bluuebunny/crossref_metadata_2025 huggingface dataset:
Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM
Authors: Boyle Evan A. , Goldberg Gabriela , Schmok Jonathan C. , Burgado Jillybeth , Layng Fabiana Izidro , Grunwald Hannah A. , Balotin Kylie M. , Cuoco Michael S. , Chang Keng-Chi , Ecklu-Mensah Gertrude , Arakaki Aleena K. S. , Ahmed Noorsher , Arceo Ximena Garcia , Jagannatha Pratibha , Pekar Jonathan , Iyer Mallika ,   DASL Alliance, Yeo Gene W.
Published: December 2021

Disparities for women and minorities in science, technology, engineering, and math (STEM) careers have continued even amidst mounting evidence for the superior performance of diverse workforces. In response, we launched the Diversity and Science Lecture series, a cross-institutional platform where junior life scientists present their research and comment on equity, diversity, and inclusion in STEM. We characterize speaker representation from 79 profiles and investigate topic noteworthiness via quantitative content analysis of talk transcripts. Nearly every speaker discussed interpersonal support, and three-fifths of speakers commented on race or ethnicity. Other topics, such as sexual and gender minority identity, were less frequently addressed but highly salient to the speakers who mentioned them. We found that significantly co-occurring topics reflected not only conceptual similarity, such as terms for racial identities, but also intersectional significance, such as identifying as a Latina/Hispanic woman or Asian immigrant, and interactions between priorities and identities, including the heightened value of friendship to the LGBTQ community, which we reproduce using transcripts from an independent seminar series. Our approach to scholar profiles and talk transcripts serves as an example for transmuting hundreds of hours of scholarly discourse into rich datasets that can power computational audits of speaker diversity and illuminate speakers’ personal and professional priorities.
Selective representations of texture and motion in mouse higher visual areas
Authors: Yu Yiyi , Stirman Jeffrey N. , Dorsett Christopher R. , Smith Spencer L.
Published: December 2021

Mice have a constellation of higher visual areas, but their functional specializations are unclear. Here, we used a data-driven approach to examine neuronal representations of complex visual stimuli across mouse higher visual areas, measured using large field-of-view two-photon calcium imaging. Using specialized stimuli, we found higher fidelity representations of texture in area LM, compared to area AL. Complementarily, we found higher fidelity representations of motion in area AL, compared to area LM. We also observed this segregation of information in response to naturalistic videos. Finally, we explored how popular models of visual cortical neurons could produce the segregated representations of texture and motion we observed. These selective representations could aid in behaviors such as visually guided navigation.
PIPP: Improving peptide identity propagation using neural networks
Authors: Hediyeh-zadeh Soroor , Martin Jarryd , Davis Melissa J. , Webb Andrew I.
Published: December 2021

Peptide identity propagation (PIP) can substantially reduce missing values in label-free mass spectrometry quantification by transferring peptides identified by tandem mass (MS/MS) spectra in one run to experimentally related runs where the peptides are not identified by MS/MS. The existing frameworks for matching identifications between runs perform peak tracing and propagation based on similarity of precursor features using only a limited number of dimensions available in MS1 data. These approaches do not produce accompanying confidence estimates and hence cannot filter probable false positive identity transfers. We introduce an embedding based PIP that uses a higher dimensional representation of MS1 measurements that is optimized to capture peptide identities using deep neural networks. We developed a propagation framework that works entirely on MaxQuant results. Current PIP workflows typically perform propagation mainly using two feature dimensions, and rely on deterministic tolerances for identification transfer. Our framework overcomes both these limitations while additionally assigning probabilities to each transferred identity. The proposed embedding approach enables quantification of the empirical false discovery rate (FDR) for peptide identification, while also increasing depth of coverage through coembedding the runs from the experiment with experimental libraries. In published datasets with technical and biological variability, we demonstrate that our method reduces missing values in MaxQuant results, maintains high quantification precision and accuracy, and low false transfer rate.
Effect of everyday discrimination on depression and suicidal ideation during the COVID-19 pandemic: a large-scale, repeated-measures study in theAll of UsResearch Program
Authors: Lee Younga H. , Liu Zhaowen , Fatori Daniel , Bauermeister Joshua R. , Luh Rebecca A. , Clark Cheryl R. , Bauermeister Sarah , Brunoni André R. , Smoller Jordan W.
Published: December 2021

Objective

The COVID-19 pandemic has coincided with an increase in depressive symptoms as well as a growing awareness of health inequities and structural racism in the United States. Here, we examine the mental health impact of everyday discrimination during the pandemic in a large and diverse cohort of theAll of UsResearch Program.

Methods

Using repeated assessments of 62,651 participants in May to July of 2020, we fitted mixed-effects models to assess the effect of everyday discrimination on moderate to severe depression (Patient Health Questionnaire (PHQ)-9 ≥ 10) and suicidal ideation (PHQ-9 item 9 > 0), and applied inverse probability weights to account for non-random probabilities of completing the voluntary survey.

