bluuebunny/crossref_metadata_2025 huggingface dataset:
Single‐cell transcriptomic profiling of maize cell heterogeneity and systemic immune responses against Puccinia polysora Underw
Authors: Yan Xiao‐Cui , Liu Qing , Yang Qian , Wang Kai‐Lai , Zhai Xiu‐Zhen , Kou Meng‐Yun , Liu Jia‐Long , Li Shang‐Tong , Deng Shu‐Han , Li Miao‐Miao , Duan Hui‐Jun
Published: November 2024

Southern corn rust (SCR), caused by Puccinia polysora Underw (P. polysora), is a catastrophic disease affecting maize, leading to significant global yield losses. The disease manifests primarily as pustules on the upper surface of corn leaves, obscuring our understanding of its cellular heterogeneity, the maize's response to its infection and the underlying gene expression regulatory mechanisms. In this study, we dissected the heterogeneity of maize's response to P. polysora infection using single‐cell RNA sequencing. We delineated cell‐type‐specific gene expression alterations in six leaf cell types, creating the inaugural single‐cell atlas of a maize leaf under fungal assault. Crucially, by reconstructing cellular trajectories in susceptible line N110 and resistant line R99 during infection, we identified diverse regulatory programs that fortify R99's resistance across different leaf cell types. This research uncovers an immune‐like state in R99 leaves, characterized by the expression of various fungi‐induced genes in the absence of fungal infection, particularly in guard and epidermal cells. Our findings also highlight the role of the fungi‐induced glycoside hydrolase family 18 chitinase 7 protein (ZmChit7) in conferring resistance to P. polysora. Collectively, our results shed light on the mechanisms of maize resistance to fungal pathogens through comparative single‐cell transcriptomics, offering a valuable resource for pinpointing novel genes that bolster resistance to P. polysora.
Effective Nitrogen Use in Wheat: A Multi‐Environment Trial Comparison of Nitrogen Utilization Efficiency Versus Nutrition Index
Authors: Lacasa Josefina , Le Gouis Jacques , Degan Francesca , Lemaire Gilles , Ciampitti Ignacio
Published: November 2024

Modern breeding programs aim to increase the effective use of nitrogen (N) in cereal grain crops such as wheat (Triticum aestivum L.) to reduce the environmental footprint of agriculture. The effective use of nitrogen may be assessed by measuring N utilization efficiency (NUtE, grain yield to N uptake ratio, both determined at harvest) or by measuring N nutrition index at anthesis (NNI, actual to critical N concentration ratio). Our main objective was to compare NUtE and NNI as metrics for phenotyping effective use of N in wheat. We used data from 11 field experiments evaluating wheat cultivars in contrasting N levels, including a revisionist analysis with historical cultivars. We found that NUtE had nearly no relationship with yield and was negatively related to grain protein concentration. In contrast, we found that NNI was positively related to yield and grain number, and was slightly related to grain protein concentration. Regarding the historical analysis, we found that the efficient use of N increased, but NUtE‐based analyses seemed to estimate greater improvements that NNI‐based analyses. In summary, NUtE may provide overoptimistic results on phenotyping and should be replaced by allometric‐based, plant physiology‐derived metrics such as NNI.
Exploring the Common Mutational Landscape in Cutaneous Melanoma and Pancreatic Cancer
Authors: Broseghini Elisabetta , Venturi Federico , Veronesi Giulia , Scotti Biagio , Migliori Marina , Marini Desy , Ricci Claudio , Casadei Riccardo , Ferracin Manuela , Dika Emi
Published: November 2024

Cutaneous melanoma (CM) and pancreatic cancer are aggressive tumors whose incidences are rapidly increasing in the last years. This review aims to provide a complete and update description about mutational landscape in CM and pancreatic cancer, focusing on similarities of these two apparently so different tumors in terms of site, type of cell involved, and embryonic origin. The familial forms of CM and pancreatic cancers are often characterized by a common mutated gene, namely CDKN2A. In fact, a germline mutation in CDKN2A gene can be responsible for the development of the familial atypical multiple mole and melanoma syndrome (FAMMM), which is characterized by melanomas and pancreatic cancer development. Sporadic melanoma and pancreatic cancer showed different key‐driven genes. The open‐access resource cBioPortal has been explored to deepen and investigate the common mutational landscape of these two tumors. We investigated the common mutated genes found in both melanoma and pancreatic cancer with a frequency of at least 5% of tested patients and copy number alterations with a frequency of at least of 3%. Data showed that 18 mutated genes and 3 copy number alterations are present in both melanoma and pancreatic cancers types. Since we found two patients that developed both melanoma and pancreatic cancer, we compared mutation landscape between the two tumors and identified a pathogenic variant in BRCA2 gene. This review gives valuable insights into the genetic underpinnings of melanoma and pancreatic cancer, urging the continued exploration and research of new genetic biomarkers able to identify patients and families at high risk of developing both cancers and to address to screening and to an effective clinical management of the patient.
Salmon Aquaculture in Chile: Production Growth and Socioeconomic Impacts
Authors: Ceballos‐Concha Adams , Asche Frank , Cárdenas‐Retamal Roberto
Published: November 2024

