bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enterohemorrhagic
Escherichia coli
effector EspF triggers oxidative DNA lesions in intestinal epithelial cells
Authors: Fang Yuting , Fu Muqing , Li Xinyue , Zhang Bao , Wan Chengsong 
Published: February 2024

ABSTRACT

Attaching/effacing (A/E) pathogens induce DNA damage and colorectal cancer by injecting effector proteins into host cells via the type III secretion system (T3SS). EspF is one of the T3SS-dependent effector proteins exclusive to A/E pathogens, which include enterohemorrhagic
Escherichia coli
. The role of EspF in the induction of double-strand breaks (DSBs) and the phosphorylation of the repair protein SMC1 has been demonstrated previously. However, the process of damage accumulation and DSB formation has remained enigmatic, and the damage response is not well understood. Here, we first showed a compensatory increase in the mismatch repair proteins MutS homolog 2 (MSH2) and MSH6, as well as poly(ADP-ribose) polymerase 1, followed by a dramatic decrease, threatening cell survival in the presence of EspF. Flow cytometry revealed that EspF arrested the cell cycle at the G2/M phase to facilitate DNA repair. Subsequently, 8-oxoguanine (8-oxoG) lesions, a marker of oxidative damage, were assayed by ELISA and immunofluorescence, which revealed the accumulation of 8-oxoG from the cytosol to the nucleus. Furthermore, the status of single-stranded DNA (ssDNA) and DSBs was confirmed. We observed that EspF accelerated the course of DNA lesions, including 8-oxoG and unrepaired ssDNA, which were converted into DSBs; this was accompanied by the phosphorylation of replication protein A 32 in repair-defective cells. Collectively, these findings reveal that EspF triggers various types of oxidative DNA lesions with impairment of the DNA damage response and may result in genomic instability and cell death, offering novel insight into the tumorigenic potential of EspF.

IMPORTANCE
Oxidative DNA lesions play causative roles in colitis-associated colon cancer. Accumulating evidence shows strong links between attaching/effacing (A/E) pathogens and colorectal cancer (CRC). EspF is one of many effector proteins exclusive to A/E pathogens with defined roles in the induction of oxidative stress, double-strand breaks (DSBs), and repair dysregulation. Here, we found that EspF promotes reactive oxygen species generation and 8-oxoguanine (8-oxoG) lesions when the repair system is activated, contributing to sustained cell survival. However, infected cells exposed to EspF presented 8-oxoG, which results in DSBs and ssDNA accumulation when the cell cycle is arrested at the G2/M phase and the repair system is defective or saturated by DNA lesions. In addition, we found that EspF could intensify the accumulation of nuclear DNA lesions through oxidative and replication stress. Overall, our work highlights the involvement of EspF in DNA lesions and DNA damage response, providing a novel avenue by which A/E pathogens may contribute to CRC.
Revised whole genome and DNA methylome of
Mycobacterium marinum
type strain ATCC 927
T
Authors: Savijoki Kirsi , Deptula Paulina , Roberts Richard J. , Hammarén Milka , Yli-Kauhaluoma Jari , Varmanen Pekka , Parikka Mataleena 
Published: February 2024

ABSTRACT

Mycobacterium marinum
, a slow-growing Actinobacterium, typically induces tuberculosis-like disease in fish. Here, we report a new reference sequence for
M. marinum
ATCC 927
T
, along with its DNA methylome. This aims to maximize the research potential of this type strain and facilitates investigations into the pathomechanisms of human tuberculosis.
The complete genome of
Vibrio
sp. 16 unveils two circular chromosomes and a distinctive 46-kb plasmid
Authors: Wu Xiaofen , Segall Anca M. , Giglione Carmela , Meinnel Thierry 
Published: February 2024

ABSTRACT

The entire 4.6-Mb genome of
Vibrio
sp. 16, encoding 4,270 genes, best matches with
Vibrio rotiferianus
. A 46-kb plasmid (pVDT1), alongside two circular chromosomes, showcases
parAB
/
repB
partition genes and three toxin/antitoxin systems potentially linked to phage infection.
Liver sinusoidal cells eliminate blood-borne phage K1F
Authors: Sánchez Romano Javier , Simón-Santamaría Jaione , McCourt Peter , Smedsrød Bård , Mortensen Kim Erlend , Sagona Antonia P. , Sørensen Karen Kristine , Larsen Anett Kristin 
Published: February 2024