Results

Everyday discrimination was associated with increased odds of depression (adjusted odds ratio (aOR) [95% CI]: 1.21 [1.20 -1.22]) and suicidal ideation (1.17 [1.16-1.18]). For depression, the effects were larger in earlier phases of the pandemic (interaction p=8.2×10−5), which varied by main reason for discrimination and self-reported race and ethnicity. Among those who identified race or ancestry/national origin(s) as a primary reason for discrimination, Asian and Black or African American participants had 24% and 17% increase in the odds of depression in May of 2020 (1.24 [1.17-1.31] and 1.17 [1.12-1.22]), respectively, versus a 3% and 7% increase in July (1.03 [0.96-1.10] and 1.07 [1.02-1.12]).

Conclusion

In this large and diverse sample, increased levels of everyday discrimination were associated with higher odds of depression, particularly during the early phase of the pandemic among participants self-identifying as Asian or Black.
Kidney failure alters parathyroid Pin1 phosphorylation and parathyroid hormone mRNA binding proteins leading to secondary hyperparathyroidism
Authors: Hasan Alia , Pollak Yael E. , Kilav-Levin Rachel , Silver Justin , London Nir , Nechama Morris , Ben-Dov Iddo Z. , Naveh-Many Tally
Published: December 2021

Parathyroid hormone (PTH) regulates calcium metabolism and bone strength. Chronic kidney disease leads to secondary hyperparathyroidism (SHP) which increases morbidity and mortality. In experimental SHP, the increasedPTHgene expression is due to enhancedPTHmRNA stability, mediated by changes in its interaction with stabilizing AUF1 and destabilizing KSRP. Pin1 isomerizes target proteins and leads to KSRP dephosphorylation. In SHP, Pin1 isomerase activity is decreased and phosphorylated KSRP fails to bindPTHmRNA, resulting in highPTHmRNA stability and levels. However, the up- and down-stream mechanisms by which kidney failure stimulates the parathyroid remain elusive. We now reveal a pathway where kidney failure induces parathyroid Pin1 phosphorylation, linking Pin1, KSRP and PTH mRNA stability as key players for the high PTH expression in SHP. We identified by mass-spectrometry, changes in rat parathyroid proteome and phosphoproteome profiles induced by impaired renal function, including KSRP phosphorylation at Pin1 target sites. Furthermore, both acute and chronic kidney failure led to parathyroid-specific Pin1 Ser16 and Ser71 phosphorylation, which disrupts Pin1 activity. Accordingly, pharmacologic Pin1 inhibition, that mimics the decreased Pin1 activity in SHP, increased PTH expression ex-vivo in parathyroid organ cultures and in transfected cells, through thePTHmRNA protein-interacting element and KSRP phosphorylation at potential Pin1-binding motifs. Therefore, kidney failure leads to loss of parathyroid Pin1 activity by inducing Pin1 phosphorylation. This predisposes parathyroids to increase PTH production through impairedPTHmRNA decay that is dependent on KSRP phosphorylation. Pin1 and KSRP phosphorylation and the Pin1-KSRP-PTHmRNA axis thus drive SHP.
N-acetyl-cysteinylated streptophenazines from Streptomyces
Authors: Vind Kristiina , Maffioli Sonia , Ciruelos Blanca Fernandez , Waschulin Valentin , Brunati Cristina , Simone Matteo , Sosio Margherita , Donadio Stefano
Published: December 2021

Here, we describe two N-acetyl-cysteinylated streptophenazines (1 and 2) produced by soil-derived Streptomyces sp. ID63040 and identified through a metabolomic approach. These metabolites attracted our interest due to their low occurrence frequency in a large library of fermentation broth extracts and their consistent presence in biological replicates of the producer strain. The compounds were found to possess broad-spectrum antibacterial activity while exhibiting low cytotoxicity. The biosynthetic gene cluster from Streptomyces sp. ID63040 was found to be highly similar to the streptophenazine reference cluster in the MIBiG database, which originates from the marine Streptomyces sp. CNB-091. Compounds 1 and 2 were the main streptophenazine products from Streptomyces sp. ID63040 at all cultivation times, but were not detected in Streptomyces sp. CNB-091. The lack of obvious candidates for cysteinylation in the Streptomyces sp. ID63040 biosynthetic gene cluster suggests that the N-acetyl-cysteine moiety derives from cellular functions, most likely from mycothiol. Overall, our data represent an interesting example on how to leverage metabolomics for the discovery of new natural products and point out to the often-neglected contribution of house-keeping cellular functions to natural product diversification.

Graphical abstract
A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)
Authors: Shi Chua Physilia Ying , Carøe Christian , Crampton-Platt Alex , Reyes-Avila Claudia Sarai , Jones Gareth , Streicker Daniel G. , Bohmann Kristine
Published: December 2021

The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n=8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and de novo mtDNA assembly) to identify prey. Further, we validated our results to detections made through metabarcoding. We accurately identified the common vampire bats’ prey in seven out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138bp to 3231bp (mean=985bp, SD=981bp). As we develop more computationally efficient bioinformatics pipelines and reduce sequencing costs, we can expect an uptake in metagenomics dietary studies in the near future.
PEDOT:PSS-Modified Cotton Conductive Thread for Mass Manufacturing of Textile-Based Electrical Wearable Sensors by Computerized Embroidery
Authors: Alshabouna Fahad , Lee Hong Seok , Barandun Giandrin , Tan Ellasia , Çotur Yasin , Asfour Tarek , Gonzalez-Macia Laura , Coatsworth Philip , Núnez-Bajo Estefanía , Kim Ji-Seon , Güder Firat
Published: December 2021

