bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanics of human embryo compaction
Authors: Firmin Julie , Ecker Nicolas , Danon Diane Rivet , Lange Virginie Barraud , Turlier Hervé , Patrat Catherine , Maître Jean-Léon
Published: January 2022

The shaping of the human embryo begins with compaction, during which cells come into close contact and form a tighter structure1,2. Assisted reproductive technology (ART) studies suggest that human embryos fail compaction primarily because of defective adhesion3,4. Based on our current understanding of animal morphogenesis5,6, other morphogenetic engines, such as cell contractility, could be involved in shaping the human embryo. However, the molecular, cellular and physical mechanisms driving human embryo morphogenesis remain uncharacterized. Using micropipette aspiration on human embryos donated to research, we have mapped cell surface tensions during compaction. This reveals a 4-fold increase of tension at the cellmedium interface while cell-cell contacts keep a steady tension. Comparison between human and mouse reveals qualitatively similar but quantitively different mechanical strategies, with human embryos being mechanically least efficient. Inhibition of cell contractility and cell-cell adhesion in human embryos reveal that only contractility controls the surface tension responsible for compaction. Interestingly, if both cellular processes are required for compaction, they exhibit distinct mechanical signatures when faulty. Analyzing the mechanical signature of naturally failing embryos, we find evidence that non-compacting embryos or partially compacting embryos with excluded cells have defective contractility. Together, our study reveals that an evolutionarily conserved increase in cell contractility is required to generate the forces driving the first morphogenetic movement shaping the human body.
Identification of domestic cat hepadnavirus from a cat blood sample in Japan
Authors: Takahashi Kazuki , Kaneko Yasuyuki , Shibanai Akiko , Yamamoto Shushi , Katagiri Ayana , Osuga Tatsuyuki , Inoue Yoshiyuki , Kuroda Kohei , Tanabe Mika , Okabayashi Tamaki , Naganobu Kiyokazu , Minobe Isao , Saito Akatsuki
Published: January 2022

The hepatitis B virus (Hepadnaviridae) induces chronic hepatitis and hepatic cancer in humans. A novel domestic cat hepadnavirus (DCH) was recently identified in several countries, however, the DCH infection status of cats in Japan is unknown. Therefore, we investigated the DCH infection rate of 139 cat samples collected in Japan. We identified one positive blood sample (0.78%) from a 17-year-old female cat with chronically elevated alanine aminotransferase. Phylogenetic analysis demonstrated that the DCH strain identified in this study is genetically distinct from strains in other countries. Further investigations are required to elucidate the evolution of DCH and the impact of DCH infection on hepatic diseases in domestic cats.
Systematic comparison of ranking aggregation methods for gene lists in experimental results
Authors: Wang Bo , Law Andy , Regan Tim , Parkinson Nicholas , Cole Joby , Russell Clark D. , Dockrell David H. , Gutmann Michael U. , Baillie J. Kenneth
Published: January 2022

A common experimental output in biomedical science is a list of genes implicated in a given biological process or disease. The results of a group of studies answering the same, or similar, questions can be combined by meta-analysis to find a consensus or a more reliable answer. Ranking aggregation methods can be used to combine gene lists from various sources in meta-analyses. Evaluating a ranking aggregation method on a specific type of dataset before using it is required to support the reliability of the result since the property of a dataset can influence the performance of an algorithm. Evaluation of aggregation methods is usually based on a simulated database especially for the algorithms designed for gene lists because of the lack of a known truth for real data. However, simulated datasets tend to be too small compared to experimental data and neglect key features, including heterogeneity of quality, relevance and the inclusion of unranked lists. In this study, a group of existing methods and their variations which are suitable for meta-analysis of gene lists are compared using simulated and real data. Simulated data was used to explore the performance of the aggregation methods as a function of emulating the common scenarios of real genomics data, with various heterogeneity of quality, noise level, and a mix of unranked and ranked data using 20000 possible entities. In addition to the evaluation with simulated data, a comparison using real genomic data on the SARS-CoV-2 virus, cancer (NSCLC), and bacteria (macrophage apoptosis) was performed. We summarise our evaluation results in terms of a simple flowchart to select a ranking aggregation method for genomics data.
Exploitation of neighbouring subsoil for nutrient acquisition under annual-perennial strip intercropping systems
Authors: Han Eusun , Czaban Weronika , Dresbøll Dorte Bodin , Thorup-Kristensen Kristian
Published: January 2022

