bluuebunny/crossref_metadata_2025 huggingface dataset:
Viral cultures, PCR Cycle threshold values and viral load estimation for COVID-19 infectious potential assessment in transplant patients: systematic review - Protocol Version 30 December 2021
Authors: Jefferson Tom , Spencer Elizabeth A. , Maltoni Susanna , Brassey Jon , Onakpoya Igho J. , Rosca Elena C. , Plüddemann Annette , Evans David H. , Conly John M. , Heneghan Carl J.
Published: January 2022

This is the protocol for a systematic review focussing on people receiving solid organ or hematopoietic stem cell transplants.

Our research questions are as follows:

What is the relationship between serial PCR Ct value or other measures of viral burden, and the likelihood and duration of the presence of infectious virus from viral culture, among transplant recipients with SARS-CoV-2 infection?

What is the influence of age, sex, underlying pathologies, degree of immunosuppression, vaccination status, COVID-19 symptoms and COVID-19 disease course on viral burden and the likelihood of presence of infectious SARS-CoV-2?

We will include single studies reporting serial Cts from sequential rt-PCR testing or other measures of viral burden such as RNA gene copies of respiratory samples (from nasopharyngeal specimens) along with viral culture data on the same samples, from patients about to receive a transplant or who are post transplant with SARS-CoV-2 infection.
Interictal SEEG resting-state connectivity localizes seizure onset zone and predicts seizure outcome
Authors: Jiang Haiteng , Kokkinos Vasileios , Ye Shuai , Urban Alexandra , Bagić Anto , Richardson Mark , He Bin
Published: January 2022

Stereotactic-electroencephalography (SEEG) is a common neurosurgical method to localize epileptogenic zone in drug resistant epilepsy patients and inform treatment recommendations. In the current clinical practice, localization of epileptogenic zone typically requires prolonged recordings to capture seizure, which may take days to weeks. Although epilepsy surgery has been proven to be effective in general, the percentage of unsatisfactory seizure outcomes is still concerning. We developed a method to identify the seizure onset zone (SOZ) and predict seizure outcome using short-time resting-state SEEG data. In a cohort of 43 drug resistant epilepsy patients, we estimated the information flow via directional connectivity and inferred the excitation-inhibition ratio from the 1/f power slope. We hypothesized that the antagonism of information flow at multiple frequencies between SOZ and non-SOZ underlying the relatively stable epilepsy resting state could be related to the disrupted excitation-inhibition balance. We found higher excitability in non-SOZ regions compared to the SOZ, with dominant information flow from non-SOZ to SOZ regions, probably reflecting inhibitory input from non-SOZ to prevent seizure initiation. Greater differences in information flow between SOZ and non-SOZ regions were associated with favorable seizure outcome. By integrating a balanced random forest model with resting-state connectivity, our method localized the SOZ with an accuracy of 85% and predicted the seizure outcome with an accuracy of 77% using clinically determined SOZ. Overall, our study suggests that brief resting-state SEEG data can significantly facilitate the identification of SOZ and may eventually predict seizure outcomes without requiring long-term ictal recordings.
Point-of-care lung ultrasound predicts severe disease and death due to COVID-19: a prospective cohort study
Authors: Blair Paul W. , Siddharthan Trishul , Liu Gigi , Bai Jiawei , East Joshua , Herrera Phabiola , Anova Lalaine , Mahadevan Varun , Hossen Shakir , Seo Stefanie , Sonuga Olamide , Lawrence Joshua , Peters Jillian , Cox Andrea , Manabe Yukari C. , Fenstermacher Katherine , Shea Sophia , Rothman Richard E. , Hansoti Bhakti , Sauer Lauren , Crainiceanu Ciprian , Clark Danielle V.
Published: January 2022

Objective

The clinical utility of point-of-care lung ultrasound (LUS) for disease severity triage of hospitalized patients with COVID-19 is unclear.

Design

Prospective cohort study

Setting

A large tertiary care center in Maryland, USA between April 2020 to September 2021.

Patients

Hospitalized adults (≥18 years of age) with positive SARS-CoV-2 RT-PCR results.

Interventions

None.

Measurements and Main Results

All patients were scanned using a standardized protocol including 12 lung zones and followed to determine clinical outcomes until hospital discharge and vital status at 28-days. Ultrasounds were independently reviewed for lung and pleural line artifacts and abnormalities, and the mean Lung Ultrasound Score (ranging from 0 to 3) across lung zones (mLUSS) was determined. The primary outcome was time to ICU-level care, defined as high flow oxygen, noninvasive, or mechanical ventilation, within 28-days of the initial ultrasound. Cox proportional hazards regression models adjusted for age and sex were fit for mLUSS and each ultrasound covariate. A total of 264 participants were enrolled in the study; the median age was 59 years and 114 (43.2) % of participants were female. The median mLUSS was 1 (interquartile range: 0.5 to 1.3). Following enrollment, 29 (11.0%) participants went on to require ICU-level care and 14 (5.3%) subsequently died by 28 days. Each increase in mLUSS at enrollment was associated with disease progression to ICU-level care (aHR = 3.63; 95% CI: 1.23 to 10.65) and 28-day mortality (aHR = 4.50; 95% CI: 1.52 to 13.31). Pleural line abnormalities were independently associated with disease progression to ICU-level care (aHR = 18.86; CI: 1.57 to 226.09).

