bluuebunny/crossref_metadata_2025 huggingface dataset:
Crafting effective messages to enhance safe infant sleep
Authors: Middlemiss Wendy , Brownstein Naomi C. , Nelson Scott P. , Manchiraju Srikant , Leddy Miranda , Steliotes Nicole , Grzywacz Joseph G.
Published: February 2020

Background:

Health care professionals are continually challenged by the need to provide health information in a way that successfully changes health practices. Research has documented this as a concern in relation to safe infant sleep health campaigns. Often, caregivers' knowledge of recommended practices is not associated with a change in infant sleep choices.

Purpose:

Health campaigns, including most safe infant sleep efforts, often share specific risk factors and steps for avoiding risk, that is, in a verbatim format. Research has shown that caregivers' behavior may be more likely to change when presented with messages based on their general understanding of risk, that is, gist-based format. This research examines caregivers' responses as related to verbatim- and gist-based safe sleep information.

Methods:

Five hundred forty-one caregivers of infants were shown 12 images depicting infants in safe or unsafe sleep spaces. Images varied across three commercially available spaces, infant race, and presence/absence of one policy-based risk factor.

Results:

Differences in caregivers' discernment of safe and unsafe sleep images paralleled reported differences in knowledge of safe sleep recommendations. Discernment of safe/unsafe images was greater for White than Black caregivers, as well as for females in comparison with male caregivers. Gist-based considerations, such as familiarity with the sleeper depicted or infant race, were also associated with caregivers' discernment of safe/unsafe images.

Implications for practice:

Attending to both gist- and verbatim-based knowledge regarding safe infant sleep campaign information may help to effectively facilitate caregivers' ability to always create safe sleep spaces for their infants.
Beyond the discipline: Nurse practitioner members and leaders of interdisciplinary research teams
Authors: Kalmakis Karen A.
Published: February 2020

Complex clinical questions and problems require expertise beyond one discipline to answer or resolve. Research teams that include members with different foundational perspectives across various disciplines are needed. In particular, the growing trend toward technological innovations to help patients self-manage health has been the impetus for the development of interdisciplinary research teams. The goal of this study was to provide guidance for nurse practitioners who are interested in developing effective and successful interdisciplinary teams to complete clinical research projects. A case example is used throughout the study to illustrate the process of interdisciplinary team building. The success of interdisciplinary teams requires team members who are fully invested in the project, available and willing to engage and communicate with other members of the team, and able to form relationships of trust and respect for each discipline's unique contributions to the project.
Development and Pilot Testing of Decision Aid for Shared Decision Making in Barrett’s Esophagus With Low-Grade Dysplasia
Authors: Krishnamoorthi Rajesh , Hargraves Ian , Gopalakrishnan Naveen , Blevins Christopher H. , Priyan Harshith , Johnson Michele L. , Maixner Kristyn A. , Wang Kenneth K. , Katzka David A. , Talwalkar Jayant A. , LeBlanc Annie , Iyer Prasad G.
Published: February 2020

Goals:

To develop an encounter decision aid [Barrett’s esophagus Choice (BE-Choice)] for patients and clinicians to engage in shared decision making (SDM) for management of BE with low-grade dysplasia (BE-LGD) and assess its impact on patient-important outcomes.

Background:

Currently, there are 2 strategies for management of BE-LGD—endoscopic surveillance and ablation. SDM can help patients decide on their preferred management option.

Study:

Phase-I: Patients and clinicians were engaged in a user-centered design approach to develop BE-Choice. Phase-I included review of evidence on BE-LGD management, observation of usual care (UC), creation, field-testing, and iterative development of BE-Choice in clinical settings. Phase-II: Impact of BE-Choice on patient-important outcomes (patient knowledge, decisional conflict, and patient involvement in decision making) was assessed using a controlled before-after study design (UC vs. BE-Choice).

Results:

Phase-I: Initial prototype was designed with observation of 8 clinical encounters. With field-testing, 3 successive iterations were made before finalizing BE-Choice. BE-Choice was paper based and fulfilled the qualifying criteria of International patient decision aid standards. Phase II: 29 patients were enrolled, 8 to UC and 21 to BE-Choice. Compared with UC, use of BE-Choice improved patient knowledge (90.4% vs. 70.5%; P=0.03), decisional comfort (89.6 vs. 71.9; P=0.01), and patient involvement (OPTION score: 27.1 vs. 19.2; P=0.01).

Conclusions:

BE-Choice is a feasible and effective decision aid to promote SDM in the management of BE-LGD. On pilot testing, BE-Choice had promising impact on patient-important outcomes. A larger multicenter trial is needed to confirm our results and promote widespread use of BE-Choice.
County-level Variation in Low Birthweight and Preterm Birth
Authors: Brown Clare C. , Moore Jennifer E. , Felix Holly C. , Stewart M. Kathryn , Tilford J. Mick
Published: February 2020

Background:

Rates of low birthweight and prematurity vary 2-fold across states in the United States, with increased rates among states with higher concentrations of racial minorities. Medicaid expansion may serve as a mechanism to reduce geographic variation within states that expanded, by improving health and access to care for vulnerable populations.

