantly, all three compounds showed significant in vivo anti-parasitic efficacies on blood stages of P. berghei mouse malaria model. Overall these results suggest that these PfClpQ targeting compounds are promising candidates to develop new anti-malarials.
An Updated Gene Regulatory Network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
Authors: da Silva Chagas Márcia , Filho Fernando Medeiros , dos Santos Marcelo Trindade , de Menezes Marcio Argollo , Carvalho-Assef Ana Paula D’Alincourt , da Silva Fabricio Alves Barbosa
Published: May 2022

BACKGROUND

Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behavior and provide novel ways to identify potential therapeutic targets and the development of new drugs. Gene regulatory networks (GRN) are an example of interaction representation in silico between regulatory genes and their targets.

OBJECTIVES

In this work, we update the reconstruction of the MDR P. aeruginosa CCBH4851 GRN, and analyze and discuss its structural properties.

METHODS

We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process.

FINDINGS

Our result is a GRN with a larger number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa.

MAIN CONCLUSIONS

Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.
HSF1 excludes CD8+ T cells from breast tumors via suppression of CCL5
Authors: Jacobs Curteisha , Shah Sakhi , Lu Wen-Cheng , Ray Haimanti , Wang John , Sandusky George , Nephew Kenneth P. , Lu Xin , Cao Sha , Carpenter Richard L.
Published: May 2022

Heat shock factor 1 (HSF1) is a stress-responsive transcription factor that promotes cancer cell malignancy. A novel HSF1 Activity Signature (HAS) was found to be negatively associated with antitumor immune cells in breast tumors. Knockdown of HSF1 decreased tumor size and caused an influx of several antitumor immune cells, most notably CD8+ T cells. Depletion of CD8+ T cells prevented tumors from shrinking after knockdown of HSF1, suggesting HSF1 prevents CD8+ T cell influx to avoid immune-mediated tumor killing. HSF1 was also found to suppress expression of CCL5, a chemokine for CD8+ T cells, that significantly contributed to the attraction of CD8+ T cells upon the loss of HSF1. This study demonstrates a model whereby HSF1 suppresses CCL5 leading to reduced CD8+ T cells in breast tumors that prevented immune-mediated destruction. For the first time, these studies indicate HSF1 suppresses antitumor immune activity within tumors.
Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal
Authors: Scarsbrook Lachie , Mitchell Kieren J. , McGee Matthew D. , Closs Gerard P. , Rawlence Nicolas J.
Published: May 2022

The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand—including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling—is poorly understood. The New Zealand grayling (Prototroctes oxyrhynchus) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis.

Here, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes ofP. oxyrhynchus, and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa.

We recovered strong evidence for a sister relationship between the New Zealand and Australian grayling (P. mareana), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1–23.2 Mya), after the height of Oligocene marine inundation in New Zealand.

Our temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance.

This study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA.
Replication stress tolerance and management differs between naïve and primed pluripotent cells
Authors: Kafer Georgia R. , O’Connor Aisling , Rogers Samuel , Osteil Pierre , Nelson Christopher B. , Pickett Hilda A. , Tam Patrick P.L. , Cesare Anthony J.
Published: May 2022

Replication stress is an endemic threat to genome stability. For reasons unknown, replication stress response factors become essential during peri-implantation development. This coincides with a stem cell potency switch from the naïve to the primed state. Using genetically matched, chimera-derived mouse naïve embryonic (mESC) and primed epiblast stem cells (mEpiSC) we found that replication stress management differs between potency states. Primed mEpiSCs rely on Atr activity to prevent replication catastrophe, minimize genomic damage, avoid apoptosis, and re-enter the cell cycle. Conversely, under replications stress, mESCs readily activate Atm regardless of Atr activity, undergo replication catastrophe, and induce apoptosis. Primed pluripotent cells therefore engage Atr to counteract replication difficulties and maintain viability, whereas cells in the naïve state are more readily cleared under the same conditions. We anticipate these divergent strategies enable pluripotent cells of different potency states to meet associated proliferative or developmental demands during early development.
A potentialToxoplasma gondiilipoxygenase is necessary for virulence and associated with the host immune response
Authors: Ramírez-Flores Carlos J. , Tibabuzo Perdomo Andrés M. , Wilson Sarah K. , Cavazos Carolina Mendoza , Flores Billy Joel Erazo , Barnes Katie L. , Knoll Laura J.
Published: May 2022

