bluuebunny/crossref_metadata_2025 huggingface dataset:
Bifurcation analysis of metabolic pathways: an illustration from yeast glycolysis
Authors: Overal Gosse , Teusink Bas , Bruggeman Frank J. , Hulshof Josephus , Planqué Robert
Published: July 2017

In microorganisms such as bacteria or yeasts, metabolic rates are tightly coupled to growth rate, and therefore to fitness. Although the topology of central pathways are largely conserved across organisms, the enzyme kinetics and their parameters generally vary. This prevents us to understand and predict (changes in) metabolic dynamics. The analytical treatment of metabolic pathways is generally restricted to small models, containing maybe two to four equations. Since such small core models involve much coarse graining, their biological interpretation is often hampered. In this paper we aim to bridge the gap between analytical, more in-depth treatment of small core models and biologically more realistic and detailed models by developing new methods. We illustrate these methods for a model of glycolysis inSaccharo-myces cerevisiaeyeast, arguably the best characterised metabolic pathway in the literature. The model is more involved than in previous studies, and involves both ATP/ADP and NADH/NAD householding.

A detailed analysis of the steady state equations sheds new light on two recently studied biological phenomena in yeast glycolysis: whether it is to be expected that fructose-1,6-biphosphate (FBP) parameterises all steady states, and the occurrence of bistability between a regular steady state and imbalanced steady state in which glycolytic intermediates keep accumulating.

This work shows that the special structure of metabolic pathways does allow for more in-depth bifurcation analyses than is currently the norm. We especially emphasise which of the techniques developed here scale to larger pathways, and which do not.
Connectome-harmonic decomposition of human brain activity reveals dynamical repertoire re-organization under LSD
Authors: Atasoy Selen , Roseman Leor , Kaelen Mendel , Kringelbach Morten L. , Deco Gustavo , Carhart-Harris Robin L.
Published: July 2017

Recent studies have started to elucidate the effects of lysergic acid diethylamide (LSD) on the human brain but the underlying dynamics are not yet fully understood. Here we used ‘connectome-harmonic decomposition’, a novel method to investigate the dynamical changes in brain states. We found that LSD alters the energy and the power of individual harmonic brain states in a frequency-selective manner. Remarkably, this leads to an expansion of the repertoire of active brain states, suggestive of a general re-organization of brain dynamics given the non-random increase in co-activation across frequencies. Interestingly, the frequency distribution of the active repertoire of brain states under LSD closely follows power-laws indicating a re-organization of the dynamics at the edge of criticality. Beyond the present findings, these methods open up for a better understanding of the complex brain dynamics in health and disease.
HtrA1 activation is driven by an allosteric mechanism of inter-monomer communication
Authors: Cabrera Alvaro Cortes , Melo Esther , Roth Doris , Topp Andreas , Delobel Frederic , Stucki Corinne , Chen Chia-yi , Jakob Peter , Banfai Balazs , Dunkley Tom , Schilling Oliver , Huber Sylwia , Iacone Roberto , Petrone Paula
Published: July 2017

The human protease family HtrA is responsible for preventing protein misfolding and mislocalization, and a key player in several cellular processes. Among these, HtrA1 is implicated in several cancers, cerebrovascular disease and age-related macular degeneration. HtrA1 activation, although very relevant for drug-targeting this protease, remains poorly characterized. Our work provides a mechanistic step-by-step description of HtrA1 activation and regulation. We report that the HtrA1 trimer is regulated by an allosteric mechanism by which monomers relay the activation signal to each other, in a PDZ-domain independent fashion. Notably, we show that inhibitor binding is precluded if HtrA1 monomers cannot communicate with each other. Our study establishes how HtrA1 oligomerization plays a fundamental role in proteolytic activity. Moreover, it offers a structural explanation for HtrA1-defective pathologies as well as mechanistic insights into the degradation of complex extracellular fibrils such as tubulin, amyloid beta and tau that belong to the repertoire of HtrA1.

Highlights

Monomeric HtrA1 is activated by a gating mechanism.

Trimeric HtrA1 is regulated by PDZ-independent allosteric monomer cross-talk.

HtrA1 oligomerization is key for proteolytic activity.

Substrate-binding is precluded if monomers cannot communicate with each other.
A method for detecting rash and fever illness‐associated viruses using multiplex reverse transcription polymerase chain reaction
Authors: Matsushima Yuki , Shimizu Tomomi , Doi Ikuko , Mizukoshi Fuminori , Nagasawa Koo , Ryo Akihide , Shimizu Hideaki , Kobayashi Masae , Funatogawa Keiji , Nagata Noriko , Ishikawa Mariko , Komane Ayako , Okabe Nobuhiko , Mori Yoshio , Takeda Makoto , Kimura Hirokazu
Published: July 2017

In this study, a new multiplex RT‐PCR method for detecting various viral genes in patients with rash and fever illnesses (RFIs) was constructed. New primer sets were designed for detection of herpes simplex viruses 1 and 2 (HSV1 and 2), and Epstein–Barr virus (EBV). The newly designed and previously reported primer sets were used to detect 13 types of RFI‐associated viruses by multiplex RT‐PCR assay systems. Moreover, to eliminate non‐specific PCR products, a double‐stranded specific DNase was used to digest double‐stranded DNA derived from the templates in clinical specimens. RFI‐associated viruses were detected in 77.0% of the patients (97/126 cases) by the presented method, multiple viruses being identified in 27.8% of the described cases (35/126 cases). Detected viruses and clinical diagnoses were compatible in 32.5% of the patients (41/126 cases). Sensitivity limits for these viruses were estimated to be 101–103 copies/assay. Furthermore, non‐specific PCR products were eliminated by a double‐stranded specific DNase with no influence on sensitivity. These results suggest that this method can detect various RFI‐associated viruses in clinical specimens with high sensitivity and specificity.
Continuing competence assessment and maintenance in occupational therapy: Scoping review with stakeholder consultation
Authors: Myers Christine T. , Schaefer Nancy , Coudron Ashley
Published: July 2017

Background/aim

Continuing competence activities hold the promise of improving health‐care service quality, especially given concerns about system inefficiencies and fragmentation. The aim of this scoping review was to describe the assessment and maintenance of occupational therapists’ continuing competence and identify knowledge gaps for future research. A secondary aim was comparing scoping review findings with those from other health‐care fields and considering possible impact of varying international regulations.

