bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying nearshore nursery habitats for sharks in the Eastern Tropical Pacific from fisheries landings and interviews
Authors: López-Angarita Juliana , Villate Melany , Díaz Juan Manuel , Cubillos Juan C. , Tilley Alexander
Published: February 2021

The Eastern Tropical Pacific (ETP) comprising the coasts of Costa Rica, Panama, Colombia and Ecuador, represents an area of high marine biodiversity that supports productive fisheries and acts as an important migratory corridor for many marine species. Despite its biological importance, the ETP is understudied and lacks sufficient data for science-based fisheries management and conservation decision-making. This study aims to consolidate understanding of the current and historical distribution of sharks and mobulid rays in the ETP. We used interviews of coastal community stakeholders to document traditional knowledge of shark and mobulid ray species and distributions. We also analysed small-scale fisheries landings data, where available, to quantify local exploitation patterns and the importance of sharks and rays in small-scale fisheries catches. All shark species landed in the dominant nearshore gillnet fishery show very low mean individuals weights (<5 kg), indicating that the fisheries are dominated by juveniles, captured. Aside from smooth-hounds (Mustelusspp.), the scalloped hammerhead shark,Sphyrna lewini, is the most frequently landed shark species in the region by weight and number, with peaks in abundance between April - July. From 132 interviews in 51 communities across the three countries, and landings data from two small-scale fisheries sites, we identified 41 sites in 12 broad geographical zones as important shark nursery habitats. Of these sites, 68% were associated closely with large mangrove systems of the ETP, highlighting the importance of this habitat for shark life history. No patterns were seen in the occurrence or distribution of mobulid rays in coastal areas. Marine protected areas and responsible fishing zones cover 37% of identified nursery habitats in the ETP, 30% in Costa Rica, 48% in Panama and 30% in Colombia. These findings provide an important benchmark of the conservation status of sharks in the ETP and allow for the prioritisation of research and policy-making.
In vivoidentification and validation of novel potential predictors for human cardiovascular diseases
Authors: Hammouda Omar T. , Wu Meng Yue , Kaul Verena , Gierten Jakob , Thumberger Thomas , Wittbrodt Joachim
Published: February 2021

Genetics crucially contributes to cardiovascular diseases (CVDs), the global leading cause of death. Since the majority of CVDs can be prevented by early intervention there is a high demand for predictive markers. While genome wide association studies (GWAS) correlate genes and CVDs after diagnosis and provide a valuable resource for such markers, preferentially those with previously known or suspected function are addressed further. To tackle the unaddressed blind spot of understudied genes, we particularly focused on the validation of heart GWAS candidates with little or no apparent connection to cardiac function. Building on the high conservation of basic heart function and underlying genetics from fish to human we combined CRISPR/Cas9 genome editing of the orthologs of human GWAS candidates in isogenic medaka with automated high-throughput heart rate analysis. Our functional analyses of understudied human candidates uncovered a prominent fraction of heart rate associated genes from adult human patients displaying a heart rate effect in embryonic medaka already in the injected generation. Following this pipeline, we identified 16 GWAS candidates with potential diagnostic and predictive power for human CVDs.
Global spread and evolutionary history of HCV subtype 3a
Authors: lin Shang-kuan , De Maio Nicola , Pedergnana Vincent , Wu Chieh-Hsi , Thézé Julien , Barnes Ellie , Ansari M. Azim
Published: February 2021

Studies have shown that HCV subtype 3a had likely been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV subtype 3a from the UK, North America, Australia and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV subtype 3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country and that they were more diverse than viruses from other host ancestries. We also inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America and the Australian continent. This initial spread happened during or soon after the end of the second world war. This was followed by an exponential growth in the effective population size of HCV subtype 3a worldwide and many independent transmissions between the UK, North America and Australian continent. Using both host and virus genomic information can be highly informative in studying the virus epidemic history especially in the context of chronic infections.
PIGNON: A protein-protein interaction-guided functional enrichment analysis for quantitative proteomics
Authors: Nadeau Rachel , Byvsheva Anastasiia , Lavallée-Adam Mathieu
Published: February 2021

Background

Quantitative proteomics studies are often used to detect proteins that are differentially expressed across different experimental conditions. Functional enrichment analyses are then typically used to detect annotations, such as biological processes that are significantly enriched among such differentially expressed proteins to provide insights into the molecular impacts of the studied conditions. While common, this analytical pipeline heavily relies on arbitrary thresholds of significance. Indeed, a functional annotation may be dysregulated in a given experimental condition, while none or very few of its proteins may be individually considered to be significantly differentially expressed. Such an annotation would therefore be missed by standard approaches.

