bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunogenicity following two doses of BBIBP-CorV vaccine and a third booster dose with viral vector and Mrna COVID-19 vaccines against delta and omicron variants in prime immunized adults with two doses of BBIBP-CorV vaccine
Authors: Chansaenroj Jira , Suntronwong Nungruthai , Kanokudom Sitthichai , Assawakosri Suvichada , Yorsaeng Ritthideach , Vichaiwattana Preeyaporn , Klinfueng Sirapa , Wongsrisang Lakana , Srimuan Donchida , Thatsanatorn Thaksaporn , Thongmee Thanunrat , Auphimai Chompoonut , Nilyanimit Pornjarim , Wanlapakorn Nasamon , Sudhinaraset Natthinee , Poovorawan Yong
Published: June 2022

Coronavirus disease 2019 (COVID-19) booster vaccination is being comprehensively evaluated globally due to waning immunity and the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Therefore, this study aimed to evaluate antibody responses in individuals vaccinated with two doses of BBIBP-CorV vaccine and to explore the boosting effect of the different vaccine platforms in BBIBP-CorV-primed healthy adults, including viral vector vaccine (AZD122) and mRNA vaccines (BNT162b2 and mRNA-1273). The results showed that, in the BBIBP-CorV prime group, the total receptor-binding domain (RBD) immuno-globulin (Ig) and anti-RBD IgG levels waned significantly at 3 months after receiving the second dose. However, after the booster, RBD-specific binding antibody levels increased. Neutralizing antibody measured by a surrogate neutralization test showed of inhibition over 90% against the SARS-CoV-2 delta variant but less than 70% against omicron variant after the third dose on day 28. All booster vaccines could induce the total IFN-□ T-cell response. The reactogenicity was acceptable and well tolerated without serious adverse events. This study supported administration of the third dose with either viral vector or mRNA vaccine for the BBIBP-CorV-primed individuals to stimulate antibody and T cell responses.
Home-use Photobiomodulation Device Treatment Outcomes for COVID-19
Authors: Lim Lew , Hosseinkhah Nazanin , Buskirk Mark V. , Berk Andrea , Loheswaran Genane , Abbaspour Zara , Karimpoor Mahta , Smith Alison , Au Yoke N. , Ho Kai F , Pushparaj Abhiram , Zahavi Michael , White Alexander , Rubine Jonathan , Zidel Brian , Henderson Christopher , Clayton Russell G. , Tingley David R. , Miller David J. , Karimpoor Mahroo , Hamblin Michael R.
Published: June 2022

BACKGROUND

There is need for non-pharmaceutical treatments for COVID-19. A home-use photobiomodulation (PBM) device was tested as Treatment in a randomized clinical trial.

METHODS

294 patients were randomized with equal allocation to Treatment or Standard of Care (Control). 199 qualified for efficacy analyses. The Treatment group self-treated for 20 minutes twice daily, for the first 5 days, and subsequently once daily for 30 days. A validated respiratory questionnaire was used, and patients were monitored remotely. The primary endpoint was the time-to-recovery (3 consecutive days of no sickness) for general sickness. The Kaplan-Meier method and the Cox Proportional Hazards model were primary methods of analyses.

RESULTS

Treatment patients with collective 0-12 days of symptoms, at moderate-to-severe level on Day 1 of Treatment, did not recover significantly faster than Control. However, for patients with 0-7 days of symptoms there was a significant mean difference of 3 days: Treatment, 18 days (95% CI, 13-20) vs. Control, 21 days (95% CI, 15-28), P=0.050. The Treatment:Control hazard ratio at 1.495 (95% CI, 0.996-2.243), P=0.054 exceeded the pre-trial target of 1.44. Treated patients exceeding 7 days symptoms duration were more tired and had lower energy. None of the patients in the Treatment group suffered death or hospitalization while the Control group had 1 death and 3 severe adverse events requiring hospitalization.

CONCLUSIONS

Patients with up to 7 days of symptoms at moderate-to-severe levels on first day of Treatment can expect faster recovery for general sickness and several respiratory symptoms. (Funded by Vielight Inc.;ClinicalTrials.govnumber,NCT04418505.)
More than Mycobacterium tuberculosis: specific site-of-disease microbial communities, functional capacities, and their distinct clinical profiles in tuberculous lymphadenitis
Authors: Nyawo Georgina , Naidoo Charissa , Wu Benjamin , Sulaiman Imran , Clemente Jose , Li Yonghua , Minnies Stephanie , Reeve Byron , Moodley Suventha , Rautenbach Cornelia , Wright Colleen , Singh Shivani , Whitelaw Andrew , Schubert Pawel , Warren Robin , Segal Leopoldo , Theron Grant
Published: June 2022

Background

Lymphadenitis is the most common extrapulmonary tuberculosis (EPTB) manifestation and a major cause of death. The microbiome is important to human health but uninvestigated in EPTB. We profiled the site-of-disease lymph node microbiome in tuberculosis lymphadenitis (TBL).

