bluuebunny/crossref_metadata_2025 huggingface dataset:
Early life stress in male mice blunts responsiveness in a translationally-relevant reward task
Authors: Hisey Erin E. , Fritsch Emma L. , Ressler Kerry J. , Kangas Brian D. , Carlezon William A.
Published: March 2023

Early-life stress (ELS) leaves signatures upon the brain that persist throughout the lifespan and increase the risk of psychiatric illnesses including mood and anxiety disorders. In humans, myriad forms of ELS—including childhood abuse, bullying, poverty, and trauma—are increasingly prevalent. Understanding the signs of ELS, including those associated with psychiatric illness, will enable improved treatment and prevention. Here we developed a novel procedure to model human ELS in mice and identify translationally-relevant biomarkers of mood and anxiety disorders. We exposed male mice (C57BL/6J) to an early-life (juvenile) chronic social defeat stress (jCSDS) and examined social interaction and responsivity to reward during adulthood. As expected, jCSDS-exposed mice showed a socially avoidant phenotype in open-field social interaction tests. However, sucrose preference tests failed to demonstrate ELS-induced reductions in choice for the sweetened solution, suggesting no effect on reward function. To explore whether other tasks might be more sensitive to changes in motivation, we tested the mice in the Probabilistic Reward Task (PRT), a procedure often used in humans to study reward learning deficits associated with depressive illness. In a touchscreen PRT variant that was reverse-translated to maximize alignment with the version used in human subjects, mice exposed to jCSDS displayed significant reductions in the tendency to develop response biases for more richly-rewarded stimuli, a hallmark sign of depression (anhedonia) when seen in humans. Our findings suggest that translationally-relevant procedures that utilize the same endpoints across species may enable the development of improved model systems that more accurately predict outcomes in humans.
Patch2MAP combines patch-clamp electrophysiology with super-resolution structural and protein imaging in identified single neurons without genetic modification
Authors: Vardalaki Dimitra , Pham Trang L. D. , Frosch Matthew P. , Cosgrove Garth Rees , Richardson Mark , Cash Sydney S. , Harnett Mark T.
Published: March 2023

Recent developments in super-resolution microscopy have revolutionized the study of cell biology. However, dense tissues require exogenous protein expression for single cell morphological contrast. In the nervous system, many cell types and species of interest – particularly human – are not amenable to genetic modification and/or exhibit intricate anatomical specializations which make cellular delineation challenging. Here, we present a method for full morphological labeling of individual neurons from any species or cell type for subsequent cell-resolved protein analysis without genetic modification. Our method, which combines patch-clamp electrophysiology with epitope-preserving magnified analysis of proteome (eMAP), further allows for correlation of physiological properties with subcellular protein expression. We applied Patch2MAP to individual spiny synapses in human cortical pyramidal neurons and demonstrated that electrophysiological AMPA-to-NMDA receptor ratios correspond tightly to respective protein expression levels. Patch2MAP thus permits combined subcellular functional, anatomical, and proteomic analyses of any cell, opening new avenues for direct molecular investigation of the human brain in health and disease.
Mesoscale volumetric light field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz
Authors: Nöbauer Tobias , Zhang Yuanlong , Kim Hyewon , Vaziri Alipasha
Published: March 2023

Various implementations of mesoscopes provide optical access for calcium imaging across multi-millimeter fields-of-view (FOV) in the mammalian brain. However, capturing the activity of the neuronal population within such FOVs near-simultaneously and in a volumetric fashion has remained challenging since approaches for imaging scattering brain tissues typically are based on sequential acquisition. Here, we present a modular, mesoscale light field (MesoLF) imaging hardware and software solution that allows recording from thousands of neurons within volumes of ⍰ 4000 × 200 µm, located at up to 400 µm depth in the mouse cortex, at 18 volumes per second. Our optical design and computational approach enable up to hour-long recording of ∼10,000 neurons across multiple cortical areas in mice using workstation-grade computing resources.
A generalizable protocol for expression and purification of membrane-bound bacterial phosphoglycosyl transferases in liponanoparticles
Authors: Dodge Greg J. , Bernstein Hannah M. , Imperiali Barbara
Published: March 2023

Phosphoglycosyl transferases (PGTs) are among the first membrane-bound enzymes involved in the biosynthesis of bacterial glycoconjugates. Robust expression and purification protocols for an abundant subfamily of PGTs remains lacking. Recent advancements in detergent-free methods for membrane protein solubilization open the door for purification of difficult membrane proteins directly from cell membranes into native-like liponanoparticles. By leveraging autoinduction,in vivoSUMO tag cleavage, styrene maleic acid co-polymer liponanoparticles (SMALPs), and Strep-Tag purification, we have established a robust workflow for expression and purification of previously unobtainable PGTs. The material generated from this workflow is extremely pure and can be directly visualized by Cryogenic Electron Microscopy (CryoEM). The methods presented here promise to be generalizable to additional membrane proteins recombinantly expressed inE. coliand should be of interest to the greater membrane proteomics community.

Highlights

Expression and purification of full-length Lg-PGTs has proven challenging.

Autoinduction andin vivoUlp1 cleavage produces active full-length Lg-PGTs.

SMA and DIBMA are vastly superior to DDM for Lg-PGT solubilization.

