bluuebunny/crossref_metadata_2025 huggingface dataset:
The 16p11.2 microdeletion influences how early-life microbiota perturbations affect hippocampal development and behavior throughout the lifespan
Authors: McDermott Courtney R. , Gao Zhan , Mirmajlesi Anya S. , Ntim Christiana , Kimbark Katherine , Thomas Divya , Mughal Zain , Zhang Xue-Song , Zhou Xiaofeng , Popov Daniel , Halchenko Alisa , Xing Jinchuan , Thakker-Varia Smita , Alder Janet , Millonig James H. , Samuels Benjamin A. , Blaser Martin J. , DiCicco-Bloom Emanuel
Published: February 2025

Neurodevelopmental disorders result from interactions between genetic predisposition and environmental risk factors, with infancy being the most vulnerable period. We designed a longitudinal study to determine how short-term antibiotic exposure during early postnatal life impacts the gut microbiome, neurodevelopment, and behavior, and whether these alterations were exacerbated by the neurodevelopmental disorder-associated 16p11.2 microdeletion (16pDel) mutation. The cephalosporin antibiotic, cefdinir, broadly altered the gut microbiome acutely, with persistent reductions in severalLachnospiraceaegenera despite overall recovery. These alterations preceded long-term behavioral changes, including reduced juvenile sociability, compromised risk assessment, and deficits in associative learning. Remarkably, only cefdinir-exposed 16pDel mice had changes in hippocampal stem cell proliferation, subsequent adolescent cell numbers, and gene expression compared to other groups, demonstrating that genetic predisposition can modulate the effects of early-life antibiotic exposure on neurodevelopment. These alterations may be mediated by gastrointestinal disturbances, as cefdinir-exposed 16pDel males had increased intestinal permeability and shifted metabolite profiles including arginine biosynthesis and glycerophospholipid metabolism. Taken together, this study highlights how early-life microbial alterations affect behavior and reveals that genetic predisposition influences antibiotic-induced changes in hippocampal development. Further, these insights identify metabolic mechanisms as potential targets for intervention and may raise concerns regarding antibiotic use during infancy.
The genetic basis for synchronised time perception in plant populations
Authors: Lock Sarah C. L. , McCarthy Kayla , Ronald James , Anwer Muhammad Usman , Davis Amanda M. , Hallstein Marc , Redmond Ethan J. , Knight Marina , Davis Seth J. , Ezer Daphne
Published: February 2025

Synchronised developmental timing is important for ensuring crop uniformity and high yields. However, climate change is leading to crops being grown at different latitudes, varying their exposures to photoperiods over seasons and impacting developmental timings. We investigated whether the response of circadian rhythms in seedlings to changes in photoperiod would enable us to predict the timing and synchronization of flowering. Indeed, we show that the same Quantitative Trait Loci (QTLs) are associated to circadian traits in seedlings and developmental traits during bolting, using the first recombinant inbred lines (RILs) between African and European Arabidopsis lineages, spanning diverse latitudes. Two QTLs contain K-Homology Domain RNA binding proteins (KH17, KH29) and are associated with splicing variants in known flowering genes, MADS AFFECTING FLOWERING2 and 3 (MAF2, MAF3), including generating chimeric transcripts, a potential mechanism for accelerated proteome evolution. Natural variants in KH17, including in its prion-like domain, are associated with de-coupling the mean and synchronization of flowering time, enabling greater adaptation of population-level heterogeneity in developmental timings. Our results suggest that circadian traits in seedlings could be used to screen for agriculturally relevant developmental traits in mature plants, enabling efficient breeding of climate-resilient crops.
Exploring Hippocampal Vulnerability: Diminished Angiogenic Capacity in the Hippocampus Compared to the Cortex
Authors: Li Xiaojie , Li Nanjing , He Yao , Zhong Qixing , Zhong Zhihui
Published: February 2025

Background

The hippocampus is one of the first regions affected in various neurodegenerative diseases. In this study, investigated the vascular factors contributing to its susceptibility, aiming to elucidate the underlying vascular mechanisms.

Method

Utilizing publicly available single-cell databases, we analyzed the differential expression of genes in blood-brain barrier (BBB)-associated cells within the hippocampus and compared them to those in the cortex. Those genes were further validated in mouse and ischemia rat models.

Results

We identified differentially expressed genes (DEGs) in endothelial cells, pericytes, and astrocytes in the BBB. Subsequent gene ontology (GO) enrichment analysis and protein-protein interaction (PPI) network analysis identified key hub genes:Kdr,Fn1,Pecam1,Cd34, andCd93,that related to angiogenesis. They differential expression was then experimentally verified using micro-vessels from mouse and rat brains: In the rat ischemia model, we observed up-regulation of angiogenesis-related genes, includingKdr,Cd34, andCd93, in the microvasculature of both the hippocampus and cortex, with relatively lower expression in the hippocampus.

