bluuebunny/crossref_metadata_2025 huggingface dataset:
Disparities in Cardiac Rehabilitation Participation in the United States
Authors: Sun Enid Y. , Jadotte Yuri T. , Halperin William
Published: September 2016

PURPOSE:

Phase 2 cardiac rehabilitation (CR) is a class I recommendation for all patients following an acute cardiac event or cardiac surgery according to the The American Heart Association and the American College of Cardiology Foundation. Studies have shown that there are differences in cardiac rehabilitation participation rates between sociodemographic groups. The purpose of this systematic review and meta-analyses was to synthesize quantitative data on the relationship between outpatient cardiac rehabilitation (OCR) attendance and various sociodemographic factors.

METHODS:

We conducted a search of PubMed, PsycINFO, CINAHL, Google Scholar, Dissertations & Theses A&I, and conference abstracts for observational studies conducted in the United States that fit our inclusion criteria. A total of 21 studies were included in our final review and meta-analyses.

RESULTS:

Our meta-analyses showed that overall, attenders were younger than nonattenders (mean difference=−3.74 years, 95% CI =−5.87 to −1.61) and the odds of participation were lower among females (OR = 0.59; 95% CI = 0.51-0.69), individuals with a high school degree or less (OR = 0.67; 95% CI = 0.50-0.91), and the uninsured or self-payers (OR = 0.32; 95% CI = 0.14-0.71). Full- or part-time employees were more likely to participate than those not employed (OR = 1.45; 95% CI = 1.08-1.95).

CONCLUSIONS:

Our systematic review and meta-analyses showed that there are significant sociodemographic disparities in CR participation. On the basis of this knowledge, clinicians and policy makers should focus on identifying and eliminating barriers to participation.
Systematic Review of Postural Assessment in Individuals With Obstructive Respiratory Conditions
Authors: Lee Annemarie L. , Zabjek Karl , Goldstein Roger S. , Brooks Dina
Published: September 2016

PURPOSE:

Changes in posture in individuals with an obstructive respiratory disease have been reported, but the extent of these deviations and their clinical significance is not well understood. This study aimed to systematically review the literature of the skeletal structural alignment in children and adults with an obstructive respiratory disease, describe the measurement techniques used, and determine the clinical relevance of any alternations.

METHODS:

Observational cohort or cross-sectional studies of postural assessment were identified, with 2 reviewers independently assessing study quality.

RESULTS:

A total of 18 studies were included, 12 in cystic fibrosis (CF), 5 in asthma, and 1 in chronic obstructive pulmonary disease (COPD). The overall quality assessment rating was 12.6 out of 16. Increased thoracic kyphosis or scoliosis was found in both children and adults with CF. Increased shoulder protraction and elevation were evident in asthma and COPD, although changes in spinal curvature were variable. The clinical impact of postural changes was diverse, with an inconsistent influence on lung function. A mix of methods was applied for postural assessment.

CONCLUSIONS:

Skeletal structural malalignment appears to be present in some individuals with an obstructive respiratory disease, although the extent of alterations and its clinical impact is variable. Photogrammetry is used to provide a comprehensive assessment of posture in these populations.
Short-Term Experience with Off-Pump Versus On-Pump Implantation of the HeartWare Left Ventricular Assist Device
Authors: Gregoric Igor D. , Radovancevic Rajko , Akay Mehmet H. , Jezovnik Mateja K. , Nathan Sriram , Patel Manish , Patel Jayeshkumar A. , Nedelcu Elena , Nguyen Nghia D. , Loyalka Pranav , Kar Biswajit
Published: September 2016

Implantation of left ventricular assist devices while avoiding cardiopulmonary bypass (CPB) may decrease bleeding and improve postoperative recovery. To understand the effectiveness of this approach, we reviewed the charts of 26 patients who underwent HeartWare left ventricular assist device (HVAD) implantation without use of CPB (off-CPB group) and 22 patients who had HVAD implanted with CPB (CPB group) with an emphasis on the 30 day postoperative period. Preoperatively, both groups had similar demographic, functional, and hemodynamic characteristics. Off-CPB patients had significantly shorter surgery times than CPB patients, 188.5 (161.5–213.3) min versus 265.0 (247.5–299.5) min, respectively; p < 0.001. Blood transfusion requirements during surgery and within the postoperative 48 hour period were significantly lower in the off-CPB group than in the CPB group (odds ratio: 5.9; 95% confidence interval: 1.1–31.1, p = 0.042). Compared with the CPB group, the off-CPB group patients had a shorter intubation time, 21 (17.4–48.5) hours versus 41 (20.6–258.4) hours; p = 0.042. Intensive care unit stay was 7.0 (4.75–13.5) days for off-CPB versus 10.0 (6.0–19.0) days for CPB (p = 0.256). The off-CPB approach allows HVAD to be implanted quickly with significantly less perioperative bleeding and transfusion requirements and facilitates postoperative rehabilitation.
Time in Therapeutic Range for Left Ventricular Assist Device Patients Anticoagulated With Warfarin: A Correlation to Clinical Outcomes
Authors: Halder Laura C. , Richardson Laura B. , Garberich Ross F. , Zimbwa Peter , Bennett Mosi K.
Published: September 2016

