bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of an Emergency Department Bruising Pathway on Disparities in Child Abuse Evaluation
Authors: Crumm Caitlin E. , Brown Emily C.B. , Vora Surabhi B. , Lowry Sarah , Schlatter Adrienne , Rutman Lori E.
Published: July 2023

Objectives

Previous research has shown racial, ethnic, and socioeconomic disparities in provider medical evaluations and reporting to child protective services (CPS) and law enforcement (LE) for cases of suspected child physical abuse. Our hospital standardized evaluation and reporting of high-risk bruising using a clinical pathway. We aimed to assess whether standardization impacted disparity.

Methods

We performed a retrospective observational study including children evaluated in the emergency department who had a social work consult for concern for child abuse or neglect between June 2012 and December 2019. From this group, we identified children with high-risk bruising. We compared outcomes (receipt of skeletal survey, CPS report, or LE report) before and after implementation of a standard bruising evaluation pathway to determine how the intervention changed practice among various racial, ethnic, and socioeconomic groups.

Results

During the study period, 2129 children presented to the ED and received a social work consult for child abuse or neglect. Of these, 333 had high-risk bruising. Children without private insurance had a higher risk of having a CPS (adjusted relative risk, 1.32; 95% confidence interval, 1.09–1.60) or LE (adjusted relative risk, 1.48; 95% confidence interval, 1.11–1.97) report prepathway, but not after pathway implementation. No significant associations were seen for race or ethnicity.

Conclusions

A standardized clinical pathway for identification and evaluation of high-risk bruising may help to decrease socioeconomic disparities in reporting high-risk bruising. Larger studies are needed to fully evaluate disparities in assessment and reporting of child abuse.
Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency
Authors: Yue Ye , Read Timothy D. , Fedirko Veronika , Satten Glen A. , Hu Yi-Juan
Published: July 2023

The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for the objective of testing differential abundance at the genus and community levels while overcoming these difficulties. We demonstrate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than twoad hocapproaches.
Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing
Authors: Xie Yi , Chen Huimei , Chellamuthu Vasuki Ranjani , Lajam Ahmad bin Mohamed , Albani Salvatore , Low Andrea Hsiu Ling , Petretto Enrico , Behmoaras Jacques
Published: July 2023

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10X Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10X data where samples are not multiplexed. Despite a relatively lower library and cell capture efficiencies, Parse can detect rare cell types (e.g. plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.
A distributed theta network of error generation and processing in aging
Authors: Kolev Vasil , Falkenstein Michael , Yordanova Juliana
Published: July 2023

Based on previous concepts that a distributed theta network with a central “hub” in the medial frontal cortex is critically involved in movement regulation, monitoring, and control, the present study explored the involvement of this network in error processing with advancing age in humans. For that aim, the oscillatory neurodynamics of motor theta oscillations was analyzed at multiple cortical regions during correct and error responses in a sample of older adults.

Response-related potentials (RRPs) of correct and incorrect reactions were recorded in a four-choice reaction task. RRPs were decomposed in the time-frequency domain to extract oscillatory theta activity. Motor theta oscillations at extended motor regions were analyzed with respect to power, temporal synchronization, and functional connectivity.

Major results demonstrated that errors had pronounced effects on motor theta oscillations at cortical regions beyond the medial frontal cortex by being associated with (1) theta power increase in the hemisphere contra-lateral to the movement, (2) suppressed spatial and temporal synchronization at pre-motor areas contra-lateral to the responding hand, (2) inhibited connections between the medial frontal cortex and sensorimotor areas, and (3) suppressed connectivity and temporal phase-synchronization of motor theta networks in the posterior left hemisphere, irrespective of the hand, left, or right, with which the error was made.

These findings reveal distributed effects of errors on motor theta oscillations in older subjects and support the hypothesis that error processing operates on a network level. They confirm the presence of aging-dependent functional disengagement of the medial frontal region and suggest that difficulties in controlling the focus of motor attention and response selection contribute to performance impairment in old individuals.
LRRK2 G2019S promotes the development of colon cancer via modulating intestinal inflammation
Authors: Wang Yuhang , Gao Joyce Z , Sakaguchi Taylor , Maretzky Thorsten , Gurung Prajwal , Short Sarah , Xiong Yiqin , Kang Zizhen
Published: July 2023

