bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovative Application of the Ilizarov Technique for Long Nerve Defect Reconstruction: A Detailed Case Report
Authors: Liang Xiajun , Xu Lei , Zhou Chunhao , Fang Jia , Sun Dawei , Qin Chenghe 
Published: August 2024

BackgroundTraditionally known for bone regeneration, the Ilizarov technique's effectiveness in nerve reconstruction, particularly for extensive nerve damage, has yet to be widely recognized.Case presentationThis report presents a case study and proposes the innovative use of the Ilizarov technique for reconstructing extended nerve defects. In this study, we reviewed a 43‐year‐old male diagnosed with an open fracture of the right tibia combined with soft tissue injury resulting in a mangled injury in which a large part of his right tibial bone and nerve were lost. The patient was cured and the sensorimotor function was recovered after distraction osteogenesis by the Ilizarov technique, which is a unique application of this technique to repair a substantial long nerve defect, a rare occurrence in medical literature. It highlights the method of nerve lengthening, which is achieved by attaching the nerve stump to the bone stump. This approach allows for significant nerve regeneration and ensures a stable progression of the nerve, as the bone stump acts as a carrier, overcoming the challenges of direct nerve lengthening.ConclusionsThe adaptability and effectiveness of the Ilizarov technique in a new area suggests the need to reconsider traditional approaches to complex nerve reconstruction. Placing this case within the context of current medical knowledge underscores the potential of this technique to revolutionize the treatment of extended nerve defects, offering hope for improved outcomes in challenging scenarios.
AaMYC3 bridges the regulation of glandular trichome density and artemisinin biosynthesis in Artemisia annua
Authors: Yuan Mingyuan , Sheng Yinguo , Bao Jingjing , Wu Wenkai , Nie Guibin , Wang Lingjian , Cao Junfeng 
Published: August 2024

SummaryArtemisinin, the well‐known natural product for treating malaria, is biosynthesised and stored in the glandular‐secreting trichomes (GSTs) of Artemisia annua. While numerous efforts have clarified artemisinin metabolism and regulation, the molecular association between artemisinin biosynthesis and GST development remains elusive. Here, we identified AaMYC3, a bHLH transcription factor of A. annua, induced by jasmonic acid (JA), which simultaneously regulates GST density and artemisinin biosynthesis. Overexpressing AaMYC3 led to a substantial increase in GST density and artemisinin accumulation. Conversely, in the RNAi‐AaMYC3 lines, both GST density and artemisinin content were markedly reduced. Through RNA‐seq and analyses conducted both in vivo and in vitro, AaMYC3 not only directly activates AaHD1 transcription, initiating GST development, but also up‐regulates the expression of artemisinin biosynthetic genes, including CYP71AV1 and ALDH1, thereby promoting artemisinin production. Furthermore, AaMYC3 acts as a co‐activator, interacting with AabHLH1 and AabHLH113, to trigger the transcription of two crucial enzymes in the artemisinin biosynthesis pathway, ADS and DBR2, ultimately boosting yield. Our findings highlight a critical connection between GST initiation and artemisinin biosynthesis in A. annua, providing a new target for molecular design breeding of traditional Chinese medicine.
Recent advances in artificial intelligent strategies for tissue engineering and regenerative medicine
Authors: Gharibshahian Maliheh , Torkashvand Mohammad , Bavisi Mahya , Aldaghi Niloofar , Alizadeh Akram 
Published: August 2024

AbstractBackgroundTissue engineering and regenerative medicine (TERM) aim to repair or replace damaged or lost tissues or organs due to accidents, diseases, or aging, by applying different sciences. For this purpose, an essential part of TERM is the designing, manufacturing, and evaluating of scaffolds, cells, tissues, and organs. Artificial intelligence (AI) or the intelligence of machines or software can be effective in all areas where computers play a role.MethodsThe “artificial intelligence,” “machine learning,” “tissue engineering,” “clinical evaluation,” and “scaffold” keywords used for searching in various databases and articles published from 2000 to 2024 were evaluated.ResultsThe combination of tissue engineering and AI has created a new generation of technological advancement in the biomedical industry. Experience in TERM has been refined using advanced design and manufacturing techniques. Advances in AI, particularly deep learning, offer an opportunity to improve scientific understanding and clinical outcomes in TERM.ConclusionThe findings of this research show the high potential of AI, machine learning, and robots in the selection, design, and fabrication of scaffolds, cells, tissues, or organs, and their analysis, characterization, and evaluation after their implantation. AI can be a tool to accelerate the introduction of tissue engineering products to the bedside.Highlights
The capabilities of artificial intelligence (AI) can be used in different ways in all the different stages of TERM and not only solve the existing limitations, but also accelerate the processes, increase efficiency and precision, reduce costs, and complications after transplantation.
ML predicts which technologies have the most efficient and easiest path to enter the market and clinic.
The use of AI along with these imaging techniques can lead to the improvement of diagnostic information, the reduction of operator errors when reading images, and the improvement of image analysis (such as classification, localization, regression, and segmentation).
AAO2 impairment enhances aldehyde detoxification by AAO3 in Arabidopsis leaves exposed to UV‐C or Rose‐Bengal
Authors: Nurbekova Zhadyrassyn , Srivastava Sudhakar , Nja Zai Du , Khatri Kusum , Patel Jaykumar , Choudhary Babita , Turečková Veronica , Strand Miroslav , Zdunek‐Zastocka Edyta , Omarov Rustem , Standing Dominic , Sagi Moshe 
Published: August 2024

