bluuebunny/crossref_metadata_2025 huggingface dataset:
Anellovirus evolution during long-term chronic infection
Authors: Kaczorowska Joanna , Timmerman Anne L , Deijs Martin , Kinsella Cormac M , Bakker Margreet , van der Hoek Lia
Published: January 2023

Human anelloviruses (AVs) are extremely genetically diverse, are widespread in the human population, and cause chronic infections. However, the evolutionary dynamics of AVs within single hosts is currently unknown, and it is unclear whether these changes have an implication on the long-term persistence of AVs in the host. Here, we assessed the evolutionary dynamics of six AV lineages during 30 years of chronic infection at single host resolution. The total number of substitutions and the number of variable sites increased over time. However, not all substitutions reached population fixation, showing that AV lineages form heterogeneous swarms within the host. Most substitutions occurred within a hypervariable region (HVR) located between nucleotide positions 800 and 1,300 of ORF1, which is known to be located within the spike domain. Different regions of the ORF1 gene undergo either positive or negative selection pressure. Sites under strong diversifying selection pressure were detected in the HVR, while the majority of the sites under purifying selection were detected outside this region. The HVR may play the role of an immunological decoy that prevents antibodies from binding to more vulnerable parts of ORF1. Moreover, the frequent substitutions in this region may increase the chances of AV particles escaping immune recognition.
Development of a Real-Time PCR Assay for the Detection and Identification of Rubus Stunt Phytoplasma in Rubus spp.
Authors: Bennypaul Harvinder , Sanderson Daniel , Donaghy Peri , Abdullahi Ismail
Published: January 2023

Rubus stunt, caused by ‘Candidatus Phytoplasma rubi’ (Rubus stunt phytoplasma; RSP), is an economically important disease of Rubus. This disease occurs in wild and cultivated Rubus spp. in Europe but has not been reported from North America; however, its major leafhopper vector is well established in western Canada and the U.S.A. RSP has the potential to impact the cane-fruit industry by significantly compromising yields and impacting export potential for Rubus propagation material. To mitigate the risk of this disease entering or establishing, import and export testing of propagation material is a phytosanitary requirement in Canada, the U.S.A., and other countries regulating RSP. In the absence of a specific test for RSP, the current testing scheme involves the use of a generic test to screen for phytoplasmas followed by additional time-consuming procedures to confirm the phytoplasma species. In this study, a real-time PCR assay, targeting a 154-bp region of tuf gene, was developed for sensitive and specific detection of RSP in Rubus spp. The developed assay detected a minimum of five target copies, and no cross-reactivity was observed even with the ‘Ca. P. rubi’-related strain associated with blackberry witches’ broom, which differs from RSP only by a single nucleotide polymorphism in the target region. Repeatability of the developed assay was checked on two real-time PCR platforms with acceptable results. In conclusion, this real-time PCR assay provides a sensitive and specific detection of RSP for mitigating the introduction and spread of Rubus stunt disease in Rubus spp.
Modulation of Cerebral Function by Muscle Afferent Activity, with Reference to Intravenous Succinylcholine
Authors: Lanier William L.
Published: January 2023

Cerebral Function and Muscle Afferent Activity Following Intravenous Succinylcholine in Dogs Anesthetized with Halothane: The Effects of Pretreatment with a Defasciculating Dose of Pancuronium. By WL Lanier, PA Iaizzo, and JH Milde. Anesthesiology 1989; 71:87–95. Reprinted with permission.

By the mid-1980s, it was widely assumed that if the depolarizing muscle relaxant, succinylcholine, given IV, produced increases in intracranial pressure, it did so because fasciculations produced increases in intrathoracic and central venous pressures that were transferred to the brain; however, there was no direct evidence that this was true. In contrast, we explored the possibility that the succinylcholine effect on the brain was explained by the afferentation theory of cerebral arousal, which predicts that agents or maneuvers that stimulate muscle stretch receptors will tend to stimulate the brain. Our research in tracheally intubated, lightly anesthetized dogs discovered that IV succinylcholine (which does not cross the blood-brain barrier) produced a doubling of cerebral blood flow that lasted for 30 min and corresponded to activation of the electroencephalogram and increases in intracranial pressure. Later, in our Classic Paper, we were able to assess simultaneously cerebral physiology and afferent nerve traffic emanating from muscle stretch receptors (primarily muscle spindles). We affirmed that the cerebral arousal response to succinylcholine was indeed driven by muscle afferent traffic and was independent of fasciculations or increases in intrathoracic or central venous pressures. Later research in complementary models demonstrated that endogenous movement (e.g., coughing, hiccups) produced a cerebral response very similar to IV succinylcholine, apparently as a result of the same muscle afferent mechanisms, independent of intrathoracic and central venous pressures. Thus, the importance of afferentation theory as a driver of the cerebral state of arousal and cerebral physiology during anesthesia was affirmed.
The Middle Rectal Artery: Revisited Anatomy and Surgical Implications of a Neglected Blood Vessel
Authors: Heinze Tillmann , Fletcher Jordan , Miskovic Danilo , Stelzner Sigmar , Bayer Andreas , Wedel Thilo
Published: January 2023

BACKGROUND:

Although the middle rectal artery is a relevant anatomical landmark for rectal resection and lateral lymph node dissection, descriptions of this entity are highly divergent.