LRRK2 G2019S is the most prevalent variant associated with Parkinson’s disease (PD), found in 1-3% of sporadic and 4-8% of familial PD cases. Intriguingly, emerging clinical studies have suggested that LRRK2 G2019S carriers have an increased risk of cancers including colorectal cancer. However, the underlying mechanisms of the positive correlation between LRRK2-G2019S and colorectal cancer remain unknown. Using a mouse model of colitis-associated cancer (CAC) and LRRK2 G2019S knockin (KI) mice, here we report that LRRK2 G2019S promotes the pathogenesis of colon cancer as evidenced by increased tumor number and tumor size in LRRK2 G2019S KI mice. LRRK2 G2019S promoted intestinal epithelial cell proliferation and inflammation within the tumor microenvironment. Mechanistically, we found that LRRK2 G2019S KI mice are more susceptible to dextran sulfate sodium (DSS)-induced colitis. Suppressing the kinase activity of LRRK2 ameliorated the severity of colitis in both LRRK2 G2019S KI and WT mice. At the molecular level, our investigation unveiled that LRRK2 G2019S promotes the production of reactive oxygen species, triggers inflammasome activation, and induces cell necrosis in the gut epithelium in a mouse model of colitis. Collectively, our data provide direct evidence that gain-of-kinase activity in LRRK2 promotes colorectal tumorigenesis, implicating LRRK2 as a potential target in colon cancer patients with hyper LRRK2 kinase activity.
Hippocampal contributions to novel spatial learning are both age-related and age-invariant
Authors: Zheng Li , Gao Zhiyao , Doner Stephanie , Oyao Alexis , Forloines Martha , Grilli Matthew D. , Barnes Carol A. , Ekstrom Arne D.
Published: July 2023

Older adults show declines in spatial memory, although the extent of these alterations is not uniform across the healthy older population. Here, we investigate the stability of neural representations for the same and different spatial environments in a sample of younger and older adults using high-resolution functional magnetic resonance imaging (fMRI) of the medial temporal lobe. Older adults showed, on average, lower neural pattern similarity for retrieving the same environment and more variable neural patterns compared to young adults. We also found a positive association between spatial distance discrimination and the distinctiveness of neural patterns between environments. Our analyses suggested that one source for this association was the extent of informational connectivity to CA1 from other subfields, which was dependent on age, while another source was the fidelity of signals within CA1 itself, which was independent of age. Together, our findings suggest both age-dependent and independent neural contributions to spatial memory performance.

Significance Statement

Spatial memory declines with age, although some older adults show little cognitive decline, even into their 80s. One important lead for age-related changes comes from electrophysiological studies of older rats, who have less stable neural representations for a spatial environment, termed “place cells.” Using high-resolution fMRI targeting the human hippocampus, we demonstrate that older adults also have less stable neural representations within the same environment. Our results reveal, however, that there are both age and performance dependent differences driving these effects. While older adults, on average, showed alterations in information flow within the hippocampal circuit, better performing individuals showed more differentiated neural representations regardless of age. Together, these findings provide novel insight into the impact of age on spatial memory.
Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
Authors: Sielemann Katharina , Schmidt Nicola , Guzik Jonas , Kalina Natalie , Pucker Boas , Viehöver Prisca , Breitenbach Sarah , Weisshaar Bernd , Heitkam Tony , Holtgräwe Daniela
Published: July 2023

Most crop plants, including sugar beet (Beta vulgarissubsp.vulgaris), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses.

Especially polyploids are interesting from an evolutionary perspective as genes undergo reorganisation after the polyploidisation event. Through neo-and subfunctionalisation, novel functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. Particularly in the face of climate change, specific stress and pathogen resistances or tolerances gain importance. To introduce such traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. The identification of genes underlying traits of interest is crucial for crop improvement.

For beets, the sectionCorollinaecontains the tetraploid speciesBeta corolliflora(2n=4x=36) that harbours salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits ofB. corolliflorais increased compared to those of the known diploids in this section (all 2n=2x=18). Nevertheless, neither the parental relationships ofB. corolliflorahave been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding.

To benefit from the resources offered by polyploid beet wild relatives, we generated a comprehensive pangenome dataset includingB. corolliflora,Beta lomatogona, andBeta macrorhiza, as well as a more distant wild beetPatellifolia procumbens(2n=2x=18). Joined analyses with publicly available genome sequences of two additional wild beets allowed the identification of genomic regions absent from cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours. In addition, we present strong evidence for the parental relationship of theB. corolliflorawild beet as an autotetraploid emerging fromB. macrorhiza.
Well-ST-seq: cost-effective spatial transcriptomics at cellular level and high RNA capture efficiency
Authors: Yu Nianzuo , Jin Zhengyang , Liang Chongyang , Zhang Junhu , Yang Bai
Published: July 2023

