bluuebunny/crossref_metadata_2025 huggingface dataset:
ERG dependence distinguishes developmental control of hematopoietic stem cell maintenance from hematopoietic specification
Authors: Taoudi Samir , Bee Thomas , Hilton Adrienne , Knezevic Kathy , Scott Julie , Willson Tracy A. , Collin Caitlin , Thomas Tim , Voss Anne K. , Kile Benjamin T. , Alexander Warren S. , Pimanda John E. , Hilton Douglas J.
Published: January 2011

Although many genes are known to be critical for early hematopoiesis in the embryo, it remains unclear whether distinct regulatory pathways exist to control hematopoietic specification versus hematopoietic stem cell (HSC) emergence and function. Due to their interaction with key regulators of hematopoietic commitment, particular interest has focused on the role of the ETS family of transcription factors; of these, ERG is predicted to play an important role in the initiation of hematopoiesis, yet we do not know if or when ERG is required. Using in vitro and in vivo models of hematopoiesis and HSC development, we provide strong evidence that ERG is at the center of a distinct regulatory program that is not required for hematopoietic specification or differentiation but is critical for HSC maintenance during embryonic development. We show that, from the fetal period, ERG acts as a direct upstream regulator of Gata2 and Runx1 gene activity. Without ERG, physiological HSC maintenance fails, leading to the rapid exhaustion of definitive hematopoiesis.
PKG-mediated MAPK signaling is necessary for long-term operant memory inAplysia
Authors: Michel Maximilian , Green Charity L. , Eskin Arnold , Lyons Lisa C.
Published: January 2011

Signaling pathways necessary for memory formation, such as the mitogen-activated protein kinase (MAPK) pathway, appear highly conserved across species and paradigms. Learning that food is inedible (LFI) represents a robust form of associative, operant learning that induces short- (STM) and long-term memory (LTM) inAplysia. We investigated the role of MAPK signaling in LFI memory in vivo. Inhibition of MAPK activation in animals prior to training blocked STM and LTM. Discontinuing MAPK signaling immediately after training inhibited LTM with no impact on STM. Therefore, MAPK signaling appears necessary early in memory formation for STM and LTM, with prolonged MAPK activity required for LTM. We found that LFI training significantly increased phospho-MAPK levels in the buccal ganglia. Increased MAPK activation was apparent immediately after training with greater than basal levels persisting for 2 h. We examined the mechanisms underlying training-induced MAPK activation and found that PKG activity was necessary for the prolonged phase of MAPK activation, but not for the early MAPK phase required for STM. Furthermore, we found that neither the immediate nor the prolonged phase of MAPK activation was dependent upon nitric oxide (NO) signaling, although expression of memory was dependent on NO as previously reported. These studies emphasize the role of MAPK and PKG in negatively reinforced operant memory and demonstrate a role for PKG-dependent MAPK signaling in invertebrate associative memory.
SPA‐1 controls the invasion and metastasis of human prostate cancer
Authors: Shimizu Yosuke , Hamazaki Yoko , Hattori Masakazu , Doi Keiko , Terada Naoki , Kobayashi Takashi , Toda Yoshinobu , Yamasaki Toshinari , Inoue Takahiro , Kajita Yoichiro , Maeno Atsushi , Kamba Tomomi , Mikami Yoshiki , Kamoto Toshiyuki , Yamada Tomomi , Kanno Toru , Yoshikawa Kiyotsugu , Ogawa Osamu , Minato Nagahiro , Nakamura Eijiro
Published: January 2011

Recent studies suggest that SIPA1 encoding a Rap GTPase‐activating protein SPA‐1 is a candidate metastasis efficiency‐modifying gene in human breast cancer. In this study, we investigated the expression and function of SPA‐1 in human prostate cancer (CaP). Immunohistochemical studies of tumor specimens from CaP patients revealed a positive correlation of SPA‐1 expression with disease progression and metastasis. The correlation was recapitulated in human CaP cell lines; LNCaP that rarely showed metastasis in SCID mice expressed an undetectable level of SPA‐1, whereas highly metastatic PC3 showed abundant SPA‐1 expression. Moreover, SIPA1 transduction in LNCaP caused prominent abdominal lymph node metastasis without affecting primary tumor size, whereas shRNA‐mediated SIPA1 knockdown or expression of a dominant‐active Rap1 mutant (Rap1V12) in PC3 suppressed metastasis. LNCaP transduced with SPA‐1 (LNCaP/SPA‐1) showed attenuated adhesion to the precoated extracellular matrices (ECM) including collagens and fibronectin, due to defective ECM‐medicated Rap1 activation. In addition, LNCaP/SPA‐1 showed a diminished level of nuclear Brd4, which is known to bind SPA‐1, resulting in reduced expression of a series of ECM‐related genes. These results suggest that SPA‐1 plays an important role in controlling metastasis efficiency of human CaP by regulating the expression of and interaction with ECM in the primary sites. (Cancer Sci 2011; 102: 828–836)
B7‐H3 expression in gastric cancer: A novel molecular blood marker for detecting circulating tumor cells
Authors: Arigami Takaaki , Uenosono Yoshikazu , Hirata Munetsugu , Yanagita Shigehiro , Ishigami Sumiya , Natsugoe Shoji
Published: January 2011

