bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitation of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes
Authors: Garcia Audrey , Le Tri , Jankowski Paul , Yanaç Kadir , Yuan Qiuyan , Uyaguari-Díaz Miguel
Published: August 2021

We investigated the potential use and quantitation of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA and RNA enteric viruses, as well as theuidAgene found inEscherichia coliwere targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantitated in the extracted samples via quantitative PCR using TaqMan assays.

The average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.0547 and 0.7986) than the average gene copies assessed in the effluents for Adenovirus and crAssphage (DNA viruses), Pepper Mild Mottle Virus (RNA virus), anduidAin terms of both volume and biomass. A significant reduction of these enteric viruses was observed consistently in activated sludge samples compared with those for raw sewage. Corresponding reductions in gene copies per volume and gene copies per biomass were also seen foruidAbut were not statistically significant (p-value = 0.8769 and p-value = 0.6353, respectively). The higher gene copy numbers of enteric viruses andE. coliobserved in the effluents may be associated with the 12-hour hydraulic retention time in the facility. Enteric viruses found in gene copy numbers were at least one order of magnitude higher than theE. colimarkeruidA. This indicate that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used as complementary viral indicators of human fecal pollution.
Bursting emerges from the complementary roles of neurons in a four-cell network
Authors: Sakurai Akira , Katz Paul S.
Published: August 2021

Reciprocally inhibitory modules that form half-center oscillators require mechanisms for escaping or being released from inhibition. The central pattern generator (CPG) underlying swimming by the nudibranch mollusc, Dendronotus iris, is composed of only four neurons that are organized into two competing modules of a half center oscillator. In this system, bursting activity in left-right alternation is not driven by any of the neurons but is an emergent property of the network as a whole. We found that the unique synaptic actions and membrane properties of the two neurons in each module (Si2 and Si3) play complementary roles in generating stable bursting in this network oscillator. Only Si2 evokes fast and strong inhibition of its contralateral counterpart, the termination of which initiates post-inhibitory rebound in the Si3 of that module. Only Si3 is responsible for the rebound excitation because it has a hyperpolarization-activated inward current. Within each module, the synaptic actions and membrane properties of the two neurons complement each other: Si3 excites Si2, which then feeds back slow inhibition to Si3, terminating the burst. Using dynamic clamp, we showed that the magnitude of the slow inhibition sets the period of the oscillator. Thus, the synaptic actions of Si2 provide the hyperpolarization needed for the other module to rebound stably, whereas the membrane properties of Si3 in each module cause it to rebound first and excite Si2 and maintain the burst until the cycle repeats and the other module becomes active.
Altered interpersonal distance regulation in autism spectrum disorder
Authors: Farkas Kinga , Pesthy Orsolya , Guttengéber Anna , Weigl Anna Szonja , Veres András , Szekely Anna , Komoróczy Eszter , Szuromi Bálint , Janacsek Karolina , Réthelyi János M. , Németh Dezső
Published: August 2021

Interpersonal distance regulation is an essential element of social communication. Its impairment in autism spectrum disorder (ASD) is widely acknowledged among practitioners, but only a handful of studies reported empirical research in real-life settings focusing mainly on children. Interpersonal distance in adults with ASD and related autonomic functions received less attention. Here, we measured interpersonal distance along with heart rate variability (HRV) in adults with ASD, and tested the modulatory effects of eye-contact and attribution. Twenty-two adults diagnosed with ASD and 21 matched neurotypical controls participated in our study from 2019 October to 2020 February. Our experimental design combined the modified version of the stop distance paradigm with HRV measurement controlling for eye contact between the experimenter and the participant to measure interpersonal distance. Our results showed a greater preferred distance in ASD. These results were altered with eye contact. Moreover, we found lower baseline HRV and reduced HRV reactivity in ASD; however, these autonomic measurements could not predict preferred interpersonal distance. Our study highlights the importance of interpersonal space regulation in ASD and the need for sophisticated experimental designs to grasp the complexity and underlying factors of distance regulation in typical and atypical populations.
Preterm birth rates during the COVID-19 lockdown in Queensland Australia
Authors: Jasper Brittany , Stillerova Tereza , Anstey Christopher , Weaver Edward
Published: August 2021

Background

Preventative strategies for preterm birth are lacking. Recent evidence proposed COVID-19 lockdowns may have contributed to changes in preterm birth. We aimed to determine the prevalence of preterm birth during the COVID-19 lockdown on the Sunshine Coast and in the state of Queensland, Australia.

Methods

Retrospective cohort analysis of all births in Queensland including the Sunshine Coast University Hospital, during two epochs, April 1–May 31, 2020 (lockdown) and June 1–July 31, 2020 (post-lockdown), compared to antecedent calendar-matched periods in 2018–2019. Prevalence of preterm birth, stillbirth, and late terminations were examined.

