bluuebunny/crossref_metadata_2025 huggingface dataset:
Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces
Authors: Oki Kaihei , Kudo Yuko , Watanabe Koichi
Published: April 2011

Two Gram-stain-positive strains, YIT 12363T and YIT 12364T, were isolated from human faeces. They were rod-shaped, non-motile, asporogenous, facultatively anaerobic and did not exhibit catalase activity. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus casei (95.3 % similarity), Lactobacillus paracasei subsp. paracasei (95.6 %), Lactobacillus paracasei subsp. tolerans (95.3 %) and Lactobacillus rhamnosus (95.4 %) were the closest neighbours to strain YIT 12363T. For strain YIT 12364T, the highest similarity values were observed with the type strains of Lactobacillus diolivorans, Lactobacillus parafarraginis and Lactobacillus rapi (95.8, 96.0 and 96.0 %, respectively). Phenotypic and genotypic features demonstrated that these strains each represent a separate novel species of the genus Lactobacillus, and the names Lactobacillus saniviri sp. nov. (type strain YIT 12363T = JCM 17471T = DSM 24301T) and Lactobacillus senioris sp. nov. (type strain YIT 12364T = JCM 17472T = DSM 24302T), respectively, are proposed.
PERSISTENT TAPETAL CELL1Encodes a PHD-Finger Protein That Is Required for Tapetal Cell Death and Pollen Development in Rice
Authors: Li Hui , Yuan Zheng , Vizcay-Barrena Gema , Yang Caiyun , Liang Wanqi , Zong Jie , Wilson Zoe A. , Zhang Dabing
Published: April 2011

In higher plants, timely degradation of tapetal cells, the innermost sporophytic cells of the anther wall layer, is a prerequisite for the development of viable pollen grains. However, relatively little is known about the mechanism underlying programmed tapetal cell development and degradation. Here, we report a key regulator in monocot rice (Oryza sativa), PERSISTANT TAPETAL CELL1 (PTC1), which controls programmed tapetal development and functional pollen formation. The evolutionary significance of PTC1 was revealed by partial genetic complementation of the homologous mutation MALE STERILITY1 (MS1) in the dicot Arabidopsis (Arabidopsis thaliana). PTC1 encodes a PHD-finger (for plant homeodomain) protein, which is expressed specifically in tapetal cells and microspores during anther development in stages 8 and 9, when the wild-type tapetal cells initiate a typical apoptosis-like cell death. Even though ptc1 mutants show phenotypic similarity to ms1 in a lack of tapetal DNA fragmentation, delayed tapetal degeneration, as well as abnormal pollen wall formation and aborted microspore development, the ptc1 mutant displays a previously unreported phenotype of uncontrolled tapetal proliferation and subsequent commencement of necrosis-like tapetal death. Microarray analysis indicated that 2,417 tapetum- and microspore-expressed genes, which are principally associated with tapetal development, degeneration, and pollen wall formation, had changed expression in ptc1 anthers. Moreover, the regulatory role of PTC1 in anther development was revealed by comparison with MS1 and other rice anther developmental regulators. These findings suggest a diversified and conserved switch of PTC1/MS1 in regulating programmed male reproductive development in both dicots and monocots, which provides new insights in plant anther development.
The Influence of Low Oxygen on Macrophage Response to Leishmania Infection
Authors: Degrossoli A. , Arrais‐Silva W. W. , Colhone M. C. , Gadelha F. R. , Joazeiro P. P. , Giorgio S.
Published: April 2011

Hypoxia (low oxygen tension) is a common feature of inflamed and infected tissues. The influence of hypoxia on macrophage responses to micro‐organisms has only recently been studied. This study demonstrates that hypoxia induced macrophages to control Leishmania amazonensis, an intracellular parasite that causes cutaneous and cutaneous metastatic lesions. The mechanisms that contribute to the control of macrophages against L. amazonensis infection under a hypoxic microenvironment are not known. Nitric oxide, TNF‐α, IL‐10 or IL‐12 is not responsible for the decrease in parasitism under hypoxia. Live L. amazonensis entry or exocytosis of internalized particles as well as energetic metabolism was not impaired in infected macrophages; no apoptosis‐like death was detected in intracellular parasites. Reactive oxygen species (ROS) is likely to be involved, because treatment with antioxidants N‐acetylcysteine (NAC) and ebselen inhibits the leishmanicidal effect of macrophages under hypoxia. Leishmania amazonensis infection induces macrophages to express hypoxia‐inducible factor‐1 (HIF‐1α) and ‐2 (HIF‐2α). Data indicate that hypoxia affects the microbial activities and protein expression of macrophages leading to a different phenotype from that of the normoxic counterpart and that it plays a role in modulating Leishmania infection.
Of Stem Cells and Germ Cells
Authors: Roelen BAJ
Published: April 2011

Contents

Stem cells have an intrinsic capacity to self‐renew and can differentiate to at least one specialized cell type. Different types of stem cells exist that can be culturedin vitro. The identity of the stem cells is marked by their origin and differentiation potential. Germ cells have similarities with pluripotent stem cells but are of a special order: They do not self‐renew and are already differentiated, but they have the capacity to form a complete new organism after fertilization. This review focuses on pluripotent stem cells and discusses possibilities of generating pluripotent stem cells from germ cell precursors and possibilities of generating germ cells from stem cells. As it accompanies a plenary lecture at the 15th annual ESDAR Conference 2011, the overview is focused on stem cells from farm animal species and on results from my own research group.
Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars
Authors: Triplett L. R. , Hamilton J. P. , Buell C. R. , Tisserat N. A. , Verdier V. , Zink F. , Leach J. E.
Published: April 2011