Objective:

The objective of this study was to identify the association of Medicaid expansion with changes in county-level geographic variation in rates of low birthweight and preterm births, overall and stratified by race/ethnicity.

Research Design:

We compared changes in the coefficient of variation and the ratio of the 80th-to-20th percentiles using bootstrap samples (n=1000) of counties drawn separately for all births and for white, black, and Hispanic births, separately.

Measures:

County-level rates of low birthweight and preterm birth.

Results:

Before Medicaid expansion, counties in expansion states were concentrated among quintiles with lower rates of adverse birth outcomes and counties in nonexpansion states were concentrated among quintiles with higher rates. In expansion states, county-level variation, measured by the coefficient of variation, declined for both outcomes among all racial/ethnic categories. In nonexpansion states, geographic variation reduced for both outcomes among Hispanic births and for low birthweight among white births, but increased for both outcomes among black births.

Conclusions:

The decrease in county-level variation in adverse birth outcomes among expansion states suggests improved equity in these states. Further reduction in geographic variation will depend largely on policies or interventions that reduce racial disparities in states that did and did not expand Medicaid.
Mortality and causes of death in people living with HIV in the era of combination antiretroviral therapy compared with the general population in Japan
Authors: Nishijima Takeshi , Inaba Yosuke , Kawasaki Yohei , Tsukada Kunihisa , Teruya Katsuji , Kikuchi Yoshimi , Gatanaga Hiroyuki , Oka Shinichi
Published: February 2020

Objectives:

To determine the mortality and causes of death in people living with HIV (PLHIV) in Japan.

Design:

A prospective cohort study at AIDS Clinical Center, Tokyo, which treats approximately 10% of PLHIV in care in Japan.

Methods:

Either PLHIV who visited our center for the first time between January 2005 and December 2014 or PLHIV who started their regular visit before January 2005 and visited us between January and March 2005 were included and followed by the end of 2016. Causes of death were defined according to the CoDe protocol.

Results:

Two thousand, seven hundred and ninety-seven PLHIV were analysed with total of 18 858 person-years of follow-up, which constitutes 14% of the estimated number of PLHIV in care in Japan. One hundred and sixty-five (5.9%) PLHIV died with all-cause mortality rate of 8.75 per 1000 person-years. All-cause mortality rate for PLHIV in care in Japan was estimated to be 8.75 per 1000 person-years (95% CI 5.53–12.0). Among causes of death, AIDS-defining illnesses accounted for 39% and malignancy contributed to 47%. Standardized mortality ratio (SMR) for all-cause mortality, malignancy-related mortality, and suicide were 5.96 (95% CI 5.05–6.87), 7.76 (95% CI 6.02–9.51), and 3.24 (95% CI 1.54–4.94), respectively. Even among the patients who were diagnosed early or without history of AIDS, SMR was four times higher than the general population.

Conclusion:

Mortality of PLHIV, even among those with early diagnosis, is substantially higher than that of the general population in Japan, highlighting the importance of further efforts towards prevention, early diagnosis and prompt treatment initiation.
The Biointegration of a Porcine Acellular Dermal Matrix in a Novel Radiated Breast Reconstruction Model
Authors: Cottler Patrick S. , Sun Naidi , Thuman Jenna M. , Bielak Kendall M. H. , Salopek Lisa S. , Piñeros-Fernandez Angela , Hu Song , Campbell Chris A.
Published: February 2020

Background

Ideal acellular dermal matrices (ADM) for breast reconstruction exhibit native extracellular matrix (ECM) structure to allow rapid biointegration and appropriate mechanical properties for desired clinical outcomes. In a novel in vivo model of irradiated breast reconstruction, we describe the cellular and vascular ingrowth of Artia, a porcine product chemically prepared to mimic the biomechanics of human ADM, with retained natural ECM structure to encourage cellular ingrowth.

Methods

Utilizing the murine dorsal skinfold model, Artia was implanted into 16 C57bl/6 mice. Eight of the mice received a single dose 35 Gy radiation to the skin, followed by 12 weeks to produce radiation fibrosis and 8 mice served as nonradiated controls. Real-time photoacoustic microscopy of vascular integration and oxygen saturation within the ADM were made over 14 days. At 21 days, vascular ingrowth (CD31), fibroblast scar tissue formation (alpha smooth-muscle actin α-SMA, vimentin), and macrophage function (M2/M1 ratio) were evaluated. Scanning electron microscopy images of Artia were produced to help interpret the potential orientation of cellular and vascular ingrowth.

