bluuebunny/crossref_metadata_2025 huggingface dataset:
Suggested role of NosZ in preventing N2O inhibition of dissimilatory nitrite reduction to ammonium
Authors: Yoon Sojung , Heo Hokwan , Han Heejoo , Song Dong-Uk , Bakken Lars R. , Frostegård Åsa , Yoon Sukhwan
Published: February 2023

Climate change and nutrient pollution are among the most urgent environmental issues. Enhancing the abundance and/or the activity of beneficial organisms is an attractive strategy to counteract these problems. Dissimilatory nitrate reduction to ammonium (DNRA), which theoretically improves nitrogen retention in soils, has been suggested as a microbial process that may be harnessed, especially since many DNRA-catalyzing organisms have been found to possess clade IInosZgenes and the ability to respire N2O. However, the selective advantages that may favor thesenosZ-harboring DNRA-catalyzing organisms is not well understood. Here, the effect of N2O on Nrf-mediated DNRA was examined in a recently isolated soil bacterium,Bacillussp. DNRA2, possessing bothnrfAandnosZgenes. The DNRA metabolism of this bacterium was observed in the presence of C2H2, a NosZ inhibitor, with or without N2O, and the results were compared with C2H2-free controls. Cultures were also exposed to repeated oxic-anoxic transitions in the sustained presence of N2O. The NO2−-to-NH4+reduction following oxic-to-anoxic transition was significantly delayed in NosZ-inhibited C2H2-amended cultures, and the inhibition was more pronounced with repeated oxic-anoxic transitions. The possible involvement of C2H2was dismissed since the cultures continuously flushed with C2H2/N2mixed gas after initial oxic incubation did not exhibit a similar delay in DNRA progression as that observed in the culture flushed with N2O-containing gas. The findings provide novel ecological and evolutionary insights into the oft-observed presence ofnosZgenes in DNRA-catalyzing microorganisms.

Importance

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3−and/or NO2−to NH4+. Interestingly, many DNRA-catalyzing microorganisms possessingnrfAgenes harbornosZgenes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms,Bacillussp. DNRA2, we have discovered that N2O may delay transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why somenrfA-possessing microorganisms have retainednosZgenes that had probably been acquired via horizontal gene transfers: to remove N2O that may otherwise interfere with the transition from O2respiration to DNRA.
Rapidly Adaptable Multiplexed Yeast Surface Display Serological Assay for Immune Escape Screening of SARS-CoV-2 Variants
Authors: Lopez-Morales Joanan , Vanella Rosario , Utzinger Tamara , Schittny Valentin , Hirsiger Julia , Osthoff Michael , Berger Christoph , Guri Yakir , Nash Michael A.
Published: February 2023

With numerous variations in the Spike protein, including concentrated mutations in the receptor-binding domain (RBD), the SARS-CoV-2 Omicron variant significantly shifted in the trajectory of the COVID-19 pandemic. To understand individual patient risk profiles in the face of rapidly emerging variants, there is an interest in sensitive serological tests capable of analyzing patient IgG response to multiple variants in parallel. Here, we present a serological test based on yeast surface display and serum biopanning that characterizes immune profiles against SARS-CoV-2 RBD variants. We used this yeast-based multi-variant serology method to examine IgG titers from 30 serum samples derived from COVID-19-convalescent and vaccinated individuals in Switzerland and assessed the relative affinity of polyclonal serum IgG for Wuhan (B lineage), Delta (B.1.617.2 lineage), and Omicron (B.1.1.529 lineage) RBD domains. We validated and benchmarked our system against a commercial lateral flow assay and showed strong concordance. Our assay demonstrates that serum IgGs from patients recovered from severe COVID-19 between March-June 2021 bound tightly to both original Wuhan and Delta RBD variants, but became indistinguishable from background when assayed against Omicron, representing an affinity loss of >10-20 fold. Our yeast immunoassay is easily tailored and parallelized with newly emerging RBD variants.
Measuring Stigma Associated with Hepatitis B Virus Infection in Sierra Leone: Validation of an Abridged Berger HIV Stigma Scale
Authors: Yendewa George A. , Sellu Edmond J. , Kpaka Rashid A. , James Peter B. , Yendewa Sahr A. , Cummings Peterlyn E. , Babawo Lawrence M. , Massaquoi Samuel P. , Ghazawi Manal , Ocama Ponsiano , Lakoh Sulaiman , Babawo Lawrence S. , Salata Robert A.
Published: February 2023