Results

Herein, we propose a novel graph theory-based method, PIGNON, for the detection of differentially expressed functional annotations in different conditions. PIGNON does not assess the statistical significance of individual genes, but rather maps protein differential expression levels onto a protein-protein interaction network and measures the clustering of proteins from a given functional annotation within the network. This process allows the detection of functional annotations for which the proteins are differentially expressed and grouped in the network. A Monte-Carlo sampling approach is used to assess the clustering of proteins in an expression-weighted network. When applied to a quantitative proteomics analysis of different molecular subtypes of breast cancer, PIGNON detects Gene Ontology terms that are both significantly clustered in a protein-protein interaction network and differentially expressed across two breast cancer subtypes. PIGNON identified 168 breast cancer pathways dysregulated and clustered within the network between the HER2+ and triple negative subtypes, 203 breast cancer pathways shared by HER2+ and hormone receptor positive subtypes, 19 breast cancer pathways shared by hormone receptor positive and triple negative breast that are not detected by standard approaches. PIGNON identifies functional annotations that have been previously associated with specific breast cancer subtypes as well as novel annotations that may be implicated in the diseases.

Conclusion

PIGNON provides an alternative to functional enrichment analyses and a more comprehensive characterization of quantitative datasets. Hence, it contributes to yielding a better understanding of dysregulated functions and processes in biological samples under different conditions.
Artificial Intelligence Approaches to Assessing Primary Cilia
Authors: Bansal Ruchi , Engle Staci E. , Kamba Tisianna K. , Brewer Kathryn , Lewis Wesley R. , Berbari Nicolas F.
Published: February 2021

Cilia are microtubule based cellular appendages that function as signaling centers for a diversity of signaling pathways in many mammalian cell types. Cilia length is highly conserved, tightly regulated, and varies between different cell types and tissues and has been implicated in directly impacting their signaling capacity. For example, cilia have been shown to alter their lengths in response to activation of ciliary G protein-coupled receptors. However, accurately and reproducibly measuring the lengths of numerous cilia is a time-consuming and labor-intensive procedure. Current approaches are also error and bias prone. Artificial intelligence (Ai) programs can be utilized to overcome many of these challenges due to capabilities that permit assimilation, manipulation, and optimization of extensive data sets. Here, we demonstrate that an Ai module can be trained to recognize cilia in images from bothin vivoandin vitrosamples. After using the trained Ai to identify cilia, we are able to design and rapidly utilize applications that analyze hundreds of cilia in a single sample for length, fluorescence intensity and colocalization. This unbiased approach increased our confidence and rigor when comparing samples from different primary neuronal prepsin vitroas well as across different brain regions within an animal and between animals. Moreover, this technique can be used to reliably analyze cilia dynamics from any cell type and tissue in a high-throughput manner across multiple samples and treatment groups. Ultimately, Ai-based approaches will likely become standard as most fields move toward less biased and more reproducible approaches for image acquisition and analysis.

The use of Artificial Intelligence (Ai) to analyze images is emerging as a powerful, less biased, and rapid approach compared with commonly used methods. Here we trained Ai to recognize a cellular organelle, primary cilia, and analyze properties such as length and staining intensity in a rigorous and reproducible manner.
Enabling multiscale variation analysis with genome graphs
Authors: Letcher Brice , Hunt Martin , Iqbal Zamin
Published: February 2021

Background

Standard approaches to characterising genetic variation revolve around mapping reads to a reference genome and describing variants in terms of differences from the reference; this is based on the assumption that these differences will be small and provides a simple coordinate system. However this fails, and the coordinates break down, when there are diverged haplotypes at a locus (e.g. one haplotype contains a multi-kilobase deletion, a second contains a few SNPs, and a third is highly diverged with hundreds of SNPs). To handle these, we need to model genetic variation that occurs at different length-scales (SNPs to large structural variants) and that occurs on alternate backgrounds. We refer to these together as multiscale variation.

Results

We model the genome as a directed acyclic graph consisting of successive hierarchical subgraphs (“sites”) that naturally incorporate multiscale variation, and introduce an algorithm for genotyping, implemented in the softwaregramtools. This enables variant calling on different sequence backgrounds. In addition to producing regular VCF files, we introduce a JSON file format based on VCF, which records variant site relationships and alternate sequence backgrounds.

We show two applications. First, we benchmark gramtools against existing state-of-the-art methods in joint-genotyping17 M. tuberculosissamples at long deletions and the overlapping small variants that segregate in a cohort of 1,017 genomes. Second, in 706 African and SE AsianP. falciparumgenomes, we analyse a dimorphic surface antigen gene which possesses variation on two diverged backgrounds which appeared to not recombine. This generates the first map of variation on both backgrounds, revealing patterns of recombination that were previously unknown.

