bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability in HIV-1 transmitted/founder virus susceptibility to combined APOBEC3F and APOBEC3G host restriction
Authors: Gaba Amit , Yousefi Maria , Bhattacharjee Shreoshri , Chelico Linda 
Published: December 2024

ABSTRACT

Several APOBEC3 enzymes restrict HIV-1 by deaminating cytosine to form uracil in single-stranded proviral (−)DNA. However, HIV-1 Vif counteracts their activity by inducing their proteasomal degradation. This counteraction by Vif is incomplete, as evidenced by footprints of APOBEC3-mediated mutations within integrated proviral genomes of people living with HIV-1. The relative contributions of multiple APOBEC3s in HIV-1 restriction are not fully understood. Here, we investigated the activity of co-expressed APOBEC3F and APOBEC3G against HIV-1 Subtype B and Subtype C transmitted/founder viruses. We determined that APOBEC3F interacts with APOBEC3G through its N-terminal domain. We provide evidence that this results in protection of APOBEC3F from Vif-mediated degradation because the APOBEC3F N-terminal domain contains residues required for recognition by Vif. We also found that HIV-1 Subtype C Vifs, but not Subtype B Vifs, were less active against APOBEC3G when APOBEC3F and APOBEC3G were co-expressed. Consequently, when APOBEC3F and APOBEC3G were expressed together in a single cycle of HIV-1 replication, only HIV-1 Subtype C viruses showed a decrease in relative infectivity compared to when APOBEC3G was expressed alone. Inspection of Vif amino acid sequences revealed that differences in amino acids adjacent to conserved sequences influenced the Vif-mediated APOBEC3 degradation ability. Altogether, the data provide a possible mechanism for how combined expression of APOBEC3F and APOBEC3G could contribute to mutagenesis of HIV-1 proviral genomes despite the presence of Vif and provide evidence for variability in the Vif-mediated APOBEC3 degradation ability of transmitted/founder viruses.

IMPORTANCE
APOBEC3 enzymes suppress HIV-1 infection by inducing cytosine deamination in proviral DNA but are hindered by HIV-1 Vif, which leads to APOBEC3 proteasomal degradation. Moving away from traditional studies that used lab-adapted HIV-1 Subtype B viruses and singular APOBEC3 enzymes, we examined how transmitted/founder isolates of HIV-1 replicated in the presence of APOBEC3F and APOBEC3G. We determined that APOBEC3F interacts with APOBEC3G through its N-terminal domain and that APOBEC3F, like APOBEC3G, has Vif-mediated degradation determinants in the N-terminal domain. This enabled APOBEC3F to be partially resistant to Vif-mediated degradation. We also demonstrated that Subtype C is more susceptible than Subtype B HIV-1 to combined APOBEC3F/APOBEC3G restriction and identified Vif variations influencing APOBEC3 degradation ability. Importantly, Vif amino acid variation outside of previously identified conserved regions mediated APOBEC3 degradation and HIV-1 Vif subtype-specific differences. Altogether, we identified factors that affect susceptibility to APOBEC3F/APOBEC3G restriction.
An insect virus differentially alters gene expression among life stages of an insect vector and enhances bacterial phytopathogen transmission
Authors: Lin Chun-Yi , Robledo Buritica Jacobo , Sarkar Poulami , Jassar Ola , Rocha Sâmara Vieira , Batuman Ozgur , Stelinski Lukasz L. , Levy Amit 
Published: December 2024

ABSTRACT

Diaphorina citri
transmits
Candidatus
Liberibacter asiaticus (CLas) between citrus plants which causes the expression of huanglongbing disease in citrus.
D. citri
flavi-like virus (DcFLV) co-occurs intracellularly with CLas in
D. citri
populations in the field. However, the impact(s) of DcFLV presence on the insect vector and its interaction with the CLas phytopathogen remain unclear. We compared CLas acquisition and transmission efficiencies as well as transcriptomic expression between viruliferous and non-viruliferous psyllids at multiple life stages. Viruliferous nymphs acquired higher titers of CLas than non-viruliferous nymphs, whereas viruliferous adults acquired less CLas than those without virus. The presence of DcFLV increased the transmission of CLas by both nymphs and adults. Furthermore, RNA-seq and functional gene expression analyses revealed that endoplasmic reticulum stress-, autophagy-, and defense-related genes were significantly upregulated in viruliferous adult psyllids, whereas most of these genes were downregulated in viruliferous nymphs. Our work demonstrates that DcFLV differentially modulates various cellular and physiological functions in
D. citri
in a life stage-dependent manner and promotes the acquisition of CLas at the nymphal stage and transmission of the pathogen at the adult stage of the vector. Collectively, our results suggest that
D. citri
vectors with DcFLV exhibit greater pathogen transmission efficiency than those without virus.