Methods

Fine needle aspiration biopsies (FNABs) were collected from 159 pre-treatment presumptive TBL patients in Cape Town, South Africa. 16S Illumina MiSeq rRNA gene sequencing was done.

Results

We analysed 89 definite TBLs (dTBLs) and 61 non-TBLs (nTBLs), which had similar α-but different β-diversities (p=0.001). Clustering identified five lymphotypes prior to TB status stratification: Mycobacterium-, Prevotella- and Streptococcus-dominant lymphotypes were more frequent in dTBLs whereas a Corynebacterium-dominantlymphotype and a fifth lymphotype (no dominant taxon) were more frequent in nTBLs. When restricted to dTBLs, clustering identified a Mycobacterium-dominant lymphotype with low α-diversity and other non-Mycobacterium-dominated lymphotypes (termed Prevotella-Corynebacterium and Prevotella-Streptococcus). The Mycobacterium dTBL lymphotype was associated with HIV-positivity and clinical features characteristic of severe lymphadenitis (e.g., node size). dTBL microbial communities were enriched with potentially proinflammatory microbial short chain fatty acid metabolic pathways (propanoate, butanoate) vs. those in nTBLs. 11% (7/61) of nTBLs had Mycobacterium reads.

Conclusions

TBL at the site-of-disease is not microbially homogenous and distinct microbial community clusters exist that are associated with different immunomodulatory potentials and clinical characteristics. Non-Mycobacterium-dominated dTBL lymphotypes, which contain taxa potentially targeted by TB treatment, represent less severe potentially earlier stage disease. These investigations lay foundations for studying the microbiome’s role in lymphatic TB and the long-term clinical significance of lymphotypes requires prospective evaluation.
Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic
Authors: Lizcano-Perret Belén , Lardinois Cécile , Wavreil Fanny , Hauchamps Philippe , Herinckx Gaëtan , Sorgeloos Frédéric , Vertommen Didier , Gatto Laurent , Michiels Thomas
Published: June 2022

Proteins from some unrelated pathogens, including viruses and bacteria can recruit and activate cellular p90-ribosomal protein S6 kinases (RSKs) through a common linear motif. Our data suggested that such pathogens’ proteins might act as adapters to dock the kinase toward specific substrates. We explored this hypothesis using the Cardiovirus leader protein (L) as a paradigm. L is known to trigger phenylalanine-glycine nucleoporins (FG-NUPs) hyperphosphorylation and nucleocytoplasmic trafficking perturbation. Using a biotin ligase fused to either RSK or to L, we identified FG-NUPs as primary partners of the L-RSK complex in infected cells. Mutant analysis shows that L uses distinct motifs to recruit RSK and to dock the L-RSK complex toward the FG-NUPs. Using an analog-sensitive RSK2 mutant kinase, we show that, in infected cells, L can trigger RSK to use NUP98 and NUP214 as direct substrates. Our data illustrate a novel virulence mechanism where pathogens’ proteins retarget cellular protein kinases toward specific substrates.
Transposable element-mediated rearrangements are prevalent in human genomes
Authors: Balachandran Parithi , Walawalkar Isha A. , Flores Jacob I. , Dayton Jacob N. , Audano Peter A. , Beck Christine R.
Published: June 2022

Transposable elements constitute about half of human genomes, and their role in generating human variation through retrotransposition is broadly studied and appreciated. Structural variants mediated by transposons, which we call transposable element-mediated rearrangements (TEMRs), are less well studied, and the mechanisms leading to their formation as well as their broader impact on human diversity are poorly understood. Here, we identify 493 unique TEMRs across the genomes of three individuals. While homology directed repair is the dominant driver of TEMRs, our sequence-resolved TEMR resource allows us to identify complex inversion breakpoints, triplications or other high copy number polymorphisms, and additional complexities. TEMRs are enriched in genic loci and can create potentially important risk alleles such as a deletion in TRIM65, a known cancer biomarker and therapeutic target. These findings expand our understanding of this important class of structural variation, the mechanisms responsible for their formation, and establish them as an important driver of human diversity.
Modelling Vaccination Strategies for the Control of Marburg Virus Disease Outbreaks
Authors: Qian George Y , Edmunds W John , Bausch Daniel G , Jombart Thibaut
Published: June 2022