The species
Xanthomonas oryzae
is comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. Although
X. oryzae
is not considered endemic in the United States, an
X. oryzae
-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterized
X. oryzae
pathovars. In the current study, a draft genome sequence from two U.S.
Xanthomonas
strains revealed that the U.S. strains form a novel clade within the
X. oryzae
species, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools.
Genotype Distribution of Human Sapoviruses in Wastewater in Japan
Authors: Kitajima Masaaki , Haramoto Eiji , Phanuwan Chanetta , Katayama Hiroyuki
Published: April 2011

Human sapovirus sequences were identified in 12 (100%) influent and 7 (58%) effluent wastewater samples collected once a month for a year. The strains were characterized based on their partial capsid gene sequences and classified into 10 genotypes, demonstrating that genetically diverse sapovirus strains infect humans in the study area.
Continuous Monitoring of Ammonia Removal Activity and Observation of Morphology of Microbial Complexes in a Microdevice
Authors: Toda Kensuke , Yawata Yutaka , Setoyama Erika , Fukuda Junji , Nomura Nobuhiko , Suzuki Hiroaki
Published: April 2011

Continuous monitoring of ammonia removal by microbial complexes and observation of their morphology were carried out using a microdevice. Consumption of NH
4
+
ions by active sludge could clearly be recorded over 48 h. Aggregation of the sludge could be observed in parallel by using confocal reflection microscopy.
Direct Image-Based Correlative Microscopy Technique for Coupling Identification and Structural Investigation of Bacterial Symbionts Associated with Metazoans
Authors: Halary Sébastien , Duperron Sébastien , Boudier Thomas
Published: April 2011

Coupling prokaryote identification with ultrastructural investigation of bacterial communities has proven difficult in environmental samples. Prokaryotes can be identified by using specific probes and fluorescencein situhybridization (FISH), but resolution achieved by light microscopes does not allow ultrastructural investigation. In the case of symbioses involving bacteria associated with metazoan tissues, FISH-based studies often indicate the co-occurrence of several bacterial types within a single host species. The ultrastructure is then relevant to address host and bacterial morphology and the intra- or extracellular localization of symbionts. A simple protocol for correlative light and electron microscopy (CLEM) is presented here which allows FISH-based identification of specific 16S rRNA phylotypes and transmission electron microscopy to be performed on a same sample. Image analysis tools are provided to superimpose images obtained and generate overlays. This procedure has been applied to two symbiont-bearing metazoans, namely, aphids and deep-sea mussels. The FISH protocol was modified to take into account constraints associated with the use of electron microscopy grids, and intense and specific signals were obtained. FISH signals were successfully overlaid with bacterial morphotypes in aphids. We thus used the method to address the question of symbiont morphology and localization in a deep-sea mussel. Signals from a type I methanotroph-related phylotype were associated with morphotypes displaying the stacked internal membranes typical for this group and three-dimensional electron tomography was performed, confirming for the first time the correspondence between morphology and phylotype. CLEM is thus feasible and reliable and could emerge as a potent tool for the study of prokaryotic communities.
Development of an Effective Method for Recovery of Viral Genomic RNA from Environmental Silty Sediments for Quantitative Molecular Detection
Authors: Miura Takayuki , Masago Yoshifumi , Sano Daisuke , Omura Tatsuo
Published: April 2011

Nine approaches to recover viral RNA from environmental silty sediments were newly developed and compared to quantify RNA viruses in sediments using molecular methods. Four of the nine approaches employed direct procedures for extracting RNA from sediments (direct methods), and the remaining five approaches used indirect methods wherein viral particles were recovered before RNA extraction. A direct method using an SDS buffer with EDTA to lyse viral capsids in sediments, phenol-chloroform-isoamyl alcohol to extract RNA, isopropanol to concentrate RNA, and magnetic beads to purify RNA resulted in the highest rate of recovery (geometric mean of 11%, with a geometric standard deviation of 0.02;
n
= 7) of poliovirus 1 (PV1) inoculated in an environmental sediment sample. The direct method exhibiting the highest rate of PV1 recovery was applied to environmental sediment samples. One hundred eight sediment samples were collected from the Takagi River, Miyagi, Japan, and its estuary from November 2007 to April 2009, and the genomic RNAs of enterovirus and human norovirus in these samples were quantified by reverse transcription (RT)-quantitative PCR (qPCR). The human norovirus genome was detected in one sample collected at the bay, although its concentration was below the quantification limit. Meanwhile, the enterovirus genome was detected in two samples at the river mouth and river at concentrations of 8.6 × 10
2
and 2.4 × 10
2
copies/g (wet weight), respectively. This is the first report to obtain quantitative data for a human pathogenic virus in a river and in estuarine sediments using RT-qPCR.
Acetate Repression of Methane Oxidation by Supplemental Methylocella silvestris in a Peat Soil Microcosm
Authors: Rahman M. Tanvir , Crombie Andrew , Moussard Hélène , Chen Yin , Murrell J. Colin
Published: April 2011