Global aquaculture production has been rapidly increasing in recent decades. Associated with this growth, there has been a discussion with respect to the industry's socioeconomic impact. In particular, the industry's ability to make a positive difference in the communities where it is conducted is often questioned. This is a difficult topic to address due to limited data availability. However, it is a critical question concerning the aquaculture industry's long‐term viability. Some recent studies have addressed specific indicators such as poverty reduction in a given country. However, no studies review the impact of an aquaculture industry on a broad set of indicators over time. In this paper, we review the impact of the Chilean salmon industry on three broad socioeconomic indicators: employment, salary level and migration; as well as several narrower indicators. While data beyond production initially are scarce and mostly found in the gray literature, the information they provide connects well with newer data sets as they become available. Not unexpectedly, employment in the Chilean aquaculture industry increases with production. The industry pays relatively well, and it has a societal impact as opportunities created by the industry first reverse outward migration and then lead to inward migration. This is also associated with reduced poverty, a more even income distribution, a higher female labor participation ratio, and higher education levels. While the overall socioeconomic impacts of the industry are positive, they are also disrupted by severe environmental crises and show that the socioeconomic benefits are conditioned on environmental sustainability.
Susceptibility of Mammals to Highly Pathogenic Avian Influenza: A Qualitative Risk Assessment From the Belgian Perspective
Authors: Van Leeuw Virginie , Depoorter Pieter , Mauroy Axel , Beck Olivier , Claeys Herman , De Regge Nick , De Waele Valérie , De Winter Paul , Heymans Jean‐François , Hooyberghs Jozef , Houdart Philippe , Houtsaeger Cyrelle , Linden Annick , Mori Marcella , Nauwynck Hans , Parys Anna , Rebolledo Romero Javiera , Rettigner Chantal , Rouffaer Lieze , Stassijns Jorgen , Steensels Mieke , Van Gucht Steven , Van Reeth Kristien , Vermeersch Katie , Vervaeke Muriel , Saegerman Claude , Dewulf Jeroen
Published: November 2024

Aims

The world experienced a huge number of outbreaks of highly pathogenic avian influenza (HPAI) in birds, which could represent one of the largest registered epidemics of infectious disease in food‐producing animals. Therefore, mammals, including humans, are continuously exposed to HPAI viruses leading to sporadic and sometimes unusual mammal infections. The aim of this paper is to assess the risk of crossing the avian/mammalian species barrier by the currently circulating HPAI viruses, focusing on the epidemiological situation of Belgium, a representative country for Western Europe.

Methods and Results

Information on transmission pathways and species susceptibility, based on the experimental and epidemiological data, was reviewed and weighted to assess the risk of mammal infection with HPAI A(H5N1) viruses of the circulating clade 2.3.4.4b. This risk is defined as the likelihood of mammal infection by birds crossed by the clinical consequences of this infection for this animal. From the Belgian perspective, it is concluded that this risk remains ‘low’ to ‘moderate’ for captive/domestic mammal species. However, this risk was categorised as ‘high’ for certain species, i.e. mammals that have the opportunity to have frequent direct or indirect close contacts with infected (dead) birds, such as wild felids, wild mustelids, foxes and wild marine carnivore mammals. For some mammal species, the uncertainty associated with the assessment remains high due to an ever‐changing situation.

Conclusions

The longer the virus will continue to circulate in wildlife/the environment the stronger the probability of contact between infected birds and mammals will become. This will increase the related risk of viral adaptation for efficient transmission between mammal, posing concerns for public health. Regular reassessments based on the field and experimental data are therefore necessary to implement and adapt risk‐based mitigation measures. This will require continuous monitoring of avian influenza viruses in both birds and mammals as well as sharing of sequence data.
The effect of female breast surface area on cutaneous thermal sensation, wetness perception and epidermal properties
Authors: Blount Hannah , Valenza Alessandro , Ward Jade , Caggiari Silvia , Worsley Peter R. , Filingeri Davide
Published: November 2024

Female development includes significant size changes across the breast. Yet, whether differences in breast surface area (BrSA) modify breast sensitivity to warm, cold and wetness, and the associated epidermal properties (skin thickness and surface roughness) remain unclear. We investigated the relationship between BrSA and thermal and wetness perception, as well as epidermal properties, in 21 females (2810 years) of varying breast sizes (BrSA range: 147–502 cm2), at multiple breast sites (i.e., nipple, above and below the nipple, and bra triangle). Associations between BrSA and the perceptual and epidermal variables were determined via correlation analyses. Differences across test sites were assessed by repeated‐measures ANOVA. Our results did not support the hypothesis that larger breasts present reduced thermal and wetness sensitivity, except for the above nipple site, which presented reduced warm sensitivity with increasing BrSA (r = −0.61, P = 0.003). We also found a heterogeneous distribution of cold, but not warm or wetness, sensitivity across the breast, with the above nipple site presenting lower cold sensitivity than any other site (P < 0.015). Our findings did not indicate any association between BrSA and epidermal properties (thickness and roughness), nor any site‐dependent variation in these anatomical parameters (P > 0.15). We conclude that, while some skin‐site (i.e., above the nipple) and perceptual modality‐dependent (i.e., warm sensitivity) differences were observed, BrSA‐dependent variations in thermal and wetness sensitivity were not a generalised feature of the skin covering the breast. These observations advance our fundamental understanding of breast sensory function, and they could inform the design of user‐centred clothing such as bras.
Rad‐mediated inhibition of CaV1.2 channel activity contributes to uterine artery haemodynamic adaptation to pregnancy
Authors: Hu Xiang‐Qun , Song Rui , Dasgupta Chiranjib , Liu Taiming , Zhang Meijuan , Twum‐Barimah Stephen , Blood Arlin B. , Zhang Lubo
Published: November 2024

