bluuebunny/crossref_metadata_2025 huggingface dataset:
Research output is low, but increasing, and focuses on public health at new universities in southern Ethiopia
Authors: Lindtjørn Bernt , Massebo Fekadu , Gari Taye , Tesfaye Solomon Hailemariam
Published: October 2021

Objective

The aim of this work is to describe the developments in research publication at three new universities in southern Ethiopia.

Design

Bibliometric analysis.

Methods

We retrieved references from 1998 to July 2021 from the Web of Science database using the authors’ affiliation. English language publications and peer-reviewed journals were included. The bibliometric analyses were conducted by using Web of Science and the bibliometrix package (version 3.1) under R version 4.0.5.

Results

We reviewed 1019 scientific papers, and there was a substantial increase in the number of publications over the years, especially since 2016. The publications were in 304 different journals with 2606 authors; the number of documents per author was 0·39. Most of the studies were descriptive, 17 (1·7%) were clinical trials, 60 (5·9%) were case-control studies, and 83 (8·1%) were cohort studies. Topics related to public health were the most often studied. The average citations per publication was 9·1. The most frequently cited papers occurred with international collaboration. A total of 886 (84%) publications were “All Open Access” and only 5% of the papers were published in Ethiopian journals. We identified ten groups that maintained scientific production for 8 years or more, mainly in research on malaria and vector borne diseases, nutrition, microbiology, and various public health issues. One of seven papers were published with support from external funding, and with collaborative links with the United States, Europe, and New Zealand.

Conclusions

There has been a remarkable increase in health research at the three universities. The institutions should enhance the research culture, strengthening their health research capacity by encouraging good research practice and ensuring connections between health research and implementation.
HPV vaccination of girls in the German model region Saarland: Insurance data-based analysis and identification of starting points for improving vaccination rates
Authors: Marthaler Anna , Berkó-Göttel Barbara , Rissland Jürgen , Schöpe Jakob , Taurian Emeline , Müller Hanna , Weber Gero , Lohse Stefan , Lamberty Thomas , Holleczek Bernd , Stoffel Harry , Hauptmann Gunter , Giesen Martin , Firk Christiane , Schanzenbach Alexandra , Brandt Florian , Hohmann Heike , Werthner Quirin , Selzer Dominik , Lehr Thorsten , Wagenpfeil Stefan , Smola Sigrun
Published: October 2021

In Germany, the incidence of cervical cancer, a disease caused by human papillomaviruses (HPV), is higher than in neighboring European countries. HPV vaccination has been recommended for girls since 2007. However, it continues to be significantly less well received than other childhood vaccines, so its potential for cancer prevention is not fully realized.

To find new starting points for improving vaccination rates, we analyzed pseudonymized routine billing data from statutory health insurers in the PRÄZIS study in the federal state Saarland serving as a model region. We show that lowering the HPV vaccination age to 9 years led to more completed HPV vaccinations already in 2015. Since then, HPV vaccination rates and the proportion of 9-to 11-year-old girls among HPV-vaccinated females have steadily increased. However, HPV vaccination rates among 15-year-old girls in Saarland remained well below 50% in 2019. Pediatricians vaccinated the most girls overall, with a particularly high proportion at the recommended vaccination age of 9-14 years, while gynecologists provided more HPV catch-up vaccinations among 15-17-year-old girls, and general practitioners compensated for HPV vaccination in Saarland communities with fewer pediatricians or gynecologists. We also provide evidence for a significant association between attendance at the U11 or J1 medical check-ups and HPV vaccination. In particular, participation in HPV vaccination is high on the day of U11. However, obstacles are that U11 is currently not funded by all statutory health insurers and there is a lack of invitation procedures for both U11 and J1, resulting in significantly lower participation rates than for the earlier U8 or U9 screenings, which are conducted exclusively with invitations and reminders.

Based on our data, we propose to restructure U11 and J1 screening in Germany, with mandatory funding for U11 and organized invitations for HPV vaccination at U11 or J1 for both boys and girls.
Model-based Bayesian inference of the ventilation distribution in patients with Cystic Fibrosis from multiple breath washout, with comparison to ventilation MRI
Authors: Whitfield Carl A. , Horsley Alexander , Jensen Oliver E. , Horn Felix C. , Collier Guilhem J. , Smith Laurie J. , Wild Jim M.
Published: October 2021

Background

Indices of ventilation heterogeneity (VH) from multiple breath washout (MBW) have been shown to correlate well with VH indices derived from hyperpolarised gas ventilation MRI. Here we report the prediction of ventilation distributions from MBW data using a mathematical model, and the comparison of these predictions with imaging data.

Methods

We developed computer simulations of the ventilation distribution in the lungs to model MBW measurement with 3 parameters: σV, determining the extent of VH; V0, the lung volume; and VD, the dead-space volume. These were inferred for each individual from supine MBW data recorded from 25 patients with cystic fibrosis (CF) using approximate Bayesian computation. The fitted models were used to predict the distribution of gas imaged by 3He ventilation MRI measurements collected from the same visit.

