bluuebunny/crossref_metadata_2025 huggingface dataset:
Ensemble learning for robust knee cartilage segmentation: data from the osteoarthritis initiative
Authors: Peake Edward J , Chevasson Raphael , Pszczolkowski Stefan , Auer Dorothee P , Arthofer Christoph
Published: September 2020

Purpose

To evaluate the performance of an ensemble learning approach for fully automated cartilage segmentation on knee magnetic resonance images of patients with osteoarthritis.

Materials and Methods

This retrospective study of 88 participants with knee osteoarthritis involved the study of three-dimensional (3D) double echo steady state (DESS) MR imaging volumes with manual segmentations for 6 different compartments of cartilage (Data available from the Osteoarthritis Initiative). We propose ensemble learning to boost the sensitivity of our deep learning method by combining predictions from two models, a U-Net for the segmentation of two labels (cartilage vs background) and a multi-label U-Net for specific cartilage compartments. Segmentation accuracy is evaluated using Dice coefficient, while volumetric measures and Bland Altman plots provide complimentary information when assessing segmentation results.

Results

Our model showed excellent accuracy for all 6 cartilage locations: femoral 0.88, medial tibial 0.84, lateral tibial 0.88, patellar 0.85, medial meniscal 0.85 and lateral meniscal 0.90. The average volume correlation was 0.988, overestimating volume by 9% ± 14% over all compartments. Simple post processing creates a single 3D connected component per compartment resulting in higher anatomical face validity.

Conclusion

Our model produces automated segmentation with high Dice coefficients when compared to expert manual annotations and leads to the recovery of missing labels in the manual annotations, while also creating smoother, more realistic boundaries avoiding slice discontinuity artifacts present in the manual annotations.

Key Results

Combining a 2-label U-Net (cartilage vs background) with a multi-class U-Net for segmentation of cartilage compartment boosts the accuracy of our deep learning model leading to the recovery of missing annotations in the manual dataset.

Automatically generated segmentations have high Dice coefficients (0.85-0.90) and reduce inter-slice discontinuity artefact caused by slice wise delineation.

Model refinement yields more anatomically plausible segmentations where each cartilage label is composed of only a single 3D region of interest.
Synchrony in the periphery: inter-subject correlation of physiological responses during live music concerts
Authors: Czepiel Anna , Fink Lauren K. , Fink Lea T. , Wald-Fuhrmann Melanie , Tröndle Martin , Merrill Julia
Published: September 2020

A concert is a common event at which people gather to share a musical experience. While techniques are increasingly offering insights into naturalistic stimuli perception, this study extended methods to a more ecological context in order to explore real-world music listening within a concert setting. Cardiorespiratory, skin conductance, and facial muscle responses were measured from participants attending one of three concerts with live chamber music performances of works of varying Western Classical styles (Viennese Classical, Contemporary, and Romantic). Collective physiological synchronisation of audience members was operationalised via inter-subject correlation (ISC). By assessing which musical features (obtained via Music Information Retrieval and music-theoretical analyses) evoked moments of high synchrony, logistic regressions revealed that tempo consistently predicted physiological synchrony across all concerts in Classical and Romantic styles, but not the Contemporary style. Highly synchronised responses across all three concert audiences seemed to occur during structural transitional passages, boundaries, and at phrase repetitions. The results support the idea that group synchronisation is linked to musical arousal, structural coherence, and familiarity. By employing physiological ISC and an inter-disciplinary musical analysis, the current study demonstrates a novel approach to gain valuable insight into experiences of naturalistic stimuli in an ecological context.
mtDNA replication in dysfunctional mitochondria promotes deleterious heteroplasmy via the UPRmt
Authors: Yang Qiyuan , Liu Pengpeng , Anderson Nadine S. , Shpilka Tomer , Du YunGuang , Naresh Nandhitha Uma , Luk Kevin , Lavelle Josh , Zeinert Rilee D. , Chien Peter , Wolfe Scot A. , Haynes Cole M.
Published: September 2020

The accumulation of deleterious mitochondrial genomes (ΔmtDNAs) underlies inherited mitochondrial diseases and contributes to the aging-associated decline in mitochondrial function. In heteroplasmic cells, oxidative phosphorylation (OXPHOS) function declines as the population of ΔmtDNAs increase relative to wildtype mtDNAs. In response to mitochondrial perturbations, the bZIP protein ATFS-1 induces a transcription program to promote the recovery of mitochondrial function. Paradoxically, ATFS-1 is also required to maintain ΔmtDNAs in heteroplasmic worms. However, the mechanism(s) by which ATFS-1 promotes ΔmtDNA accumulation relative to wildtype mtDNAs is unclear. Here, we show that mitochondrial-localized ATFS-1 binds almost exclusively to ΔmtDNAs in heteroplasmic worms. Moreover, we demonstrate that mitochondrial ATFS-1 promotes the preferential binding of the mtDNA replicative polymerase (POLG) to ΔmtDNAs. Interestingly, inhibition of the mtDNA-bound protease LONP-1 increased ATFS-1 and POLG binding to wildtype mtDNAs. Furthermore, LONP-1 inhibition inC. elegansand human cybrid cells improved the heteroplasmy ratio and restored OXPHOS function. Our findings suggest that ATFS-1 promotes mtDNA replication by recruiting POLG to mtDNA in a manner that is antagonized by LONP-1. We speculate that this mechanism promotes the repair and expansion of the mitochondrial network by synchronizing mtDNA replication with UPRmtactivation driven by nuclear ATFS-1 activity. However, this repair mechanism cannot resolve OXPHOS defects in mitochondria harboring ΔmtDNAs, resulting in an accumulation of ATFS-1 in dysfunctional mitochondria and constitutive replication of ΔmtDNAs.
THE MODEL OFPPARγDOWNREGULATED SIGNALING IN PSORIASIS
Authors: Sobolev Vladimir , Nesterova Anastasia , Soboleva Anna , Dvoriankova Evgenia , Piruzyan Anastas , Mildzikhova Dzerassa , Korsunskaya Irina , Svitich Oxana
Published: September 2020