While the asexual cycle ofToxoplasma gondiican occur in any warm-blooded animal, the sexual cycle is restricted to the feline intestine. We previously determined that because cats lack delta-6-desaturase activity in their intestines, they build up excess linoleic acid, which signalsT. gondiito undergo sexual development. We hypothesized thatT. gondiioxygenates linoleic acid to signal sexual development, so we examined theT. gondiigenome for potential lipoxygenases (TgLOX) enzymes. We identified seven potential TgLOXs that were at least 100-fold more abundant in the cat intestinal versus the tissue culture tachyzoite stage. Parasites deleted in TgLOX1 (TgΔLOX1) had no significant growth differences in tissue culture fibroblast cells. Because the sexual development assay begins with brain cysts, we infected mice with TgΔLOX1 and were surprised to find that TgΔLOX1 had reduced virulence. The TgΔLOX1 parasitemia was reduced by 3 days postinfection and largely cleared by 7 days postinfection. At 3 days postinfection, the cytokines IFNγ, IL-6, MCP-1, and TNF-α were significantly reduced in TgΔLOX1-infected mice, which prompted us to examine TgΔLOX1 in IFNγKO mice. We found that IFNγKO mice infected with TgΔLOX1 succumbed to acute infection with the same kinetics as the parental and complemented strains, suggesting the role of TgLOX1 in mice was IFNγ dependent. In tissue culture fibroblasts, TgLOX1 was localized within the parasite, but in leukocytes from infected mice and activated macrophages, TgLOX1 was localized in vesicular structures in the host cytoplasm. These results suggest that TgLOX1 in these vesicular structures modifies the host immune response.

Importance

Lipoxygenases are enzymes that catalyze the dioxygenation of polyunsaturated fatty acids such as linoleic and arachidonic acid. These modifications create signaling molecules that are best characterized for modulating the immune response. Deletion of the first lipoxygenase characterized forToxoplasma gondii(TgLOX1) generated a less virulent strain and infected mice showed a decreased immune response. This virulence defect was dependent on the mouse cytokine IFNγ. TgLOX1 changes location from inside the parasite in tissue culture conditions to vesicular structures within the host immune cells during mouse infection. These results suggest that TgLOX1 plays a role in the modification of the host immune response in mice.
Feasibility and evaluation of an emergency department-based GP streaming and treatment service
Authors: Aldus Clare , Pope Ian , Brainard Julii , Ruston Annmarie , Hughes Gareth , Everden Paul
Published: May 2022

BACKGROUND

Emergency departments (EDs) are under ever-increasing pressure. The General Practitioner Streaming and Treatment (GPST) service implemented at a large ED in England UK aimed to identify and treat patients who attended an ED but who might effectively be managed in primary care to reduce pressure on ED services.

METHODS

Patients attending ED were met by a GP nurse practitioner who ‘streamed’ them to the GPST service or usual ED care. Routinely collected electronic records, satisfaction questionnaires and interviews were used to evaluate patient outcomes, staff experiences, service outcomes and impacts on usual ED services.

RESULTS

Approximately 96% of GPST patients were seen by a clinician within one hour and all within 87 minutes. Routinely collected ED datasets indicate statistically significant reductions in patients streamed to usual ED care who had to wait > 4 hours for disposition (p=<0.005). Of 769 patients with GPST consultation (approximately 10% of all walk-in patients) 421 (55%) needed no further intervention by ED. The speed at which GPST patients were managed exceeded patients’ expectations and was a major determinant of their satisfaction. No staff expressed dissatisfaction, but some suggested possible improvements in patient eligibility criteria and built environment design features.

