bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated imaging of duckweed growth and development
Authors: Cox Kevin L. , Manchego Jordan , Meyers Blake C. , Czymmek Kirk J. , Harkess Alex
Published: July 2021

Duckweeds are some of the smallest angiosperms, possessing a simple body architecture and high rates of biomass accumulation. They can grow near-exponentially via clonal propagation. Understanding their reproductive biology, growth, and development is essential to unlock their potential for phytoremediation, carbon capture, and nutrition. However, there is a lack of non-laborious and convenient methods for spatially and temporally imaging an array of duckweed plants and growth conditions in the same experiment. We developed an automated microscopy approach to record time-lapse images of duckweed plants growing in 12-well cell culture plates. As a proof-of-concept experiment, we grew duckweed on semi-solid media with and without sucrose and monitored its effect on their growth over 3 days. Using the PlantCV toolkit, we quantified the thallus area of individual plantlets over time, and showed thatL. minorgrown on sucrose had an average growth rate four times higher than without sucrose. This method will serve as a blueprint to perform automated high-throughput growth assays for studying the development patterns of duckweeds from different species, genotypes, and conditions.
Patterns of pan-genome occupancy and gene co-expression under water-deficit in Brachypodium distachyon
Authors: Sancho Rubén , Catalán Pilar , Contreras-Moreira Bruno , Juenger Thomas E. , Des Marais David L.
Published: July 2021

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among co-expression modules. Co-expression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
The Amazon River microbiome, a story of humic carbon
Authors: Sylvain François-Étienne , Bouslama Sidki , Holland Aleicia , Leroux Nicolas , Mercier Pierre-Luc , Val Adalberto Luis , Derome Nicolas
Published: July 2021

The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear and black waters. Black waters contain important loads of allochthonous humic dissolved organic carbon (DOC), mostly coming from bacteria-mediated lignin degradation, a process that remains understudied. Here, we identified the main bacterial taxa and functions associated with contrasting Amazonian water types, and shed light on their potential implication in the lignin degradation process. We performed an extensive field bacterioplankton sampling campaign from the three Amazonian water types, and combined our observations to a meta-analysis of 90 Amazonian basin shotgun metagenomes used to build a tailored functional inference database. We showed that the overall quality of DOC is a major driver of bacterioplankton structure, transcriptional activity and functional repertory. We also showed that among the taxa mostly associated to differences between water types, Polynucleobacter sinensis particularly stood out, as its abundance and transcriptional activity was strongly correlated to black water environments, and specially to humic DOC concentration. Screening the reference genome of this bacteria, we found genes coding for enzymes implicated in all the main lignin degradation steps, suggesting that this bacteria may play key roles in the carbon cycle processes within the Amazon basin.
ELIMINATOR: Essentiality anaLysIs using MultIsystem Networks And inTeger prOgRamming
Authors: Antoranz Asier , Ortiz María , Pey Jon
Published: July 2021

A gene is considered as essential when it is indispensable for cells to grow and replicate under a certain environment. However, gene essentiality is not a structural property but rather a contextual one, which depends on the specific biological conditions affecting the cell. This circumstantial essentiality of genes is what brings the attention of scientist since we can identify genes essential for cancer cells but not essential for healthy cells. This same contextuality makes their identification extremely challenging. Huge experimental efforts such as Project Achilles where the essentiality of thousands of genes is measured in over one thousand cell lines together with a plethora of molecular data (transcriptomics, copy number, mutations, etc.) can shed light on the causality behind the essentiality of a gene in a given environment by associating the measured essentiality to molecular features of the cell line.

Here, we present an in-silico method for the identification of patient-specific essential genes using constraint-based modelling (CBM). Our method expands the ideas behind traditional CBM to accommodate multisystem networks, that is a biological network that focuses on complex interactions within several biological systems. In essence, it first calculates the minimum number of non-expressed genes required to be active by the cell to sustain life as defined by a set of requirements; and second, it performs an exhaustive in-silico gene knockout to find those that lead to the need of activating extra non-expressed genes.

We validated the proposed methodology using a set of 452 cancer cell lines derived from the Cancer Cell Line Encyclopedia where an exhaustive experimental large-scale gene knockout study using CRISPR (Achilles Project) evaluates the impact of each removal. We also show that the integration of different essentiality predictions per gene, what we called Essentiality Congruity Score, (derived from multiple pathways) reduces the number of false positives. Finally, we explored the gene essentiality predictions for a breast cancer patient dataset, and our results showed high concordance with previous publications.