OBJECTIVE:

Dissection, visualization, morphometry, and 3-dimensional reconstruction of the middle rectal artery to facilitate its management in surgery.

DESIGN:

Macroscopic dissection, histologic study, morphometric measurements, and virtual modeling.

SETTING:

University laboratory of applied surgical anatomy.

PATIENTS:

This study includes formalin-fixed hemipelvis specimens (n=37) obtained from body donors (age, 67–97 y).

MAIN OUTCOME MEASURES:

The main outcome measures are photo documentation of origin, trajectory, diameter, and branching pattern; immunolabeling of lymphatics; and 3-dimensional reconstruction of the middle rectal artery.

RESULTS:

The middle rectal artery was present in 71.4% of body donors (21.4% bilateral, 50% unilateral), originated from the anterior division of the internal iliac artery, and branched either from the internal pudendal artery (45.5%), the inferior gluteal artery (22.7%), the gluteal-pudendal trunk (22.7%), or a trifurcation (9.1%). One to 3 branches of varying diameters (0.5–3.5 mm) entered the mesorectum from the ventrolateral (35.7%), lateral (42.9%), or dorsolateral (21.4%) aspect. The middle rectal artery was accompanied by podoplanin-immunoreactive lymphatic vessels and gave off additional branches (81.8%) to the urogenital pelvic organs. Three-dimensional reconstruction revealed the complex course of the middle rectal artery from the pelvic sidewall through the pelvic nerve plexus and parietal pelvic fascia into the mesorectum.

LIMITATIONS:

Findings retrieved from body donors may be prone to age- and fixation-related processes.

CONCLUSIONS:

The investigation disclosed the rather high prevalence of the middle rectal artery, its 3-dimensional topographic anatomy, and its proximity to the autonomic pelvic nerves. These features play a role in the surgical management of this blood vessel. The data provide the anatomical rationale for the lateral lymphatic spread of rectal cancer and an anatomical basis for nerve-preserving lateral lymph node dissection.
Review of the role of bone-SPECT/CT in tarsal coalitions
Authors: van der Bruggen Wouter , de Geus-Oei Lioe-Fee , Bosmans Bas , Slart Riemer H.J.A. , Lima Thiago V.M. , Bhure Ujwal , Vriens Dennis , Strobel Klaus
Published: January 2023

Tarsal coalition (TC) is a congenital abnormal connection (fibrous, cartilaginous, or osseous) between two or more bones in the hind and midfoot, mostly consisting of calcaneonavicular or talocalcaneal coalition, and is often asymptomatic. However, TCs may result in foot motion limitation and pain with or without flatfoot (pes planus), arising in adolescents and young adults. Appropriate imaging is needed to pinpoint foot pain in the (suspected) TC, starting with plain radiographs. Still, normal radiographs do not exclude TCs. Computed tomography (CT) and MRI are frequently used advanced imaging techniques. CT alone has known limited sensitivity in cartilaginous and fibrous TCs and correlation between CT abnormalities and pain may be challenging, as solely anatomical changes in TCs are often asymptomatic. MRI can depict soft tissue abnormalities in TC with high accuracy. Nonetheless, after the implantation of metallic osteosynthesis material, MRI is often limited due to image distortion, signal loss, and misregistration. Bone scintigraphy with [99mTc]Tc-diphosphonate single photon emission computed tomography/CT (bone-SPECT/CT) is a known sensitive tool to detect osteoblastic bone pathology. However, the literature concerning bone-SPECT/CT in TC patients is limited. This article reviews bone-SPECT/CT patterns in TCs, how it complements other imaging techniques and their relation to clinical complaints. Bone-SPECT/CT excels in accurate bone pathology characterization in TC, confidently excluding synchronous lesions elsewhere, and offering optimal insight into osseous structures and 3D-localization of bone metabolism for surgery planning. Furthermore, even with implanted osteosynthesis material, bone-SPECT/CT can pinpoint the culprit pain generator, where MRI is either contra-indicated or considerably hampered.
Topographic de-adhesion in the viscoelastic limit
Authors: Nguyen Nhung , Hamm Hahn Eugenio , Velankar Sachin , Cerda Enrique , Pocivavsek Luka
Published: January 2023

The superiority of many natural surfaces at resisting soft, sticky biofoulants have inspired the integration of dynamic topography with mechanical instability to promote self-cleaning artificial surfaces. The physics behind this novel mechanism is currently limited to elastic biofoulants where surface energy, bending stiffness and topographical wavelength are key factors. However, the viscoelastic nature of many biofoulants causes a complex interplay between these factors with time-dependent characteristics such as material softening and loading rate. Here, we enrich the current elastic theory of topographic de-adhesion using analytical and finite-element models to elucidate the nonlinear, time-dependent interaction of three physical, dimensionless parameters: biofoulant’s stiffness reduction, the product of relaxation time and loading rate, and the critical strain for short-term elastic de-adhesion. Theoretical predictions, in good agreement with numerical simulations, provide insight into tuning these control parameters to optimize surface renewal via topographic de-adhesion in the viscoelastic regime.
Adaptation of prokaryotic toxins for negative selection and cloning-independent markerless mutagenesis (CIMM) inStreptococcusspecies
Authors: Li Lena , Qin Hua , Zou Zhengzhong , Kreth Jens , Merritt Justin
Published: January 2023

