bluuebunny/crossref_metadata_2025 huggingface dataset:
Bridging physiological and evolutionary time‐scales in a gene regulatory network
Authors: Marchand Gwenaëlle , Huynh‐Thu Vân Anh , Kane Nolan C. , Arribat Sandrine , Varès Didier , Rengel David , Balzergue Sandrine , Rieseberg Loren H. , Vincourt Patrick , Geurts Pierre , Vignes Matthieu , Langlade Nicolas B.
Published: May 2014

Gene regulatory networks (GRNs) govern phenotypic adaptations and reflect the trade‐offs between physiological responses and evolutionary adaptation that act at different time‐scales. To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution.

We examined the responses of 32 423 expressed sequences to drought and to abscisic acid (ABA) and selected 145 co‐expressed transcripts. We characterized their regulatory relationships in nine kinetic studies based on different hormones. From this, we inferred a GRN by meta‐analyses of a Gaussian graphical model and a random forest algorithm and studied the genetic differentiation among populations (FST) at nodes.

We identified two main hubs in the network that transport nitrate in guard cells. This suggests that nitrate transport is a critical aspect of the sunflower physiological response to drought. We observed that differentiation of the network genes in elite sunflower cultivars is correlated with their position and connectivity.

This systems biology approach combined molecular data at different time‐scales and identified important physiological processes. At the evolutionary level, we propose that network topology could influence responses to human selection and possibly adaptation to dry environments.
Investigation of Central Nervous System Dysfunction in Chronic Pelvic Pain Using Magnetic Resonance Spectroscopy and Noninvasive Brain Stimulation
Authors: Simis Marcel , Reidler Jay S. , Duarte Macea Debora , Moreno Duarte Ingrid , Wang Xiaoen , Lenkinski Robert , Petrozza John C. , Fregni Felipe
Published: May 2014

Background

Recent studies demonstrate that chronic pelvic pain is associated with altered afferent sensory input resulting in maladaptive changes in the neural circuitry of pain. To better understand the central changes associated with chronic pelvic pain, we investigated the contributions of critical pain‐related neural circuits using single‐voxel proton magnetic resonance spectroscopy (MRS) and transcranial direct current stimulation (tDCS).

Methods

We measured concentrations of neural metabolites in 4 regions of interest (thalamus, anterior cingulate cortex, primary motor, and occipital cortex [control]) at baseline and after 10 days of active or sham tDCS in patients with chronic pelvic pain. We then compared our results to those observed in healthy controls, matched by age and gender.

Results

We observed a significant increase in pain thresholds after active tDCS compared with sham conditions. There was a correlation between metabolite concentrations at baseline and quantitative sensory assessments. Chronic pelvic pain patients had significantly lower levels of NAA/Cr in the primary motor cortex compared with healthy patients.

Conclusions

tDCS increases pain thresholds in patients with chronic pelvic pain. Biochemical changes in pain‐related neural circuits are associated with pain levels as measured by objective pain testing. These findings support the further investigation of targeted cortical neuromodulatory interventions for chronic pelvic pain.
Dealing with Symptoms and Issues of Hospitalized Patients with Cancer in Indonesia: The Role of Families, Nurses, and Physicians
Authors: Effendy Christantie , Vissers Kris , Tejawinata Sunaryadi , Vernooij‐Dassen Myrra , Engels Yvonne
Published: May 2014

Objective

Patients with cancer often face physical, psychological, social, spiritual, and emotional symptoms. Our aim was to study symptoms and issues of hospitalized patients with cancer in Indonesia, a country with strong family ties, and how family members, nurses, and physicians deal with them.

Methods

In 2011, 150 hospitalized cancer patients in 3 general hospitals in Indonesia were invited to fill in a questionnaire, which was based on the validated Problems and Needs of Palliative Care (short version) questionnaire. Descriptive statistics were performed.

Results

Of 119 patients (79%) who completed the questionnaire, 85% stated that their symptoms and issues were addressed. According to these patients, financial (56%), autonomy (36%), and psychosocial (34%) issues were most often addressed by the family alone. Physical symptoms (52%) and spiritual issues (33%) were addressed mainly by a combination of family, nurses, and physicians.

Conclusions

Hospitalized patients with cancer in Indonesia felt that most of their symptoms and issues had been addressed, and the family was highly involved. The strong family ties in Indonesian culture may have contributed to this family role. More research is needed to clarify how this influences patient outcome, quality of care, and quality of life of both the patients and their families, along with the degree of partnership between families and professionals. This information might help answer the question what advantages and disadvantages the family role in caring for a hospitalized patient with cancer generates for the patient, the family, and professional caregivers.
Salt stress‐induced seedling growth inhibition coincides with differential distribution of serotonin and melatonin in sunflower seedling roots and cotyledons
Authors: Mukherjee Soumya , David Anisha , Yadav Sunita , Baluška František , Bhatla Satish Chander
Published: May 2014