These findings suggest that identifying genes whose activity are fundamental to sustain cellular life in a patient-specific manner is feasible using in-silico methods. The patient-level gene essentiality predictions can pave the way for precision medicine by identifying potential drug targets whose deletion can induce death in tumour cells.
Raptor downregulation rescues neuronal phenotypes in mouse models of Tuberous Sclerosis Complex
Authors: Karalis Vasiliki , Caval-Holme Franklin , Bateup Helen S.
Published: July 2021

Tuberous Sclerosis Complex (TSC) is a neurodevelopmental disorder caused by mutations in the TSC1 or TSC2 genes, which encode proteins that negatively regulate mTOR complex 1 (mTORC1) signaling. Current treatment strategies focus on mTOR inhibition with rapamycin and its derivatives. While effective at improving some aspects of TSC, chronic rapamycin inhibits both mTORC1 and mTORC2 and is associated with systemic side-effects. It is currently unknown which mTOR complex is most relevant for TSC-related brain phenotypes. Here we used genetic strategies to selectively reduce neuronal mTORC1 or mTORC2 activity in mouse models of TSC. We find that reduction of the mTORC1 component Raptor, but not the mTORC2 component Rictor, rebalanced mTOR signaling in Tsc1 knock-out neurons. Raptor reduction was sufficient to improve several TSC-related phenotypes including neuronal hypertrophy, macrocephaly, impaired myelination, network hyperactivity, and premature mortality. Raptor downregulation represents a promising potential therapeutic intervention for the neurological manifestations of TSC.
Fully automatic segmentation of craniomaxillofacial CT scans for computer-assisted orthognathic surgery planning using the nnU-Net framework
Authors: Dot Gauthier , Schouman Thomas , Dubois Guillaume , Rouch Philippe , Gajny Laurent
Published: July 2021

Objectives

To evaluate the performance of the nnU-Net open-source deep learning framework for automatic multi-task segmentation of craniomaxillofacial (CMF) structures in CT scans obtained for computer-assisted orthognathic surgery.

Methods

Four hundred and fifty-three consecutive patients having undergone high-resolution CT scans before orthognathic surgery were randomly distributed among a training/validation cohort (n = 300) and a testing cohort (n = 153). The ground truth segmentations were generated by 2 operators following an industry-certified procedure for use in computer-assisted surgical planning and personalized implant manufacturing. Model performance was assessed by comparing model predictions with ground truth segmentations. Examination of 45 CT scans by an industry expert provided additional evaluation. The model’s generalizability was tested on a publicly available dataset of 10 CT scans with ground truth segmentations of the mandible.

Results

In the test cohort, mean volumetric Dice Similarity Coefficient (vDSC) & surface Dice Similarity Coefficient at 1mm (sDSC) were 0.96 & 0.97 for the upper skull, 0.94 & 0.98 for the mandible, 0.95 & 0.99 for the upper teeth, 0.94 & 0.99 for the lower teeth and 0.82 & 0.98 for the mandibular canal. Industry expert segmentation approval rates were 93% for the mandible, 89% for the mandibular canal, 82% for the upper skull, 69% for the upper teeth and 58% for the lower teeth.

Conclusion

While additional efforts are required for the segmentation of dental apices, our results demonstrated the model’s reliability in terms of fully automatic segmentation of preoperative orthognathic CT scans.

Key points

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The nnU-Net deep learning framework can be trained out-of-the-box to provide robust fully automatic multi-task segmentation of CT scans performed for computer-assisted orthognathic surgery planning.

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The clinical viability of the trained nnU-Net model is shown on a challenging test dataset of 153 CT scans randomly selected from clinical practice, showing metallic artifacts and diverse anatomical deformities.

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Commonly used biomedical segmentation evaluation metrics (volumetric and surface Dice Similarity Coefficient) do not always match industry expert evaluation in the case of more demanding clinical applications.
Air travel-related outbreak of multiple SARS-CoV-2 variants
Authors: Dhanasekaran Vijaykrishna , Edwards Kimberly M , Xie Ruopeng , Gu Haogao , Adam Dillon C , Chang Lydia DJ , Cheuk Sammi SY , Gurung Shreya , Krishnan Pavithra , Ng Daisy YM , Liu Gigi YZ , Wan Carrie KC , Cheng Samuel SM , Tsang Dominic NC , Cowling Benjamin , Peiris Malik , Poon Leo LM
Published: July 2021

Background

A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of >400,000 newly confirmed cases on 7 May 2021.