Conclusions

Participants with a mLUSS ≥1 or pleural line changes on LUS had an increased likelihood of subsequent requirement of high flow oxygen or greater. LUS is a promising tool for assessing risk of COVID-19 progression at the bedside.
Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires
Authors: Mikelov Artem I. , Alekseeva Evgeniia I. , Komech Ekaterina A. , Staroverov Dmitriy B. , Turchaninova Maria A. , Shugay Mikhail , Chudakov Dmitriy M. , Bazykin Georgii A. , Zvyagin Ivan V.
Published: January 2022

The stability and plasticity of B cell-mediated immune memory ensures the ability to respond to the repeated challenges. We have analyzed the longitudinal dynamics of immunoglobulin heavy chain repertoires from memory B cells, plasmablasts, and plasma cells from the peripheral blood of generally healthy volunteers. We reveal a high degree of clonal persistence in individual memory B cell subsets, with inter-individual convergence in memory and antibody-secreting cells (ASCs). ASC clonotypes demonstrate clonal relatedness to memory B cells, and are transient in peripheral blood. We identify two clusters of expanded clonal lineages with differing prevalence of memory B cells, isotypes, and persistence. Phylogenetic analysis revealed signs of reactivation of persisting memory B cell-enriched clonal lineages, accompanied by new rounds of affinity maturation during proliferation and differentiation into ASCs. Negative selection contributes to both persisting and reactivated lineages, preserving the functionality and specificity of BCRs to protect against current and future pathogens.
Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient
Authors: Zhao Xueying , Ford Roseanne M.
Published: January 2022

In natural systems bacteria are exposed to many chemical stimulants; some attract chemotactic bacteria as they promote survival, while others repel bacteria because they inhibit survival. When faced with a mixture of chemoeffectors, it is not obvious which direction the population will migrate. Predicting this direction requires an understanding of how bacteria process information about their surroundings. We used a multiscale mathematical model to relate molecular level details of their two-component signaling system to the probability that an individual cell changes its swimming direction to the chemotactic velocity of a bacterial population. We used a microfluidic device designed to maintain a constant chemical gradient to compare model predictions to experimental observations. We obtained parameter values for the multiscale model of Escherichia coli chemotaxis to individual stimuli, α-methylaspartate and nickel ion, separately. Then without any additional fitting parameters, we predicted the response to chemoeffector mixtures. Migration of E. coli toward α-methylaspartate was modulated by adding increasing concentrations of nickel ion. Thus, the migration direction was controlled by the relative concentrations of competing chemoeffectors in a predictable way. This study demonstrated the utility of a multiscale model to predict the migration direction of bacteria in the presence of competing chemoeffectors.
A systematic characterization of intrinsically formed microglia-like cells during retinal organoid differentiation
Authors: Bartalska Katarina , Hübschmann Verena , Korkut-Demirbaş Medina , Cubero Ryan John A. , Venturino Alessandro , Rössler Karl , Czech Thomas , Siegert Sandra
Published: January 2022

Brain organoids differentiated from human induced pluripotent stem cells provide a unique opportunity to investigate the development, organization and connectivity of neurons in a complex cellular environment. However, organoids usually lack microglia, brain-resident immune cells which are both present in the early human embryonic brain and participate in neuronal circuit development.

Here, we find that microglia innately develop in unguided retinal organoid differentiation between week 3 and 4 in 2.5D culture and appear later in floating, non-pigmented, 3D-cystic compartments. We enriched for cystic structures using a low-dosed BMP4 application and performed mass spectrometry, thus defining the protein composition of microglia-containing compartments. We found that cystic compartments expressed both mesenchymal and epithelial markers with microglia enriched in the mesenchymal region. Interestingly, microglia-like cells started to express the border-associated macrophage marker CD163. The preferential localization of human microglia to a mesenchymal compartment provides insight into the behavior and migration of microglia. The model will ultimately allow detailed study of these enigmatic cells and how they enter and distribute within the human brain.
Intermittent compression increases flow through a gel: a mechanical model perhaps relevant to flow of cerebrospinal fluid
Authors: Hale Michael G. , Coles Jonathan A.
Published: January 2022

Exchange of molecules between cerebrospinal fluid (CSF) and brain cells contributes to brain function and protection from dementia. Despite widespread acceptance of the ‘glymphatic’ theory, the route by which CSF is brought close enough to the neural tissue for solutes to be exchanged by extracellular diffusion is not entirely clear. Exogenous molecules injected into CSF are observed to reach the basement lamina that surrounds the dense capillary network. Transport of solutes by diffusion along the basement lamina, a gel of macromolcules about 100 nm thick, would be too slow; bulk flow in a static geometry would require unphysiologically high pressures. However, it is known that the pulsation of blood aids transport of CSF, and we hypothesized that this is because the pulsation intermittently squeezes the pericapillary lamina. In a primitive mimicry, we have tested whether intermittent squeezing increases flow through an agar gel. In all but one of 216 tests, pulsation caused a reversible increase, sometimes by a factor of 100 or more. The enhancement was greatest for frequencies 5-11 Hz and, over the tested range of pressure heads (20 - 50 cmH2O), was greatest for the lowest pressure. The results suggest a reason why exercise slows the aging of the brain.
Structure-function relationships in mitochondrial transcriptional condensates
Authors: Feric Marina , Sarfallah Azadeh , Dar Furqan , Temiakov Dmitry , Pappu Rohit V. , Misteli Tom
Published: January 2022

