Oaks enhance early life stage longleaf pine growth and density in a subtropical xeric savanna.

The interplay of positive and negative species interactions controls species assembly in communities. Dryland plant communities, such as savannas, are important to global biodiversity and ecosystem functioning. Sandhill oaks in xeric savannas of the southeastern United States can facilitate longleaf pine by enhancing seedling survival, but the effects of oaks on recruitment and growth of longleaf pine have not been examined. We censused, mapped, and monitored nine contiguous hectares of longleaf pine in a xeric savanna to quantify oak-pine facilitation, and to examine other factors impacting recruitment, such as vegetation cover and longleaf pine tree density. We found that newly recruited seedlings and grass stage longleaf pines were more abundant in oak-dominated areas where densities were 230% (newly recruited seedlings) and 360% (grass stage) greater from lowest to highest oak neighborhood densities. Longleaf pine also grew faster under higher oak density. Longleaf pine recruitment was lowest under longleaf pine canopies. Mortality of grass stage and bolt stage longleaf pine was low (~1.0% yr-1) in the census interval without fire. Overall, our findings highlight the complex interactions between pines and oaks-two economically and ecologically important genera globally. Xeric oaks should be incorporated as a management option for conservation and restoration of longleaf pine ecosystems.

Confined Assemblies of Colloidal Particles with Soft Repulsive Interactions.

We investigate the microconfinement of charged silica nanoparticles dispersed in refractive index matching monomers in poly(dimethylsiloxane) (PDMS) porous membrane. Here, the silica colloidal particles interact with each other and the pore wall via electrostatic double layer forces. Different from the hard sphere systems where the assembled morphologies are prescribed by the diameter ratio between the cylindrical confinement and the nanoparticles, here we observe a much richer variety of assemblies that are highly sensitive to both bulk and local nanoparticle concentration with fixed particle size and channel size. The experimentally observed assembly morphologies are consistent with theoretical predictions from the literature, based on Yukawa potential in the low packing density regime. Also, most of the configurations found in the experiment are well described by computer simulations using pairwise additive long-range repulsive interactions, demonstrating the ability to control the system to obtain a desired structure.

Motor transport of self-assembled cargos in crowded environments.

Intracellular transport of cargo particles is performed by multiple motors working in concert. However, the mechanism of motor association to cargos is unknown. It is also unknown how long individual motors stay attached, how many are active, and how multimotor cargos would navigate a densely crowded filament with many other motors. Prior theoretical and experimental biophysical model systems of intracellular cargo have assumed fixed teams of motors transporting along bare microtubules or microtubules with fixed obstacles. Here, we investigate a regime of cargos transporting along microtubules crowded with free motors. Furthermore, we use cargos that are able to associate or dissociate motors as it translocates. We perform in vitro motility reconstitution experiments with high-resolution particle tracking. Our model system consists of a quantum dot cargo attached to kinesin motors, and additional free kinesin motors that act as traffic along the microtubule. Although high densities of kinesin motors hinder forward motion, resulting in a lower velocity, the ability to associate motors appears to enhance the run length and attachment time of the quantum dot, improving overall cargo transport. These results suggest that cargos that can associate new motors as they transport could overcome traffic jams.

Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium.

Two groups independently sequenced the Agrobacterium tumefaciens C58 genome in 2001. We report here consolidation of these sequences, updated annotation, and additional analysis of the evolutionary history of the linear chromosome, which is apparently limited to the biovar I group of Agrobacterium.

Management of Neuropathic Pain in Polyneuropathy.

PURPOSE OF REVIEW: Many polyneuropathies cause significant neuropathic pain, resulting in substantial morbidity and reduced quality of life. Appropriate management is crucial for maintaining quality of life for patients with painful polyneuropathies. The US Food and Drug Administration (FDA) has only approved one new drug for painful diabetic neuropathy in the past decade, a topical capsaicin patch that was initially approved for the treatment of postherpetic neuralgia in 2009. Gabapentinoids and serotonin norepinephrine reuptake inhibitors (SNRIs) continue to have an advantage in safety profiles and efficacy. Other antiepileptic medications remain second-line agents because of fewer studies documenting efficacy. RECENT FINDINGS: This article reviews recent literature on complementary and pharmacologic therapies for the management of painful polyneuropathies. Exercise has emerged as an important therapeutic tool and may also improve the underlying polyneuropathy in the setting of obesity, metabolic syndrome, and diabetes. SUMMARY: The approach to management of painful polyneuropathies is multifactorial, using both pharmacologic and nonpharmacologic measures to improve pain severity and patient quality of life.

Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria.

The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.

Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes.

Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins.

Nanoparticles binding to lipid membranes: from vesicle-based gels to vesicle tubulation and destruction.

While cells offer numerous inspiring examples in which membrane morphology and function are controlled by interactions with viruses or proteins, we still lack design principles for controlling membrane morphology in synthetic systems. With experiments and simulations, we show that spherical nanoparticles binding to lipid-bilayer membrane vesicles results in a remarkably rich set of collective morphologies that are controllable via the particle binding energy. We separately study cationic and anionic particles, where the adhesion is tuned by addition of oppositely charged lipids to the vesicles. When the binding energy is weak relative to a characteristic membrane-bending energy, vesicles adhere to one another and form a soft solid gel, a novel and useful platform for controlled release. With larger binding energy, a transition from partial to complete wrapping of the nanoparticles causes a remarkable vesicle destruction process culminating in rupture, nanoparticle-membrane tubules, and an apparent inversion of the vesicles. These findings help unify the diverse phenomena observed previously. They also open the door to a new class of vesicle-based, closed-cell gels that are more than 99% water and can encapsulate and release on demand, and show how to drive intentional membrane remodeling for shape-responsive systems.

The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

A Method Utilizing Ultra-High Performance Liquid Chromatography with Ultraviolet and Mass Spectrometric Detection for the Analysis of Material Extracts Produced during a Controlled Extraction Study.

Pharmaceutical packaging/delivery systems and medical devices are characterized via a controlled extraction study as part of the development process for new pharmaceutical products. The purpose of this study is to determine compounds that may be extracted from the packaging using various solvents and exposure conditions. Results generated from a controlled extraction study serve to evaluate the suitability of the materials in the package configuration as well as provide an assessment of compounds that may potentially leach into the drug product. Analysis of extract samples generated during a controlled extraction study is performed utilizing multiple analytical methodologies to help establish a complete extractable profile regardless of the polarity, volatility, or other unique physical properties of each compound that may be present. The work presented in this article describes a method for the analysis of non-volatile as well as thermally labile, or otherwise not suited for analysis by gas chromatography, semi-volatile compounds from extraction samples. An ultra-high performance liquid chromatographic system with both atmospheric chemical ionization mass spectrometric and ultra violet detectors is used as the platform for the method. Adequate separation and retention is achieved for a mix of model compounds representing a wide range of common extractables within a 22 min analysis time. Ionization of this diverse range of compounds is also achieved with acceptable responses in the total ion chromatography data. Finally, analysis of extraction samples directly, even those comprised of non-compatible organic solvents, is demonstrated with no significant impact on the chromatography. Three case studies are presented to further illustrate method performance and its use for controlled extraction samples. LAY ABSTRACT: Pharmaceutical packaging/delivery systems and medical devices are characterized via a controlled extraction study as part of the development process for new pharmaceutical products. The purpose of this study is to determine compounds that may be extracted from the packaging using various solvents and exposure conditions. Results of this work serve to evaluate the suitability of the material for use in the package as well as provide an assessment of compounds that may potentially contaminate the drug product. Analysis of extract samples generated during a controlled extraction study is performed utilizing multiple analytical methodologies to help establish a complete extractable profile regardless of the unique physical properties of each compound that may be present. The work presented in this article describes a method for the analysis of non-volatile as well as semi-volatile compounds from extraction samples. Separation and detection of a diverse range of extractables were demonstrated in a 22 min analysis time. Three case studies are presented to further illustrate method performance and its use for controlled extraction samples.

Fear of movement/(re)injury and activity avoidance in persons with neurogenic versus vascular claudication.