ABSTRACT

Phage treatment has regained attention due to an increase in multiresistant bacteria. For phage therapy to be successful, phages must reach their target bacteria in sufficiently high numbers. Blood-borne phages are believed to be captured by macrophages in the liver and spleen. Since liver sinusoids also consist of specialized scavenger liver sinusoidal endothelial cells (LSECs) and Kupffer cells (KCs), this study investigated the contribution of both cell types in the elimination of
Escherichia coli
phage K1Fg10b::gfp (K1F
gfp
) in mice. Circulatory half-life, organ, and hepatocellular distribution of K1F
gfp
were determined following intravenous administration. Internalization of K1F
gfp
and effects of phage opsonization on uptake were explored using primary mouse and human LSEC and KC cultures. When inoculated with 10
7
virions, >95% of the total K1F
gfp
load was eliminated from the blood within 20 min, and 94% of the total retrieved K1F
gfp
was localized to the liver. Higher doses resulted in slower elimination, possibly reflecting temporary saturation of liver scavenging capacity. Phage DNA was detected in both cell types, with a KC:LSEC ratio of 12:1 per population following cell isolation. Opsonization with plasma proteins increased time-dependent cellular uptake in both LSECs and KCs
in vitro
. Internalized phages were rapidly transported along the endocytic pathway to lysosomal compartments. Reduced viability of intracellular K1F
gfp
corroborated inactivation following endocytosis. This study is the first to identify phage distribution in the liver at the hepatocellular level, confirming clearance of K1F
gfp
performed mostly by KCs with a significant uptake also in LSECs.

IMPORTANCE
Faced with the increasing amounts of bacteria with multidrug antimicrobial resistance, phage therapy has regained attention as a possible treatment option. The phage field has recently experienced an emergence in commercial interest as research has identified new and more efficient ways of identifying and matching phages against resistant superbugs. Currently, phages are unapproved drugs in most parts of the world. For phages to reach broad clinical use, they must be shown to be clinically safe and useful. The results presented herein contribute to increased knowledge about the pharmacokinetics of the T7-like phage K1F in the mammalian system. The cell types of the liver that are responsible for rapid phage blood clearance are identified. Our results highlight the need for more research about appropriate dose regimens when phage therapy is delivered intravenously and advise essential knowledge about cell systems that should be investigated further for detailed phage pharmacodynamics.
Genomic epidemiology of the primary methicillin-resistant
Staphylococcus aureus
clones causing invasive infections in Paraguayan children
Authors: Guillén Rosa , Salinas Claudia , Mendoza-Álvarez Alejandro , Rubio Rodríguez Luis A. , Díaz-de Usera Ana , Lorenzo-Salazar José M. , González-Montelongo Rafaela , Flores Carlos , Rodríguez Fátima 
Published: February 2024

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) is one of the major human pathogens. It could carry numerous resistance genes and virulence factors in its genome, some of which are related to the severity of the infection. An observational, descriptive, cross-sectional study was designed to molecularly analyze MRSA isolates that cause invasive infections in Paraguayan children from 2009 to 2013. Ten representative MRSA isolates of the main clonal complex identified were analyzed with short-read paired-end sequencing and assessed for the virulome, resistome, and phylogenetic relationships. All the genetically linked MRSA isolates were recovered from diverse clinical sources, patients, and hospitals at broad gap periods. The pan-genomic analysis of these clones revealed three major and different clonal complexes (CC30, CC5, and CC8), each composed of clones closely related to each other. The CC30 genomes prove to be a successful clone, strongly installed and disseminated throughout our country, and closely related to other CC30 public genomes from the region and the world. The CC5 shows the highest genetic variability, and the CC8 carried the complete arginine catabolic mobile element (ACME), closely related to the USA300-NAE-ACME+, identified as the major cause of CA-MRSA infections in North America. Multiple virulence and resistance genes were identified for the first time in this study, highlighting the complex virulence profiles of MRSA circulating in the country. This study opens a wide range of new possibilities for future projects and trials to improve the existing knowledge on the epidemiology of MRSA circulating in Paraguay.

