bluuebunny/crossref_metadata_2025 huggingface dataset:
Compaction behaviour of a sandy road base contaminated with microplastics from vehicle tires
Authors: Ozhan Hakki O. , Elnemr Abdelrahman Maher Taha
Published: July 2024

Disintegrated tire particles can easily be transferred into the road bases because of the abrasion of vehicle tires on roads. The fragmented tire particles that have a grain size of smaller than 5 mm can be expressed as microplastics. In order to simulate the tire chip microplastic concentration in a sandy road base and assess the effect of microplastics on the compaction degree of the road base, standard Proctor compaction tests were performed on 0.05%, 0.1%, 0.2%, 0.4%, 1%, 2%, 4% and 8% tire chip microplastics‐amended sandy soil by dry mass. Results showed that maximum dry unit weight (ɣdmax) of the sand increased from 16.04 to 16.99 kN/m3 as the tire chip microplastic concentration increased up to 0.4%. Further increase in the microplastic concentration resulted in a decrease in ɣdmax. Contrarily, optimum water content (wopt) decreased from 15.9 to 12.5% as a result of the tire chip microplastic addition up to a concentration of 0.4%. An additional increase in the microplastic concentration led to an increase in wopt. By considering these results, a concentration of 0.4% tire chip microplastics was found to be the optimum amount that enhanced the degree of compaction. Besides contributing to the stabilization of a sandy road base, tire chip microplastics can also be assessed in terms of environmental protection. These microplastics are forced to be stacked in the sand because of compaction. As a result, they cannot easily be transferred to water resources or agricultural products that may threaten human health and cause environmental contamination.
Use of letermovir for cytomegalovirus primary prophylaxis in lung transplant recipients
Authors: Kleiboeker Hanna L. , Wang Jacob , Borkowski Nicole , Miner Brad , Prom Alyson , Paplaczyk Krista , Wright Jennifer , Subramani Mrinalini Venkata , Arunachalam Ambalavanan , Betensley Alan D. , Tomic Rade , Myers Catherine N.
Published: July 2024

Background

Cytomegalovirus (CMV) is a driver of negative outcomes after lung transplant (LTX) and primary prophylaxis (PPX) with valganciclovir (VGC) is standard‐of‐care. VGC is associated with myelosuppression, prompting interest in letermovir (LTV).

Methods

Adults receiving LTX between April 1, 2015, and July 30, 2022, at our institution were evaluated. Patients were excluded if low CMV risk (D‐/R‐), survived <90 days post‐LTX, or transferred care before PPX withdrawal. Primary outcomes were leukopenia (white blood cell count [WBC] ≤ 3.0 × 109/L), severe leukopenia (WBC ≤ 2.0 × 109/L), and neutropenia (absolute neutrophil count ≤ 1500 cells/µL) requiring granulocyte‐colony stimulating factor (GCSF) on PPX. Secondary outcomes included breakthrough CMV infection and post‐PPX CMV infection.

Results

204 patients met inclusion criteria: 175 patients on VGC and 29 patients on LTV (after VGC conversion). Most patients received bilateral LTX (62.7%) with non‐lymphocyte‐depleting induction (96.6%) and moderate‐risk serostatus (D+/R+, 48.5%). Patients transitioned from VGC to LTV after a mean of 178 days (SD 80.8 days) post‐transplant. Patients on VGC experienced significantly more leukopenia (82.3% vs. 58.6%, p = 0.008), severe leukopenia (57.1% vs. 31.0%, p = 0.016), and neutropenia requiring GCSF (70.9% vs. 51.7%, p = 0.048). Breakthrough (5.7% vs. 3.4%, p = 0.955) and post‐PPX (24.6% vs. 37.9%, p = 0.199) infections were similar. A subgroup analysis of patients with high‐risk serostatus showed similar trends, though did not reach statistical significance.

Conclusions

In this single‐center study, the incidence of leukopenia and neutropenia requiring GCSF were reduced with LTV compared to VGC. Breakthrough and post‐PPX infections were not significantly different. This evidence suggests that LTV has comparable efficacy with reduced myelosuppression compared to VGC in LTX recipients, and may be an appropriate alternative for PPX.

image
Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1
Authors: Jiang Meng , Zhang Huali , Song Yue , Chen Jiale , Bai Jianjiang , Tang Jianhao , Wang Qing , Fotopoulos Vasileios , Zhu Qian‐Hao , Yang Ruifang , Li Ruiqing
Published: July 2024

Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white‐core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi‐omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP‐Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make‐up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high‐AC in the low‐AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10–OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.
Deciphering Pteronia's evolution in the Cape Floristic Region: A comprehensive study disputes polyploid deficiency and affirms diploid radiation
Authors: Chumová Zuzana , Havlíčková Eliška , Zeisek Vojtěch , Šemberová Kristýna , Mandáková Terezie , Euston‐Brown Douglas , Trávníček Pavel
Published: July 2024