TheStreptococcus mutansgenetic system offers a variety of strategies to rapidly engineer targeted chromosomal mutations. Previously, we reported the firstS. mutansnegative selection system that functions in a wild-type background. This system utilizes induced sensitivity to the toxic amino acid analogp-chlorophenylalanine (4-CP) as a negative selection mechanism, and was developed for counterselection-based cloning-independent markerless mutagenesis (CIMM). While we have employed this system extensively for our ongoing genetic studies, we have encountered a couple limitations with the system, mainly its narrow host range and the requirement for selection on a toxic substrate. Here, we report the development of a new negative selection system that addresses both limitations, while still retaining the utility of the previous 4-CP-based markerless mutagenesis system. We placed a variety of toxin-encoding genes under the control of the xylose-inducible Xyl-S expression cassette and found the Fst-sm and ParE toxins to be suitable candidates for inducible negative selection. We combined the inducible toxins with an antibiotic resistance gene to create several different counterselection cassettes. The most broadly useful of these contained a wild-typefst-smopen reading frame transcriptionally fused to a point mutant form of the Xyl-S expression system, which we subsequently named as IFDC4. IFDC4 was shown to exhibit exceptionally low background resistance, with 3 – 4 log reductions in cell number observed when plating on xylose-supplemented media. IFDC4 also functioned similarly in multiple strains ofS. mutansas well as withS. gordoniiandS. sanguinis. We performed CIMM with IFDC4 and successfully engineered a variety of different types of markerless mutations in all three species. The counterselection strategy described here provides a template approach that should be adaptable for the creation of similar counterselection systems in many other bacteria.
Modelling the Longitudinal Dynamics of Paranoia in Psychosis: A Temporal Network Analysis Over 20 Years
Authors: Barnby J.M. , Haslbeck J.M.B. , Sharma R. , Rosen C. , Harrow M.
Published: January 2023

Paranoia is a highly debilitating, core element of psychosis, although is poorly managed. Theories of paranoia mostly interface with short-scale or cross-sectional data models, leaving the longitudinal course of paranoia underspecified. Here, we develop an empirical characterisation of two aspects of paranoia - persecutory and referential delusions - in individuals with psychosis over 20 years. We examine delusional dynamics by applying a Graphical Vector Autoregression Model to data collected from the Chicago Follow-up Study (n=135 with a range of psychosis-spectrum diagnoses). We adjusted for age, sex, IQ, and antipsychotic use. We found that referential and persecutory delusions are central themes, supported by other primary delusions, and are strongly autoregressive – the presence of referential and persecutory delusions is predictive of their future occurrence. In a second analysis we demonstrate that social factors influence the severity of referential, but not persecutory, delusions. We suggest that persecutory delusions represent central, resistant states in the cognitive landscape, whereas referential beliefs are more flexible, offering an important window of opportunity for intervention. Our data models can be collated with prior biological, computational, and social work to contribute toward a more complete theory of paranoia and provide more time-dependent evidence for optimal treatment targets.

Graphical Abstract

Highlights

Persecutory and referential delusions are central themes amongst primary delusions in chronic psychosis.

Persecutory and referential delusions share a recursive relationship and are both strongly and positively autoregressive.

Greater number and quality of friends reduce referential, but not persecutory, delusions.

Our formal data model can be used as a test bed and framework for clinical intervention.
Hepatitis B virus infection status and associated factors among health care workers in selected hospitals in Kisumu County, Kenya: a cross-sectional study
Authors: Mboya Frankline Otieno , Daud Ibrahim I. , Ondondo Raphael , Onguru Daniel
Published: January 2023

Background

Poorly managed medical waste produced at the health facilities are potential source of infections including occupational exposure to Hepatitis B Virus (HBV). This study evaluated the prevalence of HBV infection among healthcare workers (HCW) in Kisumu County.

Methods

We determined the prevalence of HBV infections among 192 HCW from nine purposively selected high volume public hospitals in Kisumu County. A structured questionnaire was administered, and 4.0 ml of venous blood sample collected for Hepatitis B surface antigen (HBsAg), hepatitis B surface antibody (anti-HBs) and total hepatitis B core antibody (anti-HBc) testing using enzyme immunoassay (EIA).

Results

Of the 192 HCW sampled, 52.1% were males and 78.7% are married, the median participants age was 34.4 years with interquartile range (IQR) of 11 years. Most participants had between 1-5 years of service while 43.8% had ≥2 doses of HBV vaccine.

The respective prevalence of HBsAg, anti HBs and anti HBc was 18.8% (95% CI: 13.5-25.0%), 63.0% (95% CI: 55.8-69.9%) and 44.8% (95% CI: 37.6-52.1%). Higher proportion of HBV positive was found in HCW who had worked for less than one year and who had not received any dose of HBV vaccine at 37.5% and 35.9 % respectively.. Significant risk of HBV lifetime exposure was noted among HCW with one vaccine dose, those with no known exposure and highest in those with knowledge on HBV transmission (aOR, 7.97; 95% CI, 2.10-153.3, p-value=0.008). HCW who had received ≥2 doses of HBV vaccine (aOR, 0.03; 95% CI, 0.01-0.10, p-value= <0.0001) had significant HBV protection. Duration of service was not associated with HBV among HCW.