Left ventricular assist devices (LVADs) require anticoagulation therapy with vitamin K antagonists to reduce the risk of thrombotic events. The quality of anticoagulation may be assessed by the time in therapeutic range (TTR). We analyzed a retrospective cohort of LVAD patients at a single institution from January 2012 to September 2014. Primary outcomes included TTR during the study time period and TTR 30 days preceding a bleeding or thrombotic event. Fifty-one patients (mean age 57.0 ± 14.6 years; 78% male) had an overall TTR of 52%. Median international normalized ratio (INR) preceding a bleeding and thrombotic event was 2.7 and 2.2, respectively (p = 0.049). In the 30 days before an event, patients with a bleeding event were more likely to be on low-dose aspirin (37% vs. 12%; p = 0.018) and spend a higher proportion of time above therapeutic range (41% vs. 17%; p = 0.007) compared with those with thrombotic events. The association between a greater percentage of time above therapeutic range in the 30 days before a bleeding event demonstrates the importance of avoiding a supratherapeutic INR in the LVAD patient population and the usefulness of TTR as a measure of the overall quality of anticoagulation and monitoring in an LVAD cohort.
Pancreatic Gastrointestinal Stromal Tumor
Authors: Liu Zhen , Tian Yangzi , Xu Guanghui , Liu Shushang , Guo Man , Lian Xiao , Fan Daiming , Zhang Hongwei , Feng Fan
Published: September 2016

Goals:

The present study aimed to investigate the clinicopathologic features and prognosis of pancreatic gastrointestinal stromal tumor (GIST).

Background:

Reports on clinicopathologic features and prognosis of pancreatic GIST are limited due to the extremely rare incidence.

Study:

One case of pancreatic GIST from our center and 44 cases reported in MEDLINE were enrolled in this study. Clinicopathologic features and prognosis of pancreatic GISTs were analyzed and compared with 297 gastric GISTs from our center.

Results:

The most common location was head of pancreas (38.5%). The majority of pancreatic GISTs exceeded 5 cm (74.4%), displayed cystic or mixed imaging features (56.4%), and were high risk (85.7%). The 5-year disease-free survival (DFS) and disease-specific survival rates were 66.1% and 95.8%, respectively. Mitotic index was the only risk factor for DFS of pancreatic GISTs. The distribution of tumor size, histologic type and National Institutes of Health risk category were significantly different between pancreatic and gastric GISTs. The 5-year DFS rate of pancreatic GISTs was significantly lower than that of gastric GISTs. Multivariate analysis showed that location was an independent prognostic factor for DFS between pancreatic and gastric GISTs.

Conclusions:

The most common location was head of pancreas. The majority of pancreatic GISTs were large and highly malignant. Pancreatic GISTs differed significantly from gastric GISTs in respect to clinicopathologic features. The DFS of pancreatic GISTs was worse than that of gastric GISTs.
Fresh versus cryopreserved oocyte donation
Authors: Kushnir Vitaly A. , Gleicher Norbert
Published: September 2016

Purpose of review

Utilization of cryopreserved instead of fresh donor oocytes has rapidly increased in recent years. Whether treatment outcomes are comparable has, however, remained controversial.

Recent findings

More than 24% of initiated oocyte donation cycles in the USA during 2013–2014 involved previously cryopreserved oocytes. The use of cryopreserved-donated oocytes may simplify logistics and lower costs per treatment cycle. Whether cryopreserved donor oocytes also lower costs per live birth is still undetermined as they result in lower live birth rates in comparison to fresh donor oocyte cycles. National data regarding the safety of donated oocytes, including miscarriage rates and neonatal health outcomes, are lacking.

Currently available data on cryopreserved-donated oocytes are incomplete and, therefore, still insufficient to claim equivalency between fresh and cryopreserved donor oocytes. Until sufficient data are available, patients should be advised about advantages and disadvantages of both methods of oocyte donation, and the use of cryopreserved oocytes should be considered only with caution and appropriate informed consent. Because banking of donated human oocytes facilities their commercial trade, it challenges basic ethical considerations, which have been the basis of oocyte donation since its inception.
Pharmacogenomic approaches to lipid-regulating trials
Authors: Bertrand Marie-Jeanne , Dubé Marie-Pierre , Tardif Jean-Claude
Published: September 2016

Purpose of review

Randomized clinical outcome trials are costly, long, and often yield neutral or modestly positive results, and these issues have impeded cardiovascular drug development in the past decade. Despite the significant reduction of cardiovascular morbidity and mortality with statins, substantial residual risk of major cardiovascular events remains. This could be because of the difficulty of demonstrating benefits of new drugs in addition to the current standard of care in unselected populations as well as the interindividual variability in drug response. Pharmacogenomics is a promising avenue for the development of novel or failed drugs and for the repurposing of other medications.