Methods

A series of database searches retrieved peer‐reviewed and grey literature on assessment and maintenance of occupational therapy continuing competence from 1995 to 2015. Themes were developed and findings shared with stakeholders, whose comments drove a second phase: searching for reviews related to continuing competence from allied health, medicine, and nursing, and reviewing websites and documents concerning regulatory requirements for occupational therapy continuing competence in seven English‐speaking nations.

Results

Twenty‐seven sources from the scoping review search met inclusion criteria. Stakeholder consultation validated the themes and preliminary knowledge gaps. Research into other health‐care specialties corresponded to findings from the scoping review. The website/document review of occupational therapy regulatory requirements revealed wide variation on both the state/province and national levels.

Conclusions

This scoping review highlights gaps in research on effective methods and assessment of occupational therapy continuing competence. Findings suggest a need for research on approaches to continuing competence that incorporate the translation of evidence to practice and address the influence of external factors. Regulatory agencies may address the quality of occupational therapy services by incorporating a variety of professional development options into requirements.
Association between universal hepatitis B prison vaccination, vaccine uptake and hepatitis B infection among people who inject drugs
Authors: Palmateer Norah E. , Goldberg David J. , Munro Alison , Taylor Avril , Yeung Alan , Wallace Lesley A. , Mitchell Alan , Shepherd Samantha J. , Gunson Rory N. , Aitken Celia , Hutchinson Sharon J.
Published: July 2017

Background and aims

In Scotland, hepatitis B virus (HBV) vaccination for all prisoners was introduced in 1999; here, we examine the impact of this programme among people who inject drugs (PWID) in the community. This study aimed to compare rates of HBV vaccine uptake before and after implementation of the prison programme and to estimate the determinants of vaccine uptake, the levels of ever/current HBV infection and the associations between vaccine uptake and ever/current HBV infection.

Design

Data collected via serial cross‐sectional surveys were used to compare the proportion who reported being vaccinated over time. For the 2013–14 survey, rates of ever/current HBV infection were calculated and the associations between vaccine uptake and ever/current HBV infection were examined using logistic regression.

Setting

Services providing injecting equipment and drug treatment and street sites in Glasgow (1993–2002) and throughout Scotland (2008–14).

Participants

More than 10 000 PWID in total were recruited in the surveys.

Measurements

Participants completed a questionnaire (all years) to ascertain self‐reported vaccine uptake and provided a blood spot (in 2013–14), tested for HBV core antibodies (anti‐HBc) and surface antigen (HBsAg).

Findings

Among recent‐onset PWID in Glasgow, vaccine uptake increased from 16% in 1993 to 59% in 2008–14 (P < 0.001). Among all PWID in Scotland, uptake increased further from 71% in 2008–09 to 77% in 2013–14 (P < 0.001) and was associated with incarceration [adjusted odds ratio (aOR) = 2.91, 95% confidence interval (CI) = 2.23–3.79]. The prevalence of anti‐HBc and HBsAg in Scotland was 2.6 and 0.3%, respectively, among PWID who had commenced injecting in the decade since the programme's introduction. Vaccination was associated with reduced odds of ever (aOR = 0.60, CI = 0.37–0.97) and current (aOR = 0.40, CI = 0.16–0.97) HBV infection.

Conclusions

In Scotland, uptake of hepatitis B virus (HBV) vaccination among people who inject drugs (PWID) in the community has increased since the 1999 introduction of universal prison vaccination, and current levels of HBV infection among PWID are low compared with other European countries.
Comparison of perioperative and functional outcomes of robotic partial nephrectomy for cT1a vs cT1b renal masses
Authors: Reynolds Christopher R. , Delto Joan C. , Paulucci David J. , Weinstein Corey , Badani Ketan , Eun Daniel , Abaza Ronney , Porter James , Bhandari Akshay , Hemal Ashok K.
Published: July 2017

Objective

To compare perioperative and functional outcomes of patients with cT1a or cT1b renal masses undergoing robotic partial nephrectomy (RPN) in a large multi‐institutional study

Patients and Methods

The present retrospective Institutional Review Board‐approved multi‐institutional study utilised a prospectively maintained database to identify patients undergoing RPN by six surgeons for a solitary cT1a (n = 1 307) or cT1b (n = 377) renal mass from 2006 to 2016. Perioperative and renal function outcomes at discharge and at a median follow‐up of 12.2 months were compared in univariable and multivariable regression analyses adjusting for surgeon performing the procedure and date of surgery.