CONCLUSIONS

Concurrent provision of GPST correlated with shorter waits for ED attenders to receive health care. Patient and staff experiences of GPST were positive. A robust assessment of safety and health economic outcomes would be useful to refine eligibility criteria and cost effectiveness.
Spondyloarthritis, acute anterior uveitis, and Crohn’s disease have both shared and distinct gut microbiota
Authors: Essex Morgan , Rios Rodriguez Valeria , Rademacher Judith , Proft Fabian , Löber Ulrike , Markó Lajos , Pleyer Uwe , Strowig Till , Marchand Jérémy , Kirwan Jennifer A. , Siegmund Britta , Forslund Sofia Kirke , Poddubnyy Denis
Published: May 2022

Objectives

Spondyloarthritis (SpA) is a group of immune-mediated diseases highly concomitant with non-musculoskeletal inflammatory disorders, such as acute anterior uveitis (AAU) and Crohn’s disease (CD). The gut microbiome represents a promising avenue to elucidate shared and distinct underlying pathophysiology.

Method

We performed 16S rRNA sequencing on stool samples of 277 patients (72 CD, 103 AAU, and 102 SpA) included in the German Spondyloarthritis Inception Cohort (GESPIC) and 62 back pain controls without any inflammatory disorder. Discriminatory statistical methods were used to disentangle microbial disease signals from one another and a wide range of potential confounders. Patients were naïve to or had not received treatment with biological disease-modifying anti-rheumatic drugs for at least three months before enrollment, providing a better approximation of a true baseline disease signal.

Results

We identified a shared, immune-mediated disease signal represented by low abundances of Lachnospiraceae taxa relative to controls, most notablyFusicatenibacter, which partially mediated higher serum CRP levels and was most abundant in controls receiving NSAID monotherapy. Patients with SpA drove an enrichment ofCollinsella, while HLA-B27+ individuals displayed enrichedFaecalibacterium. CD patients had higher abundances of aRuminococcustaxon, and previous csDMARD therapy was associated with increasedAkkermansia.

Conclusion

Our work supports the existence of a common gut dysbiosis in SpA and related inflammatory pathologies. We reveal shared and disease-specific microbial associations and potential mediators of disease activity. Validation studies are needed to clarify the role ofFusicatenibacterin gut-joint inflammation, and metagenomic resolution is needed to understand the relationship betweenFaecalibacteriumcommensals and HLA-B27.
Selective observation of semi-rigid non-core residues in dynamically complex mutant huntingtin protein fibrils
Authors: Matlahov Irina , Boatz Jennifer C. , van der Wel Patrick C. A.
Published: May 2022

Many amyloid-forming proteins, which are normally intrinsically disordered, undergo a disorder-to-order transition to form fibrils with a rigid β-sheet core flanked by disordered domains. Solid-state NMR (ssNMR) and cryogenic electron microscopy (cryoEM) excel at resolving the rigid structures within amyloid cores but studying the dynamically disordered domains remains challenging. This challenge is exemplified by mutant huntingtin exon 1 (HttEx1), which self-assembles into pathogenic neuronal inclusions in Huntington disease (HD). The mutant protein’s expanded polyglutamine (polyQ) segment forms a fibril core that is rigid and sequestered from the solvent. Beyond the core, solvent-exposed surface residues mediate biological interactions and other properties of fibril polymorphs. Here we deploy magic angle spinning ssNMR experiments to probe for semi-rigid residues proximal to the fibril core and examine how solvent dynamics impact the fibrils’ segmental dynamics. Dynamic spectral editing (DYSE) 2D ssNMR based on a combination of cross-polarization (CP) ssNMR with selective dipolar dephasing reveals the weak signals of solvent-mobilized glutamine residues, while suppressing the normally strong background of rigid core signals. This type of ‘intermediate motion selection’ (IMS) experiment based on cross-polarization (CP) ssNMR, is complementary to INEPT- and CP-based measurements that highlight highly flexible or highly rigid protein segments, respectively. Integration of the IMS-DYSE element in standard CP-based ssNMR experiments permits the observation of semi-rigid residues in a variety of contexts, including in membrane proteins and protein complexes. We discuss the relevance of semi-rigid solvent-facing residues outside the fibril core to the latter’s detection with specific dyes and positron emission tomography tracers.