Recent findings

Several variants were identified in genes that were associated with the effects of statins on plasma lipids. Genomic studies of mutations in genes that encode drug targets have the potential to inform on the link between drug therapy acting on those targets and clinical outcomes. Recently, ADCY9 gene variants were shown to be significantly associated with responses to dalcetrapib in terms of clinical outcomes, atherosclerosis imaging, cholesterol efflux, and inflammation, which provided support for the conduct of a new prospective clinical trial in a genetically determined population.

Pharmacogenomics hold great potential in future lipid trials to decrease failure rates in drug development and to identify patients who will respond with greater benefits and smaller risk.
The future of lipid guidelines
Authors: Robinson Jennifer G.
Published: September 2016

Purpose of review

Factors influencing guideline development may result in paradigm shifts in treatment recommendations.

Recent findings

The 2013 American College of Cardiology/American Heart Association cholesterol guideline provides an example of how new methodology and findings from randomized clinical trials can result in a paradigm shift in the approach to cardiovascular prevention. This guideline moved away from a treat to cholesterol goal approach. Based on strong evidence of a net benefit in randomized clinical trials, statins were recommended to reduce atherosclerotic cardiovascular disease risk in four groups of patients most likely to benefit. In addition, improved risk prediction equations and shared decision-making were recommended for guiding statin initiation in primary prevention patients with LDL cholesterol ≤190 mg/dl. Future guidelines will address the role of nonstatins for cardiovascular prevention. Improved risk prediction in statin-treated patients with and without cardiovascular disease, estimation of the potential for net benefit, and shared decision-making should be integral components of the next guideline.

Guidelines will continue to evolve as new data accumulate. New treatment paradigms will be needed to optimize patient outcomes.
Filaggrin and Periostin Expression Is Altered in Eosinophilic Esophagitis and Normalized With Treatment
Authors: Politi Ekaterini , Angelakopoulou Aspasia , Grapsa Dimitra , Zande Maria , Stefanaki Kalliopi , Panagiotou Ioanna , Roma Eleftheria , Syrigou Ekaterini
Published: September 2016

Objectives:

Previous data have suggested that filaggrin (FLG) and periostin (POSTN) genes may be dysregulated in eosinophilic esophagitis (EoE). We aimed to further evaluate the expression patterns of FLG and POSTN proteins in esophageal tissue samples of patients with EoE, as compared to those of patients with gastroesophageal reflux disease (GERD) and normal controls.

Methods:

A total of 61 prospectively collected cases, including 40 children with EoE and 21 children with GERD, and a control group of 14 sex‐ and age‐matched healthy children were enrolled. Patients with EoE were treated with skin testing–driven elimination diet and/or corticosteroids. The immunohistochemical expression of FLG and POSTN was evaluated in esophageal biopsies obtained from patients and controls, and the results were correlated with EoE‐related clinicopathological parameters.

Results:

Positive FLG and negative POSTN staining were observed in all esophageal biopsies from normal controls. In contrast, FLG and POSTN stained negative and positive, respectively, in all pretreatment biopsies obtained from patients with EoE, whereas FLG and POSTN stained positive in 57.1% and 95.2% of GERD cases, respectively (P < 0.001). A statistically significant decrease of the proportion of cases with negative FLG and positive POSTN staining was observed from the first (pretreatment) to the second (post‐treatment) biopsy in the subgroup of patients with EoE (P < 0.001 in both correlations).

Conclusions:

FLG and POSTN expression may be downregulated and upregulated, respectively, in the esophageal mucosa of patients with active EoE, and these changes may be restored with treatment in a significant percentage of cases.
Echinococcosis
Authors: Taxy Jerome B. , Gibson William E. , Kaufman Michael W.
Published: September 2016

Echinococcus is the smallest of the major tapeworms. Humans are incidental hosts who become infected by exposure to soil contaminated with ova from the feces of the canine definitive hosts. The major species are E. granulosus (cystic echinococcosis) and E. multilocularis (alveolar or sylvatic echinococcosis), both common worldwide but unusual and not reportable in the United States. Human disease is characterized by slowly growing visceral cystic masses often containing daughter cysts and hydatid sand. In nonendemic areas, the clinical evaluation includes imaging, serology, and surgery; metastatic tumor is a major consideration. The diagnosis depends on the morphologic recognition of scolices and hooklets, albeit degenerated, within the cyst or attached to the cyst wall. Highly suggestive cyst wall features are an acellular hyaline lining surrounded by focally calcific fibrous tissue and chronic inflammation. We report 7 patients encountered in the Chicago area (5 E. granulosus, 2 E. multilocularis) who presented with cystic masses affecting the liver, lung, soft tissue, and spleen. The initial diagnosis was established or suggested by intraoperative evaluation of cyst fluid or cyst wall histopathology. Organism parts were found in 5 cases; 1 patient had a hyalinized cyst wall with a positive IgG (enzyme-linked immunosorbent assay), and 1 had a positive Western blot and a 30-year history of treatment. Treatment included cyst resection, hepatic lobectomy, intraoperative cyst injection, and benzimidazole therapy. There was 1 death. In a nonendemic area, the awareness of the pathologist to the possibility of this disease will exclude a neoplasm and facilitate prompt antihelminthic treatment.
Anatomical Relationships of Burch Colposuspension Sutures
Authors: Kinman Casey L. , Agrawal Anubhav , Deveneau Nicolette E. , Meriwether Kate V. , Herring Nicole R. , Francis Sean L.
Published: September 2016

Objectives

The prevalent use of minimally invasive midurethral slings for the treatment of stress urinary incontinence in the last several decades has resulted in fewer Burch procedures being performed and diminished surgical experience in performing the Burch colposuspension. However, recent antimesh media has resulted in more patients requesting nonmesh anti-incontinence procedures and a subsequent need for surgeons to refamiliarize themselves with the Burch procedure and its relevant anatomy. The objective of this study was to evaluate the relationships of Burch sutures to surrounding neurovascular anatomic structures in the human cadaver.

