bluuebunny/crossref_metadata_2025 huggingface dataset:
Relative water content consistently predicts drought mortality risk in seedling populations with different morphology, physiology, and times to death
Authors: Sapes Gerard , Sala Anna
Published: December 2020

Predicted increases in forest drought mortality highlight the need for predictors of incipient drought-induced mortality (DIM) risk that enable proactive large-scale management. Such predictors should be consistent across plants with varying morphology and physiology. Because of their integrative nature, indicators of water status are promising candidates for real time monitoring of DIM, particularly if they standardize morphological differences among plants. We assessed the extent to which differences in morphology and physiology betweenPinus ponderosapopulations influence time to mortality and the predictive power of key indicators of DIM risk. Time to incipient mortality differed between populations but occurred at the same relative water content (RWC) and water potential (WP). RWC and WP were accurate predictors of drought mortality risk. These results highlight that variables related to water status capture critical thresholds during DIM and the associated dehydration processes. Both WP and RWC are promising candidates for large-scale assessments of DIM risk. RWC is of special interest because it allows comparisons across different morphologies and can be remotely sensed. Our results offer promise for real-time landscape-level monitoring of DIM and its global impacts in the near term.
The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Authors: Guo Chenxu , Tsai Shang-Jui , Ai Yiwei , Li Maggie , Pekosz Andrew , Cox Andrea , Atai Nadia , Gould Stephen J.
Published: December 2020

The spike D614G mutation increases SARS-CoV-2 infectivity, viral load, and transmission but the molecular mechanism underlying these effects remains unclear. We report here that spike is trafficked to lysosomes and that the D614G mutation enhances the lysosomal sorting of spike and the lysosomal accumulation of spike-positive punctae in SARS-CoV-2-infected cells. Spike trafficking to lysosomes is an endocytosis-independent, V-ATPase-dependent process, and spike-containing lysosomes drive lysosome clustering but display poor lysotracker labeling and reduced uptake of endocytosed materials. These results are consistent with a lysosomal pathway of coronavirus biogenesis and raise the possibility that a common mechanism may underly the D614G mutation’s effects on spike protein trafficking in infected cells and the accelerated entry of SARS-CoV-2 into uninfected cells.
Topological Insights into Mutant Huntingtin Exon 1 and PolyQ Aggregates by Cryo-Electron Tomography
Authors: Galaz-Montoya Jesús G. , Shahmoradian Sarah H. , Shen Koning , Frydman Judith , Chiu Wah
Published: December 2020

Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregatesin vitroare structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we observed some filaments in both types of aggregates under ∼2 nm in width, thinner than previously reported, while other regions form large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy, slab-shaped morphology in both aggregates, supportive of the “polyQ core” model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling and their identification in cells without fusion tags.
Heterogenous adhesion of follower cells affects tension profile and velocity of leader cells in primary keratocyte collective cell migration
Authors: Mukherjee Baishali , Chakraborty Madhura , Biswas Arikta , Nayak Rajesh Kumble , Sinha Bidisha
Published: December 2020

Single cell studies demonstrate membrane tension to be a central regulator of lamellipodia-driven motility bringing in front-coherence. During collective cell migration, however, tension mapping or existence of intracellular tension-gradients and the effect of cell-cell interactions have remained unexplored. In this study of membrane fluctuations and fluctuation-tension of migrating primary keratocyte cell-sheets, we first show that some leader cells are followed by followers which remain de-adhered from the substrate while being attached to other cells and thus appear to be “taking a ride”. A subtle yet significant enhanced long-timescale velocity in these leaders indicate increased directionality. Intriguingly, such leaders mostly have front-high tension gradients like single keratocytes, while followers and other leaders usually display front-low membrane tension gradients. The front-high tension gradient and higher membrane tension observed in these leaders, despite the high cell-to-cell variability in membrane tension demonstrate how leader-follower interactions and heterogenous adhesion profiles are key in collective cell migration.
Evolving Structure and Diversity of Human Narratives in the Journal of Stories in Science
Authors: Mach Reilly Q. , Tsai Jessica W. , Muindi Fanuel J.
Published: December 2020