Conclusion

These findings suggest that the hippocampus has a reduced angiogenic capacity compared to the cortex, which may contribute to its increased vulnerability to neurological disorders.
Within-Individual Precision Mapping of Brain Networks Exclusively Using Task Data
Authors: Du Jingnan , Elliott Maxwell L. , Ladopoulou Joanna , Eldaief Mark C. , Buckner Randy L.
Published: February 2025

Precision mapping of brain networks within individuals has become a widely used tool that prevailingly relies on functional connectivity analysis of resting-state data. Here we explored whether networks could be precisely estimated solely using data acquired during active task paradigms. The straightforward strategy involved extracting residualized data after application of a task-based general linear model (GLM) and then applying standard functional connectivity analysis. Functional correlation matrices estimated from task data were highly similar to those derived from traditional resting-state fixation data. The largest factor affecting similarity between correlation matrices was the amount of data. Networks estimated within-individual from task data displayed strong spatial overlap with those estimated from resting-state fixation data and predicted the same triple functional dissociation in independent data. The implications of these findings are that (1) existing task data can be reanalyzed to estimate within-individual network organization, (2) restingstate fixation and task data can be pooled to increase statistical power, and (3) future studies can exclusively acquire task data to both estimate networks and extract task responses. Most broadly, the present results suggest that there is an underlying, stable network architecture that is idiosyncratic to the individual and persists across task states.
MMP-2/9 inhibition modulates sharp wave abundance, inhibitory proteoglycan sulfation, and fear memory in juvenile zebrafish: relevance to affective disorders
Authors: Blanco I. , Deasy S. , Amontree Matthew , Gabriel M. , Caccavano A. , Vicini S. , Glasgow E. , Conant K
Published: February 2025

Sharp wave ripple (SWR) events, present in diverse species, spontaneously occur in the hippocampus during quiescent restfulness and slow-wave sleep. SWRs comprise a negative deflection, the sharp wave (SW) event with an often-superimposed ripple (R) and are the neural correlates of memory consolidation and recall. The Anterodorsolateral lobe (ADL) (zebrafish hippocampal homologue) exhibits SW and SWR events, and since SWs initiate SWRs, their abundance typically shows the same directionality. In previous work, we observed matrix metalloproteinase-9 (MMP-9)-dependent effects on depression-relevant behaviors, perineuronal net (PNN) levels, and SWR abundance in the adult rodent hippocampus. Here, we investigate MMP-2/9-dependent effects on biochemical, behavioral, and neurophysiological endpoints in juvenile zebrafish and zebrafish at the transition from the late juvenile period to early adulthood. With MMP-2/9 inhibition, juvenile zebrafish showed reduced SW amplitude and abundance together with increased fear memory retention and reduced sociability. Juvenile zebrafish also showed an increased percentage of longer-duration SW events. Except for a reduction in SW amplitude, these changes were not observed at the transition from late juvenile to early adulthood. These changes were accompanied by increased levels of chondroitin sulfate (CS) proteoglycan 4-O-sulfation, which modulates PNNs and excitatory-to-inhibitory (E/I) balance. Discontinuation of MMP-2/9 inhibition in juvenile zebrafish normalized deficits in ADL SW abundance and sociability. Together, these findings show that MMP-2/9 significantly influences E/I balance and learning and memory during the highly plastic juvenile period in zebrafish. Findings also have relevance to an emerging appreciation of PNN changes that may contribute to altered neuronal oscillations and mood or cognition.
Nonlinear breathers with crystalline symmetries
Authors: Schindler Frank , Bulchandani Vir B. , Benalcazar Wladimir A.
Published: February 2025

Nonlinear lattice models can support “discrete breather” excitations that stay localized in space for all time. By contrast, the localized Wannier states of linear lattice models are dynamically unstable. Nevertheless, symmetric and exponentially localized Wannier states are a central tool in the classification of band structures with crystalline symmetries. Moreover, the quantized transport observed in nonlinear Thouless pumps relies on the fact that—at least in a specific model—discrete breathers recover Wannier states in the limit of vanishing nonlinearity. Motivated by these observations, we investigate the correspondence between nonlinear breathers and exponentially localized Wannier states for a family of discrete nonlinear Schrödinger equations with crystalline symmetries. We develop a formalism to analytically predict the breathers' spectrum, center of mass and symmetry data, and apply this to nonlinear generalizations of the Su-Schrieffer-Heeger chain and the breathing kagome lattice.

Published by the American Physical Society
2025
Solution to the
B9(1/2+)
state problem using the
R
-matrix formalism
Authors: Brooks A. D. , Bishop J. , Kokalova Tz. , Wheldon C.
Published: February 2025

For the last 60 years researchers have struggled to unambiguously identify the first excited state in B9. Many prior experimental and theoretical results provide conflicting answers on the expected energy that this level should possess. Within these lie a trend wherein two distinct values emerge as possible solutions to this long-standing question. This dual energy mystery has now been resolved following the identification of the 3/2− ground-state ghost peak in the R-matrix spectrum of B9. Reevaluation of existing experimental data in the context of this new insight provides further proof of historical misidentification of a state at 0.8 MeV in B9.

Published by the American Physical Society
2025
Unitarity method for holographic defects
Authors: Chen Junding , Gimenez-Grau Aleix , Paul Hynek , Zhou Xinan
Published: February 2025

We initiate the study of loop-level holographic correlators in the presence of defects. We present a unitarity method that constructs loop corrections from lower order data. As an example, we apply this method to 6D N=(2,0) theories with 12-BPS surface defects and report the first holographic two-point function at one loop.