Interactions of genes in intersecting signaling pathways, as well as environmental influences, are required for the development of psoriasis. Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor and transcription factor which inhibits the expression of many proinflammatory genes. We tested the hypothesis that low levels ofPPARγexpression promote the development of psoriatic lesions. We combined experimental results and network functional analysis to reconstruct the model ofPPARγdownregulated signaling in psoriasis. We hypothesize that the expression ofIL17, STAT3, FOXP3, andRORCandFOSL1genes in psoriatic skin are correlated with the level ofPPARγexpression and they belong to the same signaling pathway that regulates the development of psoriasis lesion.
Dynamic fluctuations of the locus coeruleus-norepinephrine system underlie sleep state transitions
Authors: Kjaerby Celia , Andersen Mie , Hauglund Natalie , Ding Fengfei , Wang Wei , Xu Qiwu , Deng Saiyue , Kang Ning , Peng Sisi , Sun Qian , Dall Camilla , Jørgensen Peter Kusk , Feng Jiesi , Li Yulong , Weikop Pia , Hirase Hajime , Nedergaard Maiken
Published: September 2020

We normally regard sleep and wake as two distinct opposing brain states, where sleep requires silence of wake-promoting structures such as the locus coeruleus (LC)-norepinephrine (NE) system. We set out to investigate how cortical NE dynamics and NE-related astrocytic activity relates to LC population activity during sleep states.

We show that LC displays regular phasic activity bouts during NREM sleep leading to a slow oscillatory pattern of prefrontal NE levels of which the majority of NE increases does not lead to awakening. NE troughs link to sleep spindles and continued NE decline transitions into REM sleep. Last, we show that prefrontal astrocytes have reduced sensitivity towards NE during sleep.

Our results suggest that dynamic changes in the activity of wake-promoting systems during sleep create alternation between crucial sleep processes and broadening of sensitivity towards incoming sensory input.

Highlights

Extracellular levels of norepinephrine display dynamic changes during NREM and REM sleep

Phasic activity of locus coeruleus neurons during NREM underlies slow norepinephrine oscillations

Spindles occur at norepinephrine troughs and are abolished by norepinephrine increases

Increased spindles prior to REM reflect the beginning of a long-lasting norepinephrine decline

REM episodes are characterized by a sub-threshold continuous norepinephrine decline

The responsiveness of astrocytic Ca2+to norepinephrine is reduced during sleep
Essential role for FtsL in activation of septal PG synthesis
Authors: Park Kyung-Tae , Du Shishen , Lutkenhaus Joe
Published: September 2020

Spatiotemporal regulation of septal PG synthesis is achieved by coupling assembly and activation of the synthetic enzymes (FtsWI) to the Z ring, a cytoskeletal element required for division in most bacteria. InE. colithe recruitment of the FtsWI complex is dependent upon the cytoplasmic domain of FtsL, a component of the conserved FtsQLB complex. Once assembled, FtsWI is activated by the arrival of FtsN, which acts through FtsQLB and FtsA that are also essential for their recruitment. However, the mechanism of activation of FtsWI by FtsN is not clear. Here, we identify a region of FtsL that plays a key role in the activation of FtsWI which we designate AWI (Activation of FtsWI) and present evidence that FtsL acts through FtsI. Our results suggest that FtsN switches FtsQLB from a recruitment complex to an activator with FtsL interacting with FtsI to activate FtsW. Since FtsQLB and FtsWI are widely conserved in bacteria this mechanism is likely to be also widely conserved.