The textile industry has advanced processes that allow computerized manufacturing of garments at large volumes with precise visual patterns. The industry, however, is not able to mass fabricate clothes with seamlessly integrated wearable sensors, using its precise methods of fabrication (such as computerized embroidery). This is due to the lack of conductive threads compatible with standard manufacturing methods used in industry. In this work, we report a low-cost poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS)-modified cotton conductive thread (PECOTEX) that is compatible with computerized embroidery. The PECOTEX was produced using a crosslinking reaction between PEDOT:PSS and cotton thread using divinyl sulfone as the crosslinker. We extensively characterized and optimized our formulations to create a mechanically robust conductive thread that can be produced in large quantities in a roll-to-roll fashion. Using PECOTEX and a domestic computerized embroidery machine, we produced a series of wearable electrical sensors including a facemask for monitoring breathing, a t-shirt for monitoring heart activity and textile-based gas sensors for monitoring ammonia as technology demonstrators. PECOTEX has the potential to enable mass manufacturing of new classes of low-cost wearable sensors integrated into everyday clothes.
Response plasticity of Drosophila olfactory sensory neurons
Authors: Halty-deLeon Lorena , Pal Mahadevan Venkatesh , Hansson Bill S. , Wicher Dieter
Published: December 2021

In insect olfaction, sensitization refers to the amplification of a weak olfactory signal when the stimulus is repeated within a specific time window. In the vinegar fly, Drosophila melanogaster, his occurs already at the periphery, at the level of olfactory sensory neurons (OSNs) located in the antenna. In our study, we investigate whether sensitization is a widespread property in a set of seven types of OSNs, as well as the mechanisms involved. First, we characterize and compare differences in spontaneous activity, response velocity and response dynamics among the selected OSN types. These express different receptors with distinct tuning properties and behavioral relevance. Second, we show that sensitization is not a general property. Among our selected OSNs types, it occurs in those responding to more general food odors, while OSNs involved in very specific detection of highly specific ecological cues like pheromones and warning signals show no sensitization. Moreover, we show that mitochondria play an active role in sensitization by contributing to the increase in intracellular Ca2+ upon weak receptor activation. Thus, by using a combination of single sensillum recordings (SSR), calcium imaging and pharmacology, we widen the understanding of how the olfactory signal is processed at the periphery.

Abstract Figure
Cathelicidin-3 associated with serum extracellular vesicles enables early diagnosis of a transmissible cancer
Authors: Espejo Camila , Wilson Richard , Pye Ruth J. , Ratcliffe Julian C. , Ruiz-Aravena Manuel , Willms Eduard , Wolfe Barrett W. , Hamede Rodrigo , Hill Andrew F. , Jones Menna E. , Woods Gregory M. , Lyons A. Bruce
Published: December 2021

The identification of practical early diagnosis biomarkers is a cornerstone of improved prevention and treatment of cancers. Such a case is devil facial tumour disease (DFTD), a highly lethal transmissible cancer afflicting virtually an entire species, the Tasmanian devil (Sarcophilus harrisii). Despite a latent period that can exceed one year, to date DFTD diagnosis requires visual identification of tumour lesions. To enable earlier diagnosis, which is essential for the implementation of effective conservation strategies, we analysed the extracellular vesicle (EV) proteome of 87 Tasmanian devil serum samples. The antimicrobial peptide cathelicidin-3 (CATH3) was enriched in serum EVs of both devils with clinical DFTD (87.9% sensitivity and 94.1% specificity) and devils with latent infection (i.e., collected while overtly healthy, but 3-6 months before subsequent DFTD diagnosis; 93.8% sensitivity and 94.1% specificity). As antimicrobial peptides can play a variety of roles in the cancer process, our results suggest that the specific elevation of serum EV-associated CATH3 may be mechanistically involved in DFTD pathogenesis. This EV-based approach to biomarker discovery is directly applicable to improving understanding and diagnosis of a broad range of diseases in other species, and these findings directly enhance the capacity of conservation strategies to ensure the viability of the imperilled Tasmanian devil population.
Age, sex, and social environmental effects on immune cell composition in a free-ranging non-human primate
Authors: Rosado Mitchell R. Sanchez , Marzan-Rivera Nicole , Watowich Marina M. , Negron-Del Valle Andrea D. , Pantoja Petraleigh , Pavez-Fox Melissa A. , Siracusa Erin R. , Cooper Eve B. , Negron-Del Valle Josue E. , Phillips Daniel , Ruiz-Lambides Angelina ,   Cayo Biobank Research Unit, Martinez Melween I. , Montague Michael J. , Platt Michael L. , Higham James P. , Brent Lauren J. N. , Sariol Carlos A. , Snyder-Mackler Noah
Published: December 2021