Results

In univariable analysis, cT1b masses were associated with longer operative time (190.0 vs 159.0 min, P < 0.001), longer warm ischaemia time (18.8 vs 15.0 min, P < 0.001), higher estimated blood loss (150.0 vs 100.0 mL, P < 0.001), more intraoperative complications (5.6% vs 2.4%, P = 0.034), and more surgical postoperative complications (10.1% vs 5.7%, P =0.002). Results were similar in multivariable analysis with additional findings including more overall postoperative complications (odds ratio 1.55, P = 0.015) and longer length of stay (P < 0.001) associated with cT1b masses. There were no differences in the risk of progression of chronic kidney disease stage at 12.2 months, positive surgical margins, or major postoperative complications.

Conclusions

Although our study shows a longer operative time, longer warm ischemia time, and higher complication rate for patients undergoing RPN for cT1b renal masses, the magnitude of these differences is small. RPN should be considered for cT1b lesions when anatomical and spatial location allow for a feasible procedure.
Baseline and longitudinal plasma caveolin‐1 level as a biomarker in active surveillance for early‐stage prostate cancer
Authors: Basourakos Spyridon P. , Davis John W. , Chapin Brian F. , Ward John F. , Pettaway Curtis A. , Pisters Louis L. , Navai Neema , Achim Mary F. , Wang Xuemei , Chen Hsiang‐Chun , Choi Seungtaek , Kuban Deborah , Troncoso Patricia , Hanash Sam , Thompson Timothy C. , Kim Jeri
Published: July 2017

Objectives

To evaluate the role of caveolin‐1 (Cav‐1) as a predictor of disease reclassification (DR) in men with early prostate cancer undergoing active surveillance (AS).

Patients and Methods

We analysed archived plasma samples prospectively collected from patients with early prostate cancer in a single‐institution AS study. Of 825 patients enrolled, 542 had ≥1 year of follow‐up. Baseline and longitudinal plasma Cav‐1 levels were measured using an enzyme‐linked immunosorbent assay. Tumour volume or Gleason grade increases were criteria for DR. Logistic regression analyses were used to assess associations between clinicopathological characteristics and reclassification risk.

Results

In 542 patients, 480 (88.6%) had stage cT1c disease, 542 (100.0%) had a median prostate‐specific antigen level of 4.1 ng/mL, and 531 (98.0%) had a median Cancer of the Prostate Risk Assessment score of 1. In all, 473 (87.3%) had a Gleason score of 3+3. After a median of 3.1 years of follow‐up, disease was reclassified in 163 patients (30.1%). The mean baseline Cav‐1 level was 2.2 ± 8.5 ng/mL and the median 0.2 ng/mL (range, 0–85.5 ng/mL). In univariate analysis, baseline Cav‐1 was a significant predictor for risk of DR (odds ratio [OR] 1.82, 95% confidence interval [CI] 1.24–2.65; P = 0.002). In multivariate analysis, with adjustments for age, tumour length, group risk stratification and number of positive cores, reclassification risk associated with Cav‐1 remained significant (OR 1.91, 95% CI 1.28–2.84; P = 0.001).

Conclusion

Baseline plasma Cav‐1 level was an independent predictor of disease classification. New methods for refining AS and intervention may result.
Safety and performance of a novel collagenated xenogeneic bone block for lateral alveolar crest augmentation for staged implant placement
Authors: Ortiz‐Vigón Alberto , Suarez Iñaki , Martínez‐Villa Sergio , Sanz‐Martín Ignacio , Bollain Juan , Sanz Mariano
Published: July 2017

Objectives

To evaluate the performance and safety of placing a collagenated xenogeneic bone block (CXBB) graft for the lateral bone augmentation of the alveolar crest prior to implant placement.

Material & Methods

In patients with single or multiple tooth gaps and a severe horizontal collapse of the alveolar ridge, a ridge augmentation procedure was performed using CXBB fixated with osteosynthesis screws to the atrophic bone crest and complemented with deproteinized bovine bone mineral particles (DBBM) and a native bilayer collagen membrane (NBCM). Patients were examined with CBCT prior to and 24 weeks after the augmentation. Twenty‐six weeks postoperatively, a re‐entry procedure was performed to evaluate the bone width and availability for adequate implant placement.

Results

Fifteen patients received 28 CXBB, and in 13 patients, a re‐entry procedure was performed. Eleven patients (84.6%) gained enough bone volume for implant insertion without additional contouring or secondary bone augmentation. The mean crest width at baseline was 2.83 mm (SD 0.57), and the mean crest width at re‐entry was 6.90 mm (SD 1.22), with a mean ridge width increase of 4.12 mm (SD 1.32). Soft tissue dehiscence occurred during the follow‐up in 5 of 14 patients (35.7%) at various time points. In addition, there was a high incidence of early implant loss (30.8% [patient‐based]).

Conclusions

CXBB achieved significant horizontal crestal width gains allowing a secondary implant placement in the majority of the patients. However, the occurrence of soft tissue dehiscence may notably affect the outcome of the subsequent implant therapy.
A novel study on association between untreated hearing loss and cognitive functions of older adults: Baseline non‐verbal cognitive assessment results
Authors: Jayakody D.M.P. , Friedland P.L. , Eikelboom R.H. , Martins R.N. , Sohrabi H.R.
Published: July 2017

Background

Age‐related hearing loss (ARHL) is highly prevalent in older adults, and more than two‐thirds above age of 70 years suffer from ARHL. Recent studies have established a link between ARHL and cognitive impairment; however, most of the studies have used verbally loaded cognitive measures to investigate the association between ARHL and cognition. It is possible that due to hearing impairment, the elderly may experience difficulty in following verbal instructions or completing tasks that heavily rely on hearing during cognitive assessments. This may result in overestimation of cognitive impairment in such individuals. This baseline cross‐sectional study investigated the associations between untreated hearing loss and a number of cognitive functions using a battery of non‐verbal cognitive tests. Further, association between hearing loss and psychological status of older adults was examined.