The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR. Employing NGS‐based HybSeq and RADSeq methodologies, flow cytometry, karyology, and ecological modeling, we scrutinize the intricacies of its polyploid evolution. Phylogenetic reconstructions using 951 low‐copy nuclear genes confirm Pteronia as a well‐supported, distinct clade within the tribe Astereae. The ingroup displays a structure indicative of rapid radiation likely antedating polyploid establishment, with the two main groups demarcated by their presence or absence in the fynbos biome. Genome size analysis encompasses 1293 individuals across 347 populations, elucidating significant variation ranging from 6.1 to 34.2 pg (2C‐value). Pteronia demonstrates substantially large genome sizes within Astereae and phanerophytes. Polyploidy is identified in 31% of the studied species, with four discerned ploidy levels (2x, 4x, 6x, 8x). Cytotypes exhibit marked distinctions in environmental traits, influencing their distribution across biomes and augmenting their niche differentiation. These revelations challenge the presumed scarcity of polyploidy in the Cape flora, underscoring the imperative need for detailed population studies. The intricate evolutionary history of Pteronia, characterized by recent polyploidy and genome size variation, contributes substantially to the comprehension of diversification patterns within the GCFR biodiversity hotspot.
Volitional modulation of neuronal activity in the external globus pallidus by engagement of the cortical–basal ganglia circuit
Authors: Luo Shengtao , Zhou Xiaopeng , Zhou Hui , Li Tao , He Yutong , Chen Jiang‐Fan , Zhang Liping
Published: July 2024

Volitional modulation of neural activity is not confined to the cortex but extends to various brain regions. Yet, it remains unclear whether neurons in the basal ganglia structure, the external globus pallidus (GPe), can be volitionally controlled. Here, we employed a volitional conditioning task to compare the volitional modulation of GPe and primary motor cortex (M1) neurons as well as the underlying circuits and control mechanisms. The results revealed that the volitional modulation of GPe neuronal activity engaged both M1 and substantia nigra pars reticulata (SNr) neurons, indicating the involvement of the cortex–GPe–SNr loop. In contrast, the volitional modulation of M1 neurons primarily occurred through the engagement of M1 local circuitry. Furthermore, lesioning M1 neurons did not affect the volitional learning or volitional control signal in GPe, whereas lesioning of GPe neurons impaired the learning process for the volitional modulation of M1 neuronal activity at the intermediate stage. Additionally, lesion of GPe neurons enhanced M1 neuronal activity when performing the volitional control task without reward delivery and a random reward test. Taken together, our findings demonstrated that GPe neurons could be volitionally controlled by engagement of the cortical–basal ganglia circuit and inhibit learning process for the volitional modulation of M1 neuronal activity by regulating M1 neuronal activity. Thus, GPe neurons can be effectively harnessed for independent volitional modulation for neurorehabilitation in patients with cortical damage.

image

Key points

The cortical–basal ganglia circuit contributes to the volitional modulation of GPe neurons.

Volitional modulation of M1 neuronal activity mainly engages M1 local circuitry.

Bilateral GPe lesioning impedes volitional learning at the intermediate stages.

Lesioning of GPe neurons inhibits volitional learning process by regulating M1 neuronal activity.
Transient Radiation Heat Transfer of Thermally Compact, Lumped Bodies: An Explicit Solution
Authors: Allison Jonathan
Published: July 2024

An explicit, analytical solution is offered to the problem of transient radiation heat transfer of thermally lumped bodies. This solution is readily implemented as a calculator on a simple spreadsheet software, allowing prediction of transient radiation that can aid didactics, design, test, and operations. It is shown that transient radiation heat transfer has a few similarities, and many differences, in comparison to linear forms of transient heat transfer such as conduction and convection. Both linear and radiation forms of transient heat transfer asymptotically approach their steady-state conditions. Differences of note are that transient radiation heat transfer is nonself-similar, it depends upon two nondimensional variables, transient radiative heating is generally faster than transient radiative cooling, and externally applied heat sources substantially delay transient radiation heat transfer relative to internally applied heat sources.
Toward Smart Ultrasound Image Augmentation to Advance Tumor Treatment Monitoring: Exploring the Potential of Diffusion Generative Model
Authors: Yangue Emmanuel , Ranjan Ashish , Feng Yu , Liu Chenang
Published: July 2024