Methylocellaspp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase ofMethylocella silvestrisin laboratory culture. DNA stable-isotope probing (DNA-SIP) using13C-methane and12C-acetate, carried out withMethylocella-spiked peat soil, showed that acetate also repressed methane oxidation byMethylocellain environmental samples.
Engineering Trehalose Synthesis in Lactococcus lactis for Improved Stress Tolerance
Authors: Carvalho Ana Lúcia , Cardoso Filipa S. , Bohn Andreas , Neves Ana Rute , Santos Helena
Published: April 2011

Trehalose accumulation is a common cell defense strategy against a variety of stressful conditions. In particular, our team detected high levels of trehalose inPropionibacterium freudenreichiiin response to acid stress, a result that led to the idea that endowingLactococcus lactiswith the capacity to synthesize trehalose could improve the acid tolerance of this organism. To this end, we took advantage of the endogenous genes involved in the trehalose catabolic pathway ofL. lactis, i.e.,trePPandpgmB, encoding trehalose 6-phosphate phosphorylase and β-phosphoglucomutase, respectively, which enabled the synthesis of trehalose 6-phosphate. Given thatL. lactislacks trehalose 6-phosphate phosphatase, the respective gene,otsB, from the food-grade organismP. freudenreichiiwas used to provide the required activity. The trehalose yield was approximately 15% in resting cells and in mid-exponential-phase cells grown without pH control. The intracellular concentration of trehalose reached maximal values of approximately 170 mM, but at least 67% of the trehalose produced was found in the growth medium. The viability of mutant and control strains was examined after exposure to heat, cold or acid shock, and freeze-drying. The trehalose-producing strains showed improved tolerance (5- to 10-fold-higher survivability) to acid (pH 3) and cold shock (4°C); there was also a strong improvement in cell survival in response to heat shock (45°C), and no protection was rendered against dehydration. The insight provided by this work may help the design of food-grade strains optimized for the dairy industry as well as for oral drug delivery.
An Orphan Histidine Kinase, OhkA, Regulates Both Secondary Metabolism and Morphological Differentiation in Streptomyces coelicolor
Authors: Lu Yinhua , He Juanmei , Zhu Hong , Yu Zhenyu , Wang Rui , Chen Yunliang , Dang Fujun , Zhang Weiwen , Yang Sheng , Jiang Weihong
Published: April 2011

We report here the physiological and genetic characterization of an orphan histidine kinase (HK) (OhkA,
SCO1596
) in
Streptomyces coelicolor
and its homolog (OhkAsav,
SAV_6741
) in
Streptomyces avermitilis
. The physiological analysis showed that the
ohkA
mutant of
S. coelicolor
exhibits impaired aerial mycelium formation and sporulation and overproduction of multiple antibiotics on mannitol-soy flour (MS) medium, especially actinorhodin (ACT) and calcium-dependent antibiotic (CDA), and disruption of
ohkAsav
in
S. avermitilis
also led to the similar phenotypes of impaired morphological differentiation and significantly increased oligomycin A production. DNA microarray analysis combined with real-time reverse transcription-PCR (RT-PCR) and RNA dot blot assay in the
S. coelicolor ohkA
deletion mutant confirmed the physiological results by showing the upregulation of genes involved in the biosynthesis of ACT, CDA, undecylprodigiosin (RED), a yellow type I polyketide (CPK,
SCO6273-6289
), and a sesquiterpene antibiotic, albaflavenone (
SCO5222-5223
). The results also suggested that the increased production of ACT and RED in the mutant could be partly ascribed to the enhanced precursor malonyl coenzyme A (malonyl-CoA) supply through increased transcription of genes encoding acetyl-CoA carboxylase (ACCase). Interestingly, DNA microarray analysis also showed that deletion of
ohkA
greatly downregulated the transcription of
chpABCDEFGH
genes essential for aerial mycelium formation by
S. coelicolor
on MS medium but significantly increased transcription of
ramS
/
C
/
R
, which is responsible for SapB formation and regulation and is normally absent on MS medium. Moreover, many other genes involved in development, such as
bldM
/
N
,
whiG
/
H
/
I
,
ssgA
/
B
/
E
/
G
/
R
, and
whiE
, were also significantly downregulated upon
ohkA
deletion. The results clearly demonstrated that OhkA is an important global regulator for both morphological differentiation and secondary metabolism in
S. coelicolor
and
S. avermitilis
.
Novel Reaction of Succinyl Coenzyme A (Succinyl-CoA) Synthetase: Activation of 3-Sulfinopropionate to 3-Sulfinopropionyl-CoA in Advenella mimigardefordensis Strain DPN7
T
during Degradation of 3,3′-Dithiodipropionic Acid
Authors: Schürmann Marc , Wübbeler Jan Hendrik , Grote Jessica , Steinbüchel Alexander
Published: April 2011

The
sucCD
gene of
Advenella mimigardefordensis
strain DPN7
T
encodes a succinyl coenzyme A (succinyl-CoA) synthetase homologue (EC 6.2.1.4 or EC 6.2.1.5) that recognizes, in addition to succinate, the structural analogues 3-sulfinopropionate (3SP) and itaconate as substrates. Accumulation of 3SP during 3,3′-dithiodipropionic acid (DTDP) degradation was observed in Tn
5
::
mob-
induced mutants of
A. mimigardefordensis
strain DPN7
T
disrupted in
sucCD
and in the defined deletion mutant
A. mimigardefordensis
Δ
sucCD
. These mutants were impaired in growth with DTDP and 3SP as the sole carbon source. Hence, it was proposed that the succinyl-CoA synthetase homologue in
A. mimigardefordensis
strain DPN7
T
activates 3SP to the corresponding CoA-thioester (3SP-CoA). The putative genes coding for
A. mimigardefordensis
succinyl-CoA synthetase (SucCD