Phase separation organizes many membraneless structures in cells. The functional consequences of concentrating cellular machinery into biomolecular condensates, however, are largely unclear. One fundamental cellular function that has been linked to condensate formation is transcription. Here, we have reconstituted mitochondrial transcription in condensates from purified components. We find that the core components of the mttranscriptional machinery form multi-phasic, viscoelastic condensatesin vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than equivalent reactions in bulk solution. These condensate-mediated decreases in transcriptional rates are associated with the formation of dynamically arrested vesicular structures that are driven by the production and accumulation of RNA during transcription. Using coarse-grained, equilibrium simulations, we show that the generation of RNA alters the phase behavior and the organization of transcriptional components within condensates and that thein vitromtcondensates are non-equilibrium structures. Together, ourin vitroandin silicoapproaches shed light on how proteins and (ribo)nucleic acids biophysically self-assemble within mitochondriain vivo. Our results highlight the complex morphologies of transcribing, multicomponent condensates and they illustrate the interdependent structure-function relationships in condensates.

Significance Statement

Mitochondria condense their genome into transcriptionally active mt-nucleoids. These structures fit the definition of biomolecular condensates that form via macromolecular phase separation. We take advantage of the ability to reconstitute mitochondrial transcriptional condensates in vitro from minimal components. We find that the production and accumulation of RNA alters the phase behavior of transcriptional condensates. The altered phase behavior is linked to the formation of arrested, non-equilibrium vesicular structures. Similar changes to phase behavior of proteins and (ribo)nucleic acids can be recapitulated in live mitochondria through knockdown of mt-nucleoid core components. Computer simulations help identify biophysical mechanisms that are needed to maintain the steady-state structures of transcriptional condensates.
White-matter degradation and dynamical compensation support age-related functional alterations in human brain
Authors: Petkoski Spase , Ritter Petra , Jirsa Viktor K.
Published: January 2022

Structural connectivity of the brain at different ages is analyzed using diffusion-weighted Magnetic Resonance Imaging (MRI) data. The largest decrease of the number and average length of streamlines is found for the long inter-hemispheric links, with the strongest impact for frontal regions. From the BOLD functional MRI (fMRI) time series we identify age-related changes of dynamic functional connectivity (dFC) and spatial covariation features of the FC links captured by metaconnectivity (MC). They indicate more constant dFC, but wider range and variance of MC. Finally we applied computational whole-brain network model based on oscillators, which mechanistically expresses the impact of the spatio-temporal structure of the brain (weights and the delays) to the dynamics. With this we tested several hypothesis, which revealed that the spatio-temporal reorganization of the brain with ageing, supports the observed functional fingerprints only if the model accounts for: (i) compensation of the individual brains for the overall loss of structural connectivity, and (ii) decrease of propagation velocity due to the loss of myelination. We also show that having these two conditions, it is sufficient to decompose the time-delays as bimodal distribution that only distinguishes between intra- and inter-hemispheric delays, and that the same working point also captures the static FC the best.
A common human brain-derived neurotrophic factor polymorphism leads to sustained depression of excitatory synaptic transmission by isoflurane in hippocampus
Authors: Williams RA , Johnson KW , Lee FS , Hemmings HC , Platholi J
Published: January 2022

Multiple presynaptic and postsynaptic targets have been identified for the reversible neurophysiological effects of general anesthetics on synaptic transmission and neuronal excitability. However, the synaptic mechanisms involved in persistent depression of synaptic transmission resulting in more prolonged neurological dysfunction following anesthesia are less clear. Here, we show that brain-derived neurotrophic factor (BDNF), a growth factor implicated in synaptic plasticity and dysfunction, enhances glutamate synaptic vesicle exocytosis, and that attenuation of vesicular BDNF release by isoflurane contributes to transient depression of excitatory synaptic transmission in mice. This reduction in synaptic vesicle exocytosis was irreversible in neurons that release less endogenous BDNF due to a polymorphism (BDNF Val66Met) compared to wild-type mouse hippocampal neurons following isoflurane exposure. These effects were prevented by exogenous application of BDNF. Our findings identify a role for a common human BDNF single nucleotide polymorphism (Val66Met; rs6265) in persistent changes of synaptic function following isoflurane exposure. These persistent alterations in excitatory synaptic transmission have important implications for the role of genotype in anesthetic effects on synaptic plasticity and neurocognitive function.
Mechanical gating of the auditory transduction channel TMC1 involves the fourth and sixth transmembrane helices
Authors: Akyuz Nurunisa , Karavitaki K. Domenica , Pan Bifeng , Tamvakologos Panos I. , Brock Kelly P. , Li Yaqiao , Marks Debora S. , Corey David P.
Published: January 2022