Methods

The retropubic space of 11 unembalmed female cadavers was dissected, and a Burch procedure performed. The distance from the Burch sutures’ location through both Cooper’s ligament and the vagina to the obturator neurovascular bundle and external iliac vessels was measured.

Results

The mean distance from the most lateral stitch in Cooper’s ligament to the obturator bundle was 25.9 ± 7.6 mm and to the external iliac vessels was 28.9 ± 9.3 mm, and in some instances, these structures were less than 1.5 cm away.

Conclusions

The obturator bundle and external iliac lie, on average, within 3 cm of sutures placed during a Burch colposuspension. Knowledge of these anatomical relationships is valuable when dissecting the space of Retzius and placing sutures for a Burch to avoid injury.
Perioperative Complications and Cost of Vaginal, Open Abdominal, and Robotic Surgery for Apical Vaginal Vault Prolapse
Authors: Anand Mallika , Weaver Amy L. , Fruth Kristin M. , Borah Bijan J. , Klingele Christopher J. , Gebhart John B.
Published: September 2016

Objectives

To determine the rate of perioperative complications and cost associated with Mayo-McCall culdoplasty (MMC), open abdominal sacrocolpopexy (ASC), and robotic sacrocolpopexy (RSC) for posthysterectomy vaginal vault prolapse.

Methods

We retrospectively searched for the records of patients undergoing posthysterectomy apical vaginal prolapse surgery (MMC, ASC, or RSC) between January 1, 2000, and June 30, 2012, at our institution. For all patients identified, perioperative complications, length of hospital stay, and inpatient costs to patients were abstracted from the medical records and compared by procedure. Inverse–probability-of-procedure weighting using propensity scores was used to obtain less-biased comparisons of outcomes between procedures.

Results

A total of 512 patients met the inclusion criteria (174 MMC, 237 ASC, and 101 RSC). Using inverse-probability weighting, the MMC group had a significantly lower intraoperative complication rate (3.3% vs 11.6% for ASC, 3.4% vs 24.1% for RSC), median operative time (94 vs 217 min for ASC, 100 vs 228 min for RSC), and median cost (US $8,776 vs $12,695 for ASC, US $8,773 vs $13,107 for RSC) than the ASC and RSC groups (all P < 0.01). In addition, the MMC group had significantly fewer postoperative grade 3+ complications than the RSC group (1.1% vs 9.4%, P < 0.01).

Conclusions

In the treatment of posthysterectomy vaginal vault prolapse, MMC is associated with decreased non–urinary tract infection, less perioperative morbidity, and lower cost to patients compared with sacrocolpopexy.
Current management of low-grade gliomas
Authors: Hottinger Andreas F. , Hegi Monika E. , Baumert Brigitta G.
Published: September 2016

Purpose of review

The management of patients suffering from low-grade gliomas (LGGs) remains a challenge in absence of a definite curative therapy. The median survival is highly variable, from 2 years (high-risk disease) to over 15 years (low risk). The aim of this review is to provide a practical step-by-step evaluation of the available treatment options for patients with LGGs.

Recent findings

Next to clinical prognostic markers, both the isocitrate dehydrogenase (IDH) mutation status and the status of 1p/19q codeletion are key prognostic factors for the optimal management of patients with LGG. Two recent randomized phase III clinical trials were performed in LGGs. They first compared the efficacy of radiation versus temozolomide (TMZ) chemotherapy in high-risk LGGs. The second trial compared radiation versus radiation combined with procarbazine, lomustine and vincristine chemotherapy.

Regarding molecular prognostic factors, IDH wild-type LGGs have the worst prognosis, independent of therapy, whereas patients with mutated IDH, codeleted 1p/19q LGGs fared best regarding progression-free survival (PFS). In high-risk LGGs, PFS is similar regardless of whether patients have been treated with radiation or TMZ. In the second trial, patients who were treated with combination radiation and chemotherapy showed significant longer overall survival.
L-form bacteria, chronic diseases and the origins of life
Authors: Errington Jeff , Mickiewicz Katarzyna , Kawai Yoshikazu , Wu Ling Juan
Published: September 2016

