bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic Review: Evaluating the Efficacy of Intrathecal Fluorescein for Localizing Cerebrospinal Fluid Rhinorrhea
Authors: Romeo Dominic , Go Beatrice C. , Ng Jinggang J. , Barrette Louis-Xavier , Rhodes Isaiah J. , Rajasekaran Karthik
Published: October 2022

Objectives:

A defect in the skull base can result in leakage of cerebrospinal fluid (CSF) out of the subarachnoid space into the sinonasal cavities, termed CSF rhinorrhea. Patients presenting with CSF rhinorrhea often require surgical repair, typically performed endoscopically. Successful surgical intervention is highly reliant on accurate identification of the leak site. Identification can be enhanced by the administration of intrathecal fluorescein (IF) via a lumbar drain before surgery. The objective of this systematic review is to better characterize the benefits and limitations of IF administration.

Methods:

A systematic search was conducted for literature documenting the use of IF for CSF leak localization. The results of this search were subjected to initial review, followed by full-text evaluation of selected texts, and final inclusion based on predetermined selection criteria. Primary outcomes were specificity and sensitivity of IF administration in identifying CSF leak sites. Secondary outcomes included administration technique and safety data.

Results:

A total of 25 studies representing 3801 instances of IF administration met inclusion criteria. When injected slowly for up to 30 minutes at doses of <50 mg, IF administration results in minimal complications. A total of 25 mg doses (92.36%) of IF appear more sensitive than 10 mg (71.88%) doses of IF while maintaining a similar safety profile. Mixing fluorescein with double distilled water instead of CSF or saline may decrease waiting times before fluorescein can be identified and increase its safety profile.

Conclusions:

Intrathecal fluorescein may play an important role in the identification of CSF leak site during endoscopic repair.
Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny
Authors: Redshaw Jonathan , Ganea Patricia A.
Published: October 2022

Humans possess the remarkable capacity to imagine possible worlds and to demarcate possibilities and impossibilities in reasoning. We can think about what might happen in the future and consider what the present would look like had the past turned out differently. We reason about cause and effect, weigh up alternative courses of action and regret our mistakes. In this theme issue, leading experts from across the life sciences provide ground-breaking insights into the proximate questions of how thinking about possibilities works and develops, and the ultimate questions of its adaptive functions and evolutionary history. Together, the contributions delineate neurophysiological, cognitive and social mechanisms involved in mentally simulating possible states of reality; and point to conceptual changes in the understanding of singular and multiple possibilities during human development. The contributions also demonstrate how thinking about possibilities can augment learning, decision-making and judgement, and highlight aspects of the capacity that appear to be shared with non-human animals and aspects that may be uniquely human. Throughout the issue, it becomes clear that many developmental milestones achieved during childhood, and many of the most significant evolutionary and cultural triumphs of the human species, can only be understood with reference to increasingly complex reasoning about possibilities.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Neural differences between internal and external episodic counterfactual thoughts
Authors: Khoudary Ari , O'Neill Kevin , Faul Leonard , Murray Samuel , Smallman Rachel , De Brigard Felipe
Published: October 2022

Episodic counterfactual thoughts (eCFT) consist of imagining alternative outcomes to past experiences. A common sub-class of eCFT—
upward
eCFT—involves imagining how past negative experiences could have been
better
, either because one could have done something differently (internal) or because something about the circumstances could have been different (external). Although previous neuroimaging research has shown that the brain's default mode network (DMN) supports upward eCFT, it is unclear how it is differentially recruited during internal versus external upward eCFT. We collected functional magnetic resonance imaging data while participants remembered negative autobiographical memories, generated either internal or external upward eCFT for the memory, and then rated the plausibility, perceived control and difficulty of eCFT generation. Both internal and external eCFT engaged midline regions of cingulate cortex, a central node of the DMN. Most activity differentiating eCFT, however, occurred outside the DMN. External eCFT engaged cuneus, angular gyrus and precuneus, whereas internal eCFT engaged posterior cingulate and precentral gyrus. Angular gyrus and precuneus were additionally sensitive to perceived plausibility of external eCFT, while postcentral gyrus and insula activity scaled with perceived plausibility of internal eCFT. These results highlight the key brain regions that might be involved in cases of maladaptive mental simulations.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Moral judgements reflect default representations of possibility
Authors: Acierno Jane , Mischel Sarah , Phillips Jonathan
Published: October 2022

Moral judgement requires representing what is possible: judging that someone ought to do something implies that they actually can do that thing; and if they cannot do that thing, then it is not the case that they ought to have done it. Moral judgements are often made quickly and effortlessly, suggesting that they may rely on default, rather than deliberative, representations of what is possible. To investigate this possibility, we asked participants to make 10 different kinds of moral judgements either very fast or more slowly about 240 different actions across 12 contexts. We found that these moral judgements were more similar to one another when participants were forced to quickly assess the morality of immoral actions, suggesting a common default template for moral judgement that becomes more differentiated upon reflection. When making moral permissibility judgements quickly, participants were more likely to judge that improbable, irrational and impossible actions were not permissible, indicating that default representations of permissibility may be reflecting default representations of possibility. A direct investigation revealed a close relationship between default representations of possibility and fast judgements of moral permissibility. These findings demonstrate the role of default representations of possibility in moral cognition.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Anchored in the present: preschoolers more accurately infer their futures when confronted with their pasts
Authors: Goulding Brandon W. , Stonehouse Emily Elizabeth , Friedman Ori
Published: October 2022