Methods

Epidemiological information including date of symptom onset, date of positive-sample detection, and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021, and 1,217 reference sequences.

Results

Sequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa, and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021.

Conclusions

The broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.
Systematic mapping of small nucleolar RNA targets in human cells
Authors: Dunn-Davies Hywel , Dudnakova Tatiana , Langhendries Jean-Louis , Watkins Nicholas , Lafontaine Denis L.J. , Tollervey David
Published: July 2021

Altered expression of box C/D small nucleolar RNAs (snoRNAs) is implicated in human diseases, including cancer. Box C/D snoRNAs canonically direct site-specific, 2’-O-methylation but the extent to which they participate in other functions remains unclear. To identify RNA targets of box C/D snoRNAs in human cells, we applied two techniques based on UV crosslinking, proximity ligation and sequencing of RNA hybrids (CLASH and FLASH). These identified hundreds of novel snoRNA interactions with rRNA, snoRNAs and mRNAs. We developed an informatic pipeline to rigorously call interactions predicted to direct methylation. Multiple snoRNA-rRNA interactions identified were not predicted to direct RNA methylation. These potentially modulate methylation efficiency and/or contribute to folding dynamics. snoRNA-mRNA hybrids included 1,300 interactions between 117 snoRNA families and 940 mRNAs. Human U3 is substantially more abundant than other snoRNAs and represented about 50% of snoRNA-mRNA hybrids. The distribution of U3 interactions across mRNAs also differed from other snoRNAs. Following U3 depletion, mRNAs showing altered abundance were strongly enriched for U3 CLASH targets. Most human snoRNAs are excised from pre-mRNA introns. Enrichment for snoRNA association with branch point regions of introns that contain snoRNA genes was common, suggesting widespread regulation of snoRNA maturation.
Placental structure, function and mitochondrial phenotype relate to fetal size and sex in mice
Authors: Salazar-Petres Esteban , Carvalho Daniela Pereira , Lopez-Tello Jorge , Sferruzzi-Perri Amanda Nancy
Published: July 2021

Fetal growth depends on placental function, which requires energy from mitochondria. Here we investigated whether mitochondrial function in the placenta relates to growth of the lightest and heaviest fetuses of each sex within the litter of mice. Placentas from the lightest and heaviest fetuses were taken to evaluate placenta morphology (stereology), mitochondrial energetics (high-resolution respirometry), and mitochondrial regulators, nutrient transporters, hormone handling and signalling pathways (qPCR and western blotting). We found that mitochondrial complex I and II oxygen consumption rate was greater for placentas supporting the lightest female fetuses, although placental complex I abundance of the lightest females and complexes III and V of the lightest males were decreased compared to their heaviest counterparts. Expression of mitochondrial biogenesis (Nrf1) and fission (Drp1 and Fis1) genes was lower in the placenta from the lightest females, whilst biogenesis-related gene Tfam was greater in the placenta of the lightest male fetuses. Additionally, placental morphology and steroidogenic gene (Cyp17a1 and Cyp11a1) expression was aberrant for the lightest females, but glucose transporter (Glut1) expression was lower in only the lightest males versus their heaviest counterparts. Differences in intra-litter placental phenotype were related to sex-dependent changes in the expression of hormone responsive (androgen receptor) and metabolic signalling (AMPK, AKT, PPARγ) pathways. Thus, in normal mouse pregnancy, placental structure, function and mitochondrial phenotype are differentially responsive to growth of the female and the male fetus. This study may inform the design of sex- specific therapies for placental insufficiency and fetal growth abnormalities with life-long benefits for the offspring.
Gammaherpesvirus infection licenses age-associated B cells for pathogenicity in MS and EAE
Authors: Mouat Isobel C. , Allanach Jessica R. , Fan Vina , Girard Anna M. , Shanina Iryna , Vorobeychik Galina , Horwitz Marc S.
Published: July 2021