Results

There were 64,989 births in Queensland from April to July 2018–2020. At the Sunshine Coast University Hospital, there was a significantly higher chance of birth at term during both lockdown (OR 1.81, 95% CI 1.17, 2.79; P=0.007) and post-lockdown (OR 2.01, 95% CI 1.27, 3.18; P=0.003). At the same centre, prevalence of preterm birth was 5.5% (30/547) during lockdown, compared to 9.1% (100/1095) in previous years, a 40.0% relative reduction (P=0.016). At this centre during lockdown, emergency caesareans concurrently decreased (P=0.034) and vacuum-assisted births increased (P=0.036). In Queensland overall, there was a nonsignificant decrease in the prevalence of preterm birth during lockdown.

Conclusions

There is a link between lockdown and a reduction in the prevalence of preterm birth on the Sunshine Coast. The cause is speculative. Further research is needed to determine a causal link and assess if this can be translated into management which provides a sustained reduction in preterm birth and its associated morbidity and mortality.
Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production
Authors: Gamble Caitlin , Bryant Drew , Carrieri Damian , Bixby Eli , Dang Jason , Marshall Jacob , Doughty David , Colwell Lucy , Berndl Marc , Roberts James , Frumkin Michael
Published: August 2021

Background

Arthrospira platensis (commonly known as spirulina) is a promising new platform for low-cost manufacturing of biopharmaceuticals. However, full realization of the platform’s potential will depend on achieving both high growth rates of spirulina and high expression of therapeutic proteins.

Objective

We aimed to optimize culture conditions for the spirulina-based production of therapeutic proteins.

Methods

We used a machine learning approach called Bayesian black-box optimization to iteratively guide experiments in 96 photobioreactors that explored the relationship between production outcomes and 17 environmental variables such as pH, temperature, and light intensity.

Results

Over 16 rounds of experiments, we identified key variable adjustments that approximately doubled spirulina-based production of heterologous proteins, improving volumetric productivity between 70% to 100% in multiple bioreactor setting configurations.

Conclusion

An adaptive, machine learning-based approach to optimize heterologous protein production can improve outcomes based on complex, multivariate experiments, identifying beneficial variable combinations and adjustments that might not otherwise be discoverable within high-dimensional data.
CRISPR-Cas9-mediated Large Cluster Deletion and Multiplex Genome Editing in Paenibacillus polymyxa
Authors: Meliawati Meliawati , Teckentrup Christa , Schmid Jochen
Published: August 2021

The use of molecular tools based on the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems has rapidly advanced genetic engineering. These molecular biological tools have been applied for different genetic engineering purposes in multiple organisms, including the quite rarely explored Paenibacillus polymyxa. However, only limited studies on large cluster deletion and multiplex genome editing have been described for this highly interesting and versatile bacterium. Here, we demonstrate the utilization of a Cas9-based system to realize targeted deletions of four biosynthetic gene clusters in the range of 12 kb to 41 kb by the use of a single targeting sgRNA. Furthermore, we also harness the system for multiplex editing of genes and large genomic regions. Multiplex deletion was achieved with more than 80 % efficiency, while simultaneous integration at two distantly located sites was obtained with 58 % efficiency. The findings reported in this study are anticipated to accelerate future research in P. polymyxa and related species.
Robust somatic copy number estimation using coarse-to-fine segmentation
Authors: Culibrk Luka , Grewal Jasleen K , Pleasance Erin D , Williamson Laura , Mungall Karen , Laskin Janessa , Marra Marco A , Jones Steven JM
Published: August 2021

Cancers routinely exhibit chromosomal instability that results in copy number variants (CNVs), namely changes in the abundance of genomic material. Unfortunately, the detection of these variants in cancer genomes is difficult. We present Ploidetect, a software package that effectively identifies CNVs within whole-genome sequenced tumors. Ploidetect utilizes a coarse-to-fine segmentation approach which yields highly contiguous segments while allowing for focal CNVs to be detected with high sensitivity. We benchmark Ploidetect against popular CNV tools using synthetic data, cell line data, and real-world metastatic tumor data, and find an improvement in sensitivity and accuracy while maintaining low levels of oversegmentation. We show that the improved CNV sensitivity enables Ploidetect to recover recurrent homozygous deletions and genes associated with chromosomal instability in a multi-cancer cohort of 687 patients. Using highly contiguous CNV calls afforded by Ploidetect, we also demonstrate the use of segment N50 as a novel metric for the measurement of chromosomal instability within tumor biopsies. We propose that increasingly accurate determination of CNVs is critical for their productive study in cancer, and our work demonstrates advances made possible by progress in this regard.
An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs
Authors: Cook Ashley L. , Wyhs Nicolas , Sur Surojit , Ptak Blair , Popoli Maria , Dobbyn Laura , Papadopoulos Tasos , Bettegowda Chetan , Papadopoulos Nickolas , Vogelstein Bert , Zhou Shibin , Kinzler Kenneth W
Published: August 2021