IMPORTANCE

Huanglongbing (HLB), caused by fastidious bacteria from three
Candidatus
Liberibacter species, is the most damaging disease impacting the citrus industry worldwide. Spread by the Asian citrus psyllid (
Diaphorina citri
) in Asia and the Americas, HLB causes substantial financial losses, and has reduced citrus production in Florida by more than 90%. Although there are ongoing efforts to limit spread of the disease, effective HLB management remains elusive. Suppressing vector populations and decreasing CLas transmission are the two strategies that need to be urgently improved. Recently, a
D. citri
flavi-like virus (DcFLV) was characterized within its
D. citri
host, and it co-occurs intracellularly with CLas in psyllid populations. Here, we show that viruliferous nymphs exhibit higher CLas acquisition than non-viruliferous nymphs. Furthermore, both viruliferous adults and nymphs exhibit increased CLas transmission efficiency. We suggest the possibility of manipulating DcFLV in
D. citri
populations to reduce CLas transmission for HLB disease management.
Ethanolamine-induced assembly of microcompartments is required for
Fusobacterium nucleatum
virulence
Authors: Franklin Dana S. , Chen Yi-Wei , Chen Yimin , Wittchen Manuel , Agnew Angela , Luu Alexis , Whitelegge Julian P. , Zhou Z. Hong , Tauch Andreas , Das Asis , Ton-That Hung 
Published: December 2024

ABSTRACT

Many bacteria metabolize ethanolamine as a nutrient source through cytoplasmic organelles named bacterial microcompartments (BMCs). Here we investigated the molecular assembly, regulation, and function of BMCs in
Fusobacterium nucleatum—
a Gram-negative oral pathobiont that is associated with adverse pregnancy outcomes. The
F. nucleatum
genome harbors a conserved ethanolamine utilization (
eut
) locus with 21 genes that encode several putative BMC shell proteins and a two-component signal transduction system (TCS), in addition to the enzymes for ethanolamine transport and catabolism. We show that the expression of most of these genes and BMC formation are highly increased in wild-type fusobacteria when cultured in the presence of ethanolamine as a nutrient source. Deletion of the response regulator EutV eliminated this induction of
eut
mRNAs and BMCs, thus demonstrating that BMC formation is transcriptionally regulated by the TCS EutV-EutW in response to ethanolamine. Mass spectrometry of isolated BMCs unveiled the identity of the constituent proteins EutL, EutM
1
, EutM
2
, and EutN. Consistent with the role of these proteins in BMC assembly and metabolism, deletion of
eutN
,
eutL
/

eutM
1

/

eutM
2

, or
eutL
/

eutM
1

/

eutM
2

/
eutN
not only affected BMC formation but also ethanolamine utilization, causing cell growth defects with ethanolamine as a nutrient. BMCs are also assembled in fusobacteria cultured with placental cells or the culture media, a process that is dependent on the BMC shell proteins. Significantly, we show that the
eutN
mutant is defective in inducing preterm birth in a mouse model. Together, these results establish that the BMC-mediated metabolism of ethanolamine is critical for fusobacterial virulence.

IMPORTANCE

The oral anaerobe
Fusobacterium nucleatum
can spread to distal internal organs, such as the colon and placenta, thereby promoting the development of colorectal cancer and inducing preterm birth, respectively. Yet, how this opportunistic pathogen adapts to the various metabolically distinct host cellular niches remains poorly understood. We demonstrated here that this microbe assembles specialized metabolic organelles, termed bacterial microcompartments (BMCs), to utilize environmental ethanolamine (EA) as a key environmental nutrient source. The formation of
F. nucleatum
BMCs, containing BMC shell proteins EutLM1M2N, is controlled by a two-component system, EutV-EutW, responsive to EA. Significantly, this ability of
F. nucleatum
to form BMCs in response to EA is crucial for its pathogenicity evidenced by the fact that the genetic disruption of BMC formation reduces fusobacterial virulence in a mouse model of preterm birth.
The prebiotic potential of dietary onion extracts: shaping gut microbial structures and promoting beneficial metabolites
Authors: Yoo Yebeen , Kim Seongok , Lee WonJune , Kim Jinwoo , Son Bokyung , Lee Kwang Jun , Shin Hakdong 
Published: December 2024