Conclusion

Prevalence of HBV infection was high among HCW in Kisumu County. Ministry of health Kenya should strengthen comprehensive infection prevention and control practices to reduce lifetime exposure to HBV infection among HCW.
Predicting Ward Transfer Mortality with Machine Learning
Authors: Lezama Jose L. , Alterovitz Gil , Jakey Colleen E. , Kraus Ana L. , Kim Michael J. , Borkowski Andrew A.
Published: January 2023

Background

Predicting mortality and morbidity amongst hospitalized patients has long been a struggle for inpatient Internal Medicine physicians. To prevent physician burnout, hospital organizations are turning to shift work for the care of hospitalized patients. Such shift work frequently leads to a handoff of patients, with many physicians often being the sole provider in the hospital for close to one hundred patients.

Objectives

We propose developing an artificial intelligence model that helps predict which patients will be most at risk of increased mortality. This model would assist providers and frontline staff in focusing their efforts on improving patient outcomes.

Materials and Methods

Records of patients who were transferred from non-intensive care units to intensive care units were queried from the Veteran Affairs Corporate Data Warehouse (CDW). Two thousand four hundred twenty-five records were identified. The patient outcome was designated a dependent variable, with bad outcome defined as the patient dying within 30 days of admission and good outcome as the patient being alive within 30 days of admission. Using twenty-two independent variables, we trained sixteen machine learning models, of which six best-performing ones were fine-tuned and evaluated on the testing dataset. Finally, we repeated this process with twenty independent variables, omitting the Length of Stay and Days to Intensive Care Unit Transfer variables which are unknown at the time of admission.

Results

The best results were obtained with the LightGBM model with both datasets, one that included Length of Stay and Days to Intensive Care Unit Transfer variables and the other without these two variables. The former achieved Receiver Operating Characteristics Curve - Area Under the Curve (ROC-AUC) of 0.89, an accuracy of 0.72, a sensitivity of 0.97, and a specificity of 0.68, while the latter achieved a ROC-AUC of 0.86, an accuracy of 0.71, sensitivity of 0.94 and specificity of 0.67 respectively.

Conclusions

Our predictive mortality model may offer providers a means for optimizing the utilization of resources when managing a large caseload, especially with shift changes.
Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network
Authors: Ravan Aniket , Feng Ruopei , Gruebele Martin , Chemla Yann R.
Published: January 2023

Quantitative ethology requires an accurate estimation of an organism’s postural dynamics in three dimensions plus time. Technological progress over the last decade has made animal pose estimation in challenging scenarios possible with unprecedented detail. Here, we present (i) a fast automated method to record and track the pose of individual larval zebrafish in a 3-D environment, applicable when accurate human labeling is not possible; (ii) a rich annotated dataset of 3-D larval poses for ethologists and the general zebrafish and machine learning community; and (iii) a technique to generate realistic, annotated larval images in novel behavioral contexts. Using a three-camera system calibrated with refraction correction, we record diverse larval swims under free swimming conditions and in response to acoustic and optical stimuli. We then employ a convolutional neural network to estimate 3-D larval poses from video images. The network is trained against a set of synthetic larval images rendered using a 3-D physical model of larvae. This 3-D model samples from a distribution of realistic larval poses that we estimate a priori using a template-based pose estimation of a small number of swim bouts. Our network model, trained without any human annotation, performs larval pose estimation with much higher speed and comparable accuracy to the template-based approach, capturing detailed kinematics of 3-D larval swims.

Author Summary

Larval zebrafish swimming has been studied extensively in 2-D environments, which are restrictive compared to natural 3-D habitats. To enable rapid capture of 3-D poses, we collect three orthogonal video projections of swim behaviors in several behavioral settings and fit poses to a physical model. We then use the physical model to generate an auto-annotated stream of synthetic poses to train a convolutional neural network. The network model performs highly accurate pose predictions on over 600 real swim bouts much faster than a physical model fit. Our results show that larvae frequently exhibit motions inaccessible in a 2-D setup. The annotated dataset could be used by ethologists studying larval swimming dynamics, and by the machine learning community interested in multi-dimensional time series and 3-D reconstruction. Using the ability to render images with multiple synthetic poses, our method can be extended to collective behavior.
DNA methylation signature inNSD2loss-of-function variants appeared similar to that in Wolf-Hirschhorn syndrome
Authors: Kawai Tomoko , Kinoshita Shiori , Takayama Yuka , Onishi Eriko , Kamura Hiromi , Kojima Kazuaki , Kikuchi Hiroki , Terao Miho , Sugawara Tohru , Migita Ohsuke , Kagami Masayo , Isojima Tsuyoshi , Yamaguchi Yu , Wakui Keiko , Ohashi Hirofumi , Shimizu Kenji , Mizuno Seiji , Okamoto Nobuhiko , Fukushima Yoshimitsu , Takada Fumio , Kosaki Kenjiro , Takada Shuji , Akutsu Hidenori , Ura Kiyoe , Nakabayashi Kazuhiko , Hata Kenichiro
Published: January 2023

Purpose

Wolf-Hirschhorn syndrome (WHS), a contiguous gene syndrome caused by the hemizygous deletion of the distal short arm of chromosome 4 whereNSD2is, reportedly exhibits specific DNA methylation signatures in peripheral blood cells. However, responsible genomic loci for signatures are unreported. The objective of the study is to define the loci of WHS-related DNA methylation signatures and to explore the role ofNSD2for the signatures.