The striking increase of uterine blood flow during pregnancy is essential for normal fetal development as well as for cardiovascular well‐being of the mother. Yet, the underlying mechanisms of pregnancy‐mediated vasodilatation of the uterine artery are not fully understood. In this study, we test the hypothesis that Rad, a monomeric G protein, is a novel regulatory mechanism in inhibiting CaV1.2 channel currents in uterine artery haemodynamic adaptation to pregnancy in a sheep model. We found that pregnancy significantly upregulates Rad expression and decreases CaV1.2 channel currents in uterine arterial smooth muscle cells. Rad knockdown ex vivo and in vivo increases CaV1.2 activity and channel window currents by reducing steady‐state inactivation in uterine arteries of pregnant sheep, recapitulating the phenotype of uterine arteries in non‐pregnant animals. Moreover, Rad knockdown in vivo in pregnant sheep enhances myogenic tone and phenylephrine‐induced vasoconstriction of uterine arteries. Whereas knockdown of Rad has no effect on mesenteric arterial CaV1.2 channel activity and mean arterial blood pressure, it significantly increases uterine vascular resistance and decreases uterine artery blood flow. Our study reveals a novel cause‐and‐effect mechanism of Rad in pregnancy‐induced suppression of CaV1.2 channel activity in uterine arteries to facilitate increased uterine blood flow, providing new insights into fundamental mechanisms of uterine haemodynamic adaptation to pregnancy.

image

Key points

Pregnancy suppresses CaV1.2 channel currents in uterine arterial smooth muscle cells.

Rad, a monomeric G protein, is upregulated in uterine arteries of pregnant sheep.

Rad knockdown ex vivo or in vivo increases CaV1.2 channel currents in uterine arteries from pregnant ewes.

In vivo knockdown of Rad elevates uterine vascular resistance and decreases uterine blood flow in pregnant sheep.

The study reveals a novel mechanism of Rad in pregnancy‐induced suppression of CaV1.2 channel activity in uterine arterial haemodynamic adaptation to pregnancy.
Impact of air pollution exposure on cytokines and histone modification profiles at single-cell levels during pregnancy
Authors: Jung Youn Soo , Aguilera Juan , Kaushik Abhinav , Ha Ji Won , Cansdale Stuart , Yang Emily , Ahmed Rizwan , Lurmann Fred , Lutzker Liza , Hammond S. Katherine , Balmes John , Noth Elizabeth , Burt Trevor D. , Aghaeepour Nima , Waldrop Anne R. , Khatri Purvesh , Utz Paul J. , Rosenburg-Hasson Yael , DeKruyff Rosemarie , Maecker Holden T. , Johnson Mary M. , Nadeau Kari C.
Published: November 2024

Fine particulate matter (PM
2.5
) exposure can induce immune system pathology via epigenetic modification, affecting pregnancy outcomes. Our study investigated the association between PM
2.5
exposure and immune response, as well as epigenetic changes using high-dimensional epigenetic landscape profiling using cytometry by time-of-flight (EpiTOF) at the single cell. We found statistically significant associations between PM
2.5
exposure and levels of certain cytokines [interleukin-1RA (IL-1RA), IL-8/CXCL8, IL-18, and IL-27)] and histone posttranslational modifications (HPTMs) in immune cells (HPTMs: H3K9ac, H3K23ac, H3K27ac, H2BK120ub, H4K20me1/3, and H3K9me1/2) among pregnant and nonpregnant women. The cord blood of neonates with high maternal PM
2.5
exposure showed lower IL-27 than those with low exposure. Furthermore, PM
2.5
exposure affects the co-modification profiles of cytokines between pregnant women and their neonates, along with HPTMs in each immune cell type between pregnant and nonpregnant women. These modifications in specific histones and cytokines could indicate the toxicological mechanism of PM
2.5
exposure in inflammation, inflammasome pathway, and pregnancy complications.
Magnonic superconductivity
Authors: Nazaryan Khachatur G. , Fu Liang
Published: November 2024

We uncover a superconducting state with partial spin polarization induced by a magnetic field. This state, which we call “magnonic superconductor,” lacks a conventional pairing order parameter but is characterized instead by a composite order parameter that represents the binding of electron pairs and magnons. We rigorously demonstrate the existence of magnonic superconductivity with high transition temperature in one-dimensional and two-dimensional Hubbard models with repulsive interaction. We further show that magnonic Cooper pairs can attract to form higher-charge bound states, which can give rise to charge-6
e
superconductivity.
Elevating levels of the endocannabinoid 2-arachidonoylglycerol blunts opioid reward but not analgesia
Authors: Martínez-Rivera Arlene , Fetcho Robert N. , Birmingham Lizzie , Xu Jin , Yang Ruirong , Foord Careen , Scala-Chávez Diego , Mekawy Narmin , Pleil Kristen , Pickel Virginia M. , Liston Conor , Castorena Carlos M. , Levitz Joshua , Pan Ying-Xian , Briand Lisa A. , Rajadhyaksha Anjali M. , Lee Francis S.
Published: November 2024

