bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of pH and removed filtrate onE. coliregrowth and microbial community during storage of electro-dewatered biosolids
Authors: Navab-Daneshmand Tala , Guo Bing , Gehr Ronald , Frigon Dominic 
Published: September 2021

ABSTRACTResidual biosolids can be land applied if they meet microbiological requirements at the time of application. Electro-dewatering technology is shown to reduce biosolids bacterial counts to detection limits with little potential for bacterial regrowth during incubations. Here, we investigated the impacts onEscherichia coliregrowth and microbial communities of biosolids pH, removed nutrients via the filtrate, and inhibitory compounds produced in electro-dewatered biosolids. Findings suggest pH as the primary mechanism impactingE. coliregrowth in electro-dewatered biosolids. Propidium monoazide treatments were effective at removing DNA from dead cells, based on the removal of obligate anaerobes observed after anaerobic incubation. Analyses of high throughput sequenced data showed lower alpha-diversities associated with electro-dewatering treatment and incubation time. Moreover, biosolids pH and incubation period were the main factors contributing to the variations in microbial community compositions after incubation. Results highlight the role of electro-dewatered biosolids’ low pH on inhibiting the regrowth of culturable bacteria as well as reducing the microbial community variance.
Microbial habitability of early Mars lacustrine environments sustained by iron redox cycling
Authors: Moore Rachel A. , Carr Christopher E. 
Published: September 2021

AbstractSeveral studies have reported new data on the estimated compositions of chemical components at Gale crater; however, there is still a lack of information regarding potential past support of biomass and detectable biomarkers of ancient life. In this study we evaluate microbial habitability of early Mars constrained by the recently reconstructed water chemistry at Gale. The modeled community is based on Fe-metabolizing bacteria with the ability to utilize solid-phase iron oxides (e.g., magnetite) as an electron source or sink. Our results illustrate the plausibility of a sustained community in Gale Lake and provides suggestions for future modelled and laboratory-based studies to further evaluate the past habitability of Mars, biosignatures and their preservation potential, and hidden metabolic potential.One Sentence SummaryThis work provides an existence proof of habitability on early Mars and demonstrates modeling processes by which the habitability of extraterrestrial environments can be explored quantitatively.
A high throughput bispecific antibody discovery pipeline
Authors: Segaliny Aude I. , Jayaraman Jayapriya , Chen Xiaoming , Chong Jonathan , Luxon Ryan , Fung Audrey , Fu Qiwei , Jiang Xianzhi , Rivera Rodrigo , Ma Xiaoya , Ren Ci , Zimak Jan , Hedde Per Niklas , Shang Yonglei , Wu George , Zhao Weian 
Published: September 2021

AbstractBispecific antibodies (BsAbs) represent an emerging class of immunotherapy but inefficiency in the current BsAb discovery paradigm has limited their broad clinical availability. Here we report a high throughput, agnostic, single-cell-based BsAb functional screening pipeline, comprising molecular and cell engineering for efficient generation of BsAb library cells, followed by functional interrogation at the single-cell level to identify and sort positive clones and downstream sequence identification with single-cell PCR and sequencing and functionality characterization. Using a CD19xCD3 bispecific T cell engager (BiTE) as a model system, we demonstrate that our single cell platform possesses a high throughput screening efficiency of up to one and half million variant library cells per run and can isolate rare functional clones at low abundance of 0.008%. Using a complex CD19xCD3 BiTE-expressing cell library with approximately 22,300 unique variants comprising combinatorially varied scFvs, connecting linkers and VL/VH orientations, we have identified 98 unique clones including extremely rare ones (∼ 0.001% abundance). We also discovered BiTEs that exhibit novel properties contradictory to conventional wisdom, including harboring rigid scFv connecting peptide linkers yet with in vitro cytotoxicity comparable to that of clinically approved Blinatumomab. Through sequencing analyses on sorted BiTE clones, we discovered multiple design variable preferences for functionality including the CD19VL-VH– CD3VH-VL and CD19VH-VL–CD3VH-VL arrangements being the most favored orientation. Sequence analysis further interrogated the sequence composition of the CDRH3 domain in scFvs and identified amino acid residues conserved for function. We expect our single cell platform to not only significantly increase the development speed of high quality of new BsAb therapeutics for cancer and other disorders, but also enable identifying generalizable design principles for new BsAbs and other immunotherapeutics based on an in-depth understanding of the inter-relationships between sequence, structure, and function.
The effect of external lateral stabilization on energy cost of walking – A systematic review and meta-analysis
Authors: Mahaki Mohammadreza , Hoozemans Marco J M , Houdijk Han , van Dieën Jaap H. , Bruijn Sjoerd M 
Published: September 2021