Little is known of how the deep root systems of perennial crops contribute to deeper and better resource use when intercropped with annuals in arable fields. Therefore, we aimed at measuring the capacity of perennial deep roots, alfalfa (Medicago sativa L.) and curly dock (Rumex crispus L.) to access the nutrient source located under the neighboring annuals at 1.0 and 2.5 m of soil depth. Alfalfa and curly dock were able to access the tracer-labelled source placed at a distance under the annual crop strips. As a result, the reliance on deeper soil layer for nutrient uptake under intercroppings became greater compared with sole-croppings. Combination of an annual cereal (winter rye) and a perennial legume (alfalfa) with contrasting root systems exhibited higher resource complementarity compared with intercroppings having similar root systems or absence of legumes. Our results demonstrated that the deep-rooted perennials when intercropped with annuals can induce vertical niche complementarity, especially at deeper soil layers. This was assumed to be due to the vertically stratified root activity between the crop components, however, the magnitude of the effects depended on choice of crop combinations, and on types of tracers. Future studies should include estimates such as relative yield total and land equivalent ratio to quantitatively determine the effects of resource acquisition under annual-perennial intercropping in arable fields.
Distinct sub-second dopamine signaling in dorsolateral striatum measured by a genetically-encoded fluorescent sensor
Authors: Salinas Armando G. , Lee Jeong O. , Augustin Shana M. , Zhang Shiliang , Patriarchi Tommaso , Tian Lin , Morales Marisela , Mateo Yolanda , Lovinger David M.
Published: January 2022

Dopamine produces neuromodulation throughout the basal ganglia, cortex and other brain regions, and is implicated in movement control, neural mechanisms of reward and actions of misused substances. The efferent projections of dopaminergic neurons with somata in the substantia nigra pars compacta and ventral tegmental area strongly innervate different striatal subregions. While much is known about the function of these neurons, there is a relative deficiency of information aboutin vivodopamine dynamics in the nigrostriatal projections, especially those to the dorsolateral striatum (DLS). In past studies, subsecond dopamine changes were measured predominantly with fast-scan cyclic voltammetry (FSCV) both in brain slices andin vivo. However, traditional FSCV has limitations in discriminating among catecholamines, and cannot be used for simultaneous measurement of both slow and fast/phasic dopamine changes. In addition, FSCV has been most useful for measuring dopamine in the ventral striatumin vivowith less utility for measurement in dorsolateral striatum. The development of genetically encoded dopamine sensors has provided a new approach to measuring slow and fast dopamine dynamics both in brain slices andin vivo, raising the hope of more facile measurement ofin vivodopamine measurements, including in areas where measurement was previously difficult with FSCV. To this end, we first evaluated dLight photometry in brain slices with simultaneous FSCV. We found that both techniques yielded comparable findings. However, differences were noted in responses to dopamine transporter inhibitors, including cocaine. We then usedin vivofiber photometry with dLight to examine responses to cocaine in DLS and compared responses during Pavlovian conditioning in DLS to two other striatal subregions. These experiments show that dopamine increases are readily detectable in DLS and provide new information about dopamine transient kinetics and slowly developing signaling during conditioning. Overall, our findings indicate that dLight photometry is well suited to measuring dopamine dynamics in a striatal region of great interest where such measurements were difficult previously.
Identification of a phage display-derived peptide interacting with the N-terminal region of Factor VII activating protease (FSAP) enables characterization of zymogen activation
Authors: Seidl Sebastian , Nielsen Nis Valentin , Escheid Michael , Haug Bengt Erik , Stensland Maria , Thiede Bernd , Declerck Paul J. , Åge Løset Geir , Kanse Sandip M.
Published: January 2022

Increased Factor VII activating protease (FSAP) activity has a protective effect in diverse disease conditions as inferred from studies in FSAP−/− mice and humans deficient in FSAP activity due to a single nucleotide polymorphism. The activation of FSAP zymogen in plasma is mediated by extracellular histones that are released during tissue injury or inflammation or by positively charged surfaces. However, it is not clear if this activation mechanism is specific and amenable to manipulation. Using a phage display approach we have identified a peptide, NNKC9/41, that activates pro-FSAP in plasma. Other commonly found zymogens in the plasma were not activated. Binding studies with FSAP domain deletion mutants indicate that the N-terminus of FSAP is the key interaction site of this peptide. Blocking the contact pathway of coagulation did not influence pro-FSAP activation by the peptide. In a monoclonal antibody screen, we identified MA-FSAP-38C7 that prevented the activation of pro-FSAP by the peptide. This antibody bound to the LESLDP sequence (amino acids 30-35) in the N-terminus of FSAP. The plasma clotting time was shortened by NNKC9/41 and this was reversed by MA-FSAP-38C7 demonstrating the utility of this peptide. Identification of this peptide, and the corresponding interaction site, provides proof of principle that it is possible to activate a single protease zymogen in blood in a specific manner. Peptide NNKC/41 will be useful as a tool to delineate the molecular mechanism of activation of pro-FSAP in more detail, elucidate its biological role.

