bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting the relationship between complement and ulcerative colitis
Authors: Ma Yujie , Zhang Kaicheng , Wu Yuanyuan , Fu Xiaoyan , Liang Shujuan , Peng Meiyu , Guo Juntang , Liu Meifang
Published: September 2023

Ulcerative colitis (UC) is an inflammatory bowel disorder (IBD) characterized by relapsing chronic inflammation of the colon that causes continuous mucosal inflammation. The global incidence of UC is steadily increasing. Immune mechanisms are involved in the pathogenesis of UC, of which complement is shown to play a critical role by inducing local chronic inflammatory responses that promote tissue damage. However, the function of various complement components in the development of UC is complex and even paradoxical. Some components (e.g. C1q, CD46, CD55, CD59, and C6) are shown to safeguard the intestinal barrier and reduce intestinal inflammation, while others (e.g. C3, C5, C5a) can exacerbate intestinal damage and accelerate the development of UC. The complement system was originally thought to function primarily in an extracellular mode; however, recent evidence indicates that it can also act intracellularly as the complosome. The current study provides an overview of current studies on complement and its role in the development of UC. While there are few studies that describe how intracellular complement contributes to UC, we discuss potential future directions based on related publications. We also highlight novel methods that target complement for IBD treatment.
The RAV transcription factor TEMPRANILLO1 involved in ethylene‐mediated delay of chrysanthemum flowering
Authors: Cheng Hua , Wang Qingguo , Zhang Zixin , Cheng Peilei , Song Aiping , Zhou Lijie , Wang Likai , Chen Sumei , Chen Fadi , Jiang Jiafu
Published: September 2023

TEMPRANILLO1 (TEM1) is a transcription factor belonging to related to ABI3 and VP1 family, which is also known as ethylene response DNA‐binding factor 1 and functions as a repressor of flowering in Arabidopsis. Here, a putative homolog of AtTEM1 was isolated and characterized from chrysanthemum, designated as CmTEM1. Exogenous application of ethephon leads to an upregulation in the expression of CmTEM1. Knockdown of CmTEM1 promotes floral initiation, while overexpression of CmTEM1 retards floral transition. Further phenotypic observations suggested that CmTEM1 involves in the ethylene‐mediated inhibition of flowering. Transcriptomic analysis established that expression of the flowering integrator CmAFL1, a member of the APETALA1/FRUITFULL subfamily, was downregulated significantly in CmTEM1‐overexpressing transgenic plants compared with wild‐type plants but was verified to be upregulated in amiR‐CmTEM1 lines by quantitative RT‐PCR. In addition, CmTEM1 is capable of binding to the promoter of the CmAFL1 gene to inhibit its transcription. Moreover, the genetic evidence supported the notion that CmTEM1 partially inhibits floral transition by targeting CmAFL1. In conclusion, these findings demonstrate that CmTEM1 acts as a regulator of ethylene‐mediated delayed flowering in chrysanthemum, partly through its interaction with CmAFL1.
Dicer‐like2b suppresses the wiry leaf phenotype in tomato induced by tobacco mosaic virus
Authors: Ma Liqun , Zhang Xi , Deng Zhiqi , Zhang Peiyu , Wang Tian , Li Ran , Li Jinyan , Cheng Ke , Wang Jubin , Ma Nan , Qu Guiqin , Zhu Benzhong , Fu Daqi , Luo Yunbo , Li Feng , Zhu Hongliang
Published: September 2023

Dicer‐like (DCL) proteins are principal components of RNA silencing, a major defense mechanism against plant virus infections. However, their functions in suppressing virus‐induced disease phenotypes remain largely unknown. Here, we identified a role for tomato (Solanum lycopersicum) DCL2b in regulating the wiry leaf phenotype during defense against tobacco mosaic virus (TMV). Knocking out SlyDCL2b promoted TMV accumulation in the leaf primordium, resulting in a wiry phenotype in distal leaves. Biochemical and bioinformatics analyses showed that 22‐nt virus‐derived small interfering RNAs (vsiRNAs) accumulated less abundantly in slydcl2b mutants than in wild‐type plants, suggesting that SlyDCL2b‐dependent 22‐nt vsiRNAs are required to exclude virus from leaf primordia. Moreover, the wiry leaf phenotype was accompanied by upregulation of Auxin Response Factors (ARFs), resulting from a reduction in trans‐acting siRNAs targeting ARFs (tasiARFs) in TMV‐infected slydcl2b mutants. Loss of tasiARF production in the slydcl2b mutant was in turn caused by inhibition of miRNA390b function. Importantly, silencing SlyARF3 and SlyARF4 largely restored the wiry phenotype in TMV‐infected slydcl2b mutants. Our work exemplifies the complex relationship between RNA viruses and the endogenous RNA silencing machinery, whereby SlyDCL2b protects the normal development of newly emerging organs by excluding virus from these regions and thus maintaining developmental silencing.
Russia's spatial anxiety and the construction of geographical knowledge
Authors: Smirnova Vera
Published: September 2023