Significance

A critical step in bacterial cytokinesis is the activation of septal peptidoglycan synthesis at the Z ring. Although FtsN is the trigger and acts through FtsQLB and FtsA to activate FtsWI the mechanism is unclear. Here we find an essential role for FtsL in activating septal PG synthesis and find that it acts on FtsI. Our results suggest a model where FtsWI is recruited in an inactive form by FtsQLB and upon FtsN arrival, FtsQLB undergoes a conformational change so that a region of FtsL, that we designate the AWI domain, becomes available to interact with FtsI and activate the FtsWI complex. This mechanism for activation of the divisome has similarities to activation of the elongasome and is likely to be widely conserved in bacteria.
Regression plane concept: analysing continuous cellular processes with machine learning
Authors: Szkalisity Abel , Piccinini Filippo , Beleon Attila , Balassa Tamas , Varga Istvan Gergely , Migh Ede , Paavolainen Lassi , Timonen Sanna , Banerjee Indranil , Yamauchi Yohei , Ando Istvan , Peltonen Jaakko , Pietiäinen Vilja , Honti Viktor , Horvath Peter
Published: September 2020

Biological processes are inherently continuous, and the chance of phenotypic discovery is significantly restricted by discretising them. Using multi-parametric active regression we introduce a novel concept to describe and explore biological data in a continuous manner. We have implementedRegression Plane (RP), the first user-friendly discovery tool enabling class-free phenotypic supervised machine learning.
Coupled Control of Distal Axon Integrity and Somal Responses to Axonal Damage by the Palmitoyl Acyltransferase ZDHHC17
Authors: Niu Jingwen , Sanders Shaun S. , Jeong Hey-Kyeong , Holland Sabrina M. , Sun Yue , Collura Kaitlin M. , Hernandez Luiselys , Huang Haoliang , Hayden Michael R. , Smith George M. , Hu Yang , Jin Yishi , Thomas Gareth M.
Published: September 2020

After optic nerve crush (ONC), the cell bodies and distal axons of most retinal ganglion cells (RGCs) degenerate. RGC somal and distal axon degeneration were previously thought to be controlled by two distinct pathways, involving activation of the kinase DLK and loss of the axon survival factor NMNAT2, respectively. However, we found that mutual palmitoylation by the palmitoyl acyltransferase ZDHHC17 couples the DLK and NMNAT2 signals, which together form a “trust, but verify system”. In healthy optic nerves, ZDHHC17-dependent palmitoylation ensures NMNAT-dependent distal axon integrity, while following ONC, ZDHHC17-dependent palmitoylation is critical for DLK-dependent somal degeneration. We found that ZDHHC17 also controls survival-versus-degeneration decisions in sensory neurons and identified motifs in NMNAT2 and DLK that govern their ZDHHC17-dependent regulation. These findings suggest that the control of somal and distal axon integrity should be considered as a single, holistic process, involving two palmitoylation-dependent pathways acting in concert.
L1PA2 transposons contribute abundant regulatory sequences in MCF7 breast cancer cell line
Authors: Jiang Jiayue-Clara , Rothnagel Joseph , Upton Kyle
Published: September 2020

Transposons, a type of repetitive DNA elements, can contribute cis-regulatory sequences and regulate the expression of human genes. L1PA2 is a hominoid-specific subfamily of LINE1 transposons, with approximately 4,940 copies in the human genome. Individual transposons have been demonstrated to contribute specific biological functions, such as cancer-specific alternate promoter activity for theMEToncogene, which is correlated with enhanced malignancy and poor prognosis in cancer. Given the sequence similarity between L1PA2 elements, we hypothesise that transposons within the L1PA2 subfamily likely have a common regulatory potential and may provide a mechanism for global genome regulation. Here we show that in breast cancer, the regulatory potential of L1PA2 is not limited to single transposons, but is common within the subfamily. We demonstrate that the L1PA2 subfamily is an abundant reservoir of transcription factor binding sites, the majority of which cluster in the LINE1 5’UTR. In MCF7 breast cancer cells, over 27% of L1PA2 transposons harbour binding sites of functionally interacting, cancer-associated transcription factors. The ubiquitous and replicative nature of L1PA2 makes them an exemplary vector to disperse co-localised transcription factor binding sites, facilitating the co-ordinated regulation of genes. In MCF7 cells, L1PA2 transposons also supply transcription start sites to up-regulated transcripts. These transcriptionally active L1PA2 transposons display a cancer-specific active epigenetic profile, and likely play an oncogenic role in breast cancer aetiology. Overall, we show that the L1PA2 subfamily contributes abundant regulatory sequences in breast cancer cells, and likely plays a global role in modulating the tumorigenic state in breast cancer.
Combination of photoactivation with lattice light-sheet imaging reveals untemplated, lamellar ruffle generation by PA-Rac1
Authors: Leyden Finian , Uthishtran Sanjeev , Moorthi U K , York H M , Patil A , Gandhi H , Petrov EP , Arumugam S
Published: September 2020