Graphical abstract
Universality of Form: The Case of Retinal Cone Photoreceptor Mosaics
Authors: Beygi Alireza
Published: January 2022

Cone photoreceptor cells are wavelength-sensitive neurons in the retinas of vertebrate eyes and are responsible for color vision. The spatial distribution of these nerve cells is commonly referred to as cone photoreceptor mosaic. By applying the principle of maximum entropy, we demonstrate the universality of retinal cone mosaics in vertebrate eyes by examining various species, namely, rodent, dog, monkey, human, fish, and bird. We introduce a parameter called retinal temperature, which is conserved across the retinas of vertebrates. The virial equation of state for two-dimensional cellular networks, known as Lemaître’s law, is also obtained as a special case of our formalism. We investigate the behavior of several artificially generated networks and the natural one of the retina concerning this universal, topological law.
Structural and functional analysis of the human Cone-rod homeobox transcription factor
Authors: Clanor Penelope-Marie B. , Buchholz Christine , Hayes Jonathan E. , Friedman Michael A. , White Andrew M. , Enke Ray A. , Berndsen Christopher E.
Published: January 2022

The cone-rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone-rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 24 years since its initial characterization, there are no high-resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small-angle x-ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX-HD). We find that the CRX-HD is a compact, globular monomer in solution that can specifically bind functional cis-regulatory elements encoded upstream of retina -specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease-causing mutant protein variants.
A quantitative analysis of the similarities and differences of the HIV/FIV gag genome
Authors: Siu Charlotte , Horn Meredith , Cheng Xiao-Wen
Published: January 2022

1.

Among viruses, human immunodeficiency virus (HIV) presents the greatest challenge to humans. Here, we retrieved genome sequences from NCBI and were then run through LALIGN bioinformatics software to compute the E value, bit score, Waterman eggert score, and percent identity, which are four important indicators of how similar the sequences are. The E value was 3.1 x 10^-9, the percent identity was 54.4 percent, and the bit score was 51.9. It was also sensed that bases 1600 to 1990 in HIV and bases 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genomes are rather similar, it is unlikely that this similarity is due to random chance; therefore, there are a noticeable number of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term, it will provide new insights into the differences observed in previous studies or even facilitate the development of an effective HIV treatment.
Critical-like bistable dynamics in the resting-state human brain
Authors: Wang Sheng H. , Arnulfo Gabriele , Myrov Vladislav , Siebenhühner Felix , Nobili Lino , Breakspear Michael , Palva Satu , Palva J. Matias
Published: January 2022

Brain activity exhibits scale-free avalanche dynamics and power-law long-range temporal correlations (LRTCs) across the nervous system. This has been thought to reflect “brain criticality”, i.e., brains operating near a critical phase transition between disorder and excessive order. Neuronal activity is, however, metabolically costly and may be constrained by activity-limiting mechanisms and resource depletion, which could make the phase transition discontinuous and bistable. Observations of bistability in awake human brain activity have nonetheless remained scarce and its functional significance unclear. First, using computational modelling where bistable synchronization dynamics emerged through local positive feedback, we found bistability to occur exclusively in a regime of critical-like dynamics. We then assessed bistability in vivo with resting-state magnetoencephalography and stereo-encephalography. Bistability was a robust characteristic of cortical oscillations throughout frequency bands from δ (3-7 Hz) to high-γ (100-225 Hz). As predicted by modelling, bistability and LRTCs were positively correlated. Importantly, while moderate levels of bistability were positively correlated with executive functioning, excessive bistability was associated with epileptic pathophysiology and predictive of local epileptogenicity. Critical bistability is thus a salient feature of spontaneous human brain dynamics in awake resting-state and is both functionally and clinically significant. These findings expand the framework of brain criticality and show that critical-like neuronal dynamics in vivo involves both continuous and discontinuous phase transitions in a frequency-, neuroanatomy-, and state-dependent manner.
High-throughput direct screening of restriction endonuclease using microfluidic fluorescence-activated drop sorter based on SOS response in E. coli
Authors: Zhang Yizhe , Agresti Jeremy J. , Zheng Yu , Weitz David A.
Published: January 2022

A restriction endonuclease (RE) is an enzyme that can recognize a specific DNA sequence and cleave that DNA into fragments with double-stranded breaks. This sequence-specific cleaving ability and its ease of use have made REs commonly used tools in molecular biology since their first isolation and characterization in 1970s. While artificial REs still face many challenges in large-scale synthesis and precise activity control for practical use, searching for new REs in natural samples remains a viable route for expanding the RE pool for fundamental research and industrial applications. In this paper, we propose a new strategy to search for REs in an efficient fashion. Briefly, we construct a host bacterial cell to link the RE genotype to the phenotype of β-galactosidase expression based on the bacterial SOS response, and use a high-throughput microfluidic platform to isolate, detect and sort the REs. We employ this strategy to screen for the XbaI gene from constructed libraries of varied sizes. In single round of sorting, a 30-fold target enrichment was obtained within 1 h. The direct screening approach we propose shows potential for efficient search of desirable REs in natural samples compared to the conventional RE-screening method, and is amenable to being adapted to high-throughput screening of other genotoxic targets.
PCR-free, label-free detection of sequence-specific DNA with single-molecule sensitivity using in vitro N-hybrid system in microfluidic drops
Authors: Zhang Yizhe , Weitz David A.
Published: January 2022

We propose a novel method that can detect DNA with high specificity at the single-molecule level by employing the in vitro N-hybrid strategy realized in sub-picoliter microfluidic drops. It detects target DNA based on the specific interactions of the target-encoded proteins with their partner molecules, and achieves single-molecule sensitivity via signal-transduction and signal-amplification during gene-expression processes in a sub-picoliter droplet, therefore effectively avoiding complicated procedures in labeling-based methods or biases and artifacts in PCR-based methods.
Two subsets of circulating Ly6Clo monocytes distinguished by CD138 (syndecan-1) expression and Nr4a1 dependence in pristane-treated mice
Authors: Han Shuhong , Zhuang Haoyang , Arja Rawad Daniel , Reeves Westley H.
Published: January 2022