Methods

We conducted genome-wide methylation analysis of individuals with WHS orNSD2variants using array. We studied genome-edited knock in mice or induced pluripotent stem cells to explore the function ofNSD2variants which are observed in congenital anomaly cases.

Results

Three undiagnosed cases withNSD2variants showed WHS-related DNA methylation signatures. These variants were validated to beNSD2loss-of-function in induced pluripotent stem cells or genome-edited knock-in mice. p.Pro905Leu variant decreased Nsd2 protein levels, and changed Histone H3-Lysine 36 demethylation levels in similar way in the same genomic regions asNsd2knock out mice regulated.Nsd2knock out mice exhibited common DNA methylation changes.

Conclusion

These results revealed that WHS-related DNA methylation signatures are dependent onNSD2dysfunction and are useful in diagnosingNSD2variants of unknown significance.
APOE4, Age & Sex Regulate Respiratory Plasticity Elicited By Acute Intermittent Hypercapnic-Hypoxia
Authors: Nair Jayakrishnan , Welch Joseph F. , Marciante Alexandria B. , Hou Tingting , Lu Qing , Fox Emily J. , Mitchell Gordon S.
Published: January 2023

Rationale

Acute intermittent hypoxia (AIH) is a promising strategy to induce functional motor recovery following chronic spinal cord injuries and neurodegenerative diseases. Although significant results are obtained, human AIH trials report considerable inter-individual response variability.

Objectives

Identify individual factors (e.g., genetics, age, and sex) that determine response magnitude of healthy adults to an optimized AIH protocol, acute intermittent hypercapnic-hypoxia (AIHH).

Methods

Associations of individual factors with the magnitude of AIHH (15, 1-min O2=9.5%, CO2=5% episodes) induced changes in diaphragm motor-evoked potential amplitude (MEP) and inspiratory mouth occlusion pressures (P0.1) were evaluated in 17 healthy individuals (age=27±5 years) compared to Sham. Single nucleotide polymorphisms (SNPs) in genes linked with mechanisms of AIH induced phrenic motor plasticity (BDNF, HTR2A, TPH2, MAOA, NTRK2) and neuronal plasticity (apolipoprotein E,APOE) were tested. Variations in AIHH induced plasticity with age and sex were also analyzed. Additional experiments in humanized (h)ApoEknock-in rats were performed to test causality.

Results

AIHH-induced changes in diaphragm MEP amplitudes were lower in individuals heterozygous forAPOE4(i.e., APOE3/4) alleleversusotherAPOEgenotypes (p=0.048). No significant differences were observed between any other SNPs investigated, notablyBDNFval/met(all p>0.05). Males exhibited a greater diaphragm MEP enhancementversusfemales, regardless of age (p=0.004). Age was inversely related with change in P0.1within the limited age range studied (p=0.007). InhApoE4knock-in rats, AIHH-induced phrenic motor plasticity was significantly lower than hApoE3controls (p<0.05).

Conclusions

APOE4genotype, sex and age are important biological determinants of AIHH-induced respiratory motor plasticity in healthy adults.

ADDITION TO KNOWLEDGE BASE

Acute intermittent hypoxia (AIH) is a novel rehabilitation strategy to induce functional recovery of respiratory and non-respiratory motor systems in people with chronic spinal cord injury and/or neurodegenerative diseases. Since most AIH trials report considerable inter-individual variability in AIH outcomes, we investigated factors that potentially undermine the response to an optimized AIH protocol, acute intermittent hypercapnic-hypoxia (AIHH), in healthy humans. We demonstrate that genetics (particularly the lipid transporter,APOE), age and sex are important biological determinants of AIHH-induced respiratory motor plasticity.
Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors
Authors: Derbyshire Mark C. , Raffaele Sylvain
Published: January 2023

Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates at the subphylum level. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.
High Throughput Single Cell Proteomic Analysis of Organ Derived Heterogeneous Cell Populations by Nanoflow Dual Trap Single Column Liquid Chromatography
Authors: Kreimer Simion , Binek Aleksandra , Chazarin Blandine , Cho Jae Hyung , Haghani Ali , Hutton Alexandre , Marbán Eduardo , Mastali Mitra , Meyer Jesse G , Mesquita Thassio , Song Yang , Van Eyk Jennifer , Parker Sarah
Published: January 2023

Identification and proteomic characterization of rare cell types within complex organ derived cell mixtures is best accomplished by label-free quantitative mass spectrometry. High throughput is required to rapidly survey hundreds to thousands of individual cells to adequately represent rare populations. Here we present parallelized nanoflow dual-trap single-column liquid chromatography (nanoDTSC) operating at 15 minutes of total run time per cell with peptides quantified over 11.5 minutes using standard commercial components, thus offering an accessible and efficient LC solution to analyze 96 single-cells per day. At this throughput, nanoDTSC quantified over 1,000 proteins in individual cardiomyocytes and heterogenous populations of single cells from aorta.