Conclusions

We need new approaches to be able to jointly analyse SNP and structural variation in cohorts, and even more to handle variants on different genetic backgrounds. We have demonstrated that by modelling with a directed, acyclic and locally hierarchical genome graph, we can apply new algorithms to accurately genotype dense variation at multiple scales. We also propose a generalisation of VCF for accessing multiscale variation in genome graphs, which we hope will be of wide utility.
DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer
Authors: Zhivagui Maria , Hoda Areebah , Valenzuela Noelia , Yeh Yi-Yu , Dai Jason , He Yudou , Nandi Shuvro P. , Otlu Burcak , Van Houten Bennett , Alexandrov Ludmil B.
Published: February 2021

Ultraviolet A light is commonly emitted by UV-nail polish dryers with recent reports suggesting that long-term use may increase the risk for developing skin cancer. However, no experimental evaluation has been conducted to reveal the effect of radiation emitted by UV-nail polish dryers on mammalian cells. Here, we show that irradiation by a UV-nail polish dryer causes high levels of reactive oxygen species, consistent with 8-oxo-7,8-dihydroguanine damage and mitochondrial dysfunction. Analysis of somatic mutations reveals a dose-dependent increase of C:G>A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of mammalian cells. These results have far-reaching implications in regard to public health and to preventing skin cancer due to consumer-based exposure to ultraviolet light from artificial sources.
Rapid divergence in independent aspects of the compatibility phenotype in the Spiroplasma/Drosophila interaction
Authors: Griffin Joanne S. , Gerth Michael , Hurst Gregory D. D.
Published: February 2021

Heritable symbionts represent important components of host biology, both as antagonistic reproductive parasites and as beneficial protective partners. An important component of heritable microbes’ biology is their ability to establish in new host species, a process equivalent to a host shift for an infectiously transmitted parasite or pathogen. For a host shift to occur, the symbiont must be compatible with the host: it must not cause excess pathology, must have good vertical transmission, and possess a drive phenotype that enables spread. Classically, compatibility has been considered a declining function of genetic distance between novel and ancestral host species. Here we investigate the evolutionary lability of compatibility to heritable microbes by comparing the capacity for a symbiont to establish in two novel host species equally related to the ancestral host. Compatibility of the protectiveSpiroplasmafromD. hydeiwithD. simulansandD. melanogasterwas tested. TheSpiroplasmahad contrasting compatibility in these two host species. The transinfection showed pathology and low vertical transmission inD. melanogasterbut was asymptomatic and transmitted with high efficiency inD. simulans. These results were not affected by the presence/absence ofWolbachiain either of the two species. The pattern of protection was not congruent with that for pathology/transmission, with protection being weaker in theD. simulans, the host in whichSpiroplasmawas asymptomatic and transmitted well. Further work indicated pathological interactions occurred inD. sechelliaandD. yakuba, indicating thatD. simulanswas unusual in being able to carry the symbiont without damage. The differing compatibility of the symbiont with these closely related host species emphasises first the rapidity with which host-symbiont compatibility evolves despite compatibility itself not being subject to direct selection, and second the independence of the different components of compatibility (pathology, transmission, protection). This requirement to fit three different independently evolving aspects of compatibility, if commonly observed, is likely to be a major feature limiting the rate of host shifts. Moving forward, the variation between sibling species pairs observed above provides an opportunity to identify the mechanisms behind variable compatibility between closely related host species, which will drive hypotheses as to the evolutionary drivers of compatibility variation.
Exotic bifurcations in three connected populations with Allee effect
Authors: Röst Gergely , Sadeghimanesh AmirHosein
Published: February 2021

We consider three connected populations with strong Allee effect, and give a complete classification of the steady state structure of the system with respect to the Allee threshold and the dispersal rate, describing the bifurcations at each critical point where the number of steady states change. One may expect that by increasing the dispersal rate between the patches, the system would become more well-mixed hence simpler. However, we show that it is not always the case, and the number of steady states may (temporarily) increase by increasing the dispersal rate. Besides sequences of pitchfork and saddle-node bifurcations, we find triple-transcritical bifurcations and also a sun-ray shaped bifurcation where twelve steady states meet at a single point then disappear. The major tool of our investigations is a novel algorithm that decomposes the parameter space with respect to the number of steady states and find the bifurcation values using cylindrical algebraic decomposition with respect to the discriminant variety of the polynomial system.
Oxidant-Resistant LRRC8A/C Anion Channels Support Superoxide Production by Nox1
Authors: Choi Hyehun , Rohrbough Jeffrey , Nguyen Hong N. , Dikalova Anna , Lamb Fred S.
Published: February 2021

Tumor necrosis factor-α (TNFα) activates NADPH Oxidase 1 (Nox1) in vascular smooth muscle cells (VSMCs), producing superoxide (O2•-) required for subsequent signaling. LRRC8 family proteins A-E comprise volume-regulated anion channels (VRACs). The required subunit LRRC8A physically associates with Nox1, and VRAC activity is required for Nox activity and the inflammatory response to TNFα. LRRC8 channel currents are modulated by oxidants, suggesting that oxidant sensitivity and proximity to Nox1 may play a physiologically relevant role. In VSMCs, LRRC8C knockdown (siRNA) recapitulated the effects of siLRRC8A, inhibiting TNFα-induced extracellular and endosomal O2•-production, receptor endocytosis, NF-κB activation, and proliferation. In contrast, siLRRC8D potentiated NF-κB activation. Nox1 co-immunoprecipitated with 8C and 8D, and co-localized with 8D at the plasma membrane and in vesicles. We compared VRAC currents mediated by homomeric and heteromeric 8C and 8D channels expressed in HEK293 cells. The oxidant chloramine T (ChlorT, 1 mM) weakly inhibited LRRC8C, but potently inhibited 8D currents. ChlorT exposure also greatly reduced subsequent current block by DCPIB, implicating external sites of oxidation. Substitution of the extracellular loop domains (EL1, EL2) of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition. 8A/C channel activity is thus more effectively maintained in the oxidized microenvironment expected to result from Nox1 activation at the plasma membrane. Increased ratios of 8D:8C expression may potentially depress inflammatory responses to TNFα. LRRC8A/C channel downregulation represents a novel strategy to reduce TNFα-induced inflammation.