Strep-tag purification yields SMALPs suitable for CryoEM characterization.
Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development
Authors: Sur Abhinav , Wang Yiqun , Capar Paulina , Margolin Gennady , Farrell Jeffrey A.
Published: March 2023

During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3–120 hours post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and suggest new long-term cycling populations. Focused analyses of non-skeletal muscle and the endoderm identified transcriptional profiles of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and homologs of recently discovered humanbest4+ enterocytes. The transcriptional regulators of these populations remain unknown, so we reconstructed gene expression trajectories to suggest candidates. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
Uncovering plant microbiomes using long-read metagenomic sequencing
Authors: Masuda Sachiko , Gan Pamela , Kiguchi Yuya , Anda Mizue , Sasaki Kazuhiro , Shibata Arisa , Iwasaki Wataru , Suda Wataru , Shirasu Ken
Published: March 2023

The microbiome of plants plays a pivotal role in their growth and health. Despite its importance, many fundamental questions about the microbiome remain largely unanswered, such as the identification of colonizing bacterial species, the genes they carry, and the location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice leaf microbiome, we performed a metagenomic analysis using long-read sequences, and developed a genomic DNA extraction method that provides relatively intact DNA for long-read sequencing. 1.8 Gb reads were assembled into 26,067 contigs, including 136 circular sequences of less than 1 Mbp, as well as 172 large (≥ 1 Mbp) sequences, six of which were circularized. Within these contigs, 669 complete 16S rRNA genes were clustered into 166 bacterial species, 130 of which showed low identity to previously defined sequences, suggesting that they represent novel species. The large circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs (<1 Mbp) were defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of an uncultivated bacterium in the candidate phylumCandidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.
Vibrational Spectroscopy Identifies Myocardial Chemical Modifications in Heart Failure with Preserved Ejection Fraction
Authors: Pioppi Leonardo , Parvan Reza , Samrend Alan , da Silva Gustavo Justo , Paolantoni Marco , Sassi Paola , Cataliotti Alessandro
Published: March 2023

Background

Vibrational spectroscopy can be a valuable tool to monitor the markers of cardiovascular diseases. In the present work, we explored the vibrational spectroscopy characteristics of the cardiac tissue in an experimental model of heart failure with preserved ejection fraction (HFpEF).

Methods

We used the Fourier-transform infrared (FTIR) and Raman micro-spectroscopic techniques to provide complementary and objective tools for the histological assessment of heart tissues from an animal model of HFpEF. A new sampling technique was adopted (tissue print on a CaF2 disk) to characterize the extracellular matrix.

Results

Several spectroscopic markers (lipids, carbohydrates, and glutamate bands) were recognized in the cardiac ventricles as due to the comorbidities associated with the pathology, such as obesity and diabetes. Besides, abnormal collagen cross-linking and a decrease in tryptophan content were observed and related to the stiffening of ventricles and to the inflammatory state which is a favorable condition for HFpEF.

Conclusions

By the analyses of tissues and tissue prints, FTIR and Raman techniques were shown to be highly sensitive and selective in detecting changes in the chemistry of the heart in experimental HFpEF and its related comorbidities.
NE contribution to rebooting unconsciousness caused by midazolam
Authors: Gu LeYuan , Shao WeiHui , Liu Lu , Xu Qing , Wang YuLing , Gu JiaXuan , Yang Yue , Zhang ZhuoYue , Wu YaXuan , Shen Yue , Yu Qian , Lian XiTing , Ma Haixiang , Zhang YuanLi , Zhang HongHai
Published: March 2023

The advent of midazolam holds profound implications for modern clinical practice. The hypnotic and sedative effects of midazolam afford it broad clinical applicability. However, the specific mechanisms underlying the modulation of altered consciousness by midazolam remain elusive. Herein, using pharmacology, optogenetics, chemogenetics, fiber photometry, and gene knockdown, we revealed the role of locus coeruleus (LC)-ventrolateral preoptic nucleus (VLPO) noradrenergic neural circuit in regulating midazolam-induced altered consciousness. This effect was mediated by α1 adrenergic receptors. Moreover, gamma-aminobutyric acid receptor type A (GABAA-R) represents a mechanistically crucial binding site in the LC for midazolam. Our findings will provide novel insights into the neural circuit mechanisms underlying the recovery of consciousness after midazolam administration and will help guide the timing of clinical dosing and propose effective intervention targets for timely recovery from midazolam-induced loss of consciousness.
DISTINCT ROLES OF VIRAL US3 AND UL13 PROTEIN KINASES IN HERPES VIRUS SIMPLEX TYPE 1 (HSV-1) NUCLEAR EGRESS
Authors: Bahnamiri Masoudeh Masoud , Roller Richard J.
Published: March 2023