Marburg virus disease is an acute haemorrhagic fever caused by Marburg virus. Marburg virus is zoonotic, maintained in nature in Egyptian fruit bats, with occasional spillover infections into humans and nonhuman primates. Although rare, sporadic cases and outbreaks occur in Africa, usually associated with exposure to bats in mines or caves, and sometimes with secondary human-to-human transmission. Outbreaks outside of Africa have also occurred due to importation of infected monkeys. Although all previous Marburg virus disease outbreaks have been brought under control without vaccination, there is nevertheless the potential for large outbreaks when implementation of public health measures is not possible or breaks down. Vaccines could thus be an important additional tool and development of several candidate vaccines is under way. We developed a branching process model of Marburg virus transmission and investigated the potential effects of several prophylactic and reactive vaccination strategies in settings driven primarily by multiple spillover events as well as human-to-human transmission. Our results show a low basic reproduction number which varied across outbreaks, from 0.5 [95% CI: 0.05 – 1.8] to 1.2 [95% CI: 1.0 – 1.9] but a high case fatality ratio. Of six vaccination strategies explored, a combination of ring and targeted vaccination of high-risk groups was generally most effective, with a probability of controlling potential outbreaks of 0.88 (95% CI: 0.85 - 0.91) compared with 0.65 (0.60 - 0.69) for no vaccination, especially if the outbreak is driven by zoonotic spillovers and the vaccination campaign initiated as soon as possible after onset of the first case.

Author Summary

Marburg virus disease is a rare but acute haemorrhagic fever caused by Marburg virus. We developed a branching process model of Marburg virus transmission and used this model to investigate potential prophylactic and reactive vaccination strategies in settings driven primarily by multiple spillover events as well as human-to-human transmission. We calculate a low basic reproduction number which varied across outbreaks, from 0.5 [95% CI: 0.05 – 1.8] to 1.2 [95% CI: 1.0 – 1.9].

Of the six vaccination strategies explored, a combination of ring and targeted vaccination of high-risk groups was generally most effective, with a probability of controlling potential outbreaks of 0.88 (95% CI: 0.85 - 0.91) compared with 0.65 (0.60 - 0.69) for no vaccination, especially if the outbreak is driven by zoonotic spillovers and the vaccination campaign initiated as soon as possible after onset of the first case.
A Model for Understanding the Causes and Consequences of Walking Impairments
Authors: Schwartz Michael H. , Steele Katherine M. , Ries Andrew J. , Georgiadis Andrew G. , MacWilliams Bruce A.
Published: June 2022

Walking is an important skill with positive impacts on health, function, and well-being. Many disorders impair walking and its positive impacts through a variety of complex and interrelated mechanisms. Any attempt to understand walking impairments, or the effects of interventions intended to treat these impairments, must respect this complexity. Therefore, our main objectives in conducting this study were to (1) propose a comprehensive model for quantifying the causes and consequences of walking impairments and (2) demonstrate the potential utility of the model for supporting clinical care and addressing basic scientific questions related to walking.

To achieve these goals, we introduced a model, described by a directed acyclic graph, consisting of 10 nodes and 23 primary causal paths. We gave detailed descriptions of each node and path based on domain knowledge. We then demonstrated the model’s utility using a large sample of gait data (N = 9504) acquired as part of routine care at a regional referral center. We analyzed five relevant examples that involved many of the model’s nodes and paths. We computed causal effect magnitudes as Shapley values and displayed the overall importance of variables (mean absolute Shapley value), the variation of Shapley values with respect to underlying variables, and Shapley values for individual observations (case studies).

We showed that the model was plausible, captured some well-known cause-effect relationships, provided new insights into others, and generated novel hypotheses requiring further testing through simulation or experiment. To aid in transparency, reproducibility, and future enhancements we have included an extensively commented Rmarkdown file and a deidentified data set.
Quantitative Assessment of Aortic Hemodynamics for Varying Left Ventricular Assist Device Outflow Graft Angles and Flow Pulsation
Authors: Sahni Akshita , McIntyre Erin E. , Pal Jay D. , Mukherjee Debanjan
Published: June 2022

Left ventricular assist devices (LVADs) comprise a primary treatment choice for advanced heart failure patients. Treatment with LVAD is commonly associated with complications like stroke and gastrointestinal (GI) bleeding, which adversely impacts treatment outcomes, and causes fatalities. The etiology and mechanisms of these complications can be linked to the fact that LVAD outflow jet leads to an altered state of hemodynamics in the aorta as compared to baseline flow driven by aortic jet during ventricular systole. Here, we present a framework for quantitative assessment of aortic hemodynamics in LVAD flows realistic human vasculature, with a focus on quantifying the differences between flow driven by LVAD jet and the physiological aortic jet when no LVAD is present. We model hemodynamics in the aortic arch proximal to the LVAD outflow graft, as well as in the abdominal aorta away from the LVAD region. We characterize hemodynamics using quantitative descriptors of flow velocity, stasis, helicity, vorticity and mixing, and wall shear stress. These are used on a set of 27 LVAD scenarios obtained by parametrically varying LVAD outflow graft anastomosis angles, and LVAD flow pulse modulation. Computed descriptors for each of these scenarios are compared against the baseline flow, and a detailed quantitative characterization of the altered state of hemodynamics due to LVAD operation (when compared to baseline aortic flow) is compiled. These are interpreted using a conceptual model for LVAD flow that distinguishes between flow originating from the LVAD outflow jet (and its impingement on the aorta wall), and flow originating from aortic jet during aortic valve opening in normal physiological state.
SARS-CoV-2 infection-induced immunity and the duration of viral shedding: results from a Nicaraguan household cohort study
Authors: Maier Hannah E. , Plazaola Miguel , Lopez Roger , Sanchez Nery , Saborio Saira , Ojeda Sergio , Barilla Carlos , Kuan Guillermina , Balmaseda Angel , Gordon Aubree
Published: June 2022

