bluuebunny/crossref_metadata_2025 huggingface dataset:
How hot? How often? Getting the fire frequency and timing right for optimal management of woody cover and pasture composition in northern Australian grazed tropical savannas. Kidman Springs Fire Experiment 1993–2013
Authors: Cowley Robyn A. , Hearnden Mark H. , Joyce Karen E. , Tovar-Valencia Miguel , Cowley Trisha M. , Pettit Caroline L. , Dyer Rodd M.
Published: September 2014

A long-term (1993–2013) experiment in grazed semiarid tropical savannas in northern Australia tested the impact of varying the frequency (every 2, 4 and 6 years) and season (June – EDS versus October – LDS) of fire compared with unburnt controls on woody cover and pasture composition, in grassland and open woodland. Over an 18-year period, woody cover increased by 4% (absolute) in the woodland even with the most severe (i.e. frequent, late dry season) fire treatments. With less severe or no fire, woody cover increased by 12–17%. In the grassland, woody cover remained static when subjected to LDS fires every 2 or 4 years, but increased by 3–6% under other fire treatments, and by 8% when unburnt. Major shifts in understorey species composition occurred at both sites regardless of fire regime. The effect of fire on herbage mass and composition was compounded by higher grazing after fires. The herbage mass of perennial grasses declined and that of annual grasses and forbs increased following early or frequent fires. Brachyachne convergens, Gomphrena canescens and Flemingia pauciflora increased in response to fire while Aristida latifolia and Heteropogon contortus decreased. Four-yearly LDS fire provided the most effective management of woody cover and pasture composition. Although EDS fire is recommended for biodiversity management and reducing greenhouse gas emissions in wet tropical savannas, on grazed pastoral land, it can promote woodland thickening and pasture degradation. Optimal fire management, therefore, depends on vegetation type, land use and the prevailing seasonal timing and frequency of fire.
Cellular memory in eukaryotic chemotaxis
Authors: Skoge Monica , Yue Haicen , Erickstad Michael , Bae Albert , Levine Herbert , Groisman Alex , Loomis William F. , Rappel Wouter-Jan
Published: September 2014

Significance

Chemotaxis—the directed motion of cells in response to chemical cues—plays an important role in many biological processes. A well-known example is the migration of
Dictyostelium
cells to the source of traveling waves of chemoattractant during aggregation. A classic problem is how cells chemotax toward the wave source, even though the spatial gradient reverses direction in the back of the wave. To address this problem, we use microfluidics to expose cells to traveling waves with varying period, as well as rapid gradient switches. Our results reconcile the observed persistent motion in waves with the high sensitivity of cells to static gradients and suggest that chemotaxis to dynamic cues involves a coupling between adaptive directional sensing and bistable cellular memory.
Dysregulation of gene expression as a cause of Cockayne syndrome neurological disease
Authors: Wang Yuming , Chakravarty Probir , Ranes Michael , Kelly Gavin , Brooks Philip J. , Neilan Edward , Stewart Aengus , Schiavo Giampietro , Svejstrup Jesper Q.
Published: September 2014

Significance

Cockayne syndrome (CS) is an autosomal-recessive, multisystem disorder characterized by neurological disease, growth failure, developmental abnormalities, photosensitivity, and degeneration of organ systems such as the ear and eye, including cataracts. Most patients with CS carry mutations in Cockayne syndrome group B (CSB), best known for its role in transcription-coupled repair. Indeed, because various repair pathways are compromised in patient cells, CS is widely considered a genome instability syndrome. Here, we provide evidence from human and mouse cell models, as well as brain tissue from patients with CS, that the involvement of CSB in regulating gene expression can explain several features of CS. Together, our data suggest that dysregulation of gene regulatory networks rather than DNA repair defects may be the main cause of neurological symptoms in CS.
Chromatin reader L(3)mbt requires the Myb–MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment
Authors: Blanchard Daniel P. , Georlette Daphne , Antoszewski Lisa , Botchan Michael R.
Published: September 2014

Significance

Histone binding proteins are critical for chromosome function, and mechanisms targeting them to nucleosomes are crucial. The
Drosophila
tumor suppressor L(3)mbt binds to methylated lysines of nucleosomal histones repressing gene transcription. We show that L(3)mbt chromosomal targeting requires proteins of a site-specific DNA binding complex [Myb–MuvB (MMB)/DREAM] and Mip120, an MMB/DREAM core component, is critical for recruitment. Surprisingly, chromosome association of L(3)mbt is insufficient for repression, as other MMB/DREAM members are required for L(3)mbt-mediated repression but not its chromosome targeting. Loss of
l
(
3
)
mbt
leads to lethal malignant brain tumors. We discuss our findings in the context of complex mechanisms where specific genes activated by loss of
l
(
3
)
mbt
may help tumor progression, whereas deletion of MMB genes may suppress this phenotype.
Wasta! The long-term implications of education expansion and economic liberalisation on politics in Sudan
Authors: Mann Laura
Published: September 2014