Herpesviruses transport nucleocapsids from the nucleus to the cytoplasm by capsid envelopment into the inner nuclear membrane and de-envelopment from the outer nuclear membrane, a process that is coordinated by nuclear egress complex (NEC) proteins, pUL34, and pUL31. Both pUL31 and pUL34 are phosphorylated by the virus-encoded protein kinase, pUS3, and phosphorylation of pUL31 regulates NEC localization at the nuclear rim. pUS3 also controls apoptosis and many other viral and cellular functions in addition to nuclear egress, and the regulation of these various activities in infected cells is not well understood. It has been previously proposed that pUS3 activity is selectively regulated by another viral protein kinase, pUL13 such that its activity in nuclear egress is pUL13-dependent, but apoptosis regulation is not, suggesting that pUL13 might regulate pUS3 activity on specific substrates. We compared HSV-1 UL13 kinase-dead and US3 kinase-dead mutant infections and found that pUL13 kinase activity does not regulate the substrate choice of pUS3 in any defined classes of pUS3 substrates and that pUL13 kinase activity is not important for promoting de-envelopment during nuclear egress. We also find that mutation of all pUL13 phosphorylation motifs in pUS3, individually or in aggregate, does not affect the localization of the NEC, suggesting that pUL13 regulates NEC localization independent of pUS3. Finally, we show that pUL13 co-localizes with pUL31 inside the nucleus in large aggregates, further suggesting a direct effect of pUL13 on the NEC and suggesting a novel mechanism for both UL31 and UL13 in the DNA damage response pathway.

IMPORTANCE

Herpes simplex virus infections are regulated by two virus-encoded protein kinases, pUS3 and pUL13, which each regulate multiple processes in the infected cell, including capsid transport from the nucleus to the cytoplasm. Regulation of the activity of these kinases on their various substrates is poorly understood, but importantly, kinases are attractive targets for the generation of inhibitors. It has been previously suggested that pUS3 activity on specific substrates is differentially regulated by pUL13 and, specifically, that pUL13 regulates capsid egress from the nucleus by phosphorylation of pUS3. In this study, we determined that pUL13 and pUS3 have different effects on nuclear egress and that pUL13 may interact directly with the nuclear egress apparatus with implications both for virus assembly and egress and, possibly, the host cell DNA- damage response.
Implication ofFOXD2dysfunction in syndromic congenital anomalies of the kidney and urinary tract (CAKUT)
Authors: Riedhammer Korbinian M. , Nguyen Thanh-Minh T. , Koşukcu Can , Calzada-Wack Julia , Li Yong , Saygılı Seha , Wimmers Vera , Kim Gwang-Jin , Chrysanthou Marialena , Bakey Zeineb , Kraiger Markus , Sanz-Moreno Adrián , Amarie Oana V , Rathkolb Birgit , Klein-Rodewald Tanja , Garrett Lillian , Hölter Sabine M. , Seisenberger Claudia , Haug Stefan , Marschall Susan , Wurst Wolfgang , Fuchs Helmut , Gailus-Durner Valerie , Wuttke Matthias , Hrabe de Angelis Martin , Ćomić Jasmina , Akgün Doğan Özlem , Özlük Yasemin , Taşdemir Mehmet , Ağbaş Ayşe , Canpolat Nur , Çalışkan Salim , Weber Ruthild , Bergmann Carsten , Jeanpierre Cecile , Saunier Sophie , Lim Tze Y. , Hildebrandt Friedhelm , Alhaddad Bader , Wu Kaman , Antony Dinu , Matschkal Julia , Schaaf Christian , Renders Lutz , Schmaderer Christoph , Meitinger Thomas , Heemann Uwe , Köttgen Anna , Arnold Sebastian , Ozaltin Fatih , Schmidts Miriam , Hoefele Julia
Published: March 2023

Background

Congenital anomalies of the kidney and urinary tract (CAKUT) are the predominant cause for chronic kidney disease below 30 years of age. Many monogenic forms have been discovered mainly due to comprehensive genetic testing like exome sequencing (ES). However, disease-causing variants in known disease-associated genes still only explain a proportion of cases. Aim of this study was to unravel the underlying molecular mechanism of syndromic CAKUT in two multiplex families with presumed autosomal recessive inheritance.

Methods and Results

ES in the index individuals revealed two different rare homozygous variants inFOXD2,a transcription factor not previously implicated in CAKUT in humans: a frameshift in family 1 and a missense variant in family 2 with family segregation patterns consistent with autosomal-recessive inheritance. CRISPR/Cas9-derivedFoxd2knock-out (KO) mice presented with bilateral dilated renal pelvis accompanied by renal papilla atrophy while extrarenal features included mandibular, ophthalmologic, and behavioral anomalies, recapitulating the phenotype of humans withFOXD2dysfunction. To study the pathomechanism ofFOXD2-dysfunction-mediated developmental renal defects, in a complementary approach, we generated CRISPR/Cas9-mediated KO ofFoxd2in ureteric-bud-induced mouse metanephric mesenchyme cells. Transcriptomic analyses revealed enrichment of numerous differentially expressed genes important in renal/urogenital development, includingPax2andWnt4as well as gene expression changes indicating a cell identity shift towards a stromal cell identity. Histology ofFoxd2KO mouse kidneys confirmed increased fibrosis. Further, GWAS data (genome-wide association studies) suggests thatFOXD2could play a role for maintenance of podocyte integrity during adulthood.