Indoleamines regulate a variety of physiological functions during the growth, morphogenesis and stress‐induced responses in plants. Present investigations report the effect of NaCl stress on endogenous serotonin and melatonin accumulation and their differential spatial distribution in sunflower (Helianthus annuus) seedling roots and cotyledons using HPLC and immunohistochemical techniques, respectively. Exogenous serotonin and melatonin treatments lead to variable effect on hypocotyl elongation and root growth under NaCl stress. NaCl stress for 48 h increases endogenous serotonin and melatonin content in roots and cotyledons, thus indicating their involvement in salt‐induced long distance signaling from roots to cotyledons. Salt stress‐induced accumulation of serotonin and melatonin exhibits differential distribution in the vascular bundles and cortex in the differentiating zones of the primary roots, suggesting their compartmentalization in the growing region of roots. Serotonin and melatonin accumulation in oil body rich cells of salt‐treated seedling cotyledons correlates with longer retention of oil bodies in the cotyledons. Present investigations indicate the possible role of serotonin and melatonin in regulating root growth during salt stress in sunflower. Effect of exogenous serotonin and melatonin treatments (15 μM) on sunflower seedlings grown in the absence or presence of 120 mM NaCl substantiates their role on seedling growth. Auxin and serotonin biosynthesis are coupled to the common precursor tryptophan. Salt stress‐induced root growth inhibition, thus pertains to partial impairment of auxin functions caused by increased serotonin biosynthesis. In seedling cotyledons, NaCl stress modulates the activity of N‐acetylserotonin O‐methyltransferase (HIOMT; EC 2.1.1.4), the enzyme responsible for melatonin biosynthesis from N‐acetylserotonin.
A rare reason for liver transplantation: hepatic alveoloar echinococcosis
Authors: Kantarci M. , Pirimoglu B. , Aydinli B. , Ozturk G.
Published: May 2014

One of the rare indications for liver transplantation is hepatic alveolar echinococcosis (AE). We present a case of hepatic AE with portal vein involvement.
The pro‐inflammatory potential of microparticles in red blood cell units
Authors: Kent M. W. , Kelher M. R. , West F. B. , C. Silliman C.
Published: May 2014

Background

Microparticles (MPs) are submicron size cell fragments that are released from cells.

Objectives

We hypothesise that MPs increase during red blood cell (RBC) storage and are part of the pro‐inflammatory activity, which accumulates in the RBC supernatant.

Methods/Materials

RBC units were separated from whole blood of eight healthy donors: 5 U were split, with 50% undergoing leucoreduction (LR) and the remaining left as unmodified controls. The remaining 3 U were leucoreduced. Samples were obtained at days (D) 1 and 42 and cell‐free supernatants separated and stored. The supernatants were centrifuged at 17 000 × g (60 min) or 100 000 × g (120 min) into microparticle‐rich (MPR) and microparticle‐poor (MPP) portions, resuspended in albumin, incubated with antibodies to CD235 (RBCs), CD45 [white blood cells (WBCs)] and CD41a [platelets (Plts)], and analysed by flow cytometry. Isolated neutrophils were incubated with these samples, and priming activity measured.

Results

Total MPs increased during storage; however, MPs that marked for precursor cell types did not. Significant priming accumulated in the MPP fraction during storage with some activity present in the MPR fraction from D1 and D42 LR‐RBCs.

Conclusion

Most of the pro‐inflammatory priming activity from stored RBCs resides in the MPP supernatant, although the MPR fraction from D42 LR‐RBCs does contain some priming activity.
DIFFUSION‐WEIGHTED MAGNETIC RESONANCE IMAGING OF THE NORMAL CANINE BRAIN
Authors: Hartmann Antje , Söffler Charlotte , Failing Klaus , Schaubmar Andreas , Kramer Martin , Schmidt Martin J.
Published: May 2014

Diffusion‐weighted imaging (DWI) MRI has been primarily reported as a method for diagnosing cerebrovascular disease in veterinary patients. In humans, clinical applications for diffusion‐weighted MRI have also included epilepsy, Alzheimer's, and Creutzfeld–Jakob disease. Before these applications can be developed in veterinary patients, more data on brain diffusion characteristics are needed. Therefore, the aim of this study was to evaluate the distribution of diffusion in the normal canine brain. Magnetic resonance imaging of the brain was performed in ten, clinically normal, purpose‐bred beagle dogs. On apparent diffusion coefficient maps, regions of interest were drawn around the caudate nucleus, thalamus, piriform lobe, hippocampus, semioval center, and cerebral cortex. Statistically significant differences in mean apparent diffusion coefficient were found for the internal capsule, hippocampus, and thalamus. The highest apparent diffusion coefficient (1044.29 ± 165.21 μm2/s (mean ± SD (standard deviation)) was detected in the hippocampus. The lowest apparent diffusion coefficient was measured in the semioval center (721.39 ± 126.28 μm2/s (mean ± SD)). Significant differences in mean apparent diffusion coefficients of the caudate nucleus, thalamus, and piriform lobe were found by comparing right and left sides. Differences between brain regions may occur due to differences in myelination, neural density, or fiber orientation. The reason for the differences between right and left sides remains unclear. Data from the current study provide background for further studies of diffusion changes in dogs with brain disease.
Progressive aspect and stative verbs in Outer Circle varieties
Authors: VAN ROOY BERTUS
Published: May 2014