Highlights

Mutant huntingtin exon 1 fibrils feature a broad range of molecular dynamics.

Molecular motion is coupled to water dynamics outside the fiber core.

Dynamics-based spectral editing ssNMR reveals mobile non-core residues.

Intermediate-motion selection via dipolar dephasing of rigid sites.

Semi-mobile glutamines outside the fiber core observed and identified.
Mycorrhizas shape the evolution of plant adaptation to drought
Authors: Cosme Marco
Published: May 2022

Plant adaptation to drought facilitates major ecological transitions, and is likely to play a vital role under looming climate change. Mycorrhizas can influence the physiological capacity of plants to tolerate drought. Here, I show how mycorrhizal strategy and drought adaptation shape one another throughout the course of plant evolution.

To characterize the evolutions of both plant characters, I applied a phylogenetic comparative method using data of 1,638 extant species globally distributed.

The detected correlated evolution unveiled gains and losses of drought tolerance occurring at faster rates in lineages with an ecto- or ericoid mycorrhizal strategy, which were on average about 15 and 300 times quicker than that in lineages with the arbuscular mycorrhizal and naked root (non-mycorrhiza or facultatively arbuscular mycorrhiza) strategy, respectively. Among mycorrhiza shifts, the arbuscular mycorrhiza losses in drought sensitive lineages were more frequent than any symbiont switching or other mutualism breakdown.

My study suggests that mycorrhizas play a key facilitator role in the evolutionary process of plant adaptation to critical changes in water availability across global climates.
Pairwise sequence similarity mapping with PaSiMap: reclassification of immunoglobulin domains from titin as case study
Authors: Su Kathy , Mayans Olga , Diederichs Kay , Fleming Jennifer R.
Published: May 2022

Sequence comparison is critical for the functional assignment of newly identified protein genes. As uncharacterised protein sequences accumulate, there is an increasing need for sensitive tools for their classification. Here, we present a novel multidimensional scaling pipeline, PaSiMap, which creates a map of pairwise sequence similarities. Uniquely, PaSiMap distinguishes between unique and shared features, allowing for a distinct view of protein-sequence relationships. We demonstrate PaSiMap’s efficiency in detecting sequence groups and outliers using titin’s 169 immunoglobulin (Ig) domains. We show that Ig domain similarity is hierarchical, being firstly determined by chain location, then by the loop features of the Ig fold and, finally, by super-repeat position. The existence of a previously unidentified domain repeat in the distal, constitutive I-band is revealed. Prototypic Igs, plus notable outliers, are identified and thereby domain classification improved. This re-classification can now guide future molecular research. In summary, we demonstrate that PaSiMap is a sensitive tool for the classification of protein sequences, which adds a new perspective in the understanding of inter-protein relationships. PaSiMap is applicable to any biological system defined by a linear sequence, including nucleotides.
Asymmetric Signaling Across the Hierarchy of Cytoarchitecture within the Human Connectome
Authors: Parkes Linden , Kim Jason Z , Stiso Jennifer , Calkins Monica E , Cieslak Matthew , Gur Raquel E , Gur Ruben C , Moore Tyler M , Ouellet Mathieu , Roalf David R , Shinohara Russell T , Wolf Daniel H , Satterthwaite Theodore D , Bassett Dani S
Published: May 2022

Cortical variations in cytoarchitecture form a sensory-fugal axis that systematically shapes regional profiles of extrinsic connectivity. Additionally, this axis is thought to guide signal propagation and integration across the cortical hierarchy. While human neuroimaging work has shown that this axis constrains local properties of the human connectome, it remains unclear whether it also shapes the asymmetric signaling that arises from higher-order connectome topology. Here, we used network control theory to examine the amount of energy required to propagate dynamics across the sensory-fugal axis. Our results revealed an asymmetry in this energy indicating that bottom-up transitions were easier to complete compared to top-down transitions. Supporting analyses demonstrated that this asymmetry was underpinned by a connectome topology that is wired to support efficient bottom-up signaling. Finally, we found that this asymmetry correlated with changes in intrinsic neuronal timescales and lessened throughout youth. Our results show that cortical variation in cytoarchitecture may guide the formation of macroscopic connectome topology.
Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences
Authors: Wanchai Visanu , Jenjaroenpun Piroon , Leangapichart Thongpan , Arrey Gerard , Burnham Charles M , Tümmle Maria C , Delgado-Calle Jesus , Regenberg Birgitte , Nookaew Intawat
Published: May 2022

Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in a range of eukaryotic species and cell type including cancer where eccDNA with oncogenes appear to drive tumorigenesis. Most studies of eccDNA employ short-read sequencing to identify for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA identification. An alternative is the long-read sequencing technologies that can potentially be used to construct complete eccDNA. We present a software suite,Construction-basedRolling-circle amplification for eccDNA SequenceIdentification andLocation (CReSIL) 2.0, to identify and characterize eccDNA from long-read sequences. CReSIL’s performance in the identification of eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL’s capability in many of the long-read sequencing datasets. This includes datasets enriched for eccDNA as well as whole genome datasets from many cells that contained large eccDNA. CReSIL suite software will be a versatile tool to deeply investigate eccDNA in biological samples.
Picking winners in cell-cell collisions: wetting, speed, and contact
Authors: Zadeh Pedrom , Camley Brian A.
Published: May 2022

Groups of eukaryotic cells can coordinate their crawling motion to follow cues more effectively, stay together, or invade new areas. This collective cell migration depends on cell-cell interactions, which are often studied by colliding pairs of cells together. Can the outcome of these collisions be predicted? Recent experiments on trains of colliding epithelial cells suggest that cells with a smaller contact angle to the surface or larger speeds are more likely to maintain their direction (“win”) upon collision. When should we expect shape or speed to correlate with the outcome of a collision? We build a model for two-cell collisions within the phase field approach, which treats cells as deformable objects. We can reproduce the observation that cells with high speed and small contact angles are more likely to win with two different assumptions for how cells interact: (1) velocity-aligning, in which we hypothesize that cells sense their own velocity and align to it over a finite timescale, and (2) front-front contact repolarization, where cells polarize away from cell-cell contact, akin to contact inhibition of locomotion. Surprisingly, though we simulate collisions between cells with widely varying properties, in each case, the probability of a cell winning is completely captured by a single summary variable: its relative speed (in the velocity-aligning model) or its relative contact angle (in the contact repolarization model). Both models are currently consistent with reported experimental results, but they can be distinguished by varying cell contact angle and speed through orthogonal perturbations.
C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition
Authors: Sobeh Amr M. , Eichhorn Catherine D.
Published: May 2022

The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7), which contains an RNA recognition motif (RRM), was reported to associate with 7SK RNA and core 7SK RNP protein components in response to DNA damage. However, little is known about the mode of RBM7-7SK RNA recognition. Here, we recombinantly expressed and purified RBM7 RRM constructs and found that constructs containing extended C-termini have increased solubility and stability compared to shorter constructs. To identify potential RBM7-7SK RNA binding sites, we analyzed deposited data from in cellulo crosslinking experiments and found that RBM7 crosslinks specifically to the distal region of 7SK stem-loop 3 (SL3). Electrophoretic mobility shift assays and NMR chemical shift perturbation experiments showed weak binding to 7SK SL3 constructs in vitro. Together, these results provide new insights into RBM7 RRM folding and recognition of 7SK RNA.

Graphical abstract

Highlights

Extending the RBM7 RRM C-terminus improves protein expression and solubility

The RBM7 RRM interacts weakly with 7SK stem-loop 3 single-stranded RNA

Solution state NMR dynamics measurements support presence of additional β4’ strand
Species identification of early colonial bone artefacts excavated from Pyrmont, Australia, by mass spectrometric identification of collagen peptides
Authors: Multari Dylan H. , Sullivan Geraldine J. , Hartley Mary , Power Ronika K. , Haynes Paul A.
Published: May 2022