Fundamentally, science is about people. The stories of the people behind the science are just as important as the results themselves, even though the results are often what get more attention. Despite the growth of databases storing such stories across diverse mediums, a detailed assessment of those databases is missing. To continue innovating science storytelling, we provide the first assessment of the structure and diversity of the narratives published in the Journal of Stories in Science. In this assessment, a total of 170 published stories authored by 158 authors between 2016 and 2020 are analyzed. Majority (67%) of the authors are women from North America and in the life sciences. The narratives most commonly feature authors from academia (e.g., 23% graduate students, 13% post-doctoral fellows and 21% professors). However, there is also a growing number of authors with PhDs that are working outside of academia (15%). Nearly a quarter (23%) of the database authors come from racial groups (African American, Latino, and Hispanic) that have been shown to be underrepresented in health-related sciences in the United States. Using the industry standard Flesch Reading Ease Score, we found that 74% of the stories included in the analysis fall in the target range of 50-70, which represents readability by students in grades 8-12. The analysis here provides the first deep look into one of the databases publishing diverse stories in science using a wide range of mediums. In summary, there is a need for more emphasis on both expanding and studying such databases given the continuous demand for these stories and their inclusion into K-12 curriculums.
constclust: Consistent Clusters for scRNA-seq
Authors: Virshup Isaac , Choi Jarny , Lê Cao Kim-Anh , Wells Christine A
Published: December 2020

1

Unsupervised clustering to identify distinct cell types is a crucial step in the analysis of scRNA-seq data. Current clustering methods are dependent on a number of parameters whose effect on the resulting solution’s accuracy and reproducibility are poorly understood. The adjustment of clustering parameters is therefore ad-hoc, with most users deviating minimally from default settings.constclustis a novel meta-clustering method based on the idea that if the data contains distinct populations which a clustering method can identify, meaningful clusters should be robust to small changes in the parameters used to derive them. By reconciling solutions from a clustering method over multiple parameters, we can identify locally robust clusters of cells and their corresponding regions of parameter space. Rather than assigning cells to a single partition of the data set, this approach allows for discovery of discrete groups of cells which can correspond to the multiple levels of cellular identity. Additionallyconstclustrequires significantly fewer computational resources than current consensus clustering methods for scRNA-seq data. We demonstrate the utility, accuracy, and performance ofconstclustas part of the analysis workflow.constclustis available athttps://github.com/ivirshup/constclust1.
Pseudodesulfovibrio cashewsp. nov., a novel deep-sea sulfate-reducing bacterium, linking heavy metal resistance and sulfur cycle
Authors: Zheng Rikuan , Sun Chaomin
Published: December 2020

Sulfur cycling is primarily driven by sulfate reduction mediated by sulfate-reducing bacteria (SRB) in marine sediments. The dissimilatory sulfate reduction drives the production of enormous quantities of reduced sulfide and thereby the formation of highly insoluble metal sulfides in marine sediments. Here, a novel sulfate-reducing bacterium designatedPseudodesulfovibrio cashewSRB007 was isolated and purified from the deep-sea cold seep and proposed to represent a novel species in the genus ofPseudodesulfovibrio.A detailed description of the phenotypic traits, phylogenetic status and central metabolisms of strain SRB007, allowing the reconstruction of the metabolic potential and lifestyle of a novel member of deep-sea SRB. Notably,P. cashewSRB007 showed a strong ability to resist and remove different heavy metal ions including Fe3+, Co2+, Ni2+, Cu2+, Cd2+and Hg2+. And the dissimilatory sulfite reduction was demonstrated to contribute to the prominent removal capability ofP. cashewSRB007 against different heavy metals via forming insoluble metal sulfides.

IMPORTANCE

The dissimilatory sulfate reduction driven by sulfate-reducing bacteria (SRB) was ubiquitous in marine sediments, and was proposed to couple with heavy metal ions removal through forming insoluble metal sulfides. The deep-sea cold seep is a very special environment where is rich in sulfate and novel species of SRB that possessing many unknown mechanisms toward sulfur cycle. Here, a novel sulfate-reduction bacteriumPseudodesulfovibrio cashewSRB007 was isolated from the deep-sea cold seep and proposed as the type strain for a novel species. The taxonomy and typical physiological properties closely related to sulfur cycle, heavy metal resistance and their co-relationship were disclosed through a combination of genomic and biochemical methods. Given the absence of pure cultures of typical SRB isolated from the deep-sea cold seep, our work provides a good model to study the sulfur cycle which coupling with other elements and a potential candidate to develop bioremediation product in the future.
Protease-mediated processing of Argonaute proteins controls small RNA association
Authors: Gudipati Rajani Kanth , Braun Kathrin , Gypas Foivos , Hess Daniel , Schreier Jan , Carl Sarah H. , Ketting René F. , Großhans Helge
Published: December 2020

Small RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. We find that WAGO-1 and WAGO-3 Argonaute (Ago) proteins are matured through proteolytic processing of their unusually proline-rich N-termini. In the absence of DPF-3, a P-granule-localized N-terminal dipeptidase orthologous to mammalian DPP8/9, processing fails, causing a change of identity of 22G RNAs bound to these WAGO proteins. Desilencing of repeat- and transposon-derived transcripts, DNA damage and acute sterility ensue. These phenotypes are recapitulated when WAGO-1 and WAGO-3 are rendered resistant to DFP-3-mediated processing, identifying them as critical substrates of DPF-3. We conclude that N-terminal processing of Ago proteins regulates their activity and promotes discrimination of self from non-self by ensuring association with the proper complement of small RNAs.