Results

The MRI indices measured (I1/3, the fraction of pixels below one-third of the mean intensity and ICV, the coefficient of variation of pixel intensity) correlated strongly with those predicted by the MBW model fits (r = 0.93, 0.88 respectively). There was also good agreement between predicted and measured MRI indices (mean bias ± limits of agreement: I1/3 : − 0.003 ± 0.118 and ICV: − 0.004 ± 0.298). Fitted model parameters were robust to truncation of MBW data.

Conclusion

We have shown that the ventilation distribution in the lung can be inferred from an MBW signal, and verified this using ventilation MRI. The Bayesian method employed extracts this information with fewer breath cycles than required for LCI, reducing acquisition time required, and gives uncertainty bounds, which are important for clinical decision making.
Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests
Authors: Valley-Omar Ziyaad , Marais Gert , Iranzadeh Arash , Naidoo Michelle , Korsman Stephen , Maponga Tongai , Hussey Hannah , Davies Mary-Ann , Boulle Andrew , Doolabh Deelan , Laubscher Mariska , Deetlefs JD , Maritz Jean , Scott Lesley , Msomi Nokukhanya , Tegally Houriiyah , de Oliveira Tulio , Bhiman Jinal , Williamson Carolyn , Preiser Wolfgang , Hardie Diana , Hsiao Nei-yuan
Published: October 2021

Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.
Mental Health and Time Management Behavior among Students During COVID-19 Pandemic: Towards Persuasive Technology Design
Authors: Alhasani Mona , Alkhawaji Ali , Orji Rita
Published: October 2021

The study explored the impact of the COVID-19 pandemic on students’ mental health in higher education while capturing their perceptions and attitudes towards time management. The aim was to examine relationships between stress, anxiety, and specific time management related factors. Considering possible differences between genders and degree levels, we developed five structural equation models (SEMs) to delineate these relationships. Results of a large-scale study of 502 participants show that students suffered from stress and two types of COVID-19-related anxiety: disease and consequences. Students’ preference for organization was the only factor that significantly promoted their perceived control over time, which contributes to reducing stress, hence, anxiety. However, female students reported higher stress and anxiety levels than male students. Graduate students reported higher anxiety levels related to the consequences of the pandemic compared to undergrads. To promote students’ preference for organization, we map the three categories of organization to corresponding persuasive strategies which could be used in the design of persuasive interventions. This creates an opportunity for developing technological interventions to improve students’ perceived control over time, thus, reduce stress and anxiety.
JIA patient T cells differentiate into Th1, Th17 and Th1.17 effector cells under Th1 polarizing conditions
Authors: Patrick Anna E. , Esmond Tashawna , Shoaff Kayla , Patrick David M. , Flaherty David K. , Graham T. Brent , Crooke Philip S. , Thompson Susan , Aune Thomas M.
Published: October 2021

Objective

T helper cells develop into discrete Th1, Th2 or Th17 lineages that selectively express IFNγ, IL-4/IL-5/IL-13, or IL-17, respectively and actively silence signature cytokines expressed by opposing lineages. Our objective was to compare Th1, Th2 and Th17 polarization in cell culture models using JIA patient samples.

Methods

Peripheral blood mononuclear cells were isolated from JIA or healthy prepubescent children. T cell naïve and memory phenotypes were assessed by flow cytometry. T cell proliferation was measured using a fluorescence-based assay. Th cell cultures were generated in vitro and IFNγ, IL-17, and TNFα measured by ELISA and flow cytometry.

Results

JIA Th1 cells produced increased IFNγ and inappropriately produced IL-17. JIA Th17 cells produced increased IL-17. JIA Th1 cell cultures develop dual producers of IFNγ and IL-17, which are Th1.17 cells. JIA Th1 cultures expressed elevated levels of both T-bet and RORγT. RNA sequencing confirmed activation of immune responses and inappropriate activation of IL-17 signaling pathways in Th1 cultures. A subset of JIA patient samples was disproportionally responsible for the enhanced IFNγ and IL-17 phenotype and Th1.17 phenotype.

Conclusions

This study reveals that JIA patient uncommitted T cell precursors, but not healthy children, inappropriately develop into inflammatory effector Th1.17 and Th17 cells under Th1 polarizing conditions.

Rheumatology key messages

Th1 differentiation of JIA PBMCs generates high IFNγ, IL-17, and dual IFNγ-IL-17 producing cells.

JIA Th1 differentiation increases master transcription factor expression for Tbet and RORγT.