We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation ofTP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.
Cryo-EM Structures of Prestin and the Molecular Basis of Outer Hair Cell Electromotility
Authors: Bavi Navid , Clark Michael David , Contreras Gustavo F. , Shen Rong , Reddy Bharat , Milewski Wieslawa , Perozo Eduardo
Published: August 2021

The voltage-dependent motor protein, Prestin (SLC26A5) is responsible for the electromotive behavior of outer hair cells (OHCs). Here, we determined the structure of dolphin Prestin in six distinct states using single particle cryo-electron microscopy. Structural and functional data suggest that Prestin adopts a unique and complex set of states, tunable by the identity of bound anions. Complexes with the inhibitor salicylate show that it competes for the anion-binding site of Prestin. These conformations reveal a novel mechanism of area expansion that depends on the helix flexibility and conformational transitions at the membrane protein interface and putatively affects the physical state of the surrounding membrane. These observations illuminate the structural basis of Prestin electromotility, a key component of the mammalian cochlear amplifier.
Predictive functionality of bacteria in naturally fermented milk products of India using PICRUSt2 and Piphillin pipelines
Authors: Shingling H. Nakibapher Jones , Tamang Jyoti Prakash
Published: August 2021

Naturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from MG-RAST/NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction. MUSiCC-normalized KOs and mapped KEGG pathways from both PICRUSt2 and Piphillin resulted in higher percentage of the former in comparison to the latter. Though, functional features were compared from both the pipelines, however, there were significant differences between the predictions. Therefore, a consolidated presentation of both the algorithms presented an overall outlook into the predictive functional profiles associated with the microbiota of the NFM products of India.
A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
Authors: White Richard J , Mackay Eirinn , Wilson Stephen W , Busch-Nentwich Elisabeth M
Published: August 2021

In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation.

Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation.

Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.
Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion
Authors: Fumagalli Valeria , Ravà Micol , Marotta Davide , Di Lucia Pietro , Laura Chiara , Sala Eleonora , Grillo Marta , Bono Elisa , Giustini Leonardo , Perucchini Chiara , Mainetti Marta , Sessa Alessandro , Garcia-Manteiga José M. , Donnici Lorena , Manganaro Lara , Delbue Serena , Broccoli Vania , De Francesco Raffaele , D’Adamo Patrizia , Kuka Mirela , Guidotti Luca G. , Iannacone Matteo
Published: August 2021

The development of a tractable small animal model faithfully reproducing human COVID-19 pathogenesis would arguably meet a pressing need in biomedical research. Thus far, most investigators have used transgenic mice expressing the human ACE2 in epithelial cells (K18-hACE2 transgenic mice) that are intranasally instilled with a liquid SARS-CoV-2 suspension under deep anesthesia. Unfortunately, this experimental approach results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this model’s usefulness. Here, we describe the use of an inhalation tower system that allows exposure of unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in SARS-CoV-2- infected patients. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.
Resistance to amitraz in the parasitic honey bee mite Varroa destructor is associated with mutations in the β−adrenergic-like octopamine receptor
Authors: Hernández-Rodríguez Carmen Sara , Moreno-Martí Sara , Almecija Gabrielle , Christmon Krisztina , Johnson Josephine D. , Ventelon Marie , vanEngelsdorp Dennis , Cook Steven C. , González-Cabrera Joel
Published: August 2021

Varroa destructor is considered a major reason for high loss rate of Western honey bee (Apis mellifera) colonies. To prevent colony losses caused by V. destructor it is necessary to actively manage the mite population. Beekeepers, particularly commercial beekeepers, have few alternative treatments other than synthetic acaricides to control the parasite, resulting in intensive treatment regimens that led to the evolution of resistance in mite populations.