Am

) were cloned and heterologously expressed in
Escherichia coli
BL21(DE3)/pLysS. Purification and characterization of the enzyme confirmed its involvement during degradation of DTDP. 3SP, the cleavage product of DTDP, was converted into 3SP-CoA by the purified enzyme, as demonstrated by
in vitro
enzyme assays. The structure of 3SP-CoA was verified by using liquid chromatography-electrospray ionization-mass spectrometry. SucCD

Am

is Mg
2+
or Mn
2+
dependent and unspecific regarding ATP or GTP. In kinetic studies the enzyme showed highest enzyme activity and substrate affinity with succinate (
V
max
= 9.85 ± 0.14 μmol min
−1
mg
−1
,

K
m

= 0.143 ± 0.001 mM). In comparison to succinate, activity with 3SP was only ca. 1.2% (
V
max
= 0.12 ± 0.01 μmol min
−1
mg
−1
) and the affinity was 6-fold lower (

K
m

= 0.818 ± 0.046 mM). Based on the present results, we conclude that SucCD

Am

is physiologically associated with the citric acid cycle but is mandatory for the catabolic pathway of DTDP and its degradation intermediate 3SP.
Transcription Factor GreA Contributes to Resolving Promoter-Proximal Pausing of RNA Polymerase in Bacillus subtilis Cells
Authors: Kusuya Yoko , Kurokawa Ken , Ishikawa Shu , Ogasawara Naotake , Oshima Taku
Published: April 2011

Bacterial Gre factors associate with RNA polymerase (RNAP) and stimulate intrinsic cleavage of the nascent transcript at the active site of RNAP. Biochemical and genetic studies to date have shown that
Escherichia coli
Gre factors prevent transcriptional arrest during elongation and enhance transcription fidelity. Furthermore, Gre factors participate in the stimulation of promoter escape and the suppression of promoter-proximal pausing during the beginning of RNA synthesis in
E. coli
. Although Gre factors are conserved in general bacteria, limited functional studies have been performed in bacteria other than
E. coli
. In this investigation, ChAP-chip analysis (chromatin affinity precipitation coupled with DNA microarray) was conducted to visualize the distribution of
Bacillus subtilis
GreA on the chromosome and to determine the effects of GreA inactivation on core RNAP trafficking. Our data show that GreA is uniformly distributed in the transcribed region from the promoter to coding region with core RNAP, and its inactivation induces RNAP accumulation at many promoter or promoter-proximal regions. Based on these findings, we propose that GreA would constantly associate with core RNAP during transcriptional initiation and elongation and resolves its stalling at promoter or promoter-proximal regions, thus contributing to the even distribution of RNAP along the promoter and coding regions in
B. subtilis
cells.
Establishing a biologics service for patients with inflammatory bowel disease
Authors: Hamlin P J , Warren L , Everett S M
Published: April 2011

The use of anti-TNF therapy in the management of Crohn's disease and, to a lesser extent ulcerative colitis, is increasing. This article aims to discuss the practicalities of establishing a biologics service for patients with inflammatory bowel disease. Current guidelines on the use of these drugs are reviewed followed by a discussion on the choice of which anti-TNF agent to use based on costs and patient choice. A model for the initiation, administration, monitoring and assessment of patients receiving anti-TNF therapy is proposed. The need for a national biologics registry is highlighted in the summary.
Repair of intracranial vessel perforation with Onyx-18 using an exovascular retreating catheter technique
Authors: Kostov Dean , Kanaan Hilal , Lin Ridwan , Jovin Tudor , Horowitz Michael , Jankowitz Brian
Published: April 2011

Numerous techniques have been described to treat intracranial vessel perforation during endovascular interventions. We describe a novel application of Onyx-18 for the treatment of intracranial catheter perforations by sealing the vessel from the outside while retracting the catheter into the arterial lumen.
Under-estimation of self-reported occupational exposure by questionnaire in hospital workers
Authors: Donnay C , Denis M-A , Magis R , Fevotte J , Massin N , Dumas O , Pin I , Choudat D , Kauffmann F , Le Moual N
Published: April 2011

Objectives

The aim of the study was to determine whether self-reported occupational exposure to cleaning/disinfecting agents in hospital workers is accurate, in comparison to expert assessment, taken to be the gold standard.

Methods

In the Epidemiological Study of the Genetics and Environment of Asthma (EGEA), participants were interviewed on occupation with a specific questionnaire for hospital workers regarding tasks and cleaning/disinfecting agents. Two estimates of exposure were available: self-report and expert assessment. The expert assessment involved a standardised procedure to estimate intensity, frequency and probability of exposure for each job. The present analysis focused on eight exposures: formaldehyde, glutaraldehyde, bleach/chlorine, alcohol, quaternary ammonium components, ammonia, sprays and latex gloves. Agreement and differences between self-reported and expert estimates were studied by kappa and phi coefficients and McNemar tests, respectively.