Background

Much of the world’s population has been infected with SARS-CoV-2. Thus, infection-induced immunity will play a critical role in future SARS-CoV-2 transmission. We investigated the impact of immunity from prior infection on viral shedding duration and viral load.

Methods

We conducted a household cohort study in Managua, Nicaragua with an embedded transmission study that closely monitors participants regardless of symptom status. Real-time reverse-transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assays (ELISAs) were used to measure infections and seropositivity, respectively. Blood samples were collected in Feb/March and Oct/Nov 2020 and 2021, and surrounding household intensive monitoring periods. We used accelerated failure time models to compare shedding times. Participants vaccinated ≥14 days prior to infection were excluded from primary analyses.

Results

There were 600 RT-PCR-confirmed SARS-CoV-2 infections between May 1, 2020 and March 10, 2022 with ELISA data prior to infection. Prior infection was associated with 48% shorter shedding times, event time ratio (ETR) 0.52 (95% CI: 0.39-0.69, mean shedding: 13.7 vs 26.4 days). A 4-fold higher anti-SARS-CoV-2 spike titer was associated with 17% shorter shedding (ETR 0.83, 95% CI: 0.78-0.90). Similarly, maximum viral loads (lowest CT) were lower for previously infected individuals (mean CT 29.8 vs 28.0, p = 4.02×10−3). Shedding was shorter in previously infected adults and children ≥10 years, but not in children 0-9 years; there was little difference in CT levels for previously infected vs naïve adults above age 60.

Conclusions

Prior infection-induced immunity was associated with shorter viral shedding and lower viral loads.
Seasonal plasticity in morphology and metabolism differs between migratory North American and resident Costa Rican monarch butterflies
Authors: Tenger-Trolander Ayşe , Julick Cole R. , Lu Wei , Green Delbert André , Montooth Kristi L. , Kronforst Marcus R.
Published: June 2022

Environmental heterogeneity in temperate latitudes is expected to maintain seasonally plastic life-history strategies that include the tuning of morphologies and metabolism that support overwintering. For species that have expanded their ranges into tropical latitudes, it is unclear the extent to which the capacity for plasticity will be maintained or will erode with disuse. The migratory generations of the North American (NA) monarch butterflyDanaus plexippuslead distinctly different lives from their summer generation NA parents and their tropical descendants living in Costa Rica (CR). NA migratory monarchs postpone reproduction, travel thousands of kilometers south to overwinter in Mexico, and subsist on little food for months. Whether recently dispersed populations of monarchs such as those in Costa Rica, which are no longer subject to selection imposed by migration, retain ancestral seasonal plasticity is unclear. To investigate differences in seasonal plasticity, we reared NA and CR monarchs in summer and autumn in Illinois, USA, and measured seasonal reaction norms for aspects of morphology and metabolism related to flight. NA monarchs were seasonally plastic in forewing and thorax size, increasing wing area and thorax to body mass ratio in autumn. While CR monarchs increased thorax mass in autumn, they did not increase the area of the forewing. NA monarchs maintained similar resting and maximal flight metabolic rates across seasons. However, CR monarchs had elevated metabolic rates in autumn. Our findings suggest that the recent expansion of monarchs into habitats that support year-round breeding may be accompanied by (1) the loss of some aspects of morphological plasticity as well as (2) the underlying physiological mechanisms that maintain metabolic homeostasis in the face of temperature heterogeneity.
Functional and pharmacological analyses of visual habituation learning in larval zebrafish
Authors: Lamiré Laurie-Anne , Haesemeyer Martin , Engert Florian , Granato Michael , Randlett Owen
Published: June 2022