This commentary addresses the dimensions of Russia's ‘spatial anxiety’—its inability to come to terms with the territorial delimitations of neighbouring states and, consequently, the preoccupation of mainstream political geography with the study of Russia‐centric territorial representations. Although geographical inquiry contributed substantially to understanding Russian territorial politics, most studies are often reduced to an analysis of the official Russian geographical canon. The purpose of this commentary is to unpack these disciplinary approaches by drawing attention to the local, indigenous and peasant geographies that the statist perspectives have unearthed and utilised, while at the same time accentuating the two assumptions that this project might imply—on the re‐territorialisation of the federation and the decolonisation of Russian area studies.
Organ xenotransplantation acceptance in veterinary students: A multicentric opinion study in Spain
Authors: Martínez‐Alarcón Laura , Flores‐Medina Juan , Ramis Guillermo , Gómez‐Laguna Jaime , Moll Xavier , Falceto Victoria , San Román‐Ascaso Fidel , San Román‐Llorens Fidel , Quereda Juan José , Herrero Juan Manuel , Mendonça Livia , Martin‐Barrasa José Luis , Fernández Olga María , Muñoz Antonio , Ramírez Pablo , Gutiérrez Pedro , López‐Chicheri Isabel , López‐Navas Ana , Ríos Antonio
Published: September 2023

Background

The shortage of available transplant organs has made it necessary to search for alternatives, one of which is xenotransplantation. However, the use of animal organs could face rejection from society and the personnel involved in its implementation. Objectives: (a) to analyze the attitudes of Veterinary Degree students in six Spanish Universities towards xenotransplantation; and (b) to determine the factors that affect its acceptance.

Methods

Of the 2815 students surveyed in the degree program, 2683 valid surveys were obtained. Attitudes towards organ xenotransplantation were evaluated using a validated questionnaire of organ donation.

Results

If xenotransplantation was confirmed as a clinical reality, 93% (n = 2493) of those surveyed would accept a xenotransplanted organ, whilst 7% would not. If the results of xenotransplantation were worse than those obtained with human donors and it entailed more risk, 12% (n = 318) would be in favor. 56% (n = 1497) of the students would accept a xenotransplantation provisionally pending the arrival of a human organ. Attitudes towards xenotransplantation were affected by the academic year in which a student was studying, with more favorable attitudes among students in the last year (88% in first year vs. 95% in fifth year;p < .001). More favorable attitudes are also observed depending on the attitude they have towards organ transplantation, with those students being more in favor of donating their organs when they die (94% vs. 88%;p < .001).

Conclusion

Veterinary students would have a very favorable attitude toward xenotransplantation if these animal organs functioned as well as human organs. Therefore, these students could play an important role in the future promotion of this technique.
High-Dimensional Uncertainty Quantification of High-Pressure Turbine Vane Based on Multifidelity Deep Neural Networks
Authors: Li Zhihui , Montomoli Francesco , Casari Nicola , Pinelli Michele
Published: September 2023

In this work, a new multifidelity (MF) uncertainty quantification (UQ) framework is presented and applied to the LS89 nozzle modified by fouling. Geometrical uncertainties significantly influence the aerodynamic performance of gas turbines. One representative example is given by the airfoil shape modified by fouling deposition, as in turbine nozzle vanes, which generates high-dimensional input uncertainties. However, the traditional UQ approaches suffer from the curse of dimensionality phenomenon in predicting the influence of high-dimensional uncertainties. Thus, a new approach based on multifidelity deep neural networks (MF-DNN) was proposed in this paper to solve the high-dimensional UQ problem. The basic idea of MF-DNN is to ensure the approximation capability of neural networks based on abundant low-fidelity (LF) data and few high-fidelity (HF) data. The prediction accuracy of MF-DNN was first evaluated using a 15-dimensional benchmark function. An affordable turbomachinery UQ platform was then built based on key components including the MF-DNN model, the sampling module, the parameterization module and the statistical processing module. The impact of fouling deposition on LS89 nozzle vane flow was investigated using the proposed UQ framework. In detail, the MF-DNN was fine-tuned based on bi-level numerical simulation results: the 2D Euler flow field as low-fidelity data and the 3D Reynolds-averaged Navier–Stokes (RANS) flow field as high-fidelity data. The UQ results show that the total pressure loss of LS89 vane is increased by at most 17.1% or reduced by at most 4.3%, while the mean value of the loss is increased by 3.4% compared to the baseline. The main reason for relative changes in turbine nozzle performance is that the geometric uncertainties induced by fouling deposition significantly alter the intensity of shock waves near the throat area and trailing edge. The developed UQ platform could provide a useful tool in the design and optimization of advanced turbomachinery considering high-dimensional input uncertainties.
Quantum double structure in cold atom superfluids
Authors: Génetay Johansen Emil , Vale Chris , Simula Tapio
Published: September 2023