IMPORTANCE

The increasing prevalence of methicillin-resistant
Staphylococcus aureus
(MRSA) is a public health problem worldwide. The most frequent MRSA clones identified in Paraguay in previous studies (including community and hospital acquired) were the Pediatric (CC5-ST5-IV), the Cordobes-Chilean (CC5-ST5-I), the SouthWest Pacific (CC30-ST30-IV), and the Brazilian (CC8-ST239-III) clones. In this study, the pan-genomic analysis of the most representative MRSA clones circulating in invasive infection in Paraguayan children over the years 2009–2013, such as the CC30-ST30-IV, CC5-ST5-IV, and CC8-ST8-IV, was carried out to evaluate their genetic diversity, their repertoire of virulence factors, and antimicrobial resistance determinants. This revealed multiple virulence and resistance genes, highlighting the complex virulence profiles of MRSA circulating in Paraguay. Our work is the first genomic study of MRSA in Paraguay and will contribute to the development of genomic surveillance in the region and our understanding of the global epidemiology of this pathogen.
Characterization of a neutralizing antibody that recognizes a loop region adjacent to the receptor-binding interface of the SARS-CoV-2 spike receptor-binding domain
Authors: Anzai Itsuki , Fujita Junso , Ono Chikako , Kosaka Yoichiro , Miyamoto Yuki , Shichinohe Shintaro , Takada Kosuke , Torii Shiho , Taguwa Shuhei , Suzuki Koichiro , Makino Fumiaki , Kajita Tadahiro , Inoue Tsuyoshi , Namba Keiichi , Watanabe Tokiko , Matsuura Yoshiharu 
Published: February 2024

ABSTRACT

Although the global crisis caused by the coronavirus disease 2019 (COVID-19) pandemic is over, the global epidemic of the disease continues. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of COVID-19, initiates infection via the binding of the receptor-binding domain (RBD) of its spike protein to the human angiotensin-converting enzyme II (ACE2) receptor, and this interaction has been the primary target for the development of COVID-19 therapeutics. Here, we identified neutralizing antibodies against SARS-CoV-2 by screening mouse monoclonal antibodies and characterized an antibody, CSW1-1805, that targets a narrow region at the RBD ridge of the spike protein. CSW1-1805 neutralized several variants
in vitro
and completely protected mice from SARS-CoV-2 infection. Cryo-EM and biochemical analyses revealed that this antibody recognizes the loop region adjacent to the ACE2-binding interface with the RBD in both a receptor-inaccessible “down” state and a receptor-accessible “up” state and could stabilize the RBD conformation in the up-state. CSW1-1805 also showed different binding orientations and complementarity determining region properties compared to other RBD ridge-targeting antibodies with similar binding epitopes. It is important to continuously characterize neutralizing antibodies to address new variants that continue to emerge. Our characterization of this antibody that recognizes the RBD ridge of the spike protein will aid in the development of future neutralizing antibodies.

IMPORTANCE
SARS-CoV-2 cell entry is initiated by the interaction of the viral spike protein with the host cell receptor. Therefore, mechanistic findings regarding receptor recognition by the spike protein help uncover the molecular mechanism of SARS-CoV-2 infection and guide neutralizing antibody development. Here, we characterized a SARS-CoV-2 neutralizing antibody that recognizes an epitope, a loop region adjacent to the receptor-binding interface, that may be involved in the conformational transition of the receptor-binding domain (RBD) of the spike protein from a receptor-inaccessible “down” state into a receptor-accessible “up” state, and also stabilizes the RBD in the up-state. Our mechanistic findings provide new insights into SARS-CoV-2 receptor recognition and guidance for neutralizing antibody development.
Transdermal administration of farnesol-ethosomes enhances the treatment of cutaneous candidiasis induced by
Candida albicans
in mice
Authors: Shen Ting , Tian Baocheng , Liu Wei , Yang Xuesong , Sheng Qi , Li Mengxin , Wang Haiyan , Wang Xiuwen , Zhou Huihui , Han Yanchun , Ding Chen , Sai Sixiang 
Published: February 2024