Membrane protrusions that occur on the dorsal surface of a cell are an excellent experimental system to study actin machinery at work in a living cell. Small GTPase Rac1 controls the membrane protrusions that form and encapsulate extracellular volumes to perform pinocytic or phagocytic functions. Here, capitalizing on rapid volumetric imaging capabilities of lattice light-sheet microscopy (LLSM), we describe optogenetic approaches using photoactivable Rac1 (PA-Rac1) for controlled ruffle generation. We demonstrate that PA-Rac1 activation needs to be continuous, suggesting a threshold local concentration for sustained actin polymerization leading to ruffling. We show that Rac1 activation leads to actin assembly at the dorsal surface of the cell membrane that result in sheet-like protrusion formation without any requirement of a template. Further, this approach can be used to study the complex morpho-dynamics of the protrusions or to investigate specific proteins that may be enriched in the ruffles. Deactivating PA-Rac1 leads to complex contractile processes resulting in formation of macropinosomes. Using multicolour imaging in combination with these approaches, we find that Myo1e specifically is enriched in the ruffles.
Quantifying the impacts of urban human-wildlife conflicts – how can we solve the urban gull problem in St Andrews?
Authors: Smith Grania P.
Published: September 2020

Interactions between urban wildlife and people are increasing globally. Some of these interactions can be negative and lead to human-wildlife conflicts. In St Andrews, Scotland, residents and business owners have come into conflict with herring gulls (Larus argentatus) and lesser black-backed gulls (Larus fuscus) that nest and forage in the town. This study quantified the number, species and distribution of nesting gulls; the vulnerability of different sources of rubbish to attack; and the likelihood of negative human-gull interactions related to food. Surveys were conducted in St Andrews during the 2016 breeding season (May-July). Nesting gull density and distribution were estimated during weekly street surveys of buildings; vantage surveys were conducted for some buildings and a correction factor estimating a minimum number of nesting gulls was produced. 110 nesting gull pairs were estimated and these occupied ~10% of buildings. The vulnerability of waste sources to attack was monitored during transects recording whether or not rubbish sources were attacked. Black bin bags had the highest probability of being attacked, but placing these in secured hessian bags prevented this. The frequency of negative human-gull interactions involving food at street-level was determined during 10-minute timed watches at various locations. Incidences of gulls taking food were rare; only eight were seen in 30 hours of watches. Altering human behaviour (for example, disposing of waste securely) will mitigate potential issues with urban wildlife. Findings from this study will enable effective management of human-gull conflicts in St Andrews and have potential applications in other urban communities.
The CONDOR pipeline for simultaneous knockdown of multiple genes identifies RBBP-5 as a germ cell reprogramming barrier inC. elegans
Authors: Kazmierczak Marlon , Díaz Carlota Farré i , Ofenbauer Andreas , Tursun Baris
Published: September 2020

Multiple gene activities control complex biological processes such as cell fate specification during development and cellular reprogramming. Investigating the manifold gene functions in biological systems requires also simultaneous depletion of two or more gene activities. RNA interference-mediated knockdown (RNAi) is commonly used inC. elegansto assess essential genes, which otherwise lead to lethality or developmental arrest upon full knockout. RNAi application is straightforward by feeding worms with RNAi plasmid-containing bacteria. However, the general approach of mixing bacterial RNAi clones to deplete two genes simultaneously often yields poor results. To address this issue, we developed a bacterial conjugation-mediated double RNAi technique ‘CONDOR’. It allows combining RNAi bacteria for robust double RNAi with high-throughput. To demonstrate the power of CONDOR for large scale double RNAi screens we conjugated RNAi against the histone chaperone genelin-53with more than 700 other chromatin factor genes. Thereby, we identified the Set1/MLL methyltransferase complex member RBBP-5 as a novel germ cell reprogramming barrier. Our findings demonstrate that CONDOR increases efficiency and versatility of RNAi screens to examine interconnected biological processes inC. eleganswith high-throughput.
Potential malaria vectorAnopheles minimus(species A) still persisting in North East India
Authors: Tyagi Varun , Goswami Diganta , Dhiman Sunil , Dey Dipanjan , Rabha Bipul , Chattopadhyay P. , Dwivedi Sanjai K
Published: September 2020

Background

Vector borne infectious diseases affect two third of the world’s human population and cause mortality in millions each year. Malaria remains one of the major killers in the Indian sub-continent and transmitted uninterruptedly by many efficient vectors and their sibling species. In North East India (NE),Anopheles minimushas been recognized as an important vector which shares majority of malaria cases. This study primarily focuses on to recognize the presence and distribution of sibling species ofAn. minimusin certain endemic area of NE India.

Methods

Anophelesspecies were collected and identified using available morphological keys. The genomic DNA was extracted from the mosquito specimen and used to perform species specific PCR (ss PCR) for molecular identification of major malaria vectorAn. minimussibling species

Result

Morphological identification suggested the presence ofAn. minimus slin low density in the study area. The specimen ofAn. minimussubjected to ss PCR confirmed the prevalence of only one sibling species namely,An. minimusA in Sialmari and Chandubi.