Zooarchaeology by Mass Spectrometry (ZooMS) is a rapidly developing and increasingly utilised peptide mass fingerprinting (PMF) technique that analyses Collagen 1A1 and 1A2 marker peptides for the genus- or species-level identification of fragmentary bones in the archaeological record. Traditionally, this analysis is performed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF-MS) to identify characteristic m/z values of known marker peptides. Here we present data on the application of a modified ZooMS approach, using nanoflow liquid chromatography - tandem mass spectrometry proteomics, to the analysis of a collection of six early colonial Australian (early to mid-19th Century CE) worked bone artefacts, believed to be mostly knife handles, excavated from a site in Pyrmont, Sydney, Australia in 2017. We were successfully able to identify characteristic marker peptides for bovine COL1A1 and COL1A2 in all six bone artefacts.
Comparative Transcriptome Analysis of Hypocotyls During the Developmental Transition of C3cotyledons to C4Leaves inHalimocnemis mollissimaBunge
Authors: Zolfaghar Mahdis , Rutten Twan , Ghaffari Mohammad Reza , Banaei-Moghaddam Ali Mohammad
Published: May 2022

Identification of signaling pathways that control C4photosynthesis development is essential for introducing the C4pathway into C3crops. Species with dual photosynthesis in their life cycle are interesting models to study such regulatory mechanisms. The species used hereHalimocnemis mollissimaBunge, belonging to the Caroxyleae tribe, displays C3photosynthesis in its cotyledons and a NAD-ME subtype of C4photosynthesis in the First leaves (FLs) onwards. We explored the long-distance signaling pathways that are probably implicated in the shoot-root coordination associated with the manifestation of the C4traits, including efficient resource usage by comparing the mRNA content of hypocotyls before and after the C4first leave’s formation. Histological examination showed the presence of C3anatomy in cotyledons and C4anatomy in the FLs. Our transcriptome analyses verified the performance of the NAD-ME subtype of C4in FLs and revealed differential transcript abundance of several potential mobile regulators and their associated receptors or transporters in two developmentally different hypocotyls ofH. mollissimaBunge. These differentially expressed genes (DEGs) belong to diverse functional groups, including various transcription factor (TF) families, phytohormones metabolism, and signaling peptides, part of which could be related to hypocotyl development. Our findings support the higher nitrogen and water use efficiency associated with C4photosynthetic and provide insights into the coordinated above- and under-ground tissue communication during the developmental transition of C3to C4photosynthesis in this species.
Application and comparison of lyophilisation protocols to enhance stable long-term storage of filovirus pseudotypes for use in antibody neutralisation tests
Authors: Neto Martin Mayora , Wright Edward , Temperton Nigel , Soema Peter , ten Have Rimko , Ploemen Ivo , Scott Simon
Published: May 2022

Filoviruses encompass highly pathogenic viruses placing sporadic public health burden on countries affected. Efforts for improved diagnostics and surveillance are needed considering the recent Ebola outbreaks in Africa. The need for high containment facilities can be circumvented by the use of pseudotype viruses (PV), which can be handled in low containment, for tropism, drug screening, vaccine immunogenicity and serosurveillance studies.

In this study we assessed stability and functionality after long-term storage of lyophilised filovirus pseudotypes for use in neutralisation assays. Lyophilised Ebola and Marburg PVs retained production titres for at least two years when stored at +4°C or less. Lyophilised Ebola PVs performed similarly to non-lyophilised PVs in neutralisation assays after reconstitution. When stored at high temperatures (+37°C), lyophilised PVs did not retain titres after one-month storage, however, when lyophilised using pilot scale facilities EBOV PVs retained titres and performed well in neutralisation assays after one-month storage at 37°C suggesting removing residual moisture might be crucial for avoiding cold-chain transportation. Lyophilisation could allow reagents to be transported more efficiently as well as reducing costs for a future serological kit.
Humoral immunity to SARS-CoV-2 elicited by combination COVID-19 vaccination regimens
Authors: Wang Zijun , Muecksch Frauke , Muenn Friederike , Cho Alice , Zong Shuai , Raspe Raphael , Ramos Victor , Johnson Brianna , Tanfous Tarek Ben , DaSilva Justin , Bednarski Eva , Guzman-Cardozo Camila , Turroja Martina , Millard Katrina G. , Tober-Lau Pinkus , Hillus David , Yao Kai-Hui , Shimeliovich Irina , Dizon Juan , Kaczynska Anna , Jankovic Mila , Gazumyan Anna , Oliveira Thiago Y. , Caskey Marina , Bieniasz Paul D. , Hatziioannou Theodora , Kurth Florian , Sander Leif Erik , Nussenzweig Michel C. , Gaebler Christian
Published: May 2022