Spatial transcriptomic technologies are promising tools to reveal fine anatomical profiles of tissues. As for the methodologies based on barcoded probe arrays, improving the balance among probe barcoding complexity and cost, gene capture sensitivity, and spatial resolution can accelerate the spreading of spatial transcriptomic in basic science and clinical work. Here, based on miniaturized microfluidic and microarray technologies, we constructed a spatially cellular-level RNA-capture probe arrays. Owing to the predetermined and cost-effective probe fixation characteristics of the methodology, the consumable cost and fabrication time of the probe array can be reduced to $1.21/mm2and approximately 2 hours, and the preparation process does not rely on large precision instruments. Moreover, the efficiency of the transcript captured by the probe array is even comparable to conventional single-cell RNA sequencing. Based on this technology, we achieved the spatial transcriptome expression mapping and gained insight into spatial cell heterogeneity of the mouse hippocampus.
DrugGPT: A GPT-based Strategy for Designing Potential Ligands Targeting Specific Proteins
Authors: Li Yuesen , Gao Chengyi , Song Xin , Wang Xiangyu , Xu Yungang , Han Suxia
Published: July 2023

DrugGPT presents a ligand design strategy based on the autoregressive model, GPT, focusing on chemical space exploration and the discovery of ligands for specific proteins. Deep learning language models have shown significant potential in various domains including protein design and biomedical text analysis, providing strong support for the proposition of DrugGPT. In this study, we employ the DrugGPT model to learn a substantial amount of protein-ligand binding data, aiming to discover novel molecules that can bind with specific proteins. This strategy not only significantly improves the efficiency of ligand design but also offers a swift and effective avenue for the drug development process, bringing new possibilities to the pharmaceutical domain.

In our research, we particularly optimized and trained the GPT-2 model to better adapt to the requirements of drug design. Given the characteristics of proteins and ligands, we redesigned the tokenizer using the BPE algorithm, abandoned the original tokenizer, and trained the GPT-2 model from scratch. This improvement enables DrugGPT to more accurately capture and understand the structural information and chemical rules of drug molecules. It also enhances its comprehension of binding information between proteins and ligands, thereby generating potentially active drug candidate molecules.

Theoretically, DrugGPT has significant advantages. During the model training process, DrugGPT aims to maximize the conditional probability and employs the back-propagation algorithm for training, making the training process more stable and avoiding the Mode Collapse problem that may occur in Generative Adversarial Networks in drug design. Furthermore, the design philosophy of DrugGPT endows it with strong generalization capabilities, giving it the potential to adapt to different tasks.

In conclusion, DrugGPT provides a forward-thinking and practical new approach to ligand design. By optimizing the tokenizer and retraining the GPT-2 model, the ligand design process becomes more direct and efficient. This not only reflects the theoretical advantages of DrugGPT but also reveals its potential applications in the drug development process, thereby opening new perspectives and possibilities in the pharmaceutical field.
Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers
Authors: Zhang Junpeng , Liu Lin , Wei Xuemei , Zhao Chunwen , Li Sijing , Li Jiuyong , Le Thuc Duy
Published: July 2023

Non-coding RNAs (ncRNAs) act as important modulators of gene expression and they have been confirmed to play critical roles in the physiology and development of malignant tumors. Understanding the synergism of multiple ncRNAs in competing endogenous RNA (ceRNA) regulation can provide important insights into the mechanisms of malignant tumors caused by ncRNA regulation. In this work, we present a framework, SCOM, for identifying ncRNA synergistic competition. We systematically construct the landscape of ncRNA synergistic competition across 31 malignant tumors, and reveal that malignant tumors tend to share hub ncRNAs rather than the ncRNA interactions involved in the synergistic competition. In addition, the synergistic competition ncRNAs (i.e. ncRNAs involved in the synergistic competition) are likely to be involved in drug resistance, contribute to distinguishing molecular subtypes of malignant tumors, and participate in immune regulation. Furthermore, SCOM can help to infer ncRNA synergistic competition across malignant tumors and uncover potential diagnostic and prognostic biomarkers of malignant tumors. Altogether, the SCOM framework and the resulting web-based database SCOMdb (www.comblab.cn/SCOMdb/) serve as a useful resource for exploring ncRNA regulation and to accelerate the identification of carcinogenic biomarkers.

Author summary

Abundant evidence reveals that ncRNAs are important modulators of gene expression, and it is important for us to understand the regulation of ncRNAs in malignant tumors. In this work, we hypothesize that ncRNAs acting as ceRNAs can crosstalk with each other in the form of synergistic competition. We name the hypothesis as thencRNA synergistic competition hypothesis. To uncover potential carcinogenic biomarkers, we present a framework, SCOM, for identifying ncRNA synergistic competition in malignant tumors. From the perspective of synergistic competition, we have shown that the synergistic competition ncRNAs are likely to involve in drug resistance, contribute to distinguishing molecular subtypes of malignant tumors, and participate in immune regulation. In addition, the synergistic competition ncRNAs are potential diagnostic and prognostic biomarkers of malignant tumors. We believe that the proposed framework SCOM and the web-based database SCOMdb can contribute to the design of reliable diagnosis and treatment biomarkers for malignant tumors.
Your place or mine? The neural dynamics of personally familiar scene recognition suggests category independent familiarity encoding
Authors: Klink Hannah , Kaiser Daniel , Stecher Rico , Ambrus Géza Gergely , Kovács Gyula
Published: July 2023