Enhanced JIA Th1 IFNγ and IL-17 production occurs in a subset of JIA patients.
Localization free super-resolution microbubble velocimetry using a long short-term memory neural network
Authors: Chen Xi , Lowerison Matthew R. , Dong Zhijie , Chandra Sekaran Nathiya Vaithiyalingam , Huang Chengwu , Chen Shigao , Fan Timothy M. , Llano Daniel A. , Song Pengfei
Published: October 2021

Ultrasound localization microscopy is a super-resolution imaging technique that exploits the unique characteristics of contrast microbubbles to side-step the fundamental trade-off between imaging resolution and penetration depth. However, the conventional reconstruction technique is confined to low microbubble concentrations to avoid localization and tracking errors. Several research groups have introduced sparsity- and deep learning-based approaches to overcome this constraint to extract useful vascular structural information from overlapping microbubble signals, but these solutions have not been demonstrated to produce blood flow velocity maps of the microcirculation. Here, we introduce Deep-SMV, a localization free super-resolution microbubble velocimetry technique, based on a long short-term memory neural network, that provides high imaging speed and robustness to high microbubble concentrations, and directly outputs blood velocity measurements at a super-resolution. Deep-SMV is trained efficiently using microbubble flow simulation on real in vivo vascular data and demonstrates real-time velocity map reconstruction suitable for functional vascular imaging and pulsatility mapping at super-resolution. The technique is successfully applied to a wide variety of imaging scenarios, include flow channel phantoms, chicken embryo chorioallantoic membranes, and mouse kidney, tumor, and brain imaging.
Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells
Authors: Veling Mike T. , Nguyen Dan T. , Thadani Nicole N. , Oster Michela E. , Rollins Nathan J. , Brock Kelly P. , Bethel Neville P. , Lim Samuel , Baker David , Way Jeffrey C. , Marks Debora S. , Chang Roger L. , Silver Pamela A.
Published: October 2021

Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally-occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically-induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlight the ability for DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.
ZBP1 induces inflammatory signaling via RIPK3 and promotes SARS-CoV-2-induced cytokine expression
Authors: Peng Ruoshi , Wang-Kan Xuan , Idorn Manja , Zhou Felix Y , Orozco Susana L , McCarthy Julia , Leung Carol S , Lu Xin , Bagola Katrin , Rehwinkel Jan , Oberst Andrew , Maelfait Jonathan , Paludan Søren R , Gyrd-Hansen Mads
Published: October 2021

COVID-19 caused by the SARS-CoV-2 virus remains a threat to global health. The disease severity is mediated by cell death and inflammation, which regulate both the antiviral and the pathological innate immune responses. ZBP1, an interferon-induced cytosolic nucleic acid sensor, facilitates antiviral responses via RIPK3. Although ZBP1-mediated cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1-induced inflammatory signaling pathway that depends on ubiquitination and RIPK3’s scaffolding ability independently of cell death. In human cells, ZBP1 associates with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. RIPK1 and ZBP1 are ubiquitinated to promote TAK1- and IKK-mediated inflammatory signaling. Additionally, RIPK1 recruits the p43/41-caspase-8-p43-FLIP heterodimer to suppress RIPK3 kinase activity, which otherwise promotes inflammatory signaling in a kinase activity-dependent manner. Lastly, we show that ZBP1 contributes to SARS-CoV-2-induced cytokine production. Taken together, we describe a ZBP1-RIPK1-RIPK3-mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspase-8. Our results suggest the ZBP1 pathway contributes to inflammation in response to SARS-CoV-2 infection.
Single-cell transcriptomics reveals the identity and regulators of human mast cell progenitors
Authors: Wu Chenyan , Boey Daryl , Bril Oscar , Grootens Jennine , Vijayabaskar M. S. , Sorini Chiara , Ekoff Maria , Wilson Nicola K. , Ungerstedt Johanna S , Nilsson Gunnar , Dahlin Joakim S.
Published: October 2021

Mast cell accumulation is a hallmark of a number of diseases including allergic asthma and systemic mastocytosis. IgE-mediated crosslinking of the FcεRI receptors causes mast cell activation and contributes to disease pathogenesis. The mast cell lineage is one of the least studied among the hematopoietic cell lineages and there are still controversies about the identity of the mast cell progenitor, i.e., whether FcεRI expression appears during the hematopoietic progenitor stage or in maturing mast cells. Here, we used single-cell transcriptomics to reveal a temporal association between the appearance of FcεRI and the mast cell gene signature in CD34+hematopoietic progenitors. In agreement with these data, the FcεRI+hematopoietic progenitors formed morphologically, phenotypically and functionally mature mast cells in long-term culture assays. Single-cell transcriptomics analysis further revealed the expression patterns of prospective cytokine receptors regulating mast cell progenitor development. Culture assays showed that IL-3 and IL-5 promoted disparate effects on progenitor cell proliferation and survival, respectively, whereas IL-33 caused robust FcεRI downregulation. Taken together, we have demonstrated that FcεRI appears during the hematopoietic progenitor stage of mast cell differentiation and that external stimuli may regulate the FcεRI expression. Thus, the results resolve the controversy regarding the appearance of FcεRI during mast cell development.