ABSTRACT

Cutaneous candidiasis, caused by
Candida albicans
, is a severe and frustrating condition, and finding effective treatments can be challenging. Therefore, the development of farnesol-loaded nanoparticles is an exciting breakthrough. Ethosomes are a novel transdermal drug delivery carrier that incorporates a certain concentration (10–45%) of alcohols into lipid vesicles, resulting in improved permeability and encapsulation rates compared to conventional liposomes. Farnesol is a quorum-sensing molecule involved in morphogenesis regulation in
C. albicans
, and these ethosomes offer a promising new approach to treating this common fungal infection. This study develops the formulation of farnesol-loaded ethosomes (farnesol-ethosomes) and assesses applications in treating cutaneous candidiasis induced by
C. albicans in vitro
and
in vivo
. Farnesol-ethosomes were successfully developed by ethanol injection method. Therapeutic properties of farnesol-ethosomes, such as particle size, zeta potential, and morphology, were well characterized. According to the results, farnesol-ethosomes demonstrated an increased inhibition effect on cells’ growth and biofilm formation in
C. albicans
. In Animal infection models, treating farnesol-ethosomes by transdermal administration effectively relieved symptoms caused by cutaneous candidiasis and reduced fungal burdens in quantity. We also observed that ethosomes significantly enhanced drug delivery efficacy
in vitro
and
in vivo
. These results indicate that farnesol-ethosomes can provide future promising roles in curing cutaneous candidiasis.

IMPORTANCE

Cutaneous candidiasis attributed to
Candida
infection is a prevalent condition that impacts individuals of all age groups. As a type of microbial community, biofilms confer benefits to host infections and mitigate the clinical effects of antifungal treatments. In
C. albicans
, the yeast-to-hypha transition and biofilm formation are effectively suppressed by farnesol through its modulation of multiple signaling pathway. However, the characteristics of farnesol such as hydrophobicity, volatility, degradability, and instability in various conditions can impose limitations on its effectiveness. Nanotechnology holds the potential to enhance the efficiency and utilization of this molecule. Treatment of farnesol-ethosomes by transdermal administration demonstrated a very remarkable therapeutic effect against
C. albicans
in infection model of cutaneous candidiasis in mice. Many patients suffering fungal skin infection will benefit from this study.
Hyper-enrichment of gold via quartz fracturing and growth of polymetallic melt droplets
Authors: Jian Wei , Mao Jingwen , Lehmann Bernd , Cook Nigel J. , Li Jiankang , Song Shiwei , Zhu Lei 
Published: February 2024

Abstract
Gold precipitation in hydrothermal systems is traditionally attributed to supersaturation of gold due to decreasing gold complex stability triggered by changes in physicochemical conditions of the ore fluid. However, ultrahigh-grade gold veins in orogenic (shear zone related) gold deposits can contain kilograms per tonne of gold or more, in marked contrast to the typically very low gold concentrations (tens of parts per billion) in fluid. The gold mineral assemblage is commonly restricted to native gold and/or Au-(Ag)-tellurides and occurs in micro-fractures of sheared quartz veins. Textural and compositional characterization of such assemblages, coupled with hydrothermal diamond anvil cell experiments and heating-freezing experiments, provides evidence for an alternative ultrahigh-grade gold enrichment mechanism via growth of polymetallic melt droplets induced by quartz fracturing. We propose that polymetallic melt droplets of Au-Ag-Te-Bi–rich composition form through adsorption-reduction of metal complexes on fractured quartz surfaces, where surface silanol groups and hydrogen serve as reductants. The melt droplets subsequently grow by catalyzing reduction of metal complexes and absorbing metals from fluids percolating in the fractured quartz network. The mobile and reactive polymetallic melt droplets can repeatedly react with the fluid on protracted quartz fracturing and efficiently continue to scavenge gold from multiple pulses of gold-undersaturated ore fluids.
Association between the frailty index and readmission risk in hospitalised elderly Chinese patients: a retrospective cohort study
Authors: Wang Lina , Zhang Xiaolin , Liu Xinmin 
Published: February 2024