Converging findings have established that the endocannabinoid (eCB) system serves as a possible target for the development of new treatments as a complement to opioid-based treatments. Here, we show in male and female mice that enhancing levels of the eCB, 2-arachidonoylglycerol (2-AG), through pharmacological inhibition of its catabolic enzyme, monoacylglycerol lipase (MAGL), either systemically or in the ventral tegmental area (VTA) with JZL184, leads to a substantial attenuation of the rewarding effects of opioids in mice using conditioned place preference and self-administration paradigms, without altering their analgesic properties. These effects are driven by cannabinoid receptor 1 (CB1R) within the VTA, as VTA CB1R conditional knockout counteracts JZL184’s effects. Using fiber photometry with fluorescent sensors for calcium and dopamine (DA), we find that enhancing 2-AG levels diminishes opioid reward–related nucleus accumbens (NAc) activity and DA neurotransmission. Together, these findings reveal that 2-AG diminishes the rewarding properties of opioids and provides a potential adjunctive therapeutic strategy for opioid-related analgesic treatments.
Local chemical order enables an ultrastrong and ductile high-entropy alloy in a cryogenic environment
Authors: Sun Lifang , He Zhufeng , Jia Nan , Guo Yanxin , Jiang Shuang , Yang Yuliang , Liu Yuxin , Guan Xianjun , Shen Yongfeng , Yan Hai-Le , Liaw Peter K.
Published: November 2024

Owing to superior strength-ductility combination and great potential for applications in extreme conditions, high-entropy alloys (HEAs) with the face-centered cubic (FCC) structure have drawn enormous attention. However, the FCC structure limits yield strength and makes the alloys unable to meet ever-increasing demands for exploring the universe. Here, we report a strategy to obtain FCC materials with outstanding mechanical properties in both ambient and cryogenic environments, via exploiting dynamic development of the interstitial-driven local chemical order (LCO). Dense laths composed of the multiscaled LCO domains evolve from planar-slip bands that form in the prior thermomechanical processing, contributing to ultrahigh yield strengths over a wide temperature range. During cryogenic tensile deformation, LCO further develops and promotes remarkable dislocation cross-slip. Together with the deformation-driven transformation and twinning, these factors lead to satisfactory work hardening. The cryogenic loading–promoted LCO, also revealed by ab initio calculations, opens an avenue for designing advanced cryogenic materials.
Activity-driven polymer knotting for macromolecular topology engineering
Authors: Li Jia-Xiang , Wu Song , Hao Li-Li , Lei Qun-Li , Ma Yu-Qiang
Published: November 2024

Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here, we unexpectedly find that knots can be efficiently generated in active polymer systems. When one end of an actively reptative polymer is anchored, it undergoes continual self-knotting as a result of intermittent giant conformation fluctuations and the outward reptative motion. Once a knot is formed, it migrates to the anchoring point due to a nonequilibrium ratchet effect. Moreover, when the active polymer is grafted on a passive polymer, it can function as a self-propelling soft needle to either transfer its own knots or directly braid knots on the passive polymer. We further show that these active needles can create intermolecular bridging knots between two passive polymers. Our finding highlights the nonequilibrium effects in modifying the dynamic pathways of polymer systems, which have potential applications in macromolecular topology engineering.
Flexible mechano-optical dual-responsive perovskite molecular ferroelectric composites for advanced anticounterfeiting and encryption
Authors: Duan Shengshun , Chen Pinzhen , Xiong Yu-an , Zhao Fangzhi , Jing Zhengyin , Du Guowei , Wei Xiao , Xiang Shengxin , Hong Jianlong , Shi Qiongfeng , You Yumeng , Wu Jun
Published: November 2024

Hybrid organic-inorganic molecular ferroelectrics have emerged as promising materials for multifunctional piezoelectric devices. However, they present challenges in practical applications because of their inherent brittleness and poor ductility. Herein, we present a flexible mechano-optical dual-responsive molecular ferroelectric composite by incorporating trimethylchloromethyl ammonium (TMCM)–MnCl
3
into styrene ethylene butylene styrene (SEBS) matrix. The SEBS/TMCM-MnCl
3
exhibits excellent stretchable mechanical properties (tensile strain >1300%, thickness of 30 μm), piezoelectricity, and photoluminescence, enabling advanced visual-tactile–fused anticounterfeiting and encryption applications. Anticounterfeiting and antitampering tags are developed to judge whether the valued items are true or tampered with based on pattern recognition and piezoelectric response, respectively. Additionally, high-security password keyboards featuring triple-layer encryption are designed, offering more password combinations (524,288 times greater than those of traditional password devices relying solely on digital encryption) and enhanced security reliability against cracking attempts. This work can inspire designs of multifunctional optoelectronic materials and enable visual-tactile–fused intelligent applications in human-machine interfaces, information security, and advanced robotics.
Clinical evaluation of advanced MALDI-TOF MS for carbapenemase subtyping in Gram-negative isolates
Authors: Cheon Dong Huey , Jang Heejung , Choi Yoon Kyung , Oh Won Seok , Hwang Seohyun , Park Ju-Ri , Kim Hyojin , Park Yoonha , Lee Saeyoung , Yang Won Suk , Kim Min Jin , Lee Sun Hwa , Baek Je-Hyun
Published: November 2024