Results

In the survey of 1571 adults, 176 ever hospital workers (327 occupations) with both self-reported and expert exposure assessments were studied. An underestimation of self-reported exposure was observed especially for formaldehyde (26.5% vs 32.7%, p=0.01), ammonia (7.4% vs 18.8%, p<0.0001), alcohol (64.9% vs 93.0%, p<0.0001) and quaternary ammonium components (16.6% vs 70.9%, p<0.0001), compared to expert assessment.

Conclusion

Occupational exposure to disinfecting/cleaning agents is common and high in hospitals. A large underestimation of self-reported exposure and a lack of knowledge of product components was observed. Our results show the relevance of expert assessment in epidemiological studies to limit measurement bias. This work underlines the need for health education programmes on the occupational risks induced by these types of products.
The ecological effects of clear-cutting
Authors: Keenan Rodney J. , (Hamish) Kimmins J. P.
Published: April 2011

Clear-cutting is a controversial practice that is widely applied in forests managed for wood production in many parts of the world. This paper aims to provide an objective synthesis of the ecological effects of clear-cutting as a basis for more informed discussion of its merits and disadvantages. A definition of clear-cutting is put forward, and its place in modern productive forestry is described. Effects on microclimate, water, soil, nutrient cycling, and the diversity and composition of plant and animal species are reviewed. The effects of clear-cutting vary considerably depending on site conditions (such as climate, geology, and topography) and on the structure and composition of the forest, the extent and distribution of harvesting, the method used to extract the logs, and the length of time before the forest is removed again. However, it is evident that many of the ecological impacts commonly ascribed to clear-cutting, in fact, result from other stages of the wood-production process, such as the quality and intensity of roading, site preparation practices (such as mechanical disturbance or slash burning), and the intensity of control of noncrop vegetation. Situations where clear-cutting is inappropriate are described. It is argued that in the right situations, with appropriate safeguards, it is an environmentally sound practice that offers many advantages in terms of the production of wood fibre.Key words: clear-cutting, environmental impacts, microclimate, hydrology, soil, forest production, nutrient cycling, wildlife.
Forestry practices and biodiversity, with particular reference to the Maritime Provinces of eastern Canada
Authors: Freedman Bill , Woodley Stephen , Loo Judy
Published: April 2011

The Canadian forest industries are based on the extensive harvesting and management of forests, with attendant effects on biodiversity at all levels of organization. In large part, conflicts between forestry and biodiversity occur because lands that are harvested and managed are mostly natural and seminatural ecosystems. Prior to being affected by forestry, such lands provided habitat for native species of wild life and their communities. Some of these elements of biodiversity may not find silvicultural habitats, especially plantations, to be suitable to their needs. In addition, the longer term integrity of some natural ecosystems, for example old-growth forests, is not compatible with any but the softest types of exploitation and management. This report discusses interactions of forestry and biodiversity at three levels of organization: (i) genetic variation within populations and species; (ii) the richness of species within communities; and (iii) the richness of community types on the landscape. A broader conclusion of our report is the following: If forestry systems of harvesting and management are to be practised in an ecologically sustainable fashion, then all elements of biodiversity must be accommodated within a landscape comprised of an integration of working lands and ecological reserves. The spatial scale of this integration could be various, ranging from large watersheds, to the "woodsheds" of particular industrial facilities, to provincial and national areas. Therefore, resolution of the substantial conflicts between biodiversity and forestry requires the design of ecologically sustainable landscapes that can provide a flow of timber and other valuated forest products, while still sustaining natural biodiversity resources.Key words: forest management, biodiversity, ecological reserves, eastern Canada, harvesting practices, old growth.
Air pollution and atmospheric precipitation chemistry in Poland - a review
Authors: Grodzin'ska-Jurczak M , Godzik B
Published: April 2011

Poland, especially its southern and south-eastern parts, which are the most industrialized, has been exposed to enormous local and transboundary gaseous (SO2, NOx) and particulate (alkaline dusts, heavy metals) emissions. The fall of the communist system at the beginning of the 1980s and the economic changes that followed resulted in changes in industrial production, in the emission of pollutants, and in the pollution levels in the atmospheric precipitation. This paper describes these changes throughout Poland during the past 10 to 15 years. Increasing acidification of the atmospheric precipitation was found due to a large reduction of alkaline particulates emissions and a decrease in the concentration of acidic ions (SO42-, Cl-, NH4+, NO3-) deposited. In Poland a significant differentiation in the pollution of atmospheric precipitation as well as differentiation between urban and rural areas was observed. Despite the reduction in these emissions and in the deposition of pollutants, Poland still occupies a leading place in the pollution map of the European continent.Key words: Poland, sulphur dioxide, nitrogen oxides, alkaline particulates, acid rain, forest decline.
Historical emissions from Swedish crystal-glass production and future scenarios of soil-lead pollution
Authors: Larsson S , Bergbck B , Eklund M , Lohm Ulrik
Published: April 2011