Graphical Abstract: The role of DPF-3 in the fertility of the animals

In wild type animals, the WAGO-1 and WAGO-3 Argonaute proteins are produced as immature pro-proteins with N-termini (N) that are unusually rich in prolines (P). N-terminal processing by DPF-3 is required for loading of the proper small RNA cargo and stabilization of WAGO-3. Accordingly, loss of this processing activity causes desilencing of transposable elements (TE), cell death and sterility.
Removal of KCNQ2 from Parvalbumin-expressing Interneurons Improves Anti-Seizure Efficacy of Retigabine
Authors: Jing Junzhan , Dunbar Corrinne , Sonesra Alina , Chavez Ana , Park Suhyeorn , Soh Heun , Lee Maxwell , Tzingounis Anastasios , Cooper Edward C. , Jiang Xiaolong , Maheshwari Atul
Published: December 2020

Anti-seizure drug (ASD) targets are widely expressed in both excitatory and inhibitory neurons. It remains unknown if the action of an ASD upon inhibitory neurons could counteract its beneficial effects on excitatory neurons (or vice versa), thereby reducing the efficacy of the ASD. Here, we examine whether the efficacy of the ASD retigabine (RTG) is altered after removal of the Kv7 potassium channel subunit KCNQ2, one of its drug targets, from parvalbumin-expressing interneurons (PV-INs). Parvalbumin-Cre (PV-Cre) mice were crossed withKcnq2-floxed (Kcnq2fl/fl) mice to conditionally deleteKcnq2from PV-INs. In these conditional knockout mice (cKO, PV-Kcnq2fl/fl), RTG (10 mg/kg, i.p.) significantly delayed the onset of either picrotoxin (PTX, 10 mg/kg, i.p)- or kainic acid (KA, 30mg/kg, i.p.)-induced convulsive seizures compared to vehicle, while RTG was not effective in wild-type littermates (WT). Immunostaining for KCNQ2 and KCNQ3 revealed that both subunits were enriched at axon initial segments (AISs) of hippocampal CA1 PV-INs, and their specific expression was selectively abolished in cKO mice. Accordingly, the M-currents recorded from CA1 PV-INs and their sensitivity to RTG were significantly reduced in cKO mice. While the ability of RTG to suppress CA1 excitatory neurons in hippocampal slices was unchanged in cKO mice, its suppressive effect on the spike activity of CA1 PV-INs was significantly reduced compared with WT mice. In addition, the RTG-induced suppression on intrinsic membrane excitability of PV-INs in WT mice was significantly reduced in cKO mice. These findings suggest that preventing RTG from suppressing PV-INs improves its anticonvulsant effect.

Significance Statement

One out of three patients with epilepsy remain resistant to anti-seizure drugs (ASD). Therefore, strategies that can enhance the efficacy of current ASDs or aid in the development of novel ASDs are in high demand. Here we show that by sparing a subset of inhibitory neurons, the ASD retigabine becomes more efficacious. These findings indicate that developing the ASDs that have relatively greater effects on excitatory over inhibitory neurons may be an effective strategy to improve the efficacy of ASDs.
Sparse Coding in Temporal Association Cortex Improves Complex Sound Discriminability
Authors: Feigin L , Tasaka G , Maor I , Mizrahi A
Published: December 2020

The mouse auditory cortex is comprised of several auditory fields spanning the dorso-ventral axis of the temporal lobe. The ventral most auditory field is the temporal association cortex (TeA), which remains largely unstudied. Using Neuropixels probes, we simultaneously recorded from primary auditory cortex (AUDp), secondary auditory cortex (AUDv) and TeA, characterizing neuronal responses to pure tones and frequency modulated (FM) sweeps in awake head-restrained mice. As compared to primary and secondary auditory cortices, single unit responses to pure tones in TeA were sparser, delayed and prolonged. Responses to FMs were also sparser. Population analysis showed that the sparser responses in TeA render it less sensitive to pure tones, yet more sensitive to FMs. When characterizing responses to pure tones under anesthesia, the distinct signature of TeA was changed considerably as compared to that in awake mice, implying that responses in TeA are strongly modulated by non-feedforward connections. Together with the known connectivity profile of TeA, these findings suggest that sparse representation of sounds in TeA supports selectivity to higher-order features of sounds and more complex auditory computations.
Bacterial sirtuin CobB and PRPP synthase crosstalk in regulation of protein acetylation
Authors: Walter Beata M. , Morcinek-Orłowska Joanna , Szulc Aneta , Lovering Andrew L. , Banzhaf Manuel , Glinkowska Monika
Published: December 2020