Stigma associated with hepatitis B virus (HBV) is common in endemic countries; however; instruments are lacking to accurately measure HBV-related stigma. We therefore aimed to develop and validate a concise instrument for measuring perceived HBV-related stigma in Sierra Leone. We enrolled 220 people living with HBV (PWHB) aged ≥ 18 years from August to November 2022. The initial Likert-scale instrument entailed 12 items adapted from Berger’s HIV Stigma Scale. We included 4 additional items adapted from the USAID indicators for enacted stigma. The proposed scale’s psychometric properties were assessed. After item reduction, the final HBV Stigma Scale consisted of 10 items and had good internal consistency (overall Cronbach’s α = 0.74), discriminant and construct validity. Exploratory factor analysis produced a 3-dimensional structure accounting for 59.3% of variance: personalized stigma driven by public attitudes (6 items), negative self-image (2 items), and disclosure concerns (2 items). Overall, 72.8% of respondents reported perceived HBV stigma (mean score 29.11 ± 4.14) and a similar a proportion (73.6%) reported at least one instance of enacted stigma. In assessing criterion-related validity, perceived HBV-related stigma correlated strongly with enacted stigma (r = 0.556) and inversely with having family/friends with HBV (r = -0.059). The 10-item HBV Stigma Scale demonstrated good internal consistency and validity and is suitable for screening for HBV-related stigma in Sierra Leone. The psychometric properties of the scale can be optimized with item additions/modifications and confirmatory factor analysis. The scale may help in combating stigma as a barrier to achieving HBV global elimination goals.
The value of fetal placental ratio and placental efficiency in term human pregnancy and complications
Authors: Zhang Peilin
Published: February 2023

Background

Fetal birth weight and placental weight have been extensively studied and used for clinical assessment of fetal development and maternal health. The ratio of fetal and placental weight as a tool for clinical use in human pregnancy is less studied. We compared the fetal birth weight, placental weight and fetal placental ratio in term pregnancy to see if fetal and placental ratio is useful in assessment of maternal health and pregnancy complication as well as fetal growth and development in singleton pregnancy.

Material and methods

We have collected the fetal birth data, maternal pregnancy data and placental pathology data from March 2000 to November 2021 in a single urban hospital. We compared the fetal birth weight, placental weight and fetal placental ratio in assessment of fetal growth, maternal pregnancy complications, and placental pathology with special emphasis on the role of fetal placental ratio.

Results

A total 3302 pairs of neonates and placentas from term singleton pregnancy were reviewed and fetal birth weight and placental weight were moderately correlated with Pearman’s correlation coefficiency R=0.66. Fetal placental ratio as a proxy of placental efficiency was significantly associated with various pregnancy complications and placental pathology, and these associations were different from those of fetal birth weight or placental weight alone. High placental efficiency (90 percentile or greater) was associated with ethnic White, SARS-CoV2 status, category 2 fetal heart tracing and maternal inflammatory response in placenta while low placental efficiency (less than 10 percentile) was associated with ethnic Black, Asian and Hispanic, preeclampsia/pregnancy induced hypertension and gestational diabetes mellitus.

Conclusion

Fetal placental ratio was shown to be a useful indicator different from fetal birth weight and placental weight alone. Maternal and environmental factors were shown to have differential effects on fetal and placental growth. Understanding the mechanism of differential fetal and placental growth will help better manage the clinical relevant conditions such as IUGR and macrosomia.
Optimization of highly inclined Illumination for diffraction-limited and super-resolution microscopy
Authors: Gardini L. , Vignolini T. , Curcio V. , Pavone F.S. , Capitanio M.
Published: February 2023

In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single-molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and how this impact on the image quality complicates setting HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy. We model the beam propagation through Gaussian optics and validate the model through far- and near-field experiments, thus characterizing the main geometrical features of the beam. Further, we fully quantify the impact of a progressive reduction of the inclined beam thickness on the image quality of both diffraction-limited and super-resolution images and we show that the most relevant impact is obtained by reducing the beam thickness to sub-cellular dimensions (< 3 μm). Based on this, we present a simple optical solution to reduce the inclined beam thickness down to 2.6 μm while keeping a field-of-view dimension suited for cell imaging and allowing an increase in the number of localizations in super-resolution imaging of up to 2.6 folds.
Deep-body feelings: ingestible pills reveal gastric correlates of emotions
Authors: Porciello Giuseppina , Monti Alessandro , Panasiti Maria Serena , Aglioti Salvatore Maria
Published: February 2023