The peptidoglycan cell wall is widely conserved across the bacterial domain, suggesting that it appeared early in the evolution of bacteria. It is normally essential but under certain conditions wall-deficient or ‘L-form’ bacteria can be isolated. In
Bacillus subtilis
this normally requires two genetic changes. The first, exemplified by mutations shutting down wall precursor synthesis, works by increasing membrane synthesis. This promotes the unusual form of proliferation used by L-forms, involving a range of relatively disorganized membrane blebbing or vesiculation events. The secondary class of mutations probably work by relieving oxidative stress that L-forms may incur due to their unbalanced metabolism. Repression or inhibition of cell wall precursor synthesis can stimulate the L-form transition in a wide range of bacteria, of both Gram-positive and -negative lineages. L-forms are completely resistant to most antibiotics working specifically on cell wall synthesis, such as penicillins and cephalosporins, consistent with the many reports of their involvement in various chronic diseases. They are potentially important in biotechnology, because lack of a wall can be advantageous in a range of production or strain improvement applications. Finally, L-forms provide an interesting model system for studying early steps in the evolution of cellular life.

This article is part of the themed issue ‘The new bacteriology’.
Shedding light on biology of bacterial cells
Authors: Schneider Johannes P. , Basler Marek
Published: September 2016

To understand basic principles of living organisms one has to know many different properties of all cellular components, their mutual interactions but also their amounts and spatial organization. Live-cell imaging is one possible approach to obtain such data. To get multiple snapshots of a cellular process, the imaging approach has to be gentle enough to not disrupt basic functions of the cell but also have high temporal and spatial resolution to detect and describe the changes. Light microscopy has become a method of choice and since its early development over 300 years ago revolutionized our understanding of living organisms. As most cellular components are indistinguishable from the rest of the cellular contents, the second revolution came from a discovery of specific labelling techniques, such as fusions to fluorescent proteins that allowed specific tracking of a component of interest. Currently, several different tags can be tracked independently and this allows us to simultaneously monitor the dynamics of several cellular components and from the correlation of their dynamics to infer their respective functions. It is, therefore, not surprising that live-cell fluorescence microscopy significantly advanced our understanding of basic cellular processes. Current cameras are fast enough to detect changes with millisecond time resolution and are sensitive enough to detect even a few photons per pixel. Together with constant improvement of properties of fluorescent tags, it is now possible to track single molecules in living cells over an extended period of time with a great temporal resolution. The parallel development of new illumination and detection techniques allowed breaking the diffraction barrier and thus further pushed the resolution limit of light microscopy. In this review, we would like to cover recent advances in live-cell imaging technology relevant to bacterial cells and provide a few examples of research that has been possible due to imaging.

This article is part of the themed issue ‘The new bacteriology’.
When pathogenic bacteria meet the intestinal microbiota
Authors: Rolhion Nathalie , Chassaing Benoit
Published: September 2016

The intestinal microbiota is a large and diverse microbial community that inhabits the intestinal tract, containing about 100 trillion bacteria from 500–1000 distinct species that, collectively, provide multiple benefits to the host. The gut microbiota contributes to nutrient absorption and maturation of the immune system, and also plays a central role in protection of the host from enteric bacterial infection. On the other hand, many enteric pathogens have developed strategies in order to be able to outcompete the intestinal community, leading to infection and/or chronic diseases. This review will summarize findings describing the complex relationship occurring between the intestinal microbiota and enteric pathogens, as well as how future therapies can ultimately benefit from such discoveries.

This article is part of the themed issue ‘The new bacteriology’.
InhibitingMycobacterium tuberculosiswithin and without
Authors: Cole Stewart T.
Published: September 2016

Tuberculosis remains a scourge of global health with shrinking treatment options due to the spread of drug-resistant strains ofMycobacterium tuberculosis. Intensive efforts have been made in the past 15 years to find leads for drug development so that better, more potent drugs inhibiting new targets could be produced and thus shorten treatment duration. Initial attempts focused on repurposing drugs that had been developed for other therapeutic areas but these agents did not meet their goals in clinical trials. Attempts to find new lead compounds employing target-based screens were unsuccessful as the leads were inactive againstM. tuberculosis. Greater success was achieved using phenotypic screening against live tubercle bacilli and this gave rise to the drugs bedaquiline, pretomanid and delamanid, currently in phase III trials. Subsequent phenotypic screens also uncovered new leads and targets but several of these targets proved to be promiscuous and inhibited by a variety of seemingly unrelated pharmacophores. This setback sparked an interest in alternative screening approaches that mimic the disease state more accurately. Foremost among these were cell-based screens, often involving macrophages, as these should reflect the bacterium's niche in the host more faithfully. A major advantage of this approach is its ability to uncover functions that are central to infection but not necessarily required for growthin vitro. For instance, inhibition of virulence functions mediated by the ESX-1 secretion system severely attenuates intracellularM. tuberculosis, preventing intercellular spread and ultimately limiting tissue damage. Cell-based screens have highlighted the druggability of energy production via the electron transport chain and cholesterol metabolism. Here, I review the scientific progress and the pipeline, but warn against over-optimism due to the lack of industrial commitment for tuberculosis drug development and other socio-economic factors.