SUMMARYAmong the three active aldehyde oxidases in Arabidopsis thaliana leaves (AAO1‐3), AAO3, which catalyzes the oxidation of abscisic‐aldehyde to abscisic‐acid, was shown recently to function as a reactive aldehyde detoxifier. Notably, aao2KO mutants exhibited less senescence symptoms and lower aldehyde accumulation, such as acrolein, benzaldehyde, and 4‐hydroxyl‐2‐nonenal (HNE) than in wild‐type leaves exposed to UV‐C or Rose‐Bengal. The effect of AAO2 expression absence on aldehyde detoxification by AAO3 and/or AAO1 was studied by comparing the response of wild‐type plants to the response of single‐functioning aao1 mutant (aao1S), aao2KO mutants, and single‐functioning aao3 mutants (aao3Ss). Notably, aao3Ss exhibited similar aldehyde accumulation and chlorophyll content to aao2KO treated with UV‐C or Rose‐Bengal. In contrast, wild‐type and aao1S exhibited higher aldehyde accumulation that resulted in lower remaining chlorophyll than in aao2KO leaves, indicating that the absence of active AAO2 enhanced AAO3 detoxification activity in aao2KO mutants. In support of this notion, employing abscisic‐aldehyde as a specific substrate marker for AAO3 activity revealed enhanced AAO3 activity in aao2KO and aao3Ss leaves compared to wild‐type treated with UV‐C or Rose‐Bengal. The similar abscisic‐acid level accumulated in leaves of unstressed or stressed genotypes indicates that aldehyde detoxification by AAO3 is the cause for better stress resistance in aao2KO mutants. Employing the sulfuration process (known to activate aldehyde oxidases) in wild‐type, aao2KO, and molybdenum‐cofactor sulfurase (aba3‐1) mutant plants revealed that the active AAO2 in WT employs sulfuration processes essential for AAO3 activity level, resulting in the lower AAO3 activity in WT than AAO3 activity in aao2KO.
“
Candidatus
Uabimicrobium helgolandensis”—a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division
Authors: Wurzbacher Carmen E. , Hammer Jonathan , Haufschild Tom , Wiegand Sandra , Kallscheuer Nicolai , Jogler Christian 
Published: August 2024

ABSTRACT

The unique cell biology presented by members of the phylum
Planctomycetota
has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology—shapeshifting by members of the “
Saltatorellus
” clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium “
Candidatus
Uabimicrobium amorphum.” These recent additions to the phylum
Planctomycetota
indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like “
Ca.
U. amorphum”, we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found “
Ca.
U. amorphum” to be rather distinct in many regards. Presenting a detailed description of “
Ca.
U. amorphum,” we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second “bacterium of prey” from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with “
Ca.
U. amorphum”: phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to “
Ca.
U. amorphum” within genus thresholds, we propose the name “
Ca.
Uabimicrobium helgolandensis” for this strain.

IMPORTANCE

“
Candidatus
Uabimicrobium helgolandensis” HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be “impossible” microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.
SARS-CoV-2 Omicron subvariants progressively adapt to human cells with altered host cell entry
Authors: Sakurai Yasuteru , Okada Sayaka , Ozeki Takehiro , Yoshikawa Rokusuke , Kinoshita Takaaki , Yasuda Jiro 
Published: August 2024

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant exhibits high transmissibility with a strong immune escape ability and causes frequent large-scale global infections by producing predominant subvariants. Here, using human upper/lower airway and intestinal cells, we examined the previously dominant BA.1–BA.5 and BA.2.75 subvariants, together with the recently emerged XBB/BQ lineages, in comparison to the former Delta variant. We observed a tendency for each virus to demonstrate higher growth capability than the previously dominant subvariants. Unlike human bronchial and intestinal cells, nasal epithelial cells accommodated the efficient entry of certain Omicron subvariants, similar to the Delta variant. In contrast to the Delta’s reliance on cell-surface transmembrane protease serine 2, all tested Omicron variants depended on endosomal cathepsin L. Moreover, S1/S2 cleavage of early Omicron spikes was less efficient, whereas recent viruses exhibit improved cleavage efficacy. Our results show that the Omicron variant progressively adapts to human cells through continuous endosome-mediated host cell entry.

