bluuebunny/crossref_metadata_2025 huggingface dataset:
DUF3669, a “domain of unknown function” within ZNF746 and ZNF777, oligomerizes and contributes to transcriptional repression
Authors: Al Chiblak Mohannad , Steinbeck Felix , Thiesen Hans-Jürgen , Lorenz Peter
Published: December 2019

Background

ZNF746 and ZNF777 belong to a subset of the large Krüppel-associated box (KRAB) zinc finger (ZNF) transcription factor family. They contain, like four other members in human, an additional conserved domain, the “domain of unknown function 3669” (DUF3669). Previous work on members of this subfamily suggested involvement in transcriptional regulation and aberrant ZNF746 overexpression leads to neuronal cell death in Parkinson’s disease.

Results

Here we demonstrate that N-terminal protein segments of the ZNF746a major isoform and ZNF777 act in concert to exert moderate transcriptional repression activities. Full potency depended on the intact configuration consisting of DUF3669, a variant KRAB domain and adjacent sequences. While DUF3669 contributes an intrinsic weak inhibitory activity, the isolated KRAB-AB domains did not repress. Importantly, DUF3669 provides a novel protein-protein interaction interface and mediates direct physical interaction between the members of the subfamily in oligomers. The ZNF746 protein segment encoded by exons 5 and 6 boosted repressor potency, potentially due to the presence of an acceptor lysine for sumoylation at K189. Repressor activity of the potent canonical ZNF10 KRAB domain was not augmented by heterologous transfer of DUF3669, pointing to the importance of context for DUF3669’s impact on transcription. Neither ZNF746a nor ZNF777 protein segments stably associated with TRIM28 within cells. Isoform ZNF746b that contains, unlike the major isoform, a full-length KRAB-A subdomain, displayed substantially increased repressor potency. This increase is due to canonical mechanisms known for KRAB domains since it did not take place in HAP1 knockout models of TRIM28 and SETDB1. A glycine to glutamic acid replacement that complies with a bona fide conserved “MLE” sequence within KRAB-A led to a further strong gain in repressor potency to levels comparable to those of the canonical ZNF10 KRAB domain. Each gain of repressive activity was accompanied by an enhanced interaction with TRIM28 protein.

Conclusion

DUF3669 adds a protein-protein interaction surface to a subgroup of KRAB-ZNF proteins within an N-terminal configuration with variant KRAB and adjacent sequences likely regulated by sumoylation. DUF3669 contributes to transcriptional repression strength and its homo- and hetero-oligomerization characteristics probably extended the regulatory repertoire of KRAB-ZNF transcription factors during amniote evolution.
Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils
Authors: Heinsch Stephen C. , Hsu Szu-Yi , Otto-Hanson Lindsey , Kinkel Linda , Smanski Michael J.
Published: December 2019

Background

Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays.

Results

Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93–23, Streptomyces sp. 3211–3, and Streptomyces sp. S3–4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution.

Conclusions

Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93–23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.
Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L
Authors: Zhang Shulin , Tian Zailong , Li Haipeng , Guo Yutao , Zhang Yanqi , Roberts Jeremy A. , Zhang Xuebin , Miao Yuchen
Published: December 2019

Background

F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects.

Results

In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction.

Conclusion

The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.
Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce
Authors: Nakamura Miyuki , Köhler Claudia , Hennig Lars
Published: December 2019

Background

Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms.

Results

Here, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture.

Conclusion

Our data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.
The Safe Start trial to assess the effect of an infant hygiene intervention on enteric infections and diarrhoea in low-income informal neighbourhoods of Kisumu, Kenya: a study protocol for a cluster randomized controlled trial
Authors: Mumma Jane , Simiyu Sheillah , Aseyo Evalyne , Anderson John , Czerniewska Alexandra , Allen Elizabeth , Dreibelbis Robert , Baker Kelly K. , Cumming Oliver
Published: December 2019

Background

Symptomatic and asymptomatic enteric infections in early childhood are associated with negative effects on childhood growth and development, especially in low and middle-income countries, and food may be an important transmission route. Although basic food hygiene practices might reduce exposure to faecal pathogens and resulting infections, there have been few rigorous interventions studies to assess this, and no studies in low income urban settings where risks are plausibly very high. The aim of this study is to evaluate the impact of a novel infant food hygiene intervention on infant enteric infections and diarrhoea in peri-urban settlements of Kisumu, Kenya.

Methods

This is a cluster randomized control trial with 50 clusters, representing the catchment areas of Community Health Volunteers (CHVs), randomly assigned to intervention or control, and a total of 750 infants recruited on a rolling basis at 22 weeks of age and then followed for 15 weeks. The intervention targeted four key caregiver behaviours related to food hygiene: 1) hand washing with soap before infant food preparation and feeding; 2) bringing all infant food to the boil before feeding, including when reheating or reserving; 3) storing all infant food in sealed containers; and, 4) using only specific utensils for infant feeding which are kept separate and clean.