This article is part of the themed issue ‘The new bacteriology’.
RNA polymerase supply and flux through the
lac
operon in
Escherichia coli
Authors: Sendy Bandar , Lee David J. , Busby Stephen J. W. , Bryant Jack A.
Published: September 2016

Chromatin immunoprecipitation, followed by quantification of immunoprecipitated DNA, can be used to measure RNA polymerase binding to any DNA segment in
Escherichia coli
. By calibrating measurements against the signal from a single RNA polymerase bound at a single promoter, we can calculate both promoter occupancy levels and the flux of transcribing RNA polymerase through transcription units. Here, we have applied the methodology to the
E. coli
lactose operon promoter. We confirm that promoter occupancy is limited by recruitment and that the supply of RNA polymerase to the lactose operon promoter depends on its location in the
E. coli
chromosome. Measurements of RNA polymerase binding to DNA segments within the lactose operon show that flux of RNA polymerase through the operon is low, with, on average, over 18 s elapsing between the passage of transcribing polymerases. Similar low levels of flux were found when semi-synthetic promoters were used to drive transcript initiation, even when the promoter elements were changed to ensure full occupancy of the promoter by RNA polymerase.

This article is part of the themed issue ‘The new bacteriology’.
Molecular phenotyping of infection-associated small non-coding RNAs
Authors: Barquist Lars , Westermann Alexander J. , Vogel Jörg
Published: September 2016

Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a ‘molecular phenotype’, defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.

This article is part of the themed issue ‘The new bacteriology’.
Hypothesis: type I toxin–antitoxin genes enter the persistence field—a feedback mechanism explaining membrane homoeostasis
Authors: Gerdes Kenn
Published: September 2016

Bacteria form persisters, cells that are tolerant to multiple antibiotics and other types of environmental stress. Persister formation can be induced either stochastically in single cells of a growing bacterial ensemble, or by environmental stresses, such as nutrient starvation, in a subpopulation of cells. In many cases, the molecular mechanisms underlying persistence are still unknown. However, there is growing evidence that, in enterobacteria, both stochastically and environmentally induced persistence are controlled by the second messenger (p)ppGpp. For example, the ‘alarmone’ (p)ppGpp activates Lon, which, in turn, activates type II toxin–antitoxin (TA) modules to thereby induce persistence. Recently, it has been shown that a type I TA module,
hokB
/
sokB
, also can induce persistence. In this case, the underlying mechanism depends on the universally conserved GTPase Obg and, surprisingly, also (p)ppGpp. In the presence of (p)ppGpp, Obg stimulates
hokB
transcription and induces persistence. HokB toxin expression is under both negative and positive control: SokB antisense RNA inhibits
hokB
mRNA translation, while (p)ppGpp and Obg together stimulate
hokB
transcription. HokB is a small toxic membrane protein that, when produced in modest amounts, leads to membrane depolarization, cell stasis and persistence. By contrast, overexpression of HokB disrupts the membrane potential and kills the cell. These observations raise the question of how expression of HokB is regulated. Here, I propose a homoeostatic control mechanism that couples HokB expression to the membrane-bound RNase E that degrades and inactivates SokB antisense RNA.

This article is part of the themed issue ‘The new bacteriology’.
Logistic proliferation of cells in scratch assays is delayed
Authors: Jin Wang , Shah Esha T , Penington Catherine J , McCue Scott W , Maini Philip K , Simpson Matthew J
Published: September 2016

Scratch assays are used to study how a population of cells recolonises a vacant region on a two-dimensional substrate after a cell monolayer is scratched. These experiments are used in many applications including drug design for the treatment of cancer and chronic wounds. To provide insights into the mechanisms that drive scratch assays, solutions of continuum reaction–diffusion models have been calibrated to data from scratch assays. These models typically include a logistic source term to describe carrying capacity-limited proliferation, however the choice of using a logistic source term is often made without examining whether it is valid. Here we study the proliferation of PC-3 prostate cancer cells in a scratch assay. All experimental results for the scratch assay are compared with equivalent results from a proliferation assay where the cell monolayer is not scratched. Visual inspection of the time evolution of the cell density away from the location of the scratch reveals a series of sigmoid curves that could be naively calibrated to the solution of the logistic growth model. However, careful analysis of the per capita growth rate as a function of density reveals several key differences between the proliferation of cells in scratch and proliferation assays. Our findings suggest that the logistic growth model is valid for the entire duration of the proliferation assay. On the other hand, guided by data, we suggest that there are two phases of proliferation in a scratch assay; at short time we have adisturbance phasewhere proliferation is not logistic, and this is followed by agrowth phasewhere proliferation appears to be logistic. These two phases are observed across a large number of experiments performed at different initial cell densities. Overall our study shows that simply calibrating the solution of a continuum model to a scratch assay might produce misleading parameter estimates, and this issue can be resolved by making a distinction between the disturbance and growth phases. Repeating our procedure for other scratch assays will provide insight into the roles of the disturbance and growth phases for different cell lines and scratch assays performed on different substrates.
A fast multi-locus random-SNP-effect EMMA for genome-wide association studies
Authors: Wen Yang-Jun , Zhang Hanwen , Zhang Jin , Feng Jian-Ying , Huang Bo , Dunwell Jim M. , Zhang Yuan-Ming , Wu Rongling
Published: September 2016