The spread of carbapenemase-producing Enterobacterales (CPE) is emerging as a significant clinical concern in tertiary hospitals and, in particular, long-term care facilities with deficiencies in infection control. This study aims to evaluate an advanced matrix-assisted laser desorption/ionization (A-MALDI) mass spectrometry method for the identification of carbapenemases and further discrimination of their subtypes in clinical isolates. The A-MALDI method was employed to detect CPE target proteins. Enhancements were made to improve detectability and mass accuracy through the optimization of MALDI-TOF settings and internal mass calibration. A total of 581 clinical isolates were analyzed, including 469 CPE isolates (388
Klebsiella pneumoniae
carbapenemases [KPC], 51 NDM, 40 OXA, and 2 GES) and 112 carbapenemase-negative isolates. Clinical evaluation of the A-MALDI demonstrated 100% accuracy and precision in identifying all the collected CPE isolates. Additionally, A-MALDI successfully discriminated individual carbapenemase subtypes (KPC-2 or KPC-3/KPC-4, OXA-48 or OXA-181 or OXA-232, GES-5 or GES-24) and also differentiated co-producing carbapenemase strains (KPC and NDM, KPC and OXA, KPC and GES, and NDM and OXA), attributed to its high mass accuracy and simultaneous detection capability. A-MALDI is considered a valuable diagnostic tool for accurately identifying CPE and carbapenemase’s subtypes in clinical isolates. It may also aid in selecting appropriate antibiotics for each carbapenemase subtype. Ultimately, we expect that the A-MALDI method will contribute to preventing the spread of antibiotic resistance and improving human public health.

IMPORTANCE

A-MALDI clearly demonstrated excellent ability to identify CPEs such as KPC, NDM, OXA, and GES when carbapenemase is present in the strain (100% accuracy and precision). The method also successfully discriminated carbapenemase subtypes and simultaneous detection of co-producing multiple carbapenemases in a single strain. This is the first report for simultaneous and multiple detection of intact carbapenemases of KPC, NDM, OXA, and GES using matrix-assisted laser desorption/ionization mass spectrometry in a clinical isolate.
m
6
A demethylase CpALKBH regulates
CpZap1
mRNA stability to modulate the development and virulence of chestnut blight fungus
Authors: Zhao Lijiu , Wei Xiangyu , Chen Fengyue , Chen Baoshan , Li Ru
Published: November 2024

As the most abundant eukaryotic mRNA modification, N
6
-methyladenosine (m
6
A) plays a crucial role in regulating multiple biological processes. This methylation is regulated by methyltransferases and demethylases. However, the regulatory role and mode of action of m
6
A demethylases in fungi remain poorly understood. In this study, we demonstrate that CpALKBH is a demethylase in
Cryphonectria parasitica
that removes m
6
A modification from single-stranded RNA
in vitro
. The deletion of
CpALKBH
resulted in a significant increase in the m
6
A methylation levels, along with decreases in the growth rate, sporulation, and virulence in
C. parasitica
. Additionally, CpZap1—a transcription factor—was identified as a downstream target of CpALKBH demethylase based on RNA sequencing analysis. We confirmed that CpALKBH demethylase regulates
CpZap1
mRNA stability in an m
6
A-dependent manner. Furthermore, through MazF assay, we found that methylation of
CpZap1
at position 1935A is regulated by both CpALKBH demethylase and CpMTA1 methyltransferase.
CpZap1
significantly influences the fungal phenotype and virulence, thereby restoring the abnormal phenotype observed in ∆
CpALKBH
mutants. Collectively, our findings highlight the essential role of CpALKBH as an m
6
A demethylase in the development and virulence of
C. parasitica
, while also elucidating the molecular mechanisms through which m
6
A modification impacts
CpZap1
mRNA stability.

IMPORTANCE

N
6
-methyladenosine (m
6
A) is the most abundant eukaryotic mRNA modification and is involved in various biological processes. Methyltransferases and demethylases regulate the m
6
A modification, but the regulatory role of m
6
A demethylases in fungi remains poorly understood. Here, we demonstrated that CpALKBH functions as a demethylase in
Cryphonectria parasitica
. The deletion of
CpALKBH
leads to a significant increase in m
6
A levels and a reduction in fungal growth, sporulation, and virulence. We identified
CpZap1
as a downstream target of CpALKBH, with CpALKBH regulating
CpZap1
mRNA stability in an m
6
A-dependent manner. Additionally, our findings indicate that methylation at position 1935A of
CpZap1
is regulated by both the CpALKBH demethylase and the CpMTA1 methyltransferase. Given its critical role in fungal development and virulence, overexpression of
CpZap1
can rescue abnormal phenotypes of ∆
CpALKBH
mutant. Overall, these findings contribute to improving our understanding of the role of m
6
A demethylase in fungi.
Naturally occurring influenza reassortment in pigs facilitates the emergence of intrahost virus subpopulations with distinct genotypes and replicative fitness
Authors: Li Chong , Meliopoulos Victoria , Rendahl Aaron , Schultz-Cherry Stacey , Torremorell Montserrat
Published: November 2024