By tracking the changing nature of wasta, or personal intermediation, in the Khartoum labour market, this paper examines the impact of Islamist policies on state–society relations in Khartoum, Sudan. It argues that economic liberalisation and higher education expansion weakened sectarian control over the economy, replacing the former institutionalised system of privilege with a much more decentralised, private and transnational structure. The conclusion asks whether these policies have laid the groundwork for long-term political transformation. While education expansion and liberalisation should theoretically allow a regime to broaden patronage networks, they may also reduce the capacity of both the regime and the private sector to exercise power and establish predictability outwards.
Chronic Pathology and Longevity of Drepanocephalus spathans Infections in Juvenile Channel Catfish
Authors: Griffin Matt J. , Khoo Lester H. , Steadman James M. , Ware Cynthia , Quiniou Sylvie M. , Mischke Charles C. , Greenway Terrence E. , Wise David J.
Published: September 2014

Drepanocephalus spathans (Digenea: Echinostomatidae) is a common parasite of the double-crested cormorant Phalacrocorax auritus. The cercariae of D. spathans have been shown infective to juvenile Channel Catfish Ictalurus punctatus. The developing metacercariae concentrate in the cranial regions, often occluding blood vessels at the base of the branchial arch, occasionally resulting in death. The purpose of this study was to determine how long metacercariae of D. spathans persist in experimentally challenged Channel Catfish. Two separate infectivity trials were conducted. In both trials, metacercariae persisted at least 49 d postinfection, although prevalence and intensity of infection decreased over time. In the first trial, juvenile catfish (1–3 g) were exposed over three consecutive days to 100, 100, and 80 cercariae/fish/d, respectively. Fish were sampled 7 d after the final exposure, and metacercariae were observed in 83.3% (five of six) of challenged fish. At 21 d postexposure, metacercariae were present in only 50% of exposed fish (three of six). No metacercaria were observed in fish sampled at 35 d, however, metacercariae were present in one of six (16.7%) fish sampled 49 and 70 d postexposure, respectively. A second challenge consisted of a 24-h pooled exposure of 500 cercariae per fish. Again, metacercariae were present in most (six of seven; 85.7%) fish at 7 d postexposure. At 21 d postexposure, metacercariae were only evident in one of seven (14.3%) sampled fish. No metacercariae were present in any fish at 35 d postchallenge, yet one of seven (14.3%) fish was positive at 49 d postchallenge. The second study was terminated at 63 d postchallenge, as all fish sampled (n = 14) were negative for metacercariae. These data suggest that cercariae of D. spathans are infective to juvenile Channel Catfish, although the infection appears short lived as metacercariae rarely persisted longer than 2 months.

Received February 14, 2014; accepted May 30, 2014
Observations on Side-Swimming Rainbow Trout in Water Recirculation Aquaculture Systems
Authors: Good Christopher , Davidson John , Kinman Christin , Kenney P. Brett , Bæverfjord Grete , Summerfelt Steven
Published: September 2014

During a controlled 6-month study using six replicated water recirculation aquaculture systems (WRASs), it was observed that Rainbow Trout Oncorhynchus mykiss in all WRASs exhibited a higher-than-normal prevalence of side swimming (i.e., controlled, forward swimming but with misaligned orientation such that the fish's sagittal axis is approximately parallel to the horizontal plane). To further our understanding of this abnormality, a substudy was conducted wherein side swimmers and normally swimming fish were selectively sampled from each WRAS and growth performance (length, weight), processing attributes (fillet yield, visceral index, ventrum [i.e., thickness of the ventral “belly flap”] index), blood gas and chemistry parameters, and swim bladder morphology and positioning were compared. Side swimmers were found to be significantly smaller in length and weight and had less fillet yield but higher ventrum indices. Whole-blood analyses demonstrated that, among other things, side swimmers had significantly lower whole-blood pH and higher Pco2. Side swimmers typically exhibited swim bladder malformations, although the positive predictive value of this subjective assessment was only 73%. Overall, this study found several anatomical and physiological differences between side-swimming and normally swimming Rainbow Trout. Given the reduced weight and fillet yield of market-age side swimmers, producers would benefit from additional research to reduce side-swimming prevalence in their fish stocks.