Protein lysine acetylation, regulates a wide range of cellular functions and is controlled by protein deacetylases called sirtuins. In eukaryotes, sirtuins activity is coupled to the spatiotemporally-controlled NAD+ level. However, regulation of the bacterial sirtuin CobB and its coupling to the NAD+ metabolism is not well understood. In this work we show that such coordination inEscherichia colicells is achieved through a CobB interaction with PRPP synthase Prs, an enzyme necessary for NAD+ synthesis. Probing CobB protein-protein interactions, we demonstrate that it forms a stable complex with Prs. This assembly stimulates CobB deacetylase activity and partially protects it from inhibition by nicotinamide. We provide evidence that Prs acetylation is not necessary for CobB binding but affects the global acetylome and CobB activityin vivo. Consequently, we show that Prs acetylation status affects bacterial growth under different metabolic regimes. Therefore, we propose that CobB-Prs crosstalk orchestrates the NAD+ metabolism and protein acetylation in response to environmental cues.
The tardigradeHypsibius exemplarisas an emerging model to study the mitochondrial alternative oxidase at animal organismal level
Authors: Grobys Daria , Roszkowska Milena , Kaczmarek Łukasz , Jarmuszkiewicz Wiesława , Karachitos Andonis , Kmita Hanna
Published: December 2020

Mitochondrial alternative oxidase (AOX) is present in mitochondria of many invertebrates. Independently of the reason concerning the enzyme occurrence in animal mitochondria, expression of AOX in human mitochondria is regarded as a potential therapeutic strategy. Till now, relevant data were obtained due to heterologous AOX expression in cells and animals without natively expressed AOX. Application of animals natively expressing AOX importantly contribute the research. Thus, we investigatedHypsibius exemplarisas a model for AOX activity analysis. We observed thatH. exemplaristolerance to the blockage of the MRC complexes was diminished in the presence of AOX inhibitor and the inhibitor-sensitive respiration enabled the tardigrade respiration under condition of the blockage. Furthermore, although detection of AOX at protein level and pronounced oxygraphic registration of its activity required the MRC complex blockage, the obtained data indicated that AOX clearly contributed animal functioning. We demonstrated that AOX activity in tardigrades, can be monitored by measurement of intact specimen whole-body respiration. Furthermore, it was also possible to monitor the impact of the MRC complex IV blockage on AOX expression and AOX inhibition in the absence of the blockage on animal functioning. Thus,H. exemplarisis applied as a whole-animal model suitable to study AOX.
CLEAN AND FOLDED: OPTIMIZED PRODUCTION OF HIGH QUALITY RECOMBINANT HUMAN INTERFERON-Λ1
Authors: Shaldzhyan Aram , Yolshin Nikita , Zabrodskaya Yana , Kudling Tatiana , Lozhkov Alexey , Plotnikova Marina , Ramsay Edward , Taraskin Aleksandr , Nekrasov Peter , Grudinin Mikhail , Vasin Andrey
Published: December 2020

Type III interferons exhibit antiviral activity against influenza viruses, coronaviruses, rotaviruses, and others. In addition, this type of interferon theoretically has therapeutic advantages, in comparison with type I interferons, due to its ability to activate a narrower group of genes in a relatively small group of target cells. Hence, it can elicit more targeted antiviral or immunomodulatory responses. Obtaining biologically-active interferon lambda (hIFN-λ1) is fraught with difficulties at the stage of expression in soluble form or, in the case of expression in the form of inclusion bodies, at the stage of refolding. In this work, hIFN-λ1was expressed in the form of inclusion bodies, and a simple, effective refolding method was developed. Efficient and scalable methods for chromatographic purification of recombinant hIFN-λ1were also developed. High-yield, high-purity product was obtained through optimization of several processes including: recombinant protein expression; metal affinity chromatography; cation exchange chromatography; and an intermediate protein refolding stage. The obtained protein was shown to have expected, specific biological activity in line with published effects: induction of MxA gene expression in A549 cells.
Millimeter-resolution mapping of citrate exuded from soil grown roots using a novel, low-invasive sampling technique
Authors: Tiziani Raphael , Puschenreiter Markus , Smolders Erik , Mimmo Tanja , Herrera José Carlos , Cesco Stefano , Santner Jakob
Published: December 2020