Conclusions

In summary, our data implicate thatFOXD2dysfunction is a very rare cause of autosomal recessive syndromic CAKUT and suggest disturbances of the PAX2-WNT4 cell signaling axis contribute to this phenotype.
Endemic-epidemic modelling of school closure to prevent spread of COVID-19 in Switzerland
Authors: Dunbar M. Bekker-Nielsen , Hofmann F. , Meyer S. , Held L.
Published: March 2023

The coronavirus disease 2019 (COVID-19) pandemic disrupted daily life and changes to routines were made in accordance with public health regulations. In 2020, nonpharmaceutical interventions were put in place to reduce exposure to and spread of the disease. The goal of this work was to quantify the effect of school closure during the first year of COVID-19 pandemic in Switzerland. This allowed us to determine the usefulness of school closures as a pandemic countermeasure for emerging coronaviruses in the absence of pharmaceutical interventions. The use of multivariate endemic-epidemic modelling enabled us to analyse disease spread between age groups which we believe is a necessary inclusion in any model seeking to achieve our goal. Sophisticated time-varying contact matrices encapsulating four different contact settings were included in our complex statistical modelling approach to reflect the amount of school closure in place on a given day. Using the model, we projected case counts under various transmission scenarios (driven by implemented social distancing policies). We compared these counterfactual scenarios against the true levels of social distancing policies implemented, where schools closed in the spring and reopened in the autumn. We found that if schools had been kept open, the vast majority of additional cases would be expected among primary school-aged children with a small fraction of cases percolating into other age groups following the contact matrix structure. Under this scenario where schools were kept open, the cases were highly concentrated among the youngest age group. In the scenario where schools had remained closed, most reduction would also be expected in the lowest age group with less effects seen in other groups.
Employment outcomes of people with Long Covid symptoms: community-based cohort study
Authors: Ayoubkhani Daniel , Zaccardi Francesco , Pouwels Koen B. , Walker A. Sarah , Houston Donald , Alwan Nisreen A. , Martin Josh , Khunti Kamlesh , Nafilyan Vahé
Published: March 2023

Background

Evidence on the long-term employment consequences of SARS-CoV-2 infection is lacking. We used data from a large, community-based sample in the UK to estimate associations between Long Covid and subsequent employment outcomes.

Methods

This was an observational, longitudinal study using a pre-post design. We included survey participants from 3 February 2021 to 30 September 2022 when they were aged 16 to 64 years and not in full-time education. Using conditional logit modelling, we explored the time-varying relationship between Long Covid status ≥12 weeks after a first test-confirmed SARS-CoV-2 infection (reference: pre-infection) and labour market inactivity (neither working nor looking for work) or workplace absence lasting ≥4 weeks.

Results

Of 206,299 included participants (mean age 45 years, 54% female, 92% white), 15% were ever inactive in the labour market and 10% were ever long-term absent during follow-up. Compared with pre-infection, inactivity was higher in participants reporting Long Covid 30 to <40 weeks (adjusted odds ratio (aOR): 1.45; 95% CI: 1.17 to 1.81) or 40 to <52 weeks (1.34; 1.05 to 1.72) post-infection. Combining with official statistics on Long Covid prevalence, our estimates translate to 27,000 (95% CI: 6,000 to 47,000) working-age adults in the UK being inactive because of Long Covid in July 2022.

Conclusions

Long Covid is likely to have contributed to reduced levels of participation in the UK labour market, though it is unlikely to be the sole driver. Further research is required to quantify the contribution of other factors, such as indirect health effects of the pandemic.
The trend of hypertension-related chronic kidney disease from 1990 to 2019 and its predictions over 25 years: An analysis of the Global Burden of Disease Study 2019
Authors: Ren Yi , Zhang Honggang
Published: March 2023

Background

High blood pressure is a key pathogenetic factor that contributes to the deterioration of kidney function. However, the incidence trend of hypertension-related chronic kidney disease (CKD) has rarely been studied; therefore, we aimed to analyze the global, regional, and national patterns, temporal trends as well as burden of hypertension-related CKD.

Methods

We extracted data on hypertension-related CKD from the Global Burden of Disease (GBD) study database, including the incidence, prevalence, disability-adjusted life years (DALYs), and mortality numbers and rates (per 100,000 population) and further described according to year, location, sex, age, and socio-demographic index (SDI). The estimated annual percentage changes (EAPCs) were calculated to assess the variation in incidence, DALYs, and mortality. We used an age-period-cohort (APC) model framework to analyze the underlying trends in prevalence by age, period, and birth cohort. Nordpred APC analysis was performed to predict the future morbidity and mortality of hypertension-related CKD.

Results

In 2019, a total of over 1.57 million new hypertension-related CKD cases were reported worldwide, a 161.97% increase from 1990. Compared to 1990, the ASIR increased in all 21 regions in 2019. In all countries and territories except Iceland, the EAPC in ASIR and the lower boundary of its 95% confidence interval (CI) were higher than 0. ASIR, ASPR, ASDR, and ASMR were not identical among countries with different SDI regions in 2019; additionally, ASIR and ASMR were significantly different among sexes in all SDI regions in 2019. The predicted incidence and mortality counts globally continue to increase to 2044, and there is an upward trend in ASIR for both men and women.

Conclusions

Hypertension-related CKD cannot be ignored either as a subcategory of CKD or as a complication of hypertension. Between 1990 and 2019, the ASIR of hypertension-related CKD demonstrated an ascending trend, and according to our projections, it would remain on the rise for the next 25 years. With remarkable global population growth, aging, and an increasing number of patients with hypertension, the burden of disease caused by hypertension-related CKD continues to increase.
Prospective Assessment of Bone Marrow Involvement with Positron Emission Tomography vs Bone Marrow Biopsy in Patients with Lymphoma
Authors: Singla Suhas , Batra Sandeep , Dougall Pankaj , Dayal Nitin , Naithani Rahul
Published: March 2023

Background

Bone marrow involvement (BM involvement) in lymphoma is a known adverse prognostic factor. Bone marrow biopsy (BMB) is the gold standard for detection of bone marrow involvement but is invasive modality. Positron Emission Tomography with Computed Tomography (PET-CT) scan has the ability to assess bone marrow involvement. We aimed to assess the concordance of PET-CT for BM involvement with BMB.