To investigate the mechanism of the resistance to amitraz detected in V. destructor mites from French and U.S. apiaries, we identified and characterized octopamine and tyramine receptors (the known targets of amitraz) in this species. The comparison of sequences obtained from mites collected from different apiaries with different treatment regimens, showed that the amino acid substitutions N87S or Y215H in the OctβR were associated with treatment failures reported in French or U.S. apiaries, respectively. Based on our findings, we have developed and tested two high throughput diagnostic assays based on TaqMan® able to accurately detect mites carrying the mutations in this receptor. This valuable information may be of help for beekeepers when selecting the most suitable acaricide to manage V. destructor.
Older adults generalize their movements across walking contexts more than young during gradual and abrupt split-belt walking
Authors: Aucie Yashar , Harket Harrison. M. , Sombric Carly. J. , Torres-Oviedo Gelsy
Published: August 2021

Generalization of movements from experienced to novel situations is a critical aspect of motor learning. It has been demonstrated that the training period when a movement is learned influences the movement’s generalization to untrained situations. However, little is known about how healthy aging affects these processes. For example, young adults exhibit greater generalization of movements learned on a device (e.g. split-belt treadmill or robotic arm) to movements without it (e.g, overground walking or unconstrained reaching) when participants experience small vs. large perturbations on the training device. Here, we investigated whether a similar effect would be observed in older adults. To this end, we compared the generalization of split-belt adaptation to overground walking in older (75.9±4.8 years old) and young adults (24.7±5.9 years old) when adapted gradually (i.e., small perturbations) vs. abruptly (i.e., large perturbations). We found that both age groups adapted more to the abrupt condition compared to the gradual condition, which resulted in greater adaptation effects (i.e., aftereffects) on the treadmill in the abrupt than the gradual groups. We also found that older adults generalize more than young adults, regardless of the perturbation schedule (i.e., gradual or abrupt). Our results suggest that abrupt perturbations during adaptation do not limit the generalization of movement in older adults-perhaps because they are more likely to attribute them to their own faulty movements. These results suggest that large perturbations are better than small when training older clinical populations since abrupt disturbances would lead to more adaptation and generalization of corrected movements in older people.
Learning torus PCA based classification for multiscale RNA backbone structure correction with application to SARS-CoV-2
Authors: Wiechers Henrik , Eltzner Benjamin , Mardia Kanti V. , Huckemann Stephan F.
Published: August 2021

Motivation

Reconstructions of structure of biomolecules, for instance via X-ray crystallography or cryo-EM frequently contain clashes of atomic centers. Correction methods are usually based on simulations approximating biophysical chemistry, making them computationally expensive and often not correcting all clashes.

Results

We propose a computationally fast data-driven statistical method yielding suites free from within-suite clashes: From such a clash free training data set, devising mode hunting after torus PCA on adaptive cutting average linkage tree clustering (MINTAGE), we learn RNA suite shapes. With classification based on multiscale structure enhancement (CLEAN), for a given clash suite we determine its neighborhood on a mesoscopic scale involving several suites. As corrected suite we propose the Fréchet mean on a torus of the largest classes in this neighborhood. We validate CLEAN MINTAGE on a benchmark data set, compare it to a state of the art correction method and apply it, as proof of concept, to two exemplary suites adjacent to helical pieces of the frameshift stimulation element of SARS-CoV-2 which are difficult to reconstruct. In contrast to a recent reconstruction proposing several different structure models, CLEAN MINTAGE unanimously proposes structure corrections within the same clash free class for all suites.

Code Availability

https://gitlab.gwdg.de/henrik.wiechers1/clean-mintage-code
Increased PHOSPHO1 expression mediates cortical bone mineral density in renal osteodystrophy
Authors: Hsu Shun-Neng , Stephen Louise A , Dillon Scott , Milne Elspeth , Javaheri Behzad , Pitsillides Andrew A , Novak Amanda , Millán Jose Luis , Macrae Vicky E , Staines Katherine A , Farquharson Colin
Published: August 2021

Patients with advanced chronic kidney disease (CKD) often present with skeletal abnormalities; a condition known as renal osteodystrophy (ROD). While Tissue-nonspecific alkaline phosphatase (TNAP) and PHOSPHO1 are recognized to be critical for bone mineralization, their role in the etiology of ROD is unclear. To address this, ROD was induced in both wild-type and Phospho1 knockout (P1KO) mice using dietary adenine supplementation. The mice presented with hyperphosphatemia, hyperparathyroidism, and elevated levels of FGF23 and bone turnover markers. In particular, we noted that in CKD mice, bone mineral density (BMD) was increased in cortical bone (p < 0.05) but decreased in trabecular bone (p < 0.05). These changes were accompanied by decreased TNAP (p < 0.01) and increased PHOSPHO1 (p < 0.001) expression in wild-type CKD bones. In P1KO CKD mice, the cortical BMD phenotype was rescued, suggesting that the increased cortical BMD of CKD mice was driven by increased PHOSPHO1 expression. Other structural parameters were also improved in P1KO CKD mice. We further investigated the driver of the mineralization defects, by studying the effects of FGF23, PTH, and phosphate administration on PHOSPHO1 and TNAP expression by primary murine osteoblasts. We found both PHOSPHO1 and TNAP expression to be down-regulated in response to phosphate and PTH. While matrix mineralization was increased with phosphate (Pi), it decreased with PTH and FGF23 had no effect. The in vitro data suggest that the TNAP reduction in CKD-MBD is driven by the hyperphosphatemia and/or hyperparathyroidism noted in these mice, while the higher PHOSPHO1 expression may be a compensatory mechanism in an attempt to protect the bone from hypomineralization. We propose that increased PHOSPHO1 expression in ROD may contribute to the disordered skeletal mineralization characteristic of this progressive disorder.
Measuring the double-drift illusion and its resets with hand trajectories
Authors: ’t Hart Bernard Marius , Henriques Denise Y.P. , Cavanagh Patrick
Published: August 2021

