Biomineralization of Fungal Hyphae with Calcite (CaCO3) and Calcium Oxalate Mono- and Dihydrate in Carboniferous Limestone Microcosms

The formation of biogenic fabrics in limestone by two fungi, Serpula himantioides and a polymorphic fungal isolate from limestone identified as a Cephalotrichum (syn. Doratomyces) sp., was investigated. The fungal cultures were grown in laboratory microcosms consisting of Carboniferous limestone and after 21 d incubation at 25°C, biomineralization of fungal filaments was observed. Environmental electron scanning microscopy (ESEM) and X-ray micro-analysis (EDXA) of crystalline precipitates on the hyphae of S. himantioides demonstrated that the secondary crystals exhibited different crystalline forms but were similar in elemental composition to the original limestone. Powder X-ray diffraction (XRD) of crystalline precipitates showed they were composed of a mixture of calcite (CaCO ₃ ) and calcium oxalate monohydrate (CaC ₂ O ₄ · H ₂ O). Analysis of crystals precipitated on the hyphae of the limestone isolate, using ESEM and EDXA, showed that the crystals exhibited similar morphological characteristics and elemental composition to the original limestone. XRD showed that they were composed solely of calcite (CaCO ₃ ) or of calcite with some calcium oxalate dihydrate (CaC ₂ O ₄ · 2H ₂ O). These results provide direct experimental evidence for the precipitation of calcite (CaCO ₃ ) and also secondary mycogenic minerals, on fungal hyphae in low nutrient calcareous environments, and suggest that fungi may play a wider role in the biogeochemical carbon cycle than has previously been appreciated.     

Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates

Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%–90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.     

Intratumor heterogeneity of biomarker expression in breast carcinomas

Small biopsy samples are used increasingly to assess the biomarker expression for prognostic information and for monitoring therapeutic responses prior to and during neoadjuvant therapy. The issue of intratumor heterogeneity of expression of biomarkers, however, has raised questions about the validity of the assessment of biomarker expression based on limited tissue samples. We examined immunohistochemically the expression of HER-2neu (p185^erbB-2), epidermal growth factor receptor (EGFR), Bcl-2, p53, and proliferating cell nuclear antigen (PCNA) in 30 breast carcinomas using archived, paraffin embedded tissue and determined the extent of intratumor heterogeneity. Each section was divided into four randomly oriented discrete regions, each containing a portion of the infiltrating carcinoma. For each tumor, the entire lesion and four regions were analyzed for the expression of these markers. Scores of both membrane and cytoplasmic staining of HER-2neu and EGFR, scores of cytoplasmic staining of Bcl-2, and scores of nuclear staining of both p53 and PCNA were recorded. The intensity of staining and the proportion of immunostained cells were determined. A semiquantitative immunoscore was calculated by determining the sum of the products of the intensity and corresponding proportion of stained tumor cells. We analyzed both invasive (IDC) and in situ (DCIS) carcinomas. The Wilcoxon signed-rank test was used for paired comparisons between overall and regional immunoscores and between overall and regional percentages of stained cells. Spearman's correlation coefficients were used to assess the level of agreement of overall biomarker expression with each of the regions. Generalized linear models were used to assess overall and pair-wise differences in the absolute values of percent changes between overall and regional expression of biomarkers. For IDCs, there were no statistically significant differences in the expression of the biomarkers in terms of either the percentage of cells staining or the immunoscores when comparing the entire tumor with each region except for the lower EGFR expression of arbitrarily selected region 1 and lower p53 expression of region 1 compared to that of the entire tumor section. For DCIS, there were no statistically significant differences in the expression of the biomarkers between the entire tumor and each region except in PCNA of region 2 compared to that of entire tumor section. Positive correlation of immunoscores was observed between the entire tumor and each region as well as across all four regions for IDC. Similar observations were noted with DCIS except for HER-2neu and PCNA. No statistically significant differences were observed in the absolute values of percent changes of biomarker expression between overall and the four regions for both DCIS and IDC. Therefore, no significant intratumor heterogeneity in the expression of HER-2neu, Bcl-2, and PCNA was observed in IDC. Minor regional variations were observed for EGFR and p53 in IDC. Similarly, no significant regional variation in the expression of markers was observed in DCIS except for PCNA.     

Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination

We describe genomic structures of 59 X-chromosome segmental duplications that include the proteolipid protein 1 gene (PLP1) in patients with Pelizaeus-Merzbacher disease. We provide the first report of 13 junction sequences, which gives insight into underlying mechanisms. Although proximal breakpoints were highly variable, distal breakpoints tended to cluster around low-copy repeats (LCRs) (50% of distal breakpoints), and each duplication event appeared to be unique (100 kb to 4.6 Mb in size). Sequence analysis of the junctions revealed no large homologous regions between proximal and distal breakpoints. Most junctions had microhomology of 1-6 bases, and one had a 2-base insertion. Boundaries between single-copy and duplicated DNA were identical to the reference genomic sequence in all patients investigated. Taken together, these data suggest that the tandem duplications are formed by a coupled homologous and nonhomologous recombination mechanism. We suggest repair of a double-stranded break (DSB) by one-sided homologous strand invasion of a sister chromatid, followed by DNA synthesis and nonhomologous end joining with the other end of the break. This is in contrast to other genomic disorders that have recurrent rearrangements formed by nonallelic homologous recombination between LCRs. Interspersed repetitive elements (Alu elements, long interspersed nuclear elements, and long terminal repeats) were found at 18 of the 26 breakpoint sequences studied. No specific motif that may predispose to DSBs was revealed, but single or alternating tracts of purines and pyrimidines that may cause secondary structures were common. Analysis of the 2-Mb region susceptible to duplications identified proximal-specific repeats and distal LCRs in addition to the previously reported ones, suggesting that the unique genomic architecture may have a role in nonrecurrent rearrangements by promoting instability.     

Competition between Dunaliella species at high salinity

Information on the distribution of more than 225 species of planktonic, periphytic, and benthic rotifers from diverse waters in south and central Sweden was analyzed for pH preference. No particularly strong correlation was found between pH and any other environmental factor, with regards to rotifer distribution. However, species indicating oligotrophy generally have their pH optima at or below 7.0, while those indicating eutrophy occur at or above this level. Rotifers found in acidic waters are often non-planktonic or semiplanktonic.     

PULSES OF PHOSPHATE PROMOTE DOMINANCE OF THE TOXIC CYANOPHYTE CYLINDROSPERMOPSIS RACIBORSKII IN A SUBTROPICAL WATER RESERVOIR1

The role of dissolved inorganic phosphorus (DIP) in promoting dominance of the toxic nitrogen (N)‐fixing cyanobacterium Cylindrospermopsis raciborskii (Wo?osz.) Seenayya et Subba Raju was examined in a subtropical water reservoir, Lake Samsonvale (=North Pine reservoir). A novel in situ bioassay approach, using dialysis tubing rather than bottles or bags, was used to determine the change in C. raciborskii dominance with daily additions of DIP. A statistically significant increase in dominance of C. raciborskii was observed when DIP was added at two concentrations (0.32 μM and 16 μM) in a daily pulse over a 4 d period in three separate experiments in the summer of 2006/2007. There was an increase in both C. raciborskii cell concentrations and biovolume in two DIP treatments, but not in the ammoniacal N + DIP treatment. In addition, overall phytoplankton cell concentrations increased with DIP addition, indicating that Lake Samsonvale was DIP limited at the time of experiments. Given the bioassay response, it is likely that dominance of C. raciborskii could increase in Lake Samsonvale with periodic injections of DIP such as inflow events.     