The transmembrane channel-like (TMC) 1 and 2 proteins play a central role in auditory transduction, forming ion channels that convert sound into electrical signals. However, the molecular mechanism of their gating remains unknown. Here, using predicted structural models as a guide, we probed the effects of twelve mutations on the mechanical gating of the transduction currents in native hair cells of Tmc1/2-null mice expressing virally introduced TMC1 variants. Whole-cell electrophysiological recordings revealed that mutations within the pore-lining transmembrane (TM) helices 4 and 6 modified gating, reducing the force sensitivity or shifting the open probability of the channels, or both. For some of the mutants, these changes were accompanied by a change in single-channel conductance. Our observations are in line with a model wherein conformational changes in the TM4 and TM6 helices are involved in the mechanical gating of the transduction channel.
The synaptic organization in the C. elegans neural network suggests significant local compartmentalized computations
Authors: Ruach Rotem , Ratner Nir , Emmons Scott W. , Zaslaver Alon
Published: January 2022

Neurons are characterized by elaborate tree-like dendritic structures that support local computations by integrating multiple inputs from upstream presynaptic neurons. It is less clear if simple neurons, consisting of a few or even a single neurite, may perform local computations as well. To address this question, we focused on the compact neural network of C. elegans animals for which the full wiring diagram is available, including the coordinates of individual synapses. We find that the positions of the chemical synapses along the neurites are not randomly distributed, nor can they be explained by anatomical constraints. Instead, synapses tend to form clusters, an organization that supports local compartmentalized computations. In mutually-synapsing neurons, connections of opposite polarity cluster separately, suggesting that positive and negative feedback dynamics may be implemented in discrete compartmentalized regions along neurites. In triple-neuron circuits, the non-random synaptic organization may facilitate local functional roles, such as signal integration and coordinated activation of functionally-related downstream neurons. These clustered synaptic topologies emerge as a guiding principle in the network presumably to facilitate distinct parallel functions along a single neurite, effectively increasing the computational capacity of the neural network.
VRK1 is a Paralog Synthetic Lethal Target in VRK2-methylated Glioblastoma
Authors: Shields Julie A. , Meier Samuel R. , Bandi Madhavi , Ferdinez Maria Dam , Engel Justin L. , Mulkearns-Hubert Erin E. , Hajdari Nicole , Mitchell Kelly , Zhang Wenhai , Zhao Shan-chuan , Zhang Minjie , Tham Sjin Robert Tjin , Wilker Erik , Lathia Justin D. , Andersen Jannik N. , Chen Yingnan , Li Fang , Weber Barbara , Huang Alan , Emmanuel Natasha
Published: January 2022

Synthetic lethality — a genetic interaction that results in cell death when two genetic deficiencies co-occur but not when either deficiency occurs alone — can be co-opted for cancer therapeutics. A pair of paralog genes is among the most straightforward synthetic lethal interaction by virtue of their redundant functions. Here we demonstrate a paralog-based synthetic lethality by targeting Vaccinia-Related Kinase 1 (VRK1) in Vaccinia-Related Kinase 2 (VRK2)-methylated glioblastoma (GBM). VRK2 is silenced by promoter methylation in approximately two-thirds of GBM, an aggressive cancer with few available targeted therapies. Genetic knockdown of VRK1 in VRK2-null or VRK2-methylated cells results in decreased activity of the downstream substrate Barrier to Autointegration Factor (BAF), a regulator of post-mitotic nuclear envelope formation. VRK1 knockdown, and thus reduced BAF activity, causes nuclear lobulation, blebbing and micronucleation, which subsequently results in G2/M arrest and DNA damage. The VRK1-VRK2 synthetic lethal interaction is dependent on VRK1 kinase activity and is rescued by ectopic VRK2 expression. Knockdown of VRK1 leads to robust tumor growth inhibition in VRK2-methylated GBM xenografts. These results indicate that inhibiting VRK1 kinase activity could be a viable therapeutic strategy in VRK2-methylated GBM.
Global ecomorphological restructuring of dominant marine reptiles prior to the K/Pg mass extinction
Authors: MacLaren Jamie A. , Bennion Rebecca F. , Bardet Nathalie , Fischer Valentin
Published: January 2022

Mosasaurid squamates were the dominant amniote predators in marine ecosystems during most of the Late Cretaceous. Evidence from multiple sites worldwide of a global mosasaurid community restructuring across the Campanian–Maastrichtian transition may have wide-ranging implications for the evolution of diversity of these top oceanic predators. In this study, we use a suite of biomechanical traits and functionally descriptive ratios to investigate how the morphofunctional disparity of mosasaurids evolved through time and space prior to the Cretaceous-Palaeogene (K/Pg) mass extinction. Our results suggest that the worldwide taxonomic turnover in mosasaurid community composition from Campanian to Maastrichtian is reflected by a notable increase in morphofunctional disparity on a global scale, but especially driven the North American record. Ecomorphospace occupation becomes more polarised during the late Maastrichtian, as the morphofunctional disparity of mosasaurids plateaus in the Southern Hemisphere and decreases in the Northern Hemisphere. We show that these changes are not associated with strong modifications in mosasaurid size, but rather with the functional capacities of their skulls, and that mosasaurid morphofunctional disparity was in decline in several provincial communities before the K-Pg mass extinction. Our study highlights region-specific patterns of disparity evolution, and the importance of assessing vertebrate extinctions both globally and regionally. Ecomorphological differentiation in mosasaurid communities, coupled with declines in other formerly abundant marine reptile groups, indicates widespread restructuring of higher trophic levels in marine food webs was well underway when the K-Pg mass extinction took place.
Microglia influence neurofilament deposition in ALS iPSC-derived motor neurons
Authors: Allison Reilly L. , Adelman Jacob W. , Abrudan Jenica , Urrutia Raul A. , Zimmermann Michael T. , Mathison Angela J. , Ebert Allison D.
Published: January 2022