For Table of Contents Only
Metabolite T1relaxation times differ across the adult lifespan
Authors: Murali-Manohar Saipavitra , Gudmundson Aaron T. , Hupfeld Kathleen E. , Zöllner Helge J. , Hui Steve C.N. , Song Yulu , Davies-Jenkins Christopher W. , Gong Tao , Wang Guangbin , Oeltzschner Georg , Edden Richard A.E.
Published: January 2023

Purpose

To investigate the age-dependence of metaboliteT1relaxation times at 3T in both gray- and white-matter-rich voxels.

Methods

This manuscript analyzes publicly available metabolite and metabolite-nulled (single inversion recovery TI = 600 ms) spectra acquired at 3T using PRESS localization. Voxels were placed in posterior cingulate cortex and centrum semiovale in 102 healthy volunteers across 5 decades of life (20s to 60s). All spectra were analyzed in Osprey v2.4.0. To estimateT1relaxation times for tNAA2.0and tCr3.0, the ratio of modeled metabolite residual amplitudes in the metabolite-nulled spectrum to the full metabolite signal was calculated using the single inversion recovery signal equation. Correlations betweenT1and subject age were evaluated.

Results

Spearman correlations revealed that estimated T1relaxation times of tNAA2.0(rs= −0.43; p < 0.001) and tCr3.0(rs= −0.23; p = 0.021) decreased significantly with age in white-matter-rich CSO, and less steeply (and not significantly) for tNAA2.0(rs= −0.15; p = 0.136) and tCr3.0(rs= −0.10; p = 0.319) in gray-matter-rich PCC.

Conclusion

The analysis harnessed a large publicly available cross-sectional dataset to test an important hypothesis, that metabolite T1relaxation times change with age. This preliminary study stresses the importance of further work to measure age-normed metabolite T1relaxation times for accurate quantification of metabolite levels in studies of aging.
Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis
Authors: Alexanian Michael , Padmanabhan Arun , Nishino Tomohiro , Travers Joshua G. , Ye Lin , Lee Clara Youngna , Sadagopan Nandhini , Huang Yu , Pelonero Angelo , Auclair Kirsten , Zhu Ada , Gonzalez Teran Barbara , Flanigan Will , Kim Charis Kee-Seon , Lumbao-Conradson Koya , Costa Mauro , Jain Rajan , Charo Israel , Haldar Saptarsi M. , Pollard Katherine S. , Vagnozzi Ronald J. , McKinsey Timothy A. , Przytycki Pawel F. , Srivastava Deepak
Published: January 2023

Chronic inflammation and tissue fibrosis are common stress responses that worsen organ function, yet the molecular mechanisms governing their crosstalk are poorly understood. In diseased organs, stress-induced changes in gene expression fuel maladaptive cell state transitions and pathological interaction between diverse cellular compartments. Although chronic fibroblast activation worsens dysfunction of lung, liver, kidney, and heart, and exacerbates many cancers, the stress-sensing mechanisms initiating the transcriptional activation of fibroblasts are not well understood. Here, we show that conditional deletion of the transcription co-activatorBrd4inCx3cr1-positive myeloid cells ameliorates heart failure and is associated with a dramatic reduction in fibroblast activation. Analysis of single-cell chromatin accessibility and BRD4 occupancyin vivoinCx3cr1-positive cells identified a large enhancer proximal toInterleukin-1 beta (Il1b), and a series of CRISPR deletions revealed the precise stress-dependent regulatory element that controlled expression ofIl1bin disease. Secreted IL1B functioned non-cell autonomously to activate a p65/RELA-dependent enhancer near the transcription factorMEOX1, resulting in a profibrotic response in human cardiac fibroblasts.In vivo, antibody-mediated IL1B neutralization prevented stress-induced expression ofMEOX1, inhibited fibroblast activation, and improved cardiac function in heart failure. The elucidation of BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B provides new therapeutic strategies for heart disease and other disorders of chronic inflammation and maladaptive tissue remodeling.
A CheZ orthologue inCampylobacter jejuniplays a role in chemotaxis through conserved phosphatase activity
Authors: Jama Abdullahi S. , Ketley Julian M.
Published: January 2023

The major food-borne pathogenCampylobacter jejuniemploys chemotactic motility to colonise the avian gut, and also as a virulence mechanism in human diarrhoeal disease.

InEscherichia coliCheY activity is modulated by CheZ, a phosphatase originally thought to be absent inC. jejuni. The Hp0170 protein ofHelicobacter pyloriis a distant homologue of CheZ and, asC. jejuniCj0700 is homologous to HP0170, Cj0700 could also act as a CheZ orthologue inCampylobacter. Both theC. jejuniCheV and CheA proteins also contain a response regulator (RR) domain that may be phosphorylated. Cj0700 would therefore be predicted to dephosphorylateC. jejuniCheY and possibly also the CheV and CheA RR domains.

A mutant (Δcj0700)and complement (Δcj0700, cj0046::cj0700) were constructed inC.jejunistrains NCTC11168, NCTC11828 and 81-176. On semisolid agar the Δcj0700mutant strain showed reduced motility relative to wild-type and this phenotype was reversed in the complemented strain. In pull down and bacterial two hybrid assays, expressed Cj0700 was able to interact with CheY, CheA-RR and CheV.