Received March 20, 2014; accepted May 20, 2014
Preparation of a porcine plasma protein composite film and its application
Authors: Lee Ji-Hyun , Song Kyung Bin
Published: September 2014

To use blood released from slaughtering houses, a porcine plasma protein (PPP)/nanoclay composite film was prepared. The tensile strength and elongation at break values of the PPP composite film with 5% nanoclay were 10.01 MPa and 6.55%, respectively. The PPP composite film containing 1% grapefruit seed extract (GSE) was applied to pork meat, and the populations of inoculated Escherichia coli O157:H7 and Listeria monocytogenes in the pork meat packaged with the PPP composite film decreased by 0.8 and 1.0 log CFU/g, respectively, after 7 days of storage compared to the populations of the control. In addition, thiobarbituric acid values in the pork meat packaged with the PPP composite film were less than those of the control sample during storage. These results suggest that the PPP nanocomposite film containing 1% GSE can be used as a packaging material to maintain the quality of pork meat.
Fractal random series generated by Poisson-Voronoi tessellations
Authors: Calka Pierre , Demichel Yann
Published: September 2014

In this paper, we construct a new family of random series defined on

R

D

\mathbb {R}^D

, indexed by one scaling parameter and two Hurst-like exponents. The model is close to Takagi-Knopp functions, save for the fact that the underlying partitions of

R

D

\mathbb {R}^D

are not the usual dyadic meshes but random Voronoi tessellations generated by Poisson point processes. This approach leads us to a continuous function whose random graph is shown to be fractal with explicit and equal box and Hausdorff dimensions. The proof of this main result is based on several new distributional properties of the Poisson-Voronoi tessellation on the one hand, and an estimate of the oscillations of the function coupled with an application of a Frostman-type lemma on the other hand. Finally, we introduce two related models and provide in particular a box-dimension calculation for a derived deterministic Takagi-Knopp series with hexagonal bases.
Barnard Hampton and His Books
Authors: Rhodes Dennis E.
Published: September 2014

Barnard or Bernard Hampton is known from his inscription as the sixteenth-century owner of certain surviving Italian and Spanish books. Here, he is identified as a Clerk of the Council and Queen Mary's Spanish secretary, who died in 1572. The books that have so far been identified as his are listed and described.
A Matched Cohort Study of Postoperative Outcomes in Obstructive Sleep Apnea
Authors: Mutter Thomas C. , Chateau Dan , Moffatt Michael , Ramsey Clare , Roos Leslie L. , Kryger Meir
Published: September 2014

Background:

Obstructive sleep apnea (OSA) is associated with increased risk of postoperative complications. The authors investigated whether preoperative diagnosis and prescription of continuous positive airway pressure therapy reduces these risks.

Methods:

Matched cohort analysis of polysomnography data and Manitoban health administrative data (1987 to 2008). Postoperative outcomes in adult OSA patients up to 5 yr before (undiagnosed OSA, n = 1,571), and any time after (diagnosed OSA, n = 2,640) polysomnography and prescription of continuous positive airway pressure therapy for a new diagnosis of OSA, were compared with controls at low risk of having sleep apnea (n = 16,277). Controls were matched by exact procedure, indication, and approximate date of surgery. Procedures used to treat sleep apnea were excluded. Follow-up was at least 7 postoperative days. Results were reported as odds ratio (95% CI) for OSA or subgroup versus controls.

Results:

In multivariate analyses, the risk of respiratory complications (2.08 [1.35 to 3.19], P < 0.001) was similarly increased for both undiagnosed and diagnosed OSA. The risk of cardiovascular complications, primarily cardiac arrest and shock, was significantly different (P = 0.009) between undiagnosed OSA (2.20 [1.16 to 4.17], P = 0.02) and diagnosed OSA patients (0.75 [0.43 to 1.28], P = 0.29). For both outcomes, OSA severity, type of surgery, age, and other comorbidities were also important risk modifiers.

Conclusions:

Diagnosis of OSA and prescription of continuous positive airway pressure therapy were associated with a reduction in postoperative cardiovascular complications. Despite limitations in the data, these results could be used to justify and inform large efficacy trials of perioperative continuous positive airway pressure therapy in OSA patients.
Single-Center Experience and Short-term Outcome with the JenaValve: A Second-Generation Transapical Transcatheter Aortic Valve Implantation Device
Authors: Reuthebuch Oliver , Inderbitzin Devdas Thomas , Ruter Florian , Jeger Raban , Kaiser Christoph , Buser Peter , Fassl Jens , Eckstein Friedrich S.
Published: September 2014

Objective

We present the post-CE(Conformité Européenne)-mark single-center implantation experience and short-term outcome with the second-generation transapical JenaValve transcatheter aortic valve implantation system.

Methods

Patients [N = 27; 9 women; mean (SD) age, 80.3 (5.5) years] were operated on between November 2011 and August 2012. Via a transapical approach, the valve was positioned, in some cases, repositioned, and finally implanted. All data were collected during the hospital stay.