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease in which upper and lower motor neuron loss is the primary phenotype, leading to muscle weakness and wasting, respiratory failure, and death. Although a portion of ALS cases are linked to one of over 50 unique genes, the vast majority of cases are sporadic in nature. However, the mechanisms underlying the motor neuron loss in either familial or sporadic ALS are not entirely clear. Here we used induced pluripotent stem cells derived from a set of identical twin brothers discordant for ALS to assess the role of astrocytes and microglia on the expression and accumulation of neurofilament proteins in motor neurons. We found that motor neurons derived from the affected twin exhibited increased transcript levels of all three neurofilament isoforms and increased expression of phosphorylated neurofilament puncta. We further found that treatment of the motor neurons with astrocyte conditioned medium and microglial conditioned medium significantly impacted neurofilament deposition. Together, these data suggest that glial-secreted factors can alter neurofilament pathology in ALS iPSC-derived motor neurons.
Acoustic and vibrational signaling in true katydid Nesoecia nigrispina: three means of sound production in the one species
Authors: Korsunovskaya Olga S. , Zhantiev Rustem D.
Published: January 2022

The males of Mexican katydids Nesoecia nigrispina (Stal, 1873) produce calling songs and protest sounds using the same stridulatory apparatus as in most of the other Ensifera at the base of the elytra. It includes pars stridens on the upper elytron and plectrum on the lower. Calling sounds of two types (fast and slow) are 2-pulse series, repeated with a frequency of 1.2-4.5 s−1. Protest signals in the form of short trills from the same pulse duration males produce with tactile stimulation. The pulse repetition rate is more higher than that of the calling sounds - up to 10 (mean c. 8) s−1. The frequency spectra of these signals have maxima in the band of 14–15 kHz. However, in addition to the sounds described, both males and females are capable to produce protest signals of the second type with the help of another sound apparatus, namely with the help of the wings. Insects with removed elytra are unable to produce an audible sound. Thus, the sound is produced by the friction of the wings on the elytra, but there are no specialized stridulatory structures on them. In individuals of both sexes, in response mainly to tactile stimulation, short clicks are recorded, which they make, apparently, by the mandibles. Vibrational signals at tremulation are emitted by individuals of both sexes during courtship and males, completing the calling signal cycle and after copulation. It is possible that vibrational signals are an additional factor in reproductive isolation in sympatric species, since the calling sound signals in representatives of the genus Nesoecia are similar and exhibit significant variability.
ZC3HC1 is a structural element of the nuclear basket effecting interlinkage of TPR polypeptides
Authors: Gunkel Philip , Cordes Volker C.
Published: January 2022

The nuclear basket (NB), anchored to the nuclear pore complex (NPC), is commonly thought of as built solely of protein TPR polypeptides, the latter thus regarded as the NB’s only scaffold-forming components. In the current study, we report ZC3HC1 as a second building element of the NB. Recently described as an NB-appended protein omnipresent in vertebrates, we now show that ZC3HC1, both in vivo and in vitro, enables in a step-wise fashion the recruitment of TPR subpopulations to the NB and their linkage to already NPC-anchored TPR polypeptides. We further demonstrate that the degron-mediated rapid elimination of ZC3HC1 results in the prompt detachment of the ZC3HC1-appended TPR polypeptides from the NB and their release back into the nucleoplasm again, underscoring the role of ZC3HC1 as a natural structural element of the NB. Finally, we show that ZC3HC1 can keep TPR polypeptides positioned even at sites remote from the NB, in line with ZC3HC1 functioning as a protein connecting TPR polypeptides.
Impaired endogenous neurosteroid signaling contributes to behavioral deficits associated with chronic stress
Authors: Walton Najah L. , Antonoudiou Pantelis , Barros Lea , DiLeo Alyssa , Gabby Jenah , Howard Samantha , Paracha Rumzah , Sánchez Edgardo J. , Weiss Grant L. , Kong Dong , Maguire Jamie L.
Published: January 2022