Results

Repeated photoacoustic microscopy imaging demonstrated vascular ingrowth increasing over 14 days, with a commensurate increase in oxygen saturation within both radiated and nonradiated ADM—albeit at an insignificantly lower rate in the radiated group. By day 21, robust CD31 staining was seen that was insignificantly greater in the nonradiated group. Of the fibroblast markers, vimentin expression was significantly greater in the radiated group (P < 0.05). Macrophage lineage phenotype was consistent with remodeling physiology in both radiated and nonradiated groups. Scanning electron microscopy demonstrated transversely organized collagen fibrils with natural porous ECM structure to allow cellular ingrowth.

Conclusions

Artia demonstrates appropriate biointegration, with increased oxygen saturation by 14 days, consistent with the performance of other collagen substrates in this model. Radiation fibrosis resulted in higher vimentin expression yet did not impact macrophage phenotype while only modestly decreasing Artia biointegration suggesting that ADM may have a role in reconstructive efforts in a radiated setting. Taken together with its enhanced biomechanics, this porcine ADM product is well poised to be clinically applicable to breast reconstruction.
Geographic Variation in Outcomes After Burn Injury
Authors: Espinoza Leda F. , Friedstat Jonathan , Faoro Nicholas , Chang Philip H. , McMullen Kara A. , Simko Laura C. , Esselman Peter , Holavanahalli Radha , Ryan Colleen M. , Schneider Jeffrey C.
Published: February 2020

Background

Geography is an important yet underexplored factor that may influence the care and outcomes of burn survivors. This study aims to examine the impact of geography on physical and psychosocial function after burn injury.

Methods

Data from the Burn Model Systems National Database (1997–2015) were analyzed. Individuals 18 years and older who were alive at discharge were included. Physical and psychosocial functions were assessed at 6, 12, and 24 months postinjury using the following patient-reported outcome measures: Community Integration Questionnaire, Physical Composite Scale and Mental Composite Scale of the 12-Item Short Form Health Survey, Satisfaction with Appearance Scale, and Satisfaction with Life Scale. Descriptive statistics were generated for demographic and medical data, and mixed regression models were used to assess the impact of geography on long-term outcomes.

Results

The study included 469 burn survivors from the Centers for Medicare and Medicaid Services regions 10, 31 from region 8, 477 from region 6, 267 from region 3, and 41 from region 1. Participants differed significantly by region in terms of race/ethnicity, burn size, burn etiology, and acute care length of stay (P < 0.001). In adjusted mixed model regression analyses, scores of all 5 evaluated outcome measures were found to differ significantly by region (P < 0.05).

Conclusions

Several long-term physical and psychosocial outcomes of burn survivors vary significantly by region. This variation is not completely explained by differences in population characteristics. Understanding these geographical differences may improve care for burn survivors and inform future policy and resource allocation.
Urbanization, urbanicity, and depression: a review of the recent global literature
Authors: Sampson Laura , Ettman Catherine K. , Galea Sandro
Published: February 2020

Purpose of review

One of the defining trends of population movement in the last half century has been global urbanization. Depression is the most common mental disorder in the world, but it is unclear how urbanization and urban living affect depression outcomes. Grounded in a previously articulated conceptual framework, we systematically reviewed recently published studies on urbanization, urbanicity, and depression.

Recent findings

Eleven articles were included in this review. Four studies found that living in urban areas was associated with elevated odds or more symptoms of depression. Three studies – all done in China – estimated protective effects of urbanization or urbanicity on depression. Two studies concluded no overall clear association. The remaining two articles stratified by urbanicity and found that greenspace was inversely associated with depression in more densely populated areas relative to rural areas. Other themes discussed included global and national trends such as aging, immigration, and planned urbanization in China, as well as urban living conditions such as traffic noise, air pollution, proximity to roadways, neighborhood social capital, and social cohesion.

Urbanization may affect depression differentially across geographic regions and income levels. More research is needed, particularly in low-income and middle-income countries, and on intersections between urbanization and other emerging global trends.
The importance of faith-based mental healthcare in African urbanized sites
Authors: Ojagbemi Akin , Gureje Oye
Published: February 2020

Purpose of review

This review highlights what current research says about how local beliefs and norms can facilitate expansion of mental healthcare to meet the large unmet need for services in Africa.

Recent findings

In contemporary Africa, religious beliefs exert important influences on mental health as well as the way people with mental illnesses are viewed and cared for. Mental healthcare practices based on traditional and other religious beliefs, and offered by complementary and alternative health providers (CAPs), reflect the people's culture and are often preferentially sought by a majority of the population. Despite important differences in the worldviews of CAPs and biomedical mental healthcare practitioners in regard to causal explanations, there are nevertheless overlaps in the approaches of both sectors to the management of mental health conditions. These overlaps may provide a platform for collaboration and facilitate the scaling-up of evidence-based mental health services to underserved African populations, especially those residing in ever-expanding urban centres.