Increasing age is associated with dysregulated immune function and increased inflammation– patterns that are also observed in individuals exposed to chronic social adversity. Yet we still know little about how social adversity impacts the immune system and how it might promote age-related diseases. Here, we investigated how immune cell diversity varied with age, sex and social adversity (operationalized as low social status) in free-ranging rhesus macaques. We found age-related signatures of immunosenescence, including lower proportions of CD20+ B cells, CD20+/CD3+ ratio, and CD4+/CD8+ T cell ratio – all signs of diminished antibody production. Age was associated with higher proportions of CD3+/CD8+ Cytotoxic T cells, CD16+/CD3-Natural Killer cells, CD3+/CD4+/CD25+ and CD3+/CD8+/CD25+ T regulatory cells, and CD14+/CD16+/HLA-DR+ intermediate monocytes, and lower levels of CD14+/CD16-/HLA-DR+ classical monocytes, indicating greater amounts of inflammation and immune dysregulation. We also found an effect of exposure to social adversity (i.e., low social status) that was sex-dependent. High-status males, relative to females, had higher CD20+/CD3+ ratios and CD16+/CD3 Natural Killer cell proportions, and lower proportions of CD8+ Cytotoxic T cells. Further, low status females had higher proportions of cytotoxic T cells than high status females, while the opposite was observed in males. High status males had higher CD20+/CD3+ ratios than low status males. Together, our study identifies immune cell types that differ by age in a human-relevant primate model animal, and demonstrates a novel link between sex-dependent immunity and social adversity.
SAVED by a toxin: Structure and function of the CRISPR Lon protease
Authors: Rouillon Christophe , Schneberger Niels , Chi Haotian , Peter Martin F. , Geyer Matthias , Boenigk Wolfgang , Seifert Reinhard , White Malcolm F. , Hagelueken Gregor
Published: December 2021

CRISPR antiviral defense systems such as the well-known DNA-targeting Cas9- and the more complex RNA-targeting type III systems are widespread in bacteria and archea 1, 2. The type III systems can orchestrate a complex antiviral response that is initiated by the synthesis of cyclic oligoadenylates (cOAs) upon foreign RNA recognition 3–5. These second messenger molecules bind to the CARF (CRISPR associated Rossmann-fold) domains of dedicated effector proteins that are often DNAses, RNAses, or putative transcription factors 6. The activated effectors interfere with cellular pathways of the host, inducing cell death or a dormant state of the cell that is better suited to avoid propagation of the viral attack 7, 8. Among a large set of proteins that were predicted to be linked to the type III systems 9, 10, the CRISPR-Lon protein caught our attention. The protein was predicted to be an integral membrane protein containing a SAVED-instead of a CARF-domain as well as a Lon protease effector domain. Here, we report the crystal structure of CRISPR-Lon. The protein is a soluble monomer and indeed contains a SAVED domain that accommodates cA4. Further, we show that CRISPR-Lon forms a stable complex with the 34 kDa CRISPR-T protein. Upon activation by cA4, CRISPR-Lon specifically cleaves CRISRP-T, releasing CRISPR-T23, a 23 kDa fragment that is structurally very similar to MazF toxins and is likely a sequence specific nuclease. Our results describe the first cOA activated proteolytic enzyme and provide the first example of a SAVED domain connected to a type III CRISPR defense system. The use of a protease as a means to unleash a fast response against a threat has intriguing parallels to eukaryotic innate immunity.
MIRA: Joint regulatory modeling of multimodal expression and chromatin accessibility in single cells
Authors: Lynch Allen W. , Theodoris Christina V. , Long Henry , Brown Myles , Liu X. Shirley , Meyer Clifford A.
Published: December 2021

Rigorously comparing gene expression and chromatin accessibility in the same single cells could illuminate the logic of how coupling or decoupling of these mechanisms regulates fate commitment. Here, we present MIRA: Probabilistic Multimodal Models for Integrated Regulatory Analysis, a comprehensive methodology that systematically contrasts transcription and accessibility to infer the regulatory circuitry driving cells along developmental trajectories. MIRA leverages topic modeling of cell states and regulatory potential modeling of individual gene loci. MIRA thereby represents cell states in an efficient and interpretable latent space, infers high fidelity lineage trees, determines key regulators of fate decisions at branch points, and exposes the variable influence of local accessibility on transcription at distinct loci. Applied to epidermal maintenance differentiation and embryonic brain development from two different multimodal platforms, MIRA revealed that early developmental genes were tightly regulated by local chromatin landscape whereas terminal fate genes were titrated without requiring extensive chromatin remodeling.
Graded Variation In Cortical T1w/T2w Myelination During Adolescence
Authors: Baum Graham L. , Flournoy John C. , Glasser Matthew F. , Harms Michael P. , Mair Patrick , Sanders Ashley , Barch Deanna M. , Buckner Randy L. , Bookheimer Susan , Dapretto Mirella , Smith Stephen , Thomas Kathleen M. , Yacoub Essa , Van Essen David C. , Somerville Leah H.
Published: December 2021