IMPORTANCE
SARS-CoV-2, the causative agent of coronavirus disease 2019, has evolved into a number of variants/subvariants, which have generated multiple global waves of infection. In order to monitor/predict virological features of emerging variants and determine appropriate strategies for anti-viral development, understanding conserved or altered features of evolving SARS-CoV-2 is important. In this study, we addressed previously or recently predominant Omicron subvariants and demonstrated the gradual adaptation to human cells. The host cell entry route, which was altered from the former Delta variant, was conserved among all tested Omicron subvariants. Collectively, this study revealed both changing and maintained features of SARS-CoV-2 during the Omicron variant evolution.
Functional investigation of the two ClpPs and three ClpXs in
Myxococcus xanthus
DK1622
Authors: Wan Tianyu , Cao Ying , Lai Ya-jun , Pan Zhuo , Li Yue-zhong , Zhuo Li 
Published: August 2024

ABSTRACT

ClpXP is a protease complex that plays important roles in protein quality control and cell cycle regulation, but the functions of multiple ClpXs and multiple ClpPs in
M. xanthus
remain unknown. The genome of
Myxococcus xanthus
DK1622 contains two
clpP
s and three
clpX
s. The
clpP1
and
clpX1
genes are cotranscribed and are both essential, while the other copies are isolated in the genome and are deletable. The deletion of
clpX2
caused the mutant to be deficient in fruiting body development, while the
clpX3
gene is involved in resistance to thermal stress. Both ClpPs possess catalytic active sites, but only ClpP1 shows
in vitro
peptidase activity on the typical substrate Suc-LY-AMC. All of these
clpP
and
clpX
genes exhibit strong transcriptional upregulation in the stationary phase, and the transcription of the three
clpX
genes appears to be coordinated. Our results demonstrated that multiple ClpPs and multiple ClpXs are functionally divergent and may assist in the environmental adaptation and functional diversification of
M. xanthus
.

IMPORTANCE

ClpXP is an important protease complex of bacteria and is involved in various physiological processes.
Myxococcus xanthus
DK1622 possesses two ClpPs and three ClpXs with unclear functions. We investigated the functions of these genes and demonstrated the essential roles of
clpP1
and
clpX1
. Only ClpP1 has
in vitro
peptidase activity on Suc-LY-AMC, and the isolated
clpX
copies participate in distinct cellular processes. All of these genes exhibited significant transcriptional upregulation in the stationary phase. Divergent functions appear in multiple ClpPs and multiple ClpXs in
M. xanthus
DK1622.
A winged-helix DNA-binding protein is essential for self-fertility during sexual development of the homothallic fungus
Fusarium graminearum
Authors: Park Jiyeun , Jeon Hosung , Hwangbo Aram , Min Kyunghun , Ko Jaeho , Kim Jung-Eun , Kim Sieun , Shin Ji Young , Lee Yong-Hwan , Lee Yin-Won , Son Hokyoung 
Published: August 2024

ABSTRACT

Sexual reproduction is crucial for increasing the genetic diversity of populations and providing overwintering structures, such as perithecia and associated tissue, in the destructive plant pathogenic fungus
Fusarium graminearum
. While mating-type genes serve as master regulators in fungal sexual reproduction, the molecular mechanisms underlying this process remain elusive. Winged-helix DNA-binding proteins are key regulators of embryogenesis and cell differentiation in higher eukaryotes. These proteins are implicated in the morphogenesis and development of several fungal species. However, their involvement in sexual reproduction remains largely unexplored in
F. graminearum
. Here, we investigated the function of winged-helix DNA-binding proteins in vegetative growth, conidiation, and sexual reproduction, with a specific focus on the
FgWING27
, which is highly conserved among
Fusarium
species. Deletion of
FgWING27
resulted in an abnormal pattern characterized by a gradual increase in the expression of mating-type genes during sexual development, indicating its crucial role in the stage-specific genetic regulation of
MAT
genes in the late stages of sexual development. Furthermore, using chromatin immunoprecipitation followed by sequencing analysis, we identified
Fg17056
as a downstream gene of Fgwing27, which is essential for sexual reproduction. These findings underscore the significance of winged-helix DNA-binding proteins in fungal development and reproduction in
F. graminearum
, and highlight the pivotal role of Fgwing27 as a core genetic factor in the intricate genetic regulatory network governing sexual reproduction.