Pigs are recognized as amplifying hosts for influenza A virus (IAV) reassortant viruses. Understanding the extent of IAV reassortment occurring at the individual pig level in naturally infected pigs and how reassortment impacts virus diversity, persistence, and replicative fitness is essential for countering IAV threats to humans and animals. Here, 244 IAV plaques were isolated from 24 commercial pigs, resulting in 26 distinct genome segment constellations. About 33% (8/24) of pigs were infected with two or more different genotypes, with two pigs harboring two or more different subtypes. Our results indicate that few pigs in a population harbor significantly more genotypes than other pigs and generate most of the diversity, including the emergence of reassortants. However, detecting distinct genotypes during surveillance was dynamic, with most of the genotypes subsiding over time. All the IAV genotypes could replicate in various swine and human-sourced respiratory epithelial cells, and we observed that distinct reassortant genotypes recovered from a single pig could exhibit different growth abilities, especially in human cells. Overall, we demonstrated that multiple distinct IAV genotypes with distinct antigenic profiles and varying growth abilities on swine and human respiratory tracts can be shed simultaneously from a single pig, which contributes to the dynamic nature of IAV prevalence. The striking magnitude of IAV reassortment at the single pig level revealed in this study highlights the need to strengthen surveillance efforts and plans to eliminate IAV from swine farms because pigs have a high potential to produce diverse and potentially zoonotic influenza reassortant viruses.

IMPORTANCE

Pigs play a crucial role in driving influenza A virus (IAV) diversification and evolution by reassorting the viruses originating from different hosts. Despite IAV reassortment and diversity being well documented in pig populations at different scales (e.g., farm, region, country), limited field research has explored the extent of reassortment happening at the single pig level and how that contributes to the overall genetic and biological variation observed in populations. We provide initial information on levels of reassortment happening at the single pig level in naturally infected pigs, and that particular pigs can shed a plethora of distinct genotypes, with certain genotypes having distinct replicative fitness on swine and human respiratory tracts, which preserves the potential for IAV long-term evolution and facilitates the emergence of zoonotic/pandemic-capable reassortants.
An exacerbated phosphate starvation response triggers
Mycobacterium tuberculosis
glycerol utilization at acidic pH
Authors: Healy Claire , Ehrt Sabine , Gouzy Alexandre
Published: November 2024

The mechanisms controlling
Mycobacterium tuberculosis
(Mtb) replication and survival inside its human host remain ill-defined. Phagosome acidification and nutrient deprivation are common mechanisms used by macrophages to restrict the replication of intracellular bacteria. Mtb stops replicating at mildly acidic pH (<pH5.8), an adaptive process called “acid growth arrest,” which is thought to play an important role in Mtb virulence. Using a genome-wide mutagenesis screen, we identified 95 genes whose disruption either decreases or increases Mtb fitness during acid growth arrest. We show that the virulence-associated inorganic phosphate (Pi) uptake system (Pst-1) regulates the ability of Mtb to replicate in acidic conditions. Deletion of
pstA1
, a gene coding for a subunit of the Pst-1 system, results in the overexpression of the Pi starvation regulator
regX3,
which is sufficient to restore Mtb growth in acid conditions. Our data further support the role of limited glycerol uptake and ROS-mediated glyceraldehyde-3-phosphate dehydrogenase (GAPDH) inhibition in causing Mtb acid growth arrest. This study reveals an unexpected role of the Pi starvation response in regulating acid growth arrest and highlights the intricacy of the mechanisms regulating redox homeostasis, acid stress response, and nutrient utilization in Mtb.

IMPORTANCE

Despite the availability of antibiotic treatment,
M. tuberculosis
(Mtb), the causative agent of tuberculosis (TB), remains a major infectious disease killer worldwide. A better understanding of the environments that Mtb faces during infection and the mechanisms Mtb employs to respond and adapt may help identify currently unexplored pathways and targets for the development of novel anti-TB drugs. Here, we demonstrate that Mtb growth in acid can be restored by the over-expression of the Pi starvation response regulator
regX3
. This work paves the way toward a better understanding of the mechanisms controlling Mtb growth at acidic pH and highlights the role of inorganic phosphate in this process.
The triterpenoid curcumene mediates the relative hydrophilicity of
Bacillus subtilis
spores
Authors: Castaldi Stefany , Donadio Giuliana , Staiano Ivana , Ricca Ezio , Isticato Rachele
Published: November 2024

Spores of
Bacillus subtilis
are surrounded and protected by the coat and the crust, multi-layered structures mainly made of proteins and polysaccharides. These polysaccharides are covalently linked to some of the coat and crust proteins and influence some spore properties, such as surface adhesion and hydrophilicity. This study reports that a mutant strain lacking the
spsA-L
operon, encoding 11 enzymes involved in the synthesis of spore surface polysaccharides, produced spores exposing on their surface hydrophobic molecules that were responsible for the drastic reduction of hydrophilicity of the mutant spores. Biochemical and genetic data support the identification of the C
35
-terpenoid curcumene, a precursor of the spore-associated lipid sporulene, as the highly hydrophobic molecule present on the surface of mutant spores.