Results

The primary outcome of interest is the prevalence of one or more of 23 pre-specified enteric infections, determined using quantitative real-time polymerase chain reaction for enteric pathogen gene targets. In addition, infant food samples were collected at 33 weeks, and faecal indicator bacteria (Enterococcus) isolated and enumerated to assess the impact of the intervention on infant food contamination.

Conclusion

To our knowledge this is the first randomized controlled trial to assess the effect of an infant food hygiene intervention on enteric infections in a high burden, low income urban setting. Our trial responds to growing evidence that food may be a key pathway for early childhood enteric infection and disease and that basic food hygiene behaviours may be able to mitigate these risks. The Safe Start trial seeks to provide new evidence as to whether a locally appropriate infant food hygiene intervention delivered through the local health extension system can improve the health of young children.

Trial registration

The trial was registered at clinicaltrial.gov on March 16th 2018 before enrolment of any participants (https://clinicaltrials.gov/ct2/show/NCT03468114).
Identification of two novel COL10A1 heterozygous mutations in two Chinese pedigrees with Schmid-type metaphyseal chondrodysplasia
Authors: Kong Lingchi , Shi Li , Wang Wenbo , Zuo Rongtai , Wang Mengwei , Kang Qinglin
Published: December 2019

Background

Schmid-type metaphyseal chondrodysplasia (MCDS) is an autosomal dominant disorder caused by COL10A1 mutations, which is characterized by short stature, waddling gait, coxa vara and bowing of the long bones. However, descriptions of the expressivity of MCDS are rare.

Methods

Two probands and available family members affected with MCDS were subjected to clinical and radiological examination. Genomic DNA of all affected individuals was subjected to whole-exome sequencing, and candidate mutations were verified by Sanger sequencing in all available family members and in 250 healthy donors. A spatial model of the type X collagen (α1) C-terminal noncollagenous (NC1) domain was further constructed.

Results

We found that the phenotype of affected family members exhibited incomplete dominance. Mutation analysis indicated that there were two novel heterozygous missense mutations, [c.1765 T > A (p.Phe589Ile)] and [c.1846A > G (p.Lys616Glu)] in the COL10A1 gene in family 1 and 2, respectively. The two novel substitution sites were highly conserved and the mutations were predicted to be deleterious by in silico analysis. Furthermore, protein modeling revealed that the two substitutions were located in the NC1 domain of collagen X (α1), which potentially impacted the trimerization of collagen X (α1) and combination with molecules in the pericellular matrix.

Conclusion

Two novel mutations were identified in the present study, which will facilitate diagnosis of MCDS and further expand the spectrum of the COL10A1 mutations associated with MCDS patients. In addition, our research revealed the phenomenon of incomplete dominance in MCDS.
Psychological well-being as part of the public health debate? Insight into dimensions, interventions, and policy
Authors: Trudel-Fitzgerald Claudia , Millstein Rachel A. , von Hippel Christiana , Howe Chanelle J. , Tomasso Linda Powers , Wagner Gregory R. , VanderWeele Tyler J.
Published: December 2019

Background

Increasing evidence suggests that psychological well-being (PWB) is associated with lower disease and mortality risk, and may be enhanced with relatively low-cost interventions. Yet, dissemination of these interventions remains limited, in part because insufficient attention has been paid to distinct PWB dimensions, which may impact physical health outcomes differently.

Methods

This essay first reviews the empirical evidence regarding differential relationships between all-cause mortality and multiple dimensions of PWB (e.g., life purpose, mastery, positive affect, life satisfaction, optimism). Then, individual-level positive psychology interventions aimed at increasing PWB and tested in randomized-controlled trials are reviewed as these allow for easy implementation and potentially broad outreach to improve population well-being, in concert with efforts targeting other established social determinants of health.

Results

Several PWB dimensions relate to mortality, with varying strength of evidence. Many of positive psychology trials indicate small-to-moderate improvements in PWB; rigorous institution-level interventions are comparatively few, but preliminary results suggest benefits as well. Examples of existing health policies geared towards the improvement of population well-being are also presented. Future avenues of well-being epidemiological and intervention research, as well as policy implications, are discussed.