Myelination influences brain connectivity during sensitive periods of development by enhancing neural signaling speed and regulating synapse formation to reduce plasticity. However, in vivo studies characterizing the maturational timing of cortical myelination during human development remain scant. Here, we take advantage of recent advances in high-resolution cortical T1w/T2w myelin mapping methods, including principled correction of B1+ transmit field effects, using data from the Human Connectome Project in Development (N=628, ages 8-21) to characterize the maturational timing of myelination from childhood through early adulthood throughout the cerebral neocortex. We apply Bayesian spline models and functional latent clustering analysis to demonstrate graded variation in the rate of cortical T1w/T2w myelin growth in neocortical areas that is strongly correlated with the sensorimotor-association (S-A) axis of cortical organization reported by others. In sensorimotor areas T1w/T2w myelin starts at high levels at early ages, increases at a fast pace, and decelerates at later ages (18-21). In intermediate multimodal areas along the S-A axis, T1w/T2w myelin tends to start at intermediate levels and increase linearly at an intermediate pace. In transmodal/paralimbic association areas high along the S-A axis, T1w/T2w myelin tends to start at low levels and increase linearly at the slowest pace. These data provide evidence for graded variation along the S-A axis in the rate of cortical myelination during adolescence, which could reflect ongoing plasticity underlying the development of complex information processing and psychological functioning.

Significance Statement

Myelin is a lipid membrane that is essential to healthy brain function. Myelin wraps axons to increase neural signaling speed, enabling complex neuronal functioning underlying learning and cognition. Here we characterize the developmental timing of myelination across the cerebral cortex during adolescence using recent advances in non-invasive myelin mapping. Our results provide new evidence demonstrating graded variation across the cortex in the timing of myelination during adolescence, with rapid myelination in lower-order sensory areas and gradual myelination in higher-order association areas. This spatial pattern of microstructural brain development closely parallels the sensorimotor-to-association axis of cortical organization and plasticity during ontogeny.
Visual imagery vividness declines across the lifespan
Authors: Gulyás Erzsébet , Sütöri Sára , Lovas Andrea , Ziman Gergő , Gombos Ferenc , Kovács Ilona
Published: December 2021

The capacity to elicit vivid visual mental images varies within an extensive range across individuals between hyper- and aphantasia. It is not clear, however, whether imagery vividness is constant across the lifespan or changes during development and later in life. Without enforcing the constraints of strict experimental procedures and representativity across the entire population, our purpose was to take a first look at the self-reported level of imagery vividness and determine the relative proportion of aphantasic/hyperphantasic participants in different age-groups. Relying on the frequently used Vividness of Visual Mental Imagery questionnaire, we collected data on a random sample of 2252 participants between the ages of 12 to 60 years. We found a novel developmental pattern describing a declining ability to elicit vivid visual mental images in the group averages of different age-groups from adolescence to middle age. This effect involves both a decreasing proportion of individuals with very vivid imagery and an increasing proportion of individuals with weak imagery as maturation (assessed by boneage estimations in adolescents) and aging progresses. This finding may help to shed light on yet unknown developmental mechanisms of our internal, stimulus-independent processes, and might also help to determine genetic, maturational, and age-dependent factors in the extreme cases of hyper- and aphantasia.
CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices
Authors: Liu Shaopeng , Koslicki David
Published: December 2021

K-mer based methods are used ubiquitously in the field of computational biology. However, determining the optimal value ofkfor a specific application often remains heuristic. Simply reconstructing a newk-mer set with anotherk-mer size is computationally expensive, especially in metagenomic analysis where data sets are large. Here, we introduce a hashing-based technique that leverages a kind of bottom-msketch as well as ak-mer ternary search tree (KTST) to obtaink-mer based similarity estimates for a range ofkvalues. By truncatingk-mers stored in a pre-built KTST with a largek=kmaxvalue, we can simultaneously obtaink-mer based estimates for allkvalues up tokmax. This truncation approach circumvents the reconstruction of newk-mer sets when changingkvalues, making analysis more time and space-efficient. For example, we show that when using a KTST to estimate the containment index between a RefSeq-based microbial reference database and simulated metagenome data for 10 values ofk, the running time is close to 10x faster compared to a classic MinHash approach while using less than one-fifth the space to store the data structure. A python implementation of this method, CMash, is available athttps://github.com/dkoslicki/CMash. The reproduction of all experiments presented herein can be accessed viahttps://github.com/KoslickiLab/CMASH-reproducibles.
The SUMO protease Ulp2 regulates genome stability and drug resistance in the human fungal pathogen Candida albicans
Authors: Rizzo Marzia , Soisangwan Natthapon , Soetaert Jan , Vega-Estevez Samuel , Selmecki Anna , Buscaino Alessia
Published: December 2021

Stress-induced genome instability in microbial organisms is emerging as a critical regulatory mechanism for driving rapid and reversible adaption to drastic environmental changes. In Candida albicans, a human fungal pathogen that causes life-threatening infections, genome plasticity confers increased virulence and antifungal drug resistance. Discovering the mechanisms regulating C. albicans genome plasticity is a priority to understand how this and other microbial pathogens establish life-threatening infections and develop resistance to antifungal drugs. We identified the SUMO protease Ulp2 as a critical regulator of C. albicans genome integrity through genetic screening. Deletion of ULP2 leads to hypersensitivity to genotoxic agents and increased genome instability. This increased genome diversity causes reduced fitness under standard laboratory growth conditions but enhances adaptation to stress, making ulp2Δ/Δ cells more likely to thrive in the presence of antifungal drugs. Whole-genome sequencing indicates that ulp2Δ/Δ cells counteract antifungal drug-induced stress by developing segmental aneuploidies of chromosome R and chromosome I. We demonstrate that intrachromosomal repetitive elements drive the formation of complex novel genotypes with adaptive power.
A novel method for monitoring ground-dwelling arthropods on hard substrates: characterizing arthropod biodiversity among survey methods
Authors: McNamara Manning Katherine , Perry Kayla I. , Bahlai Christie A.
Published: December 2021