The clinical significance of B7‐H3 expression in gastric cancer remains unclear, although the B7 ligand family plays a critical role in the T cell‐mediated immune response. We therefore investigated B7‐H3 expression as a blood marker of circulating tumor cells and determined correlations with tumor progression in patients with gastric cancer. B7‐H3 expression in gastric cell lines was initially evaluated by immunocytochemistry. Furthermore, we used quantitative RT‐PCR to assess B7‐H3 mRNA expression in four cell lines and in 95 blood specimens from patients with gastric cancer, as well as in 21 samples of peripheral blood lymphocytes from healthy volunteers. B7‐H3 expression in cell lines was identified by immunocytochemistry and quantitative RT‐PCR. Blood specimens from patients with gastric cancer contained significantly more copies of B7‐H3 mRNA than those from healthy volunteers without cancer (P < 0.0001). Levels of B7‐H3 expression significantly correlated with overall stage (P = 0.013). The 5‐year survival rate was significantly lower in patients with high B7‐H3 expression than with low expression (P = 0.02). Multivariate analysis demonstrated that B7‐H3 expression was an independent prognostic factor (P = 0.046). Our results indicate that B7‐H3 appears to be a useful blood marker for predicting tumor progression in gastric cancer. (Cancer Sci 2011; 102: 1019–1024)
Prevalence and type distribution of human papillomavirus in healthy Japanese women aged 20 to 25 years old enrolled in a clinical study
Authors: Konno Ryo , Tamura Shinobu , Dobbelaere Kurt , Yoshikawa Hiroyuki
Published: January 2011

Efficacy, immunogenicity and tolerability of the human papillomavirus (HPV)‐16/18 AS04‐adjuvanted vaccine were evaluated in Japanese women aged 20–25 years, for which results have been reported previously. We analyzed the baseline data from that study and report the prevalence rates of HPV infection in young healthy Japanese women. One thousand and the forty Japanese women aged 20–25 years were enrolled in a phase II, double‐blind, controlled, randomized, multicenter study. At study entry, cervical specimens were collected from the women and tested by line probe assay for 25 HPV‐types and by HPV‐16/18‐specific polymerase chain reaction. The most frequently detected HPV‐type in baseline cervical specimens was HPV‐52 (8.1%), followed by HPV‐16 (6.5%), HPV‐51 (4.5%), HPV‐18 (4.0%) and HPV‐31 (3.8%). The proportion of HPV DNA‐positive women increased with severity of cytological abnormalities: 26.1% (237/908) in normal cytology, 93.3% (70/75) in low‐grade squamous intraepithelial lesion and 100% (7/7) in high‐grade squamous intraepithelial lesion. The relative contribution of HPV‐16 and HPV‐18 was 4.1 and 3.0% for normal cytology cases, and 20.0 and 16.0% in low‐grade squamous intraepithelial lesion, respectively. HPV‐16 was found in four of seven high‐grade squamous intraepithelial lesion cases (57.1%) and five of the six cervical intraepithelial neoplasia 2+ cases (83.3%). Multiple and single HPV infections were observed in 13.5% (140/1039) and 20.7% (215/1039) of all women, respectively. The HPV prevalence rates in Japanese women aged 20–25 years underline the importance of HPV vaccination at a young age and this report should be useful for monitoring changes in HPV prevalence after widespread HPV vaccination in Japanese women. (Cancer Sci 2011; 102: 877–882)
A spatially explicit approach to trophic interactions and landscape formation: patchiness in small‐scale variability of grazing effects along an intertidal stress gradient
Authors: Díaz Eliecer Rodrigo , McQuaid Christopher David
Published: January 2011

1. It is well known that grazing contributes to spatial and temporal patterns of algal cover on rocky shores, but this effect has traditionally been studied through grazer exclusion experiments using randomly positioned treatments at particular levels on the shore. Additionally, the effects of grazing on algal composition and biomass are expected to vary across gradients of physical stress and according to grazer size classes.

2. We examine two possible sources of spatial variability on rocky shores: (i) across‐shore variability and (ii) size class of grazers. We combined this approach with an across‐shore experiment, with experimental blocks running continuously from low to high shore, to examine the spatial structure of the effect strength of grazing for different size classes of grazers.

3. The results indicate that grazing effects vary among zones, habitats and grazer size classes. Micrograzers played a weak role in structuring the algal community and composition. Both macrograzers and mesograzers were important structuring agents on the upper low shore to the mid shore, but only mesograzers were important in tidal pools. Patterns across the shore of grazing effects were dynamic and patchy, acting simultaneously at different scales. The spatial pattern of grazing effects across the shore was also variable in time and was explained by the interactions among physical and biotic factors, often at the longer (10‐m scale) spatial intervals (or lags); mesograzers influenced almost the whole range of lags.

4. We conclude, based on cross‐semivariograms, that abiotic factors set variability at large scales, while the effects of biotic factors (in this case grazing) operate simultaneously at scales ranging from small to large.

5.Synthesis. Combining zonation and across‐shore experiments indicates that grazing effects do not follow a continuous gradient, but instead have a patchy distribution. This approach provides information about spatial variability that is not available using only the traditional approach, contributing to our understanding of zonation models.
Litter feedbacks, evolutionary change and exotic plant invasion
Authors: Eppinga Maarten B. , Kaproth Matthew A. , Collins Alexandra R. , Molofsky Jane
Published: January 2011

1. Understanding the mechanisms driving exotic plant invasions is important for designing successful invader control strategies. Previous studies have highlighted different invasion mechanisms, including alteration of nutrient cycles through plant–soil feedback and evolutionary change toward more competitive genotypes.