ABSTRACT

Onions are well-known vegetables that offer various health benefits. This study explores the impact of onion extracts on gut microbiome using an
in vitro
fecal incubation model and metabolome analysis. Fecal samples were collected from 19 healthy donors and incubated in the presence or absence of onion extracts for 24 h. To reduce inter-individual variability in the gut microbiome, we employed enterotyping based on baseline fecal microbiota: 14 subjects with a
Bacteroides
-dominant type (enterotype B) and 5 subjects with
Prevotella
-dominant type (enterotype P). Alpha diversity was significantly reduced in the onion-treated group compared to the non-treated control group in both
Bacteroides
- and
Prevotella
-dominant types. However, significant structural differences in bacterial communities were observed based on weighted UniFrac distance. Notably, short-chain fatty acid (SCFA)-producing bacteria, such as
Bifidobacterium
_388775,
Feacalibacterium
, and
Fusicatenibacter
, were overrepresented in response to onion extracts in enterotype B. Furthermore, genes related to butyrate production were significantly overrepresented in the onion-treated group within enterotype B. Consistent with the enriched taxa and the predicted metabolic pathways, SCFAs and their related metabolites were significantly enriched in the onion-treated group. Additionally, tryptophan metabolism-derived metabolites, including indolelactate (ILA) and indolepropionate (IPA), were elevated by 4- and 32-fold, respectively, in the onion-treated group compared to the control group.
In vitro
growth assays showed an increase in lactobacilli strains in the presence of onion extracts. These results provide evidence that onion extracts could serve as promising prebiotics by altering gut microbial structure and promoting the production of beneficiary metabolites, including SCFAs and indole derivatives, and enhancing the growth of probiotics.

IMPORTANCE

This study is significant as it provides compelling evidence that onion extracts have the potential to serve as effective prebiotics. Utilizing an
in vitro
fecal incubation model and enterotyping to reduce inter-individual variability, the research demonstrates how onion extracts can alter gut microbial structure and promote the production of beneficial metabolites, including SCFAs and indole derivatives like ILA and IPA. Additionally, onion extract treatment enhances the growth of beneficial probiotics. The findings underscore the potential of onion extracts to improve gut health by enriching specific beneficial bacteria and metabolic pathways, thereby supporting the development of functional foods aimed at improving gut microbiota composition and metabolic health.
Health care professionals’ views on a new postpartum contraception audiovisual animation: a survey
Authors: Simpson Janine , Cooper Michelle , Cameron Sharon 
Published: December 2024

BackgroundThe postpartum period is a high-risk time for unintended pregnancy. We developed a 2-minute audiovisual animation on postpartum contraception (PPC) including the return of fertility after birth for patients. The aim of our study was to determine the views of healthcare professionals (HCPs) involved in pregnancy care on the animation and to identify facilitators and barriers to its implementation into routine pregnancy care pathways.MethodsAn anonymous online questionnaire was circulated to 100 HCPs (midwives, doctors, health visitors) in Glasgow, Scotland, UK who provide antenatal and/or postnatal care. The aim was to collect 50 responses. The questionnaire contained 12 questions including fixed responses, categorical Likert rating scale questions and open-ended questions. Content analysis was used for the free-text responses.ResultsForty-four responses were obtained. HCPs rated the animation positively for information and inclusivity (95%), accessibility for those with a disability (81.8%) and non-English speaking (59%), and usefulness for HCPs (88.6%) and pregnant individuals (97%). Some felt the animation should contain more information or could be displayed on digital screens in clinical waiting areas. Suggestions were made as to the optimal time to view the animation in pregnancy and the importance of choice of whether/how to view and considerations on trauma-informed care. Accessibly for HCPs was mentioned, with considerations on how the resource could alleviate perceived service and financial pressures.ConclusionsThe animation was felt to be an engaging, inclusive and informative knowledge tool for patients. Consideration needs to be given to allow choice to view, timing and the appropriate digital media for delivering it.
Deleterious impacts of Western diet on jejunum function and health are reversible
Authors: Carpinelli Sarah , Ahlert John , Rubin Maxwell , Aratani Alex , Smith Emma , Floyd Dana , Potter Ross M. , Al-Nakkash Layla 
Published: December 2024