The reliable sampling of root exudates in soil grown plants is experimentally challenging. This study aimed at developing a citrate sampling and mapping technique with millimetre-resolution using DGT (diffusive gradients in thin films) ZrOH binding gels. Citrate adsorption kinetics, DGT capacity and stability of ZrOH gels were evaluated. ZrOH gels were applied to generate 2D maps of citrate exuded by white lupin roots grown in rhizotrosn in a phosphorus deficient soil. Citrate was adsorbed quantitatively and rapidly by the ZrOH gels, these gels can be stored after sampling for several weeks prior to analysis. The DGT capacity of the ZrOH gel for citrate depends on the ionic strength and the pH of the soil solution but was suitable for citrate sampling. 2D citrate maps of rhizotron grown plants have been generated for the first time at a millimetre resolution to measure an illustrated plant response to P fertilization. DGT-based citrate sampling is suitable for studying the root exudation in soil environments, at unprecedented spatial resolution. By changing binding material, the technique is also applicable to other exudate classes and might be used for the evaluation of whole root exudation crucial in specific cultivar breeding.

Highlight

We present a novel, reliable, easy to use, non-destructive citrate sampling- and two-dimensional high-resolution imaging technique for soil grown plant roots.
CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments
Authors: Seiler Christof , Ferreira Anne-Maud , Kronstad Lisa M. , Simpson Laura J. , Gars Mathieu Le , Vendrame Elena , Blish Catherine A. , Holmes Susan
Published: December 2020

Background

Flow and mass cytometry are important modern immunology tools for measuring expression levels of multiple proteins on single cells. The goal is to better understand the mechanisms of responses on a single cell basis by studying differential expression of proteins. We focus on cell-specific differential analysis and one fixed cell type. In contrast, most current methods learn cell types and perform differential analysis jointly. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees.

Results

Differential analysis of marker expressions can be difficult due to marker correlations and inter-individual heterogeneity, particularly for studies of human immunology. We address these challenges with two multiple regression strategies: A bootstrapped generalized linear model and a generalized linear mixed model. On simulated datasets, we compare the robustness towards marker correlations and heterogeneity of both strategies. For paired experiments, we find that both strategies maintain the target false discovery rate under medium correlations and that mixed models are statistically more powerful under the correct model specification. For unpaired experiments, our results indicate that much larger patient sample sizes are required to detect differences. We illustrate theCytoGLMMRpackage and workflow for both strategies on a pregnancy dataset.

Conclusions

Our approach to find differential proteins in flow and mass cytometry data reduces biases arising from maker correlations and safeguards against false discoveries induced by patient heterogeneity.
EVI/WLS function is regulated by ubiquitination and linked to ER-associated degradation by ERLIN2
Authors: Wolf Lucie , Lambert Annika , Haenlin Julie , Boutros Michael
Published: December 2020

Wnt signalling is important for development in all metazoan animals and associated with various human diseases. The Ubiquitin-Proteasome System (UPS) and regulatory ER-associated degradation (ERAD) has been implicated in the secretion of WNT proteins. Here, we investigated how the WNT secretory factor EVI/WLS is ubiquitinated, recognised by ERAD components, and subsequently removed from the secretory pathway. We performed a focused, immunoblot-based RNAi screen for factors that influence EVI/WLS protein stability. We identified the VCP-binding proteins FAF2 and UBXN4 as novel interaction partners of EVI/WLS and showed that ERLIN2 links EVI/WLS to the ubiquitination machinery. Interestingly, we found in addition that EVI/WLS is ubiquitinated and degraded in cells irrespective of their level of WNT production. K11, K48, and K63-linked ubiquitination is mediated by the E2 ubiquitin conjugating enzymes UBE2J2, UBE2N, and UBE2K, but independent of the E3 ligases HRD1/SYVN. Taken together, our study identified factors that link UPS to the WNT secretory pathway and provides mechanistic details on the fate of an endogenous substrate of regulatory ERAD in mammalian cells.
Comparative genomics provides insight into the function of broad-host range sponge symbionts
Authors: Waterworth Samantha C. , Parker-Nance Shirley , Kwan Jason C. , Dorrington Rosemary A.
Published: December 2020

As the oldest extant metazoans, sponges (PhylumPorifera) have been forming symbiotic relationships with microbes that may date back as far as 700 million years. Most symbionts are conserved within a narrow host range and perform specialized functions. However, there are widely distributed bacterial taxa such asPoribacteria, SAULandTethybacteralesthat are found in a broad range of invertebrate hosts. Here, we added eleven new genomes to theTethybacteralesorder, identified a novel family, and show that functional potential differs between the threeTethybacteralesfamilies. We compare theTethybacteraleswith the well-characterizedEntoporibacteriaand show that these broad-host range, sponge-associated bacteria likely perform distinct functions within their hosts and that their respective phylogenies are incongruent with their host phylogenies. These results suggests that ancestors of these bacteria may have undergone multiple association events, rather than a single association event followed by co-evolution.