Key Points

LRRC8A-containing anion channels associate with Nox1 and regulate superoxide production and TNFα signaling. Here we show that .LRRC8C and 8D also co-immunoprecipitate with Nox1 in vascular smooth muscle cells.

LRRC8C knockdown inhibited TNFα-induced O2•-production, receptor endocytosis, NF-κB activation, and proliferation while LRRC8D knockdown enhanced NF-κB activation. Significant changes in LRRC8 isoform expression in human atherosclerosis and psoriasis suggest compensation for increased inflammation.

The oxidant chloramine-T (ChlorT, 1 mM) weakly (∼25%) inhibited 8C currents but potently (∼80%) inhibited 8D currents. Substitution of the two extracellular loop (EL) domains of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition.

ChlorT also impaired current block by DCPIB, which occurs through interaction with EL1, further implicating external sites of oxidation.

8A/C channels most effectively maintain activity in an oxidized microenvironment, as is expected to result from Nox1 activity at the plasma membrane.
Reciprocalspaceship: A Python Library for Crystallographic Data Analysis
Authors: Greisman Jack B. , Dalton Kevin M. , Hekstra Doeke R.
Published: February 2021

Abstract

X-ray crystallography is an invaluable technique for studying the atomic structure of macromolecules. Much of crystallography’s success is due to the software packages developed to enable the automated processing of diffraction data. However, the analysis of unconventional diffraction experiments can still pose significant challenges—many existing programs are closed-source, sparsely documented, or are challenging to integrate with modern libraries for scientific computing and machine learning. Here we describereciprocalspaceship, a Python library for exploring reciprocal space. It provides a tabular representation for reflection data from diffraction experiments that extends the widely-used pandas library with built-in methods for handling space group, unit cell, and symmetry-based operations. As we illustrate, this library facilitates new modes of exploratory data analysis while supporting the prototyping, development, and release of new methods.
Understanding of the 2-oxoglutarate dehydrogenase and 2-oxoadipate dehydrogenase assembly with the E2o core relevant to a hybrid complex formation
Authors: Zhang Xu , Nemeria Natalia S. , Jordan Frank
Published: February 2021

The 2-oxoglutarate (OG) dehydrogenase complex (OGDHc) is a key enzyme in the tricarboxylic acid cycle (TCA) and comprises multiple copies of three components: 2-oxoglutarate dehydrogenase (hE1o), dihydrolipoamide succinyltransferase (hE2o), and dihydrolipoamide dehydrogenase (hE3). The OGDHc is one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels and impacts cell metabolic and cell signaling pathways through the coupling of OG metabolism to gene transcription, related to tumor cell proliferation and aging. The reduced OGDHc activity is linked to a number of neurodegenerative diseases. Evidence was obtained for the formation of a hybrid 2-oxo acid dehydrogenase complex between the OGDHc and its homologue 2-oxoadipate (OA) dehydrogenase (hE1a) in the L-lysine metabolic pathway, suggesting a potential cross-talk between the two distinct metabolic pathways. These findings raised fundamental questions about assembly of hE1a and hE1o to the hE2o core. Due to the lack of an atomic structure of the OGDHc from any sources, and of knowledge about exact distribution of components around the E2 core, hydrogen/deuterium exchange (HDX-MS) and chemical cross-linking mass spectrometry (CL-MS) have been carried out in binary hE1o-hE2o, hE1a-hE2o, hE1o-hE3 and hE2o-hE3 sub-complexes followed by structural modeling. Here we report findings that revealed some similarities in the assembly of hE1o and hE1a to the hE2o core. At the same time, three regions of the hE2o core comprising residues 191-208, 273-288, and 370-386 revealed a different binding mode to hE1o and hE1a, suggesting that hE2o can differentiate between these two proteins that may have physiological consequences.
Pelagic larval polyclads that practice macrophagous carnivory
Authors: von Dassow George , Mendes Cecili
Published: February 2021

