Culturable Airborne Bacteria in Outdoor Environments in Beijing,China

Airborne bacteria are important biological components of bioaerosol and play an important role in ecosystem. Bacteria at a high concentration in the atmosphere can result in biological air pollution and all kinds of diseases. In this study, a systematical survey on the culturable airborne bacteria was carried out for 1 year at three sites in Beijing urban area. Results showed that concentrations of culturable bacteria ranged from 71 colony forming units (CFU)/m³ to 22,100 CFU/m³, and the mean was 2,217 CFU/m³. Bacterial concentrations at the human activity-enriched site (RCEES) and the highly trafficked site (XZM) were virtually the same point. They were significantly higher than those at the greener site (BBG). Significant variation in bacterial concentrations in different seasons was observed at RCEES and XZM with higher concentrations in summer and autumn. In a single day, significantly lower concentrations were detected at 13:00 hours through all sampling sites. In this study, 165 species in 47 genera of culturable bacteria were identified. Micrococcus was one of the most dominant bacterial groups and contributed to approximately 20∼30% of the total bacterial concentration, followed by Staphylococcus, Bacillus, Corynebacterium, and Pseudomonas. The bacterial species with a high concentration percentage included Micrococcus luteus and Micrococcus roseus.     

Measurements of total and culturable bacteria in the alfresco atmosphere using a wet-cyclone sampler

Alfresco (def. clean, outdoor) airborne bacteria were collected with a commercially available wet-cyclone bioaerosol sampler to demonstrate its use, sample processing and resultant observations of total and culturable bacteria in mid-summer in the mid-Willamette River Valley, OR. Some critiques of the system are given. The maximum and minimum total and culturable airborne bacterial concentrations in the samples were 5.9 × 10⁵ and 8.8 × 10² cells m⁻³, and 1.3 × 10⁴ and 3.1 CFU m⁻³, respectively. What is thought to be a diurnal cycle was also observed for both fractions with highest concentrations during the day and lowest at dawn and dusk. The culturable bacteria as a percentage of the total, was maximal at mid-day (≈ 3%) and minimal at early morning and late evening (≈ 0.5–2%). Contrarily, the total bacteria in the downwind dust plume of a grass seed combine was 2.9 × 10⁶ cells m⁻³ and of these approximately 73% were culturable, a much greater culturable percentage than found in the alfresco outdoor atmosphere.     

The rat Ruby (<Emphasis Type="Italic">R</Emphasis>) locus is <Emphasis Type="Italic">Rab38</Emphasis>: identical mutations in Fawn-hooded and Tester-Moriyama rats derived from an ancestral Long Evans rat sub-strain

Hermansky-Pudlak syndrome (HPS) is a group of rare, recessive disorders in which oculocutaneous albinism, progressive pulmonary fibrosis, bleeding diathesis, and other abnormalities result from defective biogenesis of multiple cytoplasmic organelles. Seven different HPS genes are known in humans; in mouse, at least 16 loci are associated with HPS-like mutant phenotypes. In the rat, only two HPS models are known, Fawn-hooded (FH) and Tester Moriyama (TM), non-complementing strains in which HPS-like hypopigmentation and platelet storage pool deficiency result from a mutation of the Ruby (red eyed dilution; R) locus on Chromosome (Chr) 1. We have identified the R locus as the Rab38 gene, establishing that rat R is homologous to mouse chocolate (cht). Further, we show that FH and TM rats have identical Rab38 Met1Ile mutations, occurring on an identical Chr 1 marker allele haplotype, indicating that these two strains derive from a common ancestor. This ancestor appears to have been a sub-strain of the outbred Long Evans (LE) strain, and several modern LE sub-strains carry the Rab38 Met1Ile R mutation on the same Chr 1 marker haplotype. These findings have significant implications for the many past and ongoing studies that involve the FH and LE-derivative rat strains. Hermansky-Pudlak syndrome (HPS; MIM 203300) is a group of autosomal recessive diseases in which oculocutaneous albinism (OCA), progressive and fatal pulmonary fibrosis, and bleeding diathesis due to platelet storage pool deficiency result from defects in the biogenesis of specific cytoplasmic organelles and granules: melanosomes, lysosomes, and platelet dense granules (reviewed in Spritz 1999, 2000; Spritz et al. 2003). In humans, seven different HPS genes are known (Oh et al. 1996; DellAngelica et al. 1999; Anikster et al. 2001; Suzuki et al. 2002; Li et al. 2003; Zhang et al. 2003). In the mouse, at least 16 loci associated with HPS-like mutant phenotypes are known, seven of which are homologous to the human HPS loci (Swank et al. 1998; Bennett and Lamoreux 2003). The nucleotide sequence data reported in this paper have been submitted to GenBank and have been assigned the accession number AY425759. (Naoki Oiso) Present address: Department of Dermatology, Saiseikai Tondabayashi Hospital, Tondabayashi, Osaka 584-0082, Japan.     