One-sentence summary

Single-cell analysis of human hematopoiesis uncovers the stage at which FcεRI appears during mast cell differentiation and reveals disparate effects of IL-3, IL-5 and IL-33 on mast cell progenitor proliferation, survival, and suppression of FcεRI expression.
Structural basis for C-type inactivation in a Shaker family voltage gated K+ channel
Authors: Reddi Ravikumar , Matulef Kimberly , Riederer Erika A. , Whorton Matthew R. , Valiyaveetil Francis I.
Published: October 2021

C-type inactivation is a process by which ion flux through a voltage-gated K+ (Kv) channel is regulated at the selectivity filter. While prior studies have indicated that C-type inactivation involves structural changes at the selectivity filter, the nature of the changes have not been resolved. Here we report the crystal structure of the Kv1.2 channel in a C-type inactivated state. The structure shows that C-type inactivation involves changes in the selectivity filter that disrupt the outer two ion binding sites in the filter. The changes at the selectivity filter propagate to the extracellular mouth and the turret regions of the channel pore. The structural changes observed are consistent with the functional hallmarks of C-type inactivation. This study highlights the intricate interplay between K+ occupancy at the ion binding sites and the interactions of the selectivity filter in determining the balance between the conductive and the inactivated conformations of the filter.
Direct Reprogramming of Non-limb Fibroblasts to Cells with Properties of Limb Progenitors
Authors: Atsuta Yuji , Lee Changhee , Rodrigues Alan R. , Colle Charlotte , Tomizawa Reiko R. , Lujan Ernesto G. , Tschopp Patrick , Gorham Joshua M. , Vannier Jean-Pierre , Seidman Christine E. , Seidman Jonathan G. , Pourquié Olivier , Tabin Clifford J.
Published: October 2021

The early limb bud consists of mesenchymal progenitors (limb progenitors) derived from the lateral plate mesoderm (LPM) that produce most of the tissues of the mature limb bud. The LPM also gives rise to the mesodermal components of the trunk, flank and neck. However, the mesenchymal cells generated at these other axial levels cannot produce the variety of cell types found in the limb bud, nor can they be directed to form a patterned appendage-like structure, even when placed in the context of the signals responsible for organizing the limb bud. Here, by taking advantage of a direct reprogramming approach, we find a set of factors (Prdm16, Zbtb16, and Lin28) normally expressed in the early limb bud, that are capable of imparting limb progenitor-like properties to non-limb fibroblasts. Cells reprogrammed by these factors show similar gene expression profiles, and can differentiate into similar cell types, as endogenous limb progenitors. The further addition of Lin41 potentiates proliferation of the reprogrammed cells while suppressing differentiation. These results suggest that these same four key factors may play pivotal roles in the specification of endogenous limb progenitors.
Exploration of deep-learning based classification with human SNP image graphs
Authors: Chen Chao-Hsin , Tung Kuo-Fong , Lin Wen-Chang
Published: October 2021

Background

With the advancement of NGS platform, large numbers of human variations and SNPs are discovered in human genomes. It is essential to utilize these massive nucleotide variations for the discovery of disease genes and human phenotypic traits. There are new challenges in utilizing such large numbers of nucleotide variants for polygenic disease studies. In recent years, deep-learning based machine learning approaches have achieved great successes in many areas, especially image classifications. In this preliminary study, we are exploring the deep convolutional neural network algorithm in genome-wide SNP images for the classification of human populations.

Results

We have processed the SNP information from more than 2,500 samples of 1000 genome project. Five major human races were used for classification categories. We first generated SNP image graphs of chromosome 22, which contained about one million SNPs. By using the residual network (ResNet 50) pipeline in CNN algorithm, we have successfully obtained classification models to classify the validation dataset. F1 scores of the trained CNN models are 95 to 99%, and validation with additional separate 150 samples indicates a 95.8% accuracy of the CNN model. Misclassification was often observed between the American and European categories, which could attribute to the ancestral origins. We further attempted to use SNP image graphs in reduced color representations or images generated by spiral shapes, which also provided good prediction accuracy. We then tried to use the SNP image graphs from chromosome 20, almost all CNN models failed to classify the human race category successfully, except the African samples.

Conclusions

We have developed a human race prediction model with deep convolutional neural network. It is feasible to use the SNP image graph for the classification of individual genomes.
CDK5 influences the organization of the Circadian Machinery in peripheral clocks
Authors: Ripperger Jürgen , Albrecht Urs , Brenna Andrea
Published: October 2021

Circadian rhythms are self-sustained physiological changes that drive rhythmicity within the 24-hours cycles. Posttranslational modifications (PMTs), such as protein phosphorylation, acetylation, sumoylation, and ubiquitination, are biochemical processes that modify protein structure and functions, ensuring circadian rhythm precision. For example, phosphorylation is considered the most important hallmark of rhythmicity from cyanobacteria to mammals. Cyclin-dependent kinase 5 (CDK5) has been shown to regulate the mammalian SCN’s circadian clock via phosphorylation of PER2. Here, we show that CDK5 influences the clock machinery assembling, using immortalized mouse embryonic fibroblast as an in vitro model for studying the peripheral clock. In fact, the circadian period at the cellular level is lengthened. Furthermore, the clock-controlled gene’s expression amplitude is dampened in Cdk5 ko cell lines, while the phase is delayed about 4 hours.