Published by the American Physical Society
2025
Terahertz generation via the inverse orbital Rashba-Edelstein effect at the
Ni/CuOx
interface
Authors: Xu Renyou , Ning Xiaobai , Cheng Houyi , Yao Yuxuan , Ren Zejun , Liu Shaojie , Dai Mingcong , Xu Yong , Li Sai , Du Ao , Wu Xiaojun , Hu Fengxia , Shen Baogen , Sun Jirong , Zhang Hui , Zhao Weisheng
Published: February 2025

Orbitronics provides novel mechanisms to generate terahertz (THz) emission using the orbital angular momentum of electrons. Here, we report a systematic investigation of the THz emission from Ni/CuOx heterostructures pumped by a femtosecond laser pulse. Despite the very weak spin-orbit coupling of CuOx, considerable THz radiation from Ni/CuOx has been observed, with a polarity state that is magnetically controllable and the intensity as much as about 20% of that found in Ni/Pt spintronic THz emitter. We find conclusive evidence that THz radiation stems from the inverse orbital Rashba-Edelstein effect at the Ni/CuOx interface, which can be manipulated by tuning oxygen-induced orbital hybridization. Our experimental results of Ni thickness-dependent THz emission, combined with theoretical modeling, reveal long-range diffusion-length characteristics of orbital current within the Ni layer. This work enhances the understanding of the THz emission mechanism based on orbital-to-charge conversion, providing guidance for the development of orbitronic THz emitters.

Published by the American Physical Society
2025
Multi-Fidelity Optimization of Turbulence in a Gas Turbine Combustor Simulator
Authors: Miklaszewski Jennifer , Folk Masha , Hamlington Peter
Published: February 2025

Combustor turbulence in a gas turbine engine greatly influences the efficiency of the downstream high pressure turbine stage. Here we use a multi-fidelity computational optimization methodology to modify the geometry of a non-reacting combustor simulator such that turbulence properties are optimized at the combustor-turbine interface. We modify the size, orientation, and positioning of the primary and dilution jets to minimize turbulence intensity at the combustor exit while demonstrating negligible or favorable changes to the pressure loss and mixing characteristics of the combustor. The optimization is performed using a machine learning surrogate-assisted genetic algorithm coupled with large eddy simulations (LES) and Reynolds-averaged Navier Stokes (RANS) simulations. The optimization is performed in three phases: (i) we develop a continuously-learning artificial neural network surrogate model, (ii) we perform a stochastic optimization with RANS simulations to narrow the parameter space, and (iii) we perform a stochastic optimization with a coarse-grid LES to identify the optimal solution. Using this approach, we are able to achieve a 5.35% reduction in turbulence intensity and a 0.42% reduction in pressure loss while maintaining good mixing uniformity at the combustor exit. These changes are enabled primarily by changing the aspect ratio and diameter of the primary zone and dilution jets, as well as the chute height and spacing of the primary zone jets. This successful demonstration of multi-fidelity optimization in the combustor simulator can be extended in the future to the design of improved gas turbine combustors.
Irregular and regular honeycomb lattice structures: Effective properties and design perspectives
Authors: Kumar Anil , Jain Atul , DasGupta Anirvan
Published: February 2025

A unified approach to determine the effective elastic properties of irregular and regular honeycomb lattice structures is presented. A micromechanics model of a lattice, based on the fundamental periodic element, is developed using Castigliano's second theorem to obtain a homogenized strain energy density function that yields all elastic properties of the lattice. The lattice geometry, comprising uniform slender beam elements, is specified by six lattice parameters for irregular lattices and four lattice parameters for regular lattices. These parameters generate Honeycomb (Hc) or Re-entrant Honeycomb (RHc) structures with different symmetry properties, which can cater to different design requirements. A comprehensive validation, including comparison with available analytical and full Finite Element (FE) results for different geometries and dimensions, confirms the accuracy of the proposed approach. The influence of the geometric parameters on the effective lattice properties is clearly revealed, which leads to some novel design insights. The existence of continuous and accidental L4 symmetry axis in tuned Hc and RHc lattices (including irregular ones) is brought out for the first time from this analysis. Interestingly, it is observed that high auxeticity coincides with low shear modulus, contrary to the existing postulate of high auxeticity implies high shear stiffness. It is also shown that auxeticity is a directional property in RHc lattice structures.
Hybrid Algorithm Approach for driving Distribution Static Compensator in Multiple Renewable Energy Systems
Authors: Suryawanshi Vidhyavati , Gupta Surbhi
Published: February 2025

There has been a recent drive towards integration of the renewable energy resources to the main grid to improve the environmental aspects in the energy generation sector. The integration brings about stability and quality issues that needs to be handled in order to achieve smooth operation at the load end. This involves issues likes voltage sags, swells, and harmonic distortions which are the key focused area in our research. The Distribution Static Compensators (DSTATCOMs) is being used in this paper for a four-machine system integrated with multiple renewable energy resources like solar, wind and fuel cell in order to enhance power quality issues at the loading end. The integration of sophisticated control mechanisms, such as neural networks (NNs) and metaheuristic algorithms like the BAT Optimization Algorithm (NN_BAT) was analyzed for performance of system dynamics under disturbances. The voltage sag and swell conditions were created in the different phases of 3 phase line. It was found that adaptive and predictive adjustments to the electrical network's dynamic conditions, ensured a THD% of 1.22 % and 1.72 % in line voltage and current respectively when voltage swell occurred. Also, when the system was subjected to sag in voltage the THD% was 1.29 % and 1.86 % for voltage and current respectively. It was found that hybrid strategy NN_BAT consistently performs better, achieving lower THD percentages in both voltage and current which indicates a more effective control in mitigating distortions and maintaining power quality.
The influences of the rotor waviness on the hydrodynamic characteristics of gas porous bearings with mixed CFD boundary conditions
Authors: Xia Peng , Liu Jiabao , Song Wenlong , Huang Zhongqiang , Yang Hao , Ma Wensheng , Guo Yanling
Published: February 2025