Sampling approaches are commonly adapted to reflect the study objectives in biodiversity monitoring projects. This approach optimizes findings to be locally relevant but comes at the cost of generalizability of findings. Here, we detail a comparison study directly examining how researcher choice of arthropod trap and level of specimen identification affects observations made in small-scale arthropod biodiversity studies. Sampling efficiency of four traps: pitfall traps, yellow ramp traps, yellow sticky cards, and a novel jar ramp trap were compared with respect to an array of biodiversity metrics associated with the arthropods they captured at three levels of identification. We also outline how to construct, deploy, and collect jar ramp traps. Trapping efficiency and functional groups of arthropods (flying, crawling, and intermediate mobility) varied by trap type. Pitfalls and jar ramp traps performed similarly for most biodiversity metrics measured, suggesting that jar ramp traps provide a more comparable measurement of ground-dwelling arthropod communities to pitfall sampling than the yellow ramp traps. The jar ramp trap is a simple, inexpensive alternative when the physical aspects of an environment do not allow the use of pitfalls. This study illustrates the implications for biodiversity sampling of arthropods in environments with physical constraints on trapping, and the importance of directly comparing adapted methods to established sampling protocol. Future biodiversity monitoring schemes should conduct comparison experiments to provide important information on performance and potential limitations of sampling methodology.
Sexual and developmental variations of ecto-parasitism in damselflies
Authors: Paul Shatabdi , Khan Md Kawsar , Herberstein Marie E.
Published: December 2021

The prevalence and intensity of parasitism can have different fitness costs between sexes, and across species and developmental stages. This variation could arise because of species specific sexual and developmental differences in body condition, immunity, and resistance. Theory predicts that the prevalence of parasitism will be greater in individuals with poor body condition and the intensity of parasitism will be greater in individuals with larger body size. These predictions have been tested and verified in vertebrates. In insects, however, contradictory evidence has been found in different taxa. Here, we tested these predictions on two species ofAgriocnemis(Agriocnemis feminaandAgriocnemis pygmaea) damselflies, which are parasitized byArrenuruswater mite ectoparasites. We measured body weight, total body length, abdomen area and thorax area of non-parasitized damselflies and found body condition varied between males and females, between immature females and mature females and betweenA. feminaandA. pygmaea. Then, we calculated the parasite prevalence, i.e., the frequency of parasitism and intensity, i.e., the number of parasites per infected damselfly in eleven natural populations of both species. In line to our predictions, we observed greater prevalence in immature females than mature females but found no difference in parasite prevalence between males and females. Furthermore, we found that parasite load was higher in females than males and in immature females than mature females. Our result also showed that the frequency and intensity of parasitism varied between the two studied species, being higher inA. pygmaeathanA. femina. Our study provides evidence that parasitism impacts sexes, developmental stages and species differentially and suggests that variation may occur due to sex, developmental stage, and species-specific resistance and tolerance mechanism.
The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes
Authors: Porcellato Elena , Gonzalez Juan Carlos , Ahlmann-Eltze Constantin , Elsakka Mahmoud Ali , Shapira Itamar , Fritsch Jürgen , Navarro Juan Antonio , Anders Simon , Russell Robert B. , Wieland Felix T. , Metzendorf Christoph
Published: December 2021

Protein S-palmitoylation, the addition of a long-chain fatty acid to target proteins, is among the most frequent reversible protein modification in Metazoa, affecting subcellular protein localization, trafficking and protein-protein interactions. S-palmitoylated proteins are abundant in the neuronal system and are associated with neuronal diseases and cancer. Despite the importance of this post-translational modification, it has not been thoroughly studied in the model organism Drosophila melanogaster.

Here we present the palmitoylome of Drosophila S2R+ cells, comprising 198 proteins, an estimated 3.5% of expressed genes in these cells. Comparison of orthologs between mammals and Drosophila suggests that S-palmitoylated proteins are more conserved between these distant phyla than non-S-palmitoylated proteins. To identify putative client proteins and interaction partners of the DHHC family of protein acyl-transferases (PATs) we established DHHC-BioID, a proximity biotinylation-based method. In S2R+ cells ectopic expression of the DHHC-PAT dHip14-BioID in combination with Snap24 or an interaction-deficient Snap24- mutant, as a negative control, resulted in biotinylation of Snap24 but not the Snap24-mutant. DHHC-BioID in S2R+ cells using 10 different DHHC-PATs as bait identified 520 putative DHHC-PAT interaction partners of which 48 were S-palmitoylated and are therefore putative DHHC-PAT client proteins. Comparison of putative client protein/DHHC-PAT combinations indicates that CG8314, CG5196, CG5880 and Patsas have a preference for transmembrane proteins, while S-palmitoylated proteins with the Hip14-interaction motif are most enriched by DHHC-BioID variants of approximated and dHip14. Finally, we show that BioID is active in larval and adult Drosophila and that dHip14-BioID rescues dHip14 mutant flies, indicating that DHHC-BioID is non-toxic.