We report evidence that hatchling polyclads of several genera feed in the plankton on large prey. These ciliated swimmers, despite apparently lacking means to concentrate food or even detect it at a distance, subdue and consume fast-moving active-swimming plankters such as crustacean larvae and copepods, or molluskan veligers. We describe feeding events in captivity using videomicroscopy, and identify several wild-caught predatory pelagic polyclad larvae to genus or species level by DNA barcoding. Remarkably, one of these types is identified unambiguously with a species previously observed as Müller’s larvae, which live as conventional planktotrophs on an inferred diet of small phytoflagellates. Therefore we conclude first that while so-called “direct-developing” polyclad flatworms may hatch with juvenile-like morphology, at least some of these are functionally larvae. Second, that some species of polyclad have at least a triphasic life cycle, with a first larval stage living in the plankton on primary producers followed by a second larval stage living in the plankton by macrophagous carnivory, before presumably settling to the benthos for adult life.
Glutamatergic dysfunction precedes neuron loss in cerebral organoids withMAPTmutation
Authors: Bowles Kathryn R. , Silva M. Catarina , Whitney Kristen , Bertucci Taylor , Garza Jacob C. , Boles Nathan C. , Strang Kevin H. , Mahali Sidhartha , Marsh Jacob A. , Chen Cynthia , Pugh Derian A. , Liu Yiyuan , Berlind Joshua E. , Lai Jesse D. , Goderie Susan K. , Chowdhury Rebecca , Lotz Steven , Lane Keith , Onanuga Khadijah , Karch Celeste M. , Ichida Justin K. , Crary John F. , Haggarty Stephen J. , Goate Alison M. , Temple Sally
Published: February 2021

Frontotemporal dementia (FTD) due toMAPTmutation causes pathological accumulation of tau and glutamatergic cortical neuronal death by unknown mechanisms. We used human induced pluripotent stem cell (iPSC)-derived cerebral organoids expressing tau-V337M and isogenic corrected controls to discover early alterations due to the mutation that precede neurodegeneration. At 2 months, mutant organoids show upregulated expression ofMAPT, and glutamatergic signaling pathways and regulators including the RNA-binding proteinELAVL4. Over the following 4 months, mutant organoids accumulate splicing changes, disruption of autophagy function and build-up of tau and P-tau S396. By 6 months, tau-V337M organoids show specific loss of glutamatergic neurons of layers affected in patients. Mutant neurons are susceptible to glutamate toxicity which was rescued pharmacologically by treatment with the PIKFYVE kinase inhibitor apilimod. Our results demonstrate a sequence of events that precede cell death, revealing molecular pathways associated with glutamate signaling as potential targets for therapeutic intervention in FTD.
A high-throughput radioactivity-based assay for screening SARS-CoV-2 nsp10-nsp16 complex
Authors: Yazdi Aliakbar Khalili , Li Fengling , Devkota Kanchan , Perveen Sumera , Ghiabi Pegah , Hajian Taraneh , Bolotokova Albina , Vedadi Masoud
Published: February 2021

Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current SARS-CoV-2 pandemic, necessitate the development of therapeutics that could be easily and effectively administered world-wide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA-capping through its 2’-O-methylation activity. Like other methyltransferases, SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for methyltransferase activity of nsp10-nsp16 complex in a 384-well format, and kinetic characterization, and optimization of the assay for HTS (Z′-factor: 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.
RNA polymerase II clusters form in line with liquid phase wetting of chromatin
Authors: Pancholi Agnieszka , Klingberg Tim , Zhang Weichun , Prizak Roshan , Mamontova Irina , Noa Amra , Kobitski Andrei Yu , Nienhaus Gerd Ulrich , Zaburdaev Vasily , Hilbert Lennart
Published: February 2021

It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state and subsequent pause release to begin transcript elongation. Pol II associates with macromolecular clusters during recruitment, but it remains unclear how Pol II recruitment and pause release might affect these clusters. Here, we show that clusters exhibit morphologies that are in line with wetting of chromatin by a liquid phase enriched in recruited Pol II. Applying instantaneous structured illumination microscopy and stimulated emission double depletion microscopy to pluripotent zebrafish embryos, we find recruited Pol II associated with large clusters, and elongating Pol II with dispersed clusters. A lattice kinetic Monte Carlo model representing recruited Pol II as a liquid phase reproduced the observed cluster morphologies. In this model, chromatin is a copolymer chain containing regions that attract or repel recruited Pol II, supporting droplet formation by wetting or droplet dispersal, respectively.
Multiple indole glucosinolates and myrosinases defend Arabidopsis againstTetranychus urticaeherbivory
Authors: Widemann Emilie , Bruinsma Kristie , Walshe-Roussel Brendan , Saha Repon Kumer , Letwin David , Zhurov Vladimir , Bernards Mark A. , Grbić Miodrag , Grbić Vojislava
Published: February 2021

