bluuebunny/crossref_metadata_2025_split huggingface dataset:
CsLCD and CsDCD are involved in nitric oxide‐enhanced salt tolerance in cucumber seedlings
Authors: Li Ailing , Li Xuelian , Chen Xinfang , Pan Xuejuan , Wu Xuetong , Liao Weibiao 
Published: November 2024

AbstractNitric oxide (NO) and hydrogen sulphide (H2S) play important roles in plant growth, development and environmental adaptation. Currently, there is few information on the mechanism by which H2S may be involved in NO‐induced salt tolerance. In this study, cucumber was used to investigate the role of NO and H2S and their relationship under salt stress. The results showed that the H2S donor sodium hydrosulfide (NaHS) and the NO donor sodium nitroprusside (SNP) significantly promoted the growth of cucumber seedlings under salt stress. However, hypotaurine (HT, an H2S scavenger) inhibited the positive effects of SNP under salt stress. Meanwhile, SNP treatment significantly increased the content of endogenous H2S, the activity of H2S synthesis‐related enzymes LCD, DCD, and CAS, and the expression of H2S synthesis‐related genes (CsLCD and CsDCD). In addition, the salt tolerance of cucumber seedlings was largely eliminated after silencing the H2S synthesis‐related genes CsLCD/CsDCD, while overexpression of CsLCD/CsDCD significantly enhanced the salt tolerance. It was further found that SNP enhanced the salt tolerance of CsLCD/CsDCD overexpression lines, but it had no positive effect on the tolerance of CsLCD/CsDCD silencing lines. Therefore, NO might enhance salt tolerance in cucumber seedlings by upregulating the expression of H2S synthesis‐related gene CsLCD/CsDCD.
TaCCS1‐B expression modulates copper, enzymatic antioxidants and polyphenols contents and provides abiotic stress tolerance in transgenic Arabidopsis
Authors: Tyagi Shivi , Shumayla  , Singh Samar , Pandey Ashutosh , Upadhyay Santosh Kumar 
Published: November 2024

AbstractAbiotic stress, including osmotic and salinity stress, significantly affects plant growth and productivity. Copper chaperone for superoxide dismutase (CCS) is essential for copper homeostasis and oxidative stress management. In this study, we investigated the role of the TaCCS1‐B gene of bread wheat in enhancing stress tolerance in yeast and transgenic Arabidopsis. Expression of TaCCS1‐B increased abiotic stress tolerance in recombinant yeast cells. Phenotypic analysis of Arabidopsis TaCCS1‐B expressing lines demonstrated that they exhibited significantly higher germination rates, increased root length and better growth under osmotic and salinity stress than wild type. Additionally, the transgenic lines exhibited higher copper accumulation and enhanced photosynthetic pigments and proline level, coupled with reduced hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) contents. They also showed higher enzymatic antioxidants' activities, indicating reduced oxidative stress in transgenic lines, resulting in reduced flavonoid content. Gene expression analysis indicated modulated expression of stress‐responsive genes in the transgenic lines under stress conditions. These findings suggested the role of TaCCS1‐B in enhancing stress tolerance by improving copper homeostasis and regulating key stress‐responsive genes. This study highlights the potential of TaCCS1‐B for the development of better stress resilience crops, which is critical for sustaining agricultural productivity for food security under adverse environmental conditions.
Lipid Droplets in Aquatic Animals: Diversity, Biogenesis, and Functional Implications
Authors: Zhu Si , Lv Zhimeng , Ai Qinghui , Li Chenghua 
Published: November 2024

ABSTRACTAmid the aquaculture boom, chemical contaminants, diseases, and improper nutrition persist as threats to the sustainability of aquaculture. The accumulation of lipid droplets in different tissues has emerged as a hallmark in aquatic animals exposed to these stressors. While abundant knowledge is available on lipid droplets in mammals, relatively little is known in aquatic animals. Recently, interest in lipid droplets has grown in parallel with the recognition that they are actively engaged in the regulation of stress responses, metabolic modulation, infections, and immune response in different aquatic animals. This review first outlines the diversity of lipid droplets protein in various aquatic animals and discusses the function of lipid droplets in maintaining cellular homeostasis by contacting other organelles. Subsequently, the mechanisms of lipid droplet biogenesis in response to various chemical contaminants are summarized. Additionally, we describe the complex roles of lipid droplets in the host‐pathogen dynamic and the link between excessive lipid droplets accumulation and unwanted metabolic diseases in several aquatic animals. Finally, the potential application of lipid droplets in aquaculture is presented. A better understanding of the dynamics and functions of lipid droplets will facilitate the development of lipid droplets‐based therapeutic strategies, thereby improving the sustainability of aquaculture.
The economic costs of supply chain decoupling
Authors: Attinasi Maria‐Grazia , Boeckelmann Lukas , Meunier Baptiste 
Published: November 2024