Habituation allows animals to learn to ignore persistent but inconsequential stimuli. Despite being the most basic form of learning, a consensus model on the underlying mechanisms has yet to emerge. To probe relevant mechanisms we took advantage of a visual habituation paradigm in larval zebrafish, where larvae reduce their reactions to abrupt global dimming (a dark flash). We used Ca2+imaging during repeated dark flashes and identified 12 functional classes of neurons that differ based on their rate of adaptation, stimulus response shape, and anatomical location. While most classes of neurons depressed their responses to repeated stimuli, we identified populations that did not adapt, or that potentiated their response. These neurons were distributed across brain areas, consistent with a distributed learning process. Using a small molecule-screening approach, we confirmed that habituation manifests from multiple distinct molecular mechanisms, and we have implicated molecular pathways in habituation, including: Melatonin, Estrogen and GABA signaling. However, by combining anatomical analyses and pharmacological manipulations with Ca2+imaging, we failed to identify a simple relationship between pharmacology, altered activity patterns, and habituation behaviour. Collectively, our work indicates that habituation occurs via a complex and distributed plasticity processes that cannot be captured by a simple model. Therefore, untangling the mechanisms of habituation will likely require dedicated approaches aimed at sub-component mechanisms underlying this multidimensional learning process.
Coopting T cell proximal signaling molecules enables Boolean logic-gated CAR T cell control
Authors: Tousley Aidan M. , Rotiroti Maria Caterina , Labanieh Louai , Rysavy Lea Wenting , Rietberg Skyler P. , de la Serna Eva L. , Dalton Guillermo Nicolas , Klysz Dorota , Weber Evan W. , Kim Won-Ju , Xu Peng , Sotillo Elena , Dunn Alexander R. , Mackall Crystal L. , Majzner Robbie G.
Published: June 2022

Introductory paragraph

While CAR T cells have altered the treatment landscape for B cell malignancies, the risk of on-target, off-tumor toxicity has hampered their development for solid tumors because most target antigens are shared with normal cells1,2. Researchers have attempted to apply Boolean logic gating to CAR T cells to prevent on-target, off-tumor toxicity3–7; however, a truly safe and effective logic-gated CAR has remained elusive8. Here, we describe a novel approach to CAR engineering in which we replace traditional ITAM-containing CD3ζ domains with intracellular proximal T cell signaling molecules. We demonstrate that certain proximal signaling CARs, such as a ZAP-70 CAR, can activate T cells and eradicate tumorsin vivowhile bypassing upstream signaling proteins such as CD3ζ. The primary role of ZAP-70 is to phosphorylate LAT and SLP-76, which form a scaffold for the propagation of T cell signaling. We leveraged the cooperative role of LAT and SLP-76 to engineerLogic-gatedIntracellularNetworK(LINK) CAR, a rapid and reversible Boolean-logic AND-gated CAR T cell platform that outperforms other systems in both efficacy and the prevention of on-target, off-tumor toxicity. LINK CAR will dramatically expand the number and types of molecules that can be targeted with CAR T cells, enabling the deployment of these powerful therapeutics for solid tumors and diverse diseases such as autoimmunity9and fibrosis10. In addition, this work demonstrates that the internal signaling machinery of cells can be repurposed into surface receptors, a finding that could have broad implications for new avenues of cellular engineering.
Bioinspired Silk Fibroin Mineralization for Advanced In Vitro Bone Remodeling Models
Authors: de Wildt Bregje W.M , van der Meijden Robin , Bartels Paul A.A. , Sommerdijk Nico A.J.M. , Akiva Anat , Ito Keita , Hofmann Sandra
Published: June 2022

Human in vitro bone models can create the possibility for investigation of physiological bone remodeling while addressing the principle of replacement, reduction and refinement of animal experiments (3R). Current in vitro models lack cell-matrix interactions and their spatiotemporal complexity. To facilitate these analyses, a bone-mimetic template was developed in this study, inspired by bone’s extracellular matrix composition and organization. Silk fibroin (SF) was used as an organic matrix, poly-aspartic acid (pAsp) was used to mimic the functionality of non-collagenous proteins, and 10x simulated body fluid served as mineralization solution. By using pAsp in the mineralization solution, minerals were guided towards the SF material resulting in mineralization inside and as a coating on top of the SF. After cytocompatibility testing, remodeling experiments were performed in which mineralized scaffold remodeling by osteoclasts and osteoblasts was tracked with non-destructive micro-computed tomography and medium analyses over a period of 42 days. The mineralized scaffolds supported osteoclastic resorption and osteoblastic mineralization, in the physiological bone remodeling specific sequence. This model could therefore facilitate the investigation of cell-matrix interactions and may thus reduce animal experiments and advance in vitro drug testing for bone remodeling pathologies like osteoporosis, where cell-matrix interactions need to be targeted.
COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences
Authors: Danesh Gonché , Boennec Corentin , Verdurme Laura , Roussel Mathilde , Trombert-Paolantoni Sabine , Visseaux Benoit , Haim-Boukobza Stéphanie , Alizon Samuel
Published: June 2022

Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce theCOVFlowpipeline, accessible athttps://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in theBeast2software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.
3D single-cell shape analysis using geometric deep learning
Authors: De Vries Matt , Dent Lucas , Curry Nathan , Rowe-Brown Leo , Bousgouni Vicky , Tyson Adam , Dunsby Christopher , Bakal Chris
Published: June 2022

Abstract

Aberrations in 3D cell morphogenesis are linked to diseases such as cancer. Yet there is little systems-level understanding of cell shape determination in 3D, largely because there is a paucity of data-driven methods to quantify and describe 3D cell shapes. We have addressed this need using unsupervised geometric deep learning to learn shape representations of over 95,000 melanoma cells imaged by 3D high-throughput light-sheet microscopy. We used a dynamic graph convolutional foldingnet autoencoder with improved deep embedded clustering to simultaneously learn lower-dimensional representations and classes of 3D cell shapes. We describe a landscape of 3D cell morphology using deep learning-derived 3D quantitative morphological signatures (3DQMS) across different substrate geometries, following treatment by different clinically relevant small molecules and systematic gene depletion in high-throughput. By data integration, we predict modes of action for different small molecules providing mechanistic insights and blueprints for biological re-engineering. Finally, we provide explainability and interpretability for deep learning models.
Alternative host shapes transmission and life-history trait correlations in a multi-host plant pathogen
Authors: Susi Hanna
Published: June 2022

Most pathogens are generalists capable of infecting multiple host species or strains. Trade-offs in performance among different hosts are expected to limit the evolution of generalism. Despite the commonness of generalism, the variation in infectivity, transmission, and trade-offs in performance among host species have rarely been studied in the wild. To understand the ecological and evolutionary drivers of multi-host pathogen infectivity and transmission potential, I studied disease severity, transmission dynamics and infectivity variation of downy mildew pathogenPeronospora sparsaon its three host plantsRubus arcticus, R. chamaemorus, andR. saxatilis. In a survey of 19 wild and cultivated sites of the three host species, disease severity varied by host species and by whether the focal host species grew in shared habitat with other host species. Generally, the presence of an alternative host resulted in lower disease severity. To understand how alternative host presence and plant diversity affect on transmission of the pathogen, I conducted a trap plant experiment. In contrast to the field survey observations, the presence ofR. saxatiliswas positively correlated with transmission to trap plants. To understand how resistance toP. sparsavaries among host species and genotypes, I conducted an inoculation experiment using 10P. sparsastrains from different locations and 20 genotypes of the three host species. Significant variation in infectivity was found among host genotypes but not among host species. The pathogens strains originating form sites withR. saxatiliswere less infective than those without. When trade-offs for infectivity were tested, high infectivity in one host species correlated with high infectivity in another host species. However, when pathogen transmission-related life-history correlations were tested, a positive correlation was found inR. arcticusbut not inR. saxatilis. The results suggest that host resistance may shape pathogen life-history evolution with epidemiological consequences in a multi-host pathogen.
Influence of short and long term processes on SAR11 communities in open ocean and coastal systems
Authors: Bolaños Luis M. , Tait Karen , Somerfield Paul J. , Parsons Rachel J. , Giovannoni Stephen J. , Smyth Timothy , Temperton Ben
Published: June 2022

SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analysed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. Summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A two-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronised to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.
Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes - Insights from Simulation and Experiment
Authors: Wehrhan Leon , Leppkes Jakob , Dimos Nicole , Loll Bernhard , Koksch Beate , Keller Bettina G.
Published: June 2022

Structural waters in the S1 binding pocket ofβ-trypsin are critical for the stabilization of the complex ofβ-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced byα-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly) and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific non-covalent interactions to the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both, experimental and computational data, show a step-wise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regards to energetic properties that could explain the increase in inhibitor strength. The analysis of the enthalpy and the entropy of the water molecules in the S1 binding pocket using Grid Inhomogeneous Solvation Theory confirms this result. Overall, fluorination systematically changes the binding affinity but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.

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A comparison of methods to suppress electrocardiographic artifacts in local field potential recordings
Authors: Stam M.J. , van Wijk B.C.M. , Sharma P. , Beudel M. , Piña-Fuentes D.A. , de Bie R.M.A. , Schuurman P.R. , Neumann W.-J. , Buijink A.W.G.
Published: June 2022

Objective

Sensing-enabled neurostimulators for deep brain stimulation (DBS) therapy record neural activity directly from the stimulating electrodes in the form of local field potentials (LFPs). However, these LFPs are often contaminated with electrocardiographic (ECG) artifacts that impede the detection of physiomarkers for adaptive DBS research. This study systematically compared the ability of different ECG suppression methods to recover disease-specific electrical brain activity from ECG-contaminated LFPs.