2. We explored the possibility of these two mechanisms interactively affecting exotic plant invasion. Using data from recent experiments on the invasion of Phalaris arundinacea (Phalaris) in North American wetlands, we parameterized a classical resource competition model for nutrients and light, and expanded this model by including litter dynamics. We also examined the potential effects of evolutionary changes as observed in another set of recent experiments.

3. Both litter feedbacks and observed evolutionary changes may increase Phalaris’ performance in invasive habitats. These mechanisms may amplify each other and this synergy may accelerate Phalaris invasion in areas where it is already present, leading to a high‐litter state with Phalaris outcompeting other species. In areas with low nutrient supply where Phalaris is not yet present, a combination of litter feedbacks and evolutionary change may induce a critical transition from a low‐litter, native‐species‐dominated state toward a high‐litter, Phalaris‐dominated state.

4. Our model results suggest that the importance of litter feedbacks and evolutionary change could be verified in future empirical studies through non‐additive and nonlinear effects in litter addition experiments, and by increased litter : above‐ground biomass ratios in biogeographical comparisons between plant communities with Phalaris in invasive and native habitats. The latter result may be caused by the accumulation of more recalcitrant litter from invasive genotypes.

5.
Synthesis. Our study illustrates how exotic plant invasions may be exacerbated by the interaction between litter feedbacks and evolutionary change. This interaction may induce a positive feedback in the invasion process, suggesting that even short‐term events, such as a nutrient pulse, may lead to relatively large and rapid ecosystem shifts that could be long‐lasting and difficult to reverse.
The effect of geographic range position on demographic variability in annual plants
Authors: Gerst Katharine L. , Angert Amy L. , Venable D. Lawrence
Published: January 2011

1. The abundant centre model predicts that species abundance will decline from the centre towards the periphery of the geographic range. Thus, we expect to find decreases from the centre towards the edge in variables related to population dynamics such as population density and reproductive output. However, evidence for this pattern is contradictory, suggesting that geographically peripheral sites may not be ecologically peripheral. Populations may thrive in pockets of suitable habitat at the edge of the range or may be locally adapted to peripheral conditions.

2. This study examines how the position of a site within geographic and climatic ranges of 13 species is related to the population dynamics at one common location, The Desert Laboratory at Tumamoc Hill, Tucson, AZ, USA.

3. We used data on survival, fecundity, germination fraction and population density from a 25‐year long‐term data set on winter annual plants to determine whether there was a relationship between distance to the centre of the range and population dynamics. Geographic distance was calculated by determining the distance from the Desert Laboratory to the centre of the observed range determined from locality records. Climatic distance was calculated using the niche modelling software,maxent, and subtracting the mean climatic profile for the species range from that of the Desert Laboratory.

4. There was no relationship between mean population metrics and distance metrics. We found significant relationships between some geographic distance metrics and variance in fecundity, survival and per‐germinant fecundity, but not germination fraction or population density. We did not find a relationship with any metric of population dynamic variation and climatic distance.

5.Synthesis. Our results indicate that geographic distance from the centre of the range of 13 annual plant species more strongly predicts their population dynamics than climatic distance. This study reinforces the importance of examining vital rates and their variation in order to properly capture the effect of position within a range on population dynamics.
Resource synergy in stream periphyton communities
Authors: Hill Walter R. , Roberts Brian J. , Francoeur Steven N. , Fanta Shari E.
Published: January 2011

1. Light and nutrients play pivotal roles in determining the growth of autotrophs, yet the potential for synergistic interactions between the two resources in algal communities is poorly understood, especially in stream ecosystems. In this study, light and phosphorus were manipulated in large experimental streams to examine resource colimitation and synergy in stream periphyton.

2. Whole‐stream metabolism was simultaneously limited by light and phosphorus. Increasing the supply of either light or phosphorus resulted in significant increases in primary production and the transformation of the streams from heterotrophy to autotrophy.

3. Resource‐driven changes in periphyton community structure occurred in concert with changes in production. Algal assemblages in highly shaded streams were composed primarily of small diatoms such as Achnanthidium minutissima, whereas larger diatoms such as Melosira varians predominated at higher irradiances. Phosphorus enrichment had relatively little effect on assemblage structure, but it did substantially diminish the abundance of Meridion circulare, a diatom whose mucilaginous colonies were conspicuously abundant in phosphorus‐poor, high‐light streams. Bacterial biomass declined relative to algal biomass with increases in primary productivity, regardless of whether the increases were caused by light or phosphorus.

4. Synergistic effects on primary production appeared to occur because the availability of one resource facilitated the utilization of the other. Light increased the abundance of large diatoms, which are known to convert high concentrations of nutrients into primary production more effectively than smaller taxa. Phosphorus enrichment led to the replacement of Meridion circulare by non‐mucilaginous taxa in phosphorus‐enriched streams, and we hypothesize that this change enabled more efficient use of light in photosynthesis. Higher ratios of chlorophyll a : biomass in phosphorus‐enriched streams may have also led to more efficient photon capture and higher photosynthetic rates.