IMPORTANCE

Fusarium graminearum
is a devastating plant pathogenic fungus causing significant economic losses due to reduced crop yields. In Fusarium Head Blight epidemics, spores produced through sexual and asexual reproduction serve as inoculum, making it essential to understand the fungal reproduction process. Here, we focus on winged-helix DNA-binding proteins, which have been reported to play crucial roles in cell cycle regulation and differentiation, and address their requirement in the sexual reproduction of
F. graminearum
. Furthermore, we identified a highly conserved protein in
Fusarium
as a key factor in self-fertility, along with the discovery of its direct downstream genes. This provides crucial information for constructing the complex genetic regulatory network of sexual reproduction and significantly contribute to further research on sexual reproduction in
Fusarium
species.
Interspecies synergistic interactions mediated by cofactor exchange enhance stress tolerance by inducing biofilm formation
Authors: Wang Lvjing , Wang Xiaoyu , Wu Hao , Wang Haixia , Lu Zhenmei 
Published: August 2024

ABSTRACT

Metabolic exchange plays a crucial role in shaping microbial community interactions and functions, including the exchange of small molecules such as cofactors. Cofactors are fundamental to enzyme catalytic activities; however, the role of cofactors in microbial stress tolerance is unclear. Here, we constructed a synergistic consortium containing two strains that could efficiently mineralize di-(2-ethylhexyl) phthalate under hyperosmotic stress. Integration of transcriptomic analysis, metabolic profiling, and a genome-scale metabolic model (GEM) facilitated the discovery of the potential mechanism of microbial interactions. Multi-omics analysis revealed that the vitamin B
12
-dependent methionine-folate cycle could be a key pathway for enhancing the hyperosmotic stress tolerance of synergistic consortium. Further GEM simulations revealed interspecies exchange of S-adenosyl-L-methionine and riboflavin, cofactors needed for vitamin B
12
biosynthesis, which was confirmed by
in vitro
experiments. Overall, we proposed a new mechanism of bacterial hyperosmotic stress tolerance: bacteria might promote the production of vitamin B
12
to enhance biofilm formation, and the species collaborate with each other by exchanging cofactors to improve consortium hyperosmotic stress tolerance. These findings offer new insights into the role of cofactors in microbial interactions and stress tolerance and are potentially exploitable for environmental remediation.

IMPORTANCE
Metabolic interactions (also known as cross-feeding) are thought to be ubiquitous in microbial communities. Cross-feeding is the basis for many positive interactions (e.g., mutualism) and is a primary driver of microbial community assembly. In this study, a combination of multi-omics analysis and metabolic modeling simulation was used to reveal the metabolic interactions of a synthetic consortium under hyperosmotic stress. Interspecies cofactor exchange was found to promote biofilm formation under hyperosmotic stress. This provides a new perspective for understanding the role of metabolic interactions in microbial communities to enhance environmental adaptation, which is significant for improving the efficiency of production activities and environmental bioremediation.
Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenic
Escherichia coli
1711-4 strain of serotype O51:H40
Authors: Romão Fabiano T. , Santos Ana C. M. , Puño-Sarmiento Juan J. , Sperandio Vanessa , Hernandes Rodrigo T. , Gomes Tânia A. T. 
Published: August 2024

ABSTRACT

Atypical enteropathogenic
Escherichia coli
(aEPEC) is a significant cause of diarrhea in low- and middle-income countries. Certain aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. It can also translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of a type III secretion system for the efficiency of the invasion process was demonstrated, the expression of the locus of enterocyte effacement (LEE) genes during the invasion and intracellular persistence remains unclear. To address this question, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytes
in vitro
. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression of
eae
and
escJ
increased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 h post-infection during the persistence period. The number of actin accumulation foci formed on HeLa cells also increased during the 6-h analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that the LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.

IMPORTANCE

Atypical enteropathogenic
Escherichia coli
(aEPEC) is a major cause of diarrhea, especially in low- and middle-income countries, like Brazil. However, due to the genome heterogeneity of each clonal group, it is difficult to comprehend the pathogenicity of this strain fully. Among aEPEC strains, 1711-4 can invade eukaryotic cells
in vitro
, cross the gut barrier, and reach extraintestinal sites in animal models. By studying how different known aEPEC virulence factors are expressed during the invasion process, we can gain insight into the commonalities of this phenotype among other aEPEC strains. This will help in developing preventive measures to control infections caused by invasive strains. No known virulence-encoding genes linked to the invasion process were found. Nevertheless, additional studies are still necessary to evaluate the role of other factors in this phenotype.