The extension of the progressive form to stative verbs is a widely discussed feature of Outer Circle varieties of English. This paper examines the semantics of the stative progressive in three corpora, representing spoken and written Indian (IndE), Kenyan (KenE) and Black South African English (BSAfE). The results reveal that the progressive form is used more frequently in spoken than written data, and most frequently in BSAfE, followed by KenE, and then IndE. All three Outer Circle varieties use the progressive form proportionally more often with stative verbs than British English. The main use of the progressive form is to convey a sense of extended duration. This Outer Circle prototype is termed an on‐going state, and clearly differs from the sense of a temporary state, which is prototypical for Inner Circle varieties. There are nevertheless a substantial minority of limited duration (temporary state) uses, especially in the written data, but at the same time, a number of examples where the progressive conveys the sense of states with unlimited duration, especially in BSAfE and the spoken data. The main conclusion is that the progressive is not simply extended to stative verbs, as is argued by many previous researchers, but rather that of a different prototype, of extended duration, sanctions a wider range of uses of the progressive form with dynamic verbs and stative verbs alike.
The progressive aspect in the Netherlands and the ESL/EFL continuum
Authors: EDWARDS ALISON
Published: May 2014

This paper responds to calls to (i) approach varieties of English as a native (ENL), second (ESL) and foreign (EFL) language in an integrated fashion, and (ii) widen the scope of world Englishes analyses to the Expanding Circle. It describes the development of the Corpus of ‘Dutch English’, the first Expanding Circle corpus incorporating all text types in the written components of the ICE corpora. This corpus has implications for the description of English in the Netherlands in particular and for the investigation of ESL and EFL varieties in general. The paper then reports on a case study of the progressive aspect in this corpus compared to several ENL and ESL varieties. The results show no strict divide between the ESL varieties and the Corpus of Dutch English, which in fact displayed characteristics of both EFL and ESL. These findings provide further evidence in favour of an ESL–EFL continuum rather than a strict divide between varietal types.
Uses and functions of English in Namibia's multiethnic settings
Authors: STELL GERALD
Published: May 2014

In a context where new English varieties from the Outer Circle have been receiving increasing attention, I propose to outline a descriptive approach to their uses and functions on the basis of their patterns of co‐occurrence with local languages across intra and inter‐ethnic boundaries. The case study I offer is Namibia, a multiethnic and multilingual African country where English has been the sole official language since 1990 without having had much local history prior to that date. The general question that I pose is to what extent and how English is used in informal interactions in Namibia. Considering Namibia's ethnolinguistic diversity as well as the locally widespread practice of code‐switching, the questions I more specifically ask are: What are the patterns of code‐switching with which English finds itself associated both within and across Namibia's inter‐ethnic boundaries, and how can they be characterized in terms of social function? On the basis of a corpus of intra‐ and inter‐ethnic interactions involving a range of Namibian ethnicities, I show evidence of a continuum of linguistic usage ranging from different patterns of code‐switching involving English and local languages to more or less monolingual English varieties. I finally place that evidence within the perspective of new Englishes theory, emphasizing the possible relevance of code‐switching patterns to the emergence of indigenized English varieties in general, and of an indigenized Namibian variety in particular.
English in contemporary Poland
Authors: KASZTALSKA ALEKSANDRA
Published: May 2014

Because of its association with the West, English became a symbol of modernization and freedom during Poland's communist chapter. Since 1989, English has achieved an even higher status, as the language of international business, research, and media. Today, Polish advertisements are filled with English loan words, English‐language movies reign in theaters, and most young people study English in school. As relatively little research has examined the impact of English on contemporary Poland, this paper is an effort to begin filling this gap. I start by offering a concise history of Poland and Polish, as well as a history of English in Poland. I then provide examples of changes in Polish that are likely motivated by Poles’ use of English. In the following sections, I outline the rise to fame of English in Polish classrooms, advertisements, and media. From this review emerges a somewhat incongruous image of English, as both an economic asset and a corrupting agent on the Polish language and culture. To illustrate these dichotomous attitudes, the subsequent section reports on the findings of my preliminary, Internet‐based study of contemporary Polish discourses about English. I end the paper by identifying some unanswered questions and suggesting directions for further research.
Word juncture characteristics in world Englishes: A research report
Authors: SETTER JANE , MOK PEGGY , LOW EE LING , ZUO DONGHUI , AO RAN
Published: May 2014