Results

The implantation success rate was 100%; the mean (SD) operation time was 124.7 (43.2) minutes; and the size of the implanted prosthesis was 23 mm (n = 6), 25 mm (n = 14), and 27 mm (n = 7). The in-hospital major adverse cardiac and cerebrovascular events were as follows: intraoperative resuscitation with subsequent aortic rupture (n = 1), postoperative hemorrhage needing revision (n = 1), myocardial infarction (n = 1), atrioventricular block needing a definitive pacemaker (n = 1), new-onset renal failure needing hemodialysis (n = 1), and stroke (n = 1). The 30-day mortality was 11.1% (n = 3). The mean (SD) intensive care unit/total stay was 2.2 (1.7)/11.7 (7.9) days. Postoperative echocardiography [day 6.7 (4.8)] revealed residual para-valvular leakage of trace to grade 1 in 12 patients (44.5%) and no leakage in 15 patients, with a mean (SD) transvalvular pressure gradient of 11.6 (5.6) mm Hg with significant reduction by 36.0 (17.7) mm Hg ( P = 0.0001, Wilcoxon signed rank test).

Conclusions

This second-generation repositionable transcatheter aortic valve implantation device could safely and successfully be implanted with a fast learning curve, significant reduction in pressure gradients, overall clinical improvement at discharge, as well as an acceptable morbidity and mortality rate in this highest-risk patient cohort.
Stepping in the direction of the fall: the next foot placement can be predicted from current upper body state in steady-state walking
Authors: Wang Yang , Srinivasan Manoj
Published: September 2014

During human walking, perturbations to the upper body can be partly corrected by placing the foot appropriately on the next step. Here, we infer aspects of such foot placement dynamics using step-to-step variability over hundreds of steps of steady-state walking data. In particular, we infer dependence of the ‘next’ foot position on upper body state at different phases during the ‘current’ step. We show that a linear function of the hip position and velocity state (approximating the body center of mass state) during mid-stance explains over 80% of the next lateral foot position variance, consistent with (but not proving) lateral stabilization using foot placement. This linear function implies that a rightward pelvic deviation during a left stance results in a larger step width and smaller step length than average on the next foot placement. The absolute position on the treadmill does not add significant information about the next foot relative to current stance foot over that already available in the pelvis position and velocity. Such walking dynamics inference with steady-state data may allow diagnostics of stability and inform biomimetic exoskeleton or robot design.
Stepping inside the niche: microclimate data are critical for accurate assessment of species' vulnerability to climate change
Authors: Storlie Collin , Merino-Viteri Andres , Phillips Ben , VanDerWal Jeremy , Welbergen Justin , Williams Stephen
Published: September 2014

To assess a species' vulnerability to climate change, we commonly use mapped environmental data that are coarsely resolved in time and space. Coarsely resolved temperature data are typically inaccurate at predicting temperatures in microhabitats used by an organism and may also exhibit spatial bias in topographically complex areas. One consequence of these inaccuracies is that coarsely resolved layers may predict thermal regimes at a site that exceed species' known thermal limits. In this study, we use statistical downscaling to account for environmental factors and develop high-resolution estimates of daily maximum temperatures for a 36 000 km
2
study area over a 38-year period. We then demonstrate that this statistical downscaling provides temperature estimates that consistently place focal species within their fundamental thermal niche, whereas coarsely resolved layers do not. Our results highlight the need for incorporation of fine-scale weather data into species' vulnerability analyses and demonstrate that a statistical downscaling approach can yield biologically relevant estimates of thermal regimes.
The influence of blood on targeted microbubbles
Authors: Owen Joshua , Grove Philip , Rademeyer Paul , Stride Eleanor
Published: September 2014

The ability to successfully target the delivery of drugs and other therapeutic molecules has been a key goal of biomedical research for many decades. Despite highly promisingin vitroresults, however, successful translation of targeted drug delivery into clinical use has been extremely limited. This study investigates the significance of the characteristics of whole blood, which are rarely accounted forin vitroassays, as a possible explanation for the poor correlation betweenin vitroandin vivoexperiments. It is shown using two separate model systems employing either biochemical or magnetic targeting that blood causes a substantial reduction in targeting efficiency relative to saline under the same flow conditions. This finding has important implications for the design of targeted drug delivery systems and the assays used in their development.
Topographic cell instructive patterns to control cell adhesion, polarization and migration
Authors: Ventre Maurizio , Natale Carlo Fortunato , Rianna Carmela , Netti Paolo Antonio
Published: September 2014