AbstractPrevious studies have estimated the energy cost required for the control of medio-lateral stability in human walking by means of external lateral stabilization. Results were inconsistent, possibly due to differences in task constraints or stabilization devices. To better understand the effects of lateral stabilization on energy cost, we conducted a systematic review with meta-analysis of studies, which directly assessed effects of lateral stabilization on energy cost in healthy young adult participants (18-41 years old). We obtained individual participant data on net energy cost (J kg-1 m-1) from previously published studies. Across all studies reviewed, the net energy cost reduction during stabilized walking at preferred and zero step widths equaled to 0.05 ± 0.35 (~2-3% reduction) and 0.25 ± 0.29 J kg-1 m-1 (mean ± s.d.) (~8-9% reduction), respectively. The effect of external lateral stabilization was significant only for walking at zero step width and without arm swing. Lateral stabilization devices with short rope length increased energy cost reduction. However, spring stiffness and habituation time did not influence energy cost reduction. We provide recommendations for improvement of lateral stabilization devices to avoid some of the confounding effects. External lateral stabilization reduces energy cost during walking by a small amount. It can be concluded that a small proportion of total energy cost is required to control medio-lateral stability; this proportion is larger when walking with narrow steps and without arm swing.
Differentially optimized cell-free buffer enables robust expression from unprotected linear DNA in exonuclease-deficient extracts
Authors: Batista Angelo Cardoso , Levrier Antoine , Soudier Paul , Voyvodic Peter L. , Achmedov Tatjana , Reif-Trauttmansdorff Tristan , DeVisch Angelique , Gonsaud Martin Cohen , Faulon Jean-Loup , Beisel Chase L. , Bonnet Jerome , Kushwaha Manish 
Published: September 2021

ABSTRACTThe use of linear DNA templates in cell-free systems promises to accelerate the prototyping and engineering of synthetic gene circuits. A key challenge is that linear templates are rapidly degraded by exonucleases present in cell extracts. Current approaches tackle the problem by adding exonuclease inhibitors and DNA-binding proteins to protect the linear DNA, requiring additional time- and resource-intensive steps. Here, we delete the recBCD exonuclease gene cluster from the Escherichia coli BL21 genome. We show that the resulting cell-free systems, with buffers optimized specifically for linear DNA, enable near-plasmid levels of expression from σ70 promoters in linear DNA templates without employing additional protection strategies. When using linear or plasmid DNA templates at the buffer calibration step, the optimal potassium glutamate concentrations obtained when using linear DNA were consistently lower than those obtained when using plasmid DNA for the same extract. We demonstrate the robustness of the exonuclease deficient extracts across seven different batches and a wide range of experimental conditions across two different laboratories. Finally, we illustrate the use of the ΔrecBCD extracts for two applications: toehold switch characterization and enzyme screening. Our work provides a simple, efficient, and cost-effective solution for using linear DNA templates in cell-free systems and highlights the importance of specifically tailoring buffer composition for the final experimental setup. Our data also suggest that similar exonuclease deletion strategies can be applied to other species suitable for cell-free synthetic biology.
Transcriptome-informed reduction of protein databases: an analysis of how and when proteogenomics enhances eukaryotic proteomics
Authors: Fancello Laura , Burger Thomas 
Published: September 2021

ABSTRACTBackgroundProteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this, including the generation of reduced transcriptome-informed protein databases (i.e., built from reference protein databases only retaining proteins whose transcripts are detected in the sample-matched transcriptome), which were found to increase peptide identification sensitivity. Here, we present a detailed evaluation of this approach.ResultsFirst, we established that the increased sensitivity in peptide identification is in fact a statistical artifact, directly resulting from the limited capability of target-decoy competition to accurately model incorrect target matches when using excessively small databases. As anti-conservative FDRs are likely to hamper the robustness of the resulting biological conclusions, we advocate for alternative FDR control methods that are less sensitive to database size. Nevertheless, reduced transcriptome-informed databases are useful, as they reduce the ambiguity of protein identifications, yielding fewer shared peptides. Furthermore, searching the reference database and subsequently filtering proteins whose transcripts are not expressed reduces protein identification ambiguity to a similar extent, but is more transparent and reproducible.ConclusionIn summary, using transcriptome information is an interesting strategy that has not been promoted for the right reasons. While the increase in peptide identifications from searching reduced transcriptome-informed databases is an artifact caused by the use of an FDR control method unsuitable to excessively small databases, transcriptome information can reduce ambiguity of protein identifications.
Ustilago maydis telomere protein Pot1 harbors an extra N-terminal OB fold and regulates homology-directed DNA repair factors in a dichotomous and context-dependent manner
Authors: Zahid Syed , Aloe Sarah , Sutherland Jeanette H. , Holloman William K. , Lue Neal F. 
Published: September 2021