Methods

75 consecutive newly diagnosed cases of lymphoma were enrolled and were assessed for BM involvement with PET-CT and BMB.

Results

Of 75 patients, eighteen patients (24%) had BM involvement, with 19% (n=14) detected with BMB, and 13 (17%) with FDG 18 PET CT. There was a concordance rate of 88% amongst PET-CT and BMB. It was 92% in Hodgkin’s lymphoma (HL), 71.4% in non-Hodgkin’s lymphoma (NHL), and 91% and 70% in high-grade (HG) and low-grade (LG) NHL, respectively. Sensitivity, specificity, PPV, NPV, and accuracy of PET-CT for study population were 69.23%, 93.44%, 69.23%, 93.44%, and 89.19 % respectively. In patients with NHL sensitivity, specificity, NPV, PPV, and accuracy of PET-CT were 54.55%, 94.23%, 66.67%, 90.74%, and 87.30%, respectively; whereas in HL group these were 100%, 88.89%, 75%, 100%, and 91.67%, respectively.

Conclusions

PET-CT has got a high concordance with bone marrow biopsy in detecting bone marrow involvement with high specificity, NPV and accuracy. A high sensitivity, specificity, NPV and accuracy for detecting bone marrow involvement in patients with HL, aggressive B cell NHL, and T cell NHL was observed but the same parameters were not at par in patient with indolent (low-grade) NHL.
RNase L activating 2′–5′ oligoadenylates bind ABCF1, -3 and Decr-1
Authors: Govande Apurva A. , Babnis Aleksandra W. , Urban Christian , Habjan Matthias , Hartmann Rune , Kranzusch Philip J. , Pichlmair Andreas
Published: March 2023

A notable signaling mechanism employed by mammalian innate immune signaling pathways uses nucleotide based second messengers such as 2′–3′-cGAMP and 2′–5′-oligoadenylates (2′–5′ OA), which bind and activate STING and RNase L, respectively. Interestingly, the involvement of nucleotide second messengers to activate antiviral responses is evolutionary conserved, evidenced by the identification of an antiviral cGAMP-dependent pathway inDrosophila. Using a mass spectrometry approach, we identified several members of the ABCF family in human, mouse, andDrosophilacell lysates as 2′–5′ OA binding proteins, suggesting an evolutionary conserved function. Biochemical characterization of these interactions demonstrates high-affinity binding of 2′–5′ OA to ABCF1, which depended on phosphorylated 2′–5′ OA and an intact Walker A/B motif of the ABC cassette of ABCF1. As further support for species-specific interactions with 2′–5′ OA, we additionally identified that the metabolism enzyme Decr1 from mouse, but not human orDrosophilacells forms a high-affinity complex with 2′–5′ OA. A 1.4 Å co-crystal structure of the mouse Decr1–2′–5′ OA complex explains high-affinity recognition of 2′–5′ OA and the mechanism of species-specificity. Despite clear evidence of physical interactions, we could not identify profound antiviral functions of ABCF1, ABCF3 or Decr1 or 2′–5′ OA-dependent regulation of cellular translation rates as suggested by the engagement of ABCF proteins. Thus, although the biological consequences of the here identified interactions need to be identified, our data suggests that 2′–5′ OA can serve as signaling hub to distribute a signal to different recipient proteins.
Comparative genomics ofMycoplasma feriruminatoris, a fast-growing pathogen of wildCaprinae
Authors: Baby Vincent , Ambroset Chloé , Gaurivaud Patrice , Falquet Laurent , Boury Christophe , Guichoux Erwan , Jores Joerg , Lartigue Carole , Tardy Florence , Sirand-Pugnet Pascal
Published: March 2023

Mycoplasma feriruminatorisis a fast-growingMycoplasmaspecies isolated from wildCaprinaeand first described in 2013.M. feriruminatorisisolates have been associated with arthritis, keratoconjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017. The average chromosome size of theM. feriruminatorisstrains was 1,040 ± 0,024 kbp, with 24% G+C and 852 ± 31 CDS. The core genome and pan-genome of theM. feriruminatorisspecies contained 628 and 1,312 protein families, respectively. TheM. feriruminatorisstrains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from theM. mycoidescluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan.M. feriruminatorisgenomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyzes confirmed thatM. feriruminatoriswas closer to theM. mycoidescluster than to the ruminant speciesM. yeatsiiandM. putrefaciens. Ancestral genome reconstruction showed that the emergence of theM. feriruminatorisspecies was associated with the gain of 17 gene families, some of which encode defense enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that theM. mycoidescluster could be extended to includeM. feriruminatoris. We also find evidence that the specific organization and structure of the DnaA boxes around theoriCofM. feriruminatorismay contribute to drive the remarkable fast growth of this minimal bacterium.
Partial genome characterization of a novel potentially zoonotic parapoxvirus in a horse, Finland
Authors: Virtanen Jenni , Hautaniemi Maria , Dutra Lara , Plyusnin Ilya , Hautala Katja , Smura Teemu , Vapalahti Olli , Sironen Tarja , Kant Ravi , Kinnunen Paula M.
Published: March 2023