Recognizing a stimulus as familiar is an important capacity in our everyday life. Recent investigation of visual processes has led to important insights into the nature of the neural representations of familiarity for human faces. Still, little is known about how familiarity affects the neural dynamics of non-face stimulus processing. Here we report the results of an EEG study, examining the representational dynamics of personally familiar scenes. Participants viewed highly variable images of their own apartments and unfamiliar ones, as well as personally familiar and unfamiliar faces. Multivariate pattern analyses were used to examine the time course of differential processing of familiar and unfamiliar stimuli. Time-resolved classification revealed that familiarity is decodable from the EEG data similarly for scenes and faces. The temporal dynamics showed delayed onsets and peaks for scenes as compared to faces. Familiarity information, starting at 200 ms, generalized across stimulus categories and led to a robust familiarity effect. In addition, familiarity enhanced category representations in early (250 – 300 ms) and later (>400 ms) processing stages. Our results extend previous face familiarity results to another stimulus category and suggest that familiarity as a construct can be understood as a general, stimulus-independent processing step during recognition.

Highlights

Whether a face or scene is familiar can be decoded from the EEG signal with very similar temporal dynamics, starting at 200 ms and peaking around 400 ms after stimulus onset.

The neural dynamics of this familiarity information generalizes across stimulus categories.

Familiarity modulates stimulus category representations from 200 ms after stimulus onset, indicating deeper processing of familiar as compared to unfamiliar stimuli already during early processing stages.
Karyopherin α2 is a maternal effect gene required for early embryonic development and female fertility in mice
Authors: Rother Franziska , Depping Reinhard , Popova Elena , Huegel Stefanie , Heiler Ariane , Hartmann Enno , Bader Michael
Published: July 2023

The nuclear transport of proteins plays an important role in mediating the transition from egg to embryo and distinct karyopherins have been implicated in this process. Here, we studied the impact of KPNA2 deficiency on preimplantation embryo development in mice. Loss of KPNA2 results in complete arrest at the 2cell stage and embryos exhibit the inability to activate their embryonic genome as well as a severely disturbed nuclear translocation of Nucleoplasmin 2. Our findings define KPNA2 as a new maternal effect gene.
Autoantibody subclass predominance is not driven by aberrant class switching or impaired B cell development
Authors: Paardekooper Laurent M. , Fillié-Grijpma Yvonne E. , van der Sluijs-Gelling Alita J. , Zlei Mihaela , van Doorn Remco , Vermeer Maarten H. , Paunovic Manuela , Titulaer Maarten J. , van der Maarel Silvère M. , van Dongen Jacques J.M. , Verschuuren Jan J. , Huijbers Maartje G.
Published: July 2023

A subset of autoimmune diseases is characterized by predominant pathogenic IgG4 autoantibodies (IgG4-AIDs). Why IgG4 predominates in these disorders is unknown. We hypothesized that dysregulated B cell maturation or aberrant class switching causes overrepresentation of IgG4+B cells and plasma cells. Therefore, we compared the B cell compartment of patients with muscle-specific kinase (MuSK) myasthenia gravis (MG), pemphigus, leucine-rich glioma inactivated (LGI1) encephalitis and contactin-associated protein-like 2 (CASPR2) encephalitis (four IgG4-AIDs) to patients with acetylcholine receptor (AChR) MG, Lambert-Eaton myasthenic syndrome (LEMS) (two IgG1-3-AIDs) and age-matched healthy donors, using flow cytometry. B cell subset relative abundance at all maturation stages was normal, except for a, possibly treatment-related, reduction in immature and naïve CD5+cells in IgG4-AIDs. IgG4+B cell and plasma cell fractions were normal in IgG4-AID patients, however they had an (sub)class-independent 8-fold increase in circulating mature CD20-CD138+plasma cells. No autoreactivity was found in this subset after sorting. In conclusion, patients with IgG4-AID do not show increased numbers of IgG4-expressing cells. These results argue against aberrant B cell development in these patients and rather suggest the autoantibody subclass predominance to be antigen-driven. The similarities between B cell subset numbers among these patients suggest that these IgG4-AIDs, despite displaying variable clinical phenotypes, share a similar underlying immune profile.