Although it is generally held that gastro-intestinal (GI) signals are related to emotions, direct evidence for such a link is currently lacking. One of the reasons why the internal milieu of the GI system is poorly investigated is because visceral organs are difficult to access and monitor. To directly measure the influence of endoluminal markers of GI activity on the emotional experience, we asked a group of healthy male participants to ingest a pill that measured pH, pressure, and temperature of their GI tract while they watched video-clips that consistently induced disgust, fear, happiness, sadness, or a control neutral state. In addition to the objective physiological markers of GI activity, subjective ratings of perceived emotions and visceral (i.e. gastric, respiratory and cardiac) sensations were recorded. We found that when participants observed fearful and disgusting video-clips, they reported to perceive not only cardiac and respiratory sensations but also gastric sensations, such as nausea. Moreover, we found that there was a clear relation between the physiology of the stomach and the perceived emotions. Specifically, when disgusting video-clips were displayed, the more acidic the pH, the more participants reported feelings of disgust and fear; the less acidic the pH, the more they reported happiness. Our findings suggest that gastric signals contribute to unique emotional states and that ingestible pills may open new avenues for exploring the deep-body physiology of emotions.
Disease-specific loss of microbial cross-feeding interactions in the human gut
Authors: Marcelino Vanessa R. , Welsh Caitlin , Diener Christian , Gulliver Emily L. , Rutten Emily L. , Young Remy B. , Giles Edward M. , Gibbons Sean M. , Greening Chris , Forster Samuel C.
Published: February 2023

Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metagenome-wide metabolic models from over 1600 individuals, the MES allowed us to identify and rank metabolic interactions that were significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn’s disease case-control study, our approach identified a lack of species with the ability to consume hydrogen sulphide as the main distinguishing microbiome feature of disease. We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem.
New RoxS sRNA targets identified inB. subtilisby pulsed SILAC
Authors: Allouche Delphine , Kostova Gergana , Hamon Marion , Marchand Christophe H. , Caron Mathias , Belhocine Sihem , Christol Ninon , Charteau Violette , Condon Ciarán , Durand Sylvain
Published: February 2023

Non-coding RNAs (sRNA) play a key role in controlling gene expression in bacteria, typically by base-pairing with ribosome binding sites to block translation. The modification of ribosome traffic along the mRNA generally affects its stability. However, a few cases have been described in bacteria where sRNAs can affect translation without a major impact on mRNA stability. To identify new sRNA targets inB. subtilispotentially belonging to this class of mRNAs, we used pulsed-SILAC (stable isotope labeling by amino acids in cell culture) to label newly synthesized proteins after short expression of the RoxS sRNA, the best characterized sRNA in this bacterium. RoxS sRNA was previously shown to interfere with the expression of genes involved in central metabolism, permitting control of the NAD+/NADH ratio inB. subtilis. In this study, we confirmed most of the known targets of RoxS, showing the efficiency of the method. We further expanded the number of mRNA targets encoding enzymes of the TCA cycle and identified new targets primarily regulated at the translational level. One of these is YcsA, a tartrate dehydrogenase that uses NAD+ as co-factor, in excellent agreement with the proposed role of RoxS in Firmicutes.

Importance

Non-coding RNA (sRNA) play an important role in bacterial adaptation and virulence. The identification of the most complete set of targets for these regulatory RNAs is key to fully identify the perimeter of its function(s). Most sRNAs modify both the translation (directly) and mRNA stability (indirectly) of their targets. However, sRNAs can also influence the translation efficiency of the target primarily, with little or no impact on mRNA stability. The characterization of these targets is challenging. We describe here the application of the pulsed SILAC method to identify these targets and obtain the most complete list of targets for a defined sRNA.
An engineered electroosmotic flow transports unravelled proteins across nanopores
Authors: Sauciuc Adina , Morozzo Blasco , Tadema Matthijs , Chinappi Mauro , Maglia Giovanni
Published: February 2023

The development of a technology capable of sequencing single proteins holds promise to unravel new biological information hidden in ensemble analysis. However, new techniques must be first developed. In one approach, proteins are unfolded and translocate across a nanopore under an external bias. Unlike DNA, however, proteins do not have a uniform charge, and the electrophoretic force cannot be used to translocate proteins. Here, we show that by introducing sets of charges spaced by ~1 nm an otherwise neutral nanopore an electroosmotic force is created that induces the unidirectional transport of polypeptides, even against relatively strong electrophoretic forces. Unstructured polypeptides and native proteins unfolded with urea produce current signatures as they traversed the nanopore, which could lead to quick protein identifcation. This approach can be used to translocate and stretch proteins in non-enzymatic protein identification and enzymatic protein sequencing approaches.
The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy
Authors: Jensen Rasmus K , Miehe Michaela , Gandini Rosaria , Jørgensen Martin H , Spillner Edzard , Andersen Gregers R
Published: February 2023