BACKGROUND CONTEXT: Activity avoidance and fear of movement/(re)injury are increasingly being recognized as important factors in the rehabilitation of persons suffering from chronic low back pain, yet these factors have not been thoroughly explored in persons suffering from neurogenic claudication resulting from lumbar spinal stenosis. PURPOSE: To determine, compare, and explain differences in the degree of fear of movement/(re)injury and activity avoidance in persons with neurogenic claudication, vascular claudication, and asymptomatic volunteers. STUDY DESIGN: Prospective controlled cohort study at an academic medical center. PATIENT SAMPLE: Eighty-two adults aged between 55 and 90 years with neurogenic claudication, vascular claudication, or no back and leg symptoms. METHODS: Subjects completed a visual analog scale for pain, the Center for Epidemiological Studies Depression Scale, the Quebec Back Pain Disability Scale, Short Form 36 (SF-36), and the 13-item version of the Tampa Scale for Kinesiophobia (Tampa). They were also asked to estimate their maximum walking distance. OUTCOME MEASURES: The difference in the level of fear of movement/(re)injury and activity avoidance in the two symptomatic populations, as well as the predictive validity of self-reported measures such as pain level, functional impairment, and depression in determining fear avoidance. RESULTS: The total Tampa score was significantly higher in individuals with neurogenic claudication (M=31.68; standard deviation [SD]=7.56; N=39) than vascular claudication (M=24.07; SD=6.57; N=15) (p=.002), whereas both symptomatic groups were significantly different from controls (M=18.71; SD=6.3; N=28) (p<.001 vs. neurogenic; p<.05 vs. vascular). Tampa scores were strongly correlated to the Center for Epidemiological Studies Depression Scale score (r=0.515; p<.001), SF-36 Physical Functioning score (r=-0.632; p<.001), and the visual analog scale average level of pain in a week (r=0.461; p<.001). Using a standard multiple regression model (R²=0.406; F(3,62)=13.47; p<.001), the amount of functional impairment, that is, the SF-36 Physical Functioning score, was the strongest contributor to the variance in the Tampa total score (ß=-0.371; p=.014). The average level of pain did not make a significant or unique contribution in predicting the Tampa total score. Functional impairment as measured by the SF-36 Physical Functioning was strongly correlated with both pain (r=-0.740; p<.001) and depression (r=-0.488; p<.001). CONCLUSIONS: Persons with neurogenic claudication have important elevations in fear and avoidance, higher than those with claudication from another source (vascular insufficiency). The impact of fear and avoidance along with other factors such as depression on pain, disability, and quality of life for persons with claudication and spinal stenosis need to be explored.

Body mass index, but not blood pressure is related to the level of pain in persons with chronic pain.

OBJECTIVE: To determine whether obesity or blood pressure relate to the level of pain experienced by persons with chronic back pain. DESIGN: Retrospective Study. SETTING: University spine program. PATIENTS (OR PARTICIPANTS): Adults seeking care for back pain of more than 3 months duration. METHODS OR INTERVENTIONS (OR ASSESSMENT OF RISK FACTORS): Measurement of weight, blood pressure, and pain on a numeric scale. MAIN OUTCOME MEASUREMENTS: Relationships between body mass index (BMI) and pain, blood pressure and pain. RESULTS: 198 subjects had a mean BMI of 29.50 ± 7.12, with 33.3% obese. The relationship between pain as a continuous variable and BMI approached significance (r= 0.125, n= 175, p= 0.098). The BMI of persons with lower pain scores of 0-3 was significantly different from those with high pain scores of 7-10. No significant relationship was found between pain and systolic (r=0.126, p=0.078) or diastolic (r= 0.099, p=0.165) blood pressure. CONCLUSIONS: Contrary to assumptions about acute pain, increased chronic pain does not appear to relate to increased blood pressure. The relationship of obesity with increased pain level among persons who have chronic pain raises the possibility that psychological or physiological mechanisms may be important above and beyond the biomechanical impact of obesity.

Phosphoenolpyruvate carboxykinase is an acid-induced, chromosomally encoded virulence factor in Agrobacterium tumefaciens.

The pckA gene, encoding phosphoenolpyruvate carboxykinase, catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to form phosphoenolpyruvate. Located on the circular chromosome of Agrobacterium, this locus is adjacent to the loci chvG and chvI, encoding a two-component regulatory system that has been shown to be important in virulence. Using a reporter gene fusion, studies showed that the pckA gene is induced by acidic pH but not by acetosyringone. This acid induction is regulated by the chvG-chvI regulatory system, which controls acid-inducible genes. A pckA mutant had no demonstrable PckA enzyme activity and grew on AB minimal medium with glucose but did not grow on the same medium with succinate as the sole carbon source and was more inhibited in its growth than the wild-type strain by an acidic environment. A pckA mutant was highly attenuated in tumor-inducing ability on tobacco leaf disks and was severely attenuated in vir gene expression. Although vir gene induction was completely restored when a constitutive virG gene was introduced into the mutant strain, virulence was only partially restored. These results suggest that avirulence may be due to a combination of the inhibition of this mutant in the acidic plant wound environment and the poor induction of the vir genes.

Citrate synthase mutants of Agrobacterium are attenuated in virulence and display reduced vir gene induction.

