bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-Molecule Tracking of DNA Translocases in Bacillus subtilis Reveals Strikingly Different Dynamics of SftA, SpoIIIE, and FtsA
Authors: El Najjar Nina , El Andari Jihad , Kaimer Christine , Fritz Georg , Rösch Thomas C. , Graumann Peter L. 
Published: February 2018

ABSTRACT

Like many bacteria,
Bacillus subtilis
possesses two DNA translocases that affect chromosome segregation at different steps. Prior to septum closure, nonsegregated DNA is moved into opposite cell halves by SftA, while septum-entrapped DNA is rescued by SpoIIIE. We have used single-molecule fluorescence microscopy and tracking (SMT) experiments to describe the dynamics of the two different DNA translocases, the cell division protein FtsA and the glycolytic enzyme phosphofructokinase (PfkA), in real time. SMT revealed that about 30% of SftA molecules move through the cytosol, while a fraction of 70% is septum bound and static. In contrast, only 35% of FtsA molecules are static at midcell, while SpoIIIE molecules diffuse within the membrane and show no enrichment at the septum. Several lines of evidence suggest that FtsA plays a role in septal recruitment of SftA: an
ftsA
deletion results in a significant reduction in septal SftA recruitment and a decrease in the average dwell time of SftA molecules. FtsA can recruit SftA to the membrane in a heterologous eukaryotic system, suggesting that SftA may be partially recruited via FtsA. Therefore, SftA is a component of the division machinery, while SpoIIIE is not, and it is otherwise a freely diffusive cytosolic enzyme
in vivo
. Our developed SMT script is a powerful technique to determine if low-abundance proteins are membrane bound or cytosolic, to detect differences in populations of complex-bound and unbound/diffusive proteins, and to visualize the subcellular localization of slow- and fast-moving molecules in live cells.

IMPORTANCE
DNA translocases couple the late events of chromosome segregation to cell division and thereby play an important role in the bacterial cell cycle. The proteins fall into one of two categories, integral membrane translocases or nonintegral translocases. We show that the membrane-bound translocase SpoIIIE moves slowly throughout the cell membrane in
B. subtilis
and does not show a clear association with the division septum, in agreement with the idea that it binds membrane-bound DNA, which can occur through cell division across nonsegregated chromosomes. In contrast, SftA behaves like a soluble protein and is recruited to the division septum as a component of the division machinery. We show that FtsA contributes to the recruitment of SftA, revealing a dual role of FtsA at the division machinery, but it is not the only factor that binds SftA. Our work represents a detailed
in vivo
study of DNA translocases at the single-molecule level.
Influence of Eimeria falciformis Infection on Gut Microbiota and Metabolic Pathways in Mice
Authors: Huang Guangping , Zhang Sixin , Zhou Chunxue , Tang Xiaoli , Li Chao , Wang Chaoyue , Tang Xinming , Suo Jingxia , Jia Yonggen , El-Ashram Saeed , Yu Zhengquan , Cai Jianping , Gupta Nishith , Suo Xun , Liu Xianyong 
Published: February 2018

ABSTRACT

Coccidiosis, caused by different species of
Eimeria
parasites, is an economically important disease of poultry and livestock worldwide. Here we report previously unknown alterations in the gut microbes and metabolism of BALB/c mice infected with
Eimeria falciformis
. Specifically, we observed a significant shift in the abundance of cecal bacteria and disrupted metabolism in parasitized animals. The relative abundances of
Lachnospiraceae
bacterium NK4A136,
Ruminiclostridium
,
Alistipes
, and
Lactobacillus
declined in response to
E. falciformis
infection, whereas
Escherichia
,
Shigella
,
Helicobacter
,
Klebsiella
, and
Bacteroides
were increased. Carbohydrate and amino acid metabolites in the serum samples of infected mice were significantly altered compared to naïve controls. Levels of amino acids, including asparagine, histidine,
l
-cysteine, tryptophan, lysine, glycine, serine, alanine, proline, ornithine, methionine, and valine, decreased on day 7 postinfection before returning to baseline on day 14. In addition, increased levels of indolelactate and mannitol and a reduced amount of oxalic acid indicated impaired carbon metabolism upon parasitic infection. These data demonstrate that intestinal coccidial infection perturbs the microbiota and disrupts carbon and nitrogen metabolism.
A Plasmodium Parasite with Complete Late Liver Stage Arrest Protects against Preerythrocytic and Erythrocytic Stage Infection in Mice
Authors: Vaughan Ashley M. , Sack Brandon K. , Dankwa Dorender , Minkah Nana , Nguyen Thao , Cardamone Hayley , Kappe Stefan H. I. 
Published: February 2018