People often speculate about what the future holds. They wonder what will happen tomorrow, and what the world will be like in the distant future. Nonetheless, people's ability to consider future possibilities may be restricted when they consider their own futures. Adults show the ‘end of history’ illusion, believing they have changed more in the past than they will in the future. Further, preschoolers are even more limited in anticipating future change, as 3-year-olds insist their current desires will persist later in life. These findings suggest a deficit in children's and adults' abilities to simulate alternative possibilities that pertain to themselves. However, we report four experiments (n= 233) suggesting otherwise, at least for children. We find that 3-year-olds accurately infer their futures when prompted to consider their past rather than present preferences. Children also succeed at inferring their past preferences when not shown items they currently prefer. This shows that childrencanreason about their pasts and futures, though this ability is hindered when they are shown items that anchor them to the present. Our findings suggest that children's difficulties with mental time travel reflect a failure to shift away from the present rather than an inability to simulate alternative possibilities.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Waiting for a better possibility: delay of gratification in corvids and its relationship to other cognitive capacities
Authors: Schnell Alexandra K. , Boeckle Markus , Clayton Nicola S.
Published: October 2022

Self-control, the ability to resist temptation and wait for better but delayed possibilities, is an important cognitive skill that underpins decision-making and planning. The capacity to exert self-control has been linked to intelligence in humans, chimpanzees and most recently cuttlefish. Here, we presented 10 Eurasian jays,
Garrulus glandarius
, with a delayed maintenance task, which measured the ability to choose a preferred outcome as well as the ability to sustain the delay prior to that outcome. Jays were able to wait for better possibilities, but maximum wait times varied across the subjects. We also presented them with five cognitive tasks that assessed spatial memory, spatial relationships and learning capacity. These tasks are commonly used as measures of general intelligence within an ecological context. Individual performance was correlated across the cognitive tasks, which suggests that there was a general intelligence factor underlying their performance. Performance in these tasks was correlated significantly with the jays' capacity to wait for better possibilities. This study demonstrates that self-control and intelligence are correlated in jays. The fact that this correlation exists in diverse species suggests that self-control is a fundamental feature of cognition. Our results are discussed in the context of convergent evolution.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations
Authors: Gupta Asmita , Basu Reelina , Bashyam Murali Dharan
Published: October 2022

Despite seminal advances towards understanding its infection mechanism, SARS-CoV-2 continues to cause significant morbidity and mortality worldwide. Though mass immunization programs have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2 infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April, 2020 to October, 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this time period. We also highlight presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations (iSNVs) at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended time period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.
Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder
Authors: Phan Joann , Calvo Diana C. , Nair Divya , Jain Suneer , Montagne Thibaut , Corbitt James , Blanchard Kelsey , Treadwell Shirin , Adams James , Krajmalnik-Brown Rosa
Published: October 2022

The use of prebiotics and probiotics to improve symptoms associated with autism spectrum disorder (ASD) has varied from study to study, indicating the complex and heterogeneous nature of the disorder and the behaviors and gastrointestinal symptoms associated with ASD. There is a wide variety in the severity of symptoms and developmental impediments across the population. Gut microbiome studies have also shown unique but varied microbial signatures in ASD. While there have been successes in pre-clinical and clinical trials with prebiotic and probiotic components, the limited population sizes have promising yet inconclusive results. This study addresses this issue by 1) enrolling an ASD cohort of 296 children and adults and comparing their deep DNA metagenomic sequencing of gut microbiomes to that of an age-matched neurotypical cohort and 2) individually formulating a precision synbiotic (probiotic and prebiotic) tailored towards each individual’s needs and conducting pre/post evaluations of ASD and GI symptoms and longitudinal whole genome microbiome sequencing. At baseline, there was significantly lower microbiome diversity in the ASD group relative to controls. Microbes, pathways, and gene families significantly differed between the two populations. The ASD microbiome had higher abundances of pathogens, such asShigella, Klebsiella, Mycobacterium, andClostridium, but lower abundances of beneficial microbes, includingFaecalibacterium. With a 3-month synbiotic supplementation, the microbiome diversity of the 170 ASD participants completing the study increased and became closer to the neurotypical controls. Significant shifts in microbial and pathway abundances were also measured at the second ASD timepoint. In addition to changes in the gut microbiome, there was a significant reduction in gastrointestinal discomfort. There were also improvements in some ASD-related symptoms; however, we cannot exclude that these were potentially due to the open-label nature of the study. Changes in the gut microbiome composition and functional capacity, along with a reduction in gastrointestinal symptoms and potential changes in behavior, highlight the importance of metagenomics, longitudinal studies, and the potential for therapeutic microbial supplementation in ASD.
Rare Genetic Variants Associated with Sudden Cardiac Arrest in the Young: A Prospective, Population-Based Study
Authors: Holmstrom Lauri , Chaudhary Ninad S , Nakamura Kotoka , Chugh Harpriya , Uy-Evanado Audrey , Faye Norby F , Metcalf Ginger A , Menon Vipin K , Yu Bing , Boerwinkle Eric , Chugh Sumeet S , Akdemir Zeynep , Kransdorf Evan P
Published: October 2022