If a gabor pattern drifts in one direction while its internal texture drifts in the orthogonal direction, its perceived position deviates further and further away from its true path. We first evaluated the illusion using manual tracking. Participants followed the gabor with a stylus on a drawing tablet that coincided optically with the horizontal monitor surface. Their hand and the stylus were not visible during the tracking. The magnitude of the tracking illusion corresponded closely to previous perceptual and pointing measures indicating that manual tracking is a valid measure for the illusion. This allowed us to use it in a second experiment to capture the behavior of the illusion as it eventually degrades and breaks down in single trials. Specifically, the deviation of the gabor stops accumulating at some point and either stays at a fixed offset or resets toward the veridical position. To report the perceived trajectory of the gabor, participants drew it after the gabor was removed from the monitor. Resets were detected and analyzed and their distribution matches neither a temporal nor a spatial limit, but rather a broad gamma distribution over time. This suggests that resets are triggered randomly, about once per 1.3 s, possible by extraneous distractions or eye movements.
Multispecies phase diagram of biofilm architectures reveals biophysical principles of biofilm development
Authors: Jeckel Hannah , Díaz-Pascual Francisco , Skinner Dominic J. , Song Boya , Jiménez-Siebert Eva , Jelli Eric , Vaidya Sanika , Dunkel Jörn , Drescher Knut
Published: August 2021

Bacterial biofilms are among the most abundant multicellular structures on Earth and play essential roles in a wide range of ecological, medical, and industrial processes. However, general principles that govern the emergence of biofilm architecture across different species remain unknown. Here, we combine experiments, simulations and statistical analysis to identify shared biophysical mechanisms that determine biofilm architecture development at the single-cell level, for the speciesVibrio cholerae, Escherichia coli, Salmonella enterica, andPseudomonas aeruginosa. Our data-driven analysis reveals that despite the many molecular differences between these species, the biofilm architecture differences can be described by only two control parameters: cellular aspect ratio and cell density. Further experiments using single-species mutants for which the cell aspect ratio and the cell density are systematically varied, and mechanistic simulations, show that tuning these two control parameters reproduces biofilm architectures of different species. Altogether, our results show that early-stage biofilm architecture is determined by mechanical cell-cell interactions which are conserved across different species and, therefore, provide a unifying understanding of biofilm architecture development.
Deep learning basedkcatprediction enables improved enzyme constrained model reconstruction
Authors: Li Feiran , Yuan Le , Lu Hongzhong , Li Gang , Chen Yu , Engqvist Martin K. M. , Kerkhoven Eduard J , Nielsen Jens
Published: August 2021

Enzyme turnover numbers (kcatvalues) are key parameters to understand cell metabolism, proteome allocation and physiological diversity, but experimentally measuredkcatdata are sparse and noisy. Here we provide a deep learning approach to predictkcatvalues for metabolic enzymes in a high-throughput manner with the input of substrate structures and protein sequences. Our approach can capturekcatchanges for mutated enzymes and identify amino acid residues with great impact onkcatvalues. Furthermore, we applied the approach to predict genome scalekcatvalues for over 300 yeast species, demonstrating that the predictedkcatvalues are consistent with current evolutional understanding. Additionally, we designed an automatic pipeline using the predictedkcatvalues to parameterize enzyme-constrained genome scale metabolic models (ecGEMs) facilitated by a Bayesian approach, which outperformed the default ecGEMs in predicting phenotypes and proteomes and enabled to explain phenotype differences among yeast species. The deep learningkcatprediction approach and automatic ecGEM construction pipeline would thus be a valuable tool to uncover the global trend of enzyme kinetics and physiological diversity, and to further elucidate cell metabolism on a large scale.
Membrane Fusion can be Driven by Sec18/NSF, Sec17/αSNAP, and trans-SNARE complex without HOPS
Authors: Song Hongki , Wickner William
Published: August 2021