The theory of topological quantum computation is underpinned by two important classes of models. One is based on non-abelian Chern–Simons theory, which yields the so-called SU(2)k anyon models that often appear in the context of electrically charged quantum fluids. The physics of the other is captured by symmetry broken Yang–Mills theory in the absence of a Chern–Simons term and results in the so-called quantum double models. Extensive resources have been invested into the search for SU(2)k anyon quasi-particles, in particular, the so-called Ising anyons (k = 2) of which Majorana zero modes are believed to be an incarnation. In contrast to the SU(2)k models, quantum doubles have attracted little attention in experiments despite their pivotal role in the theory of error correction. Beyond topological error correcting codes, the appearance of quantum doubles has been limited to contexts primarily within mathematical physics, and as such, they are of seemingly little relevance for the study of experimentally tangible systems. However, recent works suggest that quantum double anyons may be found in spinor Bose–Einstein condensates. In light of this, the core purpose of this article is to provide a self-contained exposition of the quantum double structure, framed in the context of spinor condensates, by constructing explicitly the quantum doubles for various ground state symmetry groups and discuss their experimental realisability. We also derive analytically an equation for the quantum double Clebsch–Gordan coefficients from which the relevant braid matrices can be worked out. Finally, the existence of a particle-vortex duality is exposed and illuminated upon in this context.
Active intensity vortex and stagnation point singularities in a shallow underwater waveguide
Authors: Dahl Peter H. , Dall'Osto David R. , Hodgkiss William S.
Published: September 2023

Vector acoustic properties of a narrowband acoustic field are observed as a function of range from a source towed in waters of depth 77 m on the New England Mud Patch. At the source frequency (43 Hz), the waveguide supported three trapped modes, with mode 2 weakly excited owing to the towed source depth. The receiving sensor was positioned 1.45 m above the seafloor with a sampling range aperture of 2500 m. The vector acoustics observations enabled study of vortex regions that encompass two singular points for active acoustic intensity: the vortex point, which is co-located with a dislocation, and stagnation point. Interpretative modeling, based on the normal modes and using a geoacoustic model consistent with those emerging from studies conducted at this location, is in agreement with these measurements. Model-data comparisons were based on the first-order variables of acoustic pressure and velocity along with inverse Hankel transforms, which yield normalized horizontal wavenumber spectra, and second-order variables in the form of horizontal and vertical intensity as well as non-dimensional intensity-based ratios. These measures provide a degree of observational confirmation of some vortex region properties. Both observations and modeling point to a gradual deepening of such regions with increasing range owing to sediment attenuation.
Using a vertical three-mass computational model of the vocal folds to match human phonation of three adult males
Authors: Perrine Brittany L. , Scherer Ronald C.
Published: September 2023

Computer models of phonation are used to study various parameters that are difficult to control, measure, and observe in human subjects. Imitating human phonation by varying the prephonatory conditions of computer models offers insight into the variations that occur across human phonatory production. In the present study, a vertical three-mass computer model of phonation [Perrine, Scherer, Fulcher, and Zhai (2020). J. Acoust. Soc. Am. 147, 1727–1737], driven by empirical pressures from a physical model of the vocal folds (model M5), with a vocal tract following the design of Ishizaka and Flanagan [(1972). Bell Sys. Tech. J. 51, 1233–1268] was used to match prolonged vowels produced by three male subjects using various pitch and loudness levels. The prephonatory conditions of tissue mass and tension, subglottal pressure, glottal diameter and angle, posterior glottal gap, false vocal fold gap, and vocal tract cross-sectional areas were varied in the model to match the model output with the fundamental frequency, alternating current airflow, direct current airflow, skewing quotient, open quotient, maximum flow negative derivative, and the first three formant frequencies from the human production. Parameters were matched between the model and human subjects with an average overall percent mismatch of 4.40% (standard deviation = 6.75%), suggesting a reasonable ability of the simple low dimensional model to mimic these variables.
From the morphospace to the soundscape: Exploring the diversity and functional morphology of the fish inner ear, with a focus on elasmobranchs
Authors: Chapuis L. , Yopak K. E. , Radford C. A.
Published: September 2023