Manufacturing errors impacted the gas porous bearing's performance, particularly the waviness on the rotor surface that repeatedly squeezed the gas film during rotation. This study investigated the effects of waviness errors using a novel mixed computational fluid dynamics boundary condition that combined steady circumferential motion with transient radial motion. The mixed boundary condition was validated against numerical results. A transient CFD model was developed for gas porous bearings with rotor surface waviness. The transient squeezing effects from the rotating waviness significantly influenced both the hydrostatic and hydrodynamic performance of the bearing. By implementing periodic sinusoidal waviness, the effects of eccentricity, waviness amplitude, waviness number, rotor speed and supply pressure on the performances of the gas porous bearing were investigated.
Enhancement in Hydrodynamic Performance of a Quarter-Circular Breakwater Using a Porous Shield
Authors: Venkateswarlu Valliboina , Vijay K. G. , Sannasiraj Sannasi Annamalaisamy
Published: February 2025

The study evaluates the hydrodynamic performance of quarter-circular breakwaters (QCB) with various types of porous shields (say retrofits) under incident waves. The QCB with (i) vertical shield, (ii) seaside quarter-circular retrofit (QCR), (iii) shore side QCR, and (iv) partial rectangular retrofit (PRR) are proposed to enhance the performance of QCB. The effect of porous shields is analyzed using the quadratic pressure drop condition and dual boundary element method (DBEM) under the framework of linearized potential flow theory. Study results are validated with the available results reported by authors after some numerical modifications. The effect of shield porosity, and wave height on the reflection, transmission, energy loss, and vertical and horizontal forces on QCB and shield are reported as a function of relative water depth. A comparative study is performed among all the proposed breakwaters to identify an effective configuration against the incident waves. Around 39%, 30%, 31%, and 56% reduction of wave transmission is obtained for QCB with vertical shield, seaside, shoreside QCR, and PRR respectively, when compared with QCB alone for kh=1. The wave transmission KT=0.16 and energy loss KL=0.95 are obtained when kh=2 with the addition of the PRR for a QCB, which is observed as an effective porous shield against the incident waves when compared with the other types of shields. The 10%-20% retrofit porosity is recommended with clear spacing b/h=0.9 and the QCB radius of R2/h=0.7 for the effective distribution of the scattering coefficients against the incident waves.
Comparing accounts of formant normalization against US English listeners' vowel perception
Authors: Persson Anna , Barreda Santiago , Jaeger T. Florian
Published: February 2025

Human speech recognition tends to be robust, despite substantial cross-talker variability. Believed to be critical to this ability are auditory normalization mechanisms whereby listeners adapt to individual differences in vocal tract physiology. This study investigates the computations involved in such normalization. Two 8-way alternative forced-choice experiments assessed L1 listeners' categorizations across the entire US English vowel space—both for unaltered and synthesized stimuli. Listeners' responses in these experiments were compared against the predictions of 20 influential normalization accounts that differ starkly in the inference and memory capacities they imply for speech perception. This includes variants of estimation-free transformations into psycho-acoustic spaces, intrinsic normalizations relative to concurrent acoustic properties, and extrinsic normalizations relative to talker-specific statistics. Listeners' responses were best explained by extrinsic normalization, suggesting that listeners learn and store distributional properties of talkers' speech. Specifically, computationally simple (single-parameter) extrinsic normalization best fit listeners' responses. This simple extrinsic normalization also clearly outperformed Lobanov normalization—a computationally more complex account that remains popular in research on phonetics and phonology, sociolinguistics, typology, and language acquisition.
Helping teaching assistants build confidence and community through reciprocal peer observations: a no-budget, low-barrier approach
Authors: Debets Cassandra , Hay Tristyn , Barker Megan K.
Published: February 2025

Teaching assistants (TAs) are incredibly important in our teaching but are often under-supported in their roles—particularly in large courses, with large teams. Depending on instructor workload and TA contract hours, it can be challenging to support the professional development of these key members of the teaching team. To help our TAs develop their teaching and engage in a community of practice, we implemented a reciprocal peer observation. By observing each others’ tutorials in a structured way, we promoted a sense of community and collaborative learning among the TAs with only a small investment of time by instructors. We structured these peer visits using COPUS-TA, an observational tool that guides their tutorial visit and feedback conversations. From this process, our TAs increased their sense of confidence and community. This is a relatively simple approach to give TAs professional development and connection to their peers, embedded directly within a large-enrollment undergraduate course.
Passage-attenuated Powassan virus LI9P protects mice from lethal LI9 challenge and links envelope residue D308 to neurovirulence
Authors: Himmler Grace E. , Mladinich Megan C. , Conde Jonas N. , Gorbunova Elena E. , Lindner Marissa R. , Kim Hwan Keun , Mackow Erich R.
Published: February 2025