Conclusions

Although research in the fields of behavioral and psychosomatic medicine, as well as health psychology have substantially contributed to the science of PWB, this body of work has been somewhat overlooked by the public health community. Yet, the growing interest in documenting well-being, in addition to examining its determinants and consequences at a population level may provoke a shift in perspective. To cultivate optimal well-being—mental, physical, social, and spiritual—consideration of a broader set of well-being measures, rigorous studies, and interventions that can be disseminated is critically needed.
MultiSourcDSim: an integrated approach for exploring disease similarity
Authors: Deng Lei , Ye Danyi , Zhao Junmin , Zhang Jingpu
Published: December 2019

Background

A collection of disease-associated data contributes to study the association between diseases. Discovering closely related diseases plays a crucial role in revealing their common pathogenic mechanisms. This might further imply treatment that can be appropriated from one disease to another. During the past decades, a number of approaches for calculating disease similarity have been developed. However, most of them are designed to take advantage of single or few data sources, which results in their low accuracy.

Methods

In this paper, we propose a novel method, called MultiSourcDSim, to calculate disease similarity by integrating multiple data sources, namely, gene-disease associations, GO biological process-disease associations and symptom-disease associations. Firstly, we establish three disease similarity networks according to the three disease-related data sources respectively. Secondly, the representation of each node is obtained by integrating the three small disease similarity networks. In the end, the learned representations are applied to calculate the similarity between diseases.

Results

Our approach shows the best performance compared to the other three popular methods. Besides, the similarity network built by MultiSourcDSim suggests that our method can also uncover the latent relationships between diseases.

Conclusions

MultiSourcDSim is an efficient approach to predict similarity between diseases.
Selection process for botulinum toxin injections in patients with chronic-stage hemiplegic stroke: a qualitative study
Authors: Arai Sawako , Fukase Yuko , Okii Akira , Suzukamo Yoshimi , Suga Toshimitsu
Published: December 2019

Background

Botulinum toxin (BT) injection is a new treatment for spasticity with hemiplegia after stroke. How a patient decides to receive BT injections after becoming aware of the treatment remains unclear. In this exploratory qualitative study, we aimed to investigate patients’ decision-making about treatment strategies in collaboration with family and health professionals and to identify conflicts in patients’ feelings about BT treatment.

Methods

The study included six patients with stroke sequelae. Data were collected using comprehensive interviews and were analyzed using the grounded theory approach and trajectory equifinality modeling.

Results

After patients learned about BT treatment, they clearly exhibited the following two concurrent perceptions: “the restriction of one’s life due to disabilities” and “the ability to do certain things despite one’s disabilities.” Some patients reported a “fear of not being able to maintain the status quo owing to the side effects of BT.” To alleviate this fear, timely support from family members was offered, and patients overcame anxiety through creative thinking. However, there were also expressions that revealed patients’ difficulties dealing with negative events. These factors influenced the patients’ development of “expectations of BT” or “hesitations about BT.”

Conclusions

To establish treatment strategies in collaboration with patients, healthcare professionals should show supportive attitudes and have discussions with patients and their family members to help patients resolve their conflicts and should establish treatment strategies that maintain the positive aspects of patients’ lives.
Implementation of a billable transitional care model for stroke patients: the COMPASS study
Authors: Gesell Sabina B. , Bushnell Cheryl D. , Jones Sara B. , Coleman Sylvia W. , Levy Samantha M. , Xenakis James G. , Lutz Barbara J. , Bettger Janet Prvu , Freburger Janet , Halladay Jacqueline R. , Johnson Anna M. , Kucharska-Newton Anna M. , Mettam Laurie H. , Pastva Amy M. , Psioda Matthew A. , Radman Meghan D. , Rosamond Wayne D. , Sissine Mysha E. , Halls Joanne , Duncan Pamela W.
Published: December 2019

Background

The COMprehensive Post-Acute Stroke Services (COMPASS) pragmatic trial compared the effectiveness of comprehensive transitional care (COMPASS-TC) versus usual care among stroke and transient ischemic attack (TIA) patients discharged home from North Carolina hospitals. We evaluated implementation of COMPASS-TC in 20 hospitals randomized to the intervention using the RE-AIM framework.

Methods

We evaluated hospital-level Adoption of COMPASS-TC; patient Reach (meeting transitional care management requirements of timely telephone and face-to-face follow-up); Implementation using hospital quality measures (concurrent enrollment, two-day telephone follow-up, 14-day clinic visit scheduling); and hospital-level sustainability (Maintenance). Effectiveness compared 90-day physical function (Stroke Impact Scale-16), between patients receiving COMPASS-TC versus not. Associations between hospital and patient characteristics with Implementation and Reach measures were estimated with mixed logistic regression models.

Results

Adoption: Of 95 eligible hospitals, 41 (43%) participated in the trial. Of the 20 hospitals randomized to the intervention, 19 (95%) initiated COMPASS-TC.

Reach: A total of 24% (656/2751) of patients enrolled received a billable TC intervention, ranging from 6 to 66% across hospitals.