Chronic stress is a major risk factor for psychiatric illnesses, including depression; however, the pathophysiological mechanisms whereby stress leads to mood disorders remain unclear. The recent FDA approval of antidepressants with novel mechanisms of action, like Zulresso®, a synthetic neuroactive steroid analog with molecular pharmacology similar to allopregnanolone, has spurred interest in new therapeutic targets and, potentially, novel pathophysiological mechanisms for depression. Allopregnanolone acts as a positive allosteric modulator of GABAAreceptors (GABAARS), acting preferentially at δ subunit-containing receptors (δ-GABAARS). Accumulating clinical and preclinical evidence supports the antidepressant effects of exogenous administration of allopregnanolone and allopregnanolone analogs; however, the role of endogenous neurosteroids in the pathophysiology of depression remains unknown. Here, we examine whether altered neurosteroid signaling may contribute to behavioral deficits following chronic unpredictable stress (CUS) in mice. We first identified reductions in expression of δ-GABAARs, the predominant site of action of 5a-reduced neuroactive steroids, following CUS. Additionally, utilizing LC-MS/MS we discovered a decrease in levels of allopregnanolone in the BLA, but not plasma of mice following CUS, an indication of impaired neurosteroid synthesis. CRISPR knockdown the rate-limiting enzymes involved in allopregnanolone synthesis, 5α-reductase type 1 and 2, in the BLA mimicked the behavioral deficits associated with CUS in mice. Furthermore, overexpression expression of 5α-reductase type 1 and 2 in the BLA improved behavioral outcomes. Collectively, this suggests chronic stress impairs endogenous neurosteroid signaling in the BLA which is sufficient to induce behavioral deficits similar to those observed following CUS. Further, these studies suggest that the therapeutic efficacy of allopregnanolone-based treatments may be due to their ability to directly target the underlying pathophysiology of mood disorders. Therefore, targeting endogenous neurosteroidogenesis may offer a novel therapeutic strategy for the treatment of mood disorders.
Vocal traits of shorebird chicks are related to body mass and sex
Authors: Kostoglou Kristal N. , Miller Edward H. , Weston Michael A. , Wilson David R.
Published: January 2022

Acoustic communication is critical during early life phases in precocial birds. For example, adult alarm calls can elicit antipredator behaviour in young, and chick vocalisations can communicate information to parents about chick identity, condition, location, sex, or age. We investigated whether chick calls of two species of Australian Charadriidae vary with sex or body mass. We handled Red-capped PloverCharadrius ruficapillusand Southern Masked LapwingVanellus miles novaehollandiaechicks for purposes of measurement, blood sampling, and banding. We opportunistically recorded their distress calls while in the hand, and analysed the calls to determine whether call structure is related to sex or body mass (a proxy for age). We measured five traits per call, plus time intervals between successive calls, for 26 plover chicks (2600 calls) and 95 lapwing chicks (6835 calls). In plovers, inter-call intervals were shorter in males and both inter-call interval and the dominant frequency range of calls decreased with increasing body mass. In lapwings, frequency modulation (computed as the range in the rate of change of the dominant frequency) was lower in male calls. The dominant frequency range of lapwing calls decreased with mass in both sexes, but the decline was greater in males, resulting in a lower dominant frequency range in males. Frequency modulation and entropy of lapwing calls also decreased with increasing body mass. Minimum dominant frequency did not change with body mass or sex in either species. Our study provides the first evidence for charadriid chicks of (a) a sexual difference in call structure and rate and (b) gradual growth-related changes in call structure and rate, across chicks. Studies on calls from a greater range of chick ages and from more species within this large and diverse family would be valuable. We provide a foundation for further studies of shorebird vocalisations during growth, which may elucidate the development and functional significance of such vocalisations.
NETISCE: A Network-Based Tool for Cell Fate Reprogramming
Authors: Marazzi Lauren , Shah Milan , Balakrishnan Shreedula , Patil Ananya , Vera-Licona Paola
Published: January 2022

The search for effective therapeutic targets in fields like regenerative medicine and cancer research has generated interest in cell fate reprogramming. This cellular reprogramming paradigm can drive cells to a desired target state from any initial state. However, methods for identifying reprogramming targets remain limited for biological systems that lack large sets of experimental data or a dynamical characterization. We present NETISCE, a novel computational tool for identifying cell fate reprogramming targets in static networks. In combination with machine learning algorithms, NETISCE estimates the attractor landscape and predicts reprogramming targets using Signal Flow Analysis and Feedback Vertex Set Control, respectively. Through validations in studies of cell fate reprogramming from developmental, stem cell, and cancer biology, we show that NETISCE can predict previously identified cell fate reprogramming targets and identify potentially novel combinations of targets. NETISCE extends cell fate reprogramming studies to larger-scale biological networks without the need for full model parameterization and can be implemented by experimental and computational biologists to identify parts of a biological system relevant to the desired reprogramming task.
Normal Reproductive function in male mice lacking pituitary kisspeptin receptor
Authors: Ma Yaping , Awe Olubusayo , Radivick Sally , Yang Xiaofeng , Divall Sara , Wolfe Andrew , Wu Sheng
Published: January 2022

The anterior pituitary secretion of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) regulate gonadal development, gametogenesis and the secretion of the gonadal steroid hormones. The gonadotroph is primarily regulated by hypothalamic secretion of gonadotropin-releasing hormone (GnRH) from neurons of the rostral hypothalamus and is mediated by GnRH receptor signaling. Kisspeptin (KISS1)/kisspeptin receptor (KISS1R) signaling in GnRH neurons plays an essential role in reproductive function. As the kisspeptin receptor is present in the pituitary, kisspeptin signaling via the Kiss1r may regulate reproductive function at the level of pituitary. Using Cre/Lox technology, we deleted the Kiss1r gene in pituitary gonadotropes (PKiRKO). PKiRKO male and females have normal genital development, puberty onset, and fertility. Females have normal LH, FSH and estradiol while males had significantly increased basal serum FSH levels with no differences in basal serum LH, or testosterone levels. Overall, these findings indicate that the pituitary KISS1R does not play a role in male reproduction.
Oxytocin modulates social brain network correlations in resting and task state
Authors: Wu Qingyuan , Huang Qi , Liu Chao , Wu Haiyan
Published: January 2022