Powassan virus (POWV) is an emergent tick-borne flavivirus that causes lethal encephalitic disease and chronic neurologic deficits in surviving patients. POWV-LI9 is a tick-derived isolate that causes neurovirulent disease and age-dependent lethality in mice. Serial passage of VeroE6 cells infected with LI9 resulted in eight amino acid changes in a POWV strain LI9P. LI9P fails to cause neurological sequelae, or lethality in C57BL/6 mice yet elicits neutralizing POWV antibody responses and protects mice from lethal LI9 challenge. Analysis revealed that LI9, but not LI9P, is present at high levels in the CNS, suggesting that LI9P is restricted from neuroinvasion or CNS replication. LI9 and LI9P are distinguished by a D308N envelope change within a domain associated with cell attachment. We evaluated the roles of Env-Domain III residue changes in LI9 virulence and LI9P attenuation using recombinant POWVs (recPOWVs) generated by reverse genetics. Remarkably, mutating D308N in LI9 completely abolished viral lethality and neuroinvasion in 50-week-old mice, reflecting the avirulent phenotype of LI9P. Analysis of the reciprocal N308D change in LI9P only partially restored neuroinvasion and lethality to the LI9P-N308D mutant, indicating that further LI9P residue changes contribute to LI9P attenuation. Consistent with differences in neuroinvasion, we found that rapid LI9P RNA synthesis and corresponding early IFN induction may contribute to LI9P clearance. Collectively, these findings define D308 as a determinant of POWV neuroinvasion and lethality, suggest potential mechanisms for restricted LI9P CNS entry, and reveal passage-attenuated LI9P as a candidate POWV vaccine platform.

IMPORTANCE

Powassan virus (POWV) infection causes a 10% lethal encephalitis, resulting in chronic neurological symptoms in half of survivors. POWV is transmitted in as short as 15 min following tick attachment, demonstrating the need for the development of POWV vaccines and therapeutics. Mechanisms of POWV neurovirulence remain to be defined to inform vaccine and therapeutic design. Cell culture passage has successfully been used to generate live-attenuated flavivirus vaccines. Accordingly, we serially passaged POWV LI9-infected VeroE6 cells and isolated an attenuated POWV strain, LI9P, that fails to cause neurologic sequelae or murine lethality. LI9P elicits neutralizing antibody responses, protects mice from a lethal WT POWV challenge, and is a potential POWV vaccine. Analysis of attenuating mutations in LI9P revealed that changing envelope residue D308N alone in LI9 prevents POWV neurovirulence and lethality in immunocompetent mice. Altogether, this study defines viral determinants of POWV pathogenesis and attenuating mutations that inform the development of live-attenuated POWV vaccines.
Essential genes encoded by the mating-type locus of the human fungal pathogen
Cryptococcus neoformans
Authors: Bian Zhuyun , Xu Ziyan , Peer Anushka , Choi Yeseul , Priest Shelby J. , Akritidou Konstantina , Dasgupta Ananya , Dahlmann Tim A. , Kück Ulrich , Nowrousian Minou , Sachs Matthew S. , Sun Sheng , Heitman Joseph
Published: February 2025

Fungal sexual reproduction is controlled by the mating-type (
MAT
) locus. In contrast to a majority of species in the phylum Basidiomycota that have tetrapolar mating-type systems, the opportunistic human pathogen
Cryptococcus neoformans
employs a bipolar mating-type system, with two mating types (
a
and α) determined by a single
MAT
locus that is unusually large (~120 kb) and contains more than 20 genes. While several
MAT
genes are associated with mating and sexual development, others control conserved cellular processes (e.g., cargo transport and protein synthesis), of which five (
MYO2
,
PRT1
,
RPL22
,
RPL39
, and
RPO41
) have been hypothesized to be essential. In this study, through genetic analysis involving sporulation of heterozygous diploid deletion mutants, as well as in some cases construction and analyses of conditional expression alleles of these genes, we confirmed that with the exception of
MYO2
, both alleles of the other four
MAT
genes are indeed essential for cell viability. We further showed that while
MYO2
is not essential, its function is critical for infectious spore production, faithful cytokinesis, adaptation for growth at high temperature, and pathogenicity
in vivo
. Our results demonstrate the presence of essential genes in the
MAT
locus that are divergent between cells of opposite mating types. We discuss possible mechanisms to maintain functional alleles of these essential genes in a rapidly evolving genomic region in the context of fungal sexual reproduction and mating-type evolution.