Taken together, we show in vitro that CDK5 is critically involved in regulating the peripheral clocks, influencing their temporal and spatial dynamics.
Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization
Authors: Bhattacharjee Arunima , Qafoku Odeta , Richardson Jocelyn A. , Anderson Lindsey N. , Schwarz Kaitlyn , Bramer Lisa M. , Lomas Gerard X. , Orton Daniel J. , Zhu Zihua , Engelhard Mark H. , Bowden Mark E. , Nelson William C. , Jumpponen Ari , Jansson Janet K. , Hofmockel Kirsten S. , Anderton Christopher R.
Published: October 2021

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. We observed thatFusarium sp. DS 682, a representative of common saprotrophic soil fungi, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (∼12 µm) in the presence of minerals. The fungus incorporated and translocated potassium (K) from K-rich mineral interfaces, as evidenced by visualization of mineral derived nutrient transport and unique K chemical moieties following fungal induced mineral weathering. Specific membrane transport proteins were expressed in the presence of minerals, including those involved in oxidative phosphorylation pathways and transmembrane transport of small molecular weight organic acids. This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment.
Whale shark rhodopsin adapted to its vertically wide-ranging lifestyle
Authors: Yamaguchi Kazuaki , Koyanagi Mitsumasa , Sato Keiichi , Terakita Akihisa , Kuraku Shigehiro
Published: October 2021

Spectral tuning of visual pigments often facilitates adaptation to new environments, and it is intriguing to study the visual ecology of pelagic sharks with expanded habitats. The whale shark, which dives into the deep sea of nearly 2,000 meters besides near-surface filter-feeding, was previously shown to possesses the ‘blue-shifted’ rhodopsin (RHO). In this study, our spectroscopy of recombinant whale shark RHO mutants revealed the dominant effect of the novel spectral tuning amino acid site 94, which is implicated in congenital stationary night blindness of humans, accounting for the blue shift. Thermal decay profiling revealed the reduction of the thermal stability of whale shark RHO, as typically observed for cone opsins, which was experimentally shown to be achieved by the site 178, as well as 94. The results suggest that these two sites cooperatively enhance the visual capacity in both the deep sea and the sea surface, enabling exceptionally wide vertical migration of this species.
Integration of probabilistic functional networks without an external Gold Standard
Authors: James Katherine , Alsobhe Aoesha , Cockell Simon J. , Wipat Anil , Pocock Matthew
Published: October 2021

Background

Probabilistic functional integrated networks (PFINs) are designed to aid our understanding of cellular biology and can be used to generate testable hypotheses about protein function. PFINs are generally created by scoring the quality of interaction datasets against a Gold Standard dataset, usually chosen from a separate high-quality data source, prior to their integration. Use of an external Gold Standard has several drawbacks, including data redundancy, data loss and the need for identifier mapping, which can complicate the network build and impact on PFIN performance.

Results

We describe the development of an integration technique, ssNet, that scores and integrates both high-throughput and low-throughout data from a single source database in a consistent manner without the need for an external Gold Standard dataset. Using data from Saccharomyces cerevisiae we show that ssNet is easier and faster, overcoming the challenges of data redundancy, Gold Standard bias and ID mapping, while producing comparable performance. In addition ssNet results in less loss of data and produces a more complete network.

Conclusions

The ssNet method allows PFINs to be built successfully from a single database, while producing comparable network performance to networks scored using an external Gold Standard source.
Deep mutational scan of a drug efflux pump reveals its structure-function landscape
Authors: Meier Gianmarco , Thavarasah Sujani , Ehrenbolger Kai , Hutter Cedric A. J. , Hürlimann Lea M. , Barandun Jonas , Seeger Markus A.
Published: October 2021

Drug efflux is a common resistance mechanism found in bacteria and cancer cells. Although several structures of drug efflux pumps are available, they provide only limited functional information on the phenomenon of drug efflux. Here, we performed deep mutational scanning (DMS) on the bacterial ATP binding cassette (ABC) transporter EfrCD to determine the drug efflux activity profile of more than 1500 single variants. These systematic measurements revealed that the introduction of negative charges at different locations within the large substrate binding pocket results in strongly increased efflux activity towards positively charged ethidium, while additional aromatic residues did not display the same effect. Data analysis in the context of an inward-facing cryo-EM structure of EfrCD uncovered a high affinity binding site, which releases bound drugs through a peristaltic transport mechanism as the transporter transits to its outward-facing conformation. Finally, we identified substitutions resulting in rapid Hoechst influx without affecting the efflux activity for ethidium and daunorubicin. Hence, single mutations can convert the ABC exporter EfrCD into a drug-specific ABC importer.
A novel locally c-di-GMP-controlled exopolysaccharide synthase required for N4 phage infection of E. coli
Authors: Junkermeier Eike H. , Hengge Regine
Published: October 2021