IMPORTANCE

Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three know bacterial taxa (Entoporibacteria, SAULandTethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. Understanding what distinguishes these broad-host range symbionts from specialized symbionts will provide insight into the mechanisms by which sponges form these symbioses. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. This contrasts with specialized symbionts, where function is often a strain-specific trait and have co-evolved with their host following a single association event.
Limitations of DNA barcoding in determining the origin of smuggled seahorses and pipefishes
Authors: Serite Conny P. , Ntshudisane Ofentse K. , Swart Eugene , Simbine Luisa , Jaime Graça L. M. , Teske Peter R.
Published: December 2020

Seahorses and pipefishes are heavily exploited for use in Traditional Chinese Medicine (TCM), and less frequently for curio markets or as aquarium fish. A number of recent studies have used DNA barcoding to identify species sold at TCM markets in East Asia, but the usefulness of this approach in determining the region of origin remains poorly explored. Here, we generated DNA barcodes of dried seahorses and pipefishes destined for TCM that were confiscated at South Africa’s largest airport because they lacked the export permits required for the CITES-listed seahorses. These were compared with published sequences and new sequences generated for Mozambican seahorses, with the aim of determining whether it is possible to identify their country of origin. All pipefishes were identified asSyngnathoides biaculeatus, a widespread Indo-Pacific species, but the published sequence data did not provide sufficient resolution to identify the region of origin. The same was true of the majority of seahorses, which could not even be identified to species level because they clustered among an unresolved species complex whose sequences were published under the namesHippocampus kuda, H. fuscusandH. capensis. The presence of a few specimens of a second seahorse,H. camelopardalis, suggests that the shipment originated from East Africa because the range of this seahorse is centred around this region, but again, it was not possible to determine their country of origin. Even though seahorses and pipefishes have high levels of genetic population structure because of their low dispersal potential, DNA barcoding was only suitable to tentatively identify species, but not their region of origin. DNA barcoding is increasingly used to identify illegally traded wildlife, but our results show that more sophisticated methods are needed to monitor and police the trade in seahorses and pipefishes.
Short stop is a gatekeeper at the ring canals ofDrosophilaovary
Authors: Lu Wen , Lakonishok Margot , Gelfand Vladimir I.
Published: December 2020

Microtubules and actin filaments are two major cytoskeletal components essential for a variety of cellular functions. Spectraplakins are a family of large cytoskeletal proteins cross-linking microtubules and actin filaments among other components. In this study, we aim to understand how Short stop (Shot), the singleDrosophilaspectraplakin, coordinates microtubules and actin filaments for oocyte growth. The oocyte growth completely relies on the acquisition of cytoplasmic materials from the interconnected sister cells (nurse cells), through ring canals, cytoplasmic bridges that remained open after incomplete germ cell division. Given the open nature of the ring canals, it is unclear how the direction of transport through the ring canal is controlled. Here we show that Shot controls the directionality of flow of material from the nurse cells towards the oocyte. Knockdown ofshotchanges the direction of transport of many types of cargo through the ring canals from unidirectional (toward the oocyte) to bidirectional, resulting in small oocytes that fail to grow over time. In agreement with this flow-directing function of Shot, we find that it is localized at the asymmetric actin fibers adjacent to the ring canals at the nurse cell side, and controls the uniform polarity of microtubules located in the ring canals connecting the nurse cells and the oocyte. Together, we propose that Shot functions as a gatekeeper directing the material flow from the nurse cells to the oocyte, via organization of microtubule tracks.
Calculating sample size requirements for temporal dynamics in single cell proteomics
Authors: Boekweg Hannah , Guise Amanda J. , Plowey Edward D. , Kelly Ryan T. , Payne Samuel H.
Published: December 2020

Single cell measurements are uniquely capable of characterizing cell-to-cell heterogeneity, and have been used to explore the large diversity of cell types and physiological functions present in tissues and other complex cell assemblies. An intriguing application of single cell proteomics is the characterization of proteome dynamics during biological transitions, like cellular differentiation or disease progression. Time course experiments, which regularly take measurements during state transitions, rely on the ability to detect dynamic trajectories in a data series. However, in a single cell proteomics experiment, cell-to-cell heterogeneity complicates the confident identification of proteome dynamics as measurement variability may be higher than expected. Therefore, a critical question for these experiments is how many data points need to be acquired during the time course to enable robust statistical analysis. We present here an analysis of the most important variables that affect statistical confidence in the detection of proteome dynamics: fold-change, measurement variability, and the number of cells measured during the time course. Importantly, we show that datasets with less than 16 measurements across the time domain suffer from low accuracy and also have a high false-positive rate. We also demonstrate how to balance competing demands in experimental design to achieve a desired result.
Integrating continuous hypermutation with high-throughput screening for optimization ofcis,cis-muconic acid production in yeast
Authors: Jensen Emil D. , Ambri Francesca , Bendtsen Marie B. , Javanpour Alex A. , Liu Chang C. , Jensen Michael K. , Keasling Jay D.
Published: December 2020