Our data suggests that the reduced basal jejunal Isc (decreased secretory function) in Western diet-fed mice is reversible. A better understanding of Western diet-mediated intestinal disturbances may permit improved treatment options for gastrointestinal abnormalities in obese individuals.
Autonomic Inertia as a Proximal Risk Marker for Moments of Perseverative Cognition in Everyday Life in Remitted Depression
Authors: Zapetis Sarah L. , Li Jiani , Xu Ellie P. , Ye Zihua , Phanord Coralie S. , Trull Timothy J. , Schneider Stefan , Stange Jonathan P. 
Published: December 2024

Background: Trait perseverative cognition (PC) is associated with inflexible autonomic activity and risk for depressive recurrence. However, the identification of dynamic psychophysiological markers of PC that fluctuate within individuals over time could facilitate the passive detection of moments when PC occurs in daily life.Methods: Using intensively sampled data across 1 week (3x/day) in adults with remitted major depressive disorder (rMDD) and never‐depressed controls (CONs), we investigated the utility of monitoring ambulatory autonomic complexity to predict moments of PC engagement in everyday life. Autonomic complexity metrics, including the root mean square of successive difference (RMSSD), indexing vagal control, and sample entropy, indexing signal complexity, were calculated in the 30 min before each measurement of PC to enable time‐lagged analyses. Multilevel models examined proximal fluctuations in the mean level and inertia of complexity metrics as predictors of subsequent PC engagement.Results: Momentary increases in the inertia of sample entropy, but not other metrics, predicted higher levels of subsequent PC in the rMDD group, but not among never‐depressed CONs.Conclusions: The inertia of sample entropy could index autonomic rigidity and serve as a dynamic risk marker for real‐world PC in individuals with a history of depression. This could inform the development of technologies to passively detect fluctuations in risk for PC, facilitating real‐time interventions to prevent PC and reduce the risk for depressive recurrence.
ОСОБЛИВОСТІ ЕМОЦІЙНОГО ІНТЕЛЕКТУ СЕРЕД МЕДСЕСТЕР ОНКОЛОГІЧНИХ ВІДДІЛЕНЬ
Authors: Дейнека Н. Д. , Марущак М. І. 
Published: December 2024

Вступ. Незважаючи на різницю в інструментах оцінки, результати досліджень засвідчують, що емоційний інтелект (ЕІ) медсестер потребує більшої уваги, та підтверджують актуальність обраної теми дослідження.
Мета роботи – проаналізувати показники емоційного інтелекту медсестер онкологічних відділень різного профілю і встановити фактори, що на них впливають.
Основна частина. У дослідженні брали участь 60 медсестер, яких поділили на групи залежно від профілю відділення, в якому вони працюють, стажу роботи, віку, індексу маси тіла, а також залежно від наявності чи відсутності нічних змін та хронічних захворювань. Рівень емоційного інтелекту визначали за допомогою опитувальника «Емоційний інтелект» М. О. Манойлової. Встановлено вірогідно більші значення інтегрального показника ЕІ у працівників хірургічних відділень стосовно досліджуваної величини у працівників поліклінічних (на 71,58 %) і терапевтичних (на 7,89 %) відділень. За умови різного стажу роботи за спеціальністю відзначено вірогідно вищі значення інтегрального показника ЕІ та його міжособистісного аспекту в медсестер онкологічних відділень з досвідом професійної роботи понад 10 років стосовно респондентів зі стажем роботи до 10 років – в 1,43 і 2,63 раза відповідно. Відмічено вірогідно більші значення інтегрального показника ЕІ та його внутрішньоособистісного аспекту в медсестер онкологічних відділень віком до 40 років стосовно респондентів віком понад 40 років – в 1,43 і 2,63 раза відповідно. Наявність хронічних захворювань, а також позмінна робота не впливали на інтегральні індекси ЕІ медсестер онкологічних відділень. Водночас надмірна маса тіла та ожиріння респондентів, які брали участь у дослідженні, впливали на показники ЕІ медсестер онкологічних відділень.
Висновки. У медсестер онкологічних відділень хірургічного профілю інтегральний показник ЕІ вірогідно вищий від даних у працівників поліклінічних і терапевтичних відділень. На зниження інтегрального показника ЕІ та його окремих аспектів у медсестер онкологічних відділень впливають вік респондентів понад 40 років, стаж роботи до 10 років, а також ожиріння.
РОЛЬ ФІЗИЧНОЇ ТЕРАПІЇ ПРИ КОРЕКЦІЇ ПОСТАВИ В ДІТЕЙ З ДЕФОРМАЦІЯМИ СТОП
Authors: Єфремова І. С. , Гевко У. П. 
Published: December 2024