Faith-based mental healthcare is an important but informal component of the mental health system in much of Africa. Collaboration between its practitioners and biomedical practice may help to bridge the large treatment gap for mental health conditions on the continent.
Transposable elements have contributed human regulatory regions that are activated upon bacterial infection
Authors: Bogdan Lucia , Barreiro Luis , Bourque Guillaume
Published: February 2020

Transposable elements (TEs) are increasingly recognized as important contributors to mammalian regulatory systems. For instance, they have been shown to play a role in the human interferon response, but their involvement in other mechanisms of immune cell activation remains poorly understood. Here, we investigated the profile of accessible chromatin enhanced in stimulated human macrophages using ATAC-seq to assess the role of different TE subfamilies in regulating gene expression following an immune response. We found that both previously identified and new repeats belonging to the MER44, THE1, Tigger3 and MLT1 families provide 14 subfamilies that are enriched in differentially accessible chromatin and found near differentially expressed genes. These TEs also harbour binding motifs for several candidate transcription factors, including important immune regulators AP-1 and NF-κB, present in 96% of accessible MER44B and 83% of THE1C instances, respectively. To more directly assess their regulatory potential, we evaluated the presence of these TEs in regions putatively affecting gene expression, as defined by quantitative trait locus (QTL) analysis, and found that repeats are also contributing to accessible elements near QTLs. Together, these results suggest that a number of TE families have contributed to the regulation of gene expression in the context of the immune response to infection in humans.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
Authors: Farmiloe Grace , Lodewijk Gerrald A. , Robben Stijn F. , van Bree Elisabeth J. , Jacobs Frank M. J.
Published: February 2020

The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated insertions, various classes of TEs have invaded mammalian genomes at multiple timepoints throughout evolution. Even though most of the TE classes in our genome lost the capability to retrotranspose millions of years ago, it remains elusive why the KZNFs that evolved to repress them are still retained in our genome. One hypothesis is that KZNFs become repurposed for other regulatory roles. Here, we find evidence that evolutionary changes in KZNFs provide them not only with the ability to repress TEs, but also to bind to gene promoters independent of TEs. Using KZNF binding site data in conjunction with gene expression values from the Allen Brain Atlas, we show that KZNFs have the ability to regulate gene expression in the human brain in a region-specific manner. Our analysis shows that the expression of KZNFs shows correlation with the expression of their target genes, suggesting that KZNFs have a direct influence on gene expression in the developing human brain. The extent of this regulation and the impact it has on primate brain evolution are still to be determined, but our results imply that KZNFs have become widely integrated into neuronal gene regulatory networks. Our analysis predicts that gene expression networks have been repeatedly innovated throughout primate evolution, continuously gaining new layers of gene regulation mediated by both TEs and KZNFs in our genome.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity
Authors: Kauzlaric Annamaria , Jang Suk Min , Morchikh Mehdi , Cassano Marco , Planet Evarist , Benkirane Monsef , Trono Didier
Published: February 2020

KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation, notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
On transposons and totipotency
Authors: Torres-Padilla Maria-Elena
Published: February 2020

Our perception of the role of the previously considered ‘selfish’ or ‘junk’ DNA has been dramatically altered in the past 20 years or so. A large proportion of this non-coding part of mammalian genomes is repetitive in nature, classified as either satellites or transposons. While repetitive elements can be termed selfish in terms of their amplification, such events have surely been co-opted by the host, suggesting by itself a likely altruistic function for the organism at the subject of such natural selection. Indeed numerous examples of transposons regulating the functional output of the host genome have been documented. Transposons provide a powerful framework for large-scale relatively rapid concerted regulatory activities with the ability to drive evolution. Mammalian totipotency has emerged as one key stage of development in which transposon-mediated regulation of gene expression has taken centre stage in the past few years. During this period, large-scale (epigenetic) reprogramming must be accomplished in order to activate the host genome. In mice and men, one particular element murine endogenous retrovirus with leucine tRNA primer (MERVL) (and its counterpart human ERVL (HERVL)) appears to have acquired roles as a key driving force in this process. Here, I will discuss and interpret the current knowledge and its implications regarding the role of transposons, particularly of long interspersed nuclear elements (LINE-1s) and endogenous retroviruses (ERVs), in the regulation of totipotency.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Transposable elements contribute to the genomic response to insecticides in
Drosophila melanogaster
Authors: Salces-Ortiz Judit , Vargas-Chavez Carlos , Guio Lain , Rech Gabriel E. , González Josefa
Published: February 2020