A citrate synthase (CS) deletion mutant of Agrobacterium tumefaciens C58 is highly attenuated in virulence. The identity of the mutant was initially determined from its amino acid sequence, which is 68% identical to Escherichia coli and 77% identical to Brucella melitensis. The mutant lost all CS enzymatic activity, and a cloned CS gene complemented a CS mutation in Sinorhizobium. The CS mutation resulted in a 10-fold reduction in vir gene expression, which likely accounts for the attenuated virulence. When a plasmid containing a constitutive virG [virG(Con)] locus was introduced into this mutant, the level of vir gene induction was restored to nearly wild-type level. Further, the virG(Con)-complemented CS mutant strain induced tumors that were similar in size and number to those induced by the parental strain. The CS mutation resulted in only a minor reduction in growth rate in a glucose-salts medium. Both the CS mutant and the virG(Con)-complemented CS strain displayed similar growth deficiencies in a glucose-salts medium, indicating that the reduced growth rate of the CS mutant could not be responsible for the attenuated virulence. A search of the genome of A. tumefaciens C58 revealed four proteins, encoded on different replicons, with conserved CS motifs. However, only the locus that when mutated resulted in an attenuated phenotype has CS activity. Mutations in the other three loci did not result in attenuated virulence and any loss of CS activity, and none were able to complement the CS mutation in Sinorhizobium. The function of these loci remains unknown.

A new type IV secretion system promotes conjugal transfer in Agrobacterium tumefaciens.

Two DNA transfer systems encoded by the tumor-inducing (Ti) plasmid have been previously identified in Agrobacterium tumefaciens. The virB operon is required for the transfer of transferred DNA to the plant host, and the trb system encodes functions required for the conjugal transfer of the Ti plasmid between cells of Agrobacterium. Recent availability of the genome sequence of Agrobacterium allowed us to identify a third system that is most similar to the VirB type IV secretion system of Bartonella henselae. We have designated this system avhB for Agrobacterium virulence homologue virB. The avhB loci reside on pAtC58 and encode at least 10 proteins (AvhB2 through AvhB11), 7 of which display significant similarity to the corresponding virulence-associated VirB proteins of the Ti plasmid. However, the AvhB system is not required for tumor formation; rather, it mediates the conjugal transfer of the pAtC58 cryptic plasmid between cells of Agrobacterium. This transfer occurs in the absence of the Ti plasmid-encoded VirB and Trb systems. Like the VirB system, AvhB products promote the conjugal transfer of the IncQ plasmid RSF1010, suggesting that these products comprise a mating-pair formation system. The presence of plasmid TiC58 or plasmid RSF1010 reduces the conjugal transfer efficiency of pAtC58 10- or 1,000-fold, respectively. These data suggest that complex substrate interactions exist among the three DNA transfer systems of Agrobacterium.

Survival of GacS/GacA mutants of the biological control bacterium Pseudomonas aureofaciens 30-84 in the wheat rhizosphere.

GacS/GacA comprises a two-component regulatory system that controls the expression of secondary metabolites required for the control of plant diseases in many pseudomonads. High mutation frequencies of gacS and gacA have been observed in liquid culture. We examined whether gacS/gacA mutants could competitively displace the wild-type populations on roots and thus pose a threat to the efficacy of biological control. The survival of a gac mutant alone and in competition with the wild type on roots was examined in the biological control strain Pseudomonas aureofaciens 30-84. In this bacterium, GacS/GacA controls the expression of phenazine antibiotics that are inhibitory to plant pathogenic fungi and enhance the competitive survival of the bacterium. Wheat seedlings were inoculated with strain 30-84, and bacteria were recovered from roots after 21 days in sterile or nonsterile soil to check for the presence of gacS or gacA mutants. Although no mutants were detected in the inoculum, gacS/gacA mutants were recovered from 29 out of 31 roots and comprised up to 36% of the total bacterial populations. Southern hybridization analysis of the recovered gacA mutants did not indicate a conserved mutational mechanism. Replacement series analysis on roots utilizing strain 30-84 and a gacA mutant (30-84.gacA) or a gacS mutant (30-84.A2) demonstrated that although the mutant population partially displaced the wild type in sterile soil, it did not do so in natural soil. In fact, in natural soil final rhizosphere populations of wild-type strain 30-84 starting from mixtures were at least 1.5 times larger than would be predicted from their inoculation ratio and generally were greater than or equal to the population of wild type alone despite lower inoculation rates. These results indicate that although gacS/gacA mutants survive in natural rhizosphere populations, they do not displace wild-type populations. Better survival of wild-type populations in mixtures with mutants suggests that mutants arising de novo or introduced within the inoculum may be beneficial for the survival of wild-type populations in the rhizosphere.