The subtle juncture cues in older varieties of English such as Received Pronunciation can be difficult for speakers of new English varieties to perceive. This study looks at the perception of word juncture characteristics in three varieties of English (British, Hong Kong and Singapore) among British, Hong Kong and Singaporean listeners in order to widen our understanding of English juncture characteristics in general. We find that, even though reaction time data indicates that listeners perform quickest in the variety they are most familiar with, not only are juncture differences in British English difficult for Hong Kong and Singaporean listeners to perceive, they are also the most difficult for British listeners. Juncture characteristics in Hong Kong English are the easiest to distinguish among the three varieties.
Fabrication of large-scale spherical-cap structure and the application on n-GaN based light-emitting diodes
Authors: Yin Hong-Xing , Zhu Chuan-Rui , Shen Yan , Yang Hai-Fang , Liu Zhe , Gu Chang-Zhi , Liu Bao-Li , Xu Xian-Gang
Published: May 2014

An under exposure method based on Fresnel diffraction effect in a conventional optical lithography system is used to fabricate large-scale, uniform spherical-cap structures. This method provides an effective roughening technology on the top surface of light-emitting diodes (LEDs) to improve the light extraction efficiency of LEDs. LEDs with high duty cycle spherical-cap structures showed enhanced light output power by 130%–160% compared with the LED with a flat surface. This simple and easy shape control method has potential applications in other optical devices such as organic LEDs, inorganic solar cells, and laser diodes.
Tuning the oxidation states and crystallinity of copper oxide nanofibers by calcination
Authors: Park Juyun , Seo SungYong , Kang Yong-Cheol , Koh Sung-Wi
Published: May 2014

Cu oxide/polyvinyl alcohol (PVA) nanofibers were synthesized by sol–gel and electrospinning technique. The obtained Cu oxide/PVA nanofibers were heated to remove the PVA compound at 673 and 873 K. The ultrafine Cu oxide nanofibers were characterized with scanning electron microscopy (SEM), transmission electron microscopy (TEM), x-ray diffraction (XRD), and x-ray photoelectron spectroscopy (XPS). The SEM images showed that the Cu oxide nanofibers were successfully synthesized by electrospinning and calcination and the average diameters of the electrospun Cu/PVA nanofibers were 268.9 ± 97.2 nm. After the nanofibers were calcined at higher temperature than rt, the morphologies of the nanofibers changed. XRD results indicated that the crystalline structure changed from amorphous phase to monoclinic CuO through cubic Cu2O. TEM images also verified the crystal phase of Cu oxide nanofibers. XPS spectra revealed that the thermal oxidation of Cu proceeded during calcination.
Direct Relation of Acute Effects of Static Stretching on Isokinetic Torque Production With Initial Flexibility Level
Authors: Babault Nicolas , Bazine Wacef , Deley Gaëlle , Paizis Christos , Lattier Grégory
Published: May 2014

Purpose:

To examine the acute effect of a single static-stretching session of hamstring muscles on torque production in relation with individual flexibility.

Methods:

Maximal voluntary concentric torque of hamstring muscles was measured before and after a static-stretching session (6 × 30 s). Torque changes were correlated with the flexibility level determined at the onset of the experimental procedure.

Results:

The hamstring-stretching intervention significantly reduced maximal concentric torque in participants with low and high hamstring flexibility. Hamstring flexibility and torque decrease, determined immediately after the stretching procedure, were negatively correlated.

Conclusions:

Torque decrease measured after the static-stretching session is dependent on participant flexibility. Participants with low flexibility are much more likely to demonstrate large torque decreases poststretching.
Time–Motion Analysis of a 2-Hour Surfing Training Session
Authors: Secomb Josh L. , Sheppard Jeremy M. , Dascombe Ben J.
Published: May 2014

Purpose:

To provide a descriptive and quantitative time–motion analysis of surfing training with the use of global positioning system (GPS) and heart-rate (HR) technology.

Methods:

Fifteen male surfing athletes (22.1 ± 3.9 y, 175.4 ± 6.4 cm, 72.5 ± 7.7 kg) performed a 2-h surfing training session, wearing both a GPS unit and an HR monitor. An individual digital video recording was taken of the entire surfing duration. Repeated-measures ANOVAs were used to determine any effects of time on the physical and physiological measures.

Results:

Participants covered 6293.2 ± 1826.1 m during the 2-h surfing training session and recorded measures of average speed, HRaverage, and HRpeak as 52.4 ± 15.2 m/min, 128 ± 13 beats/min, and 171 ± 12 beats/min, respectively. Furthermore, the relative mean times spent performing paddling, sprint paddling to catch waves, stationary, wave riding, and recovery of the surfboard were 42.6% ± 9.9%, 4.1% ± 1.2%, 52.8% ± 12.4%, 2.5% ± 1.9%, and 2.1% ± 1.7%, respectively.