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link because of to their role in genome function and evolution. In this work, we investigate the contribution of TE insertions to the regulation of gene expression in response to insecticides. We exposed four
Drosophila melanogaster
strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that TEs can contribute to the regulation of gene expression under insecticide exposure by rewiring
cis
-regulatory networks.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
sRNA/L1 retrotransposition: using siRNAs and miRNAs to expand the applications of the cell culture-based LINE-1 retrotransposition assay
Authors: Tristan-Ramos Pablo , Morell Santiago , Sanchez Laura , Toledo Belen , Garcia-Perez Jose L. , Heras Sara R.
Published: February 2020

The cell culture-based retrotransposition reporter assay has been (and is) an essential tool for the study of vertebrate Long INterspersed Elements (LINEs). Developed more than 20 years ago, this assay has been instrumental in characterizing the role of LINE-encoded proteins in retrotransposition, understanding how ribonucleoprotein particles are formed, how host factors regulate LINE mobilization, etc. Moreover, variations of the conventional assay have been developed to investigate the biology of other currently active human retrotransposons, such as Alu and SVA. Here, we describe a protocol that allows combination of the conventional cell culture-based LINE-1 retrotransposition reporter assay with short interfering RNAs (siRNAs) and microRNA (miRNAs) mimics or inhibitors, which has allowed us to uncover specific miRNAs and host factors that regulate retrotransposition. The protocol described here is highly reproducible, quantitative, robust and flexible, and allows the study of several small RNA classes and various retrotransposons. To illustrate its utility, here we show that siRNAs to Fanconi anaemia proteins (FANC-A and FANC-C) and an inhibitor of miRNA-20 upregulate and downregulate human L1 retrotransposition, respectively.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Transposable elements as a potent source of diverse
cis
-regulatory sequences in mammalian genomes
Authors: Sundaram Vasavi , Wysocka Joanna
Published: February 2020

Eukaryotic gene regulation is mediated by
cis
-regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner. A large proportion of eukaryotic genomes, including at least half of the human genome, are composed of transposable elements (TEs), which in their ancestral form carried their own
cis
-regulatory sequences able to exploit the host
trans
environment to promote TE transcription and facilitate transposition. Although not all present-day TE copies have retained this regulatory function, the preexisting regulatory potential of TEs can provide a rich source of
cis
-regulatory innovation for the host. Here, we review recent evidence documenting diverse contributions of TE sequences to gene regulation by functioning as enhancers, promoters, silencers and boundary elements. We discuss how TE-derived enhancer sequences can rapidly facilitate changes in existing gene regulatory networks and mediate species- and cell-type-specific regulatory innovations, and we postulate a unique contribution of TEs to species-specific gene expression divergence in pluripotency and early embryogenesis. With advances in genome-wide technologies and analyses, systematic investigation of TEs'
cis
-regulatory potential is now possible and our understanding of the biological impact of genomic TEs is increasing.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Arabidopsis
RNA Polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Authors: Panda Kaushik , McCue Andrea D. , Slotkin R. Keith
Published: February 2020

The plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements (TEs), with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA methylation back to TEs to reinforce the boundary between heterochromatin and euchromatin. In the male gametophytic phase of the plant life cycle, pollen, Pol IV switches to generating primarily 21–22 nt siRNAs, but the biogenesis and function of these siRNAs have been enigmatic. In contrast to being pollen-specific, we identified that Pol IV generates these 21–22 nt siRNAs in sporophytic tissues, likely from the same transcripts that are processed into the more abundant 24 nt siRNAs. The 21–22 nt forms are specifically generated by the combined activities of DICER proteins DCL2/DCL4 and can participate in RNA-directed DNA methylation. These 21–22 nt siRNAs are also loaded into ARGONAUTE1 (AGO1), which is known to function in post-transcriptional gene regulation. Like other plant siRNAs and microRNAs incorporated into AGO1, we find a signature of genic mRNA cleavage at the predicted target site of these siRNAs, suggesting that Pol IV-generated 21–22 nt siRNAs may function to regulate gene transcript abundance. Our data provide support for the existing model that in pollen Pol IV functions in gene regulation.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae
Authors: Szuróczki Sára , Abbaszade Gorkhmaz , Szabó Attila , Bóka Károly , Schumann Peter , Tóth Erika
Published: February 2020

The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family

Verrucomicrobiaceae

of the phylum

Verrucomicrobia

, and its closest relatives are

Verrucomicrobium spinosum

DSM 4136T (94.38 %) and

Roseimicrobium gellanilyticum

DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22–28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family

Verrucomicrobiaceae

, for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.
Developing bio-technical reliability among future researchers and industrial work-force in developing countries: a success story
Authors: Acharya Kshitish K
Published: February 2020