Fishes, including elasmobranchs (sharks, rays, and skates), present an astonishing diversity in inner ear morphologies; however, the functional significance of these variations and how they confer auditory capacity is yet to be resolved. The relationship between inner ear structure and hearing performance is unclear, partly because most of the morphological and biomechanical mechanisms that underlie the hearing functions are complex and poorly known. Here, we present advanced opportunities to document discontinuities in the macroevolutionary trends of a complex biological form, like the inner ear, and test hypotheses regarding what factors may be driving morphological diversity. Three-dimensional (3D) bioimaging, geometric morphometrics, and finite element analysis are methods that can be combined to interrogate the structure-to-function links in elasmobranch fish inner ears. In addition, open-source 3D morphology datasets, advances in phylogenetic comparative methods, and methods for the analysis of highly multidimensional shape data have leveraged these opportunities. Questions that can be explored with this toolkit are identified, the different methods are justified, and remaining challenges are highlighted as avenues for future work.
Remote passive acoustic signal detection using multi-scale correlation networks and network spectrum distance in marine environment
Authors: Zhang Hongwei , Wang Haiyan , Liang Xuanming , Yan Yongsheng , Shen Xiaohong
Published: September 2023

Detecting acoustic signals in the ocean is crucial for port and coastal security, but existing methods often require informative priors. This paper introduces a new approach that transforms acoustic signal detection into network characterization using a MCN construction method. The method constructs a network representation of the acoustic signal by measuring pairwise correlations at different time scales. It proposes a network spectrum distance method that combines information geometry and graph signal processing theory to characterize these complex networks. By comparing the spectra of two networks, the method quantifies their similarity or dissimilarity, enabling comparisons of multi-scale correlation networks constructed from different time series data and tracking changes in nonlinear dynamics over time. The effectiveness of these methods is substantiated through comprehensive simulations and real-world data collected from the South China Sea. The results illustrate that the proposed approach attains a significant detection probability of over 90% when the signal-to-noise ratio exceeds −18 dB, whereas existing methods require a signal-to-noise ratio of at least −15 dB to achieve a comparable detection probability. This innovative approach holds promising applications in bolstering port security, facilitating coastal operations, and optimizing offshore activities by enabling more efficient detection of weak acoustic signals.
Oral administration of a 2-aminopyrimidine robenidine analogue (NCL195) significantly reduces
Staphylococcus aureus
infection and reduces
Escherichia coli
infection in combination with sub-inhibitory colistin concentrations in a bioluminescent mouse model
Authors: Nguyen Hang Thi , Venter Henrietta , Woolford Lucy , Young Kelly A. , McCluskey Adam , Garg Sanjay , Sapula Sylvia S. , Page Stephen W. , Ogunniyi Abiodun David , Trott Darren J.
Published: September 2023

We have previously reported promising
in vivo
activity of the first-generation 2-aminopyramidine robenidine analogue NCL195 against Gram-positive bacteria (GPB) when administered via the systemic route. In this study, we examined the efficacy of oral treatment with NCL195 (± low-dose colistin) in comparison to oral moxifloxacin in bioluminescent
Staphylococcus aureus
and
Escherichia coli
peritonitis-sepsis models. Four oral doses of 50 mg/kg NCL195, commencing immediately post-infection, were administered at 4 h intervals in the
S. aureus
peritonitis-sepsis model. We used a combination of four oral doses of 50 mg/kg NCL195 and four intraperitoneal doses of colistin at 0.125 mg/kg, 0.25 mg/kg, or 0.5 mg/kg in the
E. coli
peritonitis-sepsis model. Subsequently, the dose rates of four intraperitoneal doses of colistin were increased to 0.5 mg/kg, 1 mg/kg, or 2 mg/kg at 4 h intervals to treat a colistin-resistant
E. coli
infection. In the
S. aureus
infection model, oral treatment of mice with NCL195 resulted in significantly reduced
S. aureus
infection loads (
P
< 0.01) and longer survival times (
P
< 0.001) than vehicle-only treated mice. In the
E. coli
infection model, co-administration of NCL195 and graded doses of colistin resulted in a dose-dependent significant reduction in colistin-susceptible (
P
< 0.01) or colistin-resistant (
P
< 0.05)
E. coli
loads compared to treatment with colistin alone at similar concentrations. Our results confirm that NCL195 is a potential candidate for further preclinical development as a specific treatment for multidrug-resistant infections, either as a stand-alone antibiotic for GPB or in combination with sub-inhibitory concentrations of colistin for Gram-negative bacteria.
Expression of V-nitrogenase and Fe-nitrogenase in
Methanosarcina acetivorans
is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase
Authors: Chanderban Melissa , Hill Christopher A. , Dhamad Ahmed E. , Lessner Daniel J.
Published: September 2023

All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N
2
) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown.
Methanosarcina acetivorans
contains
nif
,
vnf
, and
anf
gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by
M. acetivorans
in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the
nif
,
vnf
, and/or
anf
gene clusters. The availability of Mo and V significantly affected growth of
M. acetivorans
with N
2
but not with NH
4
Cl.
M. acetivorans
exhibited the fastest growth rate and highest cell yield during growth with N
2
in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the
nif
operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas
vnf
and
anf
transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in
M. acetivorans
is tightly controlled and dependent on Mo-nitrogenase expression.

