bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize
Authors: Luo Bowen , Zhang Ziqi , Li Binyang , Zhang Haiying , Ma Junchi , Li Jing , Han Zheng , Zhang Chong , Zhang Shuhao , Yu Ting , Zhang Guidi , Ma Peng , Lan Yuzhou , Zhang Xiao , Liu Dan , Wu Ling , Gao Duojiang , Gao Shiqiang , Su Shunzong , Zhang Xuecai , Gao Shibin 
Published: September 2023

SUMMARYChromatin in eukaryotes folds into a complex three‐dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low‐Pi treatment led to greater chromatin volume. Furthermore, low‐Pi stress increased the insulation score and the number of TAD‐like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD‐like boundaries, whereas RdDM peak levels at conserved TAD‐like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome‐wide RdDM sites near TAD‐like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low‐Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low‐Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP‐seq results revealed that ZmDDM1A could bind to Pi‐ and root development‐related genes. Strong associations were found between interacting genes in significantly different chromatin‐interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low‐Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.
Positron emission tomography assessment of metacarpal/metatarsal condylar fractures post surgical repair: Prospective study in 14 racehorses
Authors: Bergstrom Thomas C. , Spriet Mathieu , O'Brion Julie , Carpenter Ryan 
Published: September 2023

AbstractObjectivesTo assess 18F‐sodium fluoride (18F‐NaF) positron emission tomography (PET) findings associated with metacarpal/metatarsal condylar fractures at the time of fracture repair and through healing.Study designProspective descriptive study.AnimalsFourteen Thoroughbred racehorses.Methods18F‐NaF PET was performed within 4 days of surgical metacarpal/metatarsal condylar fracture repair, on both the injured and contralateral limb. Follow‐up PET scans were offered at 3‐ and 5‐months post fracture repair. Areas of abnormal uptake were assessed using a previously validated grading system.ResultsEight fractures were located in the parasagittal groove (PSG) (six lateral and two medial) and six fractures were located abaxial to the PSG (non‐PSG) through the palmar/plantar condyle (all lateral). All horses in the latter group had uptake in the lateral palmar condyle of the contralateral limb suggestive of stress remodeling. Three horses with PSG fractures had uptake in a similar location in the contralateral limb. Horses with lateral condylar fracture only presented minimal or mild uptake in the medial condyle, which is considered atypical in the front limbs for horses in full training. Four horses developed periarticular uptake in the postoperative period suggestive of degenerative joint disease, three of these horses had persistent uptake at the fracture site. These four horses did not return to racing successfully.ConclusionThe findings of this study provide evidence of pre‐existing lesions and specific uptake patterns in racehorses suffering from metacarpal/metatarsal condylar fractures.Clinical significancePET has a possible role in the prevention, diagnosis, and postoperative monitoring of metacarpal/metatarsal condylar fractures in racehorses.
Enzymatic biodegradation and detoxification of azo and anthraquinone dyes by indigenously isolated bacterial monocultures and their synergistic behaviour in developed consortia
Authors: Hussain Khalid , Aman Afsheen , Ullah Asad , Khan Muhammad Qamar , Ansari Asma 
Published: September 2023

AbstractWastewater generated by textile industry needs to be treated to reduce its toxicity before final disposal and/or for recycling purposes. In the current study, several bacterial strains were screened for dye decolorization potential. UV–visible spectroscopy was used to determine maximum absorption wavelength of disperse dyes. HPLC and MTS assay were used to confirm the degradation and detoxification of disperse dyes, respectively. Results revealed that indigenously isolated Bacillus licheniformis, Glutamicibacter uratoxydans and Pseudomonas aeruginosa showed strong decolorization of red, blue and violet, respectively in 6–9 h. MTS assay revealed 100% viability of NIH/3T3 cell lines in presence of treated dyes. Enzyme screening assay confirmed the production of intracellular and membrane bound oxidoreductases in presence of specific dye as substrate. To resolve this issue, bacterial consortia were prepared, and better decolorization of all dyes was achieved in synergistic behaviour of Consortia 1 and 4 with 85% and 88% decolorization potential, respectively.
Recreational Runners Gain Physiological and Biomechanical Benefits From Super Shoes at Marathon Paces
Authors: Paradisis Giorgos P. , Zacharogiannis Elias , Bissas Athanassios , Hanley Brian 
Published: September 2023