Cj0700 is able to dephosphorylate the RR domain of CheY and CheA-RR, but less efficiently, CheV. These findings verify that Cj0700 plays a role inC. jejunichemotaxis through phosphatase activity with respect to CheY, and is hence likely to be a CheZ orthologue. Cj0700 also partially modulates the phosphorylation level of the RR domain on CheA and CheV, although the functional consequences of this interaction require further investigation.
HiDDEN: A machine learning label refinement method for detection of disease-relevant populations in case-control single-cell transcriptomics
Authors: Goeva Aleksandrina , Dolan Michael-John , Luu Judy , Garcia Eric , Boiarsky Rebecca , Gupta Rajat M , Macosko Evan
Published: January 2023

In case-control single-cell RNA-seq studies, sample-level labels are transferred onto individual cells, labeling all case cells as affected, but only a small fraction of them may actually be perturbed. Here, using simulations, we demonstrate that the standard approach to single cell analysis fails to isolate the subset of affected case cells and their markers when either the affected subset is small, or when the strength of the perturbation is mild. To address this fundamental limitation, we introduce HiDDEN, a computational method that refines the case-control labels to accurately reflect the perturbation status of each cell. We show HiDDEN’s superior ability to recover biological signals missed by the standard analysis workflow in simulated ground truth datasets of cell type mixtures. When applied to a dataset of human multiple myeloma precursor conditions, HiDDEN recapitulates the expert manual annotation and discovers malignancy in previously considered healthy early stage samples. When applied to a mouse model of demyelination, HiDDEN identifies an endothelial subpopulation playing a role in early stage blood-brain barrier dysfunction. We anticipate that HiDDEN should find a wide usage in contexts which require the detection of subtle changes in cell types across conditions.
An axon – T cell feedback loop enhances inflammation and axon degeneration
Authors: Liu Tingting , Wang Huanhuan , Kutsovsky Daniel Y. , Ohn Christine Y.J. , Patel Nandan , Yang Jing , Simon David J.
Published: January 2023

Inflammation is closely associated with many neurodegenerative disorders. Yet whether inflammation causes or exacerbates neurodegeneration has been challenging to define because the two processes are so closely linked. Here we disentangle inflammation from the axon damage it causes by individually blocking cytotoxic T cell function and axon degeneration. We model inflammatory damage in mouse skin, a barrier tissue that, despite frequent inflammation, must maintain proper functioning of a dense array of axon terminals. We show that sympathetic axons control skin inflammation through release of norepinephrine, which suppresses activation of gamma delta T cells via the β2 adrenergic receptor. Strong inflammatory stimulation in the form of the toll like receptor 7 (TLR7) agonist imiquimod (IMQ) causes progressive gamma delta T cell-mediated, Sarm-1-dependent loss of these immunosuppressive sympathetic axons, a positive feedback loop that removes a physiological brake on T cells, resulting in enhanced inflammation and inflammatory axon damage.
Leaf decomposing fungi influenceSaccharomyces paradoxusgrowth across carbon environments
Authors: El-Khatib Samer , Lambert Madeleine G. , Reed Meghan N. , Goncalves Melane Brito , Boynton Primrose J.
Published: January 2023

Saccharomyces paradoxusis a model organism in ecology and evolution. However, its metabolism in its native habitat remains mysterious: it is frequently found growing on leaf litter, a habitat with few carbon sources thatS. paradoxuscan metabolize. We hypothesized that leaf-decomposing fungi from the same habitat break down the cellulose in leaf litter extracellularly and release glucose, supportingS. paradoxusgrowth. We found that facilitation by leaf-decomposing fungi was possible on cellulose and inhibition was common on glucose, suggesting diverse interactions betweenS. paradoxusand other fungi that have the potential to supportS. paradoxusin nature.
C. elegansSMOC-1 interacts with both BMP and glypican to regulate BMP signaling
Authors: DeGroot Melisa S. , Williams Byron , Chang Timothy Y , Maas Gamboa Maria L. , Larus Isabel , Fromme J. Christopher , Liu Jun
Published: January 2023

ABSTRACTS

Secreted modular calcium binding (SMOC) proteins are conserved matricellular proteins found in organisms fromC. elegansto humans. SMOC homologs characteristically contain one or two extracellular calcium (EC) binding domain(s) and one or two thyroglobulin type-1 (TY) domain(s). SMOC proteins inDrosophilaand Xenopus have been found to interact with cell surface heparan sulfate protein glycans (HSPGs) to exert both positive and negative influences on the conserved bone morphogenetic protein (BMP) signaling pathway. In this study, we used a combination of biochemical, structural modeling, and molecular genetic approaches to dissect the functions of the sole SMOC protein inC. elegans. We showed that SMOC-1 binds LON-2/glypican, as well as the mature domain of DBL-1/BMP. Moreover, SMOC-1 can simultaneously bind LON-2/glypican and DBL-1/BMP. The interaction between SMOC-1 and LON-2/glypican is mediated by the EC domain of SMOC-1, while the interaction between SMOC-1 and DBL-1/BMP involves full-length SMOC-1. We further showed that while SMOC-1(EC) is sufficient to promote BMP signaling when overexpressed, both the EC and TY domains are required for SMOC-1 function at the endogenous locus. Finally, when overexpressed, SMOC-1 can promote BMP signaling in the absence of LON-2/glypican. Taken together, our findings led to a model where SMOC-1 functions both negatively in a LON-2-dependent manner and positively in a LON-2-independent manner to regulate BMP signaling. Our work provides a mechanistic basis for how the evolutionarily conserved SMOC proteins regulate BMP signaling.
Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking
Authors: Bartram Julian , Franke Felix , Kumar Sreedhar Saseendran , Buccino Alessio Paolo , Xue Xiaohan , Gänswein Tobias , Schröter Manuel , Kim Taehoon , Kasuba Krishna Chaitanya , Hierlemann Andreas
Published: January 2023