Conclusion:

The results demonstrate that a 2-h surfing training session is performed at a lower intensity than competitive heats. This is likely due to the onset of fatigue and a pacing strategy used by participants. Furthermore, surfing training sessions do not appear to appropriately condition surfers for competitive events. As a result, coaches working with surfing athletes should consider altering training sessions to incorporate repeated-effort sprint paddling to more effectively physically prepare surfers for competitive events.
Effects of Prolonged Hypertrophic Resistance Training on Acute Endocrine Responses in Young and Older Men
Authors: Walker Simon , Santolamazza Fabrizio , Kraemer William , Häkkinen Keijo
Published: May 2014

The present study investigated changes in acute serum hormone responses to a resistance exercise bout following a prolonged period of hypertrophic resistance training in young (YM) and older men (OM). Subjects performed a 5 × 10RM leg press exercise protocol before and after 20 weeks of hypertrophic resistance training. In YM, the acute responses in growth hormone were greater compared with before training (p < .05), and cortisol concentration did not increase after training. Endocrine responses in OM were similar before and after training. Greater acute growth hormone responses after training were associated with larger gains in lean mass in the entire subject group (r = .596, p = .019). These findings suggest that, in general, YM demonstrate greater adaptability within the endocrine system compared with OM. However, adaptability in growth hormone response was associated with larger training-induced gains independent of age.
Moderate Intensity Exercise Is Associated With Decreased Angiotensin-converting Enzyme, Increased β2-Adrenergic Receptor Gene Expression, and Lower Blood Pressure in Middle-Aged Men
Authors: Tartibian Bakhtyar , Botelho Teixeira Ana Maria , Baghaiee Behrouz
Published: May 2014

Purpose:

The purpose of the current study was to characterize the role of aerobic exercise in the gene expression of the angiotensin-converting enzyme (ACE) and the β2-adrenergic receptor (ADRB2) in untrained men.

Methods:

Twenty untrained middle-aged men were randomly assigned to exercise (Exe) and control (Con) groups. The Exe group performed aerobic exercises for eight weeks. ACE mRNA and ADRB2 mRNA were determined by PCR.

Results:

The expression of ACE in week 4 and in the Exe group decreased significantly (p < .001). ADRB2 in the Exe group, in week 4 and in week 8, was markedly higher, and blood pressure was significantly lower than in the Con group (p < .001). In the Con group ADRB2 mRNA decreased.

Conclusion:

These results suggest that moderate intensity exercise promotes the leukocyte expression of gene markers that may affect blood pressure by improving cardiovascular fitness levels in middle-aged men.
Walking Speed: The Functional Vital Sign
Authors: Middleton Addie , Fritz Stacy L. , Lusardi Michelle
Published: May 2014

Walking speed (WS) is a valid, reliable, and sensitive measure appropriate for assessing and monitoring functional status and overall health in a wide range of populations. These capabilities have led to its designation as the “sixth vital sign”. By synthesizing the available evidence on WS, this scholarly review article provides clinicians with a reference tool regarding this robust measure. Recommendations on testing procedures for assessing WS, including optimal distance, inclusion of acceleration and deceleration phases, instructions, and instrumentation are given. After assessing an individual’s WS, clinicians need to know what this value represents. Therefore, WS cut-off values and the corresponding predicted outcomes, as well as minimal detectable change values for specific populations and settings are provided.
The Effectiveness of Autologous Conditioned Serum in the Treatment of Knee Osteoarthritis
Authors: Astolfi Matthew , McGuire Kelly , Kaminski Thomas W.
Published: May 2014

Clinical Scenario:

Osteoarthritis (OA) is a debilitating degenerative disease affecting an estimated 27 million Americans. A systematic review found that patients with a previous history of traumatic knee injury are at increased risk of developing knee OA, regardless of specific injury. It is vital for the maintenance of quality of life for individuals affected with OA that the treatment options available be able to reduce symptoms and restore quality of living. The pain-relief benefits of traditional injection treatments are small to moderate and have a limited duration. It was found that at 2 wk postinjection that corticosteroids were more effective than hyaluronic acid (HA) injections. Autologous conditioned serum (ACS) injection is a novel treatment that has shown favorable results. However, many clinicians continue to use HA injections for reduction of symptoms in patients with osteoarthritis when the use of ACS may be more beneficial.

Focused Clinical Question:

For patients with knee OA, is an ACS injection more efficient at producing a reduction in symptoms than HA or a saline injection?
Changes in Muscle Thickness After Exercise and Biofeedback in People With Low Back Pain
Authors: Partner Shandi L. , Sutherlin Mark Alan , Acocello Shellie , Saliba Susan A. , Magrum Eric M. , Hart Joe M.
Published: May 2014

Context:

Individuals with low back pain (LBP) have reduced function of the transversus abdominis (TrA) and lumbar multifidus (LM) muscles. Biofeedback during exercise may increase the ability to contract the TrA and LM muscles compared with exercise alone.

Objective:

To compare TrA preferential activation ratio (PAR) and the percent change in LM-muscle thickness in patients with LBP history before and after exercise with or without biofeedback.

Design:

Controlled laboratory study.

Setting:

University research laboratory.

Patients:

20 LBP individuals, 10 exercise alone and 10 exercise with biofeedback.

Interventions:

Patients were allotted to tabletop exercises in isolation or tabletop exercises with visual, auditory, and tactile biofeedback.