Study design

Prospective case‐controlled study.

Methods

A total of 119 participants (54 males, M=66.33±10.50 years; 65 females M=61.51±11.46 years) were recruited. All participants completed a hearing assessment, a computerised test battery of non‐verbal cognitive functions and the depression, anxiety and stress scale.

Results

Hierarchical multiple regression analysis results revealed that hearing thresholds significantly associated with the working memory (P<0.05), paired associative learning scores (P<0.05), depression (P<0.001), and anxiety (P<0.001) and stress (P<0.001) scores. Analysis of covariance results revealed that participants with moderately‐severe hearing loss performed significantly poorer in paired associative learning and working memory tasks and psychological function tests compared to those with normal hearing.

Conclusion

Results of the current study suggest a significant relationship between ARHL and both cognition and psychological status. Our results also have some implications for using non‐verbal cognitive tests to evaluate cognitive functions in post‐lingually hearing impaired ageing adults, at least for those with more than moderately‐severe levels of hearing loss.
Effect of cellobiose supplementation on in vitro fermentation activity and bacterial numbers of porcine inocula
Authors: Heinritz S. N. , Weiss E. , Seifert J. , Mosenthin R. , Kuß S. , Degenhardt A. G. , Koch T. J.
Published: July 2017

In this in vitro study, the modified Hohenheim gas test (HGT) was applied to determine fermentation activity and bacterial composition of pig's faecal microbial inoculum using different concentrations of cellobiose. Incubation procedures included normal buffered and osmotic stress conditions (elevated medium salinity). After 24 hr of fermentation, production of gas, ammonia and short‐chain fatty acid (SCFA) was measured, and the gene copy numbers of total bacteria, Lactobacillus spp., Bifidobacterium spp., Roseburia spp., Clostridium Cluster IV spp. and Enterobacteriaceae were analysed using real‐time polymerase chain reaction. There was a significant reduction in gas production after 24 hr when comparing osmotic stress conditions with normal buffered conditions. Under osmotic stress, increasing cellobiose concentrations linearly increased gas production (p < .001), while ammonia, acetic acid and isobutyric acid concentrations decreased (p < .001, p = .012, p = .035 respectively). Under normal buffered conditions, Roseburia spp. gene copies linearly increased with increasing cellobiose concentrations (p = .048). Lactobacillus spp. and Bifidobacterium spp. numbers were higher under osmotic stress (p < .001) compared to normal conditions. Results might point towards a positive impact of cellobiose supplementation on gut health especially under osmotic stress conditions.
Fatty liver allografts are associated with primary graft non‐function and high mortality after transplantation
Authors: Mikolasevic Ivana , Milic Sandra , Filipec‐Kanizaj Tajana
Published: July 2017

See Article on Page 1219
Hepatitis C virus eradication with direct antiviral agents and liver cancer recurrence: Is the best the enemy of the good?
Authors: Colombo Massimo , Bruno Savino , Lleo Ana
Published: July 2017

See Article on Page 1122
Elfamycins: inhibitors of elongation factor‐Tu
Authors: Prezioso Samantha M. , Brown Nicole E. , Goldberg Joanna B.
Published: July 2017

Elfamycins are a relatively understudied group of antibiotics that target the essential process of translation through impairment of EF‐Tu function. For the most part, the utility of these compounds has been as laboratory tools for the study of EF‐Tu and the ribosome, as their poor pharmacokinetic profile and solubility has prevented implementation as therapeutic agents. However, due to the slowing of the antibiotic pipeline and the rapid emergence of resistance to approved antibiotics, this group is being reconsidered. Some researchers are using screens for novel naturally produced variants, while others are making directed, systematic chemical improvements on publically disclosed compounds. As an example of the latter approach, a GE2270 A derivative, LFF571, has completed phase 2 clinical trials, thus demonstrating the potential for elfamycins to become more prominent antibiotics in the future.
Disease‐modifying effect of solanezumab evaluated by delayed‐start analysis in a Japanese subpopulation with mild Alzheimer's disease
Authors: Nakamura Tomomi , Fujikoshi Shinji , Funai Jumpei , Matsumura Taka
Published: July 2017

Background

Solanezumab, an anti‐amyloid monoclonal antibody that binds soluble forms of amyloid, might have disease‐modifying properties that slow the progression of Alzheimer's disease. Delayed‐start design was proposed as a method to show a disease‐modifying effect. In the global study, delayed‐start analysis suggested that treatment advantages obtained during the placebo‐controlled period in the mild subgroup of solanezumab‐treated patients were preserved at the primary time‐point (108 weeks).

Aim

We applied the delayed‐start analysis to the Japanese subpopulation with mild Alzheimer's disease who participated in the global studies to see whether a disease‐modifying effect was also shown in the Japanese subpopulation.

Methods

A possible disease‐modifying effect of solanezumab was assessed using a new statistical method including non‐inferiority testing. Treatment differences were compared during the placebo‐controlled period with those after the placebo patients crossed over to solanezumab in the delayed‐start period.

Results

A total of 126 Japanese patients with mild Alzheimer's disease were included in the present study. Least squares mean difference for the 14‐item Alzheimer's Disease Assessment Scale‐Cognitive Subscale at the end of the placebo‐controlled period between patients with early‐ and delayed‐start of solanezumab was 2.85 (95% confidence interval 0.01–5.69) and 5.86 (95% confidence interval 2.22–9.51) at 108 weeks. Treatment difference during the placebo‐controlled period for the 14‐item Alzheimer's Disease Assessment Scale‐Cognitive Subscale was preserved at 108 weeks in the delayed‐start period.