Topographic patterns are known to affect cellular processes such as adhesion, migration and differentiation. However, the optimal way to deliver topographic signals to provide cells with precise instructions has not been defined yet. In this work, we hypothesize that topographic patterns may be able to control the sensing and adhesion machinery of cells when their interval features are tuned on the characteristic lengths of filopodial probing and focal adhesions (FAs). Features separated by distance beyond the length of filopodia cannot be readily perceived; therefore, the formation of new adhesions is discouraged. If, however, topographic features are separated by a distance within the reach of filopodia extension, cells can establish contact between adjacent topographic islands. In the latter case, cell adhesion and polarization rely upon the growth of FAs occurring on a specific length scale that depends on the chemical properties of the surface. Topographic patterns and chemical properties may interfere with the growth of FAs, thus making adhesions unstable. To test this hypothesis, we fabricated different micropatterned surfaces displaying feature dimensions and adhesive properties able to interfere with the filopodial sensing and the adhesion maturation, selectively. Our data demonstrate that it is possible to exert a potent control on cell adhesion, elongation and migration by tuning topographic features’ dimensions and surface chemistry.
Dynamics of fingertip contact during the onset of tangential slip
Authors: Delhaye Benoit , Lefèvre Philippe , Thonnard Jean-Louis
Published: September 2014

Through highly precise perceptual and sensorimotor activities, the human tactile system continuously acquires information about the environment. Mechanical interactions between the skin at the point of contact and a touched surface serve as the source of this tactile information. Using a dedicated custom robotic platform, we imaged skin deformation at the contact area between the finger and a flat surface during the onset of tangential sliding movements in four different directions (proximal, distal, radial and ulnar) and with varying normal force and tangential speeds. This simple tactile event evidenced complex mechanics. We observed a reduction of the contact area while increasing the tangential force and proposed to explain this phenomenon by nonlinear stiffening of the skin. The deformation's shape and amplitude were highly dependent on stimulation direction. We conclude that the complex, but highly patterned and reproducible, deformations measured in this study are a potential source of information for the central nervous system and that further mechanical measurement are needed to better understand tactile perceptual and motor performances.
Torsional locomotion
Authors: Bigoni D. , Dal Corso F. , Misseroni D. , Bosi F.
Published: September 2014

One edge of an elastic rod is inserted into a friction-less and fitting socket head, whereas the other edge is subjected to a torque, generating a uniform twisting moment. It is theoretically shown and experimentally proved that, although perfectly smooth, the constraint realizes an expulsive axial force on the elastic rod, which amount is independent of the shape of the socket head. The axial force explains why screwdrivers at high torque have the tendency to disengage from screw heads and demonstrates torsional locomotion along a perfectly smooth channel. This new type of locomotion finds direct evidence in the realization of a ‘torsional gun’, capable of transforming torque into propulsive force.
Using voluntary motor commands to inhibit involuntary arm movements
Authors: Ghosh Arko , Rothwell John , Haggard Patrick
Published: September 2014

A hallmark of voluntary motor control is the ability to stop an ongoing movement. Is voluntary motor inhibition a general neural mechanism that can be focused on
any
movement, including involuntary movements, or is it mere termination of a positive voluntary motor command? The involuntary arm lift, or ‘floating arm trick’, is a distinctive long-lasting reflex of the deltoid muscle. We investigated how a voluntary motor network inhibits this form of involuntary motor control. Transcranial magnetic stimulation of the motor cortex during the floating arm trick produced a silent period in the reflexively contracting deltoid muscle, followed by a rebound of muscle activity. This pattern suggests a persistent generator of involuntary motor commands. Instructions to bring the arm down voluntarily reduced activity of deltoid muscle. When this voluntary effort was withdrawn, the involuntary arm lift resumed. Further, voluntary motor inhibition produced a strange illusion of physical resistance to bringing the arm down, as if ongoing involuntarily generated commands were located in a ‘sensory blind-spot’, inaccessible to conscious perception. Our results suggest that voluntary motor inhibition may be a specific neural function, distinct from absence of positive voluntary motor commands.
Sexually selected skin colour is heritable and related to fecundity in a non-human primate
Authors: Dubuc Constance , Winters Sandra , Allen William L. , Brent Lauren J. N. , Cascio Julie , Maestripieri Dario , Ruiz-Lambides Angelina V. , Widdig Anja , Higham James P.
Published: September 2014

Sexual selection promotes the prevalence of heritable traits that increase an individual's reproductive rate. Despite theoretically strong directional selection, sexually selected traits can show inter-individual variation. Here, we investigate whether red skin ornamentation, a rare example of a male mammalian trait involved in mate attraction, influences fecundity and is heritable in rhesus macaques (
Macaca mulatta
), and explore the mechanisms that are involved in maintaining trait variation. Interestingly, the trait is expressed by and is attractive to both sexes. We collected facial images of 266 free-ranging individuals and modelled skin redness and darkness to rhesus macaque vision. We used 20 years of genetic parentage data to calculate selection gradients on the trait and perform heritability analyses. Results show that males who were both darkly coloured and high-ranking enjoyed higher fecundity. Female skin redness was positively linked to fecundity, although it remains unclear whether this influences male selectiveness. Heritability explained 10–15% of the variation in redness and darkness, and up to 30% for skin darkness when sexes are considered separately, suggesting sex-influenced inheritance. Our results suggest that inter-individual variation is maintained through condition-dependence, with an added effect of balancing selection on male skin darkness, providing rare evidence for a mammalian trait selected through inter-sexual selection.
Nocardioides daecheongensis sp. nov., isolated from soil
Authors: Lim Jun-Muk , Kim Soo-Jin , Hamada Moriyuki , Ahn Jae-Hyung , Weon Hang-Yeon , Suzuki Ken-ichiro , Ahn Tae-Young , Kwon Soon-Wo
Published: September 2014