A major target of c-di-GMP signaling is the production of biofilm-associated extracellular polymeric substances (EPS), which in Escherichia coli K-12 include amyloid curli fibres, phosphoethanolamine-modified (pEtN-)cellulose and poly-N-acetyl-glucosamine (PGA). However, the characterized c-di-GMP-binding effector systems are largely outnumbered by the 12 diguanylate cyclases (DGCs) and 13 phosphodiesterases (PDEs), which synthetize and degrade c-di-GMP, respectively. E. coli possesses a single protein with a potentially c-di-GMP-binding MshEN domain, NfrB, which – together with the outer membrane protein NfrA – is known to serve as a receptor system for phage N4. Here, we show that NfrB not only binds c-di-GMP with high affinity, but as a novel c-di-GMP-controlled glycosyltransferase synthesizes a secreted EPS, which can impede motility and is required as an initial receptor for phage N4 infection. In addition, a systematic screening of the 12 DGCs of E. coli K-12 revealed that specifically DgcJ is required for the infection with phage N4 and interacts directly with NfrB. This is in line with local signaling models, where specific DGCs and/or PDEs form protein complexes with particular c-di-GMP effector/target systems. Our findings thus provide further evidence that intracellular signaling pathways, which all use the same diffusible second messenger, can act in parallel in a highly specific manner.

Importance

Key findings in model organisms led to the concept of ‘local’ signaling, challenging the dogma of a gradually increasing global intracellular c-di-GMP concentration driving the motile-sessile transition in bacteria. In our current model, bacteria dynamically combine global as well as local signaling modes, in which specific DGCs and/or PDEs team up with effector/target systems in multiprotein complexes. Our present study highlights a novel example of how specificity in c-di-GMP signaling can be achieved by showing NfrB as a novel c-di-GMP binding effector in E. coli, which is controlled in a local manner specifically by DgcJ. We further show that NfrB (which was initially found as a part of a receptor system for phage N4) is involved in the production of a novel exopolysaccharide. Finally, our data shine new light on host interaction of phage N4, which uses this exopolysaccharide as an initial receptor for adsorption.
Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity
Authors: Reinders Alberto , Sellner Benjamin , Fadel Firas , van Berkum Margo , Kaczmarczyk Andreas , Ozaki Shogo , Rueher Johanna , Manfredi Pablo , Sangermani Matteo , Harms Alexander , Perez Camilo , Schirmer Tilman , Jenal Urs
Published: October 2021

Nucleotide-based signaling molecules (NSMs) are widespread in bacteria and eukaryotes, where they control important physiological and behavioral processes. In bacteria, NSM-based regulatory networks are highly complex, entailing large numbers of enzymes involved in the synthesis and degradation of active signaling molecules. How the converging input from multiple enzymes is transformed into robust and unambiguous cellular responses has remained unclear. Here we show that Escherichia coli converts dynamic changes of c-di-GMP into discrete binary signaling states, thereby generating heterogeneous populations with either high or low c-di-GMP. This is mediated by an ultrasensitive switch protein, PdeL, which senses the prevailing cellular concentration of the signaling molecule and couples this information to c-di-GMP degradation and transcription feedback boosting its own expression. We demonstrate that PdeL acts as a digital filter that facilitates precise developmental transitions, confers cellular memory, and generates functional heterogeneity in bacterial populations to evade phage predation. Based on our findings, we propose that bacteria apply ultrasensitive regulatory switches to convert dynamic changes of NSMs into binary signaling modes to allow robust decision-making and bet-hedging for improved overall population fitness.
Mechanical loading and hyperosmolarity as a daily resetting cue for skeletal circadian clocks
Authors: Dudek Michal , Pathiranage Dharshika , Gonçalves Cátia F. , Lawless Craig , Wang Dong , Luo Zhuojing , Yang Liu , Guilak Farshid , Hoyland Judith , Meng Qing-Jun
Published: October 2021

Daily rhythms in mammalian behaviour and physiology are generated by a multi-oscillator circadian system entrained through environmental cues (e.g. light). Presence of niche-dependent physiological time cues has been proposed, allowing local tissues flexibility of phase adjustment. However, to date, such stimuli have remained elusive. Here we show that cycles of mechanical loading and osmotic stimuli within physiological range drive rhythmic expression of clock genes and reset clock phase and amplitude in cartilage and intervertebral disc tissues. Hyperosmolarity (not hypo-osmolarity) resets clocks in young and ageing skeletal tissues through mTORC2-AKT-GSK3β pathway, leading to genome-wide induction of rhythmic genes. These results advocate diurnal patterns of mechanical loading and consequent daily surges in osmolarity as a bona fide tissue niche-specific time cue to maintain skeletal circadian rhythms in sync.