Implementation: Of eligible patients enrolled, 75.9% received two-day calls (or two attempts) and 77.5% were scheduled/offered clinic visits. Most completed visits (78% of 975) occurred within 14 days.

Effectiveness: Physical function was better among patients who attended a 14-day visit versus those who did not (adjusted mean difference: 3.84, 95% CI 1.42–6.27, p = 0.002).

Maintenance: Of the 19 adopting hospitals, 14 (74%) sustained COMPASS-TC.

Conclusions

COMPASS-TC implementation varied widely. The greatest challenge was reaching patients because of system difficulties maintaining consistent delivery of follow-up visits and patient preferences to pursue alternate post-acute care. Receiving COMPASS-TC was associated with better functional status.

Trial registration

ClinicalTrials.gov number: NCT02588664. Registered 28 October 2015.
Implementing coordinated ambulatory cardiology care in southern Germany: a mixed-methods study
Authors: Hennrich Patrick , Bölter Regine , Wensing Michel
Published: December 2019

Background

In 2009 health insurers AOK and Bosch BKK introduced the “FacharztProgramm Kardiologie” - a program for coordinated ambulatory cardiology care in the German state of Baden-Württemberg. It aims for efficient, medical guideline-oriented cardiology care to reduce avoidable hospitalizations as well as costs of care. A high number of cardiologists participate and the program has served as blueprint for programs in other medical fields. With many prerequisites and conditions involved, its implementation cannot be expected to be self-directed. Still, only little data on the actual implementation exists. We aimed to determine to what extent medical specialists and cooperating general practitioners implemented the program, which components they adapted, and which contextual factors they deemed relevant.

Methods

We collected data from primary care practices of medical specialists and general practitioners within Baden-Württemberg.

Qualitative data was obtained through structured telephone interviews with participating and non-participating medical specialists as well as general practitioners cooperating with the program and general practitioners not cooperating. Interviews were analyzed through content-structuring qualitative content analyses via MAXQDA.

Quantitative data was obtained using anonymous written questionnaires completed by participating and non-participating medical specialists as well as general practitioners cooperating with the program. Analyses were performed using SPSS Statistics, mainly with regard to differences within and between groups of physicians.

Results

Most components of the program regarding medical care were well implemented. However, access to medical care was not completely as intended due to high numbers of patients participating in the program and prioritization by physicians. Procedures for communication and cooperation between medical specialists and general practitioners were only partially adhered to and standardized communication was not implemented. A range of regional and practice-related contextual factors influenced implementation and outcomes.

Conclusions

Implementation of this program was mixed. Contextual factors posed individual challenges to participating physicians which can’t be captured by an encompassing program. Both control mechanisms and tailoring of the program to medical care seem needed.

Trial registration

Though not a clinical study, we deemed registration appropriate to ensure transparency. The study has been registered as a non-interventional observation study at the German Clinical Trials Register under ID:DRKS00013070.
Melioidosis fatalities in captive slender-tailed meerkats (Suricata suricatta): combining epidemiology, pathology and whole-genome sequencing supports variable mechanisms of transmission with one health implications
Authors: Rachlin Audrey , Shilton Cathy , Webb Jessica R. , Mayo Mark , Kaestli Mirjam , Kleinecke Mariana , Rigas Vanessa , Benedict Suresh , Gurry Ian , Currie Bart J.
Published: December 2019

Background

Melioidosis is a tropical infectious disease which is being increasingly recognised throughout the globe. Infection occurs in humans and animals, typically through direct exposure to soil or water containing the environmental bacteriumBurkholderia pseudomallei. Case clusters of melioidosis have been described in humans following severe weather events and in exotic animals imported into melioidosis endemic zones. Direct transmission ofB. pseudomalleibetween animals and/or humans has been documented but is considered extremely rare. Between March 2015 and October 2016 eight fatal cases of melioidosis were reported in slender-tailed meerkats (Suricata suricatta)on display at a Wildlife Park in Northern Australia. To further investigate the melioidosis case cluster we sampled the meerkat enclosure and adjacent park areas and performed whole-genome sequencing (WGS) on all culture-positiveB. pseudomalleienvironmental and clinical isolates.

Results

WGS confirmed that the fatalities were caused by two differentB. pseudomalleisequence types (STs) but that seven of the meerkat isolates were highly similar on the whole-genome level. Used concurrently with detailed pathology data, our results demonstrate that the seven cases originated from a single original source, but routes of infection varied amongst meerkats belonging to the clonal outbreak cluster. Moreover, in some instances direct transmission may have transpired through wounds inflicted while fighting.