Purpose: Advanced footwear technology is prevalent in distance running, with research focusing on these “super shoes” in competitive athletes, with less understanding of their value for slower runners. The aim of this study was to compare physiological and biomechanical variables between a model of super shoes (Saucony Endorphin Speed 2) and regular running shoes (Saucony Cohesion 13) in recreational athletes. Methods: We measured peak oxygen uptake (VO2peak) in 10 runners before testing each subject 4 times in a randomly ordered crossover design (ie, Endorphin shoe or Cohesion shoe, running at 65% or 80% of velocity at VO2peak [vVO2peak]). We recorded video data using a high-speed camera (300 Hz) to calculate vertical and leg stiffnesses. Results: 65% vVO2peak was equivalent to a speed of 9.4 km·h−1 (0.4), whereas 80% vVO2peak was equivalent to 11.5 km·h−1 (0.5). Two-way mixed-design analysis of variance showed that oxygen consumption in the Endorphin shoe was 3.9% lower than in the Cohesion shoe at 65% vVO2peak, with an interaction between shoes and speed (P = .020) meaning an increased difference of 5.0% at 80% vVO2peak. There were small increases in vertical and leg stiffnesses in the Endorphin shoes (P < .001); the Endorphin shoe condition also showed trivial to moderate differences in step length, step rate, contact time, and flight time (P < .001). Conclusions: There was a physiological benefit to running in the super shoes even at the slower speed. There were also spatiotemporal and global stiffness improvements indicating that recreational runners benefit from wearing super shoes.
Identification of a novel transcriptional regulator, CorR, for copper stress response in
Edwardsiella piscicida
Authors: Xia Feng , Xu Pengfei , Zhang Boya , Zhang Yibei , Liu Xiaohong , Ma Yue , Zhang Yuanxing , Wang Qiyao , Shao Shuai 
Published: September 2023

ABSTRACT

Copper plays a vital role in the host–pathogen interface, potentially making components of the bacterial copper response suitable targets for the development of innovative antimicrobial strategies. The anti-copper arsenal of intracellular pathogens has expanded as an adaptation to survive copper toxicity in order to escape intracellular killing by the host immune system. Herein, we employed transposon insertion sequencing to investigate the genetic mechanisms underlying the survival of
Edwardsiella piscicida
under copper stress. A novel transcriptional regulator, ETAE_2324 (named CorR), was identified to participate in the response to copper ions by controlling the expression of
copA,
the core component of cytoplasmic copper homeostasis. Furthermore, CorR regulated the expression of virulent determinant
eseB
, influencing the
in vivo
colonization of
E. piscicida
. Collectively, our results contribute to the comprehension of the underlying mechanism of the adaption of intracellular pathogens to copper stress during bacterial infections.

IMPORTANCE

Copper ions play a pivotal role in the interaction between bacteria and the host during infection. The host’s innate immune system employs copper ions for their bactericidal properties, thereby making bacterial copper tolerance a crucial determinant of virulence.
Edwardsiella piscicida
, a significant marine pathogen, has caused substantial losses in the global aquaculture industry. To comprehensively investigate how
E. piscicida
responds to copper stress, we utilized transposon insertion sequencing to explore genes associated with copper tolerance in culture media containing different concentrations of copper ions. A novel transcriptional regulator, CorR, was identified to respond to copper ions and regulates the expression of crucial components of copper homeostasis CopA, along with the essential virulence factor EseB. These findings offer valuable insights into the underlying mechanisms that govern bacterial copper tolerance and present novel perspectives for the development of vaccines and therapeutic strategies targeting
E. piscicida
.
PKR-mediated stress response enhances dengue and Zika virus replication
Authors: Ricciardi-Jorge Taissa , da Rocha Edroaldo Lummertz , Gonzalez-Kozlova Edgar , Rodrigues-Luiz Gabriela Flavia , Ferguson Brian J. , Sweeney Trevor , Irigoyen Nerea , Mansur Daniel Santos 
Published: September 2023

ABSTRACT
The mechanisms by which flaviviruses use non-canonical translation to support their replication in host cells are largely unknown. Here, we investigated how the integrated stress response (ISR), which promotes translational arrest by eIF2ɑ phosphorylation (p-eIF2ɑ), regulates flavivirus replication. During dengue virus (DENV) and Zika virus (ZIKV) infection, eIF2ɑ phosphorylation peaked at 24 hours post-infection and was dependent on protein kinase RNA-activated (PKR) but not type I interferon. The ISR is activated downstream of p-eIF2α during infection with either virus, but translation arrest only occurred following DENV4 infection. Despite this difference, both DENV4 and ZIKV replications were impaired in cells lacking PKR, independent of type I interferon/NF-kB signaling or cell viability. By using a ZIKV 5′-untranslated region (UTR) reporter system as a model, we found that this region of the genome is sufficient to promote an enhancement of viral mRNA translation in the presence of an active ISR. Together, we provide evidence that flaviviruses escape ISR translational arrest and co-opt this response to increase viral replication.