Chronic peritoneal inflammation following pristane injection induces lupus with diffuse alveolar hemorrhage (DAH) and pulmonary capillaritis in C57BL/6 mice. The pathogenesis involves pristane-induced microvascular lung injury. BALB/c mice are resistant to endothelial injury and DAH. Lung disease in C57BL/6 mice is abolished by depleting monocytes/macrophages. The objective of this study was to define the role of myeloid subsets in DAH. Hemorrhage and vasculitis were abolished in Ccr2-/- mice, indicating involvement of bone marrow-derived monocytes/macrophages. Along with Ly6Chi monocytes, we found two subsets of circulating Ly6Clo monocytes: one CD138- and a novel CD138+ subset. Nr4a1-dependent patrolling Ly6Clo monocytes maintain vascular integrity after endothelial injury. Circulating Ly6CloCD138+ monocytes were associated with DAH and were absent in mice without DAH. They also were absent in Nr4a1-/- mice, whereas Ly6CloCD138- monocytes were unaffected. However, Nr4a1-/- mice were susceptible to pristane-induced DAH and lung vasculitis, suggesting that disease onset does not require Ly6CloCD138- monocytes. Peritoneal Ly6CloCD138+ Mϕ were unchanged in Nr4a1-/- mice, indicating that they are not derived from Ly6CloCD138+ monocytes. We conclude that pristane-induced lung microvascular lung injury stimulates a wave of Nr4h1-dependent Ly6CloCD138+ patrolling monocytes in an ineffectual effort to maintain vascular integrity in the face of ongoing endothelial damage.
Differential response ofCandidaspecies morphologies and isolates to fluconazole and boric acid
Authors: Salama Ola E. , Gerstein Aleeza C.
Published: January 2022

Candida albicansis the most prevalent cause of vulvovaginal candidiasis (‘yeast infection’) and recurrent vulvovaginal candidiasis, though the incidence of non-albicans yeast species is increasing. The azole fluconazole is the primary antifungal drug used to treat R/VVC yet isolates from some species have intrinsic resistance to fluconazole, and recurrent infection can occur even with fluconazole-susceptible populations. The second-line broad-spectrum antimicrobial drug, boric acid, is an alternative treatment that has been found to successfully treat complicated VVC infections. Far less is known about how boric acid inhibits growth of yeast isolates in different morphologies compared to fluconazole. We found significant differences in drug resistance and drug tolerance (the ability of a subpopulation to grow slowly in high levels of drug) betweenC. albicans, C. glabrata, andC. parapsilosisisolates, with the specific relationships dependent on both drug and phenotype. Population-level variation for both susceptibility and tolerance was broader for fluconazole than boric acid in all species. Unlike fluconazole, which neither prevented hyphal formation nor disrupted mature biofilms, boric acid inhibitedC. albicanshyphal formation and reduced mature biofilm biomass and metabolic activity in all isolates in a dose-dependent manner. Variation in planktonic response did not generally predict biofilm phenotypes. Overall, our findings illustrate that boric acid is broadly effective at inhibiting growth across many isolates and morphologies, which could explain why it is an effective treatment for R/VVC.
Independent morphological variables correlate with Aging, Mild Cognitive Impairment, and Alzheimer’s Disease
Authors: de Moraes Fernanda Hansen Pacheco , Sudo Felipe , Carneiro Marina Monteiro , de Melo Bruno R. P. , Mattos Paulo , Mota Bruno , Tovar-Moll Fernanda
Published: January 2022

This manuscript presents a study with recruited volunteers that comprehends three sorts of events present in Alzheimer’s Disease (AD) evolution (structural, biochemical, and cognitive) to propose an update in neurodegeneration biomarkers for AD. The novel variables, K, I, and S, suggested based on physics properties and empirical evidence, are defined by power-law relations between cortical thickness, exposed and total area, and natural descriptors of brain morphology. Our central hypothesis is that variable K, almost constant in healthy human subjects, is a better discriminator of a diseased brain than the current morphological biomarker, Cortical Thickness, due to its aggregated information. We extracted morphological features from 3T MRI T1w images of 123 elderly subjects: 77 Healthy Cognitive Unimpaired Controls (CTL), 33 Mild Cognitive Impairment (MCI) patients, and 13 Alzheimer’s Disease (AD) patients. Moreover, Cerebrospinal Fluid (CSF) biomarkers and clinical data scores were correlated with K, intending to characterize health and disease in the cortex with morphological criteria and cognitive-behavioral profiles. K distinguishes Alzheimer’s Disease, Mild Cognitive Impairment, and Healthy Cognitive Unimpaired Controls globally and locally with reasonable accuracy (CTL-AD, 0.82; CTL-MCI, 0.58). Correlations were found between global and local K associated with clinical behavioral data (executive function and memory assessments) and CSF biomarkers (t-Tau, Aβ-40, and Aβ-42). The results suggest that the cortical folding component, K, is a premature discriminator of healthy aging, Mild Cognitive Impairment, and Alzheimer’s Disease, with significant differences within diagnostics. Despite the non-concomitant events, we found correlations between brain structural degeneration (K), cognitive tasks, and biochemical markers.
Detection and categorization of severe cardiac disorders based solely on pulse interval measurements
Authors: Shinomoto Shigeru , Tsubo Yasuhiro , Marunaka Yoshinori
Published: January 2022