Background

Sudden cardiac arrest (SCA) is a rare and tragic event among the young and often caused by inherited cardiac disease. Previous studies have investigated referral cohorts, but the prevalence of disease-associated variants is unclear at the community level. We investigated the prevalence of genetic variants among community-based cases of SCA aged <21 years.

Methods

The study sample is obtained from two prospective, community-based studies of out-of-hospital SCA ongoing in the Portland, OR metro area (population ∼1 million) and Ventura County CA (population ∼850,000). We performed next-generation whole genome sequencing and then rare variant analysis of candidate genes associated with arrhythmic syndromes and cardiomyopathy in ClinGen.

Results

The mean age of the study subjects was 11.3±8.0 (30% non-white, 45% female). We found that 36 of 52 young SCA victims (69%) harbored uncertain, likely pathogenic (LP), or pathogenic (P) variants. Eight subjects (15%) carried 9 LP/P variants. Patients with clinical histories suggesting primary arrhythmic syndromes or hypertrophic cardiomyopathy were more likely to harbor clinically actionable variants or variants of unknown significance (VUS), than subjects with myocarditis, sudden infant death syndrome, or sudden arrhythmic death. Variants were more likely to be classified as LP/P among Whites (8/9, 88.9%) as compared to non-Whites (1/9, 11.1%, p = 0.036).

Conclusions

A notable proportion of young SCA victims in the community harbor rare, potentially disease-associated gene variants, and further studies are needed to understand variants of unknown significance. We identified differences by phenotype groups and race that have potential implications for genetic testing.
Understanding Inequalities in Mental Health by Family Structure during COVID-19 Lockdowns: Evidence from the UK Household Longitudinal Study
Authors: Green Michael J , Craig Peter , Demou Evangelia , Katikireddi S Vittal , Leyland Alastair H , Pearce Anna
Published: October 2022

Background

The COVID-19 pandemic increased psychiatric distress and impacts differed by family structure. We aimed to identify mechanisms contributing to these inequalities.

Methods

Survey data were from the UK Household Longitudinal Study. Psychiatric distress (GHQ-12) was measured in April 2020 (first UK lockdown; n=10,516), and January 2021 (lockdown re-introduced following eased restrictions; n=6,893). Pre-lockdown family structure comprised partner status and presence of children (<16 years). Mediating mechanisms included: active employment, financial strain, childcare/home-schooling, caring, and loneliness. Monte Carlo g-computation simulations were used to adjust for confounding and estimate total effects and decompositions into: controlled direct effects (effects if the mediator was absent), and portions eliminated (PE; representing differential exposure and vulnerability to the mediator).

Results

In January 2021, after adjustment, we estimated increased risk of distress among couples with children compared to couples with no children (RR: 1.48; 95% CI: 1.15-1.82), largely because of childcare/home-schooling (PE RR: 1.32; 95% CI: 1.00-1.64). Single respondents without children also had increased risk of distress compared to couples with no children (RR: 1.55; 95% CI: 1.27-1.83), and the largest PE was for loneliness (RR: 1.16; 95% CI: 1.05-1.27), though financial strain contributed (RR: 1.05; 95% CI: 0.99-1.12). Single parents demonstrated the highest levels of distress, but confounder adjustment suggested uncertain effects with wide confidence intervals. Findings were similar in April 2020 and when stratified by sex.

Conclusions

Access to childcare/schooling, financial security and social connection are important mechanisms that need addressing to avoid widening mental health inequalities during public health crises.

Key Messages

Couples with young children compared to those without, had raised risk of psychiatric distress during UK lockdowns. Effect decompositions suggested this was largely due to a combination of differential exposure and vulnerability to childcare and home-schooling.

Among those without young children, being single compared to in a couple was associated with raised risk of psychiatric distress during UK lockdowns, with differential exposure to financial strain and loneliness both contributing to this inequality.