AbstractAs countries and firms increasingly seek ways to strengthen the resilience of their supply chains, this paper studies the global economic costs of a decoupling of global supply chains along geopolitical lines as well as in strategic sectors. We explore not only the long‐run effects but also the short‐run costs stemming from rigid wages and low substitutability across factors of production and input goods. We find that, in terms of welfare losses, the costs of decoupling are roughly five times higher in the short‐run compared with the long‐run, while country losses are heterogeneous. A reshaping of global supply chains increases the level of consumer prices in most countries, as well as producer prices, especially for trade‐intensive manufacturing sectors. Global supply chain decoupling entails also a reallocation of labour across skill levels. Finally, global trade would decrease substantially, driven by lower trade in intermediate inputs and a higher reliance of countries on domestic production.
Photobiomodulation studies on diabetic wound healing: An insight into the inflammatory pathway in diabetic wound healing
Authors: Mgwenya Tintswalo N. , Abrahamse Heidi , Houreld Nicolette N. 
Published: November 2024

AbstractDiabetes mellitus remains a global challenge to public health as it results in non‐healing chronic ulcers of the lower limb. These wounds are challenging to heal, and despite the different treatments available to improve healing, there is still a high rate of failure and relapse, often necessitating amputation. Chronic diabetic ulcers do not follow an orderly progression through the wound healing process and are associated with a persistent inflammatory state characterised by the accumulation of pro‐inflammatory macrophages, cytokines and proteases. Photobiomodulation has been successfully utilised in diabetic wound healing and involves illuminating wounds at specific wavelengths using predominantly light‐emitting diodes or lasers. Photobiomodulation induces wound healing through diminishing inflammation and oxidative stress, among others. Research into the application of photobiomodulation for wound healing is current and ongoing and has drawn the attention of many researchers in the healthcare sector. This review focuses on the inflammatory pathway in diabetic wound healing and the influence photobiomodulation has on this pathway using different wavelengths.
Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon
Authors: Liu Fei , Wang Shi-Hui , Cheewangkoon Ratchadawan , Zhao Rui-Lin 
Published: November 2024

ABSTRACT

Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.

IMPORTANCE
This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.
Complete genome sequence of
Mumia
sp. Pv 4-285 isolated from the rhizosphere of
Phyllostachys viridiglaucescens
(Carrière) Rivière & C. Rivière
Authors: Kachor Anna , Samborskyy Markiyan , Rebets Yuriy , Gromyko Oleksandr 
Published: November 2024

ABSTRACT

Mumia
are one of the rarest representatives of phylum Actinomycetota with only four species known. Here, we report the complete genome sequence of
Mumia
sp. Pv 4-285 isolated from a rhizosphere sample of
Phyllostachys viridiglaucescens
. The genome consists of a 4,649,352 bp circular chromosome with 4,361 protein-coding genes.
The genome sequence of a non-capsular natural
Bacillus anthracis
strain of A.Br.001/002 canSNP group isolated from permafrost in Yakutia, Russia
Authors: Goncharova Yulia , Bakhteeva Irina , Mironova Raisa , Skryabin Yuriy , Kislichkina Angelina , Solomentseva Aleksandra , Timofeev Vitalii 
Published: November 2024

ABSTRACT

We present the results of the whole-genome sequencing of a
Bacillus anthracis
strain isolated from a permafrost sample collected in Yakutia, Russia. This strain was named YakM12. Phylogenetic analysis showed that YakM12 belongs to the canSNP group A.Br.001/002 and is genetically close to the Sterne vaccine strain.
Comparative genomic analysis of ten
Elizabethkingia
anophelis
isolated from clinical patients in China
Authors: Wu Fei , Wu Yan , Zhang Miaomiao , Tian Lijun , Li Xue , Luo Xi , Zhang Yiquan , Lu Renfei 
Published: November 2024

ABSTRACT

Elizabethkingia anophelis
is an emerging pathogen that causes life-threatening infections in neonates and immunocompromised patients. In this study, we performed next-generation sequencing (NGS) to characterize 10
E. anophelis
strains isolated from clinical patients in Nantong, China. Core, accessory, and unique genomes were composed of 2,891, 1,633, and 498 genes, respectively. Based on genetic screening for antimicrobial resistance genes (AMRs), all
E. anophelis
strains carried the same AMRs, including
bla
B
,
bla
CME
, and
bla
GOB
. The virulence factors (VFs) in the 10 strains were classified into 13 functional categories, and the differences between strains were mainly in immune modulation and nutritional/metabolic factor. We further analyzed the genomic features of one of ten strains, NT06 strain. The capsule type of NT06 was X, which is rare among
E. anophelis
strains. Based on comparative analyses, we first found that NT06 carried the YclNOPQ-like operon, which is the complete transporter for petrobactin, to acquire iron. The genomic features are important for further investigations of epidemiology, resistance, virulence, and to identify appropriate treatments.