Bone tissue,lyophilized and stored at room temperature for 15 days or more,is not capable of transmitting HIV,HCV or HBV

Over the past 57 years, 17 recipients of frozen bone have been infected with: HIV (Centers for Disease Control and Prevention in Morb Mortal Wkly Rep MMWR 37(39):597–599, 1988; Li et al. in J Formos Med Assoc 100(5):350–351, 2001; Simonds et al. in NEJM 326(11):726–732, 1992; Schratt et al. in Unfallchirurg 99(9):679–684, 1996); HCV (Eggen and Nordbo in NEJM 326(6):411, 1992; Conrad et al. in J Bone Joint Surg Am 77:214–224, 1995; Trotter in J Bone Joint Surg Am 851(11):2215–2217, 2003; Tugwell et al. in Ann of Internal Med 143(9):648–654, 2005); or HBV (Shutkin in J Bone Joint Surg Am 36:160–162, 1954). However, bone, lyophilized and stored at room temperature, has never transmitted these viral diseases. A literature review was undertaken to determine whether there is any evidence that lyophilized bone is capable of transmitting HIV, HCV and HBV.     

Male Mating Interest Varies with Female Fecundity in <Emphasis Type="Italic">Pan troglodytes schweinfurthii</Emphasis> of Kanyawara,Kibale National Park

Female chimpanzees mate promiscuously during a period of extended receptivity marked by prominent sexual swelling. Recent studies of wild chimpanzees indicate that subtle variations in swelling size could act as a reliable cue of female fertilization potential both within and between cycles (Emery and Whitten Behavioral Ecology and Sociobiology, 54, 340–351, 2003; Deschner et al. Hormones and Behavior, 46, 204–215, 2004). Copulation rates increase during the periovulatory period and during conception cycles (Deschner et al. Hormones and Behavior, 46, 204–215, 2004; Emery Thompson American Journal of Primatology, 67, 137–158, 2005a), suggesting that males may be able to assess female fertilization potential. We asked whether facultative timing of copulation in Kanyawara chimpanzees was due to increased male mating interest or to increased female proceptivity during the most fecund days. We assessed multiple measures of male mating effort in cycles aligned relative to the day of detumescence and compared periovulatory days to other days of maximal swelling, and conception cycles to nonconception cycles. The rate and proportion of male initiative in soliciting sexual behavior increased during periods of highest fertilization potential. Males were also more likely to interrupt copulations, associate with estrous females, and compete with other males when females were most likely to conceive. Females initiated copulations more frequently during conception cycles but did not visibly shift mating behavior within cycles. Our results support the hypothesis that male chimpanzees have the ability to assess the profitability of mating attempts, a trait that may act as a counter-adaptation to female strategies to obscure paternity. We discuss potential cues and the implications for female reproductive strategies.     