Medical imaging is a crucial tool in clinics to monitor tumor treatment progress. In practice, many imaging tools (such as magnetic resonance imaging (MRI) and computed tomography (CT) scans) are in general costly and may also expose patients to radiation, leading to potential side effects. Recent studies have demonstrated that ultrasound imaging, which is safe, low-cost, and easy to access, can monitor the drug delivery progress in solid tumors. However, the noisy nature of ultrasound images and the high-level uncertainty of cancer disease progression are still challenging in ultrasound-based tumor treatment monitoring. To overcome these barriers, this work presents a comparative study to explore the potential advantages of the emerging diffusion generative models against the commonly applied state-of-the-art generative models. Namely, the denoising diffusion models (DDMs), against the generative adversarial networks (GAN), and variational auto-encoders (VAE), are used for analyzing the ultrasound images through image augmentation. These models are evaluated based on their capacity to augment ultrasound images for exploring the potential variations of tumor treatment monitoring. The results across different cases indicate that the denoising diffusion implicit models (DDIM)/kernel inception distance (KID)-inception score (IS) model leveraged in this work outperforms the other models in the study in terms of similarity, diversity, and predictive accuracy. Therefore, further investigation of such diffusion generative models could be considered as they can potentially serve as a great predictive tool for ultrasound image-enabled tumor treatment monitoring in the future.
Aerodynamic Impact of Secondary Air Injection Flowrates on the Main Annulus Flow Field for a Transonic High-Pressure Turbine Stage
Authors: Okita Yoji , Kazawa Junichi , Yamane Takashi , Tanaka Nozomi , Fuchigami Kazutaka , Sato Hiroki , Hamabe Masaaki , Tanimitsu Haruyuki
Published: July 2024

In this study, the influence of secondary air blowing on the main annulus flow field of a transonic high-pressure turbine (HPT) was investigated experimentally and numerically. The experimental setup was a single-stage, unshrouded turbine with a blading consistent with modern HPTs. The entire testing campaign was conducted in a full annular, rotating, continuous turbine test rig at the Japan Aerospace Exploration Agency (JAXA), which realized the most faithful matching unrivalled of both the primary and secondary stream similarity parameters to reality. An elaborate secondary air system implemented in the hardware enabled it to mimic all the dominant coolant/purge streams representative of advanced hot sections: the full coverage film-cooling on stator and rotor airfoils, disk wheelspace purge air blown forward and aft of the rotor, and coolant injection through the over-tip casing. Detailed three-dimensional flow field measurements for various secondary air flowrates were performed by traversing a pneumatic thermometric combination probe downstream of the rotor. A complete set of numerical simulations was run concurrently with the testing to determine how well they captured the flow physics, particularly the interaction of the ejected secondary streams with the primary flow. The JAXA in-house code, UPACS, and its best practice settings, based on past verification and validation efforts, were employed and not intentionally tuned to better fit the data. Given the study's primary goal, important features such as coolant holes, internal plenums, and wheelspace cavities that affect the interactions were all directly resolved in the calculation rather than simplified by the boundary conditions and/or source-term modeling. The rotor exit survey in the experiment suggested that the both disk forward hub purge and the blowing from the over-tip casing intensified the passage vortex in the cascade. In contrast, it was indicated that a positive effect also resulted from ejection from the tip casing, diminishing the tip leakage vortex. Additionally, the data suggested that coolant blown off the airfoil has an impact also on the near-endwall zone in particular and can boost (by vane coolant) or weaken (by blade coolant) the secondary flow.
Toward parametric Bayesian adaptive procedures for multi-frequency categorical loudness scaling
Authors: Shen Yi , Petersen Erik A. , Neely Stephen T.
Published: July 2024

A series of Bayesian adaptive procedures to estimate loudness growth across a wide frequency range from individual listeners was developed, and these procedures were compared. Simulation experiments were conducted based on multinomial psychometric functions for categorical loudness scaling across ten test frequencies estimated from 61 listeners with normal hearing and 87 listeners with sensorineural hearing loss. Adaptive procedures that optimized the stimulus selection based on the interim estimates of two types of category-boundary models were tested. The first type of model was a phenomenological model of category boundaries adopted from previous research studies, while the other type was a data-driven model derived from a previously collected set of categorical loudness scaling data. An adaptive procedure without Bayesian active learning was also implemented. Results showed that all adaptive procedures provided convergent estimates of the loudness category boundaries and equal-loudness contours between 250 and 8000 Hz. Performing post hoc model fitting, using the data-driven model, on the collected data led to satisfactory accuracies, such that all adaptive procedures tested in the current study, independent of modeling approach and stimulus-selection rules, were able to provide estimates of the equal-loudness-level contours between 20 and 100 phons with root-mean-square errors typically under 6 dB after 100 trials.
Phage display-derived alpaca nanobodies as potential therapeutics for
Naja atra
snake envenomation
Authors: Wang Wei-Chu , Chang Jungshan , Lee Chi-Hsin , Chiang Yu-Wei , Leu Sy-Jye , Mao Yan-Chiao , Chiang Jen-Ron , Yang Chun-Kai , Wu Chao-Jung , Yang Yi-Yuan
Published: July 2024

Naja atra
, the Chinese cobra, is a major cause of snake envenomation in Asia, causing hundreds of thousands of clinical incidents annually. The current treatment, horse serum-derived antivenom, has unpredictable side effects and presents manufacturing challenges. This study focused on developing new-generation snake venom antidotes by using microbial phage display technology to derive nanobodies from an alpaca immunized with attenuated
N. atra
venom. Following confirmation of the immune response in the alpaca, we amplified

V
H
H

genes from isolated peripheral blood mononuclear cells and constructed a phage display

V
H
H

library of 1.0 × 10
7
transformants. After four rounds of biopanning, the enriched phages exhibited increased binding activity to
N. atra
venom. Four nanobody clones with high binding affinities were selected: aNAH1, aNAH6, aNAH7, and aNAH9. Specificity testing against venom from various snake species, including two Southeast Asian cobra species, revealed nanobodies specific to the genus
Naja
. An
in vivo
mouse venom neutralization assay demonstrated that all nanobodies prolonged mouse survival and aNAH6 protected 66.6% of the mice from the lethal dosage. These findings highlight the potential of phage display-derived nanobodies as valuable antidotes for
N. atra
venom, laying the groundwork for future applications in snakebite treatment.