Graphical abstract
Amazing structural diversity of giant virus-like particles in forest soil
Authors: Fischer Matthias G. , Mersdorf Ulrike , Blanchard Jeffrey L.
Published: July 2023

Large DNA viruses of the phylumNucleocytoviricotainfect diverse eukaryotic hosts from protists to humans, with profound consequences for aquatic and terrestrial ecosystems. While nucleocytoviruses are known to be highly diverse in metagenomes, knowledge of their capsid structures is restricted to a few characterized representatives. Here, we visualize giant virus-like particles (VLPs, diameter >0.2 µm) directly from the environment using transmission electron microscopy. We found that Harvard Forest soils contain a higher diversity of giant VLP morphotypes than all hitherto isolated giant viruses combined. These included VLPs with icosahedral capsid symmetry, ovoid shapes similar to pandoraviruses, and bacilliform shapes that may represent novel viruses. We discovered giant icosahedral capsids with structural modifications that had not been described before including tubular appendages, modified vertices, tails, and capsids consisting of multiple layers or internal channels. Many giant VLPs were covered with fibers of varying lengths, thicknesses, densities, and terminal structures. These findings imply that giant viruses employ a much wider array of capsid structures and mechanisms to interact with their host cells than is currently known. We also found diverse tailed bacteriophages and filamentous VLPs, as well as ultra-small cells. Our study offers a first glimpse of the vast diversity of unexplored viral structures in soil and reinforces the potential of transmission electron microscopy for fundamental discoveries in environmental microbiology.
Non-covalent Linking Antibody to Yeast Using the Cell Surface Display of Staphylococcal Protein A
Authors: Shi Yi-Feng
Published: July 2023

Yeast surface display represents a commonly used platform suitable for the generation and screening of antibodies as well as the selection of high-producer clones. The methods of yeast display rely on the genetic fusion of recombinant antibodies to an abundant cell wall protein of yeast. Here, the study of proof of concept showed that the conventional strategy of expression of fusion antibodies was replaced by non-covalent binding to antibodies for yeast surface display. The use of cell surface display of an epitope tag will endow the cells with new arms for immobilizing, absorbing or targeting the proteins.Staphylococcalprotein A, which is characterized by its ability to bind selectively to the Fc region of IgG, was examined to be expressed on the surface ofSaccharomyces cerevisiaeusing a secretion signal ofRhizopus oryzaeglucoamylase and C-terminal half of α−agglutinin including glycosylphosphatidylinositol (GPI) anchor attachment signal under the control of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) promoter. On the other hand, an Fc-fused enzyme was created to construct a molecular fusion ofRhizopus oryzaeLipase with the spacer and the Fc region of IgG heavy chain. The secretion of fusion protein was carried out using pre-α-factor leader region as secretion signal under the control of the 5’-upstream region of theCandida tropicalisisocitrate lyase gene (UPR-ICL) inS. cerevisiae. The Fc-fused lipase was captured by Staphylococcal protein A as an adaptor protein displayed on the surface of yeast cells. The method of this switchable yeast display takes advantage of the “secretion-and-capture” strategy and can be applied to improve the efficiency of yeast display of full-length IgG.

graphical abstract

Staphylococcal protein A, which has the ability to binding to the Fc region of IgG and leaving the antigen combing site free, has been assembled on the surface of yeast cells to target antibodies or enzymes with Fc fusion.
Degradation of sulphonated mono and di-azo dye as the sole carbon source inSerratia marcescens: Insights from combined wet and dry lab analysis
Authors: Basharat Zarrin , Yasmin Azra
Published: July 2023

The high production volume of azo dyes for manufacturing and treating various consumer products leads to deleterious environmental consequences. Bacterial agents present in the environment can degrade these dyes. We, hereby, report the isolation, decolourization and degradation of a mono (Methyl orange) and di-azoic (Congo red) compound of this class of dyes by a versatile bacteriumSerratia marcescens. Our isolate showed the capability of sulphonated azo dye utilization/degradation i.e. Methyl orange and Congo red usage, with no inhibitory effects on its growth in minimal medium. The calorimetric analysis showed 80.83% decolourization of Methyl orange and 92.7% decolourization of Congo red after 7 days of incubation in a shaking incubator at pH: 7 and temperature: 37 °C. An azoreductase enzyme of ∼25 KDa was detected after SDS-PAGE analysis. Quantitative and qualitative testing of the degradation phenomenon was followed byin silicoanalysis. Structural modeling followed by molecular docking in Molecular Operating Environment revealed numerous residues involved in binding and assisting degradation. Changes in the apo, holo, and dye-bound enzyme energy profiles were also observed. This is the first study reporting the capability ofSerratia marcescensto use azo dyes/sulphonated azo dyes as the sole carbon source and the detailed computational analysis of the degradation phenomenon. We hope that these findings will be of use to environmental scientists, aid in better dye-degrading mutant creation to help craft future remediation strategies for sulphonated azo dyes.
Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803
Authors: Pfennig Tobias , Kullmann Elena , Zavřel Tomáš , Nakielski Andreas , Ebenhöh Oliver , Červený Jan , Bernát Gábor , Matuszyńska Anna Barbara
Published: July 2023

Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2 . By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.
Immunologically mediated trade-offs shaping transmission of sylvatic dengue and Zika viruses in native and novel non-human primate hosts
Authors: Hanley Kathryn A. , Cecilia Hélène , Azar Sasha R. , Moehn Brett , Yu Wanqin , Yun Ruimei , Althouse Benjamin M. , Vasilakis Nikos , Rossi Shannan L.
Published: July 2023

Mosquito-borne dengue (DENV) and Zika (ZIKV) viruses originated in Old World sylvatic cycles involving monkey hosts, spilled over into human transmission, and were translocated to the Americas, creating potential for spillback into neotropical sylvatic cycles. Studies of the trade-offs that shape within-host dynamics and transmission of these viruses are lacking, hampering efforts to predict spillover and spillback. We exposed native (cynomolgus macaque) or novel (squirrel monkey) hosts to mosquitoes infected with either sylvatic DENV or ZIKV and monitored viremia, natural killer cells, transmission to mosquitoes, cytokines, and neutralizing antibody titers. Unexpectedly, DENV transmission from both host species occurred only when serum viremia was undetectable or near the limit of detection. ZIKV replicated in squirrel monkeys to much higher titers than DENV and was transmitted more efficiently but stimulated lower neutralizing antibody titers. Increasing ZIKV viremia led to greater instantaneous transmission and shorter duration of infection, consistent with a replication-clearance trade-off.
Discovery of Eremiobacterota withnifHhomologs in tundra soil
Authors: Pessi Igor S. , Delmont Tom O. , Zehr Jonathan P. , Hultman Jenni
Published: July 2023

We describe the genome of an Eremiobacterota population from tundra soil that contains the minimal set ofnifgenes needed to fix atmospheric N2. This putative diazotroph population, which we nameCandidatusLamibacter sapmiensis, links for the first time Eremiobacterota and N2fixation. The integrity of the genome and itsnifgenes are well supported by both environmental and taxonomic signals.Ca. Lamibacter sapmiensis contains threenifHhomologs and the complementary set ofnifDKENBgenes that are needed to assemble a functional nitrogenase. The putative diazotrophic role ofCa. Lamibacter sapmiensis is supported by the presence of genes that regulate N2fixation and other genes involved in downstream processes such as ammonia assimilation. Similar to other Eremiobacterota,Ca. Lamibacter sapmiensis encodes the potential for atmospheric chemosynthesis via CO2fixation coupled with H2and CO oxidation. Interestingly, the presence of a N2O reductase indicates that this population could play a role as a N2O sink in tundra soils. Due to the lack of activity data, it remains uncertain ifCa. Lamibacter sapmiensis is able to assemble a functional nitrogenase and participate in N2fixation. Confirmation of this ability would be a testament to the great metabolic versatility of Eremiobacterota, which appears to underlie their ecological success in cold and oligotrophic environments.
Cross-species transmission and PB2 mammalian adaptations of highly pathogenic avian influenza A/H5N1 viruses in Chile
Authors: Pardo-Roa Catalina , Nelson Martha I. , Ariyama Naomi , Aguayo Carolina , Almonacid Leonardo I. , Munoz Gabriela , Navarro Carlos , Avila Claudia , Ulloa Mauricio , Reyes Rodolfo , Luppichini Eugenia Fuentes , Mathieu Christian , Vergara Ricardo , González Álvaro , González Carmen Gloria , Araya Hugo , Fernández Jorge , Fasce Rodrigo , Johow Magdalena , Medina Rafael A. , Neira Victor
Published: July 2023

H5N1 highly pathogenic avian influenza viruses (HPAIV) emerged in wild birds in Chile in December 2022 and spilled over into poultry, marine mammals, and one human. Between December 9, 2022 – March 14, 2023, a coordinated government/academic response detected HPAIV by real-time RT-PCR in 8.5% (412/4735) of samples from 23 avian and 3 mammal orders. Whole-genome sequences obtained from 77 birds and 8 marine mammals revealed that all Chilean H5N1 viruses belong to lineage 2.3.4.4b and cluster monophyletically with viruses from Peru, indicating a single introduction from North America into Peru/Chile. Mammalian adaptations were identified in the PB2 segment: D701N in two sea lions, one human, and one shorebird, and Q591K in the human and one sea lion. Minor variant analysis revealed that D701N was present in 52.9 – 70.9% of sequence reads, indicating the presence of both genotypes within hosts. Further surveillance of spillover events is warranted to assess the emergence and potential onward transmission of mammalian adapted H5N1 HPAIV in South America.
A mechanohydraulic model supports a role for plasmodesmata in cotton fiber elongation
Authors: Hernández-Hernández Valeria , Marchand Olivier C. , Kiss Annamaria , Boudaoud Arezki
Published: July 2023