While age-associated B cells (ABCs) are known to expand and persist following viral infection and during autoimmunity, their interactions are yet to be studied together in these contexts. Epstein-Barr virus (EBV) infection has long been implicated in multiple sclerosis (MS), and it is not known whether ABCs could play a role in mediating viral contribution to autoimmunity. Here, we show that the circulating ABC population is expanded in people with MS and that EBV infection and MS status differentially impact the circulating ABC phenotype. We then directly compared ABCs during viral infection and autoimmunity using mouse models of EBV, gammaherpesvirus 68 (γHV68), and MS, experimental autoimmune encephalomyelitis (EAE). We observed that splenic ABCs are expanded in a sex-biased manner during both latent virus infection and EAE, and each event drives the ABC population to opposing phenotypes. We have previously shown that latent γHV68 infection exacerbates EAE and here we show that mice lacking ABCs fail to display γHV68-enhanced disease. Collectively, these findings indicate that latent viral infection and central nervous system autoimmunity differentially impact the ABC population and suggests that viral infections such as EBV prime ABCs to contribute pathogenically in MS.
Competent immune responses to SARS-CoV-2 variants in older adults following mRNA vaccination
Authors: Jergović Mladen , Uhrlaub Jennifer L. , Watanabe Makiko , Bradshaw Christine M. , White Lisa M. , LaFleur Bonnie J. , Edwards Taylor , Sprissler Ryan , Worobey Michael , Bhattacharya Deepta , Nikolich-Žugich Janko
Published: July 2021

Aging is associated with a reduced magnitude of primary immune responses to vaccination and constriction of immune receptor repertoire diversity. Clinical trials demonstrated high efficacy of mRNA based SARS-CoV-2 vaccines in older adults but concerns about virus variant escape have not been well addressed. We have conducted an in-depth analysis of humoral and cellular immunity against an early-pandemic viral isolate and compared that to the P.1. (Gamma) and B.1.617.2 (Delta) variants in <50 and >55 age cohorts of mRNA vaccine recipients. We have further measured neutralizing antibody titers for B.1.617.1 (Kappa) and B.1.595; a SARS-CoV-2 isolate bearing Spike mutation E484Q. As reported, robust immunity required the second dose of vaccine. Older vaccinees manifested robust cellular immunity against early-pandemic SARS-CoV-2 and more recent variants, which remained statistically comparable to the adult group. The older cohort had lower neutralizing capacity at the first time point following the second dose, but at later time points immunity was indistinguishable between them. While the duration of these immune responses remains to be determined over longer periods of time, these results provide reasons for optimism regarding vaccine protection of older adults against SARS-CoV-2 variants and inform thinking about boost vaccination with variant vaccines.

eTOC summary

Vaccine responses are often diminished with aging, but we found strong responses to SARS-CoV-2 in older adults following mRNA vaccination. T cell responses were not diminished when confronted by SARS-CoV-2 variants. Neutralizing Ab were reduced but not more than those in adults.

Graphical Abstract

Created with BioRender.com
Conserved exchange of paralog proteins during neuronal differentiation
Authors: Di Fraia Domenico , Anitei Mihaela , Mackmull Marie-Therese , Parca Luca , Behrendt Laura , Andres-Pons Amparo , Gilmour Darren , Citterich Manuela Helmer , Kaether Christoph , Beck Martin , Ori Alessandro
Published: July 2021

Gene duplication enables the emergence of new functions by lowering the general evolutionary pressure. Previous studies have highlighted the role of specific paralog genes during cell differentiation, e.g., in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological functions and whether the regulation of paralog genes is conserved across species. Here, we analyze the expression of paralogs across human tissues, during development and neuronal differentiation in fish, rodents and humans. While ~80% of paralog genes are co-regulated, a subset of paralogs shows divergent expression profiles, contributing to variability of protein complexes. We identify 78 substitutions of paralog pairs that occur during neuronal differentiation and are conserved across species. Among these, we highlight a substitution between the paralogs SEC23A and SEC23B subunits of the COPII complex. Altering the ratio between these two proteins via RNAi-mediated knockdown is sufficient to influence neuron differentiation. We propose that remodeling of the vesicular transport system via paralog substitutions is an evolutionary conserved mechanism enabling neuronal differentiation.
Bassoon controls synaptic vesicle pools via regulation of presynaptic phosphorylation and cAMP homeostasis
Authors: Montenegro-Venegas Carolina , Guhathakurta Debarpan , Pina-Fernandez Eneko , Andres-Alonso Maria , Plattner Florian , Lazarevic Vesna , Gundelfinger Eckart D. , Fejtova Anna
Published: July 2021