Conclusions

Collectively, this study supports the use of high-resolution WGS to enhance epidemiological investigations into transmission modalities and pathogenesis of melioidosis, especially in the instance of a possible clonal outbreak scenario in exotic zoological collections. Such findings from an animal outbreak have important One Health implications.
Differential analysis of nutrient intake, insulin resistance and lipid profiles between healthy and premature thelarche Chinese girls
Authors: Xu Yueqin , Li Yan , Liang Shuang , Li Guimei
Published: December 2019

Background

Premature thelarche (PT) is a benevolent ailment affecting young girls. Multiple factors are reported to correlate with this condition, but the mechanisms responsible for the onset of PT have not yet been fully investigated. This study aimed to evaluate the relationship of nutrient intake, insulin resistance and lipid profile with PT.

Methods

Two hundred sixty-three girls with PT, and 222 healthy girls of similar age were enrolled into this study. Their demographics, Tanner stage of breast development, nutrient intake, insulin resistance and lipid profiles were compared.

Results

Daily protein and fat intakes, insulin resistance parameters including serum insulin-like growth factor 1, fasting glucose to insulin ratio, quantitative insulin check index and homeostasis model of assessment of insulin resistance, as well as serum levels of triacylglycerol, total cholesterol and low-density lipoprotein, were all significantly altered in PT patients. Daily intake of energy and carbohydrate, and serum level of high-density lipoprotein protein were statistically indistinguishable between PT patients and healthy controls.

Conclusion

Chinese girls with PT are potentially insulin resistant, which warrants more clinical attention and further investigation to address the underlying etiology.
Ethical issues in the design and conduct of stepped-wedge cluster randomized trials in low-resource settings
Authors: Joag Kaustubh , Ambrosio Guillermo , Kestler Edgar , Weijer Charles , Hemming Karla , Van der Graaf Rieke
Published: December 2019

Background

Stepped-wedge cluster randomized trials (SW-CRTs) are increasingly popular in health-related research in both high- and low-resource settings. There may be specific ethical issues that researchers face when designing and conducting SW-CRTs in low-resource settings. Knowledge of these issues can help to improve the ethical conduct of SW-CRTs in a global health context.

Methods

We performed an ethical analysis of two studies using SW-CRT designs in low-resource settings: the Que Vivan Las Madres study conducted from 2014 to 2017 in Guatemala and the Atmiyata study conducted from 2017 to 2018 in rural parts of India. For both case studies, we identified and evaluated the classification of the study as research or nonresearch and the ethical issues regarding the justification of the design, including the delayed rollout of an intervention that had a promising effect.

Results

In our case studies, some minor ethical issues surfaced about the registration and stakeholder pressure on the order of randomization, but both included good justification for the design and delayed rollout. Our analysis did, however, demonstrate that careful consideration of the role of randomization and registration of the trials is important.

Discussion

SW-CRTs can provide an opportunity for rigorous evaluation of interventions destined to be rolled out on the basis of limited evidence. Furthermore, in SW-CRTs, the underlying objective is often to provide a robust evaluation of the effectiveness for generalized dissemination, and this makes the SW-CRT no less a research study than any other form of cluster randomized trial.

Conclusion

The design and conduct of stepped-wedge cluster randomized trials raises at least two ethical issues that need special consideration in both high- and low-resource settings: the justification for using the design, specifically the delayed rollout of the intervention to the control group, and the classification of the study as research or nonresearch. In our case studies, these issues did not seem to raise special ethical scrutiny in low-resource settings. Further ethical evaluation will hopefully result in specific ethical guidelines for the use of SW-CRTs in both high- and low-resource settings to contribute to responsible functioning of these trials and adequate protection of participants.
Reduced H3K27me3 leads to abnormal Hox gene expression in neural tube defects
Authors: Yu Juan , Wang Lei , Pei Pei , Li Xue , Wu Jianxin , Qiu Zhiyong , Zhang Juan , Ao Ruifang , Wang Shan , Zhang Ting , Xie Jun
Published: December 2019

Background

Neural tube defects (NTDs) are severe, common birth defects that result from failure of normal neural tube closure during early embryogenesis. Accumulating strong evidence indicates that genetic factors contribute to NTDs etiology, among them, HOX genes play a key role in neural tube closure. Although abnormal HOX gene expression can lead to NTDs, the underlying pathological mechanisms have not fully been understood.

Method

We detected that H3K27me3 and expression of the Hox genes in a retinoic acid (RA) induced mouse NTDs model on E8.5, E9.5 and E10.5 using RNA-sequencing and chromatin immunoprecipitation sequencing assays. Furthermore, we quantified 10 Hox genes using NanoString nCounter in brain tissue of fetuses with 39 NTDs patients including anencephaly, spina bifida, hydrocephaly and encephalocele.