This paper aims to describe a method of estimating historical lead emissions from glassworks in the south-eastern region of Sweden from the introduction of lead in glass-making around 1870 up to the present. Three glassworks are studied, Bostorp (1872-1915), Alsterbro (1871-1969), and Kosta (1742-present). The methodological approach to the reconstruction of the lead emissions is based partly on indirect parameters, such as the use of lead oxide (red lead), the amount of glass produced, its economic value, together with recent measurements of emissions. Actual measurements of lead emissions are available from 1975, the amount of lead oxide used from 1932, the amount of glass produced in tonnes from the 1920s, and finally, the value of the production in SEK (Swedish crowns) is available for the entire period, from the 1870s up until now. The measured values are given first priority. A factor between the lead emissions and the amount of lead oxide used was calculated and used to estimate lead emissions back to the 1930s. Further back in time, the production in tonnes was used as a prediction value in a regression analysis. Finally, the production value in SEK was used to calculate the estimates back to the 1870s. The three glassworks represent different periods ofactivity but also different magnitudes of lead emissions into the air. At Bostorp about 1 tonne of lead was emitted, at Alsterbro about 10 tonnes, while the corresponding figure for Kosta is about 200 tonnes. Based on the estimated emissions of lead, future scenarios of soil-lead pollution have been approximated using different leaching factors.Key words: lead emissions, crystal leaching, soil horizons.
Temporal trends of polychlorinated biphenyls (PCBs) in Lake Ontario fish and invertebrates
Authors: Bentzen E , Mackay D , Hickie B E , Lean D RS
Published: April 2011

A comprehensive review is presented of changes of PCB concentrations in aquatic biota collected from Lake Ontario between 1977 and 1993, with emphasis on data for lake trout. Results of three major lake trout surveys from Canadian and United States agencies indicate lake trout PCBs have declined from the early 1980s, but changes in recent years are masked by interannual variability. These results also apply to other biota in the aquatic food web. PCB concentrations were consistent among the surveys after consideration of fish lipid content, age or size and analytical protocol. Variability of 20 to 30% in annual average estimates is attributed to both analytical and in situ sources. Current levels of PCBs in many salmonids exceed PCB consumption and wildlife protection advisories. The average half-life for PCBs in Lake Ontario biota is about 12 years and it will take three to four times that to reach the International Joint Commission target of 100 ng/g (ww) for protection of wildlife. It is essential that the design of monitoring programs ensures consistent, coordinated sampling and analysis. A monitoring strategy of annual sampling of key species supplemented with periodic intensive sampling of the entire food web (e.g., every 5 years) is suggested as more effective than current practices. There is a frequently neglected need for fuller interpretation of contaminant dynamics based on complementary research on the nature of the changing biotic and abiotic environments in a complex aquatic ecosystem like Lake Ontario. Key words: Lake Ontario, PCBs, fish, food webs, monitoring data, bioaccumulation.
In vitro toxicity of natural and designed peptides to tree pathogens and pollen
Authors: Jacobi V , Plourde A , Charest P J , Hamelin R C
Published: April 2011

The toxicities of four candidate peptides, which have potential for engineering disease resistance into poplars and conifers, were tested and compared in vitro. Cecropin B, (Ala8,13,18)-magainin II amide, and the two synthetic membrane interactive molecules (Peptidyl MIMs(tm)) D2A21 and D4E1 inhibited germination of spores of the fungal pathogens Cronartium ribicola J.C. Fisch., Gremmeniella abietina (Lagerberg) Morelet, Melampsora medusae Thuem., Nectria galligena Bres. in Strass., Ophiostoma ulmi (Buisman) Nannf., andSeptoria musiva Peck. Minimal inhibitory concentrations (MICs) of peptides required to achieve >95% inhibition of germination of conidia and urediniospores ranged from 0.3 to >5 µM. Permutation analyses on MICs confirmed that peptides significantly reduced germination of fungus spores (P = 0.0038) and that MICs of the two synthetic peptides were, on average, lower than those of the two natural peptides (P = 0.0012). In contrast, peptides had much less of an effect on the pollen of Picea, Pinus, and Populus species and seeds of white pine; MICs from 10 µM to >50 µM of peptide were needed to arrest germination. Peptidyl MIM(tm) D2A21 combined high antifungal activity with low pollen toxicity. Similar to some antimicrobial peptides from plants, Peptidyl MIM(tm) D2A21 could not prevent germination of fungal spores in the presence of potato dextrose broth or chloride salts with divalent cations. This may explain why the peptide had only a limited effect on fungal mycelium grown in potato dextrose broth medium.Key words: antimicrobial peptides (AMP), white pine blister rust, scleroderris canker, poplar leaf rust, Dutch elm disease, septoria canker.
Molecular systematics of Old World Apioideae (Apiaceae): relationships among some members of tribe Peucedaneae sensu lato, the placement of several island-endemic species, and resolution within the apioid superclade
Authors: Downie Stephen R , Watson Mark F , Spalik Krzysztof , Katz-Downie Deborah S
Published: April 2011