Approach

Three ECG suppression methods were evaluated: (1) QRS interpolation of the Perceive toolbox, (2) four variants of a template subtraction method, and (3) sixteen variants of a singular value decomposition (SVD) method. The performance of these methods was examined using LFPs recorded with the Medtronic PerceptTM PC system from the subthalamic nucleus in nine patients with Parkinson’s disease while stimulation was turned off (“OFF-DBS”; anode disconnected) and while stimulation was turned on at 0 mA (“ON-DBS 0 mA”; anode connected). In addition, ECG-contaminated LFPs were simulated by scaling a co-recorded external ECG signal and adding it to the OFF-DBS LFPs.

Main Results

ECG artifacts were present in 10 out of 18 ON-DBS 0 mA recordings. All ECG suppression methods were able to drastically reduce the percent difference of beta band (13 – 35 Hz) spectral power and at least partly recover the beta peak and beta burst dynamics. Using predetermined R-peaks improved the performance of the ECG suppression methods. Lengthening the time window around the R-peaks resulted in stronger reduction in artifact-induced beta band power but at an increased risk of flattening the beta peak and loss of beta burst dynamics.

Significance

The SVD method formed the preferred trade-off between artifact cleaning and signal loss, as long as its parameter settings (time window around the R-peaks; number of components) are adequately chosen.
The IgCAM BT-IgSF (IgSF11) is essential for connexin43-mediated astrocyte-astrocyte and ependymal cell-cell coupling in mice
Authors: Pelz Laura , Dossou Laura , Kompier Nine , Juttner Rene , Siemonsmeier Gabrielle , Meyer Niklas , Lowenstein Elijah David , Lahmann Ines , Kettenmann Helmut , Birchmeier Carmen , Rathjen Fritz Gunter
Published: June 2022

The type I transmembrane protein BT-IgSF is predominantly localized in the brain and testes. It belongs to the CAR subgroup of Ig cell adhesion proteins, which have been hypothesized to regulate connexin expression or localization. Here, we studied the putative link between BT-IgSF and connexins in astrocytes, ependymal cells and neurons of the mouse. Global knockout of BT-IgSF caused an increase in the clustering of connexin43 (Gja1), but not of connexin30 (Gjb6), on astrocytes and ependymal cells. Additionally, knockout animals displayed reduced expression levels of connexin43 protein in the cortex and hippocampus. Importantly, analysis of biocytin spread in hippocampal or cortical slices from mature mice of either sex revealed a decrease in astrocytic cell-cell coupling in the absence of BT-IgSF. Blocking either protein biosynthesis or proteolysis showed that the lysosomal pathway increased connexin43 degradation. Localization of connexin43 in subcellular compartments was not impaired in the mutant. In contrast to connexin43 the localization and expression of connexin36 (Gjd2) on neurons was not affected by the absence of BT-IgSF. Overall, our data indicate that the IgCAM BT-IgSF is essential for correct gap junction-mediated astrocyte-to-astrocyte and ependymal cell-to-ependymal cell communication.

Significance Statement

Astrocytes regulate a variety of physiological processes in the developing and adult brain that are essential for proper brain function. Astrocytes form extensive networks in the brain and communicate via gap junctions. Disruptions of gap junction coupling are found in several diseases such as neurodegeneration or epilepsy. Here, we demonstrate that the cell adhesion protein BT-IgSF is essential for gap junction mediated coupling between astrocytes in the cortex and hippocampus.
Spatacsin regulates directionality of lysosome trafficking
Authors: Pierga Alexandre , Matusiak Raphaël , Cauhapé Margaux , Branchu Julien , Boutry Maxime , Darios Frédéric
Published: June 2022

The endoplasmic reticulum (ER) forms contacts with the lysosomal compartment, regulating lysosome positioning and motility. The movement of lysosomes are controlled by the attachment of molecular motors to their surface. However, the molecular mechanisms by which ER controls lysosome dynamics are still elusive. Here, we demonstrate that spatacsin is an ER-resident protein that regulates ER-lysosomes contacts to promote lysosome motility, shown by the presence of tubular lysosomes. Tubular lysosomes, which are highly dynamic, are entangled in a network of tubular ER. Screening for spatacsin partners required for tubular lysosome formation showed spatacsin to act by regulating protein degradation. We demonstrate that spatacsin promotes the degradation of its partner AP5Z1, which regulates the relative amount of spastizin and AP5Z1 at lysosomes. Spastizin and AP5Z1 contribute to lysosome trafficking by interacting with anterograde and retrograde motor proteins, kinesin KIF13A and dynein/dynactin subunit p150Glued, respectively. Ultimately, investigations in polarized neurons demonstrated that spatacsin-regulated degradation of AP5Z1 controls the directionality of lysosomes trafficking. Collectively, our results identify spatacsin as a protein regulating the directionality of lysosome trafficking.
Co-immunization with pre-erythrocytic antigens alongside circumsporozoite protein can enhance sterile protection againstPlasmodiumsporozoite infection
Authors: Vigdorovich Vladimir , Patel Hardik , Watson Alexander , Raappana Andrew , Reynolds Laura , Selman William , Beeman Suzannah , Edlefsen Paul T. , Kappe Stefan H.I. , Sather D. Noah
Published: June 2022