Rapid evolution and the genomic consequences of selection against interspecific mating

While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the United States in the mid‐1980s, resulting in the displacement of A. aegypti in much of the south‐eastern United States. The rapid displacement was likely due to the superior competitive ability of A. albopictus as larvae and asymmetric mating interference competition, in which male A. albopictus mate with and sterilize A. aegypti females, a process called “satyrization.” The goal of this study was to examine the genomic responses of a resident species to an invasive species in which the mechanism of character displacement is understood. We used double‐digest restriction enzyme DNA sequencing (ddRADseq) to analyse outlier loci between selected and control lines of laboratory‐reared A. aegypti females from two populations (Tucson, AZ and Key West, Florida, USA), and individual females classified as either “resisted” or “mated with” A. albopictus males via mating trials of wild‐derived females from four populations in Florida. We found significant outlier loci in comparing selected and control lines and between mated and nonmated A. aegypti females in the laboratory and wild‐derived populations, respectively. We found overlap in specific outlier loci between different source populations that support consistent genomic signatures of selection within A. aegypti. Our results point to regions of the A. aegypti genome and potential candidate genes that may be involved in mating behaviour, and specifically in avoiding interspecific mating choices.     

Human B cell development. II. Subpopulations in the human fetus

In man, during fetal development the B cell populations show distinct phenotypes at different tissue sites. The pre-B and B lymphocytes of the fetal liver and bone marrow express IgM and B cell markers, B1 (CD20) and BA-1 (CD24). These "early" cells are negative with a number of other reagents, anti-IgD, RFB4 (CD22), RFB6 (CD21), and RFA-2, which on the other hand recognize peripheral B cells. These peripheral B lymphocytes in the developing fetus are heterogeneous. The diffusely distributed B cells in the earliest lymph node samples, 16 to 17 wk of gestational age, and from 16 to 21 wk in the spleen, are strongly IgM+ (IgD+,RFB4+,RFB6+, and RFA-2+) but lack T cell-associated markers such as T1 (CD5, p 67,000 dalton equivalent of murine Ly-1) and Tü-33. In fetal lymph nodes, primary nodules develop around the follicular dendritic (FD) cells from 17 wk onward, and contain a virtually pure population of B cells; B1+,BA1+,RFB4+,RFB6+,RFA-2+, which simultaneously express IgM,IgD together with T1 (CD5), a T cell-associated antigen. A sizeable subpopulation of these IgM+,T1+ cells are also positive for Tü-33, another T cell-associated marker. In the spleen, the B cells of the IgM+,IgD+,T1+ type appear in smaller numbers and only relatively late around wk 22. These cells are diffusely distributed at first, and start accumulating around the small FD cell clusters as soon as these emerge about the 23rd gestational wk. At that time, the IgM+,T1+B cells can also be washed out from the peritoneal and pleural cavities. The T1+,IgM+B cells may represent the normal equivalent cells of B chronic lymphoid leukemia and centrocytic lymphoma, and appear to be the counterpart of Ly-1+,IgM+B cells in the mouse.     

Variations in carbon-to-phosphorus ratios of two Australian strains of Cylindrospermopsis raciborskii

The toxic cyanobacterium Cylindrospermopsis raciborskii can form large blooms in freshwater systems, causing water quality problems. The availability of the essential macronutrient phosphorus (P), has a big impact on bloom formation but the variation in physiological response of different strains of C. raciborskii to available P has not previously been examined. This study investigated the carbon:phosphorus (C:P) ratio of two toxic Australian strains of C. raciborskii, AWT205 and NPD, under a range of P concentrations in batch and continuous cultures. P was added as a single dose to batch cultures and in continuous cultures at P concentrations of 0.032, 0.16, 0.64 and 16 μmol P l^?1. Cellular carbon and phosphorus content of both strains increased under P-limited conditions (0 μmol P l^?1 addition) with zero growth. Strain NPD had a lower C:P ratio (34:1) than AWT205 (150:1) indicating higher P storage capacity, and strain NPD survived P-limited conditions for longer. There was no significant difference in exponential growth rates (0.2 d^?1, P ≥ 0.5) under all P concentrations for both strains, with the exception of no P, demonstrating non-P-limited growth even at the lowest concentration (0.032 µmol P l^?1) and no increase in growth rate with additional P. ³³P uptake measurements were used to show that these strains both have very low half saturation constants (K_s = 0.02 μmol P l^?1) compared with other phytoplankton and strains of C. raciborskii. This is indicative of high uptake affinities and suggests that these strains are highly adapted to a low P supply. Overall the results of this study are consistent with the P strategy of storage prioritization over growth rate, and demonstrate differences between the strains in the C:P ratio under P-limitation, indicating variation in P storage.