Strain KIS2-16T was isolated from a soil sample collected from Daecheong Island of Incheon region, South Korea. KIS2-16T was Gram-staining-positive, aerobic, non-spore-forming, non-motile, catalase-positive, oxidase-negative and mesophilic. On the basis of 16S rRNA gene sequence analysis, strain KIS2-16T represented a member of the genus

Nocardioides

, being most closely related to the type strains of species of the genus

Nocardioides

,

Nocardioides maradonensis

RP-B30T (97.8 % sequence similarity) and

Nocardioides ultimimeridianus

RP-B26T (97.0 %). The fatty acid profile of KIS2-16T was dominated by C18 : 1ω9c, C17 : 1ω8c, C16 : 0, C18 : 0 10-methyl (TBSA), C16 : 0 2-OH and C17 : 0 2-OH. The major isoprenoid quinone was MK-8(H4), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The peptidoglycan structure was A3γ-type with ll-diaminopimelic acid. The genomic DNA G+C content of KIS2-16T was 64.9 mol%. Strain KIS2-16T showed DNA–DNA hybridization values of less than 70 % with the closely related species of the genus

Nocardioides

. Based on phenotypic, genotypic and phylogenetic data, the isolate represents a novel species of the genus

Nocardioides

, for which the name Nocardioides daecheongensis sp. nov. (type strain KIS2-16T = DSM 27136T = KACC 17297T = NBRC 109597T) is proposed.
Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae
Authors: Zarparvar Parisa , Amoozegar Mohammad Ali , Nikou Mahdi Moshtaghi , Schumann Peter , Ventosa Antonio
Published: September 2014

A halophilic actinomycete, strain R4S8T, was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30–50 °C (optimum 40 °C), pH 6–10 (optimum pH 7.0) and in the presence of 1–15 % (w/v) NaCl (optimum 3–5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8T contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8T belongs to the family

Thermoactinomycetaceae

and showed the closest 16S rRNA gene sequence similarity with

Desmospora activa

IMMIB L-1269T (95.5 %) and

Marininema mesophilum

SCSIO 10219T (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8T represents a novel species in a new genus within the family

Thermoactinomycetaceae

, for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8T ( = IBRC-M 10813T = CECT 8506T).
Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans
Authors: Bourhy Pascale , Collet Louis , Brisse Sylvain , Picardeau Mathieu
Published: September 2014

A group of strains representing species of the genusLeptospira,isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genusLeptospira. This was inferred from sequence analysis ofrrs(16S rRNA) and other genetic loci and suggests that they belong to a novel species. Two strains from each serogroup currently identified within this novel species were studied. Spirochaete, aerobic, motile, helix-shaped strains grew well at 30–37 °C, but not at 13 °C or in the presence of 8-azaguanine. Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genusLeptospira. The new isolates formed a distinct clade, which was most closely related toLeptospira borgpetersenii, in multilocus sequence analysis using concatenated sequences of the genesrpoB,recA,fusA,gyrB,leuSandsucA. Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA–DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. The G+C content of the genomic DNA was 39.5 mol%. These isolates are considered to represent a novel species, for which the nameLeptospira mayottensissp. nov. is proposed, with 200901116T( = CIP 110703T = DSM 28999T) as the type strain.
Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta
Authors: Miyazaki Masayuki , Sakai Sanae , Ritalahti Kirsti M. , Saito Yayoi , Yamanaka Yuko , Saito Yumi , Tame Akihiko , Uematsu Katsuyuki , Löffler Frank E. , Takai Ken , Imachi Hiroyuki
Published: September 2014

An anaerobic, psychrophilic bacterium, strain MO-SPC2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2T grew at 0–17 °C (optimally at 9 °C), at pH 6.0–8.0 (optimally at pH 6.8–7.2) and in 20–40 g NaCl l−1 (optimally at 20–30 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2T were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2T was affiliated with the genus

Sphaerochaeta

within the phylum

Spirochaetes

, and its closest relatives were

Sphaerochaeta pleomorpha

GrapesT (88.4 % sequence identity),

Sphaerochaeta globosa

BuddyT (86.7 %) and

Sphaerochaeta coccoides

SPN1T (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2T is considered to represent a novel species of the genus