IMPORTANCE

Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
Alterations in gp120 glycans or the gp41 fusion peptide-proximal region modulate the stability of the human immunodeficiency virus (HIV-1) envelope glycoprotein pretriggered conformation
Authors: Zhang Zhiqing , Wang Qian , Nguyen Hanh T. , Chen Hung-Ching , Chiu Ta-Jung , Smith III Amos B. , Sodroski Joseph G.
Published: September 2023

The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer mediates entry into host cells by binding receptors, CD4 and CCR5/CXCR4, and fusing the viral and cell membranes. In infected cells, cleavage of the gp160 Env precursor yields the mature Env trimer, with gp120 exterior and gp41 transmembrane Env subunits. Env cleavage stabilizes the State-1 conformation, which is the major target for broadly neutralizing antibodies, and decreases the spontaneous sampling of more open Env conformations that expose epitopes for poorly neutralizing antibodies. During HIV-1 entry into cells, CD4 binding drives the metastable Env from a pretriggered (State-1) conformation into more “open,” lower-energy states. Here, we report that changes in two dissimilar elements of the HIV-1 Env trimer, namely particular gp120 glycans and the gp41 fusion peptide-proximal region (FPPR), can independently modulate the stability of State 1. Individual deletion of several gp120 glycans destabilized State 1, whereas removal of a V1 glycan resulted in phenotypes indicative of a more stable pretriggered Env conformation. Likewise, some alterations of the gp41 FPPR decreased the level of spontaneous shedding of gp120 from the Env trimer and stabilized the pretriggered State-1 Env conformation. State-1-stabilizing changes were additive and could suppress the phenotypes associated with State-1-destabilizing alterations in Env. Our results support a model in which multiple protein and carbohydrate elements of the HIV-1 Env trimer additively contribute to the stability of the pretriggered (State-1) conformation. The Env modifications identified in this study will assist efforts to characterize the structure and immunogenicity of the metastable State-1 conformation.

IMPORTANCE

The elicitation of antibodies that neutralize multiple strains of HIV-1 is an elusive goal that has frustrated the development of an effective vaccine. The pretriggered shape of the HIV-1 envelope glycoprotein (Env) spike on the virus surface is the major target for such broadly neutralizing antibodies. The “closed” pretriggered Env shape resists the binding of most antibodies but is unstable and often assumes “open” shapes that elicit ineffective antibodies. We identified particular changes in both the protein and the sugar components of the Env trimer that stabilize the pretriggered shape. Combinations of these changes were even more effective at stabilizing the pretriggered Env than the individual changes. Stabilizing changes in Env could counteract the effect of Env changes that destabilize the pretriggered shape. Locking Env in its pretriggered shape will assist efforts to understand the Env spike on the virus and to incorporate this shape into vaccines.
Limiting viral replication in hepatocytes alters Rift Valley fever virus disease manifestations
Authors: Xu Lingqing , Paine Alden C. , Barbeau Dominique J. , Alencastro Frances , Duncan Andrew W. , McElroy Anita K.
Published: September 2023

Rift Valley fever virus (RVFV) causes mild to severe disease in humans and livestock. Outbreaks of RVFV have been reported throughout Africa and have spread outside Africa since 2000, calling for urgent worldwide attention to this emerging virus. RVFV directly infects the liver, and elevated transaminases are a hallmark of severe RVFV infection. However, the specific contribution of viral replication in hepatocytes to pathogenesis of RVFV remains undefined. To address this, we generated a recombinant miRNA-targeted virus, RVFVmiR-122, to limit hepatocellular replication. MicroRNAs are evolutionarily conserved non-coding RNAs that regulate mRNA expression by targeting them for degradation. RVFVmiR-122 includes an insertion of four target sequences of the liver-specific miR-122. In contrast to control RVFVmiR-184, which contains four target sequences of mosquito-specific miR-184, RVFVmiR-122 has restricted replication
in vitro
in primary mouse hepatocytes. RVFVmiR-122-infected C57BL/6 mice survived acute hepatitis and instead developed late-onset encephalitis. This difference in clinical outcome was eliminated in
Mir-122 KO
mice, confirming the specificity of the finding. Interestingly, C57BL/6 mice infected with higher doses of RVFVmiR-122 had a higher survival rate which was correlated with faster clearance of virus from the liver, suggesting a role for activation of host immunity in the phenotype. Together, our data demonstrate that miR-122 can specifically restrict the replication of RVFVmiR-122 in liver tissue both
in vitro
and
in vivo
, and this restriction alters the clinical course of disease following RVFVmiR-122 infection.