5.
Synthesis. Our results underscore the potential for resource colimitation, even in habitats where a single resource is as strongly limiting as is light in shaded streams. The capacity of autotrophic communities to respond to more than one limiting resource suggests that prevailing single‐resource models of ecosystem productivity are overly simplistic.
Linking grassland plant diversity to species pools, sorting and plant traits
Authors: Houseman Gregory R. , Gross Katherine L.
Published: January 2011

1. Variation in species pools can affect plant diversity, but it remains unclear whether the magnitude of the response varies because of resource availability, community invasibility or other environmental factors, and whether colonization along environmental gradients reflects niche‐based species sorting or neutral processes.

2. We hypothesized that unimodal diversity–productivity patterns in grasslands are dependent on species pools, with peak richness occurring at intermediate productivity due to species sorting associated with species traits. We used a seed‐addition experiment to test the influence of immigration on plant species richness across multiple grasslands (old fields), each of which encompassed a broad range in productivity. We then tested whether species sorting occurs during colonization, if this varies with site productivity, and whether sorting patterns are associated with species traits 1 and 4 years after seed addition.

3. Augmentation of species pools increased species richness across fields with the greatest increase in colonization in all fields at sites with intermediate productivity. The increased diversity following species pool augmentation during colonization (year 1) was associated with seed characteristics, seedling growth rates and allocation, and water use, suggesting that colonization and seedling establishment were the result of species sorting.

4. Although there were some changes in trait–environmental relationships between the first and fourth growing season, patterns that were observed in the first year were still apparent in the fourth year, highlighting the persistent importance of species sorting and traits that affect colonization on species distribution and diversity patterns in grasslands.

5. Synthesis. Our experimental results suggest that species richness and richness–productivity relationships in successional grasslands are at least partially determined by species sorting and trait–environmental relationships occurring during colonization.
Co‐evolutionary hot and cold spots of selective pressure move in space and time
Authors: Smith D. L. , Ericson L. , Burdon J. J.
Published: January 2011

1. A long‐term study (19 years) of a host–pathogen metapopulation involving 133–220 separate populations of the wild plantFilipendula ulmariaand its rust pathogenTriphragmium ulmariaeshows marked changes in the occurrence (32–55% demes) and severity of disease and rates of extinction and re‐establishment of individual populations (0.006–0.174 and 0.030–0.195 per annum, respectively) over time.

2. Modelling of the spatio‐temporal dynamics of disease demonstrated year‐to‐year changes associated with a range of different environmental features, but also more consistent, longer‐term patterns influenced by a complex suite of factors.

3. Both the level of disease and its spatial location varied through time and generated a changing pattern of selective pressure across the metapopulation.

4. Synthesis. Our results suggest that co‐evolutionary hot spots and cold spots can be highly dynamic within metapopulations, thereby fuelling the co‐evolutionary process even more than previously suspected.
Spatio‐temporal variations determine plant–microbe competition for inorganic nitrogen in an alpine meadow
Authors: Xu Xingliang , Ouyang Hua , Richter Andreas , Wanek Wolfgang , Cao Guangmin , Kuzyakov Yakov
Published: January 2011

1. Plant–microbe competition for available nitrogen (N) has been suggested to be an important mechanism controlling N limitation of plants in a variety of ecosystems. However, spatio‐temporal patterns of competition between plants and microbes for soil N remain unclear.

2. Short‐term 15N tracer experiments were conducted during a growing season (July, August and September) in an alpine meadow on the Tibetan Plateau to unravel spatio‐temporal patterns of plant–microbe competition for NH4+ and NO3−.

3. Alpine plants were poorer competitors than soil microorganisms for inorganic N in July compared with August and September. Occupation of soil volume by roots and root density (high in August and September) played a greater role in plant–microbe competition than air temperature or precipitation (high in July).

4. In topsoils (0–5 cm, highest root density), alpine plants effectively competed with soil microorganisms for N and showed a preference for 15NO3−, while soil microorganisms that preferentially took up 15NH4+ out‐competed plants below 5 cm soil depth (lower root density). Competition between plants and soil microorganisms for inorganic N strongly depended on root density (P < 0.0001, R2 = 0.93, exponential decay model).

5. Synthesis. Plant–microbe competition for inorganic N showed a clear spatio‐temporal pattern in alpine meadows depending on (i) root density and therefore soil depth, (ii) inorganic N form, and (iii) different periods during the growing season. These findings have important implications for our understanding of above‐ground–below‐ground interactions and plant–microbial competition for available N.
Development of Alnus tenuifolia stands on an Alaskan floodplain: patterns of recruitment, disease and succession
Authors: Nossov Dana R. , Hollingsworth Teresa N. , Ruess Roger W. , Kielland Knut
Published: January 2011

1. We investigated the population dynamics of the keystone symbiotic N‐fixing species Alnus tenuifolia (thinleaf alder) and the patterns of primary succession on the Tanana River floodplains of interior Alaska, USA. The goals of this study were to characterize (i) the variation in the population structure of thinleaf alder and its influence on ecosystem function; (ii) the role of a fungal disease outbreak in driving the population dynamics of thinleaf alder; (iii) the patterns of landscape‐scale thinleaf alder recruitment; and (iv) the variation in successional pathways across the landscape.

2. Soil N concentrations and pools increased tenfold with thinleaf alder stand age due to the accumulation of N‐rich organic material. Alder stem density varied threefold among early successional stands, and was directly related to soil N.