Yeast vacuolar membrane fusion has been reconstituted with R, Qa, Qb, and Qc-family SNAREs, Sec17/αSNAP, Sec18/NSF, and the hexameric HOPS complex. HOPS tethers membranes and catalyzes SNARE assembly into RQaQbQc trans-complexes which zipper through their SNARE domains to promote fusion. Previously, we demonstrated that Sec17 and Sec18 can bypass the requirement of complete zippering for fusion (Song et al., 2021), but it has been unclear whether this activity of Sec17 and Sec18 is directly coupled to HOPS. HOPS can be replaced for fusion by a synthetic tether when the three Q-SNAREs are pre-assembled. We now report that SNARE zippering-arrested fusion intermediates that are formed without HOPS support Sec17/Sec18-triggered fusion. This zippering-bypass fusion is thus a direct result of Sec17 and Sec18 interactions: with each other, with the platform of partially zippered SNAREs, and with the apposed tethered membranes. As these fusion elements are shared among all exocytic and endocytic traffic, Sec17 and Sec18 may have a general role in directly promoting fusion.
In vitro tau aggregation inducer molecules influence the effects of MAPT mutations on aggregation dynamics
Authors: Ingham David J. , Hillyer Kelsey M. , McGuire Madison J. , Chris Gamblin T.
Published: August 2021

Alzheimer’s disease (AD) and Alzheimer’s disease related dementias (ADRDs) affect 6 million Americans and they are projected to have an estimated health care cost of $355 billion for 2021. A histopathological hallmark of AD and many ADRDs is the aberrant intracellular accumulation of the microtubule associated protein tau. These neurodegenerative disorders that contain tau aggregates are collectively known as tauopathies and recent structural studies have shown that different tauopathies are characterized by different “strains” of tau filaments. In addition, mutations in the gene that encodes for tau protein expression have been associated with a group of tauopathies known as frontotemporal dementias with Parkinsonism linked to chromosome 17 (FTDP-17 or familial frontotemporal dementia). In vitro studies often use small molecules to induce tau aggregation as tau is extremely soluble and does not spontaneously aggregate in typical lab conditions and the use of authentic filaments to conduct in vitro studies is not feasible. This study highlights how different inducer molecules can have fundamental disparities to how disease related mutations effect the aggregation dynamics of tau. Using three different classes of tau aggregation inducer molecules we characterized disease relevant mutations in tau’s PGGG motifs at positions P301S, P332S, and P364S. When comparing these mutations to wild type tau, we found that depending on the type of inducer molecule used we saw fundamental differences in total aggregation, aggregation kinetics, immunoreactivity, and filament morphology. These data support the hypothesis that different tau aggregation inducer molecules make different polymorphs and perhaps structurally distinct strains.
Unravelling Form and Function: Improved function of engineered cardiac tissue through extra-cellular anisotropy
Authors: Cyr Jamie A. , Colzani Maria , Bayraktar Semih , Graup Vera , Farndale Richard , Sinha Sanjay , Best Serena M. , Cameron Ruth E.
Published: August 2021

Cardiac tissue engineering is a promising therapeutic option for myocardial repair after injury, however, so far engineered heart patches have shown limited translational utility due to poor electrical integration and tissue contractility. Emerging research suggests that scaffolds that recapitulate the three-dimensional structure of the native myocardium improve physiological function. Complex scaffold fabrication remains a technical challenge and the isolated impact of scaffold architecture on tissue function and cellular physiology is poorly understood. Here, we provided a direct comparison between isotropic and aligned collagen scaffold morphologies where all confounding physio-mechanical features, such as strut wall thickness and surface roughness are conserved. This enabled the independent and systematic assessment of the effects of pore macro-architecture on global tissue function and cellular maturation. We seeded our scaffolds with embryonic stem cell derived cardiomyocytes (hESC-CM) and measured tissue function through calcium signal transduction and dynamic contractile strain. The aligned tissue constructs facilitated improved signalling synchronicity and directional contractility. We further examined the influence of scaffold macrostructure on intercellular organization and intracellular development. Cells on aligned constructs conformed to the orientation of the scaffold macro-structure and were found to have phenotypic and genetic markers of increased maturity. Our results isolate the influence of scaffold macro-structure on engineered tissue function at multiple length scales. These findings inform the design of optimized cardiac tissue and expand the potential for engineered tissue in regenerative and model medical systems by reducing the gaps in tissue functionality that limit their utility.
Neuronal responses to focused ultrasound are gated by pre-stimulation brain rhythms
Authors: Nguyen Duc , Konofagou Elisa , Dmochowski Jacek P.
Published: August 2021

Background

Owing to its high spatial resolution and penetration depth, transcranial focused ultrasound stimulation (tFUS) is one of the most promising approaches to non-invasive neuromodulation. Identifying the impact of the stimulation waveform and endogenous neural activity on neuromodulation outcome is critical to harnessing the potential of tFUS.