We report a sequencing protocol and 121 kb poxvirus sequence from a clinical sample of a horse with dermatitis. Based on phylogenetic analyses, the virus is a novel parapoxvirus. We show association with recent epidemic, and previous data suggest zoonotic potential. Further characterization and development of diagnostic protocols are necessary.
Whole-body Microbiota of Newborn Calves and Their Response to Prenatal Vitamin and Mineral Supplementation
Authors: Luecke Sarah M. , Holman Devin B. , Schmidt Kaycie N. , Gzyl Katherine E. , Hurlbert Jennifer L. , Menezes Ana Clara B. , Bochantin Kerri A. , Kirsch James D. , Baumgaertner Friederike , Sedivec Kevin K. , Swanson Kendall C. , Dahlen Carl R. , Amat Samat
Published: March 2023

Here, we investigated whether initial microbial colonization at seven different anatomical locations in newborn calves and their blood cytokines are influenced by prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of beef calves that were born from dams that received diets with or without VTM supplementation throughout gestation (n=7/group). Calves were separated from their dams immediately after birth and fed colostrum and milk replacer until euthanasia at 30 h post-initial colostrum feeding. The microbiota of all samples was assessed using 16S rRNA gene sequencing and qPCR. 15 cytokines and chemokines were quantified in their serum. The hoof, ocular, liver, respiratory, and reproductive sites of newborn calves were colonized by site-specific microbiota that differed from that of the rumen (0.64 ≥ R2≥ 0.12,P≤ 0.003). Only the ruminal fluid microbiota was differed by on prenatal VTM supplementation (P<0.01 Differences (P<0.05) were detected in microbial richness (vagina), diversity (ruminal tissue and fluid, eye), composition at the phylum and genus level (ruminal tissue and fluid, and vagina), and total bacterial abundance (ocular and vagina) between VTM and control calves. The cytokine IP-10 was higher (P=0.02) in VTM calves. Overall, our results suggest that despite immediate separation from the dam upon birth, whole-body of 32-h old calves are colonized by relatively rich, diverse and site-specific bacterial communities, and that initial microbial colonization of the rumen, vagina and oculus seem to be influenced by the prenatal VTM supplementation.

IMPORTANCE

Increased appreciation of maternal nutrition and microbiome’s involvement in developmental programming and evidence supportingin uteromicrobial colonization highlight that maternal nutrition factors could impact offspring microbial colonization. Here, we investigated whether initial microbial colonization in any of 7 different anatomical sites of newborn calves was influenced by maternal vitamin and mineral (VTM) supplementation. We identified changes in ruminal, vaginal, and ocular microbiota in newborn calves in response to prenatal VTM supplementation. We provided a “holistic” view on the whole-body calf microbiota. Our data was obtained from calves of the same sex and age, and who were immediately separated from dams, and hence provides novel insights on taxonomic composition of initial bacterial microbiota colonization in those anatomical sites examined. Combined, this study provides direction for future work targeting the manipulation of early life microbiome via alteration of maternal nutrition and harnessing early life microbiota for improved cattle health and production.
Resistance to host antimicrobial peptides mediates resilience of gut commensals during infection and aging inDrosophila
Authors: Arias-Rojas Aranzazu , Frahm Dagmar , Hurwitz Robert , Brinkmann Volker , Iatsenko Igor
Published: March 2023

Resilience to short-term perturbations, like inflammation, is a fundamental feature of microbiota, yet the underlying mechanisms of microbiota resilience are incompletely understood. Here we show thatLactiplantibacillus plantarum, a majorDrosophilacommensal, stably colonizes the fruit fly gut during infection and is resistant toDrosophilaantimicrobial peptides (AMPs). By transposon screening, we identifiedL. plantarummutants sensitive to AMPs. These mutants were impaired in peptidoglycan O-acetylation or teichoic acid D-alanylation, resulting in increased negative cell surface charge and higher affinity to cationic AMPs. AMP-sensitive mutants were cleared from the gut after infection and aging-induced gut inflammation in wild-type, but not in AMP-deficient flies, suggesting that resistance to host AMPs is essential for commensal resilience in an inflamed gut environment. Thus, our work reveals that in addition to the host immune tolerance to the microbiota, commensal-encoded resilience mechanisms are necessary to maintain the stable association between host and microbiota during inflammation.
ODF2 negatively regulates CP110 levels at centrioles/basal bodies to control biogenesis of primary cilia
Authors: Otto Madeline , Hoyer-Fender Sigrid
Published: March 2023

Primary cilia are essential sensory organelles that develop when an inhibitory cap consisting of CP110 and other proteins is eliminated. Degradation of CP110 by the ubiquitin-dependent proteasome pathway mediated by NEURL4 and HYLS1 removes the inhibitory cap. Here, we investigated the suitability of rapamycin-mediated dimerization for centriolar recruitment and asked whether the induced recruitment of NEURL4 or HYLS1 to the centriole promotes primary cilia development and CP110 degradation. We used rapamycin-mediated dimerization with ODF2 to induce their targeted recruitment to the centriole. We found decreased CP110 levels in transfected cells, but independent of rapamycin-mediated dimerization. By knocking down ODF2, we show that ODF2 controls CP110 levels. Overexpression of ODF2 is not sufficient to promote the formation of primary cilia, but overexpression of NEURL4 or HYLS1 is. Co-expression of ODF2 and HYLS1 resulted in the formation of tube-like structures, indicating an interaction. Thus, ODF2 controls primary cilia formation by negatively regulating the concentration of CP110 levels. Our data suggest that ODF2 most likely acts as a scaffold for the binding of proteins such as NEURL4 or HYLS1 to mediate CP110 degradation.