Self-sustained recurrent activity in cortical networks is thought to be important for multiple crucial processes, including circuit development and homeostasis. Yet, the precise relationship between synaptic input patterns and the spiking output of individual neurons remains largely unresolved. Here, we developed, validated and applied a novel in vitro experimental platform and analytical procedures that provide – for individual neurons – simultaneous excitatory and inhibitory synaptic activity estimates during recurrent network activity. Our approach combines whole-network high-density microelectrode array (HD-MEA) recordings from rat neuronal cultures with patch clamping and enables a comprehensive mapping and characterization of active incoming connections to single postsynaptic neurons. We found that, during network states with excitation(E)-inhibition(I) balance, postsynaptic spiking often coincided with the maxima of fast fluctuations in the input E/I ratio. These spike-associated E/I ratio escalations were largely due to a rapid bidirectional change in synaptic inhibition that was modulated by the network-activity level. Our approach also uncovered the underlying circuit architecture and we show that individual neurons received a few key inhibitory connections – often from special hub neurons – that were instrumental in controlling postsynaptic spiking. Balanced network theory predicts dynamical regimes governed by small and rapid input fluctuation and featuring a fast neuronal responsiveness. Our findings – obtained in self-organized neuronal cultures – suggest that the emergence of these favorable regimes and associated network architectures is an inherent property of cortical networks in general.
Identification and Characterization of novel long non-coding RNAs in vascular smooth cells
Authors: Solomon Charles U. , McVey David G. , Andreadi Catherine , Gong Peng , Turner Lanka , Khemiri Sonja , Chamberlain Julie C. , Webb Tom R. , Samani Nilesh J. , Ye Shu
Published: January 2023

A significant portion of the RNA produced from the human genome consists of long non-coding RNAs (lncRNAs). These molecules tend to have lower levels of expression, are more specific to certain tissues, and show greater variation in expression between individuals compared to protein-coding messenger RNAs (mRNAs). LncRNAs have been linked with regulatory roles in gene expression and genome architecture. There is growing evidence that lncRNAs play important roles in many biological processes and diseases, and a number of lncRNAs have been identified as potential therapeutic targets. Here, we report the identification and characterization of the lncRNA landscape of vascular smooth muscle cells (VSMC). We used an ensemble of bioinformatics tools to identify 329 novel lncRNAs from a large VSMC RNA-Seq dataset. We found that majority of the novel lncRNAs are natural antisense transcripts of protein-coding genes. In addition, we predicted cellular localization and potential miRNAs that targets the novel lncRNAs and found that most localize in the cytoplasm and that miRNA target site ranged from 2-889 sites on each novel lncRNA. Furthermore, we identified co-expressed lncRNAs that correlate with the proliferation, migration and apoptosis of vascular smooth muscle cells. These results suggest that we have identified a diverse set of previously unknown lncRNAs that may be involved in important regulatory pathways in vascular smooth muscle cells.
Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response
Authors: Sullivan Madsen , Williams Martin M. , Studer Anthony J.
Published: January 2023

Popcorn is an important crop in the United States; however, genetic analyses of popcorn are limited and tend to utilize relatively few markers that cannot capture the total genomic variation. To improve the genomic resources in popcorn, a panel of 362 popcorn accessions was evaluated using 417,218 single nucleotide polymorphisms generated using a genotyping-by-sequencing approach. Using this genomic data, a model-based clustering analysis identified two populations. The first comprised North American Yellow Pearl Popcorns and several accessions of the Chilean Curagua landrace. The second, the Pointed and Latin American Popcorns, included all remaining North American (pointed and early popcorns), Latin American, and global accessions. The two populations exhibited large differences in population structure and genetic diversity. The North American Yellow Pearl Popcorns constitute a highly inbred population with limited genetic diversity compared to the Pointed and Latin American Popcorns. Additionally, phenotypic differences between the two populations were observed in kernel color and nicosulfuron sensitivity. A filtered set of SNPs was curated and used for genome-wide association studies and popcorn-specific candidate genes for nicosulfuron tolerance were identified. The genomic characterization described here can be used by breeding programs to accelerate the rate of genetic gain and incorporate genetic diversity into elite popcorn germplasm.

Core Ideas

North American Popcorn is composed of two distinct populations that differ genetically and phenotypically.

North American Yellow Pearl Popcorns contain limited genetic diversity and are highly inbred.

Pointed and Latin American Popcorns exhibit considerable genetic diversity and rapid linkage disequilibrium decay.

Kernel color does not affect nicosulfuron sensitivity and instead reflects differences between the populations.

Popcorn-specific candidate genes for nicosulfuron tolerance are distinct from dent corn.