Objective

Here we tested a new form of tFUS where the amplitude of the ultrasonic waveform is modulated at a rate much slower than the operating frequency. Moreover, we sought to identify the relationship between pre-stimulation neural activity and the neuronal response to tFUS.

Methods

We applied three minutes of amplitude modulated (AM) tFUS at 40 Hz to the rat hippocampus while recording local field potentials (LFP) and multi-unit activity (MUA)from the sonicated region. To assess the role of AM, we also tested continuous-wave (CW) stimulation.

Results

AM tFUS reduced firing rate during and immediately after stimulation. On the other hand, CW tFUS produced an acute firing rate increase that was abolished after sonication. For both waveforms, firing rate changes were stronger in units exhibiting high baseline LFP power, particularly in the gamma band (30-250 Hz). The neuromodulatory effect was also influenced by the prevalence of sharp wave ripples (SWR) during the pre-stimulation period, with firing rates modulated by up to 33% at units showing frequent baseline SWR.

Conclusion

Our findings suggest that AM and CW tFUS produce qualitatively different neuronal outcomes, and that baseline rhythms may effectively “gate” the response to tFUS.
Disc and Actin-Associated Protein 1 Influence Attachment in the Intestinal Parasite Giardia lamblia
Authors: Steele-Ogus Melissa C. , Obenaus Ava M. , Sniadecki Nathan J. , Paredez Alexander R.
Published: August 2021

The deep-branching eukaryote Giardia lamblia is an extracellular parasite that attaches to the host intestine via a microtubule-based structure called the ventral disc. Control of attachment is mediated in part by the movement of two regions of the ventral disc that either permit or exclude the passage of fluid under the disc. Several known disc-associated proteins (DAPs) contribute to disc structure and function, but no force-generating protein has been identified among them. We recently identified several Giardia actin (GlActin) interacting proteins at the ventral disc, which could potentially employ actin polymerization for force generation and disc conformational changes. One of these proteins, Disc and Actin Associated Protein 1 (DAAP1), is highly enriched at the two regions of the disc previously shown to be important for fluid flow during attachment. In this study, we investigate the role of both GlActin and DAAP1 in ventral disc morphology and function. We confirmed interaction between GlActin and DAAP1 through coimmunoprecipitation, and used immunofluorescence to localize both proteins throughout the cell cycle and during trophozoite attachment. Similar to other DAPs, the association of DAAP1 with the disc is stable, except during cell division when the disc disassembles. Depletion of GlActin by translation-blocking antisense morpholinos resulted in both impaired attachment and defects in the ventral disc, indicating that GlActin contributes to disc-mediated attachment. Depletion of DAAP1 through CRISPR interference resulted in intact discs but impaired attachment, gating, and flow under the disc. As attachment is essential for infection, elucidation of these and other molecular mediators is a promising area for development of new therapeutics against a ubiquitous parasite.

Author Summary

Giardia lamblia is a single-celled organism and one of the most common gastrointestinal parasites worldwide. In developing countries, recurrent Giardia infections are common, due to lack of access to clean water. Giardia infections can lead to diarrhea, vomiting, dehydration, disruption of the intestinal microbiome, and chronic infections can lead to irritable bowel syndrome. Because existing drug treatments have side effects and Giardia’s resistance to drugs is increasing, new treatment strategies are needed. The parasite’s attachment to the host’s intestine is mediated by a Giardia-specific structure that resembles a suction cup and is called the ventral adhesive disc. We previously identified DAAP1, a protein which interacts with Giardia actin and localizes to the ventral disc. Here, we explore the relationship between these two proteins and investigate their role in disc-based attachment. Most disc proteins, including DAAP1, are unrelated to any human proteins, making them appealing drug targets to inhibit parasite attachment and infection.
Modeling bottlenecks, modularity, and context-dependency in behavioral control
Authors: Nande Anjalika , Dubinkina Veronika , Ravasio Riccardo , Zhang Grace H. , Berman Gordon J.
Published: August 2021

In almost all animals, the transfer of information from the brain to the motor circuitry is facilitated by a relatively small number of neurons, leading to a constraint on the amount of information that can be transmitted. Our knowledge of how animals encode information through this pathway, and the consequences of this encoding, however, is limited. In this study, we use a simple feed-forward neural network to investigate the consequences of having such a bottleneck and identify aspects of the network architecture that enable robust information transfer. We are able to explain some recently observed properties of descending neurons – that they exhibit a modular pattern of connectivity and that their excitation leads to consistent alterations in behavior that are often dependent upon the prior behavioral state (context-dependency). Our model predicts that in the presence of an information bottleneck, such a modular structure is needed to increase the efficiency of the network and to make it more robust to perturbations. However, it does so at the cost of an increase in context-dependency. Despite its simplicity, our model is able to provide intuition for the trade-offs faced by the nervous system in the presence of an information processing constraint and makes predictions for future experiments.
AMES: Automated evaluation of sarcomere structures in cardiomyocytes
Authors: Hillemanns Maximilian , Lemcke Heiko , David Robert , Martinetz Thomas , Wolfien Markus , Wolkenhauer Olaf
Published: August 2021