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection, and amplification. While powerful, systematic searches through large sequence-spaces is a labor-intensive task, and can be further limited bya prioriknowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generates enzyme variants using the recently developed orthogonal replication system, OrthoRep, and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a ratelimiting enzymatic reaction of the biosynthetic pathway forcis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, inSaccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers >13-fold compared to reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study, is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.
Poxviruses package viral redox proteins in lateral bodies and modulate the host oxidative response
Authors: Bidgood Susanna R. , Novy Karel , Collopy Abigail , Albrecht David , Krause Melanie , Burden Jemima J. , Wollscheid Bernd , Mercer Jason
Published: December 2020

All poxviruses contain a set of proteinaceous structures termed lateral bodies (LB) that deliver viral effector proteins into the host cytosol during virus entry. To date, the spatial proteotype of LBs remains unknown. Using the prototypic poxvirus, vaccinia virus (VACV), we employed a quantitative comparative mass spectrometry strategy to determine the poxvirus LB proteome. We identified a large population of cellular proteins, the majority being mitochondrial, and 15 viral LB proteins. Strikingly, one-third of these comprise the full set of VACV redox proteins whose LB residency could be confirmed using super-resolution microscopy. We further show that VACV infection exerts an anti-oxidative effect on host cells and that artificial induction of oxidative stress impacts early gene expression and virion production. In addition to defining the spatial proteotype of these enigmatic viral structures, these findings implicate poxvirus redox proteins as modulators of host oxidative anti-viral responses and provide a solid starting point for future investigations into the role of LB resident proteins in host immunomodulation.
Genome-wide sequence data show no evidence of admixture and introgression among pollinator wasps associated with a community of Panamanian strangler figs
Authors: Satler Jordan D. , Herre Edward Allen , Heath Tracy A. , Machado Carlos A. , Gómez Zúñiga Adalberto , Nason John D.
Published: December 2020

Interactions between plants and their animal pollinators can shape processes of divergence and gene flow within associated lineages. For example, in the obligate mutualism between figs (Ficus) and fig pollinator wasps (family Agaonidae), each wasp species typically pollinates a single fig species, potentially reinforcing reproductive isolation among different wasp species. Multiple pollinator species, however, can sometimes reproduce in the same host fig species, potentially enabling hybridization and introgression between wasp species. In a community of Panamanian strangler figs (sectionAmericana), we use genome-wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and gene flow among 19 pollinator species associated with 16 host fig species. Previous studies showing ongoing pollinator sharing and a history of pollinator host switching are consistent with documented genetic admixture in their host figs. Here we investigate if host sharing and a dynamic evolutionary history including host switching has also resulted in hybridization and gene flow between pollinator species. Phylogenetic analyses recover strong support for well-delimited wasp species coupled with high interspecific divergence. There is no evidence for ongoing hybridization or introgression, even among pairs of pollinator species currently reproducing within the same host. In contrast to work suggesting admixture among Panamanian host figs, we conclude hybridization and interspecific gene flow have not been important processes shaping the evolutionary history of their pollinating wasps.
The biophysical basis of protein domain compatibility
Authors: Coyote-Maestas Willow , Nedrud David , Suma Antonio , He Yungui , Matreyek Kenneth A. , Fowler Douglas M. , Carnevale Vincenzo , Myers Chad L. , Schmidt Daniel
Published: December 2020

Understanding the biophysical mechanisms that govern the combination of protein domains into viable proteins is essential for advancing synthetic biology and biomedical engineering. Here, we use massively parallel genotype/phenotype assays to determine cell surface expression of over 300,000 variants of the inward rectifier K+channel Kir2.1 recombined with hundreds of protein motifs. We use machine learning to derive a quantitative biophysical model and practical rules for domain recombination. Insertional fitness depends on nonlinear interactions between the biophysical properties of inserted motifs and the recipient protein, which adds a new dimension to the rational design of fusion proteins. Insertion maps reveal a generalizable hierarchical organization of Kir2.1 and several other ion channels that balances stability needed for folding and dynamics required for function.

Massively parallel assays reveal interactions between donor domains and recipient proteins govern domain compatibility
A systematic conduct of POE for polyclinic facilities in Saudi Arabia
Authors: Salaheldin Mohammad H. , Hassanain Mohammad A. , Ibrahim Ahmed M.
Published: December 2020

Purpose

This paper presents a systematic conduct of post-occupancy evaluation (POE) for polyclinic facilities at public hospitals.