Conclusion

Though in low density, but malaria vectorAn. minimusis still present in certain endemic areas of NE India. The ss PCR assay employed presently suggested thatAn. minimussibling species A is prevailing in the region. Presently used ss PCR assay was simpler, faster, cheaper and more readily interpreted than earlier assays. This information could be useful in understanding of current prevalence and distribution ofAn. minimussibling species complex in NE region of India.
Maintaining robust size across environmental conditions through plastic brain growth dynamics
Authors: Cobham Ansa E. , Neumann Brent , Mirth Christen K.
Published: September 2020

Organ growth is tightly regulated across environmental conditions to generate appropriate final size. While the size of some organs is free to vary, others need to maintain constant size to function properly. This poses a unique problem: how is robust final size achieved when environmental conditions can alter some major growth processes? While we know that brain growth is “spared” from the effects of the environment from humans to fruit flies, we do not understand how this process alters growth dynamics across brain compartments. Here, we explore how this robustness in brain size is achieved by examining differences in growth patterns between the larval body, the brain, and a brain compartment – the mushroom bodies – inDrosophila melanogasteracross both thermal and nutritional conditions. We identify key differences in patterns of growth between the whole brain and mushroom bodies that are likely to underlie robustness of final organ shape. Further, we show that these differences produce distinct brain shapes across environments.

Significance of Study

A long-standing question in Biology has been how fully functional multicellular organisms with highly specialized organs are generated, given that organs initiate growth at different times across development. Although the genetic mechanisms that underlie growth has been studied extensively, we are yet to understand how growth pattern of organs produces distinct final shapes across changing environmental conditions. We use the Drosophila brain, to reveal that key differences in growth dynamics are likely to underlie robustness of final organ shape and are tuned by nutrition and temperature. Further deepening our knowledge of how final organ shape is maintained across environmental conditions.
Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms
Authors: Oude Munnink Bas B. , Sikkema Reina S. , Nieuwenhuijse David F. , Molenaar Robert Jan , Munger Emmanuelle , Molenkamp Richard , van der Spek Arco , Tolsma Paulin , Rietveld Ariene , Brouwer Miranda , Bouwmeester-Vincken Noortje , Harders Frank , der Honing Renate Hakze-van , Wegdam-Blans Marjolein C.A. , Bouwstra Ruth J. , GeurtsvanKessel Corine , van der Eijk Annemiek A. , Velkers Francisca C. , Smit Lidwien A.M. , Stegeman Arjan , van der Poel Wim H.M. , Koopmans Marion P.G.
Published: September 2020

The zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms.

One sentence summary

SARS-CoV-2 transmission on mink farms.
Ongoing evolution of KRAB zinc finger protein-coding genes in modern humans
Authors: Thorball Christian W. , Planet Evarist , de Tribolet-Hardy Jonas , Coudray Alexandre , Fellay Jacques , Turelli Priscilla , Trono Didier
Published: September 2020

Background

Krüppel-associated box (KRAB) zinc finger proteins (KZFPs) constitute the largest and fastest evolving family of gene regulators encoded by the human genome. Recent data indicate that many KZFPs serve as repressors of transposable element-embedded regulatory sequences (TEeRS) and that the evolutionary turnover of KZFP genes is mainly attributable to the changing transposable element (TE) load of their hosts. However, how natural selection and genetic variation are shaping this process is still poorly defined.

Methods

Genetic information was collected from nine primate species and 138,500 human genomes. Gene-wide as well as functional amino acid position specific constraint was calculated across all human KZFPs.

Results

We found that the most conserved KZFPs, some of which go back close to 400 million years, have been subjected to marked negative selection in the evolutionarily recent past and are very homogeneous within the human population. In contrast, younger, largely primate-restricted family members present evidence of less negative selection than the rest of genome and lower levels of coding constraint, particularly within the sequences encoding the functional sites of their zinc finger (ZF) arrays. We defined 33 sets of KZFP paralogs, which pairwise displayed a broad range of coding constraints differentials, with more recently emerged paralogs usually displaying a higher frequency of putatively deleterious mutations and missense variants within the functional sites of their ZF arrays than their source gene. Finally, we identified three KZFP genes more constrained in the genomes of individuals of African ancestry than in Europeans, with their modes of expression or DNA targets pointing to possible links between these inter-populational genetic differences and regional differences in the prevalence of some diseases.

Conclusions

This work shows how the ongoing selection of KZFPs contributes to modern human genetic variation, in particular through the constraint of putatively deleterious- and missense variants in functional protein sites, and how ongoing interplays between environment and KZFP genes might be impacting the biology of modern humans.
Confinement size determines the architecture of Ran-induced microtubule networks
Authors: Gai Ya , Setru Sagar , Cook Brian , Stone Howard A. , Petry Sabine
Published: September 2020

The organization of microtubules (MTs) within cells is critical for its internal organization during interphase and mitosis. During mitotic spindle assembly, MTs are made and organized around chromosomes in a process regulated by RanGTP. The role of RanGTP has been explored inXenopusegg extracts, which are not limited by a cell membrane. Here, we investigated whether cell-sized confinements affect the assembly of RanGTP-induced MT networks inXenopusegg extracts. We used microfluidics to encapsulate extract within monodisperse extract-in-oil droplets. Importantly, we find that the architecture of Ran-induced MT networks depends on the droplet diameter and the Ran concentration, and differs from structures formed in bulk extract. Our results highlight that both MT nucleation and physical confinement play critical roles in determining the spatial organization of the MT cytoskeleton.