3. The current outbreak of a fungal disease caused widespread branch dieback and mortality of alder. Young stems were disproportionately susceptible to disease‐induced mortality. Overall disease incidence and mortality of young stems were positively related to alder stem density.

4. Thinleaf alder age structures revealed that landscape‐scale recruitment was pulsed over time.

5. Multiple pathways of primary succession were found using indirect gradient analysis and associated environmental characteristics were described.

6. Synthesis. The population dynamics of thinleaf alder and the inter‐relationship with disease‐driven disturbance can strongly influence soil N accumulation and ecosystem function in primary succession on an active glacial floodplain. The temporal pattern of thinleaf alder recruitment across the landscape appears to reflect the influence of the hydrologic regime on silt bar development and alder dispersal limitation and population dynamics. Differential life history traits explain the predominant successional pathway, but an alternative successional pathway suggests this pattern can be altered by stochastic events, disturbance, environmental variation or other factors.
Degenerative retinopathy in captive Atlantic menhaden, Brevoortia tyrannus (L.)
Authors: NASISSE M. P. , NOGA E. J. , DAVIDSON M. G.
Published: January 2011

Abstract. Blindness developed in Atlantic menhaden, Brevoortia tyrannus (L.), within 4 weeks of captivity in an indoor open culture system. Ophthalmoscopic changes indicative of retinal degeneration were substantiated by the absence of retinal electrical activity as measured by conventional electroretinography. Results of histological evaluation suggest that photo‐receptor degeneration, occurring initially in the rods of the central retina, was the primary abnormality. With chronicity, all retinal layers degenerated, and marked pigment proliferation developed. Other pathological changes included uveal vascular engorgement, vitreal and anterior chamber haemorrhage, and cataracts. With the exception of dermal hyperpigmentation, no systemic abnormalities were consistently observed. Phototoxicity is the suspected cause of this degenerative retinopathy.
Observations on the role of the caseinase enzyme in the pathogenesis of furunculosis
Authors: DRINAN E. M. , DONLON J. , MOLLOY S. , SMITH P. R.
Published: January 2011

Abstract. The role of the caseinase extracellular enzyme in the pathogenesis of furunculosis was investigated. Natural and mutant strains of Aeromonas salmonicida which were unable, or limited, in their ability to produce this enzyme were studied. The virulence of the mutant strains of A. salmonicida was not significantly reduced by the lack of extracellular caseinase production. Furthermore, there was no difference in the toxicity of extracellular products produced by these mutant strains and the wild‐type A. salmonicida strain studied. It is reasonable to assume from these results that the caseinase enzyme has no major role in the pathogenesis of A. salmonicida infections.
CD154, a marker of antigen‐specific stimulation of CD4 T cells, is associated with response to treatment in patients with chronic HCV infection
Authors: Möller J. F. , Möller B. , Wiedenmann B. , Berg T. , Schott E.
Published: January 2011

Summary.  CD4 T‐cell function is crucial for the eradication of HCV, and insufficient function is observed in chronic carriers. The monitoring of T‐cell responses is complicated by the scarcity of antigen‐specific T cells and the relative inefficiency of virus‐specific T cells to produce effector cytokines. CD154 is a marker of activation expressed on T cells induced through their T‐cell receptor. We analysed CD4 T‐cell responses in 72 patients with chronic or resolved HCV infection (23 treatment naïve, 49 treatment experienced, including 16 who had achieved a sustained response). In an additional prospective protocol, 20 of the chronically infected patients were analysed before and after 8–12 weeks of combination therapy with peg‐interferon‐α and ribavirin. T‐cell responses were measured by detecting the expression of CD154 and Th1 cytokines after stimulation with recombinant HCV proteins and were correlated with pretreatment status and outcome of therapy. Broader T‐cell responses were observed in treatment naïve than in experienced patients, while the outcome of a preceding therapy regimen did not influence T‐cell responses. In the prospective cohort, an on‐treatment increase in CD154+ cytokine− T‐cell activity was associated with response to treatment, while a decrease was observed in nonresponders. Stronger antigen‐independent activity of CD154+ cytokine+ T cells was observed in responders than in nonresponders. Our data indicate that CD154 as a marker of activation of CD4 T cells is a suitable tool for the analysis of T‐cell responses in patients with HCV infection.
Who are the missing parents? Grandparentage analysis identifies multiple sources of gene flow into a wild population
Authors: CHRISTIE MARK R. , MARINE MELANIE L. , BLOUIN MICHAEL S.
Published: January 2011