AbstractThe telomere G-strand binding protein Pot1 plays multifaceted roles in telomere maintenance and protection. We examined the structure and activities of Pot1 in Ustilago maydis, a fungal model that recapitulates key features of mammalian telomere regulation. Compared to the well-characterized primate and fission yeast Pot1 orthologs, UmPot1 harbors an extra N-terminal OB-fold domain (OB-N), which was recently shown to be present in most metazoans. UmPot1 binds directly to Rad51 and regulates the latter’s strand exchange activity. Deleting the OB-N domain, which is implicated in Rad51-binding, caused telomere shortening, suggesting that Pot1-Rad51 interaction facilitates telomere replication. Depleting Pot1 through transcriptional repression triggered growth arrest as well as rampant recombination, leading to multiple telomere aberrations. In addition, telomere repeat RNAs transcribed from both the G- and C-strand were dramatically up-regulated, and this was accompanied by elevated levels of telomere RNA-DNA hybrids. Telomere abnormalities of pot1-deficient cells were suppressed, and cell viability was restored by the deletion of genes encoding Rad51 or Brh2 (the BRCA2 ortholog), indicating that homology-directed repair (HDR) proteins are key mediators of telomere aberrations and cellular toxicity. Together, these observations underscore the complex physical and functional interactions between Pot1 and DNA repair factors, leading to context-dependent and dichotomous effects of HDR proteins on telomere maintenance and protection.
Three-dimensional label-free histological imaging of whole organs by microtomy-assisted autofluorescence tomography
Authors: Zhang Yan , Kang Lei , Yu Wentao , Tsang Victor Tsz Chun , Wong Terence T. W. 
Published: September 2021

AbstractThree-dimensional (3D) histology is vitally important to characterize disease-induced tissue heterogeneity at the individual cell level. However, it remains a scientific challenge for both high-quality 3D imaging and volumetric reconstruction. Here we propose a label-free, automated, and ready-to-use 3D histological imaging technique, termed microtomy-assisted autofluorescence tomography with ultraviolet excitation (MATE). With the combination of block-face imaging and serial microtome sectioning, MATE can achieve rapid and label-free imaging of paraffin-embedded whole organs at an acquisition speed of 1 cm3 per 4 hours with a voxel resolution of 1.2 × 1.2 × 10 μm3. We demonstrate that MATE enables simultaneous visualization of cell nuclei, fiber tracts, and blood vessels in mouse/human brains without tissue staining or clearing. Moreover, diagnostic features, such as nuclear size and packing density, can be quantitatively extracted with high accuracy. MATE is augmented to the current slide-based 2D histology, holding great promise for facilitating histopathological interpretation at the cell level to analyze complex tissue heterogeneity in 3D.Significance StatementConventional 3D histology based on spatial registration of serial histochemically-stained thin tissue slices is fundamentally labor-intensive and inaccurate. Here, we propose a rapid and label-free 3D histological imaging technique (i.e., MATE) that enables high-resolution imaging of complex whole organs without tissue staining or clearing. MATE is fully automated to provide a series of distortion- and registration-free images with intrinsic absorption-based contrast, demonstrating great potential as a routine tissue analysis tool that can seamlessly fit into the current clinical practice to facilitate the applications of histopathological interpretation at the subcellular level.
Motivations, concerns and selection biases when posting preprints: a survey of bioRxiv authors
Authors: Fraser Nicholas , Mayr Philipp , Peters Isabella 
Published: September 2021

AbstractSince 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors’ biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find weak evidence that authors preferentially select their highest quality, most novel or most significant research to post as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.
Honest cues contribute to male choice for female guarding in a herbivorous spider mite
Authors: Goossens Steven F. , Mortier Frederik , Parmentier Thomas , Batsleer Femke , Van Leeuwen Thomas , Wybouw Nicky , Bonte Dries 
Published: September 2021