The effects of oxytocin (OT) on the social brain can be tracked upon assessing the neural activity in resting and task states, and developing a system-level framework for characterizing the state-based functional relationships of its distinct effect. Here, we contribute to this framework by examining how OT modulates social brain network correlations during resting and task states, using fMRI. First, we investigated network activation, followed by an analysis of the relationships between networks and individual differences. Subsequently, we evaluated the functional connectivity in both states. Finally, the relationship between networks across states was represented by the predictive power of networks in the resting state for task-evoked activities. The differences in the predicted accuracy between the subjects displayed individual variations in this relationship. Our results showed that the activity of the dorsal default mode network (DDMN) in the resting state had the largest predictive power for task-evoked activation of the precuneus network (PN) only in the OT group. The results also demonstrated that OT reduced the individual variation in PN in the prediction process. These findings suggest a distributed but modulatory effect of OT on the association between resting and task-dependent brain networks.
Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae
Authors: Soal Nicole C , Coetzee Martin HA , van der Nest Magriet A , Hammerbacher Almuth , Wingfield Brenda D
Published: January 2022

Fungal species of the Ceratocystidaceae grow on their host plants using a variety of different lifestyles, from saprophytic to highly pathogenic. Although many genomes of fungi in the Ceratocystidaceae are publicly available, it is not known how the genes that encode catechol dioxygenases (CDOs), enzymes involved in the degradation of phenolic plant defence compounds, differ among members of the Ceratocystidaceae. The aim of this study was therefore to identify and characterize the genes encoding CDOs in the genomes of Ceratocystidaceae representatives. We found that genes encoding CDOs are more abundant in pathogenic necrotrophic species of the Ceratocystidaceae and less abundant in saprophytic species. The loss of the CDO genes and the associated 3-oxoadipate catabolic pathway appears to have occurred in a lineage-specific manner. Taken together, this study revealed a positive association between CDO gene copy number and fungal lifestyle in Ceratocystidaceae representatives.
Roles for Mitochondrial Complex I subunits in regulating synaptic transmission and growth
Authors: Mallik Bhagaban , Frank C. Andrew
Published: January 2022

To identify conserved components of synapse function that are also associated with human diseases, we conducted a genetic screen. We used the Drosophila melanogaster neuromuscular junction (NMJ) as a model. We employed RNA interference (RNAi) on selected targets and assayed synapse function and plasticity by electrophysiology. We focused our screen on genetic factors known to be conserved from human neurological or muscle functions (300 Drosophila lines screened). From our screen, knockdown of a Mitochondrial Complex I (MCI) subunit gene (ND-20L) lowered levels of NMJ neurotransmission. Due to the severity of the phenotype, we studied MCI function further. Knockdown of core MCI subunits concurrently in neurons and muscle led to impaired neurotransmission. We localized this neurotransmission function to the muscle. Pharmacology targeting MCI phenocopied the impaired neurotransmission phenotype. Finally, MCI subunit knockdowns or pharmacological inhibition led to profound cytological defects, including reduced NMJ growth and altered NMJ morphology. Mitochondria are essential for cellular bioenergetics and produce ATP through oxidative phosphorylation. Five multi-protein complexes achieve this task, and MCI is the largest. Impaired Mitochondrial Complex I subunits in humans are associated with disorders such as Parkinson’s disease, Leigh syndrome, and cardiomyopathy. Together, our data present an analysis of Complex I in the context of synapse function and plasticity. We speculate that in the context of human MCI dysfunction, similar neuronal and synaptic defects could contribute to pathogenesis.
AXenopusneuromast bioassay for chemical ototoxicity
Authors: Knight V. Bleu , Luna Amanda R. , Serrano Elba E.
Published: January 2022

Background

Ototoxic chemicals can impair the senses of hearing and balance in mammals through irreversible damage to the mechanosensory bundles of inner ear hair cells. Fish and amphibians are useful models for investigating ototoxicity because their inner ear hair cells, like those of mammals, are susceptible to damage by ototoxins. Moreover, amphibian mechanosensation is augmented by a lateral line organ on the body surface that comprises external mechanosensory hair cells. The lateral line hair cells are arranged in clusters (neuromasts) and are structurally and functionally similar to inner ear hair cells, but are more accessible for experimental manipulation. Herein, we implemented neuromasts of the amphibian (Xenopus)lateral line as an organ system for evaluating the effects of ototoxic chemicals, such as antibiotics, on mechanosensory hair cell bundles.

Methods

We examined the ultrastructure of larvalXenopus laevisneuromasts with scanning electron microscopy (SEM) after larvae were continuously exposed to ototoxic aminoglycoside antibiotics at sub-lethal concentrations (gentamicin; streptomycin; neomycin) for 72 hours.

Results

SEM images demonstrated that 72 hours of exposure to antibiotic concentrations greater than 25 µM reduced the hair cell bundle number in lateral line neuromasts.