Design/methodology/approach

This is a mixed design research, where a review of literature was utilized, to qualitatively synthesize POE research on healthcare facilities. Three polyclinic facilities at Saudi Arabia were then assessed. The assessment was systematically conducted by the utilization of surveys and relative importance indices to solicit the experts’ and users' perspectives. The research included the conduct of physical measurements and walkthroughs inspections. Lastly, focus group meetings were conducted to generate recommendations that would improve the built environment conditions of polyclinic facilities.

Findings

The research identified unsatisfactory zoning, indoor air quality and concerns related to installations of different systems. Performance elements and subsequent indicators were identified and evaluated for their significance. The knowledge of these, enables the systematic conduct of POE, by exemplary case studies, for the managers and decision-makers of polyclinic facilities.

Originality/value

This research presents a comprehensive approach for the systematic conduct of POE at polyclinic facilities. The research enriches the literature and fulfils a contextual gap. The recommendations serve to enhance feedforward, the design and management of healthcare facilities.
Architecture students' satisfaction with and perceptions of online design studios during COVID-19 lockdown: the case of Jordan universities
Authors: Alnusairat Saba , Al Maani Duaa , Al-Jokhadar Amer
Published: December 2020

Purpose

The purpose of this study is to examine the attitudes of students in higher educational institutions in Jordan towards the use of online design studios during coronavirus disease 2019 (COVID-19) lockdown and discusses how their use could enhance the learning process.

Design/methodology/approach

615 undergraduate students studying architecture in Jordanian universities were recruited to explore the factors that constituted and affected their perceptions of online design studios.

Findings

The findings of this study highlight that many of the participants felt uncertain about aspects of their online learning experience and wanted more guidance and support. Reasons of this disengagement include technical factors, such as poor network quality and lack of familiarity with the new applications. Students and tutors' personal situations when working and studying from home are also relevant due to the tutors' lack of expertise in online teaching, and the limitations of peer interaction. Together, these factors can make the experience of the online design studio more challenging.

Research limitations/implications

The sample was nationally representative of architecture students from various institutions. However, the study was limited to an exploration of students' opinions, and it did not include the points of view of tutors and decision-makers.

Originality/value

This research was conceived during the period of the COVID-19 lockdown, whilst both tutors and students were experiencing dramatic changes in their modes of teaching and learning due to the sudden move from on-campus design studios to a virtual alternative, with only the bare minimum of resources and relevant experience. Learners' perspectives can enhance understanding of online design studios to assess their quality and effectiveness.
Management control system for corporate social responsibility implementation – a stakeholder perspective
Authors: Adib Mohamed , Zhang Xianzhi , A.A.Zaid Mohammad , Sahyouni Ahmad
Published: December 2020

Purpose

The purpose of this paper is to build a framework that intends to help organizations define, implement and control their corporate social responsibility (CSR) strategies. Based on the stakeholder perspective, this paper proposes a sustainability management control system (SMCS) specifically made for the definition and implementation of CSR strategy, by linking the firm’s material topics to its key stakeholders, thus, allowing our model to be dynamic to different business environments.

Design/methodology/approach

In this paper, the authors constructed their model based on a review of selective relevant studies about CSR and SMCSs. This paper also went through different practical concepts from leading sustainability guidelines and stakeholder’s engagement manuals, discussing the stakeholder identification and prioritization, to re-center the debate to the strategic importance of the stakeholder perspective in defining and implementing CSR strategy, as well as its importance in how organizations can define proxies to assess the performance of their CSR initiatives.

Findings

Adopting the stakeholder theory as a key lens to re-frame, organize and guide the debate over the performance consequences of CSR has the potential to overcome the simplistic and (eventual) misleading conceptions of CSR strategy implementation, thus fostering the move toward more effective and efficient CSR strategies, by developing management control system (MCS) typical for CSR issues.

Social implications

The full process of the model outlined in this paper aims to provide a comprehensive and forward-looking tool for CSR and sustainability strategy implementation and assessment. Our model could help companies to gain an overview and an understanding of the relative importance of the material topics of their business activities that should be addressed and how they are related to the key stakeholders, thus, eventually leading to more equitable and sustainable social development by giving those who have a right to be heard the opportunity to be considered in the sustainability decision-making and strategy processes, in the aim of making valuable contributions to social, economic and environmental spheres.

Originality/value

The paper answers the call for research for developing novel theoretical foundations to design MCSs for CSR implementation. Therefore, the paper suggests an innovative model of SMCS for CSR strategy definition, development and implementation and helping organizations to define and develop key sustainability indicators specific to their business environment. The model also presents an opportunity to rethink and advance the understanding of how managers can prioritize competing stakeholders’ claims, which are constrained by the company’s business activities impacts.