ObjectivesFrailty is a common and important concern of the ageing population. This study examined the association between the frailty index and negative outcomes of hospitalised elderly Chinese patients.DesignRetrospective cohort study.SettingGeriatrics Department of Peking University First Hospital.Participants470 hospitalised elderly patients.Main outcomes and measuresFrailty was measured using a 30-item deficit-accumulation frailty index. The outcomes were the hospitalisation duration and readmission.ResultsThe frailty index was available for 470 patients: 72 (15.32%) were categorised as robust, 272 (57.87%) as prefrail and 126 (26.81%) as frail. The frail group had a longer hospital stay than the robust and prefrail groups. After adjustment for age, sex and cause of hospitalisation at baseline, frailty remained a strong independent risk factor for all-cause readmission and cardiocerebrovascular disease readmission (HR 2.41, 95% CI 1.49 to 3.91, p<0.001; HR 4.92, 95% CI 1.47 to 6.31, p<0.001, respectively).ConclusionsThe frailty index predicted a longer length of stay and higher all-cause and cardiocerebrovascular disease readmission risk in hospitalised elderly patients.
Effectiveness of a Regenerative Epithelial Suspension (RES), on the pigmentation of split-thickness skin graft donor sites in children: the dRESsing pilot randomised controlled trial protocol
Authors: Bairagi Anjana , Tyack Zephanie , Kimble Roy M , McPhail Steven M , McBride Craig Antony , Patel Bhaveshkumar , Vagenas Dimitrios , Dettrick Zoe , Griffin Bronwyn 
Published: February 2024

BackgroundPaediatric donor site wounds are often complicated by dyspigmentation following a split-thickness skin graft. These easily identifiable scars can potentially never return to normal pigmentation. A Regenerative Epidermal Suspension (RES) has been shown to improve pigmentation in patients with vitiligo, and in adult patients following a burn injury. Very little is known regarding the efficacy of RES for the management of donor site scars in children.Methods and analysisA pilot randomised controlled trial of 40 children allocated to two groups (RES or no RES) standard dressing applied to donor site wounds will be conducted. All children aged 16 years or younger requiring a split thickness skin graft will be screened for eligibility. The primary outcome is donor site scar pigmentation 12 months after skin grafting. Secondary outcomes include re-epithelialisation time, pain, itch, dressing application ease, treatment satisfaction, scar thickness and health-related quality of life. Commencing 7 days after the skin graft, the dressing will be changed every 3–5 days until the donor site is ≥ 95% re-epithelialised. Data will be collected at each dressing change and 3, 6 and 12 months post skin graft.Ethics and disseminationEthics approval was confirmed on 11 February 2019 by the study site Human Research Ethics Committee (HREC) (HREC/18/QCHQ/45807). Study findings will be published in peer-reviewed journals and presented at national and international conferences. This study was prospectively registered on the Australian New Zealand Clinical Trials Registry (available athttps://anzctr.org.au/ACTRN12620000227998.aspx).Trial registration numberAustralian New Zealand Clinical Trials Registry [Available athttps://anzctr.org.au/ACTRN12620000227998.aspx]
Lived experiences of people living with HIV and hypertension or diabetes access to care in Ethiopia: a phenomenological study
Authors: Badacho Abebe Sorsa , Mahomed Ozayr Haroon 
Published: February 2024

BackgroundPeople living with HIV (PLWH) are more likely to develop hypertension and diabetes than people without HIV. Previous studies have shown that HIV stigma, discrimination and exclusion make it difficult for PLWH to access care for hypertension and diabetes.ObjectivesThis study aimed to explore the lived experiences of PLWH with comorbid hypertension or diabetes to access hypertension and diabetes care in southern Ethiopia.DesignWe conducted a qualitative study using a semistructured interview guide for an in-depth, in-person interview.SettingsFrom 5 August to 25 September 2022, PLWH with comorbid hypertension or diabetes were purposefully selected from five primary healthcare (PHC) facilities in the Wolaita zone of southern Ethiopia.ParticipantsA total of 14 PLWH with comorbid hypertension or diabetes who were receiving antiretroviral therapy from PHC were interviewed. Among them, 10 were women, and 4 were men.MethodsIn-person, in-depth interviews were conducted. Qualitative data analysis software (NVivo V.12) was used to assist with the data organisation, and Colaizzi’s (1978) inductive thematic analyses were conducted to explore key concepts.ResultThis study yielded two main themes: Theme 1: barriers to accessing care as individual barriers to access (low awareness of non-communicable diseases, misperceptions, lack of health insurance and cost of treatment); healthcare system barriers (shortage of supplies, drugs and equipment; long wait times; lack of integrated services; absence of routine screening and lack of respect from providers); community barriers (lack of support from families, friends and the community) and stigma and discrimination access to hypertension and diabetes. Theme 2: accessibility facilitators (support from family, friends and organisations; health insurance coverage).ConclusionPLWH recommended that access to services can be improved by service integration, awareness-raising activities, no user fee charges for hypertension and diabetes care and routine screening.