IMPORTANCE

Sexual reproduction is essential for long-term evolutionary success. Fungal cell-type identity is governed by the
MAT
locus, which is typically rapidly evolving and highly divergent between different mating types. In this study, we show that the
a
and α alleles of four genes encoded in the
MAT
locus of the opportunistic human fungal pathogen
C. neoformans
are essential. We demonstrate that a fifth gene,
MYO2
, which had been predicted to be essential, is in fact dispensable for cell viability. However, a functional
MYO2
allele is important for cytokinesis and fungal pathogenicity. Our study highlights the need for careful genetic analyses in determining essential genes, which is complementary to high-throughput approaches. Additionally, the presence of essential genes in the
MAT
locus of
C. neoformans
provides insights into the function, maintenance, and evolution of these fast-evolving genomic regions.
Viral protease binds to nucleosomal DNA and cleaves nuclear cGAS that attenuates type I interferon
Authors: Wu Lei , Yan Ya , Yuan Ye , Zhao Zhenchao , Qu Weiyu , Huang Xiangyu , Wang Haiwei , Li Pingwei , Li Xin
Published: February 2025

Nuclear cyclic GMP-AMP synthetase (cGAS) binds to nucleosome with high affinity to prevent its activation by self-DNA. Upon stimulation with double-stranded DNA, cGAS is activated and translocates from the nucleus to the cytoplasm, guided by its N-terminal domain. However, it remains unclear whether viruses can hijack cGAS translocation and regulate its activation. Here, we discovered that the protease 3C of picornavirus Seneca Valley virus (SVV) translocates from the cytoplasm to the nucleus upon viral infection and binds to nuclear DNA. Protease 3C specifically cleaves histone H2A while leaving other histone proteins unaffected. Additionally, DNA binding enhances the protease 3C’s ability to cleave nuclear cGAS, leading to its retention in the nucleus. This, in turn, suppresses the induction of type I interferon (IFN-I) following poly(dA:dT) stimulation. These findings reveal a novel mechanism by which a viral protease binds nuclear DNA, cleaves nuclear cGAS and histone H2A, and thereby mislocalizes cGAS, facilitating immune evasion.

IMPORTANCE

Cyclic GMP-AMP synthetase (cGAS) is robustly expressed in the nucleus and tightly tethered by chromatin to prevent its activation with self-DNA. During stimulation or infection, nuclear cGAS is activated and translocates from the nucleus to the cytoplasm. However, the viral strategies specifically targeting nuclear cGAS are completely unexplored. Here, we discovered that protease 3C of Seneca Valley virus translocates from the cytoplasm to the nucleus upon viral infection, binds to nuclear DNA, and specifically cleaves H2A. Furthermore, DNA binding to 3C enhances the cleavage of nuclear cGAS within its N-terminal domain. The hindrance of cGAS translocation from the nucleus to the cytoplasm results in the suppression of IFN-I induction and leads to immune evasion. This work uncovers a unique mechanism wherein a viral protease binds to nuclear DNA and cleaves nuclear cGAS and histone H2A, leading to viral evasion of cGAS-mediated immune restriction.
Toward the consensus of definitions for the phenomena of antifungal tolerance and persistence in filamentous fungi
Authors: Amich Jorge , Bromley Michael , Goldman Gustavo H. , Valero Clara
Published: February 2025

Antifungal drug tolerance and persistence are being increasingly recognized in fungal pathogens. Accordingly, more and more research is being carried out to characterize and understand these phenomena. However, the terminology and methodology employed in the fungal community lack consensus, particularly for filamentous fungi, as they present further complexities when compared to single-celled microorganisms. Hence, with the aim to ensure consistency in the literature, in this Perspective article, we propose tailored definitions for tolerance and persistence in filamentous fungi and suggest methods to detect and investigate these phenomena in the laboratory.
Pyruvate kinase directly generates GTP in glycolysis, supporting growth and contributing to guanosine toxicity
Authors: She Fukang , Liu Kuanqing , Anderson Brent W. , Pisithkul Tippapha , Li Yanxiu , Fung Danny K. , McCue Tyler , Mulhern William , Amador-Noguez Daniel , Wang Jue D.
Published: February 2025

Guanosine triphosphate (GTP) is essential for macromolecular biosynthesis, and its intracellular levels are tightly regulated in bacteria. Loss of the alarmone (p)ppGpp disrupts GTP regulation in
Bacillus subtilis
, causing cell death in the presence of exogenous guanosine and underscoring the critical importance of GTP homeostasis. To investigate the basis of guanosine toxicity, we performed a genetic selection for spontaneous mutations that suppress this effect, uncovering an unexpected link between GTP synthesis and glycolysis. In particular, we identified suppressor mutations in
pyk
, which encodes pyruvate kinase, a glycolytic enzyme. Metabolomic analysis revealed that inactivating pyruvate kinase prevents guanosine toxicity by reducing GTP levels. Although traditionally associated with ATP generation via substrate-level phosphorylation,
B. subtilis
pyruvate kinase
in vitro
was found to produce GTP and UTP approximately 10 and three times more efficiently than ATP, respectively. This efficient GTP/UTP synthesis extends to
Enterococcus faecalis
and
Listeria monocytogenes
, challenging the conventional understanding of pyruvate kinase’s primary role in ATP production. These findings support a model in which glycolysis directly contributes to GTP synthesis, fueling energy-demanding processes, such as protein translation. Finally, we observed a synergistic essentiality of the Δ
ndk
Δ
pyk
double mutant specifically on glucose, indicating that pyruvate kinase and nucleoside diphosphate kinase are the major contributors to nucleoside triphosphate production and complement each other during glycolysis. Our work highlights the critical role of nucleotide selectivity in pyruvate kinase and its broader implications in cellular physiology.