Conclusion

Therapeutic drug studies will benefit from the incorporation of bioassay strategies that evaluate ototoxicity across multiple species including genera of amphibian origin such asXenopus. Our outcomes support the use of theXenopuslateral line for identification of potential ototoxic chemicals and suggest thatXenopusneuromast hair cell bundles can withstand antibiotic exposure. TheXenopusbioassay presented here can be incorporated into drug discovery methodology as a high-resolution phenotypic screen for ototoxic effects.

Summary statement

Damage to sensory cells of the inner ear by chemical agents such as antibiotics contributes to the growing global prevalence of disorders of hearing and balance. Our results demonstrate that theXenopuslateral line, in conjunction with SEM, affords an accessible organ system for otoxicity screens during the drug discovery pipeline.
Cell adhesion strength and tractions are mechano-diagnostic features of cellular invasiveness
Authors: Paddillaya Neha , Ingale Kalyani , Gaikwad Chaitanya , Saini Deepak Kumar , Pullarkat Pramod , Kondaiah Paturu , Menon Gautam I. , Gundiah Namrata
Published: January 2022

The adhesion of cells to substrates occurs via integrin clustering and binding to the actin cytoskeleton. Oncogenes modify anchorage-dependent mechanisms in cells during cancer progression. Fluid shear devices provide a label-free, non-invasive way to characterize cell-substrate interactions and heterogeneities in the cell populations. We quantified the critical adhesion strengths of MCF7, MDAMB-231, A549, HPL1D, HeLa, and NIH3T3 cells using a custom fluid shear device. The detachment response was sigmoidal for each cell type. A549 and MDAMB-231 cells had significantly lower adhesion strengths at τ50 than their non-invasive counterparts, HPL1D and MCF7. Detachment dynamics was inversely correlated with cell invasion potentials. A theoretical model, based on τ50 values and the distribution of cell areas on substrates, provided good fits to data from de-adhesion experiments. Quantification of cell tractions, using the Reg-FTTC method on 10 kPa polyacrylamide gels, showed highest values for invasive, MDAMB-231 and A549, cells compared to non-invasive cells. Immunofluorescence studies show differences in vinculin distributions: non-invasive cells have distinct vinculin puncta, whereas invasive cells have more dispersed distributions. The cytoskeleton in non-invasive cells was devoid of well-developed stress fibers, and had thicker cortical actin bundles in the boundary. These correlations in adhesion strengths with cell invasiveness, demonstrated here, may be useful in cancer diagnostics and other pathologies featuring misregulation in adhesion.
DNA origami as a nanomedicine for targeted rheumatoid arthritis therapy through reactive oxygen species and nitric oxide scavenging
Authors: Ma Yuxuan , Lu Zhangwei , Shi Ye , Li Zhe
Published: January 2022

High levels of reactive oxygen species (ROS) and nitric oxide (NO) generated by M1 macrophages induce inflammation in the development of rheumatoid arthritis (RA). The eliminating of ROS and NO therefore represents an alternative strategy for RA treatment. Because DNA molecules possess ROS- and endogenous NO-scavenging capability, herein, we develop a nanomedicine based on triangular DNA origami nanostructures for targeted RA treatment. We showed that folic acid-modified triangular DNA origami nanostructures (FA-tDONs) could reduce ROS and NO simultaneously inside proinflammatory M1 macrophages, leading to their polarization into anti-inflammatory M2 subtype. Further in vivo studies confirmed that FA-tDONs could actively target inflamed joints in collagen-induced arthritis (CIA) mice, attenuate inflammatory cytokines and alleviate disease progression. This work demonstrated that DNA origami itself could act as a potential nanomedicine for targeted RA treatment.
Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages
Authors: Cohen A. , Jeng E.E. , Voorhies M. , Symington J. , Ali N. , Bassik M.C. , Sil A.
Published: January 2022

The fungal pathogen Histoplasma capsulatum (Hc) invades, replicates within, and destroys macrophages. To interrogate the molecular mechanisms underlying this interaction, we conducted a host-directed CRISPR-Cas9 screen and identified 361 genes that modify macrophage susceptibility to Hc infection, greatly expanding our understanding of host gene networks targeted by Hc. We identified pathways that have not been previously implicated in Hc interaction with macrophages, including the ragulator complex (involved in nutrient stress sensing), glycosylation enzymes, protein degradation machinery, mitochondrial respiration genes, solute transporters, and the ER membrane complex (EMC). The highest scoring protective hits included the complement C3a receptor (C3aR), a G-protein coupled receptor (GPCR) that recognizes the complement fragment C3a. Although it is known that the complement system reacts with the fungal surface, leading to opsonization and release of small peptide fragments such as C3a, a role for C3aR in macrophage susceptibility to fungi has not been elucidated. We demonstrated that whereas C3aR is dispensable for macrophage phagocytosis of bacteria and latex beads, it is critical for optimal macrophage capture of pathogenic fungi, including Hc, the ubiquitous fungal pathogen Candida albicans, and the causative agent of Valley Fever Coccidioides posadasii. We showed that C3aR localizes to the early phagosome during H. capsulatum infection where it coordinates the formation of actin-rich membrane protrusions that promote Hc capture. We also showed that the EMC promotes surface expression of C3aR, likely explaining its identification in our screen. Taken together, our results provide new insight into host processes that affect Hc-macrophage interactions and uncover a novel and specific role for C3aR in macrophage recognition of fungi.