The SARS-CoV-2 pandemic prompted a global vaccination effort and the development of numerous COVID-19 vaccines at an unprecedented scale and pace. As a result, current COVID- 19 vaccination regimens comprise diverse vaccine modalities, immunogen combinations and dosing intervals. Here, we compare vaccine-specific antibody and memory B cell responses following two-dose mRNA, single-dose Ad26.COV2.S and two-dose ChAdOx1 or combination ChAdOx1/mRNA vaccination. Plasma neutralizing activity as well as the magnitude, clonal composition and antibody maturation of the RBD-specific memory B cell compartment showed substantial differences between the vaccination regimens. While individual monoclonal antibodies derived from memory B cells exhibited similar binding affinities and neutralizing potency against Wuhan-Hu-1 SARS-CoV-2, there were significant differences in epitope specificity and neutralizing breadth against viral variants of concern. Although the ChAdOx1 vaccine was inferior to mRNA and Ad26.COV2.S in several respects, biochemical and structural analyses revealed enrichment in a subgroup of memory B cell neutralizing antibodies with distinct RBD-binding properties resulting in remarkable potency and breadth.
VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites
Authors: Subra Mélody , Dezi Manuela , Bigay Joëlle , Lacas-Gervais Sandra , Di Cicco Aurélie , Dias Araújo Ana Rita , Abélanet Sophie , Fleuriot Lucile , Debayle Delphine , Gautier Romain , Patel Amanda , Roussi Fanny , Antonny Bruno , Lévy Daniel , Mesmin Bruno
Published: May 2022

Membrane contact sites (MCSs) between organelles are heterogeneous in shape, composition and dynamics. Despite this diversity, VAP proteins act as receptors for multiple FFAT motif-containing proteins and drive the formation of most MCSs involving the endoplasmic reticulum (ER). Although the VAP‒FFAT interaction is well characterized, no model explains how VAP adapts to its partners in various MCSs. We report here that VAP-A localization to different MCSs depends on its intrinsically disordered regions (IDRs). We show that VAP-A interaction with PTPIP51 and VPS13A at ER‒mitochondria MCS conditions mitochondria fusion by promoting lipid transfer and cardiolipin buildup. VAP-A also enables lipid exchange at ER‒Golgi MCS by interacting with OSBP and CERT. However, removing IDRs from VAP-A restricts its distribution and function to ER‒ mitochondria MCS, at the expense of ER‒Golgi MCS. Our data suggest that IDRs of VAP-A do not modulate its preference towards specific partners, but adjust its geometry to the constraints linked to different MCS organization and lifetime. Thus, VAP-A conformational flexibility mediated by its IDRs ensures membrane tethering plasticity and efficiency.
Doublecortin-like kinase 1 (DCLK1) Facilitates Dendritic Spine Growth of Pyramidal Neurons in Mouse Prefrontal Cortex
Authors: Murphy Kelsey E. , Zhang Erin Y. , Wyatt Elliott V. , Sperringer Justin E. , Duncan Bryce W. , Maness Patricia F.
Published: May 2022