STATEMENT OF SIGNIFICANCE

During cell division, chromosomes are segregated by the mitotic spindle, whose framework consists of up to hundreds of thousands of microtubules (MTs). Spindle MTs are generated via several pathways, one of which is regulated by RanGTP. Yet, how Ran-induced MTs self-organize within cell-sized confinement remains unclear. This work reports unexpected architectures of Ran-induced MT networks confined in cell-sized droplets, which depend on the droplet diameter and the RanGTP concentration. Thus, MT nucleation and confinement together give rise to specific MT network architectures, which are otherwise not observed in unconfined assays. The findings provide a simple strategy to engineer the architectures of MT networks and could have direct implications in nucleation-controlled soft material processing.
Strong reduction of the chain rigidity of hyaluronan by selective binding of Ca2+ions
Authors: Giubertoni G. , Pérez de Alba Ortíz A. , Bano F. , Zhang X. , Linhardt R.J. , Green D. E. , DeAngelis P. L. , Koenderink G.H. , Richter R. P. , Ensing B. , Bakker H.J.
Published: September 2020

The biological functions of natural polyelectrolytes are strongly influenced by the presence of ions, which bind to the polymer chains and thereby modify their properties. Although the biological impact of such modifications is well-recognized, a detailed molecular picture of the binding process and of the mechanisms that drive the subsequent structural changes in the polymer is lacking. Here, we study the molecular mechanism of the condensation of calcium, a divalent cation, on hyaluronan, a ubiquitous polymer in human tissues. By combining two-dimensional infrared spectroscopy experiments with molecular dynamics simulations, we find that calcium specifically binds to hyaluronan at millimolar concentrations. Because of its large size and charge, the calcium cation can bind simultaneously to the negatively charged carboxylate group and the amide group of adjacent saccharide units. Molecular dynamics simulations and single-chain force spectroscopy measurements provide evidence that the binding of the calcium ions weakens the intra-molecular hydrogen-bond network of hyaluronan, increasing the flexibility of the polymer chain. We also observe that the binding of calcium to hyaluronan saturates at a maximum binding fraction of ~10-15 mol %. This saturation indicates that the binding of Ca2+strongly reduces the probability of subsequent binding of Ca2+at neighboring binding sites, possibly as a result of enhanced conformational fluctuations and/or electrostatic repulsion effects. Our findings provide a detailed molecular picture of ion condensation, and reveal the severe effect of a few, selective and localized electrostatic interactions on the rigidity of a polyelectrolyte chain.

TOC
New shallow water species of CaribbeanIrciniaNardo, 1833 (Porifera: Irciniidae)
Authors: Kelly Joseph B. , Thacker Robert W.
Published: September 2020

SevenIrciniagrowth forms were collected from three sites in the Caribbean (Bocas del Toro, Panama; the Mesoamerican Barrier Reef, Belize; and the Florida Keys, United States of America). Previous research used an integrative taxonomic framework to delimit species boundaries among these growth forms. Here, we present descriptions for these species, six of which are new to science (Ircinia lowisp. nov.,Ircinia bocatorensissp. nov.,Ircinia radixsp. nov.,Ircinia laeviconulosasp. nov.,Ircinia vansoestisp. nov.,Ircinia rutzlerisp. nov.) in addition to one speciesconferre(Irciniacf.reteplanaTopsent, 1923).
High-Quality Genome Assembly and Annotation of the California Harvester AntPogonomyrmex californicus(Buckley, 1867)
Authors: Bohn Jonas , Halabian Reza , Schrader Lukas , Shabardina Victoria , Steffen Raphael , Suzuki Yutaka , Ernst Ulrich R. , Gadau Jürgen R. , Makałowski Wojciech
Published: September 2020

The harvester ant genusPogonomyrmexis endemic to arid and semiarid habitats and deserts of North and South America and California harvester antPogonomyrmex californicusis the most widely distributedPogonomyrmexspecies in the North America.P. californicuscolonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation ofP. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats inP. californicus.
Bacteriophage activity against and characterisation of avian pathogenicEscherichia coliisolated from colibacillosis cases in Uganda
Authors: Kazibwe George , Katami Phionah , Alinaitwe Ruth , Alafi Stephen , Nanteza Ann , Nakavuma Jesca Lukanga
Published: September 2020