Cardiac disorders are common conditions associated with a high mortality rate. Due to their potential for causing serious symptoms, it is desirable to constantly monitor cardiac status using an accessible device such as a smartwatch. While electrocardiograms (ECGs) can make the detailed diagnosis of cardiac disorders, the examination is typically performed only once a year for each individual during health checkups, and it requires expert medical practitioners to make comprehensive judgments. Here we describe a newly developed automated system for alerting individuals about cardiac disorders solely based on pulse interval measurements. For this purpose, we examined two metrics of heart rate variability (HRV) and analyzed 1-day ECG recordings of more than 1,000 subjects in total. We found that a newly introduced metric of local variation was more efficient than conventional HRV metrics for detecting premature contraction, and furthermore, that a suitable combination of the old and new metrics resulted in much superior detectability particularly for atrial fibrillation, which requires more attention. Even with a 1-minute recording of pulse intervals, our new detection system had a diagnostic performance even better than that of the conventional analysis method applied to a 1-day recording.
Hydroxychloroquine/chloroquine for the treatment of hospitalized patients with COVID-19: An individual participant data meta-analysis
Authors: Di Stefano Leon , Ogburn Elizabeth L. , Ram Malathi , Scharfstein Daniel O. , Li Tianjing , Khanal Preeti , Baksh Sheriza N. , McBee Nichol , Gruber Joshua , Gildea Marianne R. , Clark Megan R. , Goldenberg Neil A. , Bennani Yussef , Brown Samuel M. , Buckel Whitney R. , Clement Meredith E. , Mulligan Mark J. , O’Halloran Jane A. , Rauseo Adriana M. , Self Wesley H. , Semler Matthew W. , Seto Todd , Stout Jason E. , Ulrich Robert J. , Victory Jennifer , Bierer Barbara E. , Hanley Daniel F. , Freilich Daniel
Published: January 2022

Background

Results from observational studies and randomized clinical trials (RCTs) have led to the consensus that hydroxychloroquine (HCQ) and chloroquine (CQ) are not effective for COVID-19 prevention or treatment. Pooling individual participant data, including unanalyzed data from trials terminated early, enables more detailed investigation of the efficacy and safety of HCQ/CQ among subgroups of hospitalized patients.

Methods

We searched ClinicalTrials.gov in May and June 2020 for US-based RCTs evaluating HCQ/CQ in hospitalized COVID-19 patients in which the outcomes defined in this study were recorded or could be extrapolated. The primary outcome was a 7-point ordinal scale measured between day 28 and 35 post enrollment; comparisons used proportional odds ratios. Harmonized de-identified data were collected via a common template spreadsheet sent to each principal investigator. The data were analyzed by fitting a prespecified Bayesian ordinal regression model and standardizing the resulting predictions.

Results

Eight of 19 trials met eligibility criteria and agreed to participate. Patient-level data were available from 770 participants (412 HCQ/CQ vs 358 control). Baseline characteristics were similar between groups. We did not find evidence of a difference in COVID-19 ordinal scores between days 28 and 35 post-enrollment in the pooled patient population (odds ratio, 0.97; 95% credible interval, 0.76-1.24; higher favors HCQ/CQ), and found no convincing evidence of meaningful treatment effect heterogeneity among prespecified subgroups. Adverse event and serious adverse event rates were numerically higher with HCQ/CQ vs control (0.39 vs 0.29 and 0.13 vs 0.09 per patient, respectively).

Conclusions

The findings of this individual participant data meta-analysis reinforce those of individual RCTs that HCQ/CQ is not efficacious for treatment of COVID-19 in hospitalized patients.
Plasma SARS-CoV-2 RNA levels as a biomarker of lower respiratory tract SARS-CoV-2 infection in critically ill patients with COVID-19
Authors: Jacobs Jana L. , Naqvi Asma , Shah Faraaz A. , Boltz Valerie F. , Kearney Mary F. , McVerry Bryan J. , Ray Prabir , Schaefer Caitlin , Fitzpatrick Meghan , Methé Barbara , Lee Janet , Morris Alison , Mellors John W. , Kitsios Georgios D. , Bain William
Published: January 2022