There was not sufficient evidence to indicate that being single with young children increased risk of psychiatric distress relative to couples with young children or singles without.
Forecasting Influenza-Like Illness (ILI) during the COVID-19 Pandemic
Authors: Turner Stephen D. , Hulme-Lowe Chris , Nagraj VP
Published: October 2022

Near-term probabilistic forecasts for infectious diseases such as COVID-19 and influenza play an important role in public health communication and policymaking. From 2013-2019, the FluSight challenge run by the Centers for Disease Control and Prevention invited researchers to develop and submit forecasts using influenza-like illness (ILI) as a measure of influenza burden. Here we examine how several statistical models and an autoregressive neural network model perform for forecasting ILI during the COVID-19 pandemic, where historical patterns of ILI were highly disrupted. We find that the autoregressive neural network model which forecasted ILI well pre-COVID still performs well for some locations and forecast horizons, but its performance is highly variable, and performs poorly in many cases. We found that a simple exponential smoothing statistical model is in the top half of ranked models we evaluated nearly 75% of the time. Our results suggest that even simple statistical models may perform as well as or better than more complex machine learning models for forecasting ILI during the COVID-19 pandemic. We also created an ensemble model from the limited set of time series forecast models we created here. The limited ensemble model was rarely the best or the worst performing model compared to the rest of the models assessed, confirming previous observations from other infectious disease forecasting efforts on the less variable and generally favorable performance of ensemble forecasts. Our results support previous findings that no single modeling approach outperforms all other models across all locations, time points, and forecast horizons, and that ensemble forecasting consortia such as the COVID-19 Forecast Hub and FluSight continue to serve valuable roles in collecting, aggregating, and ensembling forecasts using fundamentally disparate modeling strategies.
Automated and objective analysis of speech in premanifest and early-stage Huntington’s disease
Authors: Vogel Adam P. , Chan Cheuk S. J. , Stuart Geoffrey W. , Maruff Paul , Lie Yenni , Stout Julie C.
Published: October 2022

Background

Clinical markers that show change in performance in people with Huntington’s disease (HD) during the presymptomatic and prodromal stages remain a target of investigation in clinical medicine. Alongside genetic and neuroimaging initiatives, digital speech analytics has shown promise as a sensitive clinical marker of premanifest HD.

Objective

To investigate the sensitivity of digital speech measures for detecting subtle cognitive-linguistic and fine motor features in people carrying the expanded HD gene, with and without symptoms.

Methods

Speech data were acquired from 110 participants (55 people with the expanded HD gene including 16 presymptomatic HD; 16 prodromal HD; 14 early-stage HD; 9 mid-stage HD; and 55 matched healthy controls). Objective digital speech measures were derived from speech tasks that fit along a continuum of motor and cognitive complexity. Acoustic features quantified speakers’ articulatory agility, voice quality and speech-timing. Subjects also completed the tests of cognition and upper limb motor function.

Results

Some presymptomatic HD (furthest from disease onset) differed to healthy controls on timing measures derived from the syllable repetition and monologue. Prodromal HD presented with reduced articulatory agility, reduced speech rate and longer and variable pauses. Speech agility correlated with poorer performance on the upper limb motor test.

Conclusion

Tasks with a mix of cognitive and motor demands differentiated prodromal HD from their matched control groups. Motor speech tasks alone did not differentiate groups until participants were relatively closer to disease onset or symptomatic. Data demonstrated how ubiquitous behaviors like speech, when analyzed objectively, provide insight into disease related change.
The Novel Role of Midbody-Associated mRNAs in Regulating Abscission
Authors: Farmer Trey , Vaeth Katherine F. , Han Ke-Jun , Goering Raeann , Taliaferro J. Matthew , Prekeris Rytis
Published: October 2022

Midbodies (MBs) have been shown to function during telophase as a recruiting hub, especially for ESCRT-III complex subunits, to regulate the abscission step of cytokinesis. However, the molecular machinery governing specific protein targeting and activation at the MB remains poorly understood. Until recently, it was thought that abscission regulating proteins, such as ESCRT-III complex subunits, accumulate at the MB by directly or indirectly binding to the MB resident protein, CEP55. However, recent studies have shown that depletion of CEP55 does not fully block ESCRT-III targeting to the MB, and cells in CEP55 knock-out mice divide normally. Additionally, since MBs are microtubule-rich, proteinaceous structures, it is conceptually hard to imagine how large protein complexes, such as the ESCRT-III complex, can successfully diffuse into the MB from the cytosol in a rapid and highly regulated manner. Here, we show that MBs contain mRNAs and that these MB-associated mRNAs can be locally translated, resulting in the accumulation of abscission-regulating proteins. We also demonstrate that localized MB-associated translation of CHMP4B is required for its targeting to the abscission site and that 3′ UTR-dependent CHMP4B mRNA targeting to the MB is required for successful completion of cytokinesis. Finally, we identify regulatorycis-elements within RNAs that are necessary and sufficient for mRNA trafficking to the MB. Based on all this data, we propose a novel method of regulating cytokinesis and abscission by MB-associated targeting and localized translation of selective mRNAs.
Transformer-based deep learning integrates multi-omic data with cancer pathways
Authors: Cai Zhaoxiang , Poulos Rebecca C. , Aref Adel , Robinson Phillip J. , Reddel Roger R. , Zhong Qing
Published: October 2022

Multi-omic data analysis incorporating machine learning has the potential to significantly improve cancer diagnosis and prognosis. Traditional machine learning methods are usually limited to omic measurements, omitting existing domain knowledge, such as the biological networks that link molecular entities in various omic data types. Here we develop a Transformer-based explainable deep learning model, DeePathNet, which integrates cancer-specific pathway information into multi-omic data analysis. Using a variety of big datasets, including ProCan-DepMapSanger, CCLE, and TCGA, we demonstrate and validate that DeePathNet outperforms traditional methods for predicting drug response and classifying cancer type and subtype. Combining biomedical knowledge and state-of-the-art deep learning methods, DeePathNet enables biomarker discovery at the pathway level, maximizing the power of data-driven approaches to cancer research. DeePathNet is available on GitHub athttps://github.com/CMRI-ProCan/DeePathNet.