AbstractMate choice is a wide-spread phenomenon with important effects on ecological and evolutionary dynamics of successive generations. Increasing evidence shows that males can choose females if females vary in quality and these mating choices can strongly impact fitness. In the herbivorous spider mite Tetranychus urticae males engage in precopulatory mate guarding of quiescent females, and it is known that females vary in their time to sexual maturity and fecundity. However, our understanding of how males maximize their reproductive success and which female phenotypic traits are important cues for their mating decisions are still limited. In many arthropod species, female body size and pheromones are well known proxies for fecundity. These traits—and thus possibly male mating decisions—are however sensitive to environmental (dietary) stress. By allowing males to freely choose amongst many (synchronized) females in a controlled semi natural environment, we found that guarded females have a higher fecundity and are closer to sexual maturity than non-guarded females. Despite the fact that female body size was positively correlated with fecundity and significantly influenced by the environment, males did not discriminate on body size nor did we find evidence that they used other cues like cuticular pheromones or copying behavior (social cues). In conclusion we were able to show male mate preference for females that are closer to sexual maturity and have higher fecundity, but we were unable to identify the female traits that signal this information
Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro
Authors: Ghani Usman , Desta Israel , Jindal Akhil , Khan Omeir , Jones George , Hashemi Nasser , Kotelnikov Sergey , Padhorny Dzmitry , Vajda Sandor , Kozakov Dima 
Published: September 2021

AbstractIt has been demonstrated earlier that the neural network based program AlphaFold2 can be used to dock proteins given the two sequences separated by a gap as the input. The protocol presented here combines AlphaFold2 with the physics based docking program ClusPro. The monomers of the model generated by AlphaFold2 are separated, re-docked using ClusPro, and the resulting 10 models are refined by AlphaFold2. Finally, the five original AlphaFold2 models are added to the 10 AlphaFold2 refined ClusPro models, and the 15 models are ranked by their predicted aligned error (PAE) values obtained by AlphaFold2. The protocol is applied to two benchmark sets of complexes, the first based on the established protein-protein docking benchmark, and the second consisting of only structures released after May 2018, the cut-off date for training AlphaFold2. It is shown that the quality of the initial AlphaFold2 models improves with each additional step of the protocol. In particular, adding the AlphaFold2 refined ClusPro models to the AlphaFold2 models increases the success rate by 23% in the top 5 predictions, whereas considering the 10 models obtained by the combined protocol increases the success rate to close to 40%. The improvement is similar for the second benchmark that includes only complexes distinct from the proteins used for training the neural network.
Selective activation of BK channels in small-headed dendritic spines suppresses excitatory postsynaptic potentials
Authors: Tazerart Sabrina , Blanchard Maxime G. , Miranda-Rottmann Soledad , Mitchell Diana E. , Pina Bruno Navea , Thomas Connon I. , Kamasawa Naomi , Araya Roberto 
Published: September 2021

AbstractDendritic spines are the main receptacles of excitatory information in the brain. Their particular morphology, with a small head connected to the dendrite by a slender neck, has inspired theoretical and experimental work to understand how these structural features affect the processing, storage and integration of synaptic inputs in pyramidal neurons (PNs).The activation of glutamate receptors in spines triggers a large voltage change as well as calcium signals at the spine head. Thus, voltage-gated and calcium-activated potassium channels located in the spine head likely play a key role in synaptic transmission. Here we study the presence and function of large conductance calcium-activated potassium (BK) channels in spines from layer 5 PNs. We find that BK channels are localized to dendrites and spines regardless of their size, but their activity can only be detected in spines with small head volumes (≤ 0.09 µm3), which reduces the amplitude of two-photon (2P) uncaging (u) excitatory postsynaptic potentials (EPSPs) recorded at the soma. In addition, we find that calcium signals in spines with small head volumes are significantly larger than those observed in spines with larger head volumes. In accordance with our experimental data, numerical simulations predict that synaptic inputs impinging onto spines with small head volumes generate voltage responses and calcium signals within the spine head itself that are significantly larger than those observed in spines with bigger head volumes, which are sufficient to activate spine BK channels. These results show that BK channels are selectively activated in small-headed spines, suggesting a new level of dendritic spine-mediated regulation of synaptic processing, integration, and plasticity in cortical PNs.