Comparative sequencing of the two internal transcribed spacer regions of nuclear ribosomal DNA was carried out to examine evolutionary relationships among representatives of Old World Apiaceae (Umbelliferae) subfamily Apioideae. Emphasis was placed on delimiting groups within the previously designated apioid superclade and clarifying relationships within and among the peucedanoid genera Angelica, Ferula, Heracleum, and Peucedanum. These spacer data, and those obtained from the chloroplast rps16 intron for a subset of the taxa, also enabled hypotheses on the phylogenetic placement of several narrowly distributed endemic species. The monophyly of Drude's tribe Echinophoreae is confirmed and it is sister to the Socotran endemic genera Nirarathamnos and Rughidia; the Balearic Islands endemic genus Naufraga allies with Apium graveolens; tribes Careae and Pyramidoptereae are recognized formally to be the previously designated clades "Aegopodium" and "Crithmum"; and tribes Oenantheae and Scandiceae are each expanded to include two species of Apium, previously attributable to Helosciadium, and four species of Ferula, respectively. Within the apioid superclade, five major lineages are recognized that are consistent with all available molecular evidence: tribe Echinophoreae, the clades "Pimpinella" and "Heracleum," and the more narrowly circumscribed clades "Angelica" and "Apium." Angelica and Ferula each comprise at least two lineages; Heracleum is polyphyletic if Heracleum candicans is retained in the genus; and Peucedanum is distributed in three well-separated clades with some species allied with those species of Angelica referred to Xanthogalum.Key words: Apiaceae subfamily Apioideae, nuclear rDNA ITS, chloroplast rps16 intron, Umbelliferae.
The dendroecology and climatic impacts for old-growth white pine and hemlock on the extreme slopes of the Berkshire Hills, Massachusetts, U.S.A.
Authors: Abrams Marc D , Gevel Saskia van de , Dodson Ryan C , Copenheaver Carolyn A
Published: April 2011

Dendrochronological techniques were used to investigate the dynamics of an old-growth forest on the extreme slope (65%) at Ice Glen Natural Area in southwestern Massachusetts. The site represented a rare opportunity to study the disturbance history, successional development, and responses to climatic variation of an old-growth hemlock (Tsuga canadensis (L.) Carr) - white pine (Pinus strobus L.) - northern hardwood forest in the northeastern United States. Hemlock is the oldest species in the forest, with maximum tree ages of 305-321 years. The maximum ages for white pine and several hardwood species are 170-200 years. There was continuous recruitment of hemlock trees from 1677 to 1948. All of the existing white pine was recruited in the period between 1800 and 1880, forming an unevenly aged population within an unevenly aged, old-growth hemlock canopy. This was associated with large increases in the Master tree-ring chronologies, indicative of major stand-wide disturbances, for both hemlock and white pine. Nearly all of the hardwood species were also recruited between 1800 and 1880. After 1900, there was a dramatic decline in recruitment for all species, including hemlock, probably as a result of intensive deer browsing. White pine and hemlock tree-ring growth during the 20th century was positively correlated with the annual Palmer drought severity index (r = 0.61 and 0.39, respectively). This included reduced growth during periods of low Palmer drought severity index values, the drought years of 1895-1922, and dramatic increases during periods of high Palmer drought severity index values in the 1970s and 1990s. Significant positive and negative correlations of certain monthly Palmer drought severity index values with 20th century tree-ring chronologies also exist for white pine and hemlock using response function analysis. The results of this study suggest that old-growth forests on extreme sites in the eastern United States may be particularly sensitive to direct and indirect allogenic factors and climatic variations and represent an important resource for studying long-term ecological and climatic history.Key words: age structure, radial growth analysis, disturbance, climate, fire, tree rings.
Interpopulation variation in germination responses of Scotch thistle, Onopordum acanthium L., to various concentrations of GA3, KNO3, and NaHCO3
Authors: Qaderi Mirwais M , Cavers Paul B
Published: April 2011

The effects of GA3, KNO3, and NaHCO3 on germination percentages and rates were determined for cypselas (seeds) of four local populations of Scotch thistle, Onopordum acanthium L., collected during a 2-year period. Three (1996, stored cypselas) and four (1997, fresh cypselas) concentrations (0.025, 0.05, and 0.1% for both years, plus 0.0125% for 1997) of the three compounds were used. Both freshly collected cypselas and those stored for 67 days at room temperature exhibited a range of germination responses from readily germinable to strongly dormant. GA3, even at a very low concentration, caused most viable cypselas to germinate, but 5-6% of viable cypselas in two populations did not respond to any GA3 treatment. In general, dry-stored cypselas germinated faster than fresh ones. Populations with more germinability (= proportion of cypselas capable of germinating) responded faster to GA3 than those with less germinability. KNO3 usually increased germination percentages but reduced the rate of germination. When treated with KNO3, stored cypselas from the two populations with less germinability germinated more slowly than those of the other two. In general, germination percentage decreased with an increase in NaHCO3 concentration. Overall, stored cypselas that were treated with NaHCO3 germinated more slowly than those in the control. The large differences among four local populations in response to these chemicals suggest that the effects of germination stimulators and other chemicals should be observed on several populations per species.Key words: cypsela, germination promoters, germination inhibitors, local populations, Onopordum acanthium, Scotch thistle.
Detecting ontogenetic stages of the palmAttalea humilisin fragments of the Brazilian Atlantic forest
Authors: Souza Alexandre F , Martins Fernando R , Matos Dalva M Silva
Published: April 2011