Although the mixed linear model (MLM) such as efficient mixed model association (EMMA), has been widely used in genome-wide association studies (GWAS), relatively little is known about fast and efficient algorithms to implement multi-locus GWAS. To address this issue, we report a fast multi-locus random-SNP-effect EMMA (FASTmrEMMA). In this method, a new matrix transformation was constructed to obtain a new genetic model that includes only quantitative trait nucleotide (QTN) variation and normal residual error; letting the number of nonzero eigenvalues be one and fixing the polygenic-to-residual variance ratio was used to increase computing speed. All the putative QTNs with the ≤0.005 P-values in the first step of the new method were included in one multi-locus model for true QTN detection. Owing to the multi-locus feature, the Bonferroni correction is replaced by a less stringent selection criterion. Results from analyses of both simulated and real data showed that FASTmrEMMA is more powerful in QTN detection, model fit and robustness, has less bias in QTN effect estimation, and requires less running time than the current single- and multi-locus methodologies for GWAS, such as E-BAYES, SUPER, EMMA, CMLM and ECMLM. Therefore, FASTmrEMMA provides an alternative for multi-locus GWAS.
TheMstncmpt-Dl1abcmutation impairs secretion of promyostatin
Authors: Vásárhelyi Viktor , Trexler Mária , Patthy László
Published: September 2016

Hypermuscularity of Compact mouse is caused by a 12-bp deletion in the myostatin gene, but the molecular basis of decreased myostatin activity is unclear since the deletion does not affect the integrity of the growth factor domain. In the present work we show that the deletion causes misfolding and impaired secretion of myostatin precursor with concomitant decrease in myostatin activity. We suggest that some modifier genes that influence the expression of the Compact phenotype of myostatin mutantMstnCmpt-dl1Abcmice may exert their action through their role in the Unfolded Protein Response.
Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division
Authors: Bisson Filho Alexandre W. , Hsu Yen-Pang , Squyres Georgia R. , Kuru Erkin , Wu Fabai , Jukes Calum , Dekker Cees , Holden Seamus , VanNieuwenhze Michael S. , Brun Yves V. , Garner Ethan C.
Published: September 2016

How bacteria produce a septum to divide in two is not well understood. This process is mediated by periplasmic cell-wall producing enzymes that are positioned by filaments of the cytoplasmic membrane-associated actin FtsA and the tubulin FtsZ (FtsAZ). To understand how these components act in concert to divide cells, we visualized their movements relative to the dynamics of cell wall synthesis during cytokinesis. We find that the division septum is built at discrete sites that move around the division plane. Furthermore, FtsAZ filaments treadmill in circumferential paths around the division ring, pulling along the associated cell-wall-synthesizing enzymes. We show that the rate of FtsZ treadmilling controls both the rate of cell wall synthesis and cell division. The coupling of both the position and activity of the cell wall synthases to FtsAZ treadmilling guides the progressive insertion of new cell wall, synthesizing increasingly small concentric rings to divide the cell.

One-sentence summary

Bacterial cytokinesis is controlled by circumferential treadmilling of FtsAZ filaments that drives the insertion of new cell wall.
Synaptic vesicle glycoprotein 2C (SV2C) modulates dopamine release and is disrupted in Parkinson’s disease
Authors: Dunn Amy R. , Stout Kristen A. , Ozawa Minagi , Lohr kelly M. , Bernstein Alison I. , Li Yingjie , Wang Minzheng , Sgobio Carmelo , Sastry Namratha , Cai Huaibin , Caudle W. Michael , Miller Gary W.
Published: September 2016

The synaptic vesicle glycoprotein 2 (SV2) family of proteins are involved in synaptic function throughout the brain. The ubiquitously expressed SV2A has been widely implicated in epilepsy, though SV2C with its restricted basal ganglia distribution has no known function. SV2C is emerging as a potentially relevant protein in Parkinson’s disease, as it is a genetic modifier of nicotine neuroprotection and sensitivity to L-DOPA. Here we identify SV2C as a mediator of dopamine homeostasis and report that disrupted expression of SV2C within the basal ganglia is a pathological feature of Parkinson’s disease (PD). Genetic deletion of SV2C leads to reduced dopamine release in the dorsal striatum as measured by fast-scan cyclic voltammetry, reduced striatal dopamine content, disrupted alpha-synuclein expression, deficits in motor function, and alterations in neurochemical effects of nicotine. Further, SV2C expression is dramatically altered in postmortem brain tissue from PD cases, but not in Alzheimer’s disease, progressive supranuclear palsy or multiple system atrophy. This disruption was paralleled in mice overexpressing mutated α-synuclein. These data establish SV2C as a novel mediator of dopamine neuron function and suggest that SV2C disruption is a unique feature of PD that likely contributes to dopaminergic dysfunction
The Opiliones Tree of Life: shedding light on harvestmen relationships through transcriptomics
Authors: Fernándeza Rosa , Sharma Prashant , Tourinho Ana L.M. , Giribet Gonzalo
Published: September 2016