Immunoglobulin E is a mammal specific antibody isotype supporting the immune response against parasites and venoms, but also a driver of allergic responses. Prior studies have defined the conformation of the IgE Fc fragment bound to the cell surface receptor FcεRIα and the dynamic properties of the IgE Fc. It remains unknown, how these prior studies translate to the complex of a full antibody including the Fab arms with the receptor. Here we show that in a cryo-EM structure of the IgE FcεRIα complex, IgE adopts a T-like conformation where the antigen binding Fab arms may be parallel to the cell membrane. Two additional conformations are captured in negative stain EM (ns-EM) where the arrangements of the Fab arms differ from the cryo-EM conformation. Small angle scattering data favors the FcεRIα bound IgE conformation observed by cryo-EM, but the major IgE conformation observed by ns-EM possibly may also occur. In all observed conformations of FcεRIα bound IgE, one Fab arm is fixed relative to the IgE Fc moiety whereas the second Fab may alternate its position. Introduction of flexibility in the Fab-Fc hinge diminishes the biological activity of IgE demonstrating a functional role for the observed defined Fab-Fc hinge conformations. Our data show the organization of a full size antibody on its receptor and reveal a new layer of dynamics in FcεRIα bound IgE on top of the well established spectrum of IgE Fc conformations. Development of novel anti-IgE therapeutics may take into account these distinct FcεRIα bound IgE conformations.

Significance statement

IgE represents a canonical antibody isotype and is a key molecule for the allergic immune response to environmental triggers driven by mast cells and basophils. The requirements for efficient mediation of IgE’s effects are not fully understood. Here we elucidate the structure of the entire IgE in complex with its high affinity receptor and identify two clearly distinct and dominant conformations, in which one of the Fab arms is fixed relative to the Fc domains. Enforcing IgE flexibility impacts the biological function with potential consequences for the allergic response. This unique behavior makes IgE different from all other isotypes and its understanding sheds light on the allergenic activation of the immune response.
Reversal of drug resistance by disruption of a Gain-of-Function mutant p53 and transcriptional co-activator PC4 interaction
Authors: Mondal Priya , Roy Kumar Singha , Kundu Tapas K. , Roychoudhury Susanta , Roy Siddhartha
Published: February 2023

The positive coactivator 4 or PC4 is a chromatin-associated protein whose role in gene regulation by wild-type p53 is now well-known. During tumorigenesis, p53 is often mutated resulting in its loss of function. A sub-class of these mutants gain new pro-proliferation properties which occur largely due to the upregulation of many pro-proliferation genes. Little is known about the roles of PC4 in tumor cells bearing mutant p53 genes. In this article, we show that PC4 associates with one of the tumor-associated gain-of-function p53 mutants, R273H. This association drives its recruitment to two promoters, UBE2C, and MDR1, known to be responsible for imparting aggressive growth and resistance to many drugs. A previously reported peptide that disrupts PC4-wild-type p53 interaction also disrupts the PC4-R273Hp53 protein-protein interaction. The introduction of this peptide to tumor cells bearing the R273HTP53 gene resulted in a lowering of MDR1 expression and abrogation of drug resistance. Interestingly, cells bearing another gain-of-function mutant R248W do not show the same type of response, suggesting that the action of PC4 on mutant p53s may differ for different GOF mutants. The results presented here suggest that PC4-R273H interaction may be a promising target for reducing proliferation and tumor drug resistance.
Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background
Authors: Evangelista C. , Kamenova S. , Pauli B. Diaz , Sandkjenn J. , Vøllestad L.A. , Edeline E. , Trosvik P. , de Muinck EJ.
Published: February 2023

Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. To do so, we studied two lineages of medaka with known divergence in foraging efficiency and life history raised under antagonistic size-selective regimes for 10 generations (i.e. the largest or the smallest breeders were removed to mimic fishing-like or natural mortality). In pond mesocosms, the two lineages were subjected to contrasting population density and light intensity (used as proxies of resource availability). We observed significant differences in the gut microbiome composition and richness between the two lines, and this effect was mediated by light intensity. The bacterial richness of fishing-like medaka (small-breeder line) was reduced by 34% under low-light conditions compared to high-light conditions, while it remained unchanged in natural mortality-selected medaka (large-breeder line). However, the observed changes in bacterial richness did not correlate with changes in adult growth rate or body condition. Given the growing evidence about the gut microbiomes importance to host health, more in-depth studies are required to fully understand the role of the microbiome in size-selected organisms and the possible ecosystem-level consequences.
Predictive learning rules generate a cortical-like replay of probabilistic sensory experiences
Authors: Asabuki Toshitake , Fukai Tomoki
Published: February 2023

The brain is thought to construct an optimal internal model representing the probabilistic structure of the environment accurately. Evidence suggests that spontaneous brain activity gives such a model by cycling through activity patterns evoked by previous sensory experiences with the experienced probabilities. The brain’s spontaneous activity emerges from internally-driven neural population dynamics. However, how cortical neural networks encode internal models into spontaneous activity is poorly understood. Recent computational and experimental studies suggest that a cortical neuron can implement complex computations, including predictive responses, through soma-dendrite interactions. Here, we show that a recurrent network of spiking neurons subject to the same predictive learning principle provides a novel mechanism to learn the spontaneous replay of probabilistic sensory experiences. In this network, the learning rules minimize probability mismatches between stimulus-evoked and internally driven activities in all excitatory and inhibitory neurons. This learning paradigm generates stimulus-specific cell assemblies that internally remember their activation probabilities using within-assembly recurrent connections. Our model contrasts previous models that encode the statistical structure of sensory experiences into Markovian transition patterns among cell assemblies. We demonstrate that the spontaneous activity of our model well replicates the behavioral biases of monkeys performing perceptual decision making. Our results suggest that interactions between intracellular processes and recurrent network dynamics are more crucial for learning cognitive behaviors than previously thought.
Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity
Authors: Rohban Sara , Rafiee Mahmoud-Reza , Ule Jernej , Luscombe Nicholas M.
Published: February 2023