IMPORTANCE
One of the fundamental features that make viruses intracellular parasites is the necessity to use cellular translational machinery. Hence, this is a crucial checkpoint for controlling infections. Here, we show that dengue and Zika viruses, responsible for nearly 400 million infections every year worldwide, explore such control for optimal replication. Using immunocompetent cells, we demonstrate that arrest of protein translations happens after sensing of dsRNA and that the information required to avoid this blocking is contained in viral 5′-UTR. Our work, therefore, suggests that the non-canonical translation described for these viruses is engaged when the intracellular stress response is activated.
GlMPC
activated by GCN4 regulates secondary metabolism under nitrogen limitation conditions in
Ganoderma lucidum
Authors: Wang Zi , Chen Juhong , Ding Juan , Han Jing , Shi Liang 
Published: September 2023

ABSTRACT

Fungi actively alter their metabolic and synthetic pathways to cope with changing environmental conditions. The mitochondrial pyruvate carrier (MPC) plays a vital role in transporting pyruvate into mitochondria and regulating carbon metabolic homeostasis. However, the mechanism by which MPC regulates carbon metabolism in response to environmental stress in fungi remains unclear. In this study, yeast one-hybrid library screening assays were employed to screen for transcription factors in
Ganoderma lucidum
that may interact with GlMPC. General control non-derepressible 4 (GCN4), a key transcription factor responding to nitrogen metabolism, was found to interact with the
GlMPC
promoter region. This interaction was further confirmed by electrophoretic mobility shift assays and chromatin immunoprecipitation quantitative PCR assays, demonstrating that GCN4 is capable of binding to the
GlMPC
promoter region
in vitro
and
in vivo
. Further results indicated that GCN4 could activate
GlMPC
expression and participate in regulating the tricarboxylic acid (TCA) cycle and ganoderic acid (GA) biosynthesis under low nitrogen conditions in
G. lucidum
. These findings revealed a specific regulatory mechanism by which GCN4-activated
GlMPC
regulates the TCA cycle and secondary metabolism under nitrogen limitation conditions in
G. lucidum
, providing crucial insights into the regulation of carbon and nitrogen metabolism in fungi.

IMPORTANCE

Mitochondrial pyruvate carrier (MPC) is a pyruvate transporter that plays a crucial role in regulating the carbon metabolic flow and is considered an essential mechanism for microorganisms to adapt to environmental changes. However, it remains unclear how MPC responds to environmental stress in organisms. General control non-derepressible 4 (GCN4), a key regulator of nitrogen metabolism, plays a pivotal role in the growth and development of fungi. In this study, we report that GCN4 can directly bind to the promoter region and activate the expression of GlMPC, thereby regulating the tricarboxylic acid cycle and secondary metabolism under nitrogen limitation conditions in
Ganoderma lucidum
. These findings provide significant insights into the regulation of carbon and nitrogen metabolism in fungi, highlighting the critical role of GCN4 in coordinating metabolic adaptation to environmental stresses.
F-actin and myosin F control apicoplast elongation dynamics which drive apicoplast-centrosome association in
Toxoplasma gondii
Authors: Devarakonda Parvathi Madhavi , Sarmiento Valeria , Heaslip Aoife T. 
Published: September 2023

ABSTRACT

Toxoplasma gondii
contains an essential plastid organelle called the apicoplast that is necessary for fatty acid, isoprenoid, and heme synthesis. Perturbations affecting apicoplast function or inheritance lead to parasite death. The apicoplast is a single copy organelle and, therefore, must be divided so that each daughter parasite inherits an apicoplast during cell division. In this study, we identify new roles for F-actin and an unconventional myosin motor, TgMyoF, in this process. First, loss of TgMyoF and actin lead to an accumulation of apicoplast vesicles in the cytosol indicating a role for this actomyosin system in apicoplast protein trafficking or morphological integrity of the organelle. Second, live cell imaging reveals that during division the apicoplast is highly dynamic, exhibiting branched, U-shaped and linear morphologies that are dependent on TgMyoF and actin. In parasites where movement was inhibited by the depletion of TgMyoF, the apicoplast fails to associate with the parasite centrosomes. Thus, this study provides crucial new insight into mechanisms controlling apicoplast-centrosome association, a vital step in the apicoplast division cycle, which ensures that each daughter inherits a single apicoplast.