ABSTRACT

Genetically attenuated malaria parasites (GAP) that arrest during liver stage development are powerful immunogens and afford complete and durable protection against sporozoite infection. Late liver stage-arresting GAP provide superior protection against sporozoite challenge in mice compared to early live stage-arresting attenuated parasites. However, very few late liver stage-arresting GAP have been generated to date. Therefore, identification of additional loci that are critical for late liver stage development and can be used to generate novel late liver stage-arresting GAPs is of importance. We further explored genetic attenuation in
Plasmodium yoelii
by combining two gene deletions,
PlasMei2
and
liver-specific protein 2
(
LISP2
), that each cause late liver stage arrest with various degrees of infrequent breakthrough to blood stage infection. The dual gene deletion resulted in a synthetic lethal phenotype that caused complete attenuation in a highly susceptible mouse strain.
P. yoelii
plasmei2
−
lisp2
−
arrested late in liver stage development and did not persist in livers beyond 3 days after infection. Immunization with this GAP elicited robust protective antibody responses in outbred and inbred mice against sporozoites, liver stages, and blood stages as well as eliciting protective liver-resident T cells. The immunization afforded protection against both sporozoite challenge and blood stage challenge. These findings provide evidence that completely attenuated late liver stage-arresting GAP are achievable via the synthetic lethal approach and might enable a path forward for the creation of a completely attenuated late liver stage-arresting
P. falciparum
GAP.
Functional Overlap of
hetP
and
hetZ
in Regulation of Heterocyst Differentiation in Anabaena sp. Strain PCC 7120
Authors: Zhang He , Wang Shuai , Wang Yali , Xu Xudong 
Published: February 2018

ABSTRACT

HetR plays a key role in regulation of heterocyst differentiation and patterning in
Anabaena
. It directly regulates genes involved in heterocyst differentiation (such as
hetP
and
hetZ
), genes involved in pattern formation (
patA
), and many others. In this study, we investigated the functional relationship of
hetP
and
hetZ
and their role in HetR-dependent cell differentiation. Coexpression of
hetP
and
hetZ
from the promoter of
ntcA
, which encodes the global nitrogen regulator, enabled a
hetR
mutant to form heterocysts with low aerobic nitrogenase activity. Overexpression of
hetZ
restored heterocyst differentiation in a
hetP
mutant and vice versa. Overexpression of
hetR
restored heterocyst formation in either a
hetP
or a
hetZ
mutant but not in a
hetZ hetP
double mutant. The functional overlap of
hetP
and
hetZ
was further confirmed by reverse transcription-quantitative PCR (RT-qPCR) and transcriptomic analyses of their effects on gene expression. In addition, yeast two-hybrid and pulldown assays showed the interaction of HetZ with HetR. HetP and HetZ are proposed as the two major factors that control heterocyst formation in response to upregulation of
hetR
.

IMPORTANCE
Heterocyst-forming cyanobacteria contribute significantly to N
2
fixation in marine, freshwater, and terrestrial ecosystems. Formation of heterocysts enables this group of cyanobacteria to fix N
2
efficiently under aerobic conditions. HetR, HetP, and HetZ are among the most important factors involved in heterocyst differentiation. We present evidence for the functional overlap of
hetP
and
hetZ
and for the key role of the HetR-HetP/HetZ circuit in regulation of heterocyst differentiation. The regulatory mechanism based on HetR, HetP, and HetZ is probably conserved in all heterocyst-forming cyanobacteria.
Diagnosing Invasive Candidiasis
Authors: Clancy Cornelius J. , Nguyen M. Hong 
Published: February 2018