IMPORTANCE

In this study, we reveal that pyruvate kinase, a key glycolytic enzyme, primarily generates GTP from GDP in
Bacillus subtilis
, relative to other nucleotide triphosphates, such as ATP. This finding, uncovered through genetic selection for mutants that suppress toxic GTP overaccumulation, challenges the conventional understanding that pyruvate kinase predominantly produces ATP via substrate-level phosphorylation. The substantial role of GTP production by pyruvate kinase suggests a model where glycolysis rapidly and directly supplies GTP as the energy currency to power high GTP-demanding processes such as protein synthesis. Our results underscore the importance of nucleotide selectivity (ATP vs GTP vs UTP) in shaping the physiological state and fate of the cell, prompting further exploration into the mechanisms and broader implications of this selective nucleotide synthesis.
Carbon source, cell density, and the microbial community control inhibition of
V. cholerae
surface colonization by environmental nitrate
Authors: James Jamaurie , Santos Renato E.R.S. , Watnick Paula I.
Published: February 2025

The intestinal diarrheal pathogen
Vibrio cholerae
colonizes the host terminal ileum, a microaerophilic, glucose-poor, nitrate-rich environment. In this environment,
V. cholerae
respires nitrate and increases transport and utilization of alternative carbon sources via the cAMP receptor protein (CRP), a transcription factor that is active during glucose scarcity. Here, we show that
V. cholerae
nitrate respiration in aerated cultures is under control of CRP and, therefore, glucose availability.
V. cholerae
nitrate respiration results in extracellular accumulation of nitrite because
V. cholerae
does not possess the machinery for nitrite reduction. This nitrite inhibits
V. cholerae
biofilm formation via an as-yet unelucidated mechanism that depends on the high cell density master regulator HapR. The genome of
Paracoccus aminovorans
, an intestinal microbe identified in the microbiome of cholera patients that has been shown to enhance
V. cholerae
biofilm accumulation in the neonatal mouse gut, encodes enzymes that reduce nitrite to nitrogen gas. We report that, in nitrate-supplemented co-cultures,
P. aminovorans
metabolizes the nitrite generated by
V. cholerae
and, thereby, enhances
V. cholerae
surface accumulation. We propose that
V. cholerae
biofilm formation in the host intestine is limited by nitrite production but can be rescued by intestinal microbes such as
P. aminovorans
that have the capacity to metabolize nitrite. Such microbes increase
V. cholerae
colonization of the host ileum and predispose to symptomatic infection.

IMPORTANCE

Vibrio cholerae
colonizes the terminal ileum where both oxygen and nitrate are available as terminal electron acceptors.
V. cholerae
biofilm formation is inhibited by nitrate due to its conversion to nitrite during
V. cholerae
respiration. When co-cultured with a microbe that can further reduce nitrite,
V. cholerae
surface accumulation in the presence of nitrate is rescued. The contribution of biofilm formation to ileal colonization depends on the composition of the microbiota. We propose that the intestinal microbiota predisposes mammalian hosts to cholera by consuming the nitrite generated by
V. cholerae
in the terminal ileum. Differences in the intestinal abundance of nitrite-reducing microbes may partially explain the differential susceptibility of humans to cholera and the resistance of non-human mammalian models to intestinal colonization with
V. cholerae
.
Exploring the differential localization of protein kinase A isoforms in
Candida albicans
Authors: Hossain Saif , Liu Zhongle , Robbins Nicole , Cowen Leah E.
Published: February 2025

The cAMP-dependent protein kinase A (PKA) plays important roles in a wide range of biological processes in eukaryotic organisms. In the fungal pathogen
Candida albicans
, PKA is a critical regulator of morphological transitions, which are a key virulence trait. PKA is composed of two catalytic isoforms, Tpk1 and Tpk2, which are often thought to act together in a complex with the regulatory subunit Bcy1. Although Tpk1 and Tpk2 have some redundant functions, they also have distinct cellular functions for which the mechanistic underpinnings remain largely elusive. Here, we constructed functional GFP-tagged fusion proteins for Tpk1, Tpk2, and Bcy1 to explore the localization of PKA isoforms. We observed that the PKA holoenzyme is mainly found in the cytoplasm, as Bcy1 is always excluded from the nucleus. Under glucose-replete conditions, both Tpk1 and Tpk2 translocate into the nucleus from the cytosol. In the presence of glycerol, Tpk1 resides in the cytosol, whereas Tpk2 and Bcy1 become enriched on the vacuolar membrane. As the C-terminal domains of Tpk are highly homologous, we investigated the localization and function of hybrid Tpk proteins with exchanged N-terminal domains. We found the catalytic C-terminus of Tpk1 is required for morphogenesis in solid medium, whereas the C-terminus of Tpk2 is critical for filamentation in liquid. Interestingly, the N-terminus of Tpk2 drives its localization to the vacuolar membrane. Our work highlights environmentally contingent localization patterns for the PKA subunits and suggests that the nuclear localization of Tpk is not sufficient to induce the filamentation program in a leading fungal pathogen of humans.