Main Outcome Measures:

TrA PAR and percent change in LM-muscle thickness.

Results:

There were no differences between groups at baseline (all P > .05). Nonparametric statistics showed decreased resting muscle thickness for total lateral abdominal-wall muscles (P = .007) but not TrA (P = .410) or LM (P = .173). Percent TrA thickness increased from table to standing positions before (P = .006) and after exercise (P = .009). TrA PAR increased after exercise (pre 0.01 ± 0.02, post 0.03 ± 0.04, P = .033) for all patients and for exercise with biofeedback (pre 0.02 ± 0.01, post 0.03 ± 0.01, P = .037) but not for exercise alone (pre 0.01 ± 0.02, post 0.02 ± 0.05, P = .241). No group differences were observed for TrA PAR before (exercise 0.01 ± 0.02, exercise with biofeedback 0.02 ± 0.01, P = .290) or after exercise (exercise 0.02 ± 0.05, exercise with biofeedback 0.03 ± 0.01, P = .174). There were no group differences in LM percent change before exercise (P = .999) or after exercise (P = .597). In addition, no changes were observed in LM percent change as a result of exercise among all participants (P = .391) or for each group (exercise P = .508, exercise with biofeedback P = .575).

Conclusion:

TrA PAR increased after a single session of exercises, whereas no thickness changes occurred in LM.
A pause sequence enriched at translation start sites drives transcription dynamics in vivo
Authors: Larson Matthew H. , Mooney Rachel A. , Peters Jason M. , Windgassen Tricia , Nayak Dhananjaya , Gross Carol A. , Block Steven M. , Greenleaf William J. , Landick Robert , Weissman Jonathan S.
Published: May 2014

Transcription takes a pause to consider

A short sequence in DNA causes RNA polymerase (RNAP) to pause at thousands of previously undocumented locations in the genome. Larson
et al.
mapped these pause sites at single-nucleotide resolution in vivo in actively growing bacteria. Transcriptional pausing can be critical for the regulation of gene expression, by allowing RNA folding events and in the recruitment of other transcription factors.

Science
, this issue p.
1042
Sulfur-mediated electron shuttling during bacterial iron reduction
Authors: Flynn Theodore M. , O’Loughlin Edward J. , Mishra Bhoopesh , DiChristina Thomas J. , Kemner Kenneth M.
Published: May 2014

How bacteria manage to breathe on rust

In the absence of oxygen, anaerobic bacteria turn to other chemical compounds during respiration. This can be helpful in detoxifying heavy-metal pollution. Flynn
et al.
(see the Perspective by Friedrich and Finster) found that alkaline conditions prevent a detoxifying bug—
Shewanella oneidensis
—from using enzymes to reduce rust-like minerals. Instead, the bacteria reduce elemental sulfur compounds, generating hydrogen sulfide that reduces the iron indirectly. This interplay between anoxic biogeochemical cycles may explain why some anaerobic bacteria contain the genetic machinery necessary to reduce multiple compounds besides oxygen.

Science
, this issue p.
1039
; see also p.
974
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
Authors: Anantharaman Karthik , Duhaime Melissa B. , Breier John A. , Wendt Kathleen A. , Toner Brandy M. , Dick Gregory J.
Published: May 2014

Virus-Enhanced Sulfur Oxidation

How do microbial viruses affect subsurface microbial communities?

Anantharaman
et al.

(p.
757
, published online 1 May) investigated the interactions between ubiquitous marine lithotrophs found at hydrothermal vents and their viruses. The genes for sulfur oxidation in viruses that infect abundant marine chemosynthetic sulfur-oxidizing bacteria enhanced sulfur oxidation, thereby influencing the biogeochemical sulfur cycle.
An Introduction to the Structure and Function of the Ribosome
Authors: Dunkle Jack A. , Cate Jamie H. D.
Published: May 2014

E. coli
continues to serve as a key model for the structure and function of the ribosome, structures of ribosome from other organisms and domains of life have also greatly contributed to our knowledge of protein synthesis. Many structural models of the ribosome in a number of steps of the protein synthesis cycle have been solved by cryo-electron microscopy (cryo-EM) and x-ray crystallography. This chapter introduces the structure and dynamics of the ribosome based on these structures and ends with a brief discussion of the many questions that the structures leave unanswered. Protein synthesis is a multistep process, and the structural features of the ribosome along with the large number of cofactors reflect the complexity of translation. Numerous protein factors in addition to the ribosome contribute to translation in bacteria during the steps of initiation, elongation, termination, and recycling. These protein factors make intimate contacts to key regions of the ribosome, and this aspect is discussed in the chapter in light of our present understanding of the structure and function of the ribosome. The intact ribosome contains three binding sites for substrate tRNAs that are termed as the aminoacyl-tRNA site (A site), peptidyl-tRNA site (P site), and exit-tRNA site (E site). These three binding sites span the interface between the 30S and 50S subunits. The central activity of the ribosome is catalysis of peptide bond formation. The region of the ribosome responsible for catalyzing the reaction is called the peptidyl transferase center (PTC).
Intracellular Voyeurism: Examining the Modulation of Host Cell Activities by
Salmonella enterica Serovar Typhimurium
Authors: Szeto Jason , Brumell John H.
Published: May 2014