Arabidopsis defenses against herbivores are regulated by the jasmonate hormonal signaling pathway, which leads to the production of a plethora of defense compounds, including tryptophan-derived metabolites produced through CYP79B2/CYP79B3. Jasmonate signaling and CYP79B2/CYP79B3 limit Arabidopsis infestation by the generalist herbivore two-spotted spider mite,Tetranychus urticae. However, the phytochemicals responsible for Arabidopsis protection againstT. urticaeare unknown. Here, using Arabidopsis mutants that disrupt metabolic pathways downstream of CYP79B2/CYP79B3, and synthetic indole glucosinolates, we identified phytochemicals involved in the defense againstT. urticae. We show that Trp-derived metabolites depending on CYP71A12 and CYP71A13 are not affecting mite herbivory. Instead, the supplementation ofcyp79b2 cyp79b3mutant leaves with the 3-indolylmethyl glucosinolate and its derived metabolites demonstrated that the indole glucosinolate pathway is sufficient to assure CYP79B2/CYP79B3-mediated defenses againstT. urticae. We demonstrate that three indole glucosinolates can limitT. urticaeherbivory, but that they have to be processed by the myrosinases to hinderT. urticaeoviposition. Finally, the supplementation of the mutantmyc2 myc3 myc4with indole glucosinolates indicated that the transcription factors MYC2/MYC3/MYC4 induce additional indole glucosinolate-independent defenses that controlT. urticaeherbivory. Together, these results reveal the complexity of Arabidopsis defenses againstT. urticaethat rely on multiple indole glucosinolates, specific myrosinases, and additional MYC2/MYC3/MYC4-dependent defenses.

One sentence summary

Three indole glucosinolates and the myrosinases TGG1/TGG2 help protectArabidopsis thalianaagainst the herbivory of the two-spotted spider miteTetranychus urticae.
Natural Selection is Unlikely to Explain Why Species Get a Thin Slice ofπ
Authors: Buffalo Vince
Published: February 2021

Neutral theory predicts that genetic diversity increases with population size, yet observed levels of diversity across metazoans vary only two orders of magnitude while population sizes vary over several. This unexpectedly narrow range of diversity is known as Lewontin’s Paradox of Variation (1974). While some have suggested selection constrains diversity, tests of this hypothesis seem to fall short. Here, I revisit Lewontin’s Paradox to assess whether current models of linked selection are capable of reducing diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine previously-published estimates of pairwise diversity from 172 metazoan taxa with estimates of census sizes. Using phylogenetic comparative methods, I show this relationship is significant accounting for phylogeny, but with high phylogenetic signal and evidence that some lineages experience shifts in the evolutionary rate of diversity deep in the past. Additionally, I find a negative relationship between recombination map length and census size, suggesting abundant species have less recombination and experience greater reductions in diversity due to linked selection. However, I show that even using strong selection parameter estimates, models of linked selection are unlikely to explain the observed relationship between diversity and census sizes across species.
Examination of digital images from Macaulay Library to determine avian molt strategies: A case study on molts and plumages in eight species of North American hummingbirds
Authors: Pyle Peter
Published: February 2021

I examined a total of 27,581 images of 6.345 individuals from the Cornell Lab of Ornithology’s Macaulay Library to clarify conflicting reports on molt and plumage strategies in eight species of hummingbirds that breed or have bred primarily in the southwestern United States. Fixed replacement sequences from two nodes among primaries and two nodes among secondaries were found without exception, conforming to the findings of previous studies. I concluded that the preformative molt is limited to partial in three species, partial to incomplete in three species, partial to complete in one species, and complete in one species. These molt strategies could be interpreted as having differentiated through synapomorphy, with species between currently recognized clades varying in the extent of their preformative molts; however, given the plastic nature of molt strategies, I predict that this variation will be shaped more by environmental factors than by synapomorphy. Results of this study additionally clarify molt terminology in Trochilidae as based on homologies and establish new criteria for age determinations. The Macaulay Library clearly provides an important resource for the investigation of avian molts and plumages. The results of a validation exercise that I conducted indicate that banders and field ornithologists with a wide range of previous experience can collect accurate data in this manner. I present a road map for such studies and suggest many other questions on avian molt that can also be investigated, including how timing of molts vary geographically and by habitat and how remigial replacement sequences proceed in little-known bird families. I encourage contributors to the Macaulay Library to take and upload images of birds in molt or in worn plumages.
hC9ORF78 localizes to kinetochores and is required for proper chromosome segregation
Authors: Koranne Radhika , Brown Kayla M. , Vandenbroek Hannah E. , Taylor William R.
Published: February 2021

C9ORF78 is a poorly characterized protein found in diverse eukaryotes. Previous work indicated overexpression of hC9ORF78 (aka HCA59) in malignant tissues indicating a possible involvement in growth regulatory pathways. Additional studies in fission yeast and humans uncover a potential function in regulating the spliceosome. In studies of GFP-tagged hC9ORF78 we observed a dramatic reduction in protein abundance in cells grown to confluence and/or deprived of serum growth factors. Serum stimulation induced synchronous re-expression of the protein in HeLa cells. This effect was also observed with the endogenous protein. Overexpressing either E2F1 or N-Myc resulted in elevated hC9ORF78 expression potentially explaining the serum-dependent upregulation of the protein. Immunofluorescence analysis indicates that hC9ORF78 localizes to nuclei in interphase but does not appear to concentrate in speckles as would be expected for a splicing protein. Surprisingly, a subpopulation of hC9ORF78 co-localizes with ACA, Mad1 and Hec1 in mitotic cells suggesting that this protein may associate with kinetochores or centromeres. Furthermore, knocking-down hC9ORF78 caused mis-alignment of chromosomes in mitosis. These studies uncover novel mitotic function and subcellular localization of cancer antigen hC9ORF78.