Highlights

DeePathNet integrates biological pathways for enhanced cancer analysis.

DeePathNet utilizes Transformer-based deep learning for superior accuracy.

DeePathNet outperforms existing models in drug response prediction.

DeePathNet enables pathway-level biomarker discovery in cancer research.
Bourbon virus transmission, New York State
Authors: Dupuis Alan P. , Prusinski Melissa A. , O’Connor Collin , Maffei Joseph G. , Koetzner Cheri A. , Zembsch Tela E. , Zink Steven D. , White Alexis L. , Santoriello Michael P. , Romano Christopher L. , Xu Guang , Ribbe Fumiko , Campbell Scott R. , Rich Stephen M. , Backenson P. Bryon , Kramer Laura D. , Ciota Alexander T.
Published: October 2022

In July 2019, Bourbon virus RNA was detected in anAmblyomma americanumtick removed from a resident of Long Island, New York. Tick infection and white-tailed deer (Odocoileus virginianus) serosurvey results demonstrate active transmission in New York, especially Suffolk County, emphasizing a need for surveillance anywhereA. americanumis reported.
Extensive Dysregulation of SLK Splicing in Cancers Impacts Metastasis
Authors: Yang Ying-Qun , Hu Yue , Zhang Si-Rui , Li Jie-Fu , Guan Jia-Wen , Zhang Wen-Jing , Sun Yu , Feng Xiao-Yan , Sun Jing , Yang Yun , Wang Zefeng , Wei Huan-Huan
Published: October 2022

RNA splicing control is a pivotal aspect of gene regulation and is closely associated with cancer development. From a pan-cancer transcriptome investigation in the splicing layer, we discovered a critical cancer-associated alternative splicing (AS) event at exon 13 of SLK which produces two isoforms, SLK-L and SLK-S. The splicing is dramatically shifted towards SLK-L across multiple prevalent cancer types. We demonstrated that SLK-L plays an essential role in cancer development, especially in metastasis both in cells and in mice, whereas splicing toward SLK-S inhibits cancer development. RNA-seq revealed the two SLK isoforms play different roles in pathways related to cell migration. Furthermore, different SLK isoforms demonstrate varying binding affinities to certain cell junction markers, in part indicating the AS of SLK contributes to cancer cell migration. In addition, the splicing factor Rbfox2 was identified to specifically inhibit the inclusion of exon 13 by binding intron 12 of SLK. Collectively, our study innovatively uncovers the biological consequences and underlying mechanisms for one of the most mis-spliced genes in cancer, highlighting its potential significance in cancer diagnosis and treatment.
Ubiquitination steers SRF3 plasma membrane nano-organization to specify signaling outputs
Authors: Pierre Platre Matthieu , Matias Gleason Flores , Lukas Brent , Min Cao , Ling Zhang , Satbhai Santosh B. , Julie Neveu , Gregory Vert , Wolfgang Busch
Published: October 2022

Organisms cope with myriads of competing and conflicting environmental signals. These signals are often perceived by cell surface receptor kinases to mount appropriate adaptive responses. However, it is not well understood by which mechanism single receptor kinases can transduce different signals. The plant receptor kinase SRF3 transduces low iron and bacteria-derived signals. We found that upon these signals, ubiquitinated SRF3 is recognized by clathrin-mediated endocytosis for vacuolar targeting. Live super resolution microscopy revealed that cell surface SRF3 is present in a fast diffusible fraction, which is sustained by ubiquitination, and that non-ubiquitinated SRF3 is present in immobile nanodomains. Ubiquitination-mediated degradation of SRF3 is required for signaling only under low iron but not upon flg22 perception. Flg22-triggered SRF3 phosphorylation leads to SRF3 accumulation in the immobile fraction in which degradation is restricted, thereby preventing low iron signaling. We therefore propose that ubiquitination-dependent plasma membrane nano-organization of SRF3 specifies its signal transduction pathways.
An energy-saving glasshouse film reduces seasonal, and cultivar dependent Capsicum yield due to light limited photosynthesis
Authors: Chavan Sachin G. , He Xin , Maier Chelsea , Alagoz Yagiz , Anwar Sidra , Chen Zhong-Hua , Ghannoum Oula , Cazzonelli Christopher I. , Tissue David T.
Published: October 2022