IMPORTANCE

Chinese cobra venom bites present a formidable medical challenge, and current serum treatments face unresolved issues. Our research applied microbial phage display technology to obtain a new, effective, and cost-efficient treatment approach. Despite interest among scientists in utilizing this technology to screen alpaca antibodies against toxins, the available literature is limited. This study makes a significant contribution by introducing neutralizing antibodies that are specifically tailored to Chinese cobra venom. We provide a comprehensive and unbiased account of the antibody construction process, accompanied by thorough testing of various nanobodies and an assessment of cross-reactivity with diverse snake venoms. These nanobodies represent a promising avenue for targeted antivenom development that bridges microbiology and biotechnology to address critical health needs.
MoRgs3 functions in intracellular reactive oxygen species perception-integrated cAMP signaling to promote appressorium formation in
Magnaporthe oryzae
Authors: Zhang Ruiming , Liu Xinyu , Xu Jiayun , Chen Chen , Tang Zhaoxuan , Wu Chengtong , Li Xinyue , Su Lei , Liu Muxing , Yang Leiyun , Li Gang , Zhang Haifeng , Wang Ping , Zhang Zhengguang
Published: July 2024

Regulator of G-protein signaling (RGS) proteins exhibit GTPase-accelerating protein activities to govern G-protein function. In the rice blast fungus
Magnaporthe oryzae
, there is a family of at least eight RGS and RGS-like proteins (MoRgs1 to MoRgs8), each exhibiting distinct or shared functions in the growth, appressorium formation, and pathogenicity. MoRgs3 recently emerged as one of the crucial regulators that senses intracellular oxidation during appressorium formation. To explore this unique regulatory mechanism of MoRgs3, we identified the nucleoside diphosphate kinase MoNdk1 that interacts with MoRgs3. MoNdk1 phosphorylates MoRgs3 under induced intracellular reactive oxygen species levels, and MoRgs3 phosphorylation is required for appressorium formation and pathogenicity. In addition, we showed that MoRgs3 phosphorylation determines its interaction with MoCrn1, a coronin-like actin-binding protein homolog, which regulates MoRgs3 internalization. Finally, we provided evidence demonstrating that MoRgs3 functions in MoMagA-mediated cAMP signaling to regulate normal appressorium induction. By revealing a novel signal perception mechanism, our studies highlighted the complexity of regulation during the appressorium function and pathogenicity of the blast fungus.

IMPORTANCE

We report that MoRgs3 becomes phosphorylated in an oxidative intracellular environment during the appressorium formation stage. We found that this phosphorylation is carried out by MoNdk1, a nucleoside diphosphate kinase. In addition, this phosphorylation leads to a higher binding affinity between MoRgs3 and MoCrn1, a coronin-like actin-binding protein that was implicated in the endocytic transport of several other RGS proteins of
Magnaporthe oryzae
. We further found that the internalization of MoRgs3 is indispensable for its GTPase-activating protein function toward the Gα subunit MoMagA. Importantly, we characterized how such cellular regulatory events coincide with cAMP signaling-regulated appressorium formation and pathogenicity in the blast fungus. Our studies uncovered a novel intracellular reactive oxygen species signal-transducing mechanism in a model pathogenic fungus with important basic and applied implications.
Dependence of post-segregational killing mediated by Type II restriction–modification systems on the lifetime of restriction endonuclease effective activity
Authors: Kozlova Svetlana , Morozova Natalia , Ispolatov Yaroslav , Severinov Konstantin
Published: July 2024

Plasmid-borne Type II restriction–modification (RM) systems mediate post-segregational killing (PSK). PSK is thought to be caused by the dilution of restriction and modification enzymes during cell division, resulting in accumulation of unmethylated DNA recognition sites and their cleavage by restriction endonucleases. PSK is the likely reason for stabilization of plasmids carrying RM systems in the absence of selection for plasmid maintenance. In this study, we developed a CRISPR interference-based method to eliminate RM-carrying plasmids and study PSK-related phenomena with minimal perturbation to the
Escherichia coli
host. Plasmids carrying the EcoRV, Eco29kI, and EcoRI RM systems were highly stable, and their loss resulted in SOS response and PSK. In contrast, plasmids carrying the Esp1396I system were poorly stabilized; their loss led to a temporary cessation of growth, followed by full recovery. We demonstrate that this unusual behavior is due to a limited lifetime of the Esp1396I restriction endonuclease activity, which, upon Esp1396I plasmid loss, disappears approximately after two cycles of cell division, i.e., before unmethylated sites appear in significant numbers. Our results indicate that whenever PSK induced by a loss of RM systems, and, possibly, other toxin–antitoxin systems, is considered, the lifetimes of individual system components and the growth rate of host cells shall be taken in account. Mathematical modeling shows, that unlike the situation with classical toxin–antitoxin systems, RM system-mediated PSK is possible when the lifetimes of restriction endonuclease and methyltransferase activities are similar, as long as the toxic restriction endonuclease activity persists for more than two chromosome replication cycles.