In summary we provide the first systematic analysis of a Drosophila palmitoylome. We show that DHHC-BioID is sensitive and specific enough to identify DHHC-PAT client proteins and provide DHHC-PAT assignment for ca. 25% of the S2R+ cell palmitoylome, providing a valuable resource. In addition, we establish DHHC-BioID as a useful concept for the identification of tissue-specific DHHC-PAT interactomes in Drosophila.
Phosphorylation dynamics in a flg22-induced, heterotrimeric G-protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking
Authors: Watkins Justin M. , Clark Natalie M. , Song Gaoyuan , Oliveira Celio Cabral , Mishra Bharat , Brachova Libuse , Seifert Clara M. , Mitchell Malek S. , Reis Pedro Augusto Braga dos , Urano Daisuke , Shahid Muktar M. , Walley Justin W. , Jones Alan M.
Published: December 2021

flg22 is a 22-amino peptide released from bacterial flagellin, a Microbe-Associated Molecular Pattern (MAMP) that is recognized by the plant cell as a signal indicating that bacteria are present. On its own, flg22 initiates a rapid increase in cytoplasmic calcium, extracellular reactive oxygen species, and activation of a Mitogen Activated Protein Kinase (MAPK) cascade, all of which are activated within 15 minutes after the cell perceives flg22. Here we show a massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome within this 15-minute duration in wildtype and a mutant deficient in G-protein coupled signaling. Integration of phosphoproteome with protein-protein interactome data followed by network topology analyses discovered that many of the flg22-induced phosphoproteome changes fall on proteins that comprise the G protein interactome and on the most highly populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the G-protein interactome depend on a functional heterotrimeric G protein complex, some occur on proteins that interact directly with components of G-coupled signal transduction. One of these is ATBα, a substrate-recognition sub-unit of the PP2A Ser/Thr phosphatase and an interactor to Arabidopsis thaliana REGULATOR OF G SIGNALING 1 protein (AtRGS1), a 7-transmembrane spanning modulator of the nucleotide-binding state of the core G protein complex. AtRGS1 is phosphorylated by BAK1, a component of the flg22 receptor, to initiate AtRGS1 endocytosis. A null mutation of ATBα confers high basal endocytosis of AtRGS1, suggesting sustained phosphorylated status. Loss of ATBα confers traits associated with loss of AtRGS1. Because the basal level of AtRGS1 is lower in the atbα null mutant in a proteasome-dependent manner, we propose that phosphorylation-dependent endocytosis of AtRGS1 is part of a mechanism to degrade AtRGS1 which then sustains activation of the G protein complex. Thus, the role of ATBα is now established as a central component of phosphorylation-dependent regulation of system dynamics in innate immunity.
Distributed Feedforward and Feedback Processing across Perisylvian Cortex Supports Human Speech
Authors: Wang Ran , Chen Xupeng , Khalilian-Gourtani Amirhossein , Yu Leyao , Dugan Patricia , Friedman Daniel , Doyle Werner , Devinsky Orrin , Wang Yao , Flinker Adeen
Published: December 2021

Speech production is a complex human function requiring continuous feedforward commands together with reafferent feedback processing. These processes are carried out by distinct frontal and posterior cortical networks, but the degree and timing of their recruitment and dynamics remain unknown. We present a novel deep learning architecture that translates neural signals recorded directly from cortex to an interpretable representational space that can reconstruct speech. We leverage state-of-the-art learnt decoding networks to disentangle feedforward vs. feedback processing. Unlike prevailing models, we find a mixed cortical architecture in which frontal and temporal networks each process both feedforward and feedback information in tandem. We elucidate the timing of feedforward and feedback related processing by quantifying the derived receptive fields. Our approach provides evidence for a surprisingly mixed cortical architecture of speech circuitry together with decoding advances that have important implications for neural prosthetics.
Association of Physical Activity with the Incidence of Atrial Fibrillation in Persons >65 Years Old: The Atherosclerosis Risk In Communities (ARIC) Study
Authors: Fletcher Grace , Alam Aniqa B. , Li Linzi , Norby Faye L. , Chen Lin Y. , Soliman Elsayed Z. , Alonso Alvaro
Published: December 2021

Background

Though moderate levels of physical activity (PA) seem to reduce the risk of atrial fibrillation (AF), the association of PA with AF in the elderly remains unclear.

Methods

We studied 5,166 participants of the Atherosclerosis Risk in Communities (ARIC) cohort that took part in visit 5 (2011-2013), were free of AF and had complete information on all variables. Self-reported PA was evaluated with a validated questionnaire and weekly minutes of leisure-time moderate to vigorous physical activity (MVPA) were calculated and categorized using the 2018 Physical Activity Guidelines for Americans (no activity [0 min/week], low [>0-<150 min/week], adequate [150-<300 min/week], high [≥300 min/week]). Incident AF between the visit 5 and the end of 2019 was ascertained from hospital discharges and death certificates. Cox models were used to calculate hazard ratios (HR) and 95% confidence intervals (CI) for AF by levels of physical activity adjusting for potential confounders.