Sphaerochaeta

, for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2T ( = JCM 17281T = DSM 23952T). An emended description of the genus

Sphaerochaeta

is also proposed.
Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation
Authors: Thatcher Shawn R. , Zhou Wengang , Leonard April , Wang Bing-Bing , Beatty Mary , Zastrow-Hayes Gina , Zhao Xiangyu , Baumgarten Andy , Li Bailin
Published: September 2014

Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease fromPseudomonas aeruginosa
Authors: Nji Emmanuel , Li Dianfan , Doyle Declan A. , Caffrey Martin
Published: September 2014

The prokaryotic lysine-specific permease (LysP) belongs to the amino acid–polyamine–organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of L-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP fromPseudomonas aeruginosawas recombinantly expressed inEscherichia coliand purified to near homogeneity by immobilized metal ion-affinity chromatography (IMAC) and size-exclusion chromatography (SEC). Hexagonal- and rod-shaped crystals were obtained in the presence of L-lysine and the L-lysine analogue L-4-thialysine by vapour diffusion and diffracted to 7.5 Å resolution. The diffraction data were indexed in space groupP21, with unit-cell parametersa= 169.53,b= 169.53,c= 290.13 Å, γ = 120°.
Crystallization and preliminary X-ray crystallographic studies of CrArsM, an arsenic(III)S-adenosylmethionine methyltransferase fromChlamydomonas reinhardtii
Authors: Packianathan Charles , Pillai Jitesh K. , Riaz Ahmed , Kandavelu Palani , Sankaran Banumathi , Rosen Barry P.
Published: September 2014

Arsenic is one the most toxic environmental substances. Arsenic is ubiquitous in water, soil and food, and ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. Arsenic(III)S-adenosylmethionine methyltransferases (AS3MT in animals and ArsM in microbes) are key enzymes of arsenic biotransformation, catalyzing the methylation of inorganic arsenite to give methyl, dimethyl and trimethyl products. Arsenic methyltransferases are found in members of every kingdom from bacteria to humans (EC 2.1.1.137). In the human liver, hAS3MT converts inorganic arsenic into more toxic and carcinogenic forms. CrArsM, an ortholog of hAS3MT from the eukaryotic green algaChlamydomonas reinhardtii, was purified by chemically synthesizing the gene and expressing it inEscherichia coli. Synthetic purified CrArsM was crystallized in an unliganded form. Crystals were obtained by the hanging-drop vapor-diffusion method. The crystals belonged to space groupR3:H, with unit-cell parametersa=b= 157.8,c= 95.4 Å, γ = 120° and two molecules in the asymmetric unit. Complete data sets were collected and processed to a resolution of 2.40 Å.
Crystallization of the Ets1–Runx1–CBFβ–DNA complex formed on the TCRα gene enhancer
Authors: Shiina Masaaki , Hamada Keisuke , Inoue-Bungo Taiko , Shimamura Mariko , Baba Shiho , Sato Ko , Ogata Kazuhiro
Published: September 2014

Gene transcription is regulated in part through the assembly of multiple transcription factors (TFs) on gene enhancers. To enable examination of the mechanism underlying the formation of these complexes and their response to a phosphorylation signal, two kinds of higher-order TF–DNA assemblies were crystallized composed of an unmodified or phosphorylated Ets1 fragment, a Runx1(L94K) fragment and a CBFβ fragment on the T-cell receptor (TCR) α gene enhancer. Within these complexes, the Ets1 and Runx1 fragments contain intrinsically disordered regulatory regions as well as their DNA-binding domains. Crystals of the complex containing unmodified Ets1 belonged to space groupP212121, with unit-cell parametersa= 78.7,b= 102.1,c= 195.0 Å, and diffracted X-rays to a resolution of 2.35 Å, and those containing phosphorylated Ets1 belonged to the same space group, with unit-cell parametersa= 78.6,b= 101.7,c= 194.7 Å, and diffracted X-rays to a similar resolution. To facilitate crystallization, a Runx1 residue involved in a hydrophobic patch that was predicted to be engaged in crystal packing based on the previously reported structures of Runx1-containing crystals was mutated.
Structure of homoserineO-acetyltransferase fromStaphylococcus aureus: the first Gram-positive ortholog structure
Authors: Thangavelu Bharani , Pavlovsky Alexander G. , Viola Ronald
Published: September 2014