IMPORTANCE

Toxoplasma gondii
and most other parasites in the phylum Apicomplexa contain an apicoplast, a non-photosynthetic plastid organelle required for fatty acid, isoprenoid, iron-sulfur cluster, and heme synthesis. Perturbation of apicoplast function results in parasite death. Thus, parasite survival critically depends on two cellular processes: apicoplast division to ensure every daughter parasite inherits a single apicoplast, and trafficking of nuclear encoded proteins to the apicoplast. Despite the importance of these processes, there are significant knowledge gaps in regards to the molecular mechanisms which control these processes; this is particularly true for trafficking of nuclear-encoded apicoplast proteins. This study provides crucial new insight into the timing of apicoplast protein synthesis and trafficking to the apicoplast. In addition, this study demonstrates how apicoplast-centrosome association, a key step in the apicoplast division cycle, is controlled by the actomyosin cytoskeleton.
Complete genome sequence of an avian pathogenic
Escherichia coli
strain isolated from poultry
Authors: Jia Xinglin , Phillips Gregory J. , Lyte Joshua M. 
Published: September 2023

ABSTRACT

Avian pathogenic
Escherichia coli
found in the avian intestinal tract can cause systemic disease in birds and act as a foodborne zoonotic pathogen associated with human disease. Here, we report the complete genome sequence of
E. coli
strain H1998 isolated from a chicken with colisepticemia.
Indications for a genetic basis for big bacteria and description of the giant cable bacterium
Candidatus
Electrothrix gigas sp. nov.
Authors: Geelhoed Jeanine S. , Thorup Casper A. , Bjerg Jesper J. , Schreiber Lars , Nielsen Lars Peter , Schramm Andreas , Meysman Filip J. R. , Marshall Ian P. G. 
Published: September 2023

ABSTRACT

Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of
Candidatus
Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence
in situ
hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name
Ca
. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of
Ca
. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of
Ca
. Electrothrix gigas and other giant bacteria.

IMPORTANCE

In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name
Candidatus
Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The
bbp
gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
Phenotype and genotype analysis for
Helicobacter pylori
antibiotic resistance in outpatients: a retrospective study
Authors: Xiong Mengqiu , Mohammed Aljaberi Hend Sadeq , Khalid Ansari Nida , Sun Yalan , Yin Sijie , Nasifu Lubanga , Sun Huiling , Xu Tao , Pan Yuqin , Nie Zhenlin , Liu Caidong , Zhang Zhenyu , Jiang Zongdan , Wang Shukui , He Bangshun 
Published: September 2023

ABSTRACT

To investigate the antibiotic resistance of
Helicobacter pylori
(
H. pylori
) in outpatients and to explore the consistency between genotype and phenotype of
H. pylori
antibiotic resistance. A retrospective study on outpatients screened with urea breath test for
H. pylori
infection in Nanjing First Hospital from April 2018 to January 2022. Patients who tested positive underwent a consented upper endoscopy, and the
H. pylori
infection was confirmed by rapid urease test (RUT) and
H. pylori
culture. For antibiotic resistance phenotype analysis, the
H. pylori
strains isolated from gastric biopsy were tested for antibiotic resistance phenotype by the Kirby-Bauer disk diffusion test. In addition, the antibiotic resistance genotype of isolated
H. pylori
was tested with a real-time polymerase chain reaction. A total of 4,399 patients underwent
H. pylori
infection screening, and 3,306
H. pylori
strains were isolated. The antibiotic resistance phenotype test revealed that the resistance rates of metronidazole (MTZ), clarithromycin (CLR), levofloxacin (LEV), amoxicillin (AMX), furazolidone (FR), and tetracycline (TE) were 74.58%, 48.61%, 34.83%, 0.76%, 0.27%, and 0.09%, respectively. Additionally, the antibiotic resistance genotype test revealed that rdxA gene mutation A610G (92.96%), A91G (92.95%), C92A (93.00%), and G392A (95.07%) were predominant in
H. pylori
with MTZ resistance; 23S rRNA gene mutation A2143G (86.47%) occurred in most
H. pylori
with CLR resistance; and gyrA gene mutation 87Ile/Lys/Tyr/Arg (97.32%) and 91Asn/Gly/Tyr (90.61%) were the most popular mutations in strains with LEV resistance. The phenotypic resistance and genotypic resistance to CLR (kappa value = 0.824) and LEV (kappa value = 0.895) were in good agreement. The history of eradication with MTZ, CLR, LEV, and AMX was correlated with
H. pylori
resistance. In short, this study demonstrated that drug resistance of
H. pylori
was mainly to MTZ, CLR, and LEV in local outpatients. Three drugs can be selected for increased MICs (Minimum Inhibitory Concentration) via single chromosomal mutations. In addition, the genotype could be used to predict the phenotypic
H. pylori
resistance to CLR and LEV.

IMPORTANCE

Helicobacter pylori
is a key bacterium that causes stomach diseases. There was a high prevalence of
H. pylori
in the Chinese population. We analyzed the resistance phenotype and genotype characteristics of
H. pylori
in 4,399 outpatients at the First Hospital of Nanjing, China. We found a higher resistance rate to metronidazole (MTZ) , clarithromycin (CLR), and levofloxacin (LEV), and the genotype could be used to predict the phenotypic
H. pylori
resistance to CLR and LEV. This study provides information on
H. pylori
infection and also provides guidance for clinical doctors' drug treatment.