A laboratory-based study aimed at establishing a stock of avian pathogenicEscherichia coli(APEC) lytic bacteriophages, for future development of cocktail products for controlling colibacillosis as well as minimizing use of antimicrobial drugs in the poultry production systems in Uganda. Specifically, the study determined the antibiotic susceptibility; phylogenetic categories, occurrence of selected virulence genes amongEscherichia colistock isolates from cases of chicken colibacillosis; and isolation of specific bacteriophages. Fifty six isolates were confirmed asE. coliby standard phenotypic tests. All the 56 (100%) isolates were resistant to at least one antibiotic while 50 (89.3%) isolates were resistant to at least three classes of antimicrobial drugs and were therefore designated as multi-drug resistant. Phylogenetically, APEC isolates mainly belonged to phylogroups A and D which represented 44.6% and 39.3%, respectively. Virulence genes,ompTandiutAwere the most frequent with 33 (58.9%) and 32 (57.1%) isolates respectively; whileiroNleast occurred in 23 (41.1%) isolates. Of the 56 isolates, 69.6% harbored at least one virulence gene, while 50% had at least four virulence genes; hence confirmed as APEC. None of the isolates belonged to the selected serotypes O1, O2 and O78. Seven specific bacteriophages were isolated and their host range, varied from 1.8% to 17.9% (n=56 APEC isolates), while the combined lytic spectrum of all the phages was 25%. Phage stability was negatively affected by increasing temperatures with both UPEC04 and UPEC10 phages becoming undetectable at 70°C; however activity was detected between pH 2 and 12. The high occurrence of APEC isolates with resistance against the commonly used antibiotics supports the need for alternative strategies of bacterial infections control in poultry. The low host range exhibited by the phages calls for search for more candidates before more in-depth studies are done for phage characterization and application.
Ccr2 suppression by minocycline in Cx3cr1/Ccr2-visualized inherited retinal degeneration
Authors: Terauchi Ryo , Kohno Hideo , Watanabe Sumiko , Saito Saburo , Watanabe Akira , Nakano Tadashi
Published: September 2020

Retinal inflammation accelerates photoreceptor cell death (PCD) caused by retinal degeneration. Minocycline, a semisynthetic broad-spectrum tetracycline antibiotic, has previously been reported to show PCD rescue effect in retinal degeneration. The purpose of this study was to assess the effect of minocycline on Cx3cr1 and Ccr2 expression in retinal degeneration.Mertk-/-Cx3cr1GFP/+Ccr2RFP/+mice, which enabled observation ofCx3cr1- andCcr2-expression pattern in inherited retinal degeneration, were used to test the effect of minocycline. Minocycline was systemically administered toMertk-/-Cx3cr1GFP/+Ccr2RFP/+mice. For observing the effect of minocycline on Cx3cr1 and Ccr2 expression, administration was started on 4-week-old mice and continued for 2 weeks. To assess the PCD rescue effect, minocycline was administered to 6-week-old mice for 2 weeks. The expression pattern of Cx3cr1-GFP and Ccr2-RFP were observed on retinal and retinal pigment epithelium (RPE) flat-mounts. The severity of retinal degeneration was assessed on retinal sections. Minocycline administration suppressedCcr2expression inMertk-/-Cx3cr1GFP/+Ccr2RFP/+mice as observed in retinal and RPE flat-mounts. On the contrary, Cx3cr1 expression was not affected by minocycline administration. Retinal degeneration is ameliorated in minocycline administeredMertk-/-Cx3cr1GFP/+Ccr2RFP/+mice. In conclusions, Minocycline suppression of Ccr2 expression correlates to amelioration of retinal degeneration.
Light dependent morphological changes can tune light absorption in iridescent plant chloroplasts
Authors: Castillo Miguel A. , Wardley William P. , Lopez-Garcia Martin
Published: September 2020

Chloroplasts, the organelles responsible for photosynthesis in most plants and algae, exhibit a variety of morphological adaption strategies to changing light environments which can have important yet overlooked light scattering effects. This can be even more significant for iridoplasts, specialized chloroplasts whose tissue is arranged as a photonic multilayer producing a characteristic strong blue reflectance associated to a wavelength selective absorption enhancement relevant for photosynthesis.

In this work, we study how the photonic properties of iridoplasts are affected by light induced dynamic changes using realistic data extracted from previous reports. Our results show a reflectance red-shift from blue to green under increasing light intensity. Consequently, the light absorption enhancement induced by the photonic nanostructure is also redshifted. We also show that the photonic properties are resilient to biologically realistic levels of disorder in the structure. We extended this analysis to another photonic nanostructure-containing chloroplast, known as a bisonoplast, and found similar results, pointing towards similar properties in different plant species. We finally found that all types of chloroplasts can tune light absorption depending on light conditions. In general, our study opens the door to understanding how dynamic morphologies in chloroplasts can affect light scattering and absorption.
First evidence for an Amazonian insect migration in the butterflyPanacea prola(Lepidoptera: Nymphalidae)
Authors: Gallice Geoffrey , Mattea Riccardo , Stoiser Allison
Published: September 2020

Insect migrations rival those of vertebrates in terms of numbers of migrating individuals and even biomass, although instances of the former are comparatively poorly documented. This is especially true in the world’s tropics, which harbor the vast majority of Earth’s insect species. Understanding these mass movements is of critical and increasing importance as global climate and land use change accelerate and interact to alter the environmental cues that underlie migration, particularly in the tropics. Here, we provide the first evidence for an insect migration for the nymphalid butterflyPanacea prolain the Amazon, the world’s largest and most biodiverse rainforest that is experiencing a shifting climate and rapid forest loss.
High transmissibility and fetal pathogenicity of recent Zika virus strains from the African lineage
Authors: Aubry Fabien , Jacobs Sofie , Darmuzey Maïlis , Lequime Sebastian , Delang Leen , Fontaine Albin , Jupatanakul Natapong , Miot Elliott F. , Dabo Stéphanie , Manet Caroline , Montagutelli Xavier , Baidaliuk Artem , Gambaro Fabiana , Simon-Lorière Etienne , Gilsoul Maxime , Romero-Vivas Claudia M. , Cao-Lormeau Van-Mai , Jarman Richard G. , Diagne Cheikh T. , Faye Oumar , Faye Ousmane , Sall Amadou A. , Neyts Johan , Nguyen Laurent , Kaptein Suzanne J. F. , Lambrechts Louis
Published: September 2020