Вступ. Порушення постави є однією з найпоширеніших серед молоді проблем, що становить 90 % усіх випадків захворювань опорно-рухової системи. За статистикою, кожна четверта дитина в Україні має відхилення у поставі. Найбільшу частку деформацій хребта спостерігають у дітей, старших 7 років, а серед підлітків віком від 10 до 17 років порушення постави виявляють майже в 94 % випадків. Основ­ними чинниками такого високого рівня поширеності є сучасний спосіб життя, зокрема довготривале сидіння за комп’ютером, невідповідність меблів у навчальних закладах гігієнічним вимогам та індивідуальним морфологічним особливостям, а також недостатня фізична активність молоді.
Мета роботи – проаналізувати роль фізичної терапії у корекції постави в дітей з деформаціями стоп, визначити найбільш ефективні методи фізичної реабілітації.
Основна частина. Фізична терапія відіграє ключову роль у корекції постави в дітей з деформаціями стоп, такими, як плоскостопість, вальгусна чи варусна деформація. Порушення біомеханіки стопи впливає на формування неправильної постави, що може призвести до сколіозу, порушень ходи та інших ортопедичних проблем. Фізична терапія включає індивідуально підібрані комплекси вправ для зміцнення м’язів стопи, поліпшення рухомості суглобів та відновлення рівноваги тіла. Також застосовують методи масажу, ортези (коригувальні устілки), кінезіотейпування та фізіотерапевтичні процедури. Регулярне виконання вправ у поєднанні з контролем фахівця сприяє зменшенню симптомів деформацій і нормалізації постави, покращуючи загальний фізичний стан дитини та запобігаючи розвитку ускладнень у майбутньому.
Висновки. Фізична терапія є ефективним підходом у корекції постави в дітей з деформаціями стоп, сприяючи відновленню правильного положення тіла та покращенню моторної функції. Систематичне застосування індивідуально підібраних вправ і терапевтичних методів не лише зменшує ступінь вираження деформацій, але й запобігає розвитку вторинних ускладнень. Раннє втручання та постійний контроль фахівця підвищують ефективність лікування, забезпечуючи дитині гармонійний фізичний розвиток.
Main Component in Altimetry-Observed Response to a Tropical Cyclone
Authors: Lu Zhumin , Liang Changrong , Shang Xiaodong 
Published: December 2024

Abstract
The ocean response to a tropical cyclone (TC) generally consists of near-inertial and geostrophic components, and the geostrophic response is impliedly believed to be ignorable. This study divides and compares the geostrophic and near-inertial components in the sea surface height (SSH) response obtained by a two-layer theory and numerical experiments, revealing that the geostrophic component is dominant and the near-inertial component ignorable. This conclusion results from 1) the high ratios (approximately 70%–90%) of the geostrophic component in the upwelling where the geostrophic response occurs and/or 2) the small absolute near-inertial amplitudes, usually below 3 cm, which satellite altimeters cannot capture. The findings are first presented in a two-layer model and then confirmed to be robust using numerical experiments by considering the effects of the nonlinear process, vertical dispersion of near-inertial internal waves, and vertical structure of the geostrophic response. By testing parameter dependence, the findings are insensitive to ocean stratification and TC characteristics including moving speed, intensity, and latitude, thus being generally appropriate for any TC case. The generality is physically related to the nature of Rossby adjustment and the dispersion of TC-induced near-inertial internal waves. Finally, the evidences are provided by the SSH response to Typhoon Mawar (2023) captured by the Surface Water and Ocean Topography satellite, which demonstrates the main features of the geostrophic response and no near-inertial wavelike signals. This study lays a solid foundation for dynamically understanding altimetry-observed response, highlighting the vital role of the geostrophic response.

Significance Statement
The ocean response to a tropical cyclone generally consists of wave and quasi-steady components, and the quasi-steady component is impliedly believed to be ignorable. Based on the theory, numerical experiments, and altimetry observations, this study finds the high ratios of the quasi-steady component in sea surface height response and the relatively small wave amplitudes. Thus, the quasi-steady response is the main component, and the wave component is ignorable in the sea surface height response to a tropical cyclone observed by satellite altimeters. This study lays a solid foundation for dynamically understanding altimetry-observed response to a tropical cyclone and proves the vital importance of the quasi-steady response.