One-Sentence Summary

Circadian clocks in aneural skeletal tissues sense the passage of time through rhythmic patterns of loading and osmolarity
Balance of osmotic pressures determines the volume of the cell nucleus
Authors: Deviri Dan , Safran Samuel A.
Published: October 2021

The volume of the cell nucleus varies across cell-types and species, and is commonly thought to be determined by the size of the genome and degree of chromatin compaction. However, this notion has been challenged over the years by multiple experimental evidence. Here, we consider the physical condition of mechanical force balance as a determining condition of the nuclear volume and use quantitative, order-of-magnitude analysis to estimate the forces from different sources of nuclear and cellular pressure. Our estimates suggest that the dominant pressure within the nucleus and cytoplasm originates from the osmotic pressure of proteins and RNA molecules that are localized to the nucleus or cytoplasm by out-of-equilibrium, active nucleocytoplasmic transport rather than from chromatin or its associated ions. This motivates us to formulate a physical model for the ratio of the cell and nuclear volumes in which osmotic pressures of localized proteins determine the relative volumes. In accordance with unexplained observations that are century-old, our model predicts that the ratio of the cell and nuclear volumes is a constant, robust to a wide variety of biochemical and biophysical manipulations, and is changed only if gene expression or nucleocytoplasmic transport are modulated.
Daily ranging and den usage patterns structure fission-fusion dynamics and social associations in spotted hyenas
Authors: Strauss Eli D. , Jensen Frants H. , Gersick Andrew S. , Thomas Mara , Holekamp Kay E. , Strandburg-Peshkin Ariana
Published: October 2021

Environment structure often shapes social interactions. Spatial attractors that draw multiple individuals may play a particularly important role in dispersed groups, where individuals must first encounter one another to interact. We use GPS data recorded simultaneously from five spotted hyenas (Crocuta crocuta) within a single clan to investigate how communal dens and daily ranging patterns shape fission-fusion dynamics (subgroup splits and merges). We introduce a species-general framework for identifying and characterizing dyadic fission-fusion events and describe a taxonomy of ten possible configurations of these events. Applying this framework to the hyena data illuminates the spatiotemporal structure of social interactions within hyenas’ daily routines. The most common types of fission-fusion events involve close approaches between individuals, do not involve co-travel together, and occur at the communal den. Comparison to permutation-based reference models suggests that den usage structures broad-scale patterns of social encounters, but that other factors influence how those encounters unfold. We discuss the dual role of communal dens in hyenas as physical and social resources, and suggest that dens are an example of a general “social piggybacking” process whereby environmental attractors take on social importance as reliable places to encounter conspecifics, causing social and spatial processes to become fundamentally intertwined.
Study of Metyltetraprole, an unusual agrofungicide targeting the Qo-site of cytochrome bc1 complex
Authors: Serot Claudia , Michel Thomas , Lucas Valentine , Meunier Brigitte
Published: October 2021

The mitochondrial respiratory chain bc1 complex is a proven target of agrofungicides. Most of them are Qo-site antagonists (i.e QoIs), competing with the substrate ubiquinol, and likely share the same binding mode as the widespread Qo-site resistance mutation G143A confers cross-resistance. Metyltetraprole (MTP) presents an exception as studies with phytopathogenic fungi showed that the inhibitor was unaffected by G143A. Here, we used the yeast model to investigate its mode of action. Analysis of bc1 complex mutants supports a Qo-site binding for MTP. However the compound seems distinct to other QoIs, such as azoxystrobin, in various ways, namely; 1) G143A was without effect on MTP, as previously reported. 2) The level of MTP resistance of mutants was higher in bc1 complex activity assays than in growth assays while the opposite was observed with azoxystrobin. 3) Steady-state kinetics used to characterise the mode of action of MTP also revealed differences compared to other QoIs.
INF2-mediated actin filament reorganization confers intrinsic resilience to neuronal ischemic injury
Authors: Calabrese Barbara , Jones Steven , Yamaguchi-Shiraishi Yoko , Lingelbach Michael , Manor Uri , Svitkina Tatyana M , Higgs Henry N , Shih Andy Y , Halpain Shelley
Published: October 2021