IMPORTANCE

Elizabethkingia anophelis
strains are opportunistic pathogens causing meningitis, bloodstream infections, and endophthalmitis in vulnerable populations. There is a lack of knowledge of the genetic diversity, presence of antimicrobial resistance genes (AMRs), and virulence factors (VFs) in
E. anophelis
isolated from clinical patient
s
in China. Based on next-generation sequencing (NGS) and comparative genomic analyses, we determined the genomic features, phylogeny, and diversity of
E. anophelis
strains isolated from patients and identified a large accessory genome, intrinsic AMRs, and variable VFs. Based on comparative analyses, we identified a key strain, NT06, that carried a unique capsule type of X and the siderophore-mediated iron acquisition system (
yclNOPQ
-like genes). These findings advance our understanding of the genomic plasticity, evolution, and pathogenicity determinants of
E. anophelis
.
Differential vasoproliferative traits of
Bartonella henselae
strains associated with autotransporter BafA variants
Authors: Kondo Yuka , Suzuki Masahiro , Sato Shingo , Maruyama Soichi , Sei Akiko , Ma Xingyan , Nakano Kota , Doi Yohei , Tsukamoto Kentaro 
Published: November 2024

ABSTRACT

Bartonella henselae,
a Gram-negative facultative intracellular bacterium, is the etiological agent of cat-scratch disease and also causes bacillary angiomatosis in immunocompromised individuals. Although the ability to promote vascular endothelial cell proliferation differs among
Bartonella
species, variations among strains within
B. henselae
remain unclear.
Bartonella
angiogenic factor A (BafA) and
Bartonella
adhesin A (BadA) have been identified as autotransporters of
B. henselae
that are involved in endothelial cell proliferation. Although strain-specific differences in the expression of BadA and the VirB/D4 type IV secretion system have been reported, BafA expression among
B. henselae
strains has yet to be examined. Therefore, the present study investigated the proliferation-promoting ability of 13
B. henselae
strains from several sources in human umbilical vein endothelial cells (HUVECs). We identified BafA variants 1 and 2 based on the deduced amino acid sequences of its passenger domain. The recombinant proteins of both variants exhibited similar proliferation activity against HUVECs. However, BafA variant 2 strains showed cytotoxicity at a high bacterial inoculum in a direct coculture with HUVECs, which was attenuated in an indirect coculture. These strains, in contrast to BafA variant 1 strains, highly expressed BadA and exhibited bacterial aggregation. Based on a core genome SNP analysis of 50
B. henselae
strains, the BafA variant types corresponded to clades 1–4. These results indicate that vasoproliferative traits differ among
B. henselae
clades based on the variant types. Therefore, this study provides a new conceptual framework in which the clades of
B. henselae
may predict their pathogenicity in humans.

IMPORTANCE

Bartonella
species including
Bartonella henselae
,
Bartonella quintana
, and
Bartonella bacilliformis
cause vasoproliferative lesions. Their proliferation-promoting ability in vascular endothelial cells differs among
Bartonella
species; however, it is unclear whether these differences exist among
B. henselae
strains. We herein showed that
B. henselae
strains exhibited variable proliferation-promoting ability and cytotoxicity in vascular endothelial cells, which corresponded to the
bafA
gene variants possessed by the strains. The expression levels of
Bartonella
angiogenic factor A (BafA) and
Bartonella
adhesin A, as well as the degree of proliferation-promoting ability and cytotoxicity in endothelial cells, varied among the strains. A core genome SNP analysis of strains using whole genome sequencing data divided
B. henselae
strains into four clades, with each clade corresponding to BafA variants 1–4. These results suggest the differential vasoproliferative potency of
B. henselae
, with potential implications in clinical management, including risk stratification and predictions of the clinical course.
Comparison of lateral tail vein and retro-orbital venous sinus as routes of inoculation to study Group B streptococcal systemic infection
Authors: da Conceição Mendonça Jéssica , Lumsdaine Stephen , Burcham Lindsey R. 
Published: November 2024