Conclusion

Results from the Japanese subpopulation showed overall consistency with those from the global study, and are supportive for the possible disease‐modifying effects of solanezumab.
Identification and functional analysis of two P450 enzymes of Gossypium hirsutum involved in DMNT and TMTT biosynthesis
Authors: Liu Danfeng , Huang Xinzheng , Jing Weixia , An Xingkui , Zhang Qiang , Zhang Hong , Zhou Jingjiang , Zhang Yongjun , Guo Yuyuan
Published: July 2017

The homoterpenes (3E)‐4,8‐dimethyl‐1,3,7‐nonatriene (DMNT) and (E,E)‐4,8,12‐trimethyl‐1,3,7,11‐tridecatetraene (TMTT) are major herbivore‐induced plant volatiles that can attract predatory or parasitic arthropods to protect injured plants from herbivore attack. In this study, DMNT and TMTT were confirmed to be emitted from cotton (Gossypium hirsutum) plants infested with chewing caterpillars or sucking bugs. Two CYP genes (GhCYP82L1 and GhCYP82L2) involved in homoterpene biosynthesis in G. hirsutum were newly identified and characterized. Yeast recombinant expression and enzyme assays indicated that the two GhCYP82Ls are both responsible for the conversion of (E)‐nerolidol to DMNT and (E,E)‐geranyllinalool to TMTT. The two heterologously expressed proteins without cytochrome P450 reductase fail to convert the substrates to homoterpenes. Quantitative real‐time PCR (qPCR) analysis suggested that the two GhCYP82L genes were significantly up‐regulated in leaves and stems of G. hirsutum after herbivore attack. Subsequently, electroantennogram recordings showed that electroantennal responses of Microplitis mediator and Peristenus spretus to DMNT and TMTT were both dose dependent. Laboratory behavioural bioassays showed that females of both wasp species responded positively to DMNT and males and females of M. mediator could be attracted by TMTT. The results provide a better understanding of homoterpene biosynthesis in G. hirsutum and of the potential influence of homoterpenes on the behaviour of natural enemies, which lay a foundation to study genetically modified homoterpene biosynthesis and its possible application in agricultural pest control.
Characterization of scientific studies usually cited as evidence of adverse effects of GM food/feed
Authors: Sánchez Miguel A. , Parrott Wayne A.
Published: July 2017

GM crops are the most studied crops in history. Approximately 5% of the safety studies on them show adverse effects that are a cause for concern and tend to be featured in media reports. Although these reports are based on just a handful of GM events, they are used to cast doubt on all GM crops. Furthermore, they tend to come from just a few laboratories and are published in less important journals. Importantly, a close examination of these reports invariably shows methodological flaws that invalidate any conclusions of adverse effects. Twenty years after commercial cultivation of GM crops began, a bona fide report of an adverse health effect due to a commercialized modification in a crop has yet to be reported.
Phospholipase Dδ negatively regulates plant thermotolerance by destabilizing cortical microtubules in Arabidopsis
Authors: Zhang Qun , Song Ping , Qu Yana , Wang Peipei , Jia Qianru , Guo Liang , Zhang Chuanpeng , Mao Tonglin , Yuan Ming , Wang Xuemin , Zhang Wenhua
Published: July 2017

The pattern of cortical microtubule arrays plays an important role in plant growth and adaptation in response to hormonal and environmental changes. Cortical microtubules are connected with the plasma membrane (PM); however, how the membrane affects cortical microtubule organization is not well understood. Here, we showed that phospholipase Dδ (PLDδ) was associated with the PM and co‐localized with microtubules in cells. In vitro analysis revealed that PLDδ bound to microtubules, resulting in microtubule disorganization. Site‐specific mutations that decreased PLDδ enzymatic activity impaired its effects on destabilizing microtubule organization. Heat shock transiently activated PLDδ, without any change of its PM localization, triggering microtubule dissociation from PM and depolymerization and seedling death in Arabidopsis, but these effects were alleviated in pldδ knockout mutants. Complementation of pldδ with wild‐type PLDδ, but not mutated PLDδ, restored the phenotypes of microtubules and seedling survival to those of wild‐type Arabidopsis. Thus, we conclude that the PM‐associated PLDδ negatively regulates plant thermotolerance via destabilizing cortical microtubules, in an activity‐dependent manner, rather than its subcellular translocation.
Temperature heterogeneity over leaf surfaces: the contribution of the lamina microtopography
Authors: Saudreau Marc , Ezanic Amélie , Adam Boris , Caillon Robin , Walser Pascal , Pincebourde Sylvain
Published: July 2017

Temperature is spatially heterogeneous over leaf surfaces, yet the underlying mechanisms are not fully resolved. We hypothesized that the 3D leaf microtopography determines locally the amount of incoming irradiation flux at leaf surface, thereby driving the temperature gradient over the leaf surface. This hypothesis was tested by developing a model of leaf temperature heterogeneity that includes the development of the leaf boundary layer, the microtopography of the leaf surface and the physiological response of the leaf. Temperature distributions under various irradiation loads (1) over apple leaves based on their 3D microtopography, (2) over simulated flat (2D) apple leaves and (3) over 3D leaves with a transpiration rate distributed as in 2D leaves were simulated. Accuracy of the predictions was quantified by comparing model outputs and thermographic measurements of leaf surface temperature under controlled conditions. Only the model with 3D leaves predicted accurately the spatial heterogeneity of surface temperature over single leaves, whereas the mean temperature was well predicted by both 2D and 3D leaves. We suggest that in these conditions, the 3D leaf microtopography is the primary driver of leaf surface heterogeneity in temperature when the leaf is exposed to a light/heat source.
Photochemical Reaction Between 1,2‐Naphthoquinone and Adenine in Binary Water‐Acetonitrile Solutions
Authors: Zhou Qiaohui , Wei Yaxiong , Liu Xiang , Chen Lin , Zhou Xiaoguo , Liu Shilin
Published: July 2017