HomoserineO-acetyltransferase (HTA) catalyzes the formation of L-O-acetyl-homoserine from L-homoserine through the transfer of an acetyl group from acetyl-CoA. This is the first committed step required for the biosynthesis of methionine in many fungi, Gram-positive bacteria and some Gram-negative bacteria. The structure of HTA fromStaphylococcus aureus(SaHTA) has been determined to a resolution of 2.45 Å. The structure belongs to the α/β-hydrolase superfamily, consisting of two distinct domains: a core α/β-domain containing the catalytic site and a lid domain assembled into a helical bundle. The active site consists of a classical catalytic triad located at the end of a deep tunnel. Structure analysis revealed some important differences forSaHTA compared with the few known structures of HTA.
Expression, crystallization and preliminary X-ray analysis of McbB, a multifunctional enzyme involved in β-carboline skeleton biosynthesis
Authors: Wang Hua , Zhang Huaidong , Mi Yanling , Ju Jianhua , Chen Qi , Zhang Houjin
Published: September 2014

β-Carboline alkaloids (βCs), with tricyclic pyrido[3,4-b]indole rings, have important pharmacological and therapeutic value. In the biosynthesis of βCs, the Pictet–Spengler (PS) cyclization reaction is responsible for the formation of ring structures. McbB is one of a few enzymes that are known to catalyse PS cyclization. It can also catalyse decarboxylation and oxidation. Here, the expression, crystallization and preliminary data analysis of McbB are reported. The crystals diffracted to 2.10 Å resolution and belonged to the monoclinic space groupP21, with unit-cell parametersa= 66.06,b= 85.48,c= 106.19 Å, α = 90.00, β = 106.77, γ = 90.00°. These results provide a basis for solving the crystal structure and elucidating the catalytic mechanism for McbB.
Structure of anAspergillus fumigatusold yellow enzyme (EasA) involved in ergot alkaloid biosynthesis
Authors: Chilton Annemarie S. , Ellis Ashley L. , Lamb Audrey L.
Published: September 2014

TheAspergillus fumigatusold yellow enzyme (OYE) EasA reduces chanoclavine-I aldehyde to dihydrochanoclavine aldehyde and works in conjunction with festuclavine synthase at the branchpoint for ergot alkaloid pathways. The crystal structure of the FMN-loaded EasA was determined to 1.8 Å resolution. The active-site amino acids of OYE are conserved, supporting a similar mechanism for reduction of the α/β-unsaturated aldehyde. The C-terminal tail of one monomer packs into the active site of a monomer in the next asymmetric unit, which is most likely to be a crystallization artifact and not a mechanism of self-regulation.
Crystallization and preliminary X-ray diffraction analysis of full-length spr1814, a response regulator ofStreptococcus pneumoniae, in complex with a phosphoryl analogue
Authors: Park Aekyung , Oh Jae Soon , Chi Young Min , Jeong Seong Weon
Published: September 2014

Spr1814 ofStreptococcus pneumoniaeis a signal transduction response regulator belonging to the NarL/FixJ subfamily, which has a helix–turn–helix DNA-binding effector domain. To understand how the phosphorylation of the conserved aspartic acid residue induces conformational changes in spr1814 allowing binding to the target promoter, recombinant spr1814 expressed inEscherichia coliwas crystallized with the phosphoryl analogue beryllium fluoride BeF3−by the hanging-drop vapour-diffusion method. The crystals diffracted to 1.9 Å resolution and belonged to space groupP21, with unit-cell parametersa= 40.2,b= 114.5,c= 50.1 Å, β = 92.1°. Structure determination by the SAD method using the bromine derivative 5-amino-2,4,6-tribromoisophthalic acid (B3C) is under way.
Structure ofStreptococcus agalactiaeglyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface
Authors: Ayres Chapelle A. , Schormann Norbert , Senkovich Olga , Fry Alexandra , Banerjee Surajit , Ulett Glen C. , Chattopadhyay Debasish
Published: September 2014

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH fromStreptococcus agalactiaein complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294–307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.
Extending lean manufacturing in supply chains: a successful case in Brazil
Authors: Beatriz Lopes de Sousa Jabbour Ana , Carlos Omodei Junior José , José Chiappetta Jabbour Charbel
Published: September 2014

Purpose

– The purpose of this paper is to present the results of a success story involving the extending of lean manufacturing practices between a focal firm and its supplier, both located in Brazil, thereby configuring a case of excellence.

Design/methodology/approach

– An in-depth case study was conducted involving two companies: Company A, focal, leader in its segment, located in Brazil; and Company B, Company A's supplier, also located in Brazil.

Findings

– Results indicate there are several mechanisms for extending lean manufacturing practices in the supply chain, such as workshops, training, and integrated teams. These mechanisms are shown and guidelines are also introduced for companies seeking to successfully extend lean manufacturing practices.

Originality/value

– An original use of define, measure, analyze, improve, control for structuring the extending of lean manufacturing practices to suppliers and, consequently, the importance of the lean six-sigma relationship in this context. Furthermore, the guidelines introduced serve as a benchmark for other companies interested in the topic.