A common problem in the biotech sector of developing countries is that a large portion of students attain a poor conceptual understanding of the basic theory and/or lack proficiency in basic laboratory skills even as they complete higher studies such as a master’s degree. A small scale solution was developed in the form of a unique post-graduate diploma program that imparted reliable skills in students with good theoretical knowledge. The course of 6 to 8 months duration, with an optional 6 months internship, was successfully conducted for 8 batches. Most students of this course inculcated the right laboratory practices. This was evident by safe operations, and precise as well as accurate results of quantitative experiments conducted by them. They learned to work independently as well as in teams. They could create and follow standard operating procedures, and contribute to general laboratory maintenance. Every student also designed, prepared and conducted routine molecular biology experiments. The following aspects are suggested for successfully dealing with the patchy and varied capacities of life science students during higher (post bachelor’s) studies: a) careful selection of students, b) training with prioritized objectives, c) attention to basic lab-practices, d) opportunities to self-learn, e) structured group discussions, f) teacher(s) with genuine interest and passion, g) reasonable infrastructure, and h) maintaining a good student-instructor ratio. The course objectives, structure, teaching methods, and experiences are presented here along with some of the relevant data, including statistics about improvement in the precision and accuracy in experimental results by students. Limitations in this course and a general critical perspective of the routine higher education have also been discussed briefly.
Divide et Impera: Identification of Small-Molecule Inhibitors of HCMV Replication Interfering with Dimerization of DNA Polymerase Processivity Factor UL44
Authors: Ghassabian Hanieh , Falchi Federico , Antonio Veronica Di , Timmoneri Martina , Mercorelli Beatrice , Loregian Arianna , Palù Giorgio , Alvisi Gualtiero
Published: February 2020

Human cytomegalovirus (HCMV) is a leading cause of severe diseases in immunocompromised individuals, including AIDS and transplanted patients, and in congenitally infected newborns. Despite the availability of several antiviral drugs, their utility is limited by poor bioavailability, toxicity, and resistant strains emergence. Therefore, it is crucial to identify new targets of therapeutic intervention. The dimerization of HCMV DNA polymerase processivity factor UL44 plays an essential role in the viral life cycle being required fororiLyt-dependent DNA replication. We validated the existence of UL44 homodimers bothin vitroand in living cells by a variety of approaches, including GST pulldown, thermal shift, FRET and BRET assays. Dimerization occurred with an affinity comparable to that of the UL54/UL44 interaction, and was impaired by amino acid substitutions at the dimerization interface. Subsequently, we performed anin-silicoscreening to select 18 small molecules (SMs) potentially interfering with UL44 homodimerization. Antiviral assays using recombinant HCMV TB4-UL83-YFP in the presence of the 18 selected SMs led to the identification of four active SMs. The most active one also inhibited AD169 in plaque reduction assays, and impaired replication of an AD169-GFP reporter virus and its ganciclovir-resistant counterpart to a similar extent. As assessed by Western blotting experiments, treatment of infected cells specifically reduced viral gene expression starting from 48 h post infection, consistent with activity on viral DNA synthesis. Therefore, SMs inhibitors of UL44 dimerization could represent a new class of HCMV inhibitors, alternative to those targeting the DNA polymerase catalytic subunit or the viral terminase complex.

IMPORTANCE

HCMV is a ubiquitous infectious agent causing life-lasting infections in humans. HCMV primary infections and reactivation in non-immunocompetent individuals often result in life-threatening conditions. Antiviral therapy mainly targets the DNA polymerase catalytic subunit UL54 and is often limited by toxicity and selection of drug-resistant viral strains, making the identification of new targets of therapeutic intervention crucial for a successful management of HCMV infections. The significance of our work is in identifying the dimerization of the DNA polymerase processivity factor UL44 as an alternative antiviral target. We could show that full length UL44 dimerizes in a cellular context with high affinity and that such interaction could be targeted by small molecules, thus inhibiting the replication of several HCMV strains, including a drug-resistant mutant. Thus, our work could pave the way to the development of a new class of anti-HCMV compounds that act by targeting UL44 dimerization.
Comparison between conventional electrodes and ultrasound monitoring to measure TMS evoked muscle contraction
Authors: Kaczmarczyk Isabella , Rawji Vishal , Rothwell John C. , Hodson-Tole Emma , Sharma Nikhil
Published: February 2020

Background

Transcranial Magnetic stimulation (TMS) is a non-invasive cortical stimulation method that has been widely employed to explore cortical physiology in health and a range of diseases. At the core of many TMS protocols is the measurement of evoked muscle contractions using surface electromyography (sEMG). While sEMG is appropriate for many superficial muscles such as abductor pollicis brevis (ABP) and first dorsal interosseous (FDI), there are situations where the study of less accessible muscles may be of interest. Peripheral ultrasound is a non-invasive method that could provide a solution. We explore the relationship between TMS evoked sMEP and TMS evoked muscle contractions measured with muscle ultrasound. We hypothesise that in a healthy population, we expect a positive correlation between EMG and ultrasound measures.

Methods

In 10 participants we performed a standard TMS recruitment curve and simultaneously measured MEP and peripheral muscle ultrasound (pUS). We targeted the following muscles: biceps (BI), first dorsal interosseous (FDI), tibialis anterior (TA) and the tongue (TO).