Integrator is a multi-subunit complex that directly interacts with the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Through its RNA endonuclease activity, Integrator is required for 3′-end processing of both non-coding and coding transcripts. Here we demonstrate that depleting Integrator subunit 11 (INTS11), the main catalytic subunit of the Integrator complex, leads to a global elongation defect as a result of decreased polymerase processivity. We observe this defect in the region approximately 12 to 35 kb downstream of the transcription start site (TSS), where RNAPII normally transitions to its maximum processivity. We also identify an important role for INTS11, possibly in association with RNAPII CTD phospho-Tyr1, in repressing antisense transcription upstream of active promoters, as well as repressing transcription of genic regions near AsiSI-induced double-strand breaks.

Altogether, this study points toward a novel function of Integrator in promoting termination of incompetent RNAPII molecules while facilitating the transition to fully processive polymerase in order to enable efficient elongation.
NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons
Authors: Hamagami Nicole , Wu Dennis Y. , Clemens Adam W. , Nettles Sabin A. , Gabel Harrison W.
Published: February 2023

During postnatal development the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). The mechanisms determining genomic non-CG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, the H3K36 methyltransferase mutated in the NDD, Sotos syndrome, is required for megabase-scale patterning of H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes alterations in DNA methylation that overlap with models of DNMT3A disorders and define convergent disruption in the expression of key neuronal genes in these models that may contribute to shared phenotypes in NSD1- and DNMT3A-associated NDD. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome.

Highlights

Topology-associated DNA methylation and gene expression independently contribute to neuronal gene body and enhancer non-CG DNA methylation patterns.

Topology-associated H3K36me2 patterns and local enrichment of H3K4 methylation impact deposition of non-CG methylation by DNMT3A.

Disruption of NSD1in vivoleads to alterations in H3K36me2, DNA methylation, and gene expression that overlap with models of DNMT3A disorders.
Ergosterol distribution controls surface structure formation and fungal pathogenicity
Authors: Choy Hau Lam , Gaylord Elizabeth A. , Doering Tamara L.
Published: February 2023

Ergosterol, the major sterol in fungal membranes, is critical for defining membrane fluidity and regulating cellular processes. Although ergosterol synthesis has been well defined in model yeast, little is known about sterol organization in the context of fungal pathogenesis. We identified a retrograde sterol transporter, Ysp2, in the opportunistic fungal pathogenCryptococcus neoformans. We found that the lack of Ysp2 under host-mimicking conditions leads to abnormal accumulation of ergosterol at the plasma membrane, invagination of the plasma membrane, and malformation of the cell wall, which can be functionally rescued by inhibiting ergosterol synthesis with the antifungal drug fluconazole. We also observed that cells lacking Ysp2 mislocalize the cell surface protein Pma1 and have thinner and more permeable capsules. As a result of perturbed ergosterol distribution and its consequences,ysp2Δ cells cannot survive in physiologically-rele-vant environments such as host phagocytes and are dramatically attenuated in virulence. These findings expand our knowledge of cryptococcal biology and underscore the importance of sterol homeostasis in fungal pathogenesis.

IMPORTANCE

Cryptococcus neoformansis an opportunistic fungal pathogen that kills over 100,000 people worldwide each year. Only three drugs are available to treat cryptococcosis, and these are variously limited by toxicity, availability, cost, and resistance. Ergosterol is the most abundant sterol in fungi and a key component in modulating membrane behavior. Two of the drugs used for cryptococcal infection, amphotericin B and fluconazole, target this lipid and its synthesis, highlighting its importance as a therapeutic target. We discovered a cryptococcal ergosterol transporter, Ysp2, and demonstrated its key roles in multiple aspects of cryptococcal biology and pathogenesis. These studies demonstrate the role of ergosterol homeostasis inC. neoformansvirulence, deepen our understanding of a pathway with proven therapeutic importance, and open a new area of study.
Pathology of naturally acquired high pathogenicity avian influenza virus H5N1 infection in seabirds
Authors: Lean Fabian ZX , Falchieri Marco , Furman Natalia , Tyler Glen , Robinson Caroline , Holmes Paul , Reid Scott M , Banyard Ashley C , Brown Ian H , Man Catherine , Núñez Alejandro
Published: February 2023