Results

Here, our results showed differential expression in 26 genes with a > 20-fold change in the level of expression, including 10 upregulated Hox genes. RT-qPCR revealed that these 10 Hox genes were all upregulated in RA-induced mouse NTDs as well as RA-treated embryonic stem cells (ESCs). Using ChIP-seq assays, we demonstrate that a decrease in H3K27me3 level upregulates the expression of Hox cluster A–D in RA-induced mouse NTDs model on E10.5. Interestingly, RA treatment led to attenuation of H3K27me3 due to cooperate between UTX and Suz12, affecting Hox gene regulation. Further analysis, in human anencephaly cases, upregulation of 10 HOX genes was observed, along with aberrant levels of H3K27me3. Notably, HOXB4, HOXC4 and HOXD1 expression was negatively correlated with H3K27me3 levels.

Conclusion

Our results indicate that abnormal HOX gene expression induced by aberrant H3K27me3 levels may be a risk factor for NTDs and highlight the need for further analysis of genome-wide epigenetic modification in NTDs.
The effect of cassia seed extract on the regulation of the LKB1–AMPK–GLUT4 signaling pathway in the skeletal muscle of diabetic rats to improve the insulin sensitivity of the skeletal muscle
Authors: Wang Qiu-Ying , Tong Ai-Hua , Pan Ying-Ying , Zhang Xian-Dang , Ding Wen-Yu , Xiong Wen
Published: December 2019

Background

This study aimed to observe the hypoglycemic effect of cassia seed extract in rats with type-2 diabetes mellitus and its effect on reducing insulin resistance in the skeletal muscle.

Methods

50 rats were randomly divided into the normal, model, high-dose, middle-dose, and low-dose groups of cassia seed extract (n = 10 each). A high-fat diet combined with streptozotocin administration was adopted to build type 2 diabetes models. The cassia seed extract groups were fed different concentrations cassia seed extract while the normal and model groups were fed the same volume of normal saline. The weight, FINS, GIR, insulin tolerance, blood glucose and blood lipid level, oxidative stress indices and expressions related to the LKB1–AMPK–GLUT4 pathway were detected and compared between the two groups.

Results

Compared with the normal group, the model group showed lower weight, glucose infusion rate and expressions related to LKB1–AMPK–GLUT4 pathway and higher FINS, insulin tolerance, blood glucose and blood lipid level and oxidative stress indices (all P < 0.05). Compared with the model group, higher weight, glucose infusion rate and expressions related to LKB1–AMPK–GLUT4 pathway and lower FINS, insulin tolerance, blood glucose and blood lipid level and oxidative stress indices were observed in all groups that were administered cassia see extract (all P < 0.05).

Conclusion

Cassia seed extract could noticeably improve the insulin resistance of diabetic rats and enhance the insulin sensitivity of their skeletal muscles. Its mechanism may be related to damage repair of the LKB1–AMPK–GLUT4 signaling pathway and oxidative stress in the skeletal muscle.
Effects of exercise training on markers of adipose tissue remodeling in patients with coronary artery disease and type 2 diabetes mellitus: sub study of the randomized controlled EXCADI trial
Authors: Zaidi Hani , Byrkjeland Rune , Njerve Ida U. , Åkra Sissel , Solheim Svein , Arnesen Harald , Seljeflot Ingebjørg , Opstad Trine B.
Published: December 2019

Background

Investigate effects of long-term exercise on the remodeling markers MMP-9, TIMP-1, EMMPRIN and Galectin-3 in combined type 2 diabetes mellitus (T2DM) and coronary artery disease (CAD) patients. Any associations between these biomarkers and glucometabolic variables were further assessed at baseline.

Methods

137 patients (age 41–81 years, 17.2% females) were included and randomized to a 12-months exercise program or to a control group. Fasting blood samples and subcutaneous adipose tissue (AT) samples were taken at inclusion and after 12-months. The intervention was a combination of aerobic and strength training for a minimum of 150 min per week. Circulating protein levels were measured by ELISA methods and RNA was extracted from AT and circulating leukocytes. Expression levels were relatively quantified by PCR.

Results

After 12 months of intervention, both AT-expression and circulating levels of EMMPRIN were increased in the exercise group (p < 0.05, both) with significant difference in change between the two groups (p < 0.05 both). No significant effect was observed on MMP-9, TIMP-1 and Galectin-3. Levels of TIMP-1 (AT-expression and circulating) were significantly correlated to insulin, and HOMA2- after Bonferroni correction (p = 0.001, by 48 performed correlations).

Conclusion

The increase in levels of EMMPRIN after long-term exercise training, might indicate some degree of AT remodeling in these patients after 12-months of exercise, whether beneficial or not. The remodeling markers were to some extent associated with glucometabolic variables in our population with the combined disease.