Plant cell growth depends on turgor pressure, the cell hydrodynamic pressure, which drives expansion of the extracellular matrix (the cell wall). Turgor pressure regulation depends on several physical, chemical and biological factors, including: vacuolar invertases, which modulate osmotic pressure of the cell, aquaporins, which determine the permeability of the plasma membrane to water, cell wall remodeling factors, which determine cell wall extensibility (inverse of effective viscosity), and plasmodesmata, which are membrane-lined channels that allow free movement of water and solutes between cytoplasms of neighbouring cells, like gap junctions in animals. Plasmodesmata permeability varies during plant development and experimental studies have correlated changes in the permeability of plasmodesmal channels to turgor pressure variations. Here we study the role of plasmodesmal permeability in cotton fiber growth, a type of cell that increases in length by at least 3 orders of magnitude in a few weeks. We incorporated plasmodesma-dependent movement of water and solutes into a classical model of plant cell expansion. We performed a sensitivity analysis to changes in values of model parameters and found that plasmodesmal permeability is among the most important factors for building up turgor pressure and expanding cotton fibers. Moreover, we found that non-monotonic behaviors of turgor pressure that have been reported previously in cotton fibers cannot be recovered without accounting for dynamic changes of the parameters used in the model. Altogether, our results suggest an important role for plasmodesmal permeability in the regulation of turgor pressure.

Significance Statement

The cotton fiber is among the plant cells with the highest growth rates. In cultivars, a single fiber cell generally reaches a few centimeters in length. How such size is achieved is still poorly understood. In order to tackle this question, we built a comprehensive mathematical model of fiber elongation, considering cell mechanics and water entry into the cell. Model predictions agree with experimental observations, provided that we take into account active opening and closure of plasmodesmata, the nano-channels that connect the fiber with neighboring cells. Because cotton fiber length is a key factor for yarn quality, our work may help understanding the mechanisms behind an important agronomic trait.
SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity
Authors: Zhang Fengwen , Schmidt Fabian , Muecksch Frauke , Wang Zijun , Gazumyan Anna , Nussenzweig Michel C. , Gaebler Christian , Caskey Marina , Hatziioannou Theodora , Bieniasz Paul D.
Published: July 2023

The glycosylation of viral envelope proteins can play important roles in virus biology and immune evasion. The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 22 N-linked glycosylation sequons and 17 O-linked glycosites. Here, we investigated the effect of individual glycosylation sites on SARS-CoV-2 S function in pseudotyped virus infection assays and on sensitivity to monoclonal and polyclonal neutralizing antibodies. In most cases, removal of individual glycosylation sites decreased the infectiousness of the pseudotyped virus. For glycosylation mutants in the N-terminal domain (NTD) and the receptor binding domain (RBD), reduction in pseudotype infectivity was predicted by a commensurate reduction in the level of virion-incorporated spike protein. Notably, the presence of a glycan at position N343 within the RBD had diverse effects on neutralization by RBD-specific monoclonal antibodies (mAbs) cloned from convalescent individuals. The N343 glycan reduced overall sensitivity to polyclonal antibodies in plasma from COVID-19 convalescent individuals, suggesting a role for SARS-CoV-2 spike glycosylation in immune evasion. However, vaccination of convalescent individuals produced neutralizing activity that was resilient to the inhibitory effect of the N343 glycan.
Rational design of structure-based vaccines targeting misfolded alpha-synuclein conformers of Parkinson’s disease and related disorders
Authors: Flores-Fernandez Jose Miguel , Pesch Verena , Sriraman Aishwarya , Chimal-Juarez Enrique , Amidian Sara , Wang Xiongyao , Reithofer Sara , Ma Liang , Tamgüney Gültekin , Wille Holger
Published: July 2023

Background

Synucleinopathies, including Parkinson’s disease, multiple system atrophy, and dementia with Lewy bodies, are neurodegenerative disorders caused by the accumulation of misfolded alpha-synuclein protein. Developing effective vaccines against synucleinopathies has been challenging due to the difficulty of stimulating an immune-specific response against alpha-synuclein, conferring neuroprotection without causing harmful autoimmune reactions, and selectively targeting only pathological forms of alpha-synuclein. Previous attempts using linear peptides and epitopes without control of the antigen structure for immunization failed in clinical trials. The immune system was unable to distinguish between the native alpha-synuclein and its amyloid form.

Results

The prion domain of the fungal HET-s protein was selected as a scaffold to introduce select epitopes from the surface of alpha-synuclein fibrils. Four vaccine candidates were generated by introducing specific amino acid substitutions onto the surface of the scaffold protein in regions that showed structural similarity to alpha-synuclein fibril structures. Each vaccine candidate had unique amino acid substitutions that imitated a specific epitope from alpha-synuclein amyloid fibrils. The approach successfully mimicked the stacking of the parallel in-register beta-sheet structure seen in alpha-synuclein fibrils as the vaccine candidates were found to be structurally stable and self-assembling into the desired conformations. All vaccine candidates induced substantial levels of IgG antibodies that recognized pathological alpha-synuclein fibrils derived from a synucleinopathy mouse model. Furthermore, the resulting anti-sera recognized pathological alpha-synuclein aggregates in brain lysates from patients who died from dementia with Lewy bodies, multiple system atrophy, or Parkinson’s disease, but did not recognize linear alpha-synuclein peptides. Each vaccine candidate induced a unique pattern of reactivity toward alpha-synuclein aggregates contained in distinct disease pathologies.