IMPORTANCE

Bacterial spores are the most resistant cell forms on Earth. The metabolically quiescent spores withstand conditions that would be lethal for other cells, maintaining the capacity to sense the environment and respond to the presence of favorable conditions by germinating. Such remarkable resistance is also due to the complex layers that surround the spore cytoplasm and protect it against damaging factors. Altogether, the spore surface layers form a complex cell structure composed of proteins, polysaccharides, and, as highlighted by this study, also of lipids. Understanding the complexity of the spore surface and the specific molecules involved in its structure is an essential step for unraveling the mechanisms underlying the spore’s resistance to environmental assaults.
The dynamin-related protein PfDyn2 is essential for both apicoplast and mitochondrial fission in
Plasmodium falciparum
Authors: Morano Alexander A. , Xu Wei , Navarro Francesca M. , Shadija Neeta , Dvorin Jeffrey D. , Ke Hangjun
Published: November 2024

Dynamins, or dynamin-related proteins (DRPs), are large mechano-sensitive GTPases that mediate membrane dynamics or organellar fission/fusion events.
Plasmodium falciparum
encodes three dynamin-like proteins whose functions are poorly understood. Here, we demonstrate that one of these dynamin-related proteins, PfDyn2, is required to divide both the apicoplast and the mitochondrion, a striking divergence from the biology of related parasites. Using super-resolution and ultrastructure expansion microscopy (U-ExM), we show that PfDyn2 is expressed in dividing schizonts, and that it localizes to both the apicoplast and the mitochondrion. Our use of long-term, live-cell microscopy allows for the visualization of apicoplast and mitochondrial division in live parasites at super resolution for the first time, and demonstrates that in PfDyn2-deficient parasites, while the apicoplast and mitochondrion increase in size and complexity, they do not undergo fission. We also show that these organellar fission defects prevent successful individualization of the schizont mass and the formation of new daughter cells, or merozoites because the basal complex, the cytokinetic ring of
Plasmodium
, cannot fully contract in PfDyn2-deficient parasites, a phenotype secondary to physical blockage by undivided organelles occluding the ring. PfDyn2’s singular role in mediating both apicoplast and mitochondrial fission has not been observed in other organisms possessing two endosymbiotic organelles, including other Apicomplexans, thus reflecting a unique, potentially exploitable method of organellar division in
P. falciparum
.

IMPORTANCE

Plasmodium falciparum
remains a significant global pathogen, causing over 200 million infections and over 600,000 deaths per year. One significant obstacle to the control of malaria is increasing resistance to first-line artemisinin-based antimalarials. Another is a lack of basic knowledge about the cell biology of the parasite. Along with the mitochondrion,
Plasmodium
contains a second organelle descended from an endosymbiotic event, the apicoplast. Both organelles are common targets for antimalarials, but because many proteins involved in organellar fission are not conserved in
Plasmodium
, until now, the mechanisms underlying apicoplast and mitochondrial division have been unknown. In this study, we demonstrate that PfDyn2, a dynamin-related protein (DRP), is required for the division of both organelles. We also show that defects in organellar division hinder segmentation of the schizont and formation of invasive merozoites by preventing full contraction of the basal complex. By demonstrating its necessity for the proper division of both the apicoplast and the mitochondria, this study highlights PfDyn2 as a potential target for new antimalarials.
Complete genome sequences of six coliphages isolated from local water systems in the Philippines
Authors: Sabban Emilia Andrea V. , Eclipse Adonis N. , Arcan Stephen Kyle C. , Esliza Dexter Bryan L. , Lanete Paul Jeremy C. , Susi Lindley C. , Sikat Gelito Joseph M.
Published: November 2024

Complete genome sequences of six coliphages (genomic size: 87–347 Kbp; GC content: 35.10%–45.27%) belonging to the
Felixounavirus
,
Tequintavirus
, and
Asteriusvirus
genera were isolated from Philippine wastewater facilities and drainage systems. These phages offer potential for development as diagnostic and therapeutic tools for food and water safety.
Complete genome sequence of a methanotrophic bacterium,
Methylomicrobium lacus
strain 22M6SE5-12 isolated from a freshwater sediment environment
Authors: Kim Eui-Jin , Yim Kyung June , Bae Mi-Jung , Han Kook-IL
Published: November 2024

We assembled the complete genome of
Methylomicrobium lacus
strain 22M6SE5-12 isolated from a freshwater sediment in South Korea. The genome consists of a 4.36-Mbp chromosome and two plasmids and has 3,961 coding sequences, 12 rRNA genes, and 55 tRNA genes. We identified a gene set encoding the particulate methane monooxygenase subunits.
Draft genome sequences of two multidrug-resistant
Enterobacter soli
strains isolated from wastewater in Spain
Authors: Lois Marta , Rodríguez Sergio , Romalde Jesús L.
Published: November 2024

We report the draft genome sequences of two
Enterobacter soli
strains isolated from wastewater in Galicia (NW Spain). Genomic analysis revealed that both
E. soli
strains harbor multiple genes associated with resistance to sulfonamides, fluoroquinolones, β-latamics, and other drugs.
Virulence is not directly related to strain success
in planta
in
Clavibacter nebraskensis
Authors: Veregge Molly , Hirsch Cory D. , Moscou Matthew J. , Burghardt Liana , Tiffin Peter , Khokhani Devanshi
Published: November 2024

Goss’s wilt and leaf blight of maize is an economically important disease caused by the Gram-positive bacterium,
Clavibacter nebraskensis
(
Cn
). Little is known about the ecology and pathogenesis of this bacterium. Here, we used phenotypic assays and a high-throughput whole-genome sequencing approach to explore among-strain variation in virulence and multistrain reproductive success
in planta
. Our survey of 41 strains revealed that more recently sampled strains tended to have higher virulence than strains sampled before 2010 and tended to be more genetically divergent from the reference strain, isolated in 1971. More detailed assays with a representative sample of 13 of these strains revealed that host genotype (resistant or susceptible) did not strongly affect strain success and that strain success
in planta
in multi-strain communities was not closely associated with virulence in single-strain assays. Two weakly virulent strains, CIC354 and CIC370, had the greatest reproductive success, whereas the most highly virulent strains did not significantly change in frequency in any host genotype. A genomic analysis revealed candidate genes, including putative virulence factors (i.e., a secreted cellulase), responsible for among-strain variation in reproductive success.