Spore-forming bacteria in soil cultivated with GM white poplars: Isolation and characterization

The impact of transgenic white poplars (Populus alba L. cv. ‘Villafranca’) was assessed on the soil aerobic spore-forming bacteria (SFB). The genetically modified poplars, expressing either the StSy gene for resveratrol production or the bar gene for herbicide tolerance, were cultivated in greenhouse. The occurrence of SFB was monitored in soil samples collected at eight different timepoints over a two-year period. The total culturable bacterial population of the StSy and bar trials underwent significant seasonal fluctuations in the range of 10⁶−2.5 × 10⁸ CFU/g dry soil and of 10⁴−5 × 10⁸ CFU/g dry soil, respectively. Changes occurred also within the culturable SFB population with size varying at 10³−5 × 10⁴ CFU/g dry soil and 10²−2 × 10⁵ CFU/g dry soil in the StSy and bar trials, respectively. No significant differences in the size of the total and SFB culturable populations were observed when comparing each transgenic line with the nontransformed control line while seasonal shifts of soil bacterial populations were evident in both trials. The culturable SFB fraction included three isolates (SFB-1, SFB-2 and SFB-3) classified by 16S rDNA sequence analysis as members of the Bacillus genus. According to the reported data, cultivation of both herbicide-resistant and resveratrol-producing GM white poplars did not affect the culturable SFB population at the soil level.     

Cancer models,genomic instability and somatic cellular Darwinian evolution

   

The biology of cancer is critically reviewed and evidence adduced that its development can be modelled as a somatic cellular Darwinian evolutionary process. The evidence for involvement of genomic instability (GI) is also reviewed. A variety of quasi-mechanistic models of carcinogenesis are reviewed, all based on this somatic Darwinian evolutionary hypothesis; in particular, the multi-stage model of Armitage and Doll (Br. J. Cancer 1954:8;1-12), the two-mutation model of Moolgavkar, Venzon, and Knudson (MVK) (Math. Biosci. 1979:47;55-77), the generalized MVK model of Little (Biometrics 1995:51;1278-1291) and various generalizations of these incorporating effects of GI (Little and Wright Math. Biosci. 2003:183;111-134; Little et al. J. Theoret. Biol. 2008:254;229-238).     

Temperature controls a latitudinal gradient in the proportion of watershed nitrogen exported to coastal ecosystems

Increased export of biologically available nitrogen (N) to the coastal zone is strongly linked to eutrophication, which is a major problem in coastal marine ecosystems (NRC (2000) Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution. National Academy Press, Washington, DC; Bricker et al. (1999) National Estuarine Eutrophication Assessment. Effects of nutrient enrichment in the nation’s estuaries. NOAA-NOS Special Projects Office, Silver Spring, MD). However, not all of the nitrogen input to a watershed is exported to the coast (Howarth et al. (1996) Biogeochemistry 35:75–139; Jordan and Weller (1996) Bioscience 46:655–664). Global estimates of nitrogen export to coasts have been taken to be 25% of watershed input, based largely on northeastern U.S. observations (Galloway et al. (2004) Biogeochemistry 70:153–226; Boyer et al. (2006) Global Biogeochem Cycle 20:Art. No. GB1S91). We applied the N budgeting methodology developed for the International SCOPE Nitrogen project (Howarth et al. (1996) Biogeochemistry 35:75–139; Boyer et al. (2002) Biogeochemistry 57:137–169) to 12 watersheds in the southeastern U.S., and compared them with estimates of N export for 16 watersheds in the northeastern U.S. (Boyer et al. (2002) Biogeochemistry 57:137–169). In southeastern watersheds, average N export was only 9% of input, suggesting the need for downward revision of global estimates. The difference between northern and southern watersheds is not a function of the absolute value of N inputs, which spanned a comparable range and were positively related to export in both cases. Rather, the proportion of N exported was significantly related to average watershed temperature (% N export = 58.41 e^{−0.11 * temperature}; R ² = 0.76), with lower proportionate nitrogen export in warmer watersheds. In addition, we identified a threshold in proportionate N export at 38°N latitude that corresponds to a reported breakpoint in the rate of denitrification at 10–12°C. We hypothesize that temperature, by regulating denitrification, results in increased proportionate N export at higher latitudes. Regardless of the mechanism, these observations suggest that temperature increases associated with future climate change may well reduce the amount of nitrogen that reaches estuaries, which will have implications for coastal eutrophication.     