The re-emergence of the high pathogenicity avian influenza virus (HPAIV) subtype H5N1 in the United Kingdom in 2021-2022 has caused unprecedented epizootic events in wild birds and poultry. During the summer of 2022 there was a shift in virus transmission dynamics resulting in increased HPAIV infection in seabirds and consequently a profound impact on seabird populations. To understand the pathological impact of HPAIV in seabirds, we have evaluated the virus distribution and associated pathological changes in the tissues of great skua (Stercorarius skua, n=8), long tailed skua (Stercorarius longicaudus, n=1), European herring gull (Larus argentatus, n=5), and black-headed gull (Chroicocephalus ridibundus, n=4). Grossly there was gizzard ulceration in one great skua and pancreatic necrosis in four herring gulls, which were confirmed for virus infectionin situby immunohistochemistry. Microscopical analysis revealed neuro-, pneumo-, lymphoidand cardiotropism of HPAIV H5N1, with the most common virus-associated pathological changes being pancreatic and splenic necrosis. Examination of the reproductive tract of the great skua revealed HPAIV-associated oophoritis and salpingitis, and virus replication within the oviductal epithelium. Across the birds, epitheliotropism was evident in the intestine, nasal turbinate, and trachea. This was, in contrast, not observed in the 2021 summer mortality event in great skuas and may be significant for the disease epidemiology observed in 2022. The emergence of HPAIV in seabirds, particularly during summer 2022, has challenged the dogma of HPAIV dynamics, posing a significant threat to wild bird life with potential implications to the reproductive performance of seabirds of conservation importance.
A Single Cell Time Course of Senescence Uncovers Discrete Cell Trajectories and Transcriptional Heterogeneity
Authors: Ciotlos Serban , Wimer Lauren , Campisi Judy , Melov Simon
Published: February 2023

Senescent cells (SnCs) are typically studied as endpoints of a complex transformational process, owing to their frequent maladaptive effects on surrounding tissue and cells. SnCs accumulate with age, and while they ultimately comprise a small percentage of cells in tissues, they have important roles in age associated pathologies. Several obstacles remain in understanding the heterogeneous nature of senescence, and formulating potent beneficial intervention strategies. One approach targets senescent cells and kills them (“senolytic” approach), and is often driven by a low resolution understanding of SnC identity, which risks both incomplete clearance and off-target effects. Cellular senescence is not a singular binary response, but a suite of response trajectories that vary by multiple parameters including inducer and initial cell state. In order to elucidate the developmental trajectories of SnCs, we performed single-cell RNA sequencing on IMR90 lung fibroblasts senescencing across a 12 day time period. Our analysis reveals substantial heterogeneity in gene expression within timepoints and across the full time-course. We uncovered unique markers and differentially regulated pathways in cell populations within each timepoint. Supervised trajectory inference of the time-course data uncovered the root-origin and fates of distinct SnC lineages over 3 stages of senescence induction. Altogether our data provide a novel approach to stud SnC development, identifying cell states of interest, and differentiating between SnCs and quiescent cells. This will aid in identifying key targets for therapeutic intervention in senescence.
Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen
Authors: Joubert Pierre M. , Krasileva Ksenia V.
Published: February 2023

Background

Fungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts.

Results

We analyzed gene PAV in the rice and wheat blast fungus,Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in rice-infectingM. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes ofM. oryzaediffered in their number and their genomic context.

Conclusions

Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.
Rate versus synchrony codes for cerebellar control of motor behavior
Authors: Herzfeld David J. , Joshua Mati , Lisberger Stephen G.
Published: February 2023

Control of movement requires the coordination of multiple brain areas, each containing populations of neurons that receive inputs, process these inputs via recurrent dynamics, and then relay the processed information to downstream populations. Information transmission between neural populations could occur through either coordinated changes in firing rates or the precise transmission of spike timing. We investigate the nature of the code for transmission of signals to downstream areas from a part of the cerebellar cortex that is crucial for the accurate execution of a quantifiable motor behavior. Simultaneous recordings from Purkinje cell pairs in the cerebellar flocculus of rhesus macaques revealed how these cells coordinate their activity to drive smooth pursuit eye movements. Purkinje cells show millisecond-scale coordination of spikes (synchrony), but the level of synchrony is small and likely insufficient to impact the firing of downstream neurons in the vestibular nucleus. Further, analysis of previous metrics for assaying Purkinje cell synchrony demonstrates that these metrics conflate changes in firing rate and neuron-neuron covariance. We conclude that the output of the cerebellar cortex uses primarily a rate code rather than synchrony code to drive activity of downstream neurons and thus control motor behavior.