Plasma SARS-CoV-2 viral RNA (vRNA) levels are predictive of COVID-19 outcomes in hospitalized patients, but whether plasma vRNA reflects lower respiratory tract (LRT) vRNA levels is unclear. We compared plasma and LRT vRNA levels in simultaneously collected longitudinal samples from mechanically-ventilated patients with COVID-19. LRT and plasma vRNA levels were strongly correlated at first sampling (r=0.83, p<10−8) and then declined in parallel except in non-survivors who exhibited delayed vRNA clearance in LRT samples. Plasma vRNA measurement may offer a practical surrogate of LRT vRNA burden in critically ill patients, especially early in severe disease.
Medical domain knowledge in domain-agnostic generative AI
Authors: Kather Jakob Nikolas , Laleh Narmin Ghaffari , Foersch Sebastian , Truhn Daniel
Published: January 2022

The text-guided diffusion model GLIDE (Guided Language to Image Diffusion for Generation and Editing) is the state of the art in text-to-image generative artificial intelligence (AI). GLIDE has rich representations, but medical applications of this model have not been systematically explored. If GLIDE had useful medical knowledge, it could be used for medical image analysis tasks, a domain in which AI systems are still highly engineered towards a single use-case. Here we show that the publicly available GLIDE model has reasonably strong representations of key topics in cancer research and oncology, in particular the general style of histopathology images and multiple facets of diseases, pathological processes and laboratory assays. However, GLIDE seems to lack useful representations of the style and content of radiology data. Our findings demonstrate that domain-agnostic generative AI models can learn relevant medical concepts without explicit training. Thus, GLIDE and similar models might be useful for medical image processing tasks in the future - particularly with additional domain-specific fine-tuning.
Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma
Authors: Thind Amarinder S. , Ashford Bruce , Strbenac Dario , Gupta Ruta , Clark Jonathan R , Iyer N. Gopalakrishna , Mitchell Jenny , Lee Jenny , Mueller Simon A , Minaei Elahe , Perry Jay R. , Ranson Marie
Published: January 2022

Metastatic cutaneous squamous cell carcinoma (cSCC) is a highly morbid disease requiring radical surgery and adjuvant therapy that is associated with reduced overall survival. Yet compared to other advanced malignancies, relatively little is known of the genomic landscape of metastatic cSCC. We have previously reported the mutational signatures and mutational patterns of CCCTC-binding factor (CTCF) regions in metastatic cSCC. However, many other genomic components (indel signatures, non-coding drivers, and structural variants) of metastatic cSCC have not been reported. To this end, we performed whole genome sequencing on lymph node metastases and blood DNA from 25 cSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic cSCC.

In the noncoding genome, 3’UTR regions ofEVC(48% of specimens),PPP1R1A(48% of specimens) andABCA4(20% of specimens) along with the tumor-suppressing lncRNA LINC01003 (64% of specimens) were significantly functionally altered (Q-value < 0.05) and represent potential noncoding biomarkers of cSCC. Recurrent copy number loss in the tumor suppressor genePTPRDwas observed. Gene amplification was much less frequent and few genes were recurrently amplified. Single nucleotide variants driver analyses from 3 tools confirmedTP53andCDKN2Aas recurrently mutated genes but also identifiedC9as potential novel driver in this disease. Further, indel signature analysis highlighted the dominance of ID signature 13 (ID13) followed by ID8 and ID9. ID 9 has previously been shown to have no association with skin melanoma, unlike ID 13 and 8, suggesting a novel pattern of indel variation in metastatic cSCC. The enrichment analysis of various genetically altered candidates shows enrichment of ‘TGF-beta regulation of extracellular matrix’ and ‘Cell cycle G1 to S check points’. These enriched terms are associated with genetic instability, cell proliferation, and migration providing mechanisms of genomic drivers of metastatic cSCC.
Recognition of HIV-1 Capsid Licenses Innate Immune Response to Viral Infection
Authors: Yoh Sunnie M , Mamede João I. , Lau Derrick , Ahn Narae , Sánchez-Aparicio Maria T , Temple Joshua , Tuckwell Andrew , Fuchs Nina V. , Cianci Gianguido C. , Riva Laura , Curry Heather , Yin Xin , Gambut Stéphanie , Simons Lacy M. , Hultquist Judd F. , König Renate , Xiong Yong , García-Sastre Adolfo , Böcking Till , Hope Thomas J. , Chanda Sumit K.
Published: January 2022

Cyclic GMP-AMP synthase (cGAS) is a primary sensor of aberrant DNA that governs an innate immune signaling cascade, leading to the induction of the type-I interferon response. We have previously identified polyglutamine binding protein 1, PQBP1, as an adaptor molecule required for cGAS-mediated innate immune response of lentiviruses, including the human immunodeficiency virus 1 (HIV-1), but dispensable for the recognition of DNA viruses. HIV-1- encoded DNA is synthesized as a single copy from its RNA genome, and is subsequently integrated into the host chromatin. HIV-1 then produces progeny through amplification and packaging of its RNA genome, thus, in contrast to DNA viruses, HIV-1 DNA is both transient and of low abundance. However, the molecular basis for the detection and verification of this low abundance HIV-1 DNA pathogen-associated molecular pattern (PAMP) is not understood. Here, we elucidate a two-factor authentication strategy that is employed by the innate immune surveillance machinery to selectively respond to the low concentration of PAMP, while discerning these species from extranuclear DNA molecules. We find that, upon HIV-1 infection, PQBP1 decorates intact viral capsid, which serves as a primary verification step for the viral nucleic acid cargo. As the reverse transcription and capsid disassembly initiate, cGAS protein is then recruited to the capsid in a PQBP1-dependent manner, enabling cGAS molecules to be co-positioned at the site of PAMP generation. Thus, these data indicate that PQBP1 recognition of the HIV-1 capsid sanctions a robust cGAS-dependent response to a limited abundance and short-lived DNA PAMP. Critically, this illuminates a molecular strategy wherein the modular recruitment of co-factors to germline encoded pattern recognition receptors (PRRs) serves to enhance repertoire of pathogens that can be sensed by the innate immune surveillance machinery.
Potent protease inhibitors of deadly lagoviruses: rabbit hemorrhagic disease virus and European brown hare syndrome virus
Authors: Perera Krishani Dinali , Johnson David , Lovell Scott , Groutas William , Chang Kyeong-Ok , Kim Yunjeong
Published: January 2022