ABSTRACT

Cultures are negative in ∼50% of invasive candidiasis. Data are emerging for the performance of nonculture tests such as mannan/antimannan,
Candida albicans
germ tube antibody, 1,3-β-
d
-glucan, PCR, and the T2Candida panel in diagnosing both candidemia and deep-seated candidiasis. In most settings, positive predictive values of nonculture test are low, and negative predictive values are high. For tests to be useful, clinicians must understand the pretest likelihood of invasive candidiasis and test performance for the most common disease manifestation in a given patient. This paper reviews nonculture
Candida
diagnostics and discusses how they might be used effectively in patient care.
Intranasal Live Influenza Vaccine Priming Elicits Localized B Cell Responses in Mediastinal Lymph Nodes
Authors: Jegaskanda Sinthujan , Mason Rosemarie D. , Andrews Sarah F. , Wheatley Adam K. , Zhang Ruijun , Reynoso Glennys V. , Ambrozak David R. , Santos Celia P. , Luke Catherine J. , Matsuoka Yumiko , Brenchley Jason M. , Hickman Heather D. , Talaat Kawsar R. , Permar Sallie R. , Liao Hua-Xin , Yewdell Jonathan W. , Koup Richard A. , Roederer Mario , McDermott Adrian B. , Subbarao Kanta 
Published: February 2018

ABSTRACT
Pandemic live attenuated influenza vaccines (pLAIV) prime subjects for a robust neutralizing antibody response upon subsequent administration of a pandemic inactivated subunit vaccine (pISV). However, a difference was not detected in H5-specific memory B cells in the peripheral blood between pLAIV-primed and unprimed subjects prior to pISV boost. To investigate the mechanism underlying pLAIV priming, we vaccinated groups of 12 African green monkeys (AGMs) with H5N1 pISV or pLAIV alone or H5N1 pLAIV followed by pISV and examined immunity systemically and in local draining lymph nodes (LN). The AGM model recapitulated the serologic observations from clinical studies. Interestingly, H5N1 pLAIV induced robust germinal center B cell responses in the mediastinal LN (MLN). Subsequent boosting with H5N1 pISV drove increases in H5-specific B cells in the axillary LN, spleen, and circulation in H5N1 pLAIV-primed animals. Thus, H5N1 pLAIV primes localized B cell responses in the MLN that are recalled systemically following pISV boost. These data provide mechanistic insights for the generation of robust humoral responses via prime-boost vaccination.

IMPORTANCE
We have previously shown that pandemic live attenuated influenza vaccines (pLAIV) prime for a rapid and robust antibody response on subsequent administration of inactivated subunit vaccine (pISV). This is observed even in individuals who had undetectable antibody (Ab) responses following the initial vaccination. To define the mechanistic basis of pLAIV priming, we turned to a nonhuman primate model and performed a detailed analysis of B cell responses in systemic and local lymphoid tissues following prime-boost vaccination with pLAIV and pISV. We show that the nonhuman primate model recapitulates the serologic observations from clinical studies. Further, we found that pLAIVs induced robust germinal center B cell responses in the mediastinal lymph node. Subsequent boosting with pISV in pLAIV-primed animals resulted in detection of B cells in the axillary lymph nodes, spleen, and peripheral blood. We demonstrate that intranasally administered pLAIV elicits a highly localized germinal center B cell response in the mediastinal lymph node that is rapidly recalled following pISV boost into germinal center reactions at numerous distant immune sites.
Adaptive design clinical trials: a review of the literature and ClinicalTrials.gov
Authors: Bothwell Laura E , Avorn Jerry , Khan Nazleen F , Kesselheim Aaron S 
Published: February 2018