Results

The mean (SD) age for the sample was 75 (5) years; 59% were female and 22% were Black. During a mean (SD) follow-up time of 6.3 (2.0) years, 703 AF events were identified. The association of MVPA with AF incidence showed a U-shaped relationship. Compared to those not engaging in MVPA, individuals with low MVPA had a 23% lower hazard of AF (HR= 0.77; 95% CI: 0.61, 0.96), while those with adequate MVPA had a 14% lower hazard (HR 0.86; 95% CI: 0.69, 1.06). High levels of MVPA were not associated with AF risk (HR 0.97; 95% CI: 0.78, 1.20). There was no evidence of heterogeneity when stratified by race and sex.

Conclusion

This study suggests that being involved in low to moderate levels of MVPA was associated with a reduced hazard of AF. There was no evidence of increased risk of AF in those with higher levels of MVPA.
Influence of protonation on the geometry of 2-{[(2,6-dimethylphenoxy)ethyl]amino}-1-phenylethan-1-ol: crystal structures of the free base and of its chloride and 3-hydroxybenzoate salt forms
Authors: Nitek Wojciech , Kania Agnieszka , Marona Henryk , Waszkielewicz Anna M. , Żesławska Ewa
Published: December 2021

The aroxyalkylaminoalcohol derivatives are a group of compounds known for their pharmacological action. The crystal structures of four new xylenoxyaminoalcohol derivatives having anticonvulsant activity are reported, namely, 2-{[2-(2,6-dimethylphenoxy)ethyl]amino}-1-phenylethan-1-ol, C18H23NO2, 1, the salt N-[2-(2,6-dimethylphenoxy)ethyl]-1-hydroxy-1-phenylethan-2-aminium 3-hydroxybenzoate, C18H24NO2
+·C7H5O3
−, 2, and two polymorphs of the salt (R)-N-[2-(2,6-dimethylphenoxy)ethyl]-1-hydroxy-1-phenylethan-2-aminium chloride, C18H24NO2
+·Cl−, 3 and 3p. Both polymorphs crystallize in the space group P21212 and each has two cations and two anions in the asymmetric unit (Z′ = 2). The molecules in the polymorphs show differences in their molecular conformations and intermolecular interactions. The crystal packing of neutral 1 is dominated by intermolecular O—H...N hydrogen bonds, resulting in the formation of one-dimensional chains. In the crystal structures of the salt forms (2, 3 and 3p), each protonated N atom is engaged in a charge-assisted hydrogen bond with the corresponding anion. The protonation of the N atom also influences the conformation of the molecular linker between the two aromatic rings and changes the orientation of the rings. The crystal packing of the salt forms is dominated by intermolecular O—H...O hydrogen bonds, resulting in the creation of chains and rings. Structural studies have been enriched by the calculation of Hirshfeld surfaces and the corresponding fingerprint plots.
Advertising with scarcity messages and attitudes for luxury skin-care products
Authors: Fogel Joshua , Setton Marcelle Kim
Published: December 2021

Purpose

A number of types of scarcity messages are often used in Internet advertisements, but all these types have not been directly compared to each other.

Design/methodology/approach

College students (n = 789) were surveyed about five advertising choices for luxury skin-care products consisting of scarcity messages of high-demand, low-stock, limited-time, countdown timer and regular advertising without any scarcity message. Outcomes were product classification attitudes of functional and symbolic and psychological attitudes of persuasion knowledge and advertising skepticism.

Findings

The study found that high-demand message had greater functional attitudes and greater symbolic attitudes than regular advertising. Limited-time message had greater symbolic attitudes than regular advertising. High-demand message had lower advertising skepticism attitudes than regular advertising.

Practical implications

The authors recommend that when a luxury skin-care product is in high demand, that marketers should use high-demand messages in their advertising. Marketers of luxury skin-care products may also benefit from using limited-time message advertisements.

Originality/value

This is the first study to directly compare the scarcity message advertising types of high-demand, low-stock, limited-time, countdown timer with regular advertising without any scarcity message.
Suitability of passive RC-network-based inductorless bridged-T as a bandpass NGD circuit
Authors: Lalléchére Sébastien , Nebhen Jamel , Liu Yang , Chan George , Fontgalland Glauco , Rahajandraibe Wenceslas , Wan Fayu , Ravelo Blaise
Published: December 2021

Purpose

The purpose of this paper is to study, a bridged-T topology with inductorless passive network used as a bandpass (BP) negative group delay (NGD) function.

Design/methodology/approach

The BP NGD topology under study is composed of an inductorless passive resistive capacitive network. The circuit analysis is elaborated from the equivalent impedance matrix. Then, the analytical model of the C-shunt bridged-T topology voltage transfer function is established. The BP NGD analysis of the considered topology is developed in function of the bridged-T parameters. The NGD properties and characterizations of the proposed topology are analytically expressed. Moreover, the relevance of the BP NGD theory is verified with the design and fabrication of surface mounted device components-based proof-of-concept (PoC).

Findings

From measurement results, the BP NGD network with −151 ns at the center frequency of 1 MHz over −6.6 dB attenuation is in very good agreement with the C-shunt bridged-T PoC.

Originality/value

This paper develops a mathematical modeling theory and measurement of a C-shunt bridged-T network circuit.