Trial registration clinicaltrials.gov, NCT01232608. Registered 2 November 2010
Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity
Authors: Saenz-de-Juano Maria Desemparats , Ivanova Elena , Billooye Katy , Herta Anamaria-Cristina , Smitz Johan , Kelsey Gavin , Anckaert Ellen
Published: December 2019

Background

In vitro follicle culture (IFC), as applied in the mouse system, allows the growth and maturation of a large number of immature preantral follicles to become mature and competent oocytes. In the human oncofertility clinic, there is increasing interest in developing this technique as an alternative to ovarian cortical tissue transplantation and to preserve the fertility of prepubertal cancer patients. However, the effect of IFC and hormonal stimulation on DNA methylation in the oocyte is not fully known, and there is legitimate concern over epigenetic abnormalities that could be induced by procedures applied during assisted reproductive technology (ART).

Results

In this study, we present the first genome-wide analysis of DNA methylation in MII oocytes obtained after natural ovulation, after IFC and after superovulation. We also performed a comparison between prepubertal and adult hormonally stimulated oocytes. Globally, the distinctive methylation landscape of oocytes, comprising alternating hyper- and hypomethylated domains, is preserved irrespective of the procedure. The conservation of methylation extends to the germline differential methylated regions (DMRs) of imprinted genes, necessary for their monoallelic expression in the embryo. However, we do detect specific, consistent, and coherent differences in DNA methylation in IFC oocytes, and between oocytes obtained after superovulation from prepubertal compared with sexually mature females. Several methylation differences span entire transcription units. Among these, we found alterations in Tcf4, Sox5, Zfp521, and other genes related to nervous system development.

Conclusions

Our observations show that IFC is associated with altered methylation at specific set of loci. DNA methylation of superovulated prepubertal oocytes differs from that of superovulated adult oocytes, whereas oocytes from superovulated adult females differ very little from naturally ovulated oocytes. Importantly, we show that regions other than imprinted gDMRs are susceptible to methylation changes associated with superovulation, IFC, and/or sexual immaturity in mouse oocytes. Our results provide an important reference for the use of in vitro growth and maturation of oocytes, particularly from prepubertal females, in assisted reproductive treatments or fertility preservation.
18F-Fluorodeoxyglucose positron emission tomography may not visualize radiation pneumonitis
Authors: Guo Meiying , Qi Liang , Zhang Yun , Shang Dongping , Yu Jinming , Yue Jinbo
Published: December 2019

Background

Radiation pneumonitis is a common and potentially fatal complication of radiotherapy (RT). Some patients with radiation pneumonitis show increases in uptake of fluorodeoxyglucose (FDG) on positron emission tomography (PET), but others do not. The exact relationship between radiation pneumonitis and 18F-FDG PET findings remains controversial.

Methods

We used an animal model of radiation pneumonitis involving both radiation and simulated bacterial infection in Wistar rats. Treatment groups (10 rats/group) were as follows: control, RT-only, lipopolysaccharide (LPS)-only, and RT+LPS. All rats had micro-PET scans at 7 weeks after RT (or sham). Histologic, immunohistochemical, and biochemical analyses were performed to evaluate potential mechanisms.

Results

Irradiated rats had developed radiation pneumonitis at 7 weeks after RT based on pathology and CT scans. Maximum and mean standardized uptake values (SUVmax and SUVmean) at that time were significantly increased in the LPS group (P < 0.001 for both) and the RT+LPS group (P < 0.001 for both) relative to control, but were not different in the RT-only group (P = 0.156 SUVmax and P = 0.304 SUVmean). The combination of RT and LPS increased the expression of the aerobic glycolysis enzyme PKM2 (P < 0.001) and the glucose transporter GLUT1 (P = 0.004) in lung tissues. LPS alone increased the expression of PKM2 (P = 0.018), but RT alone did not affect PKM2 (P = 0.270) or GLUT1 (P = 0.989).

Conclusions

Aseptic radiation pneumonitis could not be accurately assessed by 18F-FDG PET, but was visualized after simulated bacterial infection via LPS. The underlying mechanism of the model of bacterial infection causing increased FDG uptake may be the Warburg effect.
Melatonin-loaded lipid-core nanocapsules protect against lipid peroxidation caused by paraquat through increased SOD expression in Caenorhabditis elegans
Authors: Charão Mariele F. , Goethel Gabriela , Brucker Natália , Paese Karina , Eifler-Lima Vera L. , Pohlmann Adriana R. , Guterres Silvia S. , Garcia Solange C.
Published: December 2019

Background

Melatonin has been described in the literature as a potent antioxidant. However, melatonin presents variable, low bioavailability and a short half-life. The use of polymeric nanoparticulated systems has been proposed for controlled release. Thus, the purpose of this study was to investigate the action of melatonin-loaded lipid-core nanocapsules (Mel-LNC) in the antioxidant system ofCaenorhabditis elegans,and the possible protective effect of this formulation against lipid peroxidation caused by paraquat (PQ).