SUMMARY STATEMENT

hC9ORF78 regulates chromosome segregation.
Single molecule tracking of AMPA receptors shows the role of synaptic insertion during maintenance of chemical LTP
Authors: Jin Chaoyi , Jang Sung-Soo , Ge Pinghua , Chung Hee Jung , Selvin Paul
Published: February 2021

Long term potentiation (LTP) likely contributes to memory formation. Early expression of LTP involves insertion of AMPA receptors (AMPARs) to the extrasynaptic membrane followed by their lateral diffusion into the synaptic membrane. However, whether a similar mechanism mediates the maintenance of LTP is unclear. Using single-molecule microscopy, we quantified that 6 GluA1- and 11 GluA2-containing endogenous AMPARs were added per synapse in cultured hippocampal neurons at 20 min following chemical LTP (cLTP) induction for 10 min, resulting in a 54% increase for both subunits. Single molecular tracking of transfected subunits revealed that the number of exocytosed subunits at the synapse increased by 15-18% from 5 to 20 min following cLTP induction, but their lateral exchange between synaptic and extrasynaptic membranes was minimal. These findings suggest that cLTP maintenance is contributed largely by synaptic insertion of AMPARs rather than the surface diffusion of exocytosed AMPARs from extrasynaptic to synaptic regions.
Essential role of CFAP53 in sperm flagellum biogenesis
Authors: Wu Bingbing , Yu Xiaochen , Liu Chao , Wang Lina , Huang Tao , Lu Gang , Chen Zi-Jiang , Li Wei , Liu Hongbin
Published: February 2021

The sperm flagellum is essential for male fertility. Despite vigorous research progress towards understanding the pathogenesis of flagellum-related diseases, much remains unknown about the mechanisms underlying the flagellum biogenesis itself. Here, we show that the cilia and flagella associated protein 53 (Cfap53) gene is predominantly expressed in testes, and it is essential for sperm flagellum biogenesis. The knockout of this gene resulted in complete infertility in male mice but not in the females. CFAP53 localized to the manchette and sperm tail during spermiogenesis, the knockout of this gene impaired flagellum biogenesis. Furthermore, we identified two manchette and sperm tail-associated proteins that interacted with CFAP53 during spermiogenesis. The disruption ofCfap53decreased the expression level of these two proteins and disrupted their localization in spermatids. Together, our results suggest that CFAP53 is an essential protein for sperm flagellum biogenesis, and its mutations might be associated with MMAF.
The role of extracurricular activities in shaping university students' employment self-efficacy perceptions
Authors: Kanar Adam , Bouckenooghe Dave
Published: February 2021

Purpose

The present study aimed to understand how participation in university extracurricular activities has a beneficial or detrimental impact on students’ employment self-efficacy through the intervening mechanism of information search strategy.

Design/methodology/approach

The authors collected data from active job-searching university students across two time-points and hypothesized that the breadth of extracurricular activity participation would positively impact employment self-efficacy perceptions and information search strategies (focused, exploratory and haphazard) would mediate this relationship.

Findings

Results indicate that the breadth of students' participation in extracurricular activities was positively associated with employment self-efficacy perceptions, and this relationship was mediated by focused and exploratory information-search strategies. Extracurricular activities exhibited a negative relationship with a haphazard search strategy.

Research limitations/implications

This research extends the understanding of the role of participation in extracurricular activities for influencing a job search. Future research may replicate these findings with different samples of job seekers.

Practical implications

Extracurricular activities are typically offered at universities as a way for students to develop skills and to improve employers' perceptions of students. The present results suggest that participating in extracurricular activities may also help university students to effectively conduct a self-directed job search.

Originality/value

We examined the role of extracurricular activities from the applicant's perspective, extending prior research examining extracurricular activities from the employer's perspective. The present results suggest that extracurricular activities play an important role in shaping the job search process of university students by influencing students' confidence for finding employment. Information search strategies mediated the effects of extracurricular activities on employment self-efficacy perceptions, suggesting that participating in extracurricular activities changed the way that applicants searched for jobs.
Adolescent English language learners’ digitally mediated multimodal compositions: multimodal enactment across different genres of writing in the EFL context
Authors: Kang Joohoon
Published: February 2021

Purpose

This paper aims to investigate adolescent English as a foreign language (EFL) learners’ digitally mediated multimodal compositions across different genres of writing.

Design/methodology/approach

Three Korean high school students participated in the study and created multiple multimodal texts over the course of one academic semester. These texts and other materials were the basis for this study’s qualitative case studies. Multiple sources of data (e.g. class observations, demographic surveys, interviews, field notes and students’ artifacts) were collected. Drawing upon the inductive approach, a coding-oriented analysis was used for the collected data. In addition, a multimodal text analysis was conducted for the students’ multimodal texts and their storyboards.