In order to increase the size of declining salmonid populations, supplementation programmes intentionally release fish raised in hatcheries into the wild. Because hatchery‐born fish often have lower fitness than wild‐born fish, estimating rates of gene flow from hatcheries into wild populations is essential for predicting the fitness cost to wild populations. Steelhead trout (Oncorhynchus mykiss) have both freshwater resident and anadromous (ocean‐going) life history forms, known as rainbow trout and steelhead, respectively. Juvenile hatchery steelhead that ‘residualize’ (become residents rather than go to sea as intended) provide a previously unmeasured route for gene flow from hatchery into wild populations. We apply a combination of parentage and grandparentage methods to a three‐generation pedigree of steelhead from the Hood River, Oregon, to identify the missing parents of anadromous fish. For fish with only one anadromous parent, 83% were identified as having a resident father while 17% were identified as having a resident mother. Additionally, we documented that resident hatchery males produced more offspring with wild anadromous females than with hatchery anadromous females. One explanation is the high fitness cost associated with matings between two hatchery fish. After accounting for all of the possible matings involving steelhead, we find that only 1% of steelhead genes come from residualized hatchery fish, while 20% of steelhead genes come from wild residents. A further 23% of anadromous steelhead genes come from matings between two resident parents. If these matings mirror the proportion of matings between residualized hatchery fish and anadromous partners, then closer to 40% of all steelhead genes come from wild trout each generation. These results suggest that wild resident fish contribute substantially to endangered steelhead ‘populations’ and highlight the need for conservation and management efforts to fully account for interconnected Oncorhynchus mykiss life histories.
and D do not replace FST
Authors: WHITLOCK MICHAEL C.
Published: January 2011

The genetic differentiation among populations is affected by mutation as well as by migration, drift and selection. For loci with high mutation rates, such as microsatellites, the amount of mutation can influence the values of indices of differentiation such as GST and FST. For many purposes, this effect is undesirable, and as a result, new indices such as and D have been proposed to measure population differentiation. This paper shows that these new indices are not effective measures of the causes or consequences of population structure. Both and D depend heavily on mutation rate, but both are insensitive to any population genetic process when the mutation rate is high relative to the migration rate. Furthermore, D is specific to the locus being measured, and so little can be inferred about the population demography from D. However, at equilibrium, D may provide an index of whether a particular marker is more strongly affected by mutation than by migration. I argue that FST is a more important summary of the effects of population structure than D and that RST or other measures that explicitly account for the mutation process are much better than GST, , or D for highly mutable markers. Markers with lower mutation rates will often be easier to interpret.
Proteins encoded by the mre gene cluster in Streptomyces coelicolor A3(2) cooperate in spore wall synthesis
Authors: Kleinschnitz Eva‐Maria , Heichlinger Andrea , Schirner Kathrin , Winkler Juliane , Latus Annette , Maldener Iris , Wohlleben Wolfgang , Muth Günther
Published: January 2011

It is still an open question how an intracellular cytoskeleton directs the synthesis of the peptidoglycan exoskeleton. In contrast to MreB of rod‐shaped bacteria, which is essential for lateral cell wall synthesis, MreB of Streptomyces coelicolor has a role in sporulation. To study the function of the S. coelicolor mre gene cluster consisting of mreB, mreC, mreD, pbp2 and sfr, we generated non‐polar replacement mutants. The individual mutants were viable and growth of substrate mycelium was not affected. However, all mutants produced enlarged spores, which frequently germinated prematurely and were sensitive to heat, high osmolarity and cell wall damaging agents. Protein–protein interaction assays by bacterial two‐hybrid analyses indicated that the S. coelicolor Mre proteins form a spore wall synthesizing complex, which closely resembles the lateral wall synthesizing complex of rod‐shaped bacteria. Screening of a genomic library identified several novel putative components of this complex. One of them (sco2097) was deleted. The Δsco2097 mutant formed sensitive spores with an aberrant morphology, demonstrating that SCO2097 is a new player in cell morphogenesis of Streptomyces. Our results suggest that all Mre proteins cooperate with the newly identified proteins in the synthesis of the thickened spore wall required to resist detrimental environmental conditions.
The outer membrane protein LptO is essential for the O‐deacylation of LPS and the co‐ordinated secretion and attachment of A‐LPS and CTD proteins in Porphyromonas gingivalis
Authors: Chen Yu‐Yen , Peng Benjamin , Yang Qiaohui , Glew Michelle D. , Veith Paul D. , Cross Keith J. , Goldie Kenneth N. , Chen Dina , O'Brien‐Simpson Neil , Dashper Stuart G , Reynolds Eric C.
Published: January 2011

Protein substrates of a novel secretion system of Porphyromonas gingivalis contain a conserved C‐terminal domain (CTD) essential for secretion and attachment to the cell surface. Inactivation of lptO (PG0027) or porT produced mutants that lacked surface protease activity and an electron‐dense surface layer. Both mutants showed co‐accumulation of A‐LPS and unmodified CTD proteins in the periplasm. Lipid profiling by mass spectrometry showed the presence of both tetra‐ and penta‐acylated forms of mono‐phosphorylated lipid A in the wild‐type and porT mutant, while only the penta‐acylated forms of mono‐phosphorylated lipid A were found in the lptO mutant, indicating a specific role of LptO in the O‐deacylation of mono‐phosphorylated lipid A. Increased levels of non‐phosphorylated lipid A and the presence of novel phospholipids in the lptO mutant were also observed that may compensate for the missing mono‐phosphorylated tetra‐acylated lipid A in the outer membrane (OM). Molecular modelling predicted LptO to adopt a β‐barrel structure characteristic of an OM protein, supported by the enrichment of LptO in OM vesicles. The results suggest that LPS deacylation by LptO is linked to the co‐ordinated secretion of A‐LPS and CTD proteins by a novel secretion and attachment system to form a structured surface layer.
tRNA accumulation and suppression of the bldA phenotype during development in Streptomyces coelicolor
Authors: Pettersson B. M. Fredrik , Kirsebom Leif A.
Published: January 2011