Salmonella
spp. can infect host cells by gaining entry through phagocytosis or by inducing host cell membrane ruffling that facilitates bacterial uptake. With its wide host range,
Salmonella enterica
serovar Typhimurium has proven to be an important model organism for studying intracellular bacterial pathogenesis. Upon entry into host cells, serovar Typhimurium typically resides within a membrane-bound compartment termed the
Salmonella
-containing vacuole (SCV). From the SCV, serovar Typhimurium can inject several effector proteins that subvert many normal host cell systems, including endocytic trafficking, cytoskeletal rearrangements, lipid signaling and distribution, and innate and adaptive host defenses. The study of these intracellular events has been made possible through the use of various imaging techniques, ranging from classic methods of transmission electron microscopy to advanced livecell fluorescence confocal microscopy. In addition, DNA microarrays have now been used to provide a "snapshot" of global gene expression in serovar Typhimurium residing within the infected host cell. This review describes key aspects of
Salmonella
-induced subversion of host cell activities, providing examples of imaging that have been used to elucidate these events. Serovar Typhimurium engages specific host cell machinery from initial contact with the host cell to replication within the SCV. This continuous interaction with the host cell has likely contributed to the extensive arsenal that serovar Typhimurium now possesses, including two type III secretion systems, a range of ammunition in the form of TTSS effectors, and a complex genetic regulatory network that coordinates the expression of hundreds of virulence factors.
Imaging Techniques for the Study of
Escherichia coli
and
Salmonella
Infections
Authors: Torstensson Elisabeth , KjÄll Peter , Richter-Dahlfors Agneta
Published: May 2014

Infectious diseases are among the leading causes of mortality worldwide, and numerous bacterial species are included in the vast array of causative agents. This review describes microscopy-based techniques that can be used to study interactions between bacteria and infected host cells, bacterial gene expression in the infected animal, and bacteria-induced cell signaling in eukaryotic cells. As infectious model systems, urinary tract infections caused by uropathogenic
Escherichia coli
(UPEC) and a mouse model of typhoid fever caused by
Salmonella enterica
serovar Typhimurium are used. To study the interaction mechanism between bacteria and eukaryotic cells, one commonly uses cell lines, primary cells, and animal models. Within the host, bacteria can be located in various organs where they are exposed to different cell types, ranging from epithelial cells at the mucosal linings to phagocytic white blood cells. In each site, bacteria are exposed to specific sets of innate immune defense mechanisms, and to survive these threats, bacteria must rapidly adapt their gene expression profile to maximize their chance of survival in any situation. The rapid development of fluorescent reporter proteins and advances in microscopy-based techniques have provided new and promising approaches not only to locate bacteria in tissues, but also to analyze expression of virulence factors in individual bacteria and host cells during the progression of disease. These techniques enable, for the first time, studies of the complex microenvironments within infected organs and will reveal the alterations of bacterial physiology that occur during bacterial growth within a host.
How We Got to Where We Are: the Ribosome in the 21st Century
Authors: Moore Peter B.
Published: May 2014

This article is a short, informal history of the ribosome field that begins with the emergence of the field in the 1930s and ends with a description of its state in 2007, the year this essay was written. The growth in our understanding of both the role of the ribosome in protein synthesis and its structure is emphasized. Starting in 2000, the field experienced a massive upheaval as a result of the publication of the first atomic-resolution crystal structures for ribosomes. However, by 2007, the field had recovered sufficiently so that one could begin to understand how it was likely to evolve in its "poststructural" era. For that reason, this essay is about as useful as a short history of the ribosome field today as it was several years ago, when it was written.
Structural Basis for the Decoding Mechanism
Authors: Gregory Steven T.
Published: May 2014

The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.
The Nucleoid: an Overview
Authors: Ishihama Akira
Published: May 2014

This review provides a brief review of the current understanding of the structure-function relationship of the
Escherichia coli
nucleoid developed after the overview by Pettijohn focusing on the physical properties of nucleoids. Isolation of nucleoids requires suppression of DNA expansion by various procedures. The ability to control the expansion of nucleoids in vitro has led to purification of nucleoids for chemical and physical analyses and for high-resolution imaging. Isolated
E. coli
genomes display a number of individually intertwined supercoiled loops emanating from a central core. Metabolic processes of the DNA double helix lead to three types of topological constraints that all cells must resolve to survive: linking number, catenates, and knots. The major species of nucleoid core protein share functional properties with eukaryotic histones forming chromatin; even the structures are different from histones. Eukaryotic histones play dynamic roles in the remodeling of eukaryotic chromatin, thereby controlling the access of RNA polymerase and transcription factors to promoters. The
E. coli
genome is tightly packed into the nucleoid, but, at each cell division, the genome must be faithfully replicated, divided, and segregated. Nucleoid activities such as transcription, replication, recombination, and repair are all affected by the structural properties and the special conformations of nucleoid. While it is apparent that much has been learned about the nucleoid, it is also evident that the fundamental interactions organizing the structure of DNA in the nucleoid still need to be clearly defined.
The Aerobic and Anaerobic Respiratory Chain of
Escherichia coli
and
Salmonella enterica
: Enzymes and Energetics
Authors: Unden Gottfried , Dünnwald Pia
Published: May 2014