Results

We report a very close relationship between the MEP and pUS contraction. Resting motor threshold (RMT) measurements and recruitment curves are consistent in sEMG and pUS. A key aspect of this work is the ability to examine clinically relevant muscles that are difficult to probe using surface EMG electrodes, such as the tongue.

Conclusion

We find that TMS muscle contractions can be measured with muscle ultrasound in superficial and deep muscles, enable additional, previously hard to study muscles, to be investigated. This could be valuable for allowing TMS to be used to explore a new range of muscles in disorders such as ALS. In muscles less accessible by sEMG, such as the tongue, it may be possible to use pUS as an alternative output. This may be useful in conditions such as ALS and stroke that can differentially affect the tongue.
Single cell mutational profiling delineates clonal trajectories in myeloid malignancies
Authors: Miles Linde A. , Bowman Robert L. , Merlinsky Tiffany R. , Csete Isabelle S. , Ooi Aik , Durruthy-Durruthy Robert , Bowman Michael , Famulare Christopher , Patel Minal A. , Mendez Pedro , Ainali Chrysanthi , Manivannan Mani , Sahu Sombeet , Goldberg Aaron D. , Bolton Kelly , Zehir Ahmet , Rampal Raajit , Carroll Martin P. , Meyer Sara E. , Viny Aaron D. , Levine Ross L.
Published: February 2020

Myeloid malignancies, including acute myeloid leukemia (AML), arise from the proliferation and expansion of hematopoietic stem and progenitor cells which acquire somatic mutations. Bulk molecular profiling studies on patient samples have suggested that somatic mutations are obtained in a step-wise fashion, where mutant genes with high variant allele frequencies (VAFs) are proposed to occur early in disease development and mutations with lower VAFs are thought to be acquired later in disease progression1–3. Although bulk sequencing informs leukemia biology and prognostication, it cannot distinguish which mutations occur in the same clone(s), accurately measure clonal complexity and clone size, or offer definitive evidence of mutational order. To elucidate the clonal framework of myeloid malignancies, we performed single cell mutational profiling on 146 samples from 123 patients. We found AML is most commonly comprised of a small number of dominant clones, which in many cases harbor co-occurring mutations in epigenetic regulators. Conversely, mutations in signaling genes often occur more than once in distinct subclones consistent with increasing clonal diversity. We also used these data to map the clonal trajectory of each patient and found that specific mutation combinations (FLT3-ITD+NPM1c) synergize to promote clonal expansion and dominance. We combined cell surface protein expression with single cell mutational analysis to map somatic genotype and clonal architecture with immunophenotype. Our studies of clonal architecture at a single cell level provide novel insights into the pathogenesis of myeloid transformation and how clonal complexity contributes to disease progression.
Mapping microglia and astrocytes activationin vivousing diffusion MRI
Authors: Garcia-Hernandez Raquel , Cerdán Cerdá Antonio , Carpena Alejandro Trouve , Drakesmith Mark , Koller Kristin , Jones Derek K. , Canals Santiago , De Santis Silvia
Published: February 2020

Glia, and particularly microglia, are increasingly implicated in the pathophysiology of psychiatric and neurodegenerative disorders. However, to date the only methods for imaging these cells in vivo involve either invasive procedures (e.g. multi-photon imaging in rodents) or TSPO-PET radiotracers, which afford low resolution and specificity, since TSPO expresses across multiple cell types. Here, we present a non-invasive diffusion-weighted MRI method to image changes in glia morphometryin vivo. Using two rat models of neuroinflammation, with and without neurodegeneration, we demonstrate that diffusion-weighted MRI carries the fingerprint of microglia and astrocytes activation, and that specific signatures from each population can be quantified non-invasively. We demonstrate that the method can further detect glia proliferation, and provide a quantitative account of neuroinflammation regardless of the existence of a concomitant neuronal loss. We prove the translational value of the approach showing significant correlations between MRI and histological microglia markers measured across different brain regions in humans. This framework holds the potential to transform basic and clinical research by providing a tool to clarify the role of inflammation in health and disease across the lifespan.
Inhibiting LXRαPhosphorylation in Hematopoietic Cells Reduces Inflammation and Attenuates Atherosclerosis and Obesity
Authors: Voisin Maud , Shrestha Elina , Rollet Claire , Josefs Tatjana , Barrett Tessa J. , Chang Hye Rim , Ruoff Rachel , Nikain Cyrus A. , Garabedian Michela L. , Brown Emily J. , Goldberg Ira J. , Pineda-Torra Inés , Fisher Edward A. , Garabedian Michael J.
Published: February 2020