Findings

The study participants’ perceptions of multimodal composing practices seemed to be positively reshaped as a result of them creating multimodal texts. Some participants created multimodal products in phases (e.g. selecting or changing a topic, constructing a storyboard and editing). Especially, although the students’ creative processes had a similarly fixed and linear flow from print-based writing to other modalities, their creative processes proved to be flexible, recursive and/or circular.

Originality/value

This study contributes to the understanding of adolescent English language learners’ multimodal composing practices in the EFL context, which has been underexplored in the literature. It also presents the students’ perspectives on these practices. In short, it provides theoretical and methodological grounds for future L2 literacy researchers to conduct empirical studies on multimodal composing practices.
Thermosolutal convection of a nanofluid in ∧-shaped cavity saturated by a porous medium
Authors: Aly Abdelraheem M. , Raizah Zehba
Published: February 2021

Purpose

The purpose of this study is to simulate the thermo-solutal convection resulting from a circular cylinder hanging in a rod inside a ∧-shaped cavity.

Design/methodology/approach

The two dimensional ∧-shaped cavity is filled by Al2O3-water nanofluid and saturated by three different levels of heterogeneous porous media. An incompressible smoothed particle hydrodynamics (ISPH) method is adopted to solve the governing equations of the present problem. The present simulations have been performed for the alteration of buoyancy ratio

(−2≤N≤2), radius of a circular cylinder

(0.05≤Rc≤0.3), a height of a rod

(0.1≤Lh≤0.4), Darcy parameter

(10−3≤Da≤10−5), Lewis number

(1≤Le≤40), solid volume fraction

(0≤ϕ≤0.06), porous levels

(0≤η1=η2≤1.5)and various boundary-wall conditions.

Findings

The performed numerical simulations indicated the importance of embedded shapes on the distributions of temperature, concentration and velocity fields inside ∧-shaped cavity. Increasing buoyancy ratio parameter enhances thermo-solutal convection and nanofluid velocity. Adiabatic conditions of the vertical-walls of ∧-shaped cavity augment the distributions of the temperature and concentration. Regardless the Darcy parameter, a homogeneous porous medium gives the lowest values of a nanofluid velocity.

Originality/value

ISPH method is used to simulate thermo-solutal convection of a nanofluid inside a novel ∧-shaped cavity containing a novel embedded shape and heterogeneous porous media.
Female entrepreneurs’ cognitive attributes and venture growth in Japan: the moderating role of perceived social legitimacy
Authors: Kawai Norifumi , Kazumi Tomoyo
Published: February 2021

Purpose

By drawing upon social cognitive and legitimacy perspectives, this study aims to explore the role of perceived social legitimacy as an informal institutional force that moderates the effects of female entrepreneurs’ self-efficacy and entrepreneurial tenacity on venture growth.

Design/methodology/approach

This study uses a data set of 308 Japanese female entrepreneurs, who are a subject of limited extant scholarly attention, to test the hypothesised relationships empirically.

Findings

Consistent with the unified framework, the study was able to identify that the acquisition of social legitimacy required by female entrepreneurs serves as a crucial safety net under which entrepreneurial self-efficacy and tenacity can significantly affect venture growth.

Research limitations/implications

The study highlights that high levels of entrepreneurial traits alone are not necessarily sufficient to guarantee women’s venture growth. In doing so, this study stimulates the development of theory on the complementary role of the social legitimacy of entrepreneurship in fueling and mobilising the female entrepreneurs’ cognitive resources as the key to venture growth in the Japanese context.

Practical implications

Policymakers should be dedicated to implementing more gender-specific policies designed to continually cultivate women’s cognitive attributes in tandem with the promotion of social awareness to embrace entrepreneurship as a promising career option.

Originality/value

The originality of this study lies in stimulating a debate on the underlying heterogeneity of female entrepreneurs in the performance outcomes of two entrepreneurial cognitive attributes. By integrating the concept of perceived social legitimacy, the study can respond to Miaoet al.(2017), who sought further examination of untested boundary conditions in the cognitive characteristics-venture growth equation.
Conceptualizing financial capability: evidence from Indonesia
Authors: Lubis Arief Wibisono
Published: February 2021

Purpose

This paper aims to investigate how microfinance institutions’ clients in Indonesia conceptualize financial capability. Previous investigations on the concept were mostly in the lenses of those in the developed economies.

Design/methodology/approach

A qualitative method was used, in which focus group discussions (FGDs) and interviews were conducted with microfinance institutions’ clients and management in four provinces in Indonesia: DKI Jakarta, DI Yogyakarta, West Nusa Tenggara and South Sulawesi.

Findings

The results exhibit some similarities with those of previous studies that highlight the importance of financial management and financial planning for strategic purposes. However, financial literacies perceived as less important due to the lack of awareness of the concept and its benefits.

Research limitations/implications

This research is only focused on certain groups of the population which implies its limited generalizability. One important implication is for policymakers and scholars to re-examine the value of financial literacy within the context of Indonesia. Although the interviews reveal skepticisms on the instrumental value of financial literacy, robust investigations are further needed.

Originality/value

This study is the first that uses the participatory method to define financial capability as understood by microfinance institutions’ clients in Indonesia.