Glasshouse films can be used to reduce energy costs by limiting non-productive heat-generating radiation, but the impact on yield of greenhouse horticultural crops remains unknown. The effects of energy-saving film ULR-80 (referred to as Smart Glass; SG) designed to block long wavelength light that generates heat also reduced photosynthetically active radiation (PAR) consequently affecting crop morphology, photosynthesis, leaf pigments, and yield of two hydroponically grown capsicum (Capsicum annuumL.) cultivars (Red and Orange). The crops were grown in four high-tech glasshouse bays over two seasons of similar daily light integrals (DLI) during ascending (Autumn) and descending (Summer) photoperiods. The Red cultivar exhibited higher photosynthetic rates (light saturated -Asatand maximal -Amax) and yield than the Orange cultivar in control but displayed stronger reductions in modelled photosynthetic rates at growth light and yield in SG without changes in photosynthetic capacity. Foliar pigment ratios of chlorophyll a/b and carotenoid: chlorophyll remained unaffected by the SG during both seasons indicating that chloroplast homeostasis was similar between SG and control. The seasonal differences in photosynthetic pigments and xanthophyll de-epoxidation state (DPS) revealed that cultivars were able to sense the SG-altered light environment during the ascending, but not descending photoperiod. The descending photoperiod correlated with a lower daily light level and a substantial yield reduction of 29 % and 13 % in Red and Orange cultivars, respectively. Thus, SG-induced higher reductions in yield during the descending photoperiod indicate that SG may be more beneficial for capsicum crops planted during Autumn with an ascending photoperiod.

Highlights

A potential energy saving SG film limited net photosynthesis of capsicum

The SG film reduced yield of two capsicum cultivars that can be mitigated by planting during the low light growth season with a shorter photoperiod

SG reduced genotype-dependent capsicum yield was associated with alterations in the level of foliar pigments required for photoprotection under adverse light conditions
Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow
Authors: Kim YeEun , Calderon Ariel A. , Favaro Patricia , Glass David R. , Tsai Albert G. , Borges Luciene , Greenleaf William J. , Bendall Sean C.
Published: October 2022

Lymphoid specification in human hematopoietic progenitors is not fully understood. To better associate lymphoid identity with protein-level cell features, we conducted a highly multiplexed single-cell proteomic screen on human bone marrow progenitors. This screen identified terminal deoxynucleotidyl transferase (TdT), a specialized DNA polymerase intrinsic to VDJ recombination, broadly expressed within CD34+ progenitors prior to B/T cell emergence. While these TdT+ cells coincided with granulocyte-monocyte progenitor (GMP) immunophenotype, their accessible chromatin regions showed enrichment for lymphoid-associated transcription factor (TF) motifs. TdT expression on GMPs was inversely related to the SLAM family member CD84. Prospective isolation of CD84loGMPs demonstrated robust lymphoid potentialex vivo, while still retaining significant myeloid differentiation capacity, akin to LMPPs. This multi-omic study identifies previously unappreciated lymphoid-primed progenitors, redefining the lympho-myeloid axis in human hematopoiesis.
Virulence factors among isolates of extraintestinalEscherichia coli(ExPEC) from hospitals in the United Kingdom
Authors: Turton Jane F
Published: October 2022

182 genes associated with virulence were sought from the whole genome sequences of all non-duplicate isolates ofEscherichia colireceived by the UK Health Security Agency’s Antimicrobial Resistance and HealthCare Associated Infections laboratory for typing between June 2019 and March 2021 from hospitals in the United Kingdom and Republic of Ireland (n=593). These were from healthcare associated investigations and were not associated with diarrhoeal disease. Genes that were very common or very rare were excluded from further analysis. The frequency of detection of genes was compared among isolates from invasive infection, screening, urine samples and from neonates.cnf1(coding for cytotoxic necrotising factor),clbK(coding for colibactin),focCDF(coding for F1 fimbriae),kpsM_K1,neuBD(associated with the K1 capsule),mchBC,mcmA(coding for microcins),papG_alleleIII (part of a cluster encoding P fimbriae),pic(protein involved in intestinal colonization),sfaE/sfafoCDE(coding for S fimbriae),tcpC(encoding TLR domain containing-protein C) andvat(encoding toxin vacuolating autotransporter) were 4 to 28 times more prevalent among isolates from invasive infections than among those from carriage. Representatives of sequence types (ST) 12, 73, 998 and 127 carried multiple of these virulence factors, no matter whether they were from screening swabs or from blood or other infection sites. Isolates carrying multiple virulence factors were more prevalent from neonatal screens than those from general screens. Genes associated with the K1 capsule (ibeA,neuBD,kpsM_K1) were particularly found in STs 1193, 10, 998, 538, 80 and 141. Nanopore sequencing of 14 isolates representing 10 different STs showed that the virulence elements sought were largely carried in chromosomal genomic islands, which were mosaic in nature. Some 9 % of isolates carried more than six of the main virulence genes/gene sets sought, highlighting the potential for significant numbers of carriage isolates to cause extraintestinal infections.
LSR Targets YAP to Modulate Intestinal Paneth Cell Differentiation
Authors: An Yanan , Wang Chao , Fan Baozhen , Li Ying , Kong Feng , Zhou Chengjun , Cao Zhang , Liu Jieying , Wang Mingxia , Sun Hui , Zhao Shengtian , Gong Yongfeng
Published: October 2022