IMPORTANCE

Rift Valley fever virus (RVFV) is a hemorrhagic fever virus that causes outbreaks in humans and livestock throughout Africa and has spread to continents outside Africa since 2000. However, no commercial vaccine or treatment is currently available for human use against RVFV. Although the liver has been demonstrated as a key target of RVFV, the contribution of viral replication in hepatocytes to overall RVFV pathogenesis is less well defined. In this study we addressed this question by using a recombinant miRNA-targeted virus with restricted replication in hepatocytes. We gained a better understanding of how this individual cell type contributes to the development of disease caused by RVFV. Techniques used in this study provide an innovative tool to the RVFV field that could be applied to study the consequences of limited RVFV replication in other target cells.
PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell- and tissue-specific manner
Authors: Kerr Catherine M. , Parthasarathy Srivatsan , Schwarting Nancy , O'Connor Joseph J. , Pfannenstiel Jessica J. , Giri Emily , More Sunil , Orozco Robin C. , Fehr Anthony R.
Published: September 2023

ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD
+
to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a murine hepatitis virus (MHV) Mac1 mutant virus in bone-marrow-derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture and
in vivo
, we produced PARP12
−/−
mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and mice. In addition, liver pathology was also increased in A59-infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice.

IMPORTANCE

Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
The major role of
Listeria monocytogenes
folic acid metabolism during infection is the generation of N-formylmethionine
Authors: Feng Ying , Chang Shannon K. , Portnoy Daniel A.
Published: September 2023

Folic acid and its derivatives (folates) play central roles in one-carbon metabolism, necessary for the synthesis of purines, pyrimidines, and some amino acids. Antifolate drugs are widely used as broad-spectrum antibiotics for bacterial infections, including listeriosis, a disease caused by the facultative intracellular pathogen
Listeria monocytogenes
. However, folate-derived metabolites required during bacterial infection are poorly understood. Here, we report that
L. monocytogenes
encodes two enzymes, methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (FolD) and formyltetrahydrofolate synthetase (Fhs), that catalyze the formation of N10-formyltetrahydrofolate, a critical intermediate in folate metabolism. N10-formyltetrahydrofolate is an essential carbon donor for biosynthesis of purines and N-formylmethionine, the amino acid used during initiation of bacteria translation. While
L. monocytogenes
mutants lacking Fhs had no observable defects and mutants lacking FolD had moderate virulence defects, mutants lacking both were highly attenuated in mice, especially in the liver. We compared the growth and virulence of mutants that were unable to synthesize folates with mutants unable to generate folate downstream products, including purines, thymidine, and N-formylmethionine. Mutants unable to synthesize N-formylmethionine behaved almost identically to FolD/Fhs double mutants during growth in broth or macrophages, but most importantly, were similarly attenuated to mutants unable to make folates, both of which had approximately 4-log
10
less colony-forming units in the livers compared with wild-type
L. monocytogenes
. The purine auxotrophic mutants were only 1.5-log
10
less virulent, and the thymidine mutants were fully virulent in the mouse infection model. These results strongly suggest that the main role of
L. monocytogenes
folates during infection is the generation of N-formylmethionine.

Importance

Folic acid is an essential vitamin for bacteria, plants, and animals. The lack of folic acid leads to various consequences such as a shortage of amino acids and nucleotides that are fundamental building blocks for life. Though antifolate drugs are widely used for antimicrobial treatments, the underlying mechanism of bacterial folate deficiency during infection is unclear. This study compares the requirements of different folic acid end-products during the infection of
Listeria monocytogenes
, a facultative intracellular pathogen of animals and humans. The results reveal the critical importance of N-formylmethionine, the amino acid used by bacteria to initiate protein synthesis. This work extends the current understanding of folic acid metabolism in pathogens and potentially provides new insights into antifolate drug development in the future.
Targeted curation of the gut microbial gene content modulating human cardiovascular disease
Authors: Borton Mikayla A. , Shaffer Michael , Hoyt David W. , Jiang Ruisheng , Ellenbogen Jared B. , Purvine Samuel , Nicora Carrie D. , Eder Elizabeth K. , Wong Allison R. , Smulian A. George , Lipton Mary S. , Krzycki Joseph A. , Wrighton Kelly C.
Published: September 2023