Impact statement

Information transmission in the brain can occur via changes in firing rate or via the precise timing of spikes. Simultaneous recordings from pairs of Purkinje cells in the floccular complex reveals that information transmission out of the cerebellar cortex relies almost exclusively on changes in firing rates rather than millisecond-scale coordination of spike timing across the Purkinje cell population.
Segmental infralesional lower motor neuron abnormalities in patients with sub-acute traumatic spinal cord injury
Authors: Berger Michael J. , Adewuyi Adenike A. , Doherty Christopher , Hanlan Amy K. , Morin Cynthia , O’Connor Russ , Sharma Radhika , Sproule Shannon , Swong Kevin N. , Wu Harvey , Franz Colin K. , Brown Erin
Published: February 2023

The health of the infralesional lower motor neuron (LMN) has received little attention in individuals with traumatic cervical spinal cord injuries (SCI). Infralesional LMN health is clinically relevant in the context of nerve transfer surgery to restore critical upper limb functions, as those demonstrating LMN damage below the neurological level of injury may experience irreversible sequelae of denervation (e.g., atrophy, fibrosis) without timely intervention. In this two-centre retrospective cohort study, we examined the health of the infralesional LMN in individuals with traumatic cervical SCI, using data derived from the clinical electrodiagnostic examination performed early after SCI. We assessed 66 limbs in 42 individuals with traumatic cervical SCI (40 males, mean age = 43.6±17.2, mean duration from injury = 3.3±1.5 months, 25 with motor complete injuries). Analysis was stratified by injury level as 1) C4 and above, 2) C5 and 3) C6-7. EMG performed on representative muscles from C5-6, C6-7, C7-8 and C8-T1, were included in analysis. LMN abnormality was dichotomized as present (abnormal spontaneous activity) or absent. Data were pooled for the most caudal infralesional segment (C8-T1). Overall, a high frequency of denervation potentials was seen in all infralesional segments for all injury levels. The pooled frequency of denervation potentials at C8-T1 was 74.6% of limbs tested. There was also evidence of denervation potentials at the rostral border of the neurological level of injury, as high as 64.3% of C5-6 muscles for C5 injuries. These data support a high prevalence of infralesional LMN abnormality following SCI, which has implications to candidacy, timing of the intervention, donor nerve options and motor prognosis following SCI.
Somatodendritic orientation determines tDCS-induced neuromodulation of Purkinje cell activity in awake mice
Authors: Sánchez-León Carlos A , Campos Guillermo Sánchez-Garrido , Fernández Marta , Sánchez-López Alvaro , Medina Javier F , Márquez-Ruiz Javier
Published: February 2023

Transcranial direct-current stimulation (tDCS) of the cerebellum is a promising non-invasive neuromodulatory technique being proposed for the treatment of neurological and neuropsychiatric disorders. However, there is a lack of knowledge about how externally applied currents affect neuronal spiking activity in cerebellar circuitsin vivo. We investigated how Cb-tDCS affects the firing rate of Purkinje cells (PC) and non-PC in the mouse cerebellar cortex to understand the underlying mechanisms behind the polarity-dependent modulation of neuronal activity induced by tDCS.

Mice (n = 9) were prepared for the chronic recording of LFPs to assess the actual electric field gradient imposed by Cb-tDCS in our experimental design. Single-neuron extracellular recording of PCs in awake (n = 24) and anesthetized (n = 27) mice was combined with juxtacellular recordings and subsequent staining of PC with neurobiotin under anesthesia (n = 8) to correlate their neuronal orientation with their response to Cb-tDCS. Finally, a high-density Neuropixels recording system was used to demonstrate the relevance of neuronal orientation during the application of Cb-tDCS in awake mice (n = 6).

In this study, we observe that Cb-tDCS induces a heterogeneous polarity-dependent modulation of the firing rate of Purkinje cells (PC) and non-PC in the mouse cerebellar cortex. We demonstrate that the apparently heterogeneous effects of tDCS on PC activity can be explained by taking into account the somatodendritic orientation relative to the electric field. Our findings highlight the need to consider neuronal orientation and morphology to improve tDCS computational models, enhance stimulation protocol reliability, and optimize effects in both basic and clinical applications.
Arousal state transitions occlude sensory-evoked neurovascular coupling in neonatal mice
Authors: Gheres Kyle W. , Ünsal Hayreddin S , Han Xu , Zhang Qingguang , Turner Kevin L. , Zhang Nanyin , Drew Patrick J.
Published: February 2023

In the adult sensory cortex, increases in neural activity elicited by sensory stimulation usually drives vasodilation mediated by neurovascular coupling. However, whether neurovascular coupling is the same in neonatal animals as adults is controversial, as both canonical and inverted responses have been observed. We investigated the nature of neurovascular coupling in unanesthetized neonatal mice using optical imaging, electrophysiology, and BOLD fMRI. We find in neonatal (postnatal day 15, P15) mice, sensory stimulation induces a small increase in blood volume/BOLD signal, often followed by a large decrease in blood volume. An examination of arousal state of the mice revealed that neonatal mice were asleep a substantial fraction of the time, and that stimulation caused the animal to awaken. As cortical blood volume is much higher during REM and NREM sleep than the awake state, awakening occludes any sensory-evoked neurovascular coupling. When neonatal mice are stimulated during an awake period, they showed relatively normal (but slowed) neurovascular coupling, showing that that the typically observed constriction is due to arousal state changes. These result show that sleep-related vascular changes dominate over any sensory-evoked changes, and hemodynamic measures need to be considered in the context of arousal state changes.