Rabbit hemorrhagic disease (RHD) and European brown hare syndrome (EBHS) are highly contagious diseases caused by lagoviruses in theCaliciviridaefamily and mainly affect rabbits and hares, respectively. These infectious diseases are associated with high mortality and a serious threat to domesticated and wild rabbits and hares, including endangered species such as Riparian brush rabbits. In the US, only isolated cases of RHD had been reported until Spring 2020. However, RHD caused by RHD type 2 virus (RHDV2) was unexpectedly reported in April 2020 in New Mexico and has subsequently spread to several US states infecting wild rabbits and hares, making it highly likely that RHD will become endemic in the US. Vaccines are available for RHD, however, there is no specific treatment for these diseases. RHDV and EBHSV encode a 3C-like protease (3CLpro), which is essential for virus replication and a promising target for antiviral drug development. We have previously generated focused small molecule libraries of 3CLpro inhibitors and demonstrated thein vitropotency andin vivoefficacy of some protease inhibitors against viruses that encode 3CLpro including caliciviruses and coronaviruses. Here we established the enzyme and cell-based assays for these uncultivable viruses to determine thein vitroactivity of 3CLpro inhibitors, including GC376, a protease inhibitor being developed for feline infectious peritonitis, and identified potent inhibitors of RHDV1 and 2 and EBHSV. In addition, structure-activity relationship study and homology modelling of the 3CLpros and inhibitors revealed that lagoviruses share similar structural requirements for 3CLpro inhibition with other caliciviruses.
The Salmonella transmembrane effector SteD hijacks AP1-mediated vesicular trafficking for delivery to antigen-loading MHCII compartments
Authors: Godlee Camilla , Cerny Ondrej , Liu Mei , Blundell Samkeliso , Gallagher Alanna E. , Shahin Meriam , Holden David W.
Published: January 2022

SteD is a transmembrane effector of the Salmonella SPI-2 type III secretion system that inhibits T cell activation by reducing the amounts of at least three proteins – major histocompatibility complex II (MHCII), CD86 and CD97 – from the surface of antigen-presenting cells. SteD specifically localises at the trans-Golgi network (TGN) and MHCII compartments; however, the targeting, membrane integration and trafficking of SteD are not understood. Using systematic mutagenesis, we identify distinct regions of SteD that are required for these processes. We show that SteD integrates into membranes of the ER/Golgi through a two-step mechanism of membrane recruitment from the cytoplasm followed by integration. SteD then migrates to and accumulates within the TGN. From here it hijacks the host adaptor protein (AP)1-mediated trafficking pathway from the TGN to MHCII compartments. AP1 binding and post-TGN trafficking require a short sequence in the N-terminal cytoplasmic tail of SteD that resembles the AP1-interacting dileucine sorting signal, but in inverted orientation, suggesting convergent evolution.
Live imaging of Yersinia translocon formation and immune recognition in host cells
Authors: Rudolph Maren , Carsten Alexander , Aepfelbacher Martin , Wolters Manuel
Published: January 2022

Yersinia enterocolitica employs a type three secretion system (T3SS) to translocate immunosuppressive effector proteins into host cells. To this end, the T3SS assembles a translocon/pore complex composed of the translocator proteins YopB and YopD in host cell membranes serving as an entry port for the effectors. The translocon is formed in a Yersinia-containing pre-phagosomal compartment that is connected to the extracellular space. As the phagosome matures, the translocon and the membrane damage it causes are recognized by the cell-autonomous immune system. We infected cells in the presence of fluorophore-labeled ALFA-tag-binding nanobodies with a Y. enterocolitica strain expressing YopD labeled with an ALFA-tag. Thereby we could record the integration of YopD into translocons and its intracellular fate in living host cells. YopD was integrated into translocons around 2 min after uptake of the bacteria into a phosphatidylinositol-4,5-bisphosphate enriched pre-phagosomal compartment and remained there for 27 min on average. Damaging of the phagosomal membrane as visualized with recruitment of GFP-tagged galectin-3 occurred in the mean around 14 min after translocon formation. Shortly after recruitment of galectin-3, guanylate-binding protein 1 (GBP-1) was recruited to phagosomes, which was accompanied by a decrease in the signal intensity of translocons, suggesting their degradation. In sum, we were able for the first time to film the spatiotemporal dynamics of Yersinia T3SS translocon formation and degradation and its sensing by components of the cell-autonomous immune system.
Privacy-Preserving Federated Neural Network Learning for Disease-Associated Cell Classification
Authors: Sav Sinem , Bossuat Jean-Philippe , Troncoso-Pastoriza Juan R. , Claassen Manfred , Hubaux Jean-Pierre
Published: January 2022