The photochemical reaction between 1,2‐naphthoquinone (NQ) and adenine was investigated using nanosecond time‐resolved laser flash photolysis. With photolysis at 355 nm, the lowest triplet state T1 of NQ was produced via intersystem crossing from its singlet excited state. The triplet‐triplet absorption of the state contributes three bands of transient spectra at 374, 596 and 650 nm, respectively, in pure acetonitrile and binary water‐acetonitrile solutions. In the presence of adenine, the observation of + (at 363 nm) and radical (at 343 and 485 nm) indicates a multistep mechanism of electron transfer process followed by a proton transfer between 3NQ* and adenine. By fitting with the Stern‐Volmer relationship, the quenching rate constant kq of 3NQ* by adenine in binary water‐acetonitrile solutions (4/1, volume ratio, v/v) is determined as 1.66 × 109 m−1 s−1. Additionally, no spectral evidence confirms the existence of electron transfer between 3NQ* with thymine, cytosine and uracil.
Low root‐to‐root transmission of a tobamovirus, yellow tailflower mild mottle virus, and resilience of its virions
Authors: Koh S. H. , Li H. , Sivasithamparam K. , Admiraal R. , Jones M. G. K. , Wylie S. J.
Published: July 2017

Tobamoviruses are serious pathogens because they have extremely stable virions, they are transmitted by contact, and they often induce severe disease in crops. Knowledge of the routes of transmission and resilience of tobamovirus virions is essential in understanding the epidemiology of this group of viruses. Here, an isolate of the tobamovirus yellow tailflower mild mottle virus (YTMMV) was used to examine root‐to‐root transmission in soil and in a hydroponic growth environment. Root‐to‐root transmission occurred rarely, and when it occurred plants did not exhibit systemic movement of the virus from the roots to the shoots over a 30‐day period. The resilience of YTMMV virions was tested in dried leaf tissue over time periods from one hour to one year under temperatures ranging from −80 to 160 °C. Infectivity was maintained for at least a year when incubated at −80 or 22 °C, or at fluctuating ambient temperatures of 0.8 to 44.4 °C, but incubation under dry conditions at 160 °C for >4 days eliminated infectivity. Exposure of virions to 0.1 m sodium hydroxide or 20% w/v skimmed milk solution for 30 min, treatments recommended for tobamovirus inactivation, did not abolish infectivity of YTMMV.
Tunable and laser-reconfigurable 2D heterocrystals obtained by epitaxial stacking of crystallographically incommensurate Bi
2
Se
3
and MoS
2
atomic layers
Authors: Vargas Anthony , Liu Fangze , Lane Christopher , Rubin Daniel , Bilgin Ismail , Hennighausen Zachariah , DeCapua Matthew , Bansil Arun , Kar Swastik
Published: July 2017

Heterocrystals: rotationally oriented stacks of incommensurate 2D materials with tunable and laser-reconfigurable properties.
Global conditions in the solar corona from 2010 to 2017
Authors: Morgan Huw , Taroyan Youra
Published: July 2017

Analysis of a huge data set reveals global solar cycle variation of the solar coronal temperature and other properties.
Metal nanoparticle film–based room temperature Coulomb transistor
Authors: Willing Svenja , Lehmann Hauke , Volkmann Mirjam , Klinke Christian
Published: July 2017

A new transistor concept exploits the colloidal synthesis of metal nanoparticles and their Coulomb charging energy.
Superconductivity across Lifshitz transition and anomalous insulating state in surface K–dosed (Li
0.8
Fe
0.2
OH)FeSe
Authors: Ren Mingqiang , Yan Yajun , Niu Xiaohai , Tao Ran , Hu Die , Peng Rui , Xie Binping , Zhao Jun , Zhang Tong , Feng Dong-Lai
Published: July 2017

Surface K–dosed (Li
0.8
Fe
0.2
OH)FeSe provides new clues to understand the mechanism of FeSe-based superconductors.
Dual-color single-mode lasing in axially coupled organic nanowire resonators
Authors: Zhang Chunhuan , Zou Chang-Ling , Dong Haiyun , Yan Yongli , Yao Jiannian , Zhao Yong Sheng
Published: July 2017

Dual-color single-mode nanolasers were experimentally achieved in axially coupled organic nanowire heterogeneous resonators.
Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments
Authors: Thakur Madhav P. , Tilman David , Purschke Oliver , Ciobanu Marcel , Cowles Jane , Isbell Forest , Wragg Peter D. , Eisenhauer Nico
Published: July 2017

Climate warming reduces biodiversity in simpler environments but enhances it in complex environments.
Molecular Mechanism and Genetic Determinants of Buprofezin Degradation
Authors: Chen Xueting , Ji Junbin , Zhao Leizhen , Qiu Jiguo , Dai Chen , Wang Weiwu , He Jian , Jiang Jiandong , Hong Qing , Yan Xin
Published: July 2017