IMPORTANCE

Non-pathogenic strains of many bacterial pathogens are reported to coexist with pathogenic strains in symptomatic plants. To understand the ecology and pathogenesis of the pathogen population, it is essential to study strain dynamics in the context of the host. We created a community of 13 strains exhibiting diverse virulence phenotypes and used this community to infect the host plant. We compared the strain frequency of these strains before and after the host infection. Contrary to our hypothesis of highly virulent strains being selected by the susceptible host, we found that weakly virulent strains were selected by both resistant and susceptible host lines. We identified several genes associated with strain frequency shifts suggesting their role in strain colonization, virulence, and fitness.
Multi-omics mechanical analysis of gut microbiota, carboxylic acids, and cardiac gene expression interaction triggering diabetic cardiomyopathy
Authors: Shi Meixin , Zhao Bingbing , Cai Wenjie , Yuan Hui , Liang Xiao , Li Zhitao , Liu Xinyu , Jin Ye , Liu Xi , Wei Can
Published: November 2024

It is well known that gut microbial imbalance is a potential factor for the occurrence and development of diabetes mellitus (DM) and its complications. Moreover, the heart and gut microbiota can regulate each other through the gut–metabolite–heart axis. In this study, metagenomics, metabolomics, and transcriptomics were chosen to sequence the changes in gut microbiota, serum metabolite levels, and differentially expressed genes (DEGs) in leptin receptor-deficient db/db mice and analyze the correlation between serum metabolites and gut microbiota or DEGs. According to the results, there were significant differences in the 1,029 cardiac genes and 353 serum metabolites in diabetic mice of the db/db group, including DEGs enriched in the PPAR signaling pathway and increased short-chain carboxylic acids (CAs), when compared with the normal db/m group. According to metagenomics, the gut microbiota of mice in the db/db group were disrupted, and particularly Lachnospiraceae bacteria and Oscillospiraceae bacteria significantly decreased. Also, according to the Pearson correlation analysis, a significant positive correlation was found between CAs and PPAR signaling pathway-related DEGs, and a negative correlation was found between CAs and the abundance of the above-mentioned species. To sum up, type 2 diabetes mellitus (T2DM) can upregulate the expression of partial cardiac genes through the levels of serum short-chain CAs affected by gut microbiota, thus playing a role in the occurrence and development of diabetic cardiomyopathy (DCM).

IMPORTANCE

Our research results clearly link the changes in heart genes of T2DM and normal mice with changes in serum metabolites and gut microbiota, indicating that some genes in biological processes are closely related to the reduction of protective microbiota in the gut microbiota. This study provides a theoretical basis for investigating the mechanism of DCM and may provide preliminary evidence for the future use of gut microbiota therapy for DCM.
Effects of temporal, spatial, and environmental factors on ciliates community in northeastern South China Sea, with notes on co-occurrence patterns of environment, phytoplankton, and ciliate
Authors: Liu Weiwei , Cheng Zijun , Wen Shaowei , Li Gang , Ke Zhixin , Li Daning , Tan Yehui
Published: November 2024

Little is known about temp-spatial variations and determining mechanism of microplankton community from continental shelf to deep basin. Here, the distribution and determinants of ciliates in the northeastern South China Sea were investigated in summer and winter. We found that the alpha diversity were generally similar, but community composition showed clear difference in summer and winter. For spatial dimension, the alpha diversity significantly decreased from neritic water to deep, and the variations of community composition were only detected between upper and deep water. The determinants of community varied depending on the research scale. For entire community, the variations were higher explained by environmental factors than by temp-spatial factors. Specially, physical factors were the main determinants, which may attribute to the effects of physical processes occurred in the research area. For the three spatial subareas, season showed more significant influences on communities than other factors. Network analyses revealed that the ciliate exhibited more relationships with phytoplankton than with environment factors. Diatom and physical factors accounted for most of the ciliate-phytoplankton-environment co-occurrence relationships, suggesting their significant influences to the community stability of the microbial food web. This study improves our understanding for the mechanisms of community structuring of microzooplankton in the open sea across both space and time.

IMPORTANCE

Ciliates are important components of microplanktons and play a crucial role in global nutrient cycling. There is still large knowledge gap on their structuring mechanisms from continental shelf to deep basin. We revealed the distribution patterns of ciliate community in neSCS and assessed the relative contribution of temporal, spatial, and environmental factors for their community structuring. Compared with temp-spatial factors, environmental factors take more responsibilities for the ciliate distribution. Among the environmental factors, physical factors showed the largest contribution to community variation. Moreover, the ciliate-environment co-occurrence pattern showed that physical factors contributed more for their relationships. These findings suggested that the physical processes play key roles in temp-spatial dynamics of ciliate community in open ocean.