Malaria-causingPlasmodiumparasites have a complex life cycle and present numerous antigen targets that may contribute to protective immune responses. The currently recommended vaccine—RTS,S—functions by targeting theP. falciparumcircumsporozoite protein (CSP), which is the most abundant surface protein of the sporozoite form responsible for initiating infection of the human host. Despite showing only moderate efficacy, RTS,S has established a strong foundation for the development of next-generation subunit vaccines. Our previous work characterizing the sporozoite surface proteome identified additional non-CSP antigens that may be useful as immunogens individually or in combination with CSP. In this study, we examined eight such antigens using the rodent malaria parasiteP. yoeliias a model system. We demonstrate that despite conferring weak protection individually, co-immunizing each of several of these antigens alongside CSP, could significantly enhance the sterile protection achieved by CSP immunization alone. Thus, our work provides compelling evidence that a multi-antigen pre-erythrocytic vaccine approach may enhance protection compared to CSP-only vaccines. This lays the groundwork for further studies aimed at testing the identified antigen combinations in human vaccination trials that assess efficacy with controlled human malaria infection.

Importance

The currently approved malaria vaccine targets a single parasite protein (CSP) and only results in partial protection. We tested several additional vaccine targets in combination with CSP to identify those that could enhance protection from infection upon challenge in the mouse malaria model. In identifying several such enhancing vaccine targets, our work indicates that a multi-protein immunization approach may be a promising avenue to achieving higher levels of protection from infection. Our work identified several candidate leads for follow-up in the models relevant for human malaria, and provides an experimental framework for efficiently carrying out such screens for other combinations of vaccine targets.
Selection for translational efficiency in genes associated with alphaproteobacterial gene transfer agents
Authors: Kogay Roman , Zhaxybayeva Olga
Published: June 2022

Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by the carbon depletion and results in host lysis and release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for the GTA-mediated DNA acquisition. Here, we detect a codon usage bias towards codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with similar trends in codon usage biases to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs were it appeared missing, and 13 genes previously not implicated in GTA lifecycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in evolution of GTA genes, and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome.

Importance

Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result a rapid dissemination of beneficial genes within and among microbial communities, and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses “domesticated” by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts’ genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in DNA incorporation into a genome are under similar selection pressure, suggesting that they may facilitate integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.
In vivoseamless genetic engineering via CRISPR-triggered single-strand annealing
Authors: Aguilar Gustavo , Bauer Milena , Vigano M. Alessandra , Schnider Sophie T. , Brügger Lukas , Jiménez-Jiménez Carlos , Guerrero Isabel , Affolter Markus
Published: June 2022

Precise genome engineering is essential for both basic and applied research. CRISPR/Cas accelerated the speed and ease by which defined exogenous sequences are integrated into specific loci. Nevertheless, knock-in generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Even when achieved, the analysis of protein localization can still be unfeasible in highly packed tissues, where spatial and temporal control of gene labeling would be ideal. Here, we describe SEED/Harvest, an efficient knock-in method based on homology-directed (HDR) and single-strand annealing (SSA) repair pathways. HDR mediates the integration of a switchable cassette. Upon a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knock-in generation with both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatio-temporal control of protein labelling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knock-ins, we have developed a toolbox based on rational engineering and functionalization of the ALFA nanobody.
Structural basis for RNA-mediated assembly of type V CRISPR-associated transposons
Authors: Schmitz Michael , Querques Irma , Oberli Seraina , Chanez Christelle , Jinek Martin
Published: June 2022

CRISPR systems have been co-opted by Tn7-like elements to direct RNA-guided transposition. Type V-K CRISPR-associated transposons rely on the concerted activities of the pseudonuclease Cas12k, the AAA+ ATPase TnsC, the Zn-finger protein TniQ, and the transposase TnsB. Here we present a cryo-electron microscopic structure of a target DNA-bound Cas12k-transposon recruitment complex comprising RNA-guided Cas12k, TniQ, TnsC and, unexpectedly, the ribosomal protein S15. Complex assembly on target DNA results in complete R-loop formation mediated by critical interactions between TniQ and the trans-activating crRNA, and is coupled with TniQ-dependent nucleation of a TnsC filament. In vivo transposition assays corroborate our structural findings, and biochemical and functional analyses of S15 supports its role as a bona fide component of the type V crRNA-guided transposition machinery. Altogether, our work uncovers key aspects of the mechanisms underpinning RNA-mediated assembly of CRISPR-associated transposons that will guide their development as programmable site-specific gene insertion tools.