Training accurate and robust machine learning models requires a large amount of data that is usually scattered across data-silos. Sharing or centralizing the data of different healthcare institutions is, however, unfeasible or prohibitively difficult due to privacy regulations. In this work, we address this problem by using a novel privacy-preserving federated learning-based approach, PriCell, for complex machine learning models such as convolutional neural networks. PriCell relies on multiparty homomorphic encryption and enables the collaborative training of encrypted neural networks with multiple healthcare institutions. We preserve the confidentiality of each institutions’ input data, of any intermediate values, and of the trained model parameters. We efficiently replicate the training of a published state-of-the-art convolutional neural network architecture in a decentralized and privacy-preserving manner. Our solution achieves an accuracy comparable to the one obtained with the centralized solution, with an improvement of at least one-order-of-magnitude in execution time with respect to prior secure solutions. Our work guarantees patient privacy and ensures data utility for efficient multi-center studies involving complex healthcare data.
Anti-thrombotic treatment enhances antibiotic efficiency in a humanized model of meningococcemia
Authors: Corre Jean-Philippe , Obino Dorian , Nivoit Pierre , Yatim Aline , Schmitt Taliah , Duménil Guillaume
Published: January 2022

Meningococcal infections remain particularly difficult to treat. Despite antibiotic therapy, the state of the patients often rapidly deteriorates. Early clinical studies suggest that meningococci acquire a form of resistance to antibiotic treatments during infections. Taking advantage of a humanized animal model of infection, we confirm that adherent bacteria become highly resistant to antibiotic treatments as early as 3-6 hours post infection, although fully sensitivein vitro. Within this time frame, meningococci adhere to the endothelium via their type IV pili, proliferate and eventually fill the vessel lumen. Using intravital imaging, we show that rapidly upon infection blood flow is dramatically decreased, thus limiting antibiotic access to infected vessels. Concomitantly, fibrin is deposited inside infected vessels in proximity to bacterial aggregates. Pharmacologically impairing thrombin generation by inhibiting Factor X activity not only improves blood flow in infected vessels, but also enhances the efficacy of the antibiotic treatment. Our results indicate that the combined administration of anticoagulants together with antibiotics might represent a therapeutic approach to treat meningococcal sepsis more efficiently.
Establishment of a transparent soil system to study Bacillus subtilis chemical ecology
Authors: Lozano-Andrade Carlos N. , Nogueira Carla G. , Wibowo Mario , Kovács Ákos T.
Published: January 2022

Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.
Bacterial lifestyle switch in response to algal metabolites
Authors: Barak-Gavish Noa , Dassa Bareket , Kuhlisch Constanze , Nussbaum Inbal , Rosenberg Gili , Avraham Roi , Vardi Assaf
Published: January 2022

Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly recognized that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during its interaction with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. To unravel the bacterial lifestyle switch, we profiled bacterial transcriptomes in response to infochemicals derived from algae in exponential and stationary growth, which induced the Sulfitobacter D7 coexistence and pathogenicity lifestyles, respectively. We found that algal dimethylsulfoniopropionate (DMSP) was a pivotal signaling molecule that mediated the transition between the lifestyles. However, the coexisting and pathogenic lifestyles were evident only in the presence of additional algal metabolites. In the pathogenic mode, Sulfitobacter D7 upregulated flagellar motility and many transport systems, presumably to maximize assimilation of E. huxleyi-derived metabolites released by algal cells upon cell death. Specifically, we discovered that algae-produced benzoate promoted the growth of Sulfitobacter D7, and negated the DMSP-inducing lifestyle switch to pathogenicity, demonstrating that benzoate is important for maintaining the coexistence of algae and bacteria. We propose that bacteria can sense the physiological status of the algal host through changes in the metabolic composition, which will determine the bacterial lifestyle during the interactions.

Significance Statement

Microorganisms in the marine environment play crucial roles in the regulation of Earth’s climate and elemental cycling. Understanding microbial interactions and the metabolic exchange that drives them is necessary for disentangling the complexity of the marine ecosystem. Here we demonstrate how the opportunistic pathogen Sulfitobacter D7 switches its lifestyle from coexistence to pathogenicity in response to metabolites released by Emiliania huxleyi, a bloom-forming unicellular alga. By mapping bacterial transcriptional profiles, we show that the algal metabolite dimethylsulfoniopropionate (DMSP), an important signaling molecule in the marine environment, is essential for the bacterial lifestyle switch. However, the activity of DMSP depended on additional algal signals. This work emphasizes how metabolic crosstalk can influence the nature and fate of microbial interactions, which have cascading effects on large-scale oceanic processes.