Neuronal presynaptic terminals contain hundreds of neurotransmitter-filled synaptic vesicles (SVs). The morphologically uniform SVs differ in their release competence segregating into functional pools that differentially contribute to neurotransmission. The presynaptic scaffold bassoon is required for neurotransmission, but the underlying molecular mechanisms are unknown. We report that glutamatergic synapses lacking bassoon featured a decreased SV release competence and increased resting pool of SV as observed by imaging of SV release in cultured neurons. Further analyses in vitro and in vivo revealed a dysregulation of CDK5/calcineurin and cAMP/PKA presynaptic signalling resulting in an aberrant phosphorylation of their downstream effectors synapsin 1 and SNAP25, which are well-known regulators of SV release competence. An acute pharmacological restoration of physiological CDK5 and cAMP/PKA activity fully normalised the SV pools in neurons lacking bassoon. Finally, we demonstrated that CDK5-dependent regulation of PDE4 activity controls SV release competence by interaction with cAMP/PKA signalling. These data reveal that bassoon organises SV pools via regulation of presynaptic phosphorylation and indicate an involvement of PDE4 in the control of neurotransmitter release.
Learning the rules of collective cell migration using deep attention networks
Authors: LaChance Julienne , Suh Kevin , Cohen Daniel J.
Published: July 2021

Collective, coordinated cellular motions underpin key processes in all multicellular organisms, yet it has been difficult to express the ‘rules’ behind these motions in clear, interpretable forms. Here we apply deep attention networks to analyze several canonical living tissues systems and present the underlying collective migration rules for each tissue type using only cell migration trajectory data. We use these networks to learn the behaviors of key tissue types with distinct collective behaviors—epithelial, endothelial, and metastatic breast cancer cells—and show how the results complement traditional biophysical approaches. In particular, we present attention maps indicating the relative influence of neighboring cells to the learned turning decisions of a focal cell. These attention networks reveal distinct patterns of influence and attention unique to each model tissue. Endothelial cells exhibit tightly focused attention on their immediate forward-most neighbors, while cells in more expansile epithelial tissues are more broadly influenced by neighbors in a relatively large forward sector. Attention maps of ensembles of more mesenchymal, metastatic cells reveal completely symmetric attention patterns, indicating the lack of any particular coordination or direction of interest. Moreover, we show how attention networks are capable of detecting and learning how these rules changes based on biophysical context, such as location within the tissue and cellular crowding. That these results require only cellular trajectories and no modeling assumptions highlights the potential of attention networks for providing further biological insights into complex cellular systems.

Author Summary

Collective behaviors are crucial to the function of multicellular life, with large-scale, coordinated cell migration enabling processes spanning organ formation to coordinated skin healing. However, we lack effective tools to discover and cleanly express collective rules at the level of an individual cell. Here, we employ a carefully structured neural network to extract collective information directly from cell trajectory data. The network is trained on data from various systems, including well-studied cell types (HUVEC and MDCK cells) which display visually distinct forms of collective motion, and metastatic cancer cells (MDA-MB-231) which are highly uncoordinated. Using these trained networks, we can produce attention maps for each system, which indicate how a cell within a tissue takes in information from its surrounding neighbors, as a function of weights assigned to those neighbors. Thus for a cell type in which cells tend to follow the path of the cell in front, the attention maps will display high weights for cells spatially forward of the focal cell. We present results in terms of additional metrics, such as accuracy plots and number of interacting cells, and encourage future development of improved metrics.
Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes
Authors: Zhang Lanxin , Wang Junyu , von Kleist Max
Published: July 2021

Pre-exposure prophylaxis (PrEP) is an important pillar to prevent HIV transmission. Because of experimental and clinical shortcomings, mathematical models that integrate pharmacological, viral- and host factors are frequently used to quantify clinical efficacy of PrEP. Stochastic simulations of these models provides sample statistics from which the clinical efficacy is approximated. However, many stochastic simulations are needed to reduce the associated sampling error. To remedy the shortcomings of stochastic simulation, we developed three numerical methods that allow predicting the efficacy of arbitrary prophylactic regimen directly from a viral dynamics model, without sampling. We apply the methods to various hypothetical dolutegravir (DTG) prophylaxis scenarios. The approaches are verified against one another, as well as state-of-the-art stochastic simulation. While the methods are more accurate than stochastic simulation, they are superior in terms of computational performance. For example, a continuous 6-month prophylactic profile is computed within a few seconds on a laptop computer. The methods’ computational performance, therefore, substantially expands the horizon of feasible analysis in the context of PrEP, and possibly other applications.

Author summary

Pre-exposure prophylaxis (PrEP) is an important tool to prevent HIV transmission. However, experimental identification of parameters that determine prophylactic efficacy is extremely difficult. Clues about these parameters could prove essential for the design of next-generation PrEP compounds. Integrative mathematical models can fill this void: Based on stochastic simulation, a sample statistic can be generated, from which the prophylactic efficacy is estimated. However, for this sample statistic to be accurate, many simulations need to be performed.