The global emergence of Zika virus (ZIKV) in the last decade revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects such as microcephaly. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compared the transmissibility and pathogenicity of seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We found that recent African ZIKV strains largely outperformed their Asian counterparts in mosquito transmission kinetics experiments, which translated into a markedly higher epidemic potential in outbreak computer simulations. In addition, African ZIKV strains were significantly more lethal than Asian ZIKV strains in immunocompromised adult mice. Finally, prenatal infection of immunocompetent mouse embryos with an African ZIKV strain resulted in embryonic death whereas it caused microcephaly with Asian ZIKV strains. Together, our results demonstrate the high epidemic potential and pathogenicity of recent ZIKV strains from Africa. Importantly, they also imply that the African ZIKV lineage could more easily go unnoticed by public health surveillance systems than the Asian ZIKV lineage due to its propensity to cause fetal loss rather than birth defects.
The importance of charge in perturbing the aromatic glue stabilizing the protein-protein interface of homodimeric tRNA-guanine transglycosylase
Authors: Nguyen Andreas , Nguyen Dzung , Nguyen Tran Xuan Phong , Sebastiani Maurice , Dörr Stefanie , Hernandez-Alba Oscar , Debaene François , Cianférani Sarah , Heine Andreas , Klebe Gerhard , Reuter Klaus
Published: September 2020

Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine and tyrosine. Inactivation of thetgtgene leads to decreased pathogenicity ofShigellabacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each exchange with respect to dimer and thermal stability or enzyme activity applying native mass spectrometry, thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate strong influence of pH on homodimer stability. Obviously, protonation of a histidine within the aromatic cluster promotes the collapse of an essential structural motif within the dimer interface at slightly acidic pH.

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Rabaptin5 targets autophagy to damaged endosomes and SCVs by interaction with FIP200 and ATG16L1
Authors: Millarte Valentina , Schlienger Simon , Kälin Simone , Spiess Martin
Published: September 2020

Selective autophagy of damaged organelles is an important process for cellular homeostasis. The mechanisms how autophagy selects specific targets is often poorly understood. Rabaptin5 was previously known as a major regulator of early endosome identity and maturation. Here we identified two novel Rabaptin5 interactors: FIP200, a subunit of the ULK1 autophagy initiator complex, and ATG16L1, a central component of the E3-like enzyme in LC3 lipidation. Indeed, autophagy of early endosomes damaged by chloroquine or monensin treatment was found to require Rabaptin5 and particularly a specific short sequence motif binding to the WD domain of ATG16L1. Rabaptin5 and this interaction with ATG16L1 is further required for much of autophagic elimination ofSalmonella entericain phagosomes with early endosomal characteristics early after infection. Our results demonstrate a novel function of Rabaptin5 in quality control of early endosomes in the selective recruitment of autophagy to damaged early endosomes and phagosomes.
Gradual development of non-adjacent dependency learning during early childhood
Authors: Paul Mariella , Männel Claudia , van der Kant Anne , Mueller Jutta L. , Höhle Barbara , Wartenburger Isabell , Friederici Angela D.
Published: September 2020

In order to become proficient native speakers, children have to learn the morpho-syntactic relations between distant elements in a sentence, so-called non-adjacent dependencies (NADs). Previous research suggests that NAD learning in children comprises different developmental stages, where until 2 years of age children are able to learn NADs associatively under passive listening conditions, while starting around the age of 3 to 4 years children fail to learn NADs during passive listening. To test whether the transition between these developmental stages occurs gradually, we tested children’s NAD learning in a foreign language using event-related potentials (ERPs). We found ERP evidence of NAD learning across the ages of 1, 2 and 3 years. The amplitude of the ERP effect indexing NAD learning, however, decreased with age. These findings might indicate a gradual transition in children’s ability to learn NADs associatively. Cognitively, this transition might be driven by children’s increasing knowledge of their native language, hindering NAD learning in novel contexts. Neuroanatomically, maturation of the prefrontal cortex might play a crucial role, promoting top-down learning, affecting bottom-up, associative learning. In sum, our study suggests that NAD learning under passive listening conditions undergoes a gradual transition between different developmental stages during early childhood.

Research Highlights

Transition between developmental stages of non-adjacent dependency (NAD) learning

Children between 1 and 3 years of age showed learning of NADs in a foreign language

Brain responses revealed associative NAD learning, triggered by passive listening

Gradual decrease of the strength of associative non-adjacent dependency learning