IMPORTANCE

It is widely accepted that many Type II restriction–modification (RM) systems mediate post-segregational killing (PSK) if plasmids that encode them are lost. In this study, we harnessed an inducible CRISPR-Cas system to remove RM plasmids from
Escherichia coli
cells to study PSK while minimally perturbing cell physiology. We demonstrate that PSK depends on restriction endonuclease activity lifetime and is not observed when it is less than two replication cycles. We present a mathematical model that explains experimental data and shows that unlike the case of toxin–antitoxin-mediated PSK, the loss of an RM system induced PSK even when the RM enzymes have identical lifetimes.
The spliceosome impacts morphogenesis in the human fungal pathogen
Candida albicans
Authors: Lash Emma , Maufrais Corinne , Janbon Guilhem , Robbins Nicole , Herzel Lydia , Cowen Leah E.
Published: July 2024

At human body temperature, the fungal pathogen
Candida albicans
can transition from yeast to filamentous morphologies in response to host-relevant cues. Additionally, elevated temperatures encountered during febrile episodes can independently induce
C. albicans
filamentation. However, the underlying genetic pathways governing this developmental transition in response to elevated temperatures remain largely unexplored. Here, we conducted a functional genomic screen to unravel the genetic mechanisms orchestrating
C. albicans
filamentation specifically in response to elevated temperature, implicating 45% of genes associated with the spliceosome or pre-mRNA splicing in this process. Employing RNA-Seq to elucidate the relationship between mRNA splicing and filamentation, we identified greater levels of intron retention in filaments compared to yeast, which correlated with reduced expression of the affected genes. Intriguingly, homozygous deletion of a gene encoding a spliceosome component important for filamentation (
PRP19
) caused even greater levels of intron retention compared with wild type and displayed globally dysregulated gene expression. This suggests that intron retention is a mechanism for fine-tuning gene expression during filamentation, with perturbations of the spliceosome exacerbating this process and blocking filamentation. Overall, this study unveils a novel biological process governing
C. albicans
filamentation, providing new insights into the complex regulation of this key virulence trait.

IMPORTANCE

Fungal pathogens such as
Candida albicans
can cause serious infections with high mortality rates in immunocompromised individuals. When
C. albicans
is grown at temperatures encountered during human febrile episodes, yeast cells undergo a transition to filamentous cells, and this process is key to its virulence. Here, we expanded our understanding of how
C. albicans
undergoes filamentation in response to elevated temperature and identified many genes involved in mRNA splicing that positively regulate filamentation. Through transcriptome analyses, we found that intron retention is a mechanism for fine-tuning gene expression in filaments, and perturbation of the spliceosome exacerbates intron retention and alters gene expression substantially, causing a block in filamentation. This work adds to the growing body of knowledge on the role of introns in fungi and provides new insights into the cellular processes that regulate a key virulence trait in
C. albicans
.
Immunological correlates of protection mediated by a whole organism,
Cryptococcus neoformans
, vaccine deficient in chitosan
Authors: Specht Charles A. , Wang Ruiying , Oliveira Lorena V. N. , Hester Maureen M. , Gomez Christina , Mou Zhongming , Carlson Diana , Lee Chrono K. , Hole Camaron R. , Lam Woei C. , Upadhya Rajendra , Lodge Jennifer K. , Levitz Stuart M.
Published: July 2024

The global burden of infections due to the pathogenic fungus
Cryptococcus
is substantial in persons with low CD4
+
T-cell counts. Previously, we deleted three chitin deacetylase genes from
Cryptococcus neoformans
to create a chitosan-deficient, avirulent strain, designated as
cda1∆2∆3∆
, which, when used as a vaccine, protected mice from challenge with virulent
C. neoformans
strain KN99. Here, we explored the immunological basis for protection. Vaccine-mediated protection was maintained in mice lacking B cells or CD8
+
T cells. In contrast, protection was lost in mice lacking α/β T cells or CD4
+
T cells. Moreover, CD4
+
T cells from vaccinated mice conferred protection upon adoptive transfer to naive mice. Importantly, while monoclonal antibody-mediated depletion of CD4
+
T cells just prior to vaccination resulted in complete loss of protection, significant protection was retained in mice depleted of CD4
+
T cells after vaccination but prior to challenge. Vaccine-mediated protection was lost in mice genetically deficient in interferon-γ (IFNγ), tumor necrosis factor alpha (TNFα), or interleukin (IL)-23p19. A robust influx of leukocytes and IFNγ- and TNFα-expressing CD4
+
T cells was seen in the lungs of vaccinated and challenged mice. Finally, a higher level of IFNγ production by lung cells stimulated ex vivo correlated with lower fungal burden in the lungs. Thus, while B cells and CD8
+
T cells are dispensable, IFNγ and CD4
+
T cells have overlapping roles in generating protective immunity prior to
cda1∆2∆3∆
vaccination. However, once vaccinated, protection becomes less dependent on CD4
+
T cells, suggesting a strategy for vaccinating HIV
+
persons prior to loss of CD4
+
T cells.