Shotgun Crystallization Strategy for Structural Genomics II: Crystallization Conditions that Produce High Resolution Structures for T. maritima Proteins

Currently, 119 high resolution structures of Thermotoga maritima proteins have been determined by the Joint Center for Structural Genomics (JCSG, www.jcsg.org). Sixty-seven of these were solved using the first implementation of the multi-tiered crystallization strategy at the JCSG for the efficient crystallization of large numbers of protein targets. Previously, we reported the analysis of all proteins crystallized using this multi-tiered strategy [Lesley, S.A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 11664–11669; Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037]. Here, we extend the analysis and describe the crystallization characteristics of those proteins that produced diffraction quality crystals, ultimately resulting in high resolution structures. First, we found that over 77% (52) of the crystals used for structure determination were produced directly from high-throughput coarse screens, indicating that less than one quarter of the crystals (15) required fine screening. In addition, as observed for the proteome screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037], the majority of conditions that produced crystals for natively expressed proteins, whose structures have been determined, were distinct from those of their more extensively purified and selenomethionine-labeled counterparts. Finally, 99% of the proteins whose structures were solved crystallized in conditions contained in the JCSG Minimal Core Screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037; Page, R. and Stevens, R.C. (2004) Methods 34, 373–389], a set of 67 conditions previously identified as those most likely to produce crystals of a diverse set of proteins, confirming its success for rapid identification of proteins with a natural propensity to crystallize.     

1H, 13C and 15N NMR assignments of the C1A and C1B subdomains of PKC-delta

The Protein Kinase C family of enzymes is a group of serine/threonine kinases that play central roles in cell-cycle regulation, development and cancer. A key step in the activation of PKC is translocation to membranes and binding of membrane-associated activators including diacylglycerol (DAG). Interaction of novel and conventional isotypes of PKC with DAG and phorbol esters occurs through the two C1 regulatory domains (C1A and C1B), which exhibit distinct ligand binding selectivity that likely controls enzyme activation by different co-activators. PKC has also been implicated in physiological responses to alcohol consumption and it has been proposed that PKCα (Slater et al. J Biol Chem 272(10):6167–6173, 1997; Slater et al. Biochemistry 43(23):7601–7609, 2004), PKCε (Das et al. Biochem J 421(3):405–413, 2009) and PKCδ (Das et al. J Biol Chem 279(36):37964–37972, 2004; Das et al. Protein Sci 15(9):2107–2119, 2006) contain specific alcohol-binding sites in their C1 domains. We are interested in understanding how ethanol affects signal transduction processes through its affects on the structure and function of the C1 domains of PKC. Here we present the ¹H, ¹⁵N and ¹³C NMR chemical shift assignments for the Rattus norvegicus PKCδ C1A and C1B proteins.     

Incidence of allergenically significant fungal aerosol in a rural bakery of West Bengal,India

The frequency of fungal spores in the air of three different sections of a rural bakery was analyzed using a Burkard personal slide sampler and Andersen two stage viable sampler. In average concentration of spores (No./m³) was 228–26770/m³ and concentration of viable colony forming units (CFU/m³) was 65-2061 CFU/m³. Dominant fungus species both culturable and nonculturable, were species of Aspergillus and Penicillium, Cladosporiumsp., Aspergillus niger, Aspergillus flavus, Aspergillus fumigatus, Cladosporium cladosporioides, Penicillium citrinum and Alternaria alternata. Seasonal variations in the spore concentrations were clearly observed in case of some fungi. Total culturable mould concentration of different bakery sections sometimes exceeded the acceptable limit for a healthy indoor environment. Antigenic extracts prepared from some dominant culturable fungi showed high level of allergenicity in skin prick tests indicating that they could be responsible for allergic respiratory dysfunction of bakery workers.This revised version was published online in October 2005 with corrections to the Cover Date.     