Here, we introduce three numerical methods to directly compute the prophylactic efficacy from a viral dynamics model, without the need for sampling. Based on several examples with dolutegravir (DTG) -based short- and long-term PrEP, as well as post-exposure prophylaxis we demonstrate the correctness of the new methods and their outstanding computational performance. Due to the methods’ computational performance, a number of analysis, including formal sensitivity analysis are becoming feasible with the proposed methods.
Proton-mediated gating mechanism of anion channelrhodopsin-1
Authors: Tsujimura Masaki , Kojima Keiichi , Kawanishi Shiho , Sudo Yuki , Ishikita Hiroshi
Published: July 2021

Anion channelrhodopsin from Guillardia theta (GtACR1) has Asp234 (3.2 Å) and Glu68 (5.3 Å) near the protonated Schiff base. Here we investigate mutant GtACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths were also analyzed, using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shortens and lengthens the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild type GtACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients towards the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism.
Binocular Benefit Following Monocular Subretinal AAV Injection in a Mouse Model of Autosomal Dominant Retinitis Pigmentosa (adRP)
Authors: Ahmed Chulbul M , Massengill Michael T , Ildefonso Cristhian J , Zhu Ping , Li Hong , Patel Anil P. , Lewin Alfred S
Published: July 2021

Autosomal dominant retinitis pigmentosa (adRP) is frequently caused by mutations in RHO, the gene for rhodopsin. In previous experiments in dogs with the T4R mutation in RHO, an AAV2/5 vector expressing both an shRNA directed to human and dog RHO mRNA and an shRNA-resistant human RHO cDNA (AAV-RHO820-shRNA820) prevented retinal degeneration for more than 8 months following injection. To confirm that this same vector could protect the retinas of a different species and bearing a different RHO mutation, we injected mice transgenic for human P23H RHO at postnatal day 30 in one eye. For nine months, we monitored their retinal structure using spectral- domain optical coherence tomography (SD-OCT) and retinal function using electroretinography (ERG). We compared these to P23H RHO transgenic mice injected with AAV-GFP. Though retinas continued to thin over time, compared to control injected eyes, AAV-RHO820-shRNA820 slowed the loss of photoreceptor cells and decreased ERG amplitudes in AAV-RHO820-shRNA820 eyes during the nine-month study period. Unexpectedly, we also observed preservation of retinal structure and function in the untreated contralateral eyes of AAV-RHO820-shRNA820 treated mice. PCR analysis and western blots provided evidence that a low amount of vector from injected eyes was present in uninjected eyes.
TMT-based proteomic analysis of the antibiotic effects of ShangKeHuangShui against Straphylococcus aureus
Authors: Liu Lichu , Zhao Na , Yang Kuangyang , Liao Honghong , Liu Xiaofang , Wu Ying , Lei Lei , Peng Xiao , Wu Yuanyan
Published: July 2021

Post-traumatic infection is a serious orthopedic trauma complication commonly caused by Staphylococcus aureus (SAU). ShangKeHuangShui, also known as Yellow Aqueous Concentrate of Traumatology Herbs (YACTH), is prepared from six Chinese herbal medicines, which has been used for decades in our hospital to prevent post-traumatic infection.

In the present study, we investigated the in vitro antibacterial effects and underlying mechanism of YACTH against SAU. YACTH exhibited significant antibacterial activity against SAU with the minimum inhibitory concentration (MIC) of 8.625 mg/mL. Proteomic analysis based on Tandem mass tag (TMT) showed different protein expression levels in SAU under the YACTH and control conditions. Compared to the control group, the expression level of 490 proteins of YACTH treated group significantly changed (>1.2 fold, P <0.05). Biological informatics analysis showed that these differential proteins were widely involved in a variety of biological processes and multiple metabolic pathways. We then selected 26 target proteins to further conduct Parallel reaction monitoring (PRM). The results revealed that the 9 down-regulated proteins were mainly involved in RNA polymerase, oxidative phosphorylation, ABC transporter and glycolysis; whereas, the 17 up-regulated proteins are related to RNA degradation, mismatch repair and ribosome.