Significance Statement

In the adult brain, increases in neural activity are often followed by vasodilation, allowing activity to be monitored using optical or magnetic resonance imaging. However, in neonates, sensory stimulation can drive vasoconstriction, whose origin was not understood. We used optical and magnetic resonance imaging approaches to investigate hemodynamics in neonatal mice. We found that sensory-induced vasoconstriction occurred when the mice were asleep, as sleep is associated with dilation of the vasculature of the brain relative to the awake state. The stimulus awakens the mice, causing a constriction due to the arousal state change. Our study shows the importance of monitoring arousal state, particularly when investigating subjects that may sleep, and the dominance arousal effects on brain hemodynamics.
The power of family? Family social capital and the risk of externalising behaviours among youth with multiple childhood adversities
Authors: Kysar‐Moon Ashleigh
Published: February 2023

Externalising behaviour problems (EBP), or aggressive and delinquent behaviours, among youth pose a significant problem for their peers, parents, teachers and society. Many types of childhood adversities increase the risk of EBP, including maltreatment, physical punishment, domestic violence, family poverty and living in violent neighbourhoods. This study asks, to what extent do children who face multiple adversities during childhood suffer an increased risk of EBP and is family social capital (FSC) associated with a lower risk? Using seven waves of panel data from the Longitudinal Studies of Child Abuse and Neglect, I examine the accumulation of adversities associated with greater risk of EBP among youth and investigate whether FSC—family network, support and cohesion—in early childhood is associated with a reduction in EBP risk. Experiencing early and multiple adversities resulted in the worst EBP trajectories throughout childhood. Although, among youth with the highest adversities, if early family support was also high, their EBP trajectories are more favourable than their disadvantaged peers with less support. FSC may protect against EBP when multiple childhood adversities are experienced. The need for early EBP interventions and bolstering FSC are discussed.
Fetal heart rate responses in chronic hypoxaemia with superimposed repeated hypoxaemia consistent with early labour: a controlled study in fetal sheep
Authors: Lear C. A. , Georgieva A. , Beacom M. J. , Wassink G. , Dhillon S. K. , Lear B. A. , Mills O. J. , Westgate J. A. , Bennet L. , Gunn A. J.
Published: February 2023

Objective

Deceleration area (DA) and capacity (DC) of the fetal heart rate can help predict risk of intrapartum fetal compromise. However, their predictive value in higher risk pregnancies is unclear. We investigated whether they can predict the onset of hypotension during brief hypoxaemia repeated at a rate consistent with early labour in fetal sheep with pre‐existing hypoxaemia.

Design

Prospective, controlled study.

Setting

Laboratory.

Sample

Chronically instrumented, unanaesthetised near‐term fetal sheep.

Methods

One‐minute complete umbilical cord occlusions (UCOs) were performed every 5 minutes in fetal sheep with baseline paO2 <17 mmHg (hypoxaemic, n = 8) and >17 mmHg (normoxic, n = 11) for 4 hours or until arterial pressure fell <20 mmHg.

Main outcome measures

DA, DC and arterial pressure.

Results

Normoxic fetuses showed effective cardiovascular adaptation without hypotension and mild acidaemia (lowest arterial pressure 40.7 ± 2.8 mmHg, pH 7.35 ± 0.03). Hypoxaemic fetuses developed hypotension (lowest arterial pressure 20.8 ± 1.9 mmHg, P < 0.001) and acidaemia (final pH 7.07 ± 0.05). In hypoxaemic fetuses, decelerations showed faster falls in FHR over the first 40 seconds of UCOs but the final deceleration depth was not different to normoxic fetuses. DC was modestly higher in hypoxaemic fetuses during the penultimate (P = 0.04) and final (P = 0.012) 20 minutes of UCOs. DA was not different between groups.

Conclusion

Chronically hypoxaemic fetuses had early onset of cardiovascular compromise during labour‐like brief repeated UCOs. DA was unable to identify developing hypotension in this setting, while DC only showed modest differences between groups. These findings highlight that DA and DC thresholds need to be adjusted for antenatal risk factors, potentially limiting their clinical utility.