Lipolysis-stimulated lipoprotein receptor (LSR) is a multi-functional protein that is best known for its roles in assembly of epithelial tricellular tight junctions and hepatic clearance of lipoproteins. Here, we investigated whether LSR contributes to intestinal epithelium homeostasis and pathogenesis of intestinal disease. By using multiple conditional deletion mouse models andex vivocultured organoids, we find that LSR elimination in intestinal stem cells results in disappearance of Paneth cell without affecting the differentiation of other cell lineages. Mechanistic studies reveal that LSR deficiency increases abundance and nuclear localization of YAP by modulating its phosphorylation and proteasomal degradation. Using gain- and loss-of-function studies we show that LSR protects against necrotizing enterocolitis through enhancement of Paneth cell differentiation in small intestinal epithelium. Thus, this study identifies LSR as an upstream negative regulator of YAP activity, an essential factor for Paneth cell differentiation, and a potential novel therapeutic target for inflammatory bowel disease.
Striatal neurons are recruited dynamically into collective representations of self-initiated and learned actions in freely-moving mice
Authors: Tiroshi Lior , Atamna Yara , Gilin Naomi , Goldberg Joshua A.
Published: October 2022

Striatal spiny projection neurons are hyperpolarized-at-rest (HaR) and are driven to spike threshold by a small number of powerful inputs – an input-output configuration that is detrimental to response reliability. Because the striatum is important for habitual behaviors and goal-directed learning, we conducted microendoscopic imaging in freely-moving mice that express a genetically-encoded calcium indicator sparsely in striatal HaR neurons to compare their response reliability during self-initiated movements and operant conditioning. The sparse expression was critical for longitudinal studies of response reliability, and for studying correlations among HaR neurons while minimizing spurious correlations arising from contamination by the background neuropil signal. We found that HaR neurons are recruited dynamically into action representation through a moment-by-moment formation of distinct cell assemblies. While individual neurons respond with little reliability, the population response remained reliable. Moreover, we found evidence for the formation of correlated cell assemblies during conditioned (but not innate) behaviors, but this correlation was independent of the distance between neurons.
Development of a yeast whole-cell biocatalyst for MHET conversion into terephthalic acid and ethylene glycol
Authors: Loll-Krippleber Raphael , Sajtovich Victoria , Ferguson Michael W. , Ho Brandon , Payliss Brandon J. , Bellissimo Joseph , Peters Sydney , Wyatt Haley D. M. , Brown Grant W.
Published: October 2022

Background

Over the 70 years since the introduction of plastic into everyday items, plastic waste has become an increasing problem. With over 360 million tonnes of plastics produced every year, solutions for plastic recycling and plastic waste reduction are sorely needed. Recently, multiple enzymes capable of degrading PET (polyethylene teraphthalate) plastic have been identified and engineered. In particular, the enzymes PETase and MHETase fromIdeonella sakaiensisdepolymerize PET into the two building blocks used for its synthesis, ethylene glycol (EG) and terephthalic acid (TPA). Importantly, EG and TPA can be re-used for PET synthesis allowing complete and sustainable PET recycling.

Results

In this study, we usedSaccharomyces cerevisiaeas a platform to develop a whole-cell catalyst expressing the MHETase enzyme, which converts MHET (monohydroxyethyl terephthalate) into TPA and EG. We assessed six expression architectures and identified those resulting in efficient MHETase expression on the yeast cell surface. We show that the MHETase whole-cell catalyst has activity comparable to recombinant MHETase purified fromEscherichia coli. Finally, we demonstrate that surface displayed MHETase is stable to pH, temperature, and for at least 12 days at room temperature.

Conclusions

We demonstrate the feasibility of usingS. cerevisiaeas a platform for the expression and surface display of PET degrading enzymes and predict that the whole-cell catalyst will viable alternatives to protein purification-based approaches for plastic degradation.
Understanding the necessity of regulatory protein machinery in heterologous expression of class-III type of Ocins
Authors: Choyam Shilja , Kammara Rajagopal.
Published: October 2022