Despite the promise of the gut microbiome to predict human health, few studies expose the molecular-scale processes underpinning such forecasts. We mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages to inventory the gut microorganisms and their gene content that control trimethylamine-induced cardiovascular disease. We assigned an atherosclerotic profile to the 6,341 microbial genomes that encoded metabolisms associated with heart disease, creating the Methylated Amine Gene Inventory of Catabolism database (MAGICdb). From microbiome gene expression data sets, we demonstrate that MAGICdb enhanced the recovery of disease-relevant genes and identified the most active microorganisms, unveiling future therapeutic targets. From the feces of healthy and diseased subjects, we show that MAGICdb predicted cardiovascular disease status as effectively as traditional lipid blood tests. This functional microbiome catalog is a public, exploitable resource, designed to enable a new era of microbiota-based therapeutics and diagnostics.

IMPORTANCE

One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.
Differential innate immune responses of human macrophages and bronchial epithelial cells against
Talaromyces marneffei
Authors: Tan Yen-Pei , Tsang Chi-Ching , Chan Ka-Fai , Fung Siu-Leung , Kok Kin-Hang , Lau Susanna K. P. , Woo Patrick C. Y.
Published: September 2023

Talaromyces marneffei
is a thermally dimorphic fungal pathogen endemic in Southeast Asia. As inhalation of airborne conidia is believed as the major infection route, airway epithelial cells followed by pulmonary macrophages are the first cell types which the fungus encounters inside the host. In this study, we established an
in vitro
infection model based on human peripheral blood-derived macrophages (hPBDMs) cultured with the supplementation of autologous plasma. Using this model, we determined the transcriptomic changes of hPBDMs in response to
T. marneffei
infection by quantitative real-time reverse-transcription polymerase chain reaction as well as high-throughput RNA sequencing. Results showed that
T. marneffei
infection could activate hPBDMs to the M1-like phenotype and trigger a potent induction of chemokine and pro-inflammatory cytokine production as well as the expression of other immunoregulatory genes. In contrast to hPBDMs, there was no detectable innate cytokine response against
T. marneffei
in human bronchial epithelial cells (hBECs). Using a green fluorescent protein-tagged
T. marneffei
strain and confocal microscopy, internalization of the fungus by hBECs was confirmed. Live cell imaging further demonstrated that the infected cells exhibited normal cellular physiology, especially that the process of cell division could be observed. Moreover,
T. marneffei
also survived better inside hBECs than hPBDMs. Our results illustrated a potential role of hBECs to serve as reservoir cells for
T. marneffei
to evade immunosurveillance by phagocytes, from which the fungus reactivates when the host immunity is weakened and causes infection. Such immunoevasion and reactivation may also help explain the long incubation period observed for talaromycosis, in particular the travel-related cases.

IMPORTANCE

Talaromyces marneffei
is an important fungal pathogen especially in Southeast Asia. To understand the innate immune response to talaromycosis, a suitable infection model is needed. Here, we established an
in vitro T. marneffei
infection model using human peripheral blood-derived macrophages (hPBDMs). We then examined the transcriptomic changes of hPBDMs in response to
T. marneffei
infection with this model. We found that contact with
T. marneffei
could activate hPBDMs to the M1-like phenotype and induced mRNA expressions of five cytokines and eight immunoregulatory genes. Contrary to hPBDMs, such immunoresponse was not elicited in human bronchial epithelial cells (hBECs), despite normal physiology observed in infected cells. We also found that infected hBECs did not eliminate
T. marneffei
as efficiently as hPBDMs. Our observation suggested that hBECs may potentially serve as reservoir cells for
T. marneffei
to evade immunosurveillance. When the host immunity deteriorates later, then the fungus reactivates and causes infection.
Adaptation mechanisms of
Listeria monocytogenes
to quaternary ammonium compounds
Authors: Schulz Lisa Maria , Dreier Fabienne , de Sousa Miranda Lisa Marie , Rismondo Jeanine
Published: September 2023