IMPORTANCE

The fungus
Cryptococcus neoformans
is responsible for >100,000 deaths annually, mostly in persons with impaired CD4
+
T-cell function such as AIDS. There are no approved human vaccines. We previously created a genetically engineered avirulent strain of
C. neoformans
, designated as
cda1∆2∆3∆
. When used as a vaccine,
cda1∆2∆3∆
protects mice against a subsequent challenge with a virulent
C. neoformans
strain. Here, we defined components of the immune system responsible for vaccine-mediated protection. We found that while B cells and CD8
+
T cells were dispensible, protection was lost in mice genetically deficient in CD4
+
T cells and the cytokines IFNγ, TNFα, or IL-23. A robust influx of cytokine-producing CD4
+
T cells was seen in the lungs of vaccinated mice following infection. Importantly, protection was retained in mice depleted of CD4
+
T cells following vaccination, suggesting a strategy to protect persons who are at risk of future CD4
+
T-cell dysfunction.
Genomic sequences of
Mycobacterium smegmatis
A cluster phages LBerry, Pembroke, and Zolita
Authors: Berry Nathan E. , Cassford Marly S. , Agostino Colby J. , Dionne Ethan N. , Schmitt Olivia J. , Butela Kristen A. , Jacobs-Sera Deborah , DeGiorgis Joseph A. , Cornely Kathleen
Published: July 2024

LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect
Mycobacterium smegmatis
mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.
The direct and indirect drivers shaping RNA viral communities in grassland soils
Authors: Wu Ruonan , Zimmerman Amy E. , Hofmockel Kirsten S.
Published: July 2024

Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were
Mitoviridae
with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes.

IMPORTANCE

Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.
Species pool and soil properties in mangrove habitats influence the species-immigration process of diazotrophic communities across southern China
Authors: Liao Nengjian , Pan Lianghao , Zhao Huaxian , Yang Shu , Qin Xinyi , Huang Jiongqing , Li Xiaoli , Dong Ke , Shi Xiaofang , Hou Qinghua , Chen Qingxiang , Wang Pengbin , Jiang Gonglingxia , Li Nan
Published: July 2024

Microbial immigration is an ecological process in natural environments; however, the ecological trade-off mechanisms that govern the balance between species extinction and migration are still lacking. In this study, we investigated the mechanisms underlying the migration of diazotrophic communities from soil to leaves across six natural mangrove habitats in southern China. The results showed that the diazotrophic alpha and beta diversity exhibited significant regional and locational variations. The diazotrophic species pool gradually increased from the leaves to nonrhizosphere soil at each site, exhibiting a vertical distribution pattern. Mantel test analyses suggested that climate factors, particularly mean annual temperature, significantly influenced the structure of the diazotrophic community. The diazotrophic community assembly was mainly governed by dispersal limitation in soil and root samples, whereas dispersal limitation and ecological drift were dominant in leaves. Partial least squares path modeling revealed that the species pool and soil properties, particularly the oxidation-reduction potential and pH, were closely linked to the species-immigration ratio of diazotrophic communities. Our study provides novel insights for understanding the ecological trait diversity patterns and spread pathways of functional microbial communities between below- and aboveground habitats in natural ecosystems.

IMPORTANCE

Environmental selection plays key roles in microbial transmission. In this study, we have provided a comprehensive framework to elucidate the driving patterns of the ecological trade-offs in diazotrophic communities across large-scale mangrove habitats. Our research revealed that
Bradyrhizobium japonicum
,
Marinobacterium lutimaris
, and
Agrobacterium tumefaciens
were more abundant in root-associated soil than in leaves by internal and external pathways. The nonrhizospheric and rhizospheric soil samples harbored the most core amplicon sequence variants, indicating that these dominant diazotrophs could adapt to broader ecological niches. Correlation analysis indicated that the diversities of the diazotrophic community were regulated by biotic and abiotic factors. Furthermore, this study found a lower species immigration ratio in the soil than in the leaves. Both species pool and soil properties regulate the species-immigration mechanisms of the diazotrophic community. These results suggest that substantial species immigration is a widespread ecological process, leading to alterations in local community diversity across diverse host environments.
Dietary L-arabinose-induced gut dysbiosis exacerbates
Salmonella
infection outcome
Authors: Yu Jingchen , Tang Huang , Zhou Ning , Wang Zuoqiang , Huang Wanqiu , Chen Yana , Wang Danni , Ni Jinjing , Lu Jie , Yao Yu-Feng
Published: July 2024