Streptomyces coelicolor undergoes distinct morphological changes as it grows on solid media where spores differentiate into vegetative and aerial mycelium that is followed by the production of spores. Deletion of bldA, encoding the rare tRNALeuUAA, blocks development at the stage of vegetative mycelium formation. From previous data it appears that tRNALeuUAA accumulates relatively late during growth while two other tRNAs do not. Here, we studied the expression of 17 different tRNAs including bldA tRNA, and the RNA subunit of the tRNA processing endoribonuclease RNase P. Our results showed that all selected tRNAs and RNase P RNA increased with time during development. However, accumulation of bldA tRNA and another rare tRNALeu isoacceptor started at an earlier stage compared with the other tRNAs. We also introduced the bldA tRNA anticodon (UAA) into other tRNAs and introduced these into a bldA deletion strain. In particular, one such mutant tRNA derived from the tRNALeuCAA isoacceptor suppressed the bldA phenotype. Thus, the bldA tRNA scaffold is not critical for function as a regulator of S. coelicolor cell differentiation. Further substitution experiments, in which the 5′‐ and 3′‐flanking regions of the suppressor tRNA were changed, indicated that these regions were important for the suppression.
Magnesium depletion triggers production of an immune modulating diterpenoid in Mycobacterium tuberculosis
Authors: Mann Francis M. , VanderVen Brian C. , Peters Reuben J.
Published: January 2011

Mycobacterium tuberculosis (Mtb) is the causative agent of the human disease Tuberculosis, and remains a worldwide health threat responsible for ∼ 1.7 million deaths annually. During infection, Mtb prevents acidification of the engulfing phagosome, thus blocking endocytic progression and eventually leading to stable residence. The diterpenoid metabolite isotuberculosinol (isoTb) exhibits biological activity indicative of a role in this early arrest of phagosome maturation. Presumably, isoTb production should be induced by phagosomal entry. However, the relevant enzymatic genes are not transcriptionally upregulated during engulfment. Previous examination of the initial biosynthetic enzyme (Rv3377c/MtHPS) involved in isoTb biosynthesis revealed striking inhibition by its Mg2+ cofactor, leading to the hypothesis that the depletion of Mg2+ observed upon phagosomal engulfment may act to trigger isoTb biosynthesis. While Mtb is typically grown in relatively high levels of Mg2+ (0.43 mM), shifting Mtb to media with phagosomal levels (0.1 mM) led to a significant (∼ 10‐fold) increase in accumulation of the MtHPS product, halimadienyl diphosphate, as well as easily detectable amounts of the derived bioactive isoTb. These results demonstrate isoTb production by Mtb specifically under conditions that mimic phagosomal cation concentrations, and further support a role for isoTb in the Mtb infection process.
Downregulation of katG expression is associated with isoniazid resistance in Mycobacterium tuberculosis
Authors: Ando Hiroki , Kitao Tomoe , Miyoshi‐Akiyama Tohru , Kato Seiya , Mori Toru , Kirikae Teruo
Published: January 2011

Isoniazid (INH) is a key agent in the treatment of tuberculosis. In Mycobacterium tuberculosis, INH is converted to its active form by KatG, a catalase‐peroxidase, and attacks InhA, which is essential for the synthesis of mycolic acids. We sequenced furA–katG and fabG1–inhA in 108 INH‐resistant (INHr) and 51 INH‐susceptible (INHs) isolates, and found three mutations in the furA–katG intergenic region (Intg‐7a, Inta‐10c and Intg‐12a) in four of 108 INHr isolates (4%), and the furAc41t mutation with an amino acid substitution in 18 INHr isolates (17%). These mutations were not found in any of 51 INHs isolates tested. We reconstructed these mutations in isogenic strains to determine whether they conferred INH resistance. We found that the Intg‐7a, Inta‐10c and Intg‐12a single mutations in the furA–katG intergenic region decreased katG expression and conferred INH resistance. In contrast, the furAc41t mutation was not sufficient to confer INH resistance. These results suggested that downregulation of katG is a mechanism of INH resistance in M. tuberculosis and that mutations in the furA–katG intergenic region play a role in this resistance mechanism.
The morphogene AmiC2 is pivotal for multicellular development in the cyanobacterium Nostoc punctiforme
Authors: Lehner Josef , Zhang Yao , Berendt Susanne , Rasse Tobias M. , Forchhammer Karl , Maldener Iris
Published: January 2011

Filamentous cyanobacteria of the order Nostocales are primordial multicellular organisms, a property widely considered unique to eukaryotes. Their filaments are composed of hundreds of mutually dependent vegetative cells and regularly spaced N2‐fixing heterocysts, exchanging metabolites and signalling molecules. Furthermore, they may differentiate specialized spore‐like cells and motile filaments. However, the structural basis for cellular communication within the filament remained elusive. Here we present that mutation of a single gene, encoding cell wall amidase AmiC2, completely changes the morphology and abrogates cell differentiation and intercellular communication. Ultrastructural analysis revealed for the first time a contiguous peptidoglycan sacculus with individual cells connected by a single‐layered septal cross‐wall. The mutant forms irregular clusters of twisted cells connected by aberrant septa. Rapid intercellular molecule exchange takes place in wild‐type filaments, but is completely abolished in the mutant, and this blockage obstructs any cell differentiation, indicating a fundamental importance of intercellular communication for cell differentiation in Nostoc. AmiC2–GFP localizes in the cell wall with a focus in the cross walls of dividing cells, implying that AmiC2 processes the newly synthesized septum into a functional cell–cell communication structure during cell division. AmiC2 thus can be considered as a novel morphogene required for cell–cell communication, cellular development and multicellularity.
Assembly and stability of flagellar motor in Escherichia coli
Authors: Li Hui , Sourjik Victor
Published: January 2011