Atherosclerosis and obesity share pathological features including inflammation mediated by innate and adaptive immune cells. LXRα, a nuclear receptor, plays a central role in the transcription of inflammatory and lipid metabolic genes. LXRαis modulated by phosphorylation at serine 196 (LXRαpS196), however, the functional consequences of LXRαpS196 in hematopoietic cell precursors in atherosclerosis and obesity have not been investigated. To assess the importance of LXRαphosphorylation, bone marrow from LXRαWT and S196A mice was transplanted intoLdlr-/-mice, which were fed a high fat, high cholesterol diet prior to evaluation of atherosclerosis and obesity. Plaques from S196A mice showed reduced inflammatory monocyte recruitment, lipid accumulation, and macrophage proliferation. Expression profiling of CD68+ cells from S196A mouse plaques revealed downregulation of pro-inflammatory genes and upregulation of mitochondrial genes characteristic of anti-inflammatory macrophages. Furthermore, S196A mice had lower body weight and less visceral adipose tissue; this was associated with transcriptional reprograming of the adipose tissue macrophages and resolution of inflammation resulting in less fat accumulation within adipocytes. Thus, reducing LXRαpS196 in hematopoietic cells attenuates atherosclerosis and obesity by reprogramming the transcriptional activity of LXRαto an anti-inflammatory phenotype.
Understanding the Effect of Left Prefrontal Stimulation on Positive Symptoms of Schizophrenia: A Dynamic Causal Modeling Study of Ultra-high field (7-Tesla) Resting-state fMRI
Authors: Limongi Roberto , Mackinley Michael , Dempster Kara , Khan Ali R. , Gati Joseph S. , Palaniyappan Lena
Published: February 2020

Repetitive transcranial magnetic stimulation (rTMS), when applied to left dorsolateral prefrontal cortex (LDLPFC), reduces negative symptoms of schizophrenia, but has no effect on positive symptoms. In a small number of cases, it appears to worsen the severity of positive symptoms. It has been hypothesized that high frequency rTMS of the LDLPFC might increase the dopaminergic neurotransmission by driving the activity of the left striatum in the basal ganglia (LSTR)—increasing striatal dopaminergic activity. This hypothesis relies on the assumption that either the frontal-striatal connection or the intrinsic frontal and/or striatal connections covary with the severity of positive symptoms. The current work aimed to evaluate this assumption by studying the association between positive and negative symptoms severity and the effective connectivity within the frontal and striatal network using dynamic causal modeling (DCM) of ultra-high field (7 Tesla) resting state fMRI in a sample of 19 first episode psychosis (FEP) subjects. We found that of all core symptoms of schizophrenia, only delusions are strongly associated with the fronto striatal circuitry. Stronger intrinsic inhibitory tone of LDLPFC and LSTR, as well as a pronounced backward inhibition of the LDLPFC on the LSTR related to the severity of delusions. We interpret that an increase in striatal dopaminergic tone that underlies delusional symptoms, is likely associated with increased prefrontal inhibitory tone, strengthening the frontostriatal ‘brake’. Furthermore, based on our model, we propose that lessening of positive symptoms could be achieved by means of continuous theta-burst or low frequency (1Hz) rTMS of the prefrontal area.
Chemogenetic stimulation of mouse central amygdala corticotropin-releasing factor neurons: Effects on cellular and behavioral correlates of alcohol dependence
Authors: Kreifeldt Max , Herman Melissa A , Sidhu Harpreet , de Macedo Giovana C , Shahryari Roxana , Roberto Marisa , Contet Candice
Published: February 2020

Background

Corticotropin-releasing factor (CRF) signaling in the central nucleus of the amygdala (CeA) plays a critical role in rodent models of excessive alcohol drinking. However, the source of CRF acting in the CeA during alcohol withdrawal remains to be identified. In the present study, we hypothesized that CeA CRF interneurons may represent a behaviorally relevant source of CRF to the CeA increasing motivation for alcohol via negative reinforcement.

Methods

We tested this hypothesis in male mice and used chemogenetics to stimulate CeA CRF neurons in vitro and in vivo.

Results

We first observed that Crh mRNA expression in the anterior part of the mouse CeA, at the junction with the interstitial nucleus of the posterior limb of the anterior commissure, correlates positively with alcohol intake in C57BL/6J males with a history of chronic binge drinking. We then found that chemogenetic activation of CeA CRF neurons in Crh-IRES-Cre mouse brain slices increases gamma-aminobutyric acid (GABA) release in the medial CeA in part via CRF1 receptor activation, indicating local CRF release. While chemogenetic stimulation of CeA CRF neurons exacerbated novelty-induced feeding suppression, as seen in C57BL/6J males withdrawn from chronic intermittent alcohol inhalation, it had no effect on voluntary alcohol consumption, following either acute or chronic manipulation.

Conclusions

Altogether, these findings indicate that hyperactivity of CeA CRF neurons may contribute to elevated CeA GABA levels and negative affect during alcohol withdrawal but is not sufficient to drive alcohol intake escalation in dependent mice.