To date, there have been no or just a few reports of successful cloning and expression to create biologically active ocins or bacteriocins. Cloning, expression, and production of class I ocins are problematic because of their structural arrangements, coordinated functions, size, and posttranslational modifications. In the case of class III ocins, there are no reports of obtaining biological active proteins to date. Because of their growing importance, use and rapid functions require understanding mechanistic aspects to obtain biological active protein. As a result, we intend to clone and express the class III type. Also, by fusion or chimaera, they reshape class I types that lack posttranslational modifications into class III. Therefore, this construct resembles a class III type ocin. With the exception of Zoocin, expression of the proteins was found to be physiologically ineffective after cloning. But, few cell morphological changes such as elongation, aggregation, and the formation of terminal hyphae were observed. However, it was discovered that the target indicator had been altered toVibrio spp. in a few. Finally, we confirm the existence of unidentified additional intrinsic factors for succesful expression to obtain biologically active protein.
An Optimized Electrotransformation Protocol forLactobacillus jensenii
Authors: Fristot Elsa , Bessede Thomas , Rufino Miguel Camacho , Mayonove Pauline , Chang Hung-Ju , Zuniga Ana , Michon Anne-Laure , Godreuil Sylvain , Bonnet Jérôme , Cambray Guillaume
Published: October 2022

Engineered bacteria are promising candidates forin situdetection and treatment of diseases. The female uro-genital tract presents several pathologies, such as sexually transmitted diseases or genital cancer, that could benefit from such technology. While bacteria from the gut microbiome are increasingly engineered, the use of chassis isolated from the female uro-genital resident flora has been limited. A major hurdle to implement the experimental throughput required for efficient engineering in these non-model bacteria is their low transformability. Here we report an optimized electrotransformation protocol forLactobacillus jensenii, one the most widespread species across vaginal microflora. Starting from classical conditions, we optimized buffers, electric field parameters, cuvette type and DNA quantity to achieve an 80-fold improvement in transformation efficiency, with up to 3.5·103CFUs/µg of DNA inL. jensenii ATCC 25258. We also identify several plasmids that are maintained and support reporter gene expression inL. jensenii. Finally, we demonstrate that our protocol provides increased transformability in three independent clinical isolates ofL. jensenii. This work will facilitate the genetic engineering ofL. jenseniiand enable its use for addressing challenges in gynecological healthcare.
SMDT1variants impair EMRE-mediated mitochondrial calcium uptake in patients with muscle involvement
Authors: Bulthuis Elianne P. , Adjobo-Hermans Merel J.W. , de Potter Bastiaan , Hoogstraten Saskia , Wezendonk Lisanne H.T. , Tutakhel Omar A.Z. , Wintjes Liesbeth T. , van den Heuvel Bert , Willems Peter H.G.M. , Kamsteeg Erik-Jan , Rubio Gozalbo M. Estela , Sallevelt Suzanne C.E.H. , Koudijs Suzanne M. , Nicolai Joost , de Bie Charlotte I. , Hoogendijk Jessica E. , Koopman Werner J.H. , Rodenburg Richard J.
Published: October 2022

Ionic calcium (Ca2+) is a key messenger in signal transduction and its mitochondrial uptake plays an important role in cell physiology. This uptake is mediated by the mitochondrial Ca2+uniporter (MCU), which is regulated by EMRE (essential MCU regulator) encoded by theSMDT1(single-pass membrane protein with aspartate rich tail 1) gene. This work presents the genetic, clinical and cellular characterization of two patients harbouringSMDT1variants and presenting with muscle problems. Analysis of patient fibroblasts and complementation experiments provide evidence that these variants lead to absence of EMRE protein, induce MCU subcomplex formation and impair mitochondrial Ca2+uptake. However, the activity of the oxidative phosphorylation enzymes, mitochondrial morphology and membrane potential, as well as routine/ATP-linked respiration were not affected. We hypothesize that the muscle-related symptoms in the patients withSMDT1variants result from aberrant mitochondrial Ca2+uptake.
The molecular principles governing HCMV infection outcome
Authors: Schwartz Michal , Shnayder Miri , Nachshon Aharon , Arazi Tamar , Kitsberg Yaarit , Samia Roi Levi , Lavi Michael , Kuint Rottem , Tsabari Reuven , Stern-Ginossar Noam
Published: October 2022

Infection with Human cytomegalovirus (HCMV) can result in either productive or non-productive infection, the latter potentially leading to establishment of latency, but the molecular factors that dictate these different infection outcomes are elusive. Macrophages are known targets of HCMV and considered to be permissive for productive infection, while monocytes, their precursors, are latently infected. Here we reveal that infection of macrophages is more complex than previously appreciated and can result in either productive or non-productive infection. By analyzing the progression of HCMV infection in monocytes and macrophages using single cell transcriptomics, we uncover that the level of viral gene expression, and specifically the expression of the major immediate early proteins, IE1 and IE2, is the principal barrier for establishing productive infection. On the cellular side, we reveal that the cell intrinsic levels of interferon stimulated genes (ISG), but not their induction, is a main determinant of infection outcome and that intrinsic ISG levels are downregulated with monocyte differentiation, partially explaining why macrophages are more susceptible to productive HCMV infection. We further show that, compared to monocytes, non-productive macrophages maintain higher levels of viral transcripts and are able to reactivate, raising the possibility that they may serve as latency reservoirs. Overall, by harnessing the tractable system of monocyte differentiation we decipher underlying principles that control HCMV infection outcome, and propose macrophages as a potential HCMV reservoir in tissues.