ObjectivesThis review investigates characteristics of implemented adaptive design clinical trials and provides examples of regulatory experience with such trials.DesignReview of adaptive design clinical trials in EMBASE, PubMed, Cochrane Registry of Controlled Clinical Trials, Web of Science and ClinicalTrials.gov. Phase I and seamless Phase I/II trials were excluded. Variables extracted from trials included basic study characteristics, adaptive design features, size and use of independent data monitoring committees (DMCs) and blinded interim analyses. We also examined use of the adaptive trials in new drug submissions to the Food and Drug Administration (FDA) and European Medicines Agency (EMA) and recorded regulators’ experiences with adaptive designs.Results142 studies met inclusion criteria. There has been a recent growth in publicly reported use of adaptive designs among researchers around the world. The most frequently appearing types of adaptations were seamless Phase II/III (57%), group sequential (21%), biomarker adaptive (20%), and adaptive dose-finding designs (16%). About one-third (32%) of trials reported an independent DMC, while 6% reported blinded interim analysis. We found that 9% of adaptive trials were used for FDA product approval consideration, and 12% were used for EMA product approval consideration. International regulators had mixed experiences with adaptive trials. Many product applications with adaptive trials had extensive correspondence between drug sponsors and regulators regarding the adaptive designs, in some cases with regulators requiring revisions or alterations to research designs.ConclusionsWider use of adaptive designs will necessitate new drug application sponsors to engage with regulatory scientists during planning and conduct of the trials. Investigators need to more consistently report protections intended to preserve confidentiality and minimise potential operational bias during interim analysis.
Is socioeconomic segregation of the poor associated with higher premature mortality under the age of 60? A cross-sectional analysis of survey data in major Indian cities
Authors: Chandola Tarani , Mikkilineni Sitamma , Chandran Anil , Bandyopadhyay Souvik Kumar , Zhang Nan , Bassanesi Sergio Luiz 
Published: February 2018

ObjectivesAlthough urbanisation is generally associated with poverty reduction in low-income and middle-income countries, it also results in increased socioeconomic segregation of the poor. Cities with higher levels of socioeconomic segregation tend to have higher mortality rates, although the evidence is based on ecological associations. The paper examines whether socioeconomic segregation of the poor is associated with higher under-60 years (‘premature’) mortality risk in Indian cities and whether this association is confounded by contextual and compositional sociodemographic and socioeconomic factors.Setting and participantsA population representative sample of over one million from 39 427 households living in 1876 urban wards within 59 Indian districts (cities) from the third (2008) District Level Household Survey (DLHS-3).Primary outcome and other measuresThe outcome was any death under the age of 60 reported by households in the preceding 4years of the DLHS-3. Socioeconomic segregation, estimated at the district (city) level, was measured using an isolation index of the poor and the index of dissimilarity.ResultsPoor households living in cities where the poor were more isolated had higher probabilities of premature mortality than poor households living in cities where the poor were less isolated. In contrast, it did not matter whether rich households lived in more or less socioeconomically segregated cities. A 1 SD increase in the isolation index was associated with an absolute increase of 1.1% in the probability of premature mortality for the poorest households.ConclusionIncreasing segregation of the poor may result in higher premature mortality. As low-income and middle-income countries become increasingly urbanised, there is a risk that this may lead to increased segregation of the poor as well as increased premature mortality.
Sequelae of multidrug-resistant tuberculosis: protocol for a systematic review and meta-analysis
Authors: Alene Kefyalew Addis , Clements Archie C A , McBryde Emma S , Jaramillo Ernesto , Lonnroth Knut , Shaweno Debebe , Viney Kerri 
Published: February 2018

IntroductionThe sequelae of multidrug-resistant tuberculosis (MDR-TB) are poorly understood and inconsistently reported. We will aim to assess the existing evidence for the clinical, psychological, social and economic sequelae of MDR-TB and to assess the health-related quality of life in patients with MDR-TB.Methods and analysisWe will perform a systematic review and meta-analysis of published studies reporting sequelae of MDR-TB. We will search PubMed, SCOPUS, ProQuest, Web of Science and PsychINFO databases up to 5 September 2017. MDR-TB sequelae will include any clinical, psychological, social and economic effects as well as health-related quality of life that occur after MDR-TB treatment or illness. Two researchers will screen the titles and abstracts of all citations identified in our search, extract data, and assess the scientific quality using standardised formats. Providing there is appropriate comparability in the studies, we will use a random-effects meta-analysis model to produce pooled estimates of MDR-TB sequelae from the included studies. We will stratify the analyses based on treatment regimen, comorbidities (such as HIV status and diabetes mellitus), previous TB treatment history and study setting.Ethics and disseminationAs this study will be based on published data, ethical approval is not required. The final report will be disseminated through publication in a peer-reviewed scientific journal and will also be presented at relevant conferences.PROSPERO registration numberCRD42017073182.
Severity and management of postabortion complications among women in Zimbabwe, 2016: a cross-sectional study
Authors: Madziyire Mugove Gerald , Polis Chelsea B , Riley Taylor , Sully Elizabeth A , Owolabi Onikepe , Chipato Tsungai 
Published: February 2018