The gut microbiota is essential for providing colonization resistance against pathogens. Dietary sugars markedly shift the composition of the intestinal microbiota and alter host susceptibility to enteric infections. Here, we demonstrate the effect of L-arabinose on bacterial infection by using a mouse infection model with
Salmonella enterica
serovar Typhimurium (
S
. Tm). In the presence of microbiota, L-arabinose induces a dramatic expansion of
Enterobacteriaceae
, thereby decreasing the microbiota diversity and causing more severe systemic infection. However, L-arabinose supplementation does not alter the disease progression of
Salmonella
infection in a microbiota-depleted mouse model. More importantly, short-term supplementation of L-arabinose fails to exert anti-diabetic effects in
Salmonella
-infected hyperglycemia mice and still promotes infection. Overall, our work reveals that a high intake of dietary L-arabinose supports a bloom of
Enterobacteriaceae
in
Salmonella
-infected gut, further accelerating the process of systemic infection.

IMPORTANCE

L-arabinose is a promising natural sweetener and food additive for the regulation of hyperglycemia. Since diabetic subjects are more susceptible to infections, the safety of dietary L-arabinose in diabetic patients experiencing infection remains a concern. Our findings reveal that L-arabinose exacerbates
Salmonella
infection outcome by inducing gut microbiota dysbiosis in mice. High dietary intake of L-arabinose may be deleterious for diabetic individuals undergoing infection.
Changes in the microbial community of semen exposed to different simulated forensic situations
Authors: Zheng Yangyang , Ye Linying , Du Jieyu , Huang Litao , Lun Miaoqiang , He Meiyun , Xiao Guichao , Du Weian , Liu Chao , Chen Ling
Published: July 2024

Semen is one of the common body fluids in sexual crime cases. The current methods of semen identification have certain limitations, so it is necessary to search for other methods. In addition, there are few reports of microbiome changes in body fluids under simulated crime scenes. It is essential to further reveal the changes in semen microbiomes after exposure to various simulated crime scenes. Semen samples from eight volunteers were exposed in closed plastic bags, soil, indoor, cotton, polyester, and wool fabrics. A total of 68 samples (before and after exposure) were collected, detected by 16S rDNA sequencing, and analyzed for the microbiome signature. Finally, a random forest model was constructed for body fluid identification. After exposure, the relative abundance of
Pseudomonas
and
Rhodococcus
changed dramatically in almost all groups. In addition, the treatment with the closed plastic bags or soil groups had a greater impact on the semen microbiome. According to the Shannon indices, the alpha diversity of the closed plastic bags and soil groups was much lower than that of the other groups. Attention should be given to the above two scenes in practical work of forensic medicine. In this study, the accuracy of semen recognition was 100%. The exposed semen can still be correctly identified as semen based on its microbiota characteristics. In summary, semen microbiomes exposed to simulated crime scenes still have good application potential for body fluid identification.

IMPORTANCE

In this study, the microbiome changes of semen exposed to different environments were observed, and the exposed semen microbiome still has a good application potential in body fluid identification.
Candida
spp.: the burden of a microorganism in a microbiology department
Authors: Soriano-Martín Ana , Alonso Roberto , Machado Marina , Reigadas Elena , Muñoz Patricia , Bouza Emilio
Published: July 2024

There is no precise information available on the entire workload of isolating a specific microorganism in a clinical microbiology laboratory, and the costs associated with it have not been specifically estimated. In this descriptive retrospective study conducted at the microbiology department of a general teaching hospital from January 2021 to December 2022, we assessed the workload associated with identifying
Candida
species in all types of clinical samples and patients. Costs were estimated from data obtained from the hospital’s finance department and microbiology laboratory cost records. In 2 years, 1,008,231 samples were processed at our microbiology department, of which 8,775 had one or more
Candida
spp. isolates (9,683 total isolates). Overall, 5,151 samples with
Candida
spp. were identified from 2,383 inpatients. We isolated
Candida
spp. from 515.3 samples/100,000 population/year and from 92 samples/1,000 hospital admissions/year. By sample type, 90.8% were superficial, mainly mucosal. Only 9.1%
Candida
spp. were isolated from deep, usually sterile, samples, being mostly from ordinarily sterile fluids.
Candida albicans
was the main species (58.5%) identified, followed by
C. parapsilosis
complex,
C. glabrata
,
C. tropicalis,
and
C. krusei
. In admitted patients, the incidences of samples with
Candida
spp. isolates were 302.7 samples/100,000 population/year and 54 samples/1,000 admissions/year. The average cost of isolating and identifying
Candida
spp. was estimated at 25€ per culture-positive sample. To our knowledge, this is the first attempt to gage the workload and costs of
Candida
spp. isolation at a hospital microbiology department. These data can help assess the burden and significance of
Candida
isolation at other institutions and also help design measures for streamlining.