During early stages of ischemic brain injury, glutamate receptor hyperactivation mediates neuronal death via osmotic cell swelling. Here we show that ischemia and excess NMDA receptor activation – conditions that trigger neuronal swelling -- cause actin filaments to undergo a rapid and extensive reorganization within the somatodendritic compartment. Normally, F-actin is concentrated within dendritic spines, with relatively little F-actin in the dendrite shaft. However, beginning <5 min after incubation of neurons with NMDA, F-actin depolymerizes within dendritic spines and polymerizes into long, stable filament bundles within the dendrite shaft and soma. A similar “actinification” of the somatodendritic compartment occurs after oxygen/glucose deprivation in vitro, and in mouse brain after photothrombotic stroke in vivo. Following transient, sub-lethal NMDA exposure these actin changes spontaneously reverse within 1-2 hours. A combination of Na+, Cl-, water, and Ca2+ entry are all necessary, but not individually sufficient, for induction of actinification. Spine F-actin depolymerization is also required. Actinification is driven by activation of the F-actin polymerization factor inverted formin-2 (INF2). Silencing of INF2 renders neurons more vulnerable to NMDA-induced membrane leakage and cell death, and formin inhibition markedly increases ischemic infarct severity in vivo. These results show that ischemia-induced actin filament reorganization within the dendritic compartment is an intrinsic pro-survival response that protects neurons from death induced by swelling.
Dcp2 C-terminal Cis-Binding Elements Control Selective Targeting of the Decapping Enzyme by Forming Distinct Decapping Complexes
Authors: He Feng , Wu Chan , Jacobson Allan
Published: October 2021

A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5’ to 3’ decay, but the molecular mechanisms controlling selective mRNA targeting by the enzyme remain elusive. Through extensive genetic analyses we uncover cis-regulatory elements in the Dcp2 C-terminal domain that control selective targeting of the decapping enzyme by forming distinct decapping complexes. Two Upf1-binding motifs target the decapping enzyme to NMD substrates, and a single Edc3-binding motif targets both Edc3 and Dhh1 substrates. Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Xrn1 also has a specific Dcp2 binding site, allowing it to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its targeting specificity and enzymatic activation.

Highlights

Loss of Dcp2 cis-binding elements causes selective stabilization of distinct decapping substrates

Dcp2 cis-binding elements promote the assembly of target-specific decapping complexes in vivo

Xrn1 binds to Dcp2, and both Edc3 and Xrn1 are common components of multiple decapping complexes

Upf1, Edc3, and Pat1 function as unique targeting subunits of the yeast holo-decapping enzyme
Improving Martini 3 for disordered and multidomain proteins
Authors: Thomasen F. Emil , Pesce Francesco , Roesgaard Mette Ahrensback , Tesei Giulio , Lindorff-Larsen Kresten
Published: October 2021

Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small angle X-ray scattering (SAXS) data, and that increasing the strength of protein-water interactions favours more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multi-domain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.
IMPROVED SSRs-BASED GENETIC DIVERSITY ASSESSMENT OF COCONUTS (COCOS NUCIFERA L) ALONG THE COAST OF KENYA
Authors: Masha Justus C. , Muhammed Najya , Njung’e Vincent , Oyoo Maurice E. , Miheso Manfred
Published: October 2021

Coconut is the most important cash crop along the Coast of Kenya, yet its genetic diversity has not been fully established. A genetic diversity study of 48 coconut genotypes that were collected along the Coast of Kenya was conducted with 13 polymorphic short sequence repeats (SSRs) markers. SSR analysis was performed using GeneMapper while data analysis was done with PowerMarker and DARwin softwares.

The results revealed a total of 68 alleles ranging from 2 to 11 per locus with a mean of 5.23 per marker. Gene diversity and polymorphic information content (PIC) ranged between 0.41 to 0.83 and 0.33 to 0.79, respectively. A neighbour-joining dendrogram grouped the genotypes into three major clusters containing distinct sub-clusters. This study underscored that capillary electrophoresis is a more accurate and informative technique for SSRs allele scoring than agarose gels, which was reported in a previous study with the same SSRs markers and coconut genotypes in Kenya. The clusters observed forms the basis to isolate conservation blocks, which are the key to establishing a genebank, since there is no documented coconut genebank for ex-situ conservation in Kenya.
Effects of productive management of an agroforestry system on the associated diversity of parasitoids (Hymenoptera: Braconidae)
Authors: Pech Cutis Cecilia Marisol , Castillo Sánchez Luis Enrique , Canul Solís Jorge Rodolfo , López Coba Ermilo , Ruz Febles Nery Maria , Campos-Navarrete Maria Jose
Published: October 2021

Tropical agroecosystems have emerged from the continuous modification of natural environments, as a sustainability alternative for food production and biodiversity conservation. This work explores how the diversity of parasitoids is modified in environments where plant diversity is limited e.g. crops and when these are adjacent to secondary vegetation, i.e. a scenario fragmented continuously in a limited space. It was found that there is no direct effect of plant diversity in the group of parasitoids studied; but the number of specialist species is high, which indicates that in diversified agroecosystems these probably function as remnants of natural habitat or as a refuge for parasitoids that disperse to different types of management within the agroecosystem. Therefore, it is necessary to consider in future studies the controls exerted by the plant diversity effects bottom-up and consumer top-down. Adding to this the context of the interactions that occur in agroecosystems.