A study of the ontogenetic stages of the acaulescent palm Attalea humilis Mart. ex. Spreng was conducted in three fragments (1.6, 6.4, and 9.9 ha) of the Atlantic forest in southeastern Brazil. The fragments were damaged by fire during the study period (1996-1999). External macromorphology and quantitative measures of leaf number and length of the newest leaf's rachis allowed the distinction of five ontogenetic stages. Seedlings were attached to buried fruit remains and presented entire leaves. Juveniles possessed incomplete segmentation of the blade. Pinnatifid-leafed, non-reproducing individuals were morphometrically divided in two groups: immature, with fewer leaves and smaller but highly variable youngest leaf length, and virginile, with more and larger leaves, but more constant youngest leaf length; the critical crown size by which immature and virginile stages could be identified varied according to fragment and year. Reproductive palms bore identifiable reproductive structures. Seedlings, juveniles, and immatures had fewer leaves than virginile and reproductive individuals. Leaf length was similar between seedlings and juveniles but increased in later stages. The characteristics of each stage were fairly constant throughout the study years in the three fragments and were little affected by fire, indicating that the stages we define in this study are important in the developmental program of A. humilis.Key words: stage-structured populations, ontogenetic stages, forest fragments, fire, leaf size, leaf number.
Dormancy-breaking and germination requirements for seeds ofDiervilla lonicera(Caprifoliaceae), a species with underdeveloped linear embryos
Authors: Hidayati Siti N , Baskin Jerry M , Baskin Carol C
Published: April 2011

Dormancy-breaking requirements and type of dormancy were determined for seeds of Diervilla lonicera Mill. Seeds have an underdeveloped linear embryo that is about 35% of the length of the seed at maturity. Embryos (in intact seeds) grew at 25:15°C but not at 5°C. Up to 85% of the freshly matured seeds had morphological dormancy (MD), and thus, they germinated within about 30 days on a moist substrate in light at 30:15°C; a maximum of 3% of the seeds germinated in constant darkness. The other portion of fresh seeds had nondeep simple morphophysiological dormancy (MPD) and required a period of warm stratification or treatment with GA3to break dormancy. These seeds also required light to germinate. In contrast, cold stratification induced dormancy, and dry storage for up to 1 year did not effectively break dormancy. Seeds with MD germinated to significantly higher percentages on soil than on filter paper or on sand. Seeds sown on soil in a non-temperature-controlled greenhouse in mid-November germinated mostly in late May, whereas those sown in mid-April germinated in early May. Apparently, embryos of November-sown seeds were induced into physiological dormancy during winter. Thus, seeds had MPD in spring and needed several weeks of warm temperatures for dormancy break, embryo growth, and germination. This is the first report on seed dormancy in the genus Diervilla.Key words: embryo growth, germination phenology, Diervilla lonicera, morphological seed dormancy, morphophysiological seed dormancy, underdeveloped linear embryo.
Leaf anatomy and chlorophyll content of 12 woody species in contrasting light conditions in a Bornean heath forest
Authors: Cao Kun-Fang
Published: April 2011

This paper reports the anatomy, chlorophyll content, and some optical properties of leaves of 12 tree species in sun and shade conditions in a tropical heath forest in Brunei (northern Borneo). These plants displayed some xeromorphic leaf features, e.g., relatively low stomata density compared with lowland rain forest plants and sun leaves usually with two or more layers of palisade cells. Most species displayed substantial plasticity in leaf structure and chlorophyll concentration in response to different light conditions. Dipterocarp leaves had thinner palisade mesophyll and greater spongy to palisade thickness ratios than non-dipterocarp leaves. The chlorophyll content per unit leaf area of the species studied was within the range quoted for American tropical rainforest trees. Their chlorophyll a : chlorophyll b ratios, however, were much lower than those for forest plants in humid temperate and subtropical regions. This could be attributed to the regular soil water deficits of this forest. Despite large variation in leaf structure and chlorophyll concentration among species and within species on the two distinct conditions, their absorptance of photosynthetic active light was similar. Chlorophyll concentration per unit weight was adversely and nonlinearly related to leaf thickness for the data pooled from all species in both light conditions (R2 = 0.49, P < 0.001).Key words: chlorophyll concentration, leaf anatomy, kerangas, light acclimation, leaf plasticity, tropical heath forest.
Variability in litter quality and its relationship to litter decay in Canadian forests
Authors: Preston Caroline M , Trofymow JA (Tony) , Working Group the Canadian Intersite Decompositio
Published: April 2011

Predicting the effects of climate change on litter decomposition requires an improved understanding of the link between organic composition and the parameters used to define litter quality. Carbon-13 nuclear magnetic resonance spectroscopy with cross-polarization and magic-angle spinning (CPMAS NMR) was used to characterize 36 foliar litters, including the species used in the Canadian Intersite Decomposition Experiment (CIDET), a Canada-wide long-term litter decomposition study. The litters showed a wide range of organic composition, qualitatively interpreted as the sum of component biopolymers (mainly carbohydrates, cutin, tannins, and lignin). Only weak correlations were found between NMR parameters and Klason lignin (KLIG); however, cluster analysis based on elemental, NMR, and proximate analysis gave good separation of botanical classes. NMR also had little predictive value for 3-year CIDET mass losses, which were negatively correlated with both KLIG and KLIG/N. Mass loss generally decreased in the following order: grass > pioneer broad-leafed deciduous > conifer (deciduous and evergreen) > American beech (a fagaceae) > wood. Predictive models for 3-year CIDET mass loss derived from linear regression with elemental, proximate, and NMR analyses were superior to those using only NMR parameters, with the best model based on KLIG, N, and Ca. Although providing no molecular-level understanding, KLIG integrates the most insoluble lignin, cutin, and tannin components. Limitations and possible improvements for NMR evaluation of litter quality are discussed.Key words: Klason lignin, 13C CPMAS NMR, proximate analysis, litter decomposition, tannin, cutin, CIDET.