NEURL4 and HYLS1 mediate the degradation of CP110 to allow cilium formation. We used rapamycin-mediated dimerization with ODF2 to recruit NEURL4 and HYLS1 to the centriole and show that ODF2 controls CP110 levels.
Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites
Authors: Delgado-Tejedor Anna , Medina Rebeca , Begik Oguzhan , Cozzuto Luca , Ponomarenko Julia , Novoa Eva Maria
Published: March 2023

The biological relevance and dynamics of mRNA modifications have been extensively studied in the past few years, revealing their key roles in major cellular processes, such as cellular differentiation or sex determination. However, whether rRNA modifications are dynamically regulated, and under which conditions, remains largely unclear. Here, we performed a systematic characterization of bacterial rRNA modification dynamics upon exposure to diverse antibiotics using native RNA nanopore sequencing. To identify significant rRNA modification changes, we developedNanoConsensus, a novel pipeline that integrates the estimates from multiple RNA modification detection algorithms, predicting differentially modified rRNA sites with very low false positive rates and high replicability. We showed thatNanoConsensusis robust across RNA modification types, stoichiometries and coverage, and outperforms all individual algorithms tested. Using this approach, we identified multiple rRNA modifications that are lost upon the presence of antibiotics, showing that rRNA modification profiles are altered in an antibiotic-specific manner. We found that significantly altered rRNA modified sites upon antibiotic exposure are located in the vicinity of the A and P-sites of the ribosome, possibly contributing to antibiotic resistance. We then systematically examined whether loss of ‘antibiotic-sensitive’ rRNA modifications may be sufficient to confer antibiotic resistance, finding that depletion of some rRNA modification enzymes guiding dysregulated rRNA modifications confers increased antibiotic resistance. Altogether, our work reveals that rRNA modification profiles can be rapidly altered in response to environmental exposures, and that nanopore sequencing can accurately identify dysregulated rRNA modifications, contributing to the mechanistic dissection of antibiotic resistance. Moreover, we provide a novel, robust workflow to study rRNA modification dynamics in any species using nanopore sequencing in a scalable and reproducible manner.
Effects of alertness on perceptual detection and discrimination
Authors: Xu Yanzhi , Wokke Martijn , Noreika Valdas , Bareham Corinne , Jagannathan Sridhar , Georgieva Stanimira , Trentin Caterina , Bekinschtein Tristan
Published: March 2023

The level of alertness fluctuates throughout the day, exerting modulatory effects on human cognitive processes at any moment. However, our knowledge of how alertness level interacts with specific cognitive demands and perceptual rules of the task is still limited. Here we use perceptual decision-making paradigms to understand how alertness modulates the detection of a stimulus and the capacity to discriminate one stimulus from another. We analyzed data from four different experiments (113 participants in total): 1 - auditory masking detection; 2 - sensorimotor detection; 3 - auditory spatial discrimination; and 4 - auditory phoneme discrimination, and examined the performance of participants during the natural transition from awake (high alertness) to drowsy (low alertness). First, we fitted psychometric functions to the hit rates across different conditions of difficulty for EEG-defined high and low alertness metastable states, respectively. Second, we performed modelling of slope and threshold for the fitted curves as well as signal detection theory measures of perceptual sensitivity (d’) and response bias (criterion). We found lower detection and discrimination sensitivity to stimuli as alertness level decreases, signalled by a shallower slope of the sigmoidal curve and a lower d’, while the threshold increases slightly and equivalently across experiments during lower alertness. There was no change in the criterion to make the decision during the transition. These results suggest that reduced alertness generally decreases the quality of perceptual decision-making. Zooming in, we observed that the decrease in sensitivity measured by slope was stronger for discrimination than for detection decisions, indicating that lower alertness impairs the precision of decisions in discriminating alternatives more than identifying the presence of a stimulus around the threshold. Taken together, these results suggest that alertness has a common effect on perceptual decision-making and differentially modulates detection and discrimination decisions.
Distinct Electrophysiological Signatures of Intentional and Unintentional Mind-Wandering Revealed by Low-Frequency EEG Markers
Authors: Martel Adrien , Bruno Nicolas , Robertson Ian H , Dockree Paul M , Sitt Jacobo D , Valero-Cabré Antoni
Published: March 2023