IMPORTANCE

We believe that this work is of interest because at present, there is no really accurate information available on the total workload involved in isolating a specific microorganism in a clinical microbiology laboratory. The costs related to this have also not been described. We have described the unrestricted workload of Candida spp. in all types of samples for all types of species and patients. We believe that this information would be necessary to collect and share this information as well as to collect it in a standardized way to know the current situation of Candida spp. workload in all clinical microbiology laboratories.
Effects of forest age and season on soil microbial communities in Chinese fir plantations
Authors: Hu Yuxin , Zhang Xiongqing , Chen Hanyue , Jiang Yihang , Zhang Jianguo
Published: July 2024

Understanding changes in the distribution patterns and diversity of soil microbial communities from the perspectives of age-related changes, seasonal variations, and the interaction between the two factors can facilitate the management of plantations. In Chinese fir plantations, we collected soils from different depths in over-mature forests, mature forests, near-mature forests, middle-aged forests, and young forests in summer, autumn, and winter in China’s subtropical regions. As the forests developed, bacterial and fungal communities’ diversity changed, reached a minimum value at near-mature forests, and then increased in mature forests or over-mature forests. Near-mature forests had the lowest topological properties. The Shannon index of microbial communities varied with seasonal changes (
P
< 0.05). Bacterial and fungal community composition at genus level was more closely related to temperature indicators (including daily average temperature, daily maximum temperature, and daily minimum temperature) (
P
< 0.01, 0.5554 <
R
2
<0.8185) than daily average precipitation (
P
> 0.05, 0.0321 <
R
2
<0.6773). Bacteria were clustered by season and fungi were clustered by forest age. We suggested that extending the tree cultivation time of plantations could promote microbial community recovery. In addition, we found some species worthy of attention, including Bacteroidetes in autumn in over-mature forests, and Firmicutes in summer in young forests.

IMPORTANCE

Chinese fir [
Cunninghamia lanceolata
(Lamb.) Hook] is an important fast-growing species with the largest artificial forest area in China, with the outstanding problems of low quality in soil. Soil microorganisms play a crucial role in soil fertility by decomposing organic matter, optimizing soil structure, and releasing essential nutrients for plant growth. In order to maintain healthy soil quality and prevent nutrient depletion and land degradation, it is crucial to understand the changes of soil microbial composition and diversity. Our study determined to reveal the change of soil microbial community from stand age, season, and the interaction between the two aspects, which is helpful to understand how interannual changes in different years and seasonal changes in one year affect soil fertility restoration and sustainable forest plantation management. It is a meaningful exploration of soil microbial communities and provides new information for further research.
F8variants and their genotype-phenotype correlations in Thai patients with haemophilia A: a nationwide multicentre study
Authors: Trirut Chayanit , Sosothikul Darintr , Ittiwut Rungnapa , Ittiwut Chupong , Pongsewalak Sureeporn , Songthawee Natsaruth , Natesirinilkul Rungrote , Banjerdlak Pallapa , Na Songkhla Pokpong , Komvilaisak Patcharee , Moonla Chatphatai , Suphapeetiporn Kanya
Published: July 2024

Aims

Analysis of theF8gene helps predict the risk of developing factor VIII (FVIII) inhibitors and the depth of phenotype in haemophilia A (HA) patients. Since data in Southeast Asian countries remain scarce, we aim to studyF8variation correlated with HA phenotypes in Thailand.

Methods

Thai patients with HA were enrolled from seven haemophilia treatment centres during 2022–2023. Using peripheral blood DNA, inverse shifting-polymerase chain reaction (IS-PCR) forF8-intron 22 inversion (Inv22) andF8-intron 1 inversion (Inv1) was performed. Whole exome sequencing (WES) was explored in cases without Inv22/Inv1.

Results

Of 124 patients with HA, 91.9% were detected with a causativeF8variant, including Inv22 (30.6%), Inv1 (1.6%), missense (23.4%), nonsense (16.9%) and small insertion/deletion (16.1%) mutations. Inv22, small insertion/deletion and nonsense were associated with severe HA, compared with missense variants, by the ORs of 13.9 (95% CI, 4.2 to 56.7), 14.7 (95% CI, 3.4 to 104.7) and 15.6 (95% CI, 3.6 to 110.2), respectively. While nonsense variants affecting the light chain increased the risk of developing FVIII inhibitors (OR, 6.8; 95% CI, 1.5 to 32.6) compared with the low-risk (small insertion/deletion, missense and splice-site) variants. Twelve patients (9.7%) harboured novelF8variants, comprising five missense (p.Pro540Leu, p.Ser564Pro, p.Leu668Pro, p.Ala1721Glu, p.His2024Pro), five small insertion/deletion (p.Val502SerfsTer13, p.Ile522PhefsTer13, p.Phe992LysfsTer11, p.Leu1223PhefsTer18, c.6427_6429+3delATGGTA) and one nonsense mutations (p.Glu1292Ter).

Conclusions

IS-PCR followed by WES successfully assessesF8alterations in most HA cases. With several unique variants, severe HA in Thailand is considerably caused by Inv22, small insertion/deletion and nonsense, whereas missense variants are more responsible for nonsevere HA phenotypes.