The L1 cell adhesion molecule NrCAM (Neuron-glia related cell adhesion molecule) functions as a co-receptor for secreted class 3 Semaphorins to prune subpopulations of dendritic spines on apical dendrites of pyramidal neurons in the developing mouse neocortex. The developing spine cytoskeleton is enriched in actin filaments but a small number of microtubules have been shown to enter the spine apparently trafficking vesicles to the membrane. Doublecortin-like kinase 1 (DCLK1) is a member of the Doublecortin (DCX) family of microtubule-binding proteins with serine/threonine kinase activity. To determine if DCLK1 plays a role in spine remodeling, we generated a tamoxifen-inducible mouse line (Nex1Cre-ERT2: DCLK1flox/flox : RCE) to delete microtubule binding isoforms of DCLK1 from pyramidal neurons during postnatal stages of spine development. Homozygous DCLK1 conditional mutant mice exhibited decreased spine density on apical dendrites of pyramidal neurons in the prefrontal cortex (layer 2/3). Mature mushroom spines were selectively decreased upon DCLK1 deletion but dendritic arborization was unaltered. Mutagenesis and binding studies revealed that DCLK1 bound NrCAM at the conserved FIGQY1231 motif in the NrCAM cytoplasmic domain, a known interaction site for the actin-spectrin adaptor Ankyrin. These findings demonstrate that DCLK1 facilitates spine growth and maturation on cortical pyramidal neurons in the mouse prefrontal cortex potentially through microtubule and NrCAM interactions.
PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea-level change on island archipelagos
Authors: Tan David J.X. , Gyllenhaal Ethan F. , Andersen Michael J.
Published: May 2022

Pleistocene sea-level change played a significant role in the evolution and assembly of island biotas. The formation of land bridges between islands during Quaternary glacial maxima, when sea levels were up to 120 metres below present-day sea levels, often facilitated historical dispersal and gene flow between islands that are today geographically disconnected.

Despite this, relatively few studies have attempted to quantify the effects of Pleistocene sea-level change on the evolution of island species assemblages.

Here we present PleistoDist, an R package that allows users to visualise and quantify the effects of Pleistocene sea-level change on islands over time, and test multiple temporally explicit hypotheses of inter-island dispersal and community assembly.

Re-analysing published datasets, we demonstrate how using PleistoDist to account for historical sea-level change can provide greater explanatory power when analysing extant island communities, and show how population genetic simulations can be used to generate spatiotemporally explicit neutral expectations of population genetic structure across island archipelagos.
Flexing the principal gradient of the cerebral cortex to suit changing semantic task demands
Authors: Gao Zhiyao , Zheng Li , Krieger-Redwood Katya , Halai Ajay , Margulies Daniel S. , Smallwood Jonathan , Jefferies Elizabeth
Published: May 2022

Understanding how thought emerges from the topographical structure of the cerebral cortex is a primary goal of cognitive neuroscience. Recent work has revealed a principal gradient of intrinsic connectivity capturing the separation of sensory-motor cortex from transmodal regions of the default mode network (DMN); this is thought to facilitate memory-guided cognition. However, studies have not explored how this dimension of connectivity changes when conceptual retrieval is controlled to suit the context. We used gradient decomposition of informational connectivity in a semantic association task to establish how the similarity in connectivity across brain regions changes during familiar and more original patterns of retrieval. Multivoxel activation patterns at opposite ends of the principal gradient were more divergent when participants retrieved stronger associations; therefore, when long-term semantic information is sufficient for ongoing cognition, regions supporting heteromodal memory are functionally separated from sensory-motor experience. In contrast, when less related concepts were linked, this dimension of connectivity was reduced in strength as semantic control regions separated from the DMN to generate more flexible and original responses. We also observed fewer dimensions within the neural response towards the apex of the principal gradient when strong associations were retrieved, reflecting less complex or varied neural coding across trials and participants. In this way, the principal gradient explains how semantic cognition is organised in the human cerebral cortex: the separation of DMN from sensory-motor systems is a hallmark of the retrieval of strong conceptual links that are culturally shared.

Significance statement

A central task in neuroscience is to understand how cognition emerges from the topographical structure of cerebral cortex. We used fMRI during a semantic task to assess informational connectivity as participants retrieved stereotypical or more unusual associations. The principal gradient of variation in informational connectivity captured the separation of heteromodal memory regions from unimodal cortex. This separation was reduced when weaker associations were retrieved; these trials also produced higher-dimensional neural responses in heteromodal regions. We conclude that the separation of DMN from sensory-motor systems is a hallmark of the retrieval of strong conceptual links that are culturally shared, while more complex and diverse cognition can be generated as this separation in connectivity is reduced.