IMPORTANCE

Fungal pathogens have a devastating impact on human health worldwide. They infect billions of people and kill more than 2.5 million per year.
Candida albicans
is a leading human fungal pathogen responsible for causing life-threatening systemic disease in immunocompromised individuals. A key virulence trait in
C. albicans
is the ability to switch between yeast and filamentous forms. The conserved protein kinase A (PKA) regulates diverse functions in the cell, including growth and filamentation. Although PKA has been studied in
C. albicans
for decades, the subcellular localization of PKA has not been thoroughly investigated. Here, we constructed functional GFP-tagged PKA subunits to explore their localization. We identified differential localization patterns for the PKA subunits that are carbon-source dependent and report that these proteins localize into foci in response to diverse environmental stresses. These findings further our understanding of a critical regulator of growth and virulence in
C. albicans
.
Performance of ddPCR-GNB for microbial diagnosis of suspected bloodstream infection due to the four most common gram-negative bacteria: a prospective, multicenter study
Authors: Weng Shan-shan , Lin Ling , Xie Jian-feng , Hu Bang-chuan , Ma Xue-qing , Xia Jiang , Jiang Yan , Zhou Hua , wu Xiao-yan , Jin Yu-hong , Wu Guo-qiu , Yang Yi , Sun Ren-Hua , Yu Yun-song , Zhao Dong-dong
Published: February 2025

We aimed to validate the performance of ddPCR-GNB, a plasma droplet digital PCR panel targeting the four most common gram-negative bacteria, for patients with suspected bloodstream infection (BSI). Patients suspected of having BSIs were prospectively enrolled. The results of blood culture and ddPCR-GNB were compared, and cases with discordant results were arbitrated on the basis of additional microbiological results and clinical evidence. A total of 1,041 patients were enrolled. Blood culture and ddPCR-GNB results were positive for targeted bacteria in 6.3% and 31.7% of patients, respectively. The overall per-patient sensitivity and specificity of ddPCR-GNB for proven BSIs were 98.5% (95% CI, 91.9% to 99.9%) and 72.8% (95% CI, 69.9% to 75.5%), respectively; the negative predictive value was 99.9% (95% CI, 99.2% to 100%). The discordant results included 265 cases (25.5%) with negative companion blood culture results but positive ddPCR-GNB results and one case vice versa. A total of 23.7% of the cases were attributed to probable (
n
= 126) or possible (
n
= 121) BSIs. If both probable and possible BSIs were assumed to be true positives, the per-patient specificity of ddPCR-GNB would be 97.5%. The ddPCR-GNB panel demonstrated excellent microbial diagnostic performance in identifying targeted bacteria for patients with suspected BSI.

IMPORTANCE

This is the first multicentral study to validate the clinical performance of ddPCR in etiological diagnosis of bloodstream infection. The results showed that ddPCR has high sensitivity and increased detection rate compared with blood culture. The study proved the potential of the ddPCR method in microbial diagnoses.
Synergistic impact of macrolide resistance and H3N2 infection on
M. pneumoniae
outbreak in children
Authors: Chen Jiali , Wang Yingdan , Cheng Juan , Ma Yunping , Zhang Xin , Bai Xuezhou , Rehati Palizhati , Cui Huashun , Wu Fan , Pan Qiuhui , Huang Jinghe
Published: February 2025

In November 2023, there was a substantial increase in the incidence of
Mycoplasma pneumoniae
infections in China following waves of SARS-CoV-2 Omicron variant and influenza outbreaks. This study aimed to elucidate the epidemiological features and clinical implications of
M. pneumoniae
infections in children and explore the potential influence of SARS-CoV-2 Omicron variants and influenza A infections on the
M. pneumoniae
outbreak. Among 38,668 children with lower respiratory tract infections from January to December 2023, 11,919 tested positive for
M. pneumoniae
, predominantly between October and December. The majority of the children with
M. pneumoniae
were aged 5–10 years, with type 1 strains and macrolide-resistant
M. pneumoniae
strains having the highest prevalence rates. Statistical analysis revealed elevated C-reactive protein, neutrophil, and monocyte levels and decreased lymphocyte, basophil, and eosinophil counts in
M. pneumoniae
-positive children.
M. pneumoniae
-positive children also presented significantly increased neutralizing antibody levels against preceding influenza A (H3N2) but not against SARS-CoV-2 Omicron variants. A parallel trend was observed between
M. pneumoniae
and H3N2 prevalence from June to December 2023. The emergence of macrolide-resistant strains and prior influenza A (H3N2) epidemics notably contributed to the
M. pneumoniae
outbreak. These findings suggested that H3N2 infection facilitates
M. pneumoniae
infection through various mechanisms. This study underscores the complex interactions between respiratory pathogens and highlights the need for comprehensive surveillance and response strategies.

IMPORTANCE

This study identified key factors contributing to an outbreak of
Mycoplasma pneumoniae
that affected 11,919 children. The influencing factors included a high prevalence of macrolide-resistant epidemic strains (94.2%) and significantly higher H3N2 neutralizing antibody levels (
P
< 0.0001) stimulated by the preceding H3N2 influenza epidemic. These findings highlight the complex relationship between the prevalence of
M. pneumoniae
and H3N2 infection in children, indicating that it is necessary to consider pathogen interactions in respiratory disease management by continuously monitoring respiratory pathogens. The emergence of macrolide-resistant strains in China and the previous H3N2 influenza epidemic significantly exacerbated the severity of the
M. pneumoniae
outbreak. H3N2 infection potentially amplifies Mycoplasma transmission. This study elucidates the epidemiological and clinical aspects of
M. pneumoniae
infections in children, yields insights regarding the cause of the outbreak, and provides guidance for improving respiratory infection management.