Conclusions

This new approach, based on the rational design of vaccines using the secondary and tertiary structure of alpha-synuclein amyloid fibrils and strict control over the exposed antigen structure used for immunization, as well as the ability to mimic aggregated alpha-synuclein, provides a promising avenue towards developing effective vaccines against alpha-synuclein fibrils, which may be crucial for the prevention and treatment of synucleinopathies.
TREX reveals proteins that bind to specific RNA regions in living cells
Authors: Dodel Martin , Guiducci Giulia , Dermit Maria , Krishnamurthy Sneha , Stojic Lovorka , Mardakheh Faraz K.
Published: July 2023

Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells under endogenous settings. Here, we introduce TREX (Targeted RNase H-mediated extraction of crosslinked RBPs), a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors ofU1snRNA, and reveals endogenous region-specific interactors ofNORADlncRNA. Using TREX, we generated a comprehensive region-by-region interactome for45SrRNA, uncovering both established and novel interactions that regulate ribosome biogenesis. With its applicability to any RNA in any cell-type, TREX is the first RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
Wound microbiota-mediated correction of matrix metalloproteinase expression promotes re-epithelialization of diabetic wounds
Authors: White Ellen K. , Uberoi Aayushi , Pan Jamie Ting-Chun , Ort Jordan T. , Campbell Amy E. , Murga-Garrido Sofia M. , Harris Jordan C. , Bhanap Preeti , Wei Monica , Robles Nelida Y. , Gardner Sue E. , Grice Elizabeth A.
Published: July 2023

Chronic wounds are a common and costly complication of diabetes, where multifactorial defects contribute to dysregulated skin repair, inflammation, tissue damage, and infection. We previously showed that aspects of the diabetic foot ulcer microbiota were correlated with poor healing outcomes, but many microbial species recovered remain uninvestigated with respect to wound healing. Here we focused onAlcaligenes faecalis, a Gram-negative bacterium that is frequently recovered from chronic wounds but rarely causes infection. Treatment of diabetic wounds withA. faecalisaccelerated healing during early stages. We investigated the underlying mechanisms and found thatA. faecalistreatment promotes re-epithelialization of diabetic keratinocytes, a process which is necessary for healing but deficient in chronic wounds. Overexpression of matrix metalloproteinases in diabetes contributes to failed epithelialization, and we found thatA. faecalistreatment balances this overexpression to allow proper healing. This work uncovers a mechanism of bacterial-driven wound repair and provides a foundation for the development of microbiota-based wound interventions.
The efficient induction of human retinal ganglion-like cells provides a platform for studying optic neuropathies
Authors: Liou Roxanne Hsiang-Chi , Chen Shih-Wei , Cheng Hui-Chen , Wu Pei-Chun , Chang Yu-Fen , Wang An-Guor , Fann Ming-Ji , Wong Yu-Hui
Published: July 2023

Retinal ganglion cells (RGCs) are essential for vision perception. In glaucoma and other optic neuropathies, RGCs and their optic axons undergo degenerative change and cell death; this can result in irreversible vision loss. Here we developed a rapid protocol for directly inducing RGC differentiation from human induced pluripotent stem cells (iPSCs) by the overexpression ofATOH7,BRN3BandSOX4. The hiPSC-derived RGC-like cells (iRGCs) show robust expression of various RGC-specific markers by whole transcriptome profiling. A functional assessment was also carried out and this demonstrated that these iRGCs display stimulus-induced neuronal activity, as well as spontaneous neuronal activity. Ethambutol (EMB), an effective first-line anti-tuberculosis agent, is known to cause serious visual impairment and irreversible vision loss due to the RGC degeneration in a significant number of treated patients. Using our iRGCs, EMB was found to induce significant dose-dependent and time-dependent increases in cell death and neurite degeneration. Western blot analysis revealed that the expression levels of p62 and LC3-II were upregulated, and further investigations revealed that EMB caused a blockade of lysosome-autophagosome fusion; this indicates that impairment of autophagic flux is one of the adverse effects of that EMB has on iRGCs. In addition, EMB was found to elevate intracellular reactive oxygen species (ROS) levels increasing apoptotic cell death. This could be partially rescued by the co-treatment with the ROS scavenger NAC. Taken together, our findings suggest that this iRGC model, which achieves both high yield and high purity, is suitable for investigating optic neuropathies, as well as being useful when searching for potential drugs for therapeutic treatment and/or disease prevention.