Mind-wandering is typically characterized by the common experience wherein attention veers off into thoughts unrelated to the task at hand. Recent research highlights the intentionality dimension of mind-wandering as a key predictor of adverse functional outcomes with intentional and unintentional task-unrelated thought (TUT) differentially linked to neural, behavioral, clinical, and functional correlates. We here aimed to elucidate the electrophysiological underpinnings of intentional and unintentional TUT by systematically examining the individual and collective discriminative power of a large set of EEG markers to distinguish between attentional states. Univariate and multivariate analyses were conducted on 54 predefined markers belonging to four conceptual families: ERP, spectral, information theory and connectivity measures, extracted from scalp EEG recordings prior to multidimensional reports of ongoing thought from participants performing a sustained attention task. We report here that on-task, intentional and unintentional TUT exhibit distinct electrophysiological signatures in the low frequency range. More specifically, increased features of the theta frequency range were found to be most discriminative between on-task and off-task states, while features within the alpha band were characteristic of intentional TUT when compared to unintentional TUT. This result is theoretically well aligned with contemporary accounts describing alpha activity as an index of internally oriented attention and a potential mechanism to shield internal processes from sensory input. Our study verifies the validity of the intentionality dimension of mind-wandering and represents a step forward towards real-time detection and mitigation of maladaptive mind-wandering.
ZCCHC17 modulates neuronal RNA splicing and supports cognitive resilience in Alzheimer’s disease
Authors: Bartosch Anne Marie W. , Youth Elliot H. H. , Hansen Shania , Kaufman Maria E. , Xiao Harrison , Koo So Yeon , Ashok Archana , Sivakumar Sharanya , Soni Rajesh K. , Dumitrescu Logan C. , Lam Tiffany G. , Ropri Ali S. , Lee Annie J. , Klein Hans-Ulrich , Vardarajan Badri N. , Bennett David A. , Young-Pearse Tracy L. , De Jager Philip L. , Hohman Timothy J. , Sproul Andrew A. , Teich Andrew F.
Published: March 2023

ZCCHC17 is a putative master regulator of synaptic gene dysfunction in Alzheimer’s Disease (AD), and ZCCHC17 protein declines early in AD brain tissue, before significant gliosis or neuronal loss. Here, we investigate the function of ZCCHC17 and its role in AD pathogenesis. Co-immunoprecipitation of ZCCHC17 followed by mass spectrometry analysis in human iPSC-derived neurons reveals that ZCCHC17’s binding partners are enriched for RNA splicing proteins. ZCCHC17 knockdown results in widespread RNA splicing changes that significantly overlap with splicing changes found in AD brain tissue, with synaptic genes commonly affected. ZCCHC17 expression correlates with cognitive resilience in AD patients, and we uncover an APOE4 dependent negative correlation of ZCCHC17 expression with tangle burden. Furthermore, a majority of ZCCHC17 interactors also co-IP with known tau interactors, and we find significant overlap between alternatively spliced genes in ZCCHC17 knockdown and tau overexpression neurons. These results demonstrate ZCCHC17’s role in neuronal RNA processing and its interaction with pathology and cognitive resilience in AD, and suggest that maintenance of ZCCHC17 function may be a therapeutic strategy for preserving cognitive function in the setting of AD pathology.

Significance

Abnormal RNA processing is an important component of AD pathophysiology. We show here that ZCCHC17, a previously identified putative master regulator of synaptic dysfunction in AD, plays a role in neuronal RNA processing, and illustrate that ZCCHC17 dysfunction is sufficient to explain some of the splicing abnormalities seen in AD brain tissue, including synaptic gene splicing abnormalities. Using data from human patients, we demonstrate that ZCCHC17 mRNA levels correlate with cognitive resilience in the setting of AD pathology. These results suggest that maintenance of ZCCHC17 function may be a therapeutic strategy for supporting cognitive function in AD patients, and motivate future work examining a possible role of abnormal RNA processing in AD-related cognitive decline.
Unrecognized Potent Activities of Colistin Against Clinically Importantmcr+ Enterobacteriaceae Revealed in Synergy with Host Immunity
Authors: Kumaraswamy Monika , Riestra Angelica , Flores Anabel , Uchiyama Satoshi , Dahesh Samira , Bondsäter Gunnar , Nilsson Victoria , Chang Melanie , Seo Hideya , Sakoulas George , Nizet Victor
Published: March 2023

Colistin (COL) is a cationic cyclic peptide that disrupts negatively-charged bacterial cell membranes and frequently serves as an antibiotic of last resort to combat multidrug-resistant Gram-negative bacterial infections. Emergence of the horizontally transferable plasmid-borne mobilized colistin resistance (mcr) determinant and its spread to Gram-negative strains harboring extended-spectrum β-lactamase and carbapenemase resistance genes threatens futility of our chemotherapeutic arsenal. COL is widely regarded to have zero activity againstmcr+patients based on standard antimicrobial susceptibility testing (AST) performed in enriched bacteriological growth media; consequently, the drug is withheld from patients withmcr+infections. However, these standard testing media poorly mimic in vivo physiology and omit host immune factors. Here we report previously unrecognized bactericidal activities of COL againstmcr-1+isolates ofEscherichia coli(EC),Klebsiella pneumoniae(KP), andSalmonella enterica(SE) in standard tissue culture media containing the physiological buffer bicarbonate. Moreover, COL promoted serum complement deposition on themcr-1+Gram-negative bacterial surface and synergized potently with active human serum in pathogen killing. At COL concentrations readily achievable with standard dosing, the peptide antibiotic killedmcr-1+EC, KP, and SE in freshly isolated human blood proved effective as monotherapy in a murine model ofmcr-1+EC bacteremia. Our results suggest that COL, currently ignored as a treatment option based on traditional AST, may in fact benefit patients withmcr-1+Gram negative infections based on evaluations performed in a more physiologic context. These concepts warrant careful consideration in the clinical microbiology laboratory and for future clinical investigation of their merits in high risk patients with limited therapeutic options.