Methods

The suspensions were prepared by interfacial deposition of the polymer and were physiochemically characterized.C. elegansN2 wild type and transgenic worm CF1553, muls84 [sod-3p::gfp; rol6(su1006)] were obtained from the Caenorhabditis Genetics Center (CGC). The worms were divided into 5 groups: Control, PQ 0.5 mM, PQ 0.5 mM + Mel-LNC 10 μg/mL, PQ + unloaded lipid-core nanocapsules (LNC), and PQ + free melatonin (Mel) 10 μg/mL. The lipid peroxidation was assessed through thiobarbituric acid (TBARS) levels and the fluorescence levels of the transgenic worms expressing GFP were measured.

Results

The LNC and Mel-LNC presented a bluish-white liquid, with pH values of 5.56 and 5.69, respectively. The zeta potential was − 6.4 ± 0.6 and − 5.2 ± 0.2, respectively. The mean particle diameter was 205 ± 4 nm and 203 ± 3 nm, respectively. The total melatonin content was 0.967 mg/ml. The TBARS levels were significantly higher in the PQ group when compared to the control group (p < 0.001). Mel-LNC reduced TBARS levels to similar levels found in the control group. Moreover, only Mel-LNC significantly enhanced the SOD-3 expression (p < 0.05). Mel-LNC was capable of protectingC. elegansfrom lipid peroxidation caused by PQ and this was not observed when free melatonin was used. Moreover, Mel-LNC increased the fluorescence intensity of the transgenic strain that encodes the antioxidant enzyme SOD-3, demonstrating a possible mechanism of protection from PQ-induced damage.

Conclusion

These findings demonstrated that melatonin, when associated with nanocapsules, had improved antioxidant properties and the protective activity against PQ-induced lipid peroxidation could be associated with the activation of antioxidant enzymes by Mel-LNC inC. elegans.
Hormonal status affects plasma exposure of tamoxifen and its main metabolites in tamoxifen-treated breast cancer patients
Authors: Ximenez João Paulo Bianchi , de Andrade Jurandyr Moreira , Marques Maria Paula , Coelho Eduardo Barbosa , Suarez-Kurtz Guilherme , Lanchote Vera Lucia
Published: December 2019

Background

Tamoxifen is considered a prodrug of its active metabolite endoxifen, which is dependent on the CYP2D6 and CYP3A enzymes. Tamoxifen pharmacokinetic variability influences endoxifen exposure and, consequently, its clinical outcome. This study investigated the impact of hormonal status on the pharmacokinetics of tamoxifen and its metabolites in TAM-treated breast cancer patients.

Methods

TAM-treated breast cancer patients (n = 40) previously believed to have CYP3A activity within the normal range based on oral midazolam and phenotyped as CYP2D6 normal metabolizers using oral metoprolol were divided into two groups according to premenopausal (n = 20; aged 35–50 years) or postmenopausal (n = 20; aged 60–79 years) status. All patients were treated with 20 mg/day tamoxifen for at least three months. Serial plasma samples were collected within the 24 h dose interval for analysis of unchanged tamoxifen, endoxifen, 4-hydroxytamoxifen and N-desmethyltamoxifen quantified by LC-MS/MS. CYP activities were assessed using midazolam apparent clearance (CYP3A) and the metoprolol/alfa-hydroxymetoprolol plasma metabolic ratio (CYP2D6). CYP3A4, CYP3A5 and CYP2D6 SNPs and copy number variation were investigated using TaqMan assays.

Results

Postmenopausal status increased steady-state plasma concentrations (Css) of tamoxifen (116.95 vs 201.23 ng/mL), endoxifen (8.01 vs 18.87 ng/mL), N-desmethyltamoxifen (485.16 vs 843.88 ng/mL) and 4-hydroxytamoxifen (2.67 vs 4.11 ng/mL). The final regression models included hormonal status as the only predictor for Css of tamoxifen [β-coef ± SE, p-value (75.03 ± 17.71, p = 0.0001)] and 4-hydroxytamoxifen (1.7822 ± 0.4385, p = 0.0002), while endoxifen Css included hormonal status (8.578 ± 3.402, p = 0.02) and race (11.945 ± 2.836, p = 0.007). For N-desmethyltamoxifen Css, the final model was correlated with hormonal status (286.259 ± 76.766, p = 0.0007) and weight (− 8.585 ± 3.060, p = 0.008).

Conclusion

The premenopausal status was associated with decreased endoxifen plasma concentrations by 135% compared to postmenopausal status. Thus, the endoxifen plasma concentrations should be monitored mainly in the premenopausal period to maintain plasma levels above the efficacy threshold value.

Trial registration

RBR-7tqc7k.