Airborne dust,bacteria, actinomycetes and fungi at a flourmill

A study was carried out on suspended dust, bacterial and fungal aerosols in a four-storey flourmill building located in Giza, Egypt. Airborne microorganisms were quantitatively isolated using liquid impinger and gravimetric samplers during the period from March 2004 to February 2005. Suspended dust varied from 1.96 to 16.3 mg m⁻³ and 0.69 to 1.8 mg m⁻³ in the indoor and outdoor environments, respectively. Suspended dust was significantly greater (P < 0.05) at bran package, double roller, purifiers and flour storage units in comparison to the outdoor reference site. The dust levels exceed the occupational exposure limit (OEL) of 0.5 mg m⁻³ for flour dust. Airborne microbial counts were found at median values, between sampling locations, ranged from 0 to >10⁴ CFU m⁻³. Gram-negative bacteria were found in small numbers (0–10² CFU m⁻³). The highest concentration of actinomycetes (>10³ CFU m⁻³) was detected in the storage unit. Airborne fungal counts were found at the median values, between sampling locations, varied from 10³ to 10⁴ CFU m⁻³. The counts of airborne bacteria and fungi were significantly greater (P < 0.05) at the purifiers and double roller mill units in comparison to the outdoor reference site using the liquid impinger sampler. Microbial levels associated with bulk deposited dust averaged between 10⁵ and 10⁶ CFU g⁻¹. Alcaligenes (5.4%) Pseudomonas (3.87%) and Enterobacter (3.1%) were the predominant Gram-negative species while Bacillus (29.4%) and Micrococci (13.9%) were the major components of Gram-positive bacteria. Aspergillus and Penicillium were the predominant fungal types indoor whereas Cladosporium (35.2%) and Aspergillus species (22.2%) were the predominant fungal types outdoor. A number of allergenic and toxigenic bioaerosols were found in the flourmill workplace.     

Kinetic models of photosystem II should accommodate the effect of donor side quenching on variable chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence in the microseconds time range

Quantitative data on laser flash-induced variable fluorescence in the 100 ns to 1 ms time range (Belyaeva et al. in Photosynth Res 98:105–119, 2008) confirming those of others (Steffen et al. in Biochemistry 40:173–180, 2001, Biochemistry 44:3123–3132, 2005; Belyaeva et al. in Biophysics 51(6):976–990, 2006), need a substantial correction with respect to magnitude of the normalized variable fluorescence associated with single turnover-induced charge separation in RCs of PS II. Their data are conclusive with the involvement of donor side quenching, the release of which occurs with a rate constant in the range of tens of ms⁻¹, and presumed to be associated with reduction of Y_\textz ⁺ Y_{\text{z}}^{ + } by the OEC.     

Genome-wide meta-analysis for rheumatoid arthritis

Meta-analysis is being increasingly used as a tool for integrating data from different studies of complex phenotypes, because the power of any one study to identify causal loci is limited. We applied a novel meta-analytical approach (Loesgen et al. in Genet Epidemiol 21(Suppl 1):S142–S147, 2001) in compiling results from four studies of rheumatoid arthritis in Caucasians including two studies from NARAC (Jawaheer et al. in Am J Hum Genet 68:927–936, 2001; Jawaheer et al. in Arthritis Rheum 48:906–916, 2003), one study from the UK (MacKay et al. in Arthritis Rheum 46:632–639, 2001) and one from France (Cornelis et al. in Proc Natl Acad Sci USA 95:10746–10750, 1998). For each study, we obtained NPL scores by performing interval mapping (2 cM intervals) using GeneHunter2 (Kruglyak et al. in Am J Hum Genet 58:1347–1363, 1996; Markianos et al. in Am J Hum Genet 68:963–977, 2001). The marker maps differed among the three consortium groups, therefore, the marker maps were aligned after the interval mapping was completed and the NPL scores that were within 1 cM of each other were combined using the method of Loesgen et al. (Genet Epidemiol 21(Suppl 1):S142–S147, 2001) by calculating the weighted average of the NPL score. This approach avoids some problems in analysis encountered by using GeneHunter2 when some markers in the sample are not genotyped. This procedure provided marginal evidence (P<0.05) of linkage on chromosome 1, 2, 5 and 18, strong evidence (P<0.01) on chromosomes 8 and 16, and overwhelming evidence in the HLA region of chromosome 6.     