Buprofezin is a widely used insect growth regulator whose residue has been frequently detected in the environment, posing a threat to aquatic organisms and nontarget insects. Microorganisms play an important role in the degradation of buprofezin in the natural environment. However, the relevant catabolic pathway has not been fully characterized, and the molecular mechanism of catabolism is still completely unknown.
Rhodococcus qingshengii
YL-1 can utilize buprofezin as a sole source of carbon and energy for growth. In this study, the upstream catabolic pathway in strain YL-1 was identified using tandem mass spectrometry. Buprofezin is composed of a benzene ring and a heterocyclic ring. The degradation is initiated by the dihydroxylation of the benzene ring and continues via dehydrogenation, aromatic ring cleavage, breaking of an amide bond, and the release of the heterocyclic ring 2-
tert
-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one (2-BI). A buprofezin degradation-deficient mutant strain YL-0 was isolated. A comparative genomic analysis combined with gene deletion and complementation experiments revealed that the gene cluster
bfzBA3A4A1A2C
is responsible for the upstream catabolic pathway of buprofezin. The
bfzA3A4A1A2
cluster encodes a novel Rieske nonheme iron oxygenase (RHO) system that is responsible for the dihydroxylation of buprofezin at the benzene ring;
bfzB
is involved in dehydrogenation, and
bfzC
is in charge of benzene ring cleavage. Furthermore, the products of
bfzBA3A4A1A2C
can also catalyze dihydroxylation, dehydrogenation, and aromatic ring cleavage of biphenyl, flavanone, flavone, and bifenthrin. In addition, a transcriptional study revealed that
bfzBA3A4A1A2C
is organized in one transcriptional unit that is constitutively expressed in strain YL-1.

IMPORTANCE
There is an increasing concern about the residue and environmental fate of buprofezin. Microbial metabolism is an important mechanism responsible for the buprofezin degradation in the natural environment. However, the molecular mechanism and genetic determinants of microbial degradation of buprofezin have not been well identified. This work revealed that gene cluster
bfzBA3A4A1A2C
is responsible for the upstream catabolic pathway of buprofezin in
Rhodococcus qingshengii
YL-1. The products of
bfzBA3A4A1A2C
could also degrade bifenthrin, a widely used pyrethroid insecticide. These findings enhance our understanding of the microbial degradation mechanism of buprofezin and benefit the application of strain YL-1 and
bfzBA3A4A1A2C
in the bioremediation of buprofezin contamination.
Med15B Regulates Acid Stress Response and Tolerance in Candida glabrata by Altering Membrane Lipid Composition
Authors: Qi Yanli , Liu Hui , Yu Jiayin , Chen Xiulai , Liu Liming
Published: July 2017

Candida glabrata
is a promising producer of organic acids. To elucidate the physiological function of the Mediator tail subunit Med15B in the response to low-pH stress, we constructed a deletion strain,
C. glabrata
med15B
Δ, and an overexpression strain,
C. glabrata HTU
Δ/
CgMED15B
. Deletion of
MED15B
caused biomass production, glucose consumption rate, and cell viability to decrease by 28.3%, 31.7%, and 26.5%, respectively, compared with those of the parent (
HTU
Δ) strain at pH 2.0. Expression of lipid metabolism-related genes was significantly downregulated in the
med15B
Δ strain, whereas key genes of ergosterol biosynthesis showed abnormal upregulation. This caused the proportion of C
18:1
fatty acids, the ratio of unsaturated to saturated fatty acids (UFA/SFA), and the total phospholipid content to decrease by 11.6%, 27.4%, and 37.6%, respectively. Cells failed to synthesize fecosterol and ergosterol, leading to the accumulation and a 60.3-fold increase in the concentration of zymosterol. Additionally, cells showed reductions of 69.2%, 11.6%, and 21.8% in membrane integrity, fluidity, and H
+
-ATPase activity, respectively. In contrast, overexpression of Med15B increased the C
18:1
levels, total phospholipids, ergosterol content, and UFA/SFA by 18.6%, 143.5%, 94.5%, and 18.7%, respectively. Membrane integrity, fluidity, and H
+
-ATPase activity also increased by 30.2%, 6.9%, and 51.8%, respectively. Furthermore, in the absence of pH buffering, dry weight of cells and pyruvate concentrations were 29.3% and 61.2% higher, respectively, than those of the parent strain. These results indicated that in
C. glabrata
, Med15B regulates tolerance toward low pH via transcriptional regulation of acid stress response genes and alteration in lipid composition.

IMPORTANCE
This study explored the role of the Mediator tail subunit Med15B in the metabolism of
Candida glabrata
under acidic conditions. Overexpression of
MED15B
enhanced yeast tolerance to low pH and improved biomass production, cell viability, and pyruvate yield. Membrane lipid composition data indicated that Med15B might play a critical role in membrane integrity, fluidity, and H
+
-ATPase activity homeostasis at low pH. Thus, controlling membrane composition may serve to increase
C. glabrata
productivity at low pH.
Stabilization of Multimeric Proteins via Intersubunit Cyclization
Authors: Zhu Lu , Wang Shuwen , Tian Wenya , Zhang Yeqi , Song Yang , Zhang Jun , Mu Bo , Peng Chao , Deng Zixin , Ma Hongmin , Qu Xudong
Published: July 2017

Proteins with high catalytic efficiency and selectivity under mild conditions have long been appreciated by industrial and medicinal fields. These proteins, which are commonly multimeric, often possess low stability, impeding wider application. Currently, strategies to improve the stability of multimeric proteins concentrate on enhancing the interaction at internal interface of the subunits. In this report, we confirmed that the largely underestimated subunit terminal ends are as significant as the internal interface for protein stability. By connecting both the terminal ends and internal interface of subunits, the tetrameric
Leifsonia
alcohol dehydrogenase (
Ln
ADH) protein can been cyclized into a rigid form with significantly improved thermostability and resilience. The improvement in the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment (
T
50
15
) and melting temperature (

T
m

) of the modified protein was 18°C and 23.3°C, respectively, which is superior to the results achieved by normal protein engineering. Our study provided a novel strategy to effectively improve the stability of multimeric proteins, which is suitable not only for the short-chain dehydrogenase/reductase (SDR) family but also other classes of proteins with close terminal ends.