Opiliones are iconic arachnids with a Paleozoic origin and a diversity that reflects ancient biogeographical patterns dating back at least to the times of Pangea. Due to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to systematics. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here we analyze a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing ca. 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families are precisely placed. Our dating analyses also using alternative calibration points, methods, and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as a general overview of the general biogeographic patterns of this ancient arthropod group.
GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell-wall synthesis
Authors: Yang Xinxing , Lyu Zhixin , Miguel Amanda , McQuillen Ryan , Huang Kerwyn Casey , Xiao Jie
Published: September 2016

The bacterial tubulin FtsZ is the central component of the division machinery, coordinating an ensemble of proteins involved in septal cell-wall synthesis to ensure successful constriction. How cells achieve this coordination is unknown. We used a combination of imaging, genetic and biochemical approaches to demonstrate that inEscherichia colicells FtsZ exhibits dynamic treadmilling predominantly determined by its GTPase activity, and that the treadmilling dynamics directs processive movement of the septal cell-wall synthesis machinery. In FtsZ mutants with severely reduced treadmilling, the spatial distribution of septal synthesis and the molecular composition and ultrastructure of the septal cell wall are substantially altered. Thus, the treadmilling of FtsZ provides a novel and robust mechanism for achieving uniform septal cell-wall synthesis to enable correct new pole morphology.

One-sentence summary

The bacterial tubulin FtsZ uses GTP hydrolysis to power treadmilling, driving processive synthesis of the septal cell wall.
The appressorium ofMagnaporthe oryzaeremains mitotically active during post-penetration hyphal growth in rice cells
Authors: Jones Kiersun , Jenkinson Cory B. , Zhu Jie , Dorhmi Sara , Khang Chang Hyun
Published: September 2016

To investigate the mitotic dynamics of an appressorium, we used time-lapse confocal imaging of a fluorescence-based mitotic reporter strain ofMagnaporthe oryzae. We present evidence that: (i) appressoria remain viable and mitotically active after host penetration, (ii) appressorial mitosis, like invasive hyphal mitosis, is semi-closed, (iii) sister chromatids separate within the appressorium, (iv) a mitotic appressorial nucleus undergoes extreme constriction and elongation as it migrates through the penetration peg in a manner analogous to mitosis during cell-to-cell movement of invasive hyphae. These results provide new insight into the potential roles of the appressorium after host penetration and highlight the unique mitotic dynamics during rice blast infection.
“In-silico studies of facilitated VEGF(s) – VEGFR(s) bindings for assessment of Lysine as an indirect Low-Mol-Wt angiogen: Experimental validation of a potential synthetic Low-Mol-Wt angiogen”
Authors: Verma Priyanshu , Bir Aritri , Banerjee Anindita , Basu Joy , Kar Sujoy , Samanta Sujoy Kumar , Datta Debatosh
Published: September 2016

In-vivo angiogenesis process is highly conserved and is mediated through a family of peptides having VEGF-A as the lead member. A respective receptor family comprising of members VEGFR-1, 2, 3 gets expressed on the endothelial cell membrane of the vascular bed in ischemic zone along with parallel expressions of VEGF-A, B, C, D and PlGF. Degree of ischaemia is the main regulator of these coupled expressions of angiogenic peptides/factors (AFs) and respective receptor(s) for a paracrine angiogenic process to take place. Physiological angiogenesis in intrauterine growth phase is the lead process in foetal growth, organogenesis and cellular specialization. Post birth and with aging, this process gets gradually inefficient and slow. In the present in-silico study, all angiogenic factors and receptor species are examined as for their binding stability in basal unaided condition and in presence of a possible Low-Mol-Wt linkage molecule–Lysine. Also a Lysine analogue 1,6-diaminohexanoic acid has been examined for its angiogenic potential both in dry docking experiment and in cell culture assay.
[N-Benzyl-N-(2-phenylethyl)dithiocarbamato-κ2
S,S′]triphenyltin(IV) and [bis(2-methoxyethyl)dithiocarbamato-κ2
S,S′]triphenyltin(IV): crystal structures and Hirshfeld surface analysis
Authors: Mohamad Rapidah , Awang Normah , Kamaludin Nurul Farahana , Jotani Mukesh M. , Tiekink Edward R. T.
Published: September 2016

The crystal and molecular structures of two triphenyltin dithiocarbamates, [Sn(C6H5)3(C16H16NS2)], (I), and [Sn(C6H5)3(C7H14NO2S2)], (II), are described. In (I), the dithiocarbamate ligand coordinates the SnIV atom in an asymmetric manner, leading to a highly distorted trigonal–bipyramidal coordination geometry defined by a C3S2 donor set with the weakly bound S atom approximately trans to one of the ipso-C atoms. A similar structure is found in (II), but the dithiocarbamate ligand coordinates in an even more asymmetric fashion. The packing in (I) features supramolecular chains along the c axis sustained by C—H...π interactions; chains pack with no directional interactions between them. In (II), supramolecular layers are formed, similarly sustained by C—H...π interactions; these stack along the b axis. An analysis of the Hirshfeld surfaces for (I) and (II) confirms the presence of the C—H...π interactions but also reveals the overall dominance of H...H contacts in the respective crystals.