ObjectivesAbortion complications cause significant morbidity and mortality. We aimed to assess the severity and factors associated with abortion complications (induced or spontaneous), and the management of postabortion care (PAC) in Zimbabwe.DesignProspective, facility-based 28 day survey among women seeking PAC and their providers.Setting127 facilities in Zimbabwe with the capacity to provide PAC, including all central and provincial hospitals, and a sample of primary health centres (30%), district/general/mission hospitals (52%), private (77%) and non-governmental organisation (NGO) (68%) facilities.Participants1002 women presenting with abortion complications during the study period.Main outcome measuresSeverity of abortion complications and associated factors, delays in care seeking, and clinical management of complications.ResultsOverall, 59% of women had complications classified as mild, 19% as moderate, 19% as severe, 3% as near miss and 0.2% died. A median of 47 hours elapsed between experiencing complication and receiving treatment; many delays were due to a lack of finances. Women who were rural, younger, not in union, less educated, at later gestational ages or who had more children were significantly more likely to have higher severity complications. Most women were treated by doctors (91%). The main management procedure used was dilatation and curettage/dilatation and evacuation (75%), while 12% had manual vacuum aspiration (MVA) or electrical vacuum aspiration and 11% were managed with misoprostol. At discharge, providers reported that 43% of women received modern contraception.ConclusionZimbabwean women experience considerable abortion-related morbidity, particularly young, rural or less educated women. Abortion-related morbidity and concomitant mortality could be reduced in Zimbabwe by liberalising the abortion law, providing PAC in primary health centres, and training nurses to use medical evacuation with misoprostol and MVA. Regular in-service training on PAC guidelines with follow-up audits are needed to ensure compliance and availability of equipment, supplies and trained staff.
Differing associations for sport versus occupational physical activity and cardiovascular risk
Authors: Ferrario Marco Mario , Roncaioli Mattia , Veronesi Giovanni , Holtermann Andreas , Clays Els , Borchini Rossana , Cavicchiolo Marco , Grassi Guido , Cesana Giancarlo 
Published: February 2018

ObjectivesWe investigate the independent and interacting long-term associations of occupational physical activity (OPA) and sport physical activity (SpPA) with the incidence of coronary heart disease (CHD) and cardiovascular diseases (CVD; CHD plus ischaemic stroke) in North Italian male workers.Methods3574 employed men aged 25–64 years, free of CVD at baseline, recruited in three population-based and one factory-based cohorts, were included in the analysis. The Baecke Questionnaire was used to assess OPA and SpPA in ‘minutes per week’ of moderate or vigorous PA. We estimated the associations between different domains of PA and the endpoints, adjusting for major CVD risk factors, using Cox models.ResultsDuring a median follow-up of 14 years, 135 and 174 first CHD and CVD events, fatal and non-fatal, occurred. Compared with the intermediate OPA tertile, the HRs for CHD among low and high OPA workers were 1.66 (95% CI 1.06 to 2.59) and 1.18 (0.72 to 1.94), respectively (P value=0.07). Decreasing trends in CHD and CVD rates across increasing levels of SpPA were also found, with an HR for CVD of 0.68 (0.46 to 0.98) for intermediate/recommended SpPA compared with poor SpPA. We also found a statistically significant SpPA-OPA interaction, and the protective effect of SpPA was only found among sedentary workers, for both endpoints. Conversely, high OPA workers with intermediate/recommended SpPA levels had increased CHD and CVD rates compared with the poor SpPA category.ConclusionsOur results provide further evidence on the health paradox of OPA, with higher CVD rates among workers with intense PA at work. Moreover, the protective effect on CVDs of SpPA is prominent in sedentary workers, but it attenuates and even reverses in moderate and strenuous OPA workers.