Escherichia coli
contains a versatile respiratory chain which oxidizes ten different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors.
Salmonella
is able to use even two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. Various respiratory pathways can be established by combining the oxidation of different electron donors and acceptors which are linked by respiratory quinones. The enzymes vary largely with respect to architecture, membrane topology, and mode of energy conservation. Most of the energy-conserving dehydrogenases (e.g., FdnGHI, HyaABC, and HybCOAB) and of the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox loop mechanism. Only two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases (e.g., Ndh, SdhABCD, and GlpD) and of terminal reductases (e.g., FrdABCD and DmsABC) do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known from structural and biochemical studies or can be predicted from sequence information. The H
+
/2e
−
ratios of proton translocation for most respiratory chains are in the range from 2 to 6 H
+
/2e
−
. The energetics of the individual redox reactions and of the respiratory chains is described. In contrast to the knowledge on enzyme function are physiological aspects of respiration such as organization and coordination of the electron transport and the use of alternative respiratory enzymes, not well characterized.
NADH as Donor
Authors: Friedrich Thorsten , Pohl Thomas
Published: May 2014

The number of NADH dehydrogenases and their role in energy transduction in
Escherchia coli
have been under debate for a long time. Now it is evident that
E. coli
possesses two respiratory NADH dehydrogenases, or NADH:ubiquinone oxidoreductases, that have traditionally been called NDH-I and NDH-II. This review describes the properties of these two NADH dehydrogenases, focusing on the mechanism of the energy converting NADH dehydrogenase as derived from the high resolution structure of the soluble part of the enzyme. In
E. coli
, complex I operates in aerobic and anaerobic respiration, while NDH-II is repressed under anaerobic growth conditions. The insufficient recycling of NADH most likely resulted in excess NADH inhibiting tricarboxylic acid cycle enzymes and the glyoxylate shunt.
Salmonella enterica
serovar Typhimurium complex I mutants are unable to activate ATP-dependent proteolysis under starvation conditions. NDH-II is a single subunit enzyme with a molecular mass of 47 kDa facing the cytosol. Despite the absence of any predicted transmembrane segment it has to be purified in the presence of detergents, and the activity of the preparation is stimulated by an addition of lipids.
Oxygen as Acceptor
Authors: Borisov Vitaliy B. , Verkhovsky Michael I.
Published: May 2014

Like most bacteria,
Escherichia coli
has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophoshate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and demethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O
2
is served by two major oxidoreductases (oxidases), cytochrome
bo3
and cytochrome
bd
. Terminal oxidases of aerobic respiratory chains of bacteria, which use O
2
as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome
c
or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome
bo3
and cytochrome
bd
in
E. coli
. It also presents a discussion on the genetics and the prosthetic groups of cytochrome
bo3
and cytochrome
bd
. The
E. coli
membrane contains three types of quinones which all have an octaprenyl side chain (C
40
). It has been proposed that the
bo
3
oxidase can have two ubiquinone-binding sites with different affinities. The spectral properties of cytochrome
bd
-II closely resemble those of
cydAB
-encoded cytochrome
bd
.
Binding Protein-Dependent Uptake of Maltose into Cells via an ATP-Binding Cassette Transporter
Authors: Davidson Amy L. , Alvarez Frances Joan D.
Published: May 2014

Maltose and maltodextrins are actively transported across the cytoplasmic membrane of
Escherichia coli
and
Salmonella
by a periplasmic binding protein (BP)- dependent transport system. Since 1996, there have been many advances in the understanding of the structure and mechanism of the maltose transporter, in the assembly of the membrane-associated transporter complex, and in the mechanism of regulation of transport both at the DNA and the protein level. The transporter has been studied in detergent and reconstituted in liposome vesicles, and while many features, including the ability of maltose-binding protein (MBP) to stimulate ATPase activity, are retained in detergent, it has been noted that the basal ATPase activity of the transporter is elevated in detergent compared with liposomes. This review focuses on these recent developments, which have culminated in a high resolution structure of MBP in a complex with the MalFGK
2
transporter. While this review focuses on the maltose system, complementary work has been carried out on many different ATP binding cassette (ABC) transporters, all of which has contributed in important ways to the understanding of the maltose transport system. The regulation of the maltose transport system, at the DNA level, is implemented by the synergistic action of MalT and cAMP/CAP complex and, at the protein level, by interactions of MalK with unphosphorylated EIIA
glc
, a signal-transducing component of the phosphoenolpyruvate-glucose phosphotransferase system.