IMPORTANCE
Industrially interesting proteins are generally multimeric proteins; however, their applications are often restricted due to low stability caused by the natural tendency of subunit disassociation. Current approaches targeting this problem mainly focus on enhancing the internal interfaces of the subunits to avoid their disassociation. In this study, we identified and confirmed the external interface to be significant for improving the stability of multimeric proteins. By connecting the terminal ends and internal interface with disulfide bonds, we found that the multimeric protein
Ln
ADH cyclized into a robust monomeric-like form, resulting in superior thermostability compared to traditional protein engineering. This intersubunit cyclization approach is efficient and easy to perform, providing a novel method for engineering many important classes of multimeric proteins.
Francisella-Like Endosymbionts and Rickettsia Species in Local and Imported Hyalomma Ticks
Authors: Azagi Tal , Klement Eyal , Perlman Gidon , Lustig Yaniv , Mumcuoglu Kosta Y. , Apanaskevich Dmitry A. , Gottlieb Yuval
Published: July 2017

Hyalomma
ticks (Acari: Ixodidae) are hosts for
Francisella
-like endosymbionts (FLE) and may serve as vectors of zoonotic disease agents. This study aimed to provide an initial characterization of the interaction between
Hyalomma
and FLE and to determine the prevalence of pathogenic
Rickettsia
in these ticks.
Hyalomma marginatum
,
Hyalomma rufipes
,
Hyalomma
dromedarii
,
Hyalomma
aegyptium
, and
Hyalomma
excavatum
ticks, identified morphologically and molecularly, were collected from different hosts and locations representing the distribution of the genus
Hyalomma
in Israel, as well as from migratory birds. A high prevalence of FLE was found in all
Hyalomma
species (90.6%), as well as efficient maternal transmission of FLE (91.8%), and the localization of FLE in Malpighian tubules, ovaries, and salivary glands in
H. marginatum
. Furthermore, we demonstrated strong cophylogeny between FLE and their host species. Contrary to FLE, the prevalence of
Rickettsia
ranged from 2.4% to 81.3% and was significantly different between
Hyalomma
species, with a higher prevalence in ticks collected from migratory birds. Using
ompA
gene sequences, most of the
Rickettsia
spp. were similar to
Rickettsia
aeschlimannii
, while a few were similar to
Rickettsia
africae
of the spotted fever group (SFG). Given their zoonotic importance, 249 ticks were tested for Crimean Congo hemorrhagic fever virus infection, and all were negative. The results imply that
Hyalomma
and FLE have obligatory symbiotic interactions, indicating a potential SFG
Rickettsia
zoonosis risk. A further understanding of the possible influence of FLE on
Hyalomma
development, as well as on its infection with
Rickettsia
pathogens, may lead to novel ways to control tick-borne zoonoses.

IMPORTANCE
This study shows that
Francisella
-like endosymbionts were ubiquitous in
Hyalomma
, were maternally transmitted, and cospeciated with their hosts. These findings imply that the interaction between FLE and
Hyalomma
is of an obligatory nature. It provides an example of an integrative taxonomy approach to simply differentiate among species infesting the same host and to identify nymphal and larval stages to be used in further studies. In addition, it shows the potential of imported
Hyalomma
ticks to serve as a vector for spotted fever group rickettsiae. The information gathered in this study can be further implemented in the development of symbiont-based disease control strategies for the benefit of human health.
Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi
Authors: Gladyshev Eugene
Published: July 2017

Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance. Recent studies of the filamentous fungus
Neurospora crassa
have shown that the process of repeat recognition for RIP apparently involves interactions between coaligned double-stranded segments of chromosomal DNA. These studies have also shown that RIP can be mediated by the conserved pathway that establishes transcriptional (heterochromatic) silencing of repetitive DNA. In light of these new findings, RIP emerges as a specialized case of the general phenomenon of heterochromatic silencing of repetitive DNA.
Long-Distance Dispersal of Fungi
Authors: Golan Jacob J. , Pringle Anne
Published: July 2017

Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most research on fungal dispersal focuses on only a small fraction of species. Thus, any discussion of the dispersal dynamics of fungi as a whole is problematic. While abundant morphological and biogeographic data are available for hundreds of species, researchers have yet to integrate this information into a unifying paradigm of fungal dispersal, especially in the context of long-distance dispersal (LDD). Fungal LDD is mediated by multiple vectors, including meteorological phenomena (e.g., wind and precipitation), plants (e.g., seeds and senesced leaves), animals (e.g., fur, feathers, and gut microbiomes), and in many cases humans. In addition, fungal LDD is shaped by both physical constraints on travel and the ability of spores to survive harsh environments. Finally, fungal LDD is commonly measured in different ways, including by direct capture of spores, genetic comparisons of disconnected populations, and statistical modeling and simulations of dispersal data. To unify perspectives on fungal LDD, we propose a synthetic three-part definition that includes (i) an identification of the source population and a measure of the concentration of source inoculum and (ii) a measured and/or modeled dispersal kernel. With this information, LDD is defined as (iii) the distance found within the dispersal kernel beyond which only 1% of spores travel.