Bacterial flagellar motor is a highly ordered and complex supramolecular structure that powers rotation of flagella and serves as a type III export apparatus for flagellar assembly. Motor biogenesis represents a formidable example of self‐assembly, but little is known about early steps of the motor structure formation. Here we used a combination of fluorescence microscopy techniques to dissect the order of the motor assembly in Escherichia coli cells, to map in vivo the underlying protein interactions and to investigate dynamics of protein exchange in the assembled motor structure. Our data suggest that motor self‐assembly is initiated by oligomerization of the membrane export apparatus protein FlhA, which is followed by the recruitment of the MS ring component FliF and by the ordered association of other motor proteins. The assembly process combines the hierarchy with cooperativity, whereby the association of each subsequent motor structure stabilizes the growing assembly. Our results provide a novel and so far the most complete view of the early steps in flagellar motor assembly and improve understanding of the motor structure and regulation.
A multifaceted genomics approach allows the isolation of the rice Pia‐blast resistance gene consisting of two adjacent NBS‐LRR protein genes
Authors: Okuyama Yudai , Kanzaki Hiroyuki , Abe Akira , Yoshida Kentaro , Tamiru Muluneh , Saitoh Hiromasa , Fujibe Takahiro , Matsumura Hideo , Shenton Matt , Galam Dominique Clark , Undan Jerwin , Ito Akiko , Sone Teruo , Terauchi Ryohei
Published: January 2011

The Oryza sativa (rice) resistance gene Pia confers resistance to the blast fungus Magnaporthe oryzae carrying the AVR‐Pia avirulence gene. To clone Pia, we employed a multifaceted genomics approach. First, we selected 12 R‐gene analog (RGA) genes encoding nucleotide binding site‐leucine rich repeats (NBS‐LRRs) proteins from a region on chromosome 11 that shows linkage to Pia. By using seven rice accessions, we examined the association between Pia phenotypes and DNA polymorphisms in the 10 genes, which revealed three genes (Os11gRGA3–Os11gRGA5) exhibiting a perfect association with the Pia phenotypes. We also screened ethyl methane sulfonate (EMS)‐treated mutant lines of the rice cultivar ‘Sasanishiki’ harboring Pia, and isolated two mutants that lost the Pia phenotype. DNA sequencing of Os11gRGA3–Os11gRGA5 from the two mutant lines identified independent mutations of major effects in Os11gRGA4. The wild‐type ‘Sasanishiki’ allele of Os11gRGA4 (SasRGA4) complemented Pia function in both mutants, suggesting that SasRGA4 is necessary for Pia function. However, when the rice cultivar ‘Himenomochi’ lacking Pia was transfected with SasRGA4, the Pia phenotype was not recovered. An additional complementation study revealed that the two NBS‐LRR‐type R genes, SasRGA4 and SasRGA5, that are located next to each other and oriented in the opposite direction are necessary for Pia function. A population genetics analysis of SasRGA4 and SasRGA5 suggests that the two genes are under long‐term balancing selection.
Arabidopsis homologues of the histone chaperone ASF1 are crucial for chromatin replication and cell proliferation in plant development
Authors: Zhu Yan , Weng Minjie , Yang Yue , Zhang Chi , Li Ziyu , Shen Wen‐Hui , Dong Aiwu
Published: January 2011

Anti‐silencing function1 (ASF1) is an evolutionarily conserved histone chaperone. Studies in yeast and animals indicate that ASF1 proteins play important roles in various chromatin‐based processes, including gene transcription, DNA replication and repair. While two genes encoding ASF1 homologues, AtASF1A and AtASF1B, are found in the Arabidopsis genome, their function has not been studied. Here we report that both AtASF1A and AtASF1B proteins bind histone H3, and are localized in the cytoplasm and the nucleus. Loss‐of‐function of either AtASF1A or AtASF1B did not show obvious defects, whereas simultaneous knockdown of both genes in the double mutant Atasf1ab drastically inhibited plant growth and caused abnormal vegetative and reproductive organ development. The Atasf1ab mutant plants exhibit cell number reduction, S‐phase delay/arrest, and reduced polyploidy levels. Selective up‐regulation of expression of a subset of genes, including those involved in S‐phase checkpoints and the CYCB1;1 gene at the G2‐to‐M transition, was observed in Atasf1ab. Furthermore, the Atasf1ab‐triggered replication fork stalling constitutively activates the DNA damage checkpoint and repair genes, including ATM, ATR, PARP1 and PARP2 as well as several genes of the homologous recombination (HR) pathway but not genes of the non‐homologous end joining (NHEJ) pathway. In spite of the activation of repair genes, an increased level of DNA damage was detected in Atasf1ab, suggesting that defects in the mutant largely exceed the available capacity of the repair machinery. Taken together, our study establishes crucial roles for the AtASF1A and AtASF1B genes in chromatin replication, maintenance of genome integrity and cell proliferation during plant development.