ABSTRACT

Murine models are commonly used to understand pathogen and host determinants of systemic infection. While these models have proven beneficial for uncovering bacterial mechanisms required for progression to invasive disease, it can be challenging to draw comparisons across studies as several different routes of infection are standardly used for these experiments. In this study, one of the leading bacterial meningeal pathogens,
Streptococcus agalactiae
, or Group B
Streptococcus
(GBS), was used to compare experimental outcomes of two commonly used routes of hematogenous infection, lateral tail vein injection and retro-orbital venous sinus injection. Here we demonstrate that both routes of infection result in systemic disease and the onset of clinical symptoms of infection. We show that retro-orbital venous sinus injection results in an initial increase in bacterial dissemination to the spleen and brain tissue of GBS-infected mice, while an increased bacterial burden was only detected in brain tissues at a later time point. Despite differences in initial dissemination and brain bacterial burden, we found that the route of infection did not significantly impact bacterial burden in the blood, kidney, spleen, heart, and lung tissues at experimental endpoints; and similarly did not impact animal health scores during infection; cytokine and proinflammatory protein abundance in the brain tissue; or overall animal survival. In summary, these findings suggest that both tail vein injection and retro-orbital venous sinus injection are viable models to study Group B streptococcal systemic infection and result in largely similar disease outcomes within our tested parameters.

IMPORTANCE

Streptococcus agalactiae
or Group B
Streptococcus
(GBS) is the leading cause of invasive disease in neonates and immunocompromised adults and is implicated in severe cases of sepsis, pneumonia, and meningitis. Established murine models of hematogenous systemic infection allow for better understanding and investigation of bacterial dispersion, pathogenesis, meningeal inflammation, and interaction with the host. Here we compared two routes of infection, intravenous lateral tail vein and retro-orbital venous sinus, demonstrating that similar experimental outcomes can be observed, regardless of the route of infection for GBS, specifically. These findings help to reinforce the utility of different systemic infection models and provide insight into comparisons across different established models and how these models can be applied in microbial research.
Legionella pneumophila
IrsA, a novel, iron-regulated exoprotein that facilitates growth in low-iron conditions and modulates biofilm formation
Authors: Lopez Alberto E. , Mayoral Joshua , Zheng Huaixin , Cianciotto Nicholas P. 
Published: November 2024

ABSTRACT

To discover new factors that are involved in iron acquisition by
Legionella pneumophila
, we used RNA-Seq to identify the genes that are most highly induced when virulent strain 130b is cultured in a low-iron chemically defined medium. Among other things, this revealed
14915
, a heretofore uncharacterized gene that is predicted to be transcriptionally regulated by Fur and to encode a novel, ~15 kDa protein.
14915
was present in all
L. pneumophila
strains examined and had homologs in a subset of the other
Legionella
species. Compatible with it containing a classic signal sequence, the 14915 protein was detected in bacterial culture supernatants in a manner dependent upon the
L. pneumophila
type II secretion system. Thus, we designated 14915 as IrsA for
ir
on-
r
egulated,
s
ecreted protein
A
. Based on mutant analysis, the
irsA
gene was not required for optimal growth of strain 130b in low-iron media. However, after discovering that the commonly used laboratory-derived strain Lp02 has a much greater requirement for iron, we uncovered a growth-enhancing role for IrsA after examining an Lp02 mutant that lacked both IrsA and the Fe
2+
-transporter FeoB. The
irsA
mutant of 130b, but not its complemented derivative, did, however, display increased biofilm formation on both plastic and agar surfaces, and compatible with this, the mutant hyper-aggregated. Thus, IrsA is a novel, iron-regulated exoprotein that modulates biofilm formation and, under some circumstances, promotes growth in low-iron conditions. For this study, we determined and deposited in the database a complete and fully assembled genome sequence for strain 130b.

IMPORTANCE

The bacterium
Legionella pneumophila
is the principal cause of Legionnaires’ disease, a potentially fatal form of pneumonia that is increasing in incidence.
L. pneumophila
exists in many natural and human-made water systems and can be transmitted to humans through inhalation of contaminated water droplets.
L. pneumophila
flourishes within its habitats by spreading planktonically, assembling into biofilms, and growing in larger host cells. Iron acquisition is a key determinant for
L. pneumophila
persistence in water and during infection. We previously demonstrated that
L. pneumophila
assimilates iron both by secreting a non-protein iron chelator (siderophore) and by importing iron through membrane transporters. In this study, we uncovered a novel, secreted protein that is highly iron-regulated, promotes
L. pneumophila
’s growth in low-iron media, and impacts biofilm formation. We also identified uncharacterized, IrsA-related proteins in other important human and animal pathogens. Thus, our results have important implications for understanding iron assimilation, biofilm formation, and pathogenesis.