Seasonal abundance and distribution of <Emphasis Type="Italic">Vibrio</Emphasis> species in the treated effluent of wastewater treatment facilities in suburban and urban communities of Eastern Cape Province,South Africa

We assessed the seasonal abundance and distribution of Vibrio species as well as some selected environmental parameters in the treated effluents of two wastewater treatment plants (WWTP), one each located in a suburban and urban community of Eastern Cape Province, South Africa. Vibrio population density ranged from 2.1×10⁵ to 4.36×10⁴ CFU/ml in the suburban community and from 2.80×10⁵ to 1.80×10⁵ CFU/ml in the urban community. Vibrio species associated with 180 μ, 60 μ, and 20 μ plankton sizes were observed at densities of 0–136×10³ CFU/ml, 0–8.40×10² CFU/ml, and 0–6.80×10² CFU/ml, respectively at the suburban community’s WWTP. In the urban community, observed densities of culturable Vibrio were 0–2.80×10² CFU/ml (180 μ), 0–6.60×10² CFU/ml (60 μm), and 0–1.80× 10³ CFU/ml (20 μm). The abundance of free-living Vibrio species ranged from 0 to 1.0×10² and 1.0×10³ CFU/ml in the suburban and urban communities’ WWTPs, respectively. Molecular confirmation of the presumptive Vibrio isolates revealed the presence of V. fluvialis (41.38%), V. vulnificus (34.48%), and V. parahaemolyticus (24.14%) in the suburban community effluents. In the urban community molecular confirmation revealed that the same species were present at slightly different percentages, V. fluvialis (40%), V. vulnificus (36%), and V. parahaemolyticus (24%). There was no significant correlation between Vibrio abundance and season, either as free-living or plankton-associated entities, but Vibrio species abundance was positively correlated with temperature (r=0.565; p<0.01), salinity, and dissolved oxygen (p<0.05). Turbidity and pH showed significant seasonal variation (p<0.05) across the seasons in both locations. This study underscores the potential of WWTPs to be sources of Vibrio pathogens in the watershed of suburban and urban communities in South Africa.     

Air biocontamination in a variety of agricultural industry environments in Egypt: a pilot study

Inhalation of airborne microorganisms and organic dust is an occupational concern among workers in agricultural industries. Airborne microorganisms and particulate matter samples were collected from poultry house, flourmill, textile, and food industry sites by use of liquid impinger and gravimetric samplers. Particulate matter concentrations were recorded at median concentrations of 1.56, 1.92, 4.39, and 0.7 mg/m³ in the occupied poultry house, textile, flourmill, and food indoor working environments, respectively. The highest median particulate matter concentration (27.9 mg/m³) was detected at the flourmill’s stack site. The highest median indoor concentration of culturable airborne bacteria (6.23 × 10⁵ CFU/m³) was found at the occupied poultry-house site and the lowest concentration (4.6 × 10³ CFU/m³) was found at the food industry site. The highest median indoor concentration of culturable airborne fungi (3.15 × 10⁴ CFU/m³) was found at the flourmill site whereas the lowest (1.24 × 10³ CFU/m³) was found at the textile industry site. Bacillus and Staphylococcus were the predominant Gram-positive bacteria whereas Acinetobacter and Klebsiella were the predominant Gram-negative bacteria. Escherichia coli and Salmonella were only detected in the indoor air at the poultry house site. Aspergillus flavus, Aspergillus niger, Penicillium, and yeast were the predominant fungal types at flourmill, textile, food industry, and poultry house, respectively. Workers were continuously exposed to airborne microorganisms at a median value of 10⁴ CFU/m³ in all the industries studied.     

Last days in the old radiation laboratory (ORL), Berkeley,California, 1954

Govindjee, the founding editor of the Historical Corner of Photosynthesis Research, invited me 3 years ago to tell the story of why I left Melvin Calvin’s laboratory in the mid 1950s long before the 1961 Nobel Prize in Chemistry was awarded to Calvin for the path of carbon in photosynthesis. I have already written my scientific perspective on this topic (see Benson (Photosynth Res 73:29–49, 2002); also see Bassham (Photosynth Res 76:35–52, 2003) as he was also a major player in this research). Here, I present my recollections of my last days in the old radiation laboratory (ORL) at Berkeley, California. References have been added by Govindjee for the benefit of the readers.