Listeria monocytogenes
is ubiquitously found in nature and can easily enter food-processing facilities due to contaminations of raw materials. Several countermeasures are used to combat contamination of food products, for instance, the use of disinfectants that contain quaternary ammonium compounds, such as benzalkonium chloride (BAC) and cetyltrimethylammonium bromide (CTAB). In this study, we assessed the potential of the commonly used wild-type strain EGD-e to adapt to BAC and CTAB under laboratory growth conditions. All BAC-tolerant suppressors exclusively carried mutations in
fepR
, encoding a TetR-like transcriptional regulator, or its promoter region, likely resulting in the overproduction of the efflux pump FepA. In contrast, CTAB tolerance was associated with mutations in
sugR
, which regulates the expression of the efflux pumps SugE1 and SugE2.
L. monocytogenes
strains lacking either FepA or SugE1/2 could still acquire tolerance toward BAC and CTAB. Genomic analysis revealed that the overproduction of the remaining efflux system could compensate for the deleted one, and even in the absence of both efflux systems, tolerant strains could be isolated, which all carried mutations in the diacylglycerol kinase-encoding gene
lmo1753
(
dgkB
). DgkB converts diacylglycerol to phosphatidic acid, which is subsequently reused for the synthesis of phospholipids, suggesting that alterations in membrane composition could be the third adaptation mechanism.

IMPORTANCE

Survival and proliferation of
Listeria monocytogenes
in the food industry are ongoing concerns, and while there are various countermeasures to combat contamination of food products, the pathogen still successfully manages to withstand the harsh conditions present in food-processing facilities, resulting in reoccurring outbreaks, subsequent infection, and disease. To counteract the spread of
L. monocytogenes
, it is crucial to understand and elucidate the underlying mechanism that permits their successful evasion. We present various adaptation mechanisms of
L. monocytogenes
to withstand two important quaternary ammonium compounds.
Approaches for timeline reductions in pathogenesis studies using genetically modified mice
Authors: Skavicus Samantha , Heaton Nicholas S.
Published: September 2023

Although genetically modified mouse models have long been a powerful tool for microbiology research, the manipulation of the mouse genome is expensive, time consuming, and has historically remained the domain of dedicated animal facilities. The recent use of
in vivo
clustered regularly interspaced short palindromic repeats (CRISPR)-based editing technology has been reported to reduce the expertise, cost, and time required to generate novel mouse lines; it has remained unclear, however, if this new technology could meaningfully alter experimental timelines. Here, we report the optimization of an in oviduct murine genetic manipulation technique for use by microbiologists. We use this approach to generate a series of knockout mice and detail a protocol using an influenza A virus infection model to test the preliminary importance of a host factor in as short as 11 weeks (with a fully backcrossed knockout line in ~22 weeks) from initiation of the study. Broader use of this approach by the microbiology community will allow for more efficient, and rapid, definition of novel pathogenic mechanisms
in vivo
.

Importance

Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have already begun to revolutionize biomedical science. An emerging application of this technology is in the development of genetically modified model organisms to study the mechanisms underlying infectious disease. Here, we describe a protocol using an
in vivo
CRISPR-based approach that can be used to test the importance of a candidate host factor for microbial pathogenesis in less than 3 months and before complete establishment of a new mouse line. Adoption of this approach by the broader microbiology community will help to decrease the resources and time required to understand how pathogens cause disease which will ultimately speed up the development of new clinical interventions and therapies.
Comment on Rogozin et al., (2023), Morphology of Lakes of the Central Tunguska Plateau (Krasnoyarsk krai, Evenkiya): New Data on the Problem of the Tunguska Event of 1908
Authors: Gasperini Luca , Bellucci Luca Giorgio , Stanghellini Carlo , Stanghellini Giuseppe , Polonia Alina
Published: September 2023

In a recent paper, Rogozin and coauthors present a morphologic/seismostratigraphic study of two small lakes, Lake Zapovednoye (LZ) and Lake Peyungda (LP), located 50‒60 km east from the alleged epicenter of the 1908 Tunguska Event (TE), a large explosion believed to have been caused by an extraterrestrial impact. Data presented in that paper suggest a similar (although not specified) origin of these two lakes and Lake Cheko, located close to the TE epicenter. This led Rogozin et al., to question the impact crater origin of Lake Cheko, whose depression was interpreted by Gasperini et al., as caused by the freefall of an extraterrestrial fragment, which survived an atmospheric explosion. We analyze Rogozin et al., data, focusing on similarities and differences between Lake Cheko, LZ and LP, to determine whether their findings are relevant to the TE problem.
Seronegative paraneoplastic encephalomyelitis in occult colonic carcinoma
Authors: Joy Shiny , Agarwal Ayush , Shamim Shamim Ahmed , Garg Ajay
Published: September 2023

Paraneoplastic neurological syndromes are immune-mediated neurological attacks triggered by malignancies. They are commonly associated with lung, breast, thymus, gynaecological and haematological malignancies. We report a case of a male patient in his late 40s with paraneoplastic encephalomyelitis due to a colonic adenocarcinoma emphasising a low threshold for extensive cancer evaluation in all subacutely presenting neurological syndromes. We also emphasise that the absence of a positive onconeural antibody does not preclude the diagnosis of a paraneoplastic syndrome.