In conclusion, YACTH, which contains the water-soluble components of six Chinese herbs, is first reported to exhibit antibacterial activity against SAU in vitro. The results provide novel insights into the antibacterial mechanisms of YACTH on protein networks, which may help us find new potential antibiotic targets.
Reconstruction of a generic genome-scale metabolic network for chicken: investigating network connectivity and finding potential biomarkers
Authors: Salehabadi Ehsan , Motamedian Ehsan , Shojaosadati Seyed Abbas
Published: July 2021

Chicken is the first sequenced avian that has a crucial role in human life for its meat and egg production. Because of various metabolic disorders, study the metabolism of chicken cell is important. Herein, the first genome-scale metabolic model of a chicken cell named iES1300, consists of 2427 reactions, 2569 metabolites, and 1300 genes, was reconstructed manually based on databases. Interactions of metabolic genes for growth were examined for E. coli, S. cerevisiae, human, and chicken metabolic models. The results indicated robustness to genetic manipulation for iES1300 similar to the results for human. iES1300 was integrated with transcriptomics data using algorithms and Principal Component Analysis was applied to compare context-specific models of the normal, tumor, lean and fat cell lines. It was found that the normal model has notable metabolic flexibility in the utilization of various metabolic pathways, especially in metabolic pathways of the carbohydrate metabolism, compared to the others. It was also concluded that the fat and tumor models have similar growth metabolisms and the lean chicken model has a more active lipid and carbohydrate metabolism.
Insertion sequences associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia
Authors: Udaondo Zulema , Abram Kaleb Z. , Kothari Atul , Jun Se-Ran
Published: July 2021

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of antibiotic resistance phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over four days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events, and IS-medicated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the IS in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium offering a new paradigm for the study of daptomycin-resistance and novel insights into the route of daptomycin resistance dissemination. In conclusion, our study highlights the role ISs and other transposable elements play in rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.
De novo mutations in KIF1A-associated neuronal disorder (KAND) dominant-negatively inhibit motor activity and axonal transport of synaptic vesicle precursors
Authors: Anazawa Yuzu , Kita Tomoki , Iguchi Rei , Hayashi Kumiko , Niwa Shinsuke
Published: July 2021

KIF1A is a kinesin superfamily molecular motor that transports synaptic vesicle precursors in axons. Mutations in Kif1a lead to a group of neuronal diseases called KIF1A-associated neuronal disorder (KAND). KIF1A forms a homodimer and KAND mutations are mostly de novo and autosomal dominant; however, it is not known whether the function of wild-type KIF1A is inhibited by disease-associated KIF1A when they are dimerized. No reliable in vivo model systems to analyze the molecular and cellular biology of KAND caused by loss of function mutations have been developed; therefore, here, we established Caenorhabditis elegans models for KAND using CRISPR/cas9 technology and analyzed defects in axonal transport. In the C. elegans models, heterozygotes and homozygotes exhibited reduced axonal transport phenotypes. Suppressor screening using the disease model worm identified a mutation that recovers the motor activity of disease-associated human KIF1A. In addition, we developed in vitro assays to analyze the motility of single heterodimers composed of wild-type KIF1A and disease-associated KIF1A. Disease-associated KIF1A significantly inhibited the motility of wild-type KIF1A when heterodimers were formed. These data indicate the molecular mechanism underlying the dominant nature of de novo KAND mutations.

Significance Statement

KIF1A is a molecular motor that transports synaptic vesicle precursors in axons. Recent studies have identified many KIF1A mutations in congenital neuropathy patients; however, the molecular mechanism of pathogenesis remains largely elusive. This study established loss of function models for KIF1A-associated neuronal disorder (KAND) in Caenorhabditis elegans to analyze the molecular and cell biology of the disease in vivo. Genetic screening using the disease model could find a mutation that recovers the motor activity of disease-associated KIF1A. This study also established in vitro single-molecule assays to quantitatively analyze the effect of KAND mutations when mutant KIF1A forms heterodimers with wild-type KIF1A. Our findings provide a foundation for future genetic screening and for drug screening to search for KAND treatments.
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
Authors: Roodgar Morteza , Good Benjamin H. , Garud Nandita R. , Martis Stephen , Avula Mohan , Zhou Wenyu , Lancaster Samuel M. , Lee Hayan , Babveyh Afshin , Nesamoney Sophia , Pollard Katherine S. , Snyder Michael P.
Published: July 2021

Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal trajectories of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We found that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. These genetic changes were frequently observed in species without obvious changes in species abundance, emphasizing the importance of monitoring diversity below the species level. We also found that many sweeping variants quickly reverted to their baseline levels once antibiotic treatment had concluded, demonstrating that the ecological resilience of the microbiota can sometimes extend all the way down to the genetic level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.
Genome-wide variability in recombination activity is associated with meiotic chromatin organization
Authors: Jin Xiaofan , Fudenberg Geoff , Pollard Katherine S.
Published: July 2021

Recombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes during meiosis. Errors in this process lead to negative health outcomes, whereas variability in recombination rate affects genome evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, although PRDM9 binding peaks are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are linked to recombination activity. We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand-break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active, spatially accessible genomic regions during meiotic prophase are associated with DSB-favored loci, which further adopt a transient locally active configuration in early prophase. Conversely, crossover formation is depleted among DSBs in spatially accessible regions during meiotic prophase, particularly within gene bodies. We also find evidence that active chromatin regions have smaller average loop sizes in mammalian meiosis. Collectively, these findings establish that differences in chromatin architecture along chromosomal axes are associated with variable recombination activity. We propose an updated framework describing how 3D organization of brush-loop chromosomes during meiosis may modulate recombination.
Crystal structure and Hirshfeld surface analysis of (2Z)-N,N-dimethyl-2-(pentafluorophenyl)-2-(2-phenylhydrazin-1-ylidene)acetamide
Authors: Atioğlu Zeliha , Akkurt Mehmet , Shikhaliyev Namiq Q. , Askerova Ulviyya F. , Niyazova Aytan A. , Mlowe Sixberth
Published: July 2021

In the title compound, C16H12F5N3O, the dihedral angle between the aromatic rings is 31.84 (8)°. In the crystal, the molecules are linked into dimers possessing crystallographic twofold symmetry by pairwise N—H...O hydrogen bonds and weak C—H...O hydrogen bonds and aromatic π–π stacking interactions link the dimers into a three-dimensional network. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from F...H/H...F (41.1%), H...H (21.8%), C...H/H...C (9.7%) C...C (7.1%) and O...H/H...O (7.1%) contacts. The contribution of some disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. The solvent contribution was not included in the reported molecular weight and density.
The on-orbit mission analysis of OTV based on DoDAF
Authors: Zheng Hongxing , Liu Xin , Wu Junhui , Man Yiyun , Xu Xibao , Guo Jifeng
Published: July 2021

Purpose

The purpose of this paper is to improve the efficiency of on-orbit operations through the top-level task design based on DoDAF. Based on the existing upper stage rocket technology, orbit transfer vehicles (OTVs) have developed rapidly in recent years. However, the lack of decision guidance based on overall task analysis requires integrating top-level analysis and bottom-level execution to achieve the smooth development of full-process tasks.

Design/methodology/approach

Using the Department of Defense Architecture Framework (DoDAF) as a reference, this paper performs the top-level mission analysis modeling of the on-orbit rendezvous and capture of the OTV. Moreover, the typical operational view products are obtained, and the cooperative relations among the mission requirements, the system requirements, and the functional requirements are also analyzed.

Findings

The results show that the attitude of the OTV changes violently during the maneuver and rendezvous phases. In addition, the view products can be optimized based on the results.

Originality/value

The proposed DoDAF-based on-orbit task integration analysis method achieves the effective fusion of high-level analysis and bottom-level execution of OTV on-orbit rendezvous and capture task through the top-level task modeling, operation view generation and task relationship analysis. According to the requirements and constraints of the on-orbit rendezvous and capture task, the control instructions of the vehicle are efficiently generated under the DoDAF framework.
Predefined-time control for a horizontal takeoff and horizontal landing reusable launch vehicle
Authors: Zhang Liang , Jing Liang , Ye Liheng , Gao Xing
Published: July 2021

Purpose

This paper aims to investigate the problem of attitude control for a horizontal takeoff and horizontal landing reusable launch vehicle.

Design/methodology/approach

In this paper, a predefined-time attitude tracking controller is presented for a horizontal takeoff and horizontal landing reusable launch vehicle (HTHLRLV). Firstly, the attitude tracking error dynamics model of the HTHLRLV is developed. Subsequently, a novel sliding mode surface is designed with predefined-time stability. Furthermore, by using the proposed sliding mode surface, a predefined-time controller is derived. To compensate the external disturbances or model uncertainties, a fixed-time disturbance observer is developed, and its convergence time can be defined as a prior control parameter. Finally, the stability of the proposed sliding mode surface and the controller can be proved by the Lyapunov theory.

Findings

In contrast to other fixed-time methods, this controller only requires three control parameters, and the convergence time can be predefined instead of being estimated. The simulation results also demonstrate the effectiveness of the proposed controller.

Originality/value

A novel predefined-time attitude tracking controller is developed based on the predefined-time sliding mode surface (SMS) and fixed-time disturbance observer (FxTDO). The convergence time of the system can be selected as a prior control parameter for SMS and FxTDO.