Background

Arrhythmias are severe cardiac diseases and lethal if untreated. To serve as an in vitro drug testing option for anti-arrhythmic agents, cardiomyocytes are being generated in vitro from induced pluripotent stem cells (iPSCs). Unfortunately, these generated cardiomyocytes resemble fetal cardiac tissue rather than adult cardiomyocytes. An automated tool for an unbiased evaluation of cardiomyocytes would highly facilitate the establishment of new differentiation protocols to increase cellular maturity.

Results

In this work, a novel deep learning-based approach for this task is presented and evaluated. Different convolutional neural networks (CNNs) including 2D and 3D models were trained on fluorescence images of human iPSC-derived cardiomyocytes, which were rated based on their sarcomere content (sarcomerisation) and the orientation of sarcomere filaments (directionality) beforehand by a domain expert. The CNNs were trained to perform classifications on sarcomerisation, directionality ratings, and cell source, including primary adult and differentiated cardiomyocytes. The best accuracies are reached by a 3D model with a classification accuracy of about 90 % for sarcomerisation classification, 63 % for directionality classification, and 80 % for cell source classification. The trained models were additionally evaluated using two explanatory algorithms, IGrad and Grad-CAM. The heatmaps computed by those explainability algorithms show that the important regions in the image occur inside the cell and at the cellular borders for the classifier, and, therefore, validate the calculated regions.

Conclusion

In summary, we showed that cellular fluorescence images can be analyzed with CNNs and subsequently used to predict different states of sarcomere maturation. Our developed prediction tool AMES (https://github.com/maxhillemanns/AMES) can be used to make trustworthy predictions on the quality of a cardiomyocyte, which ultimately facilitates the optimized generation of cardiomyocytes from iPSCs and improves the quality control in an automated, unbiased manner. The applied workflow of testing different CNN models, adjusting parameters, and using a variety of explanatory algorithms can be easily transferred to further image based quality control, stratification, or analysis setups.
Thalamocortical and intracortical contributions to stimulus-evoked and oscillatory activity in rodent primary auditory cortex
Authors: Jeschke Marcus , Ohl Frank W.
Published: August 2021

Intracortical, horizontal connections seem ideally suited to contribute to cortical processing by spreading information across cortical space and coordinating activity between distant cortical sites. In sensory systems experiments have implicated horizontal connections in the generation of receptive fields and have in turn led to computational models of receptive field generation that rely on the contribution of horizontal connections. Testing the contribution of horizontal connections at the mesoscopic level has been difficult due to the lack of a suitable method to observe the activity of intracortical horizontal connections. Here, we develop such a method based on the analysis of the relative residues of the cortical laminar current source density reconstructions. In the auditory cortex of Mongolian gerbils, the method is then tested by manipulating the contribution of horizontal connections by surgical dissection. Our results indicate that intracortical horizontal connections contribute to the frequency-tuning of mesoscopic cortical patches. Futhermore, we dissociated a type of cortical gamma oscillation based on horizontal connections between mesoscopic patches from gamma oscillations locally generated within mesoscopic patches. The data further imply that global and local coordination of activity during sensory stimulation occur in a low and high gamma frequency band, respectively. Taken together the present data demonstrate that intracortical horizontal connections play an important role in generating cortical feature tuning and coordinate neuronal oscillations across cortex.
Binding of Monomeric and Polymeric Alzheimer’s Aβ peptides to Exosomes
Authors: Coughlan Christina , Lindenberger Jared , Jacot Jeffrey , Johnson Noah , Anton Paige , Bevers Shaun , Graner Michael , Potter Huntington
Published: August 2021

Exosomes are secreted by every cell in our body under both physiological and pathological conditions. They travel in the blood, CSF, and all studied biofluids. Their biological roles have been reported to include delivery of important physiological cargo between organs and cells, clearance of toxic proteins; maintenance of cellular stasis, and the propagation of disease pathology. In the case of Alzheimer’s disease (AD) exosomes have been shown to carry pathological proteins such as amyloid, yet the specificity of this association of amyloid and exosomes is unclear. To address this deficiency, we utilized Isothermal Titration Calorimetry (ITC) to measure the binding of amyloid to exosomes. Here we report that Aβ40 and Aβ42 bind to exosomes in a saturable and endothermic manner, a phenomenon not observed with the scrambled versions of either peptide. This points to this interaction being more specific than previously understood, and to amyloid associated with exosomes as an important pool of this peptide in the plasma.