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We replaced a control peat medium with up to 75% biochar on a volumetric basis in three different forms (powder, BC; pyrolyzed softwood pellets, PP; composite wood-biochar pellets, WP), and under two supplies of nitrogen fertilizer (20 or 80 mg N) subsequently grew seedlings with a comparable morphology to the control. Using gravimetric methods to determine irrigation frequency and exponential fertilization to ensure all treatments received the same amount of N at a given point in the growing cycle, we successfully replaced peat with 25% BC and up to 50% PP. Increasing the proportion of biochar in the media significantly increased pH and bulk density and reduced effective cation exchange capacity and air-filled porosity, although none of these variables was consistent with resultant seedling growth. Adherence to gravimetric values for irrigation at an 80% water mass threshold in the container revealed that the addition of BC and WP, but not PP, required adjustments to the irrigation schedule. For future studies, we encourage researchers to provide more details about bulk density, porosity, and irrigation regime to improve the potential inference provided by this line of biochar and growing media work. [ABSTRACT FROM AUTHOR]

Presents a response by the author to a letter to the editor about the article "Smoking Cessation, Decline in Pulmonary Function and Total Mortality: A 30 Year Follow Up Study Among Finnish Cohorts of the Seven Countries," published in the 2001 issue of the journal "Thorax."

Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions. Weldenegodguad et al. performed transcriptome profiling of adipose tissues from the bone marrow, perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. They identified candidate genes potentially involved in immune responses, fat deposition, and energy metabolism that provide insight into the mechanisms by which reindeer adapt to harsh arctic conditions. [ABSTRACT FROM AUTHOR]

In vitro models mimicking the human respiratory system are essential when investigating the toxicological effects of inhaled indoor air particulate matter (PM). We present a pulmonary cell culture model for studying indoor air PM toxicity. We exposed normal human bronchial epithelial cells, grown on semi‐permeable cell culture membranes, to four doses of indoor air PM in the air‐liquid interface. We analyzed the chemokine interleukin‐8 concentration from the cell culture medium, protein concentration from the apical wash, measured tissue electrical resistance, and imaged airway constructs using light and transmission electron microscopy. We sequenced RNA using a targeted RNA toxicology panel for 386 genes associated with toxicological responses. PM was collected from a non‐complaint residential environment over 1 week. Sample collection was concomitant with monitoring size‐segregated PM counts and determination of microbial levels and diversity. PM exposure was not acutely toxic for the cells, and we observed up‐regulation of 34 genes and down‐regulation of 17 genes when compared to blank sampler control exposure. The five most up‐regulated genes were related to immunotoxicity. Despite indications of incomplete cell differentiation, this model enabled the comparison of a toxicological transcriptome associated with indoor air PM exposure. [ABSTRACT FROM AUTHOR]

Summary: Calamine accessions of the zinc/cadmium/nickel hyperaccumulator, Noccaea caerulescens, exhibit striking variation in foliar cadmium accumulation in nature. The Ganges accession (GA) from Southern France displays foliar cadmium hyperaccumulation (>1000 μg g−1 DW), whereas the accession La Calamine (LC) from Belgium, with similar local soil metal composition, does not (<100 μg g−1 DW). All calamine accessions are cadmium hypertolerant. To find out the differences between LC and GA in their basic adaptation mechanisms, we bypassed the cadmium excluding phenotype of LC by exposing the plants to 50 μm cadmium in hydroponics, achieving equal cadmium accumulation in the shoots. The iron content increased in the roots of both accessions. GA exhibited significant decreases in manganese and zinc contents in the roots and shoots, approaching those in LC. Altogether 702 genes responded differently to cadmium exposure between the accessions, 157 and 545 in the roots and shoots, respectively. Cadmium‐exposed LC showed a stress response and had decreased levels of a wide range of photosynthesis‐related transcripts. GA showed less changes, mainly exhibiting an iron deficiency‐like response. This included increased expression of genes encoding five iron deficiency‐regulated bHLH transcription factors, ferric reduction oxidase FRO2, iron transporters IRT1 and OPT3, and nicotianamine synthase NAS1, and decreased expression of genes encoding ferritins and NEET (a NEET family iron‐sulfur protein), which is possibly involved in iron transfer, distribution and/or management. The function of the IRT1 gene in the accessions was compared. We conclude that the major difference between the two accessions is in the way they cope with iron under cadmium exposure. Significance statement: Both the cadmium hyperaccumulator and the cadmium excluder Noccaea caerulescens of the 'cabbage' family (Brassicaceae) can have a full capacity to accumulate cadmium under certain conditions, while exhibiting major differences in their transcriptome response. This study highlights the critical importance of understanding the mechanisms of metal accumulation in order to prevent the uptake of toxic metals and maintain proper metal homeostasis in crops cultivated in contaminated soils and also in the increasingly popular hydroponic systems. [ABSTRACT FROM AUTHOR]

Abstract: Botanical air filtration is a promising technology for reducing indoor air contaminants, but the underlying mechanisms need better understanding. Here, we made a set of chamber fumigation experiments of up to 16 weeks of duration, to study the filtration efficiencies for seven volatile organic compounds (VOCs; decane, toluene, 2‐ethylhexanol, α‐pinene, octane, benzene, and xylene) and to monitor microbial dynamics in simulated green wall systems. Biofiltration functioned on sub‐ppm VOC levels without concentration‐dependence. Airflow through the growth medium was needed for efficient removal of chemically diverse VOCs, and the use of optimized commercial growth medium further improved the efficiency compared with soil and Leca granules. Experimental green wall simulations using these components were immediately effective, indicating that initial VOC removal was largely abiotic. Golden pothos plants had a small additional positive impact on VOC filtration and bacterial diversity in the green wall system. Proteobacteria dominated the microbiota of rhizosphere and irrigation water. Airborne VOCs shaped the microbial communities, enriching potential VOC‐utilizing bacteria (especially Nevskiaceae and Patulibacteraceae) in the irrigation water, where much of the VOC degradation capacity of the biofiltration systems resided. These results clearly show the benefits of active air circulation and optimized growth media in modern green wall systems. [ABSTRACT FROM AUTHOR]

Abstract: We found that peat moss, amended with various ratios of pellets comprised of equal proportions of biochar and wood flour, generally had chemical and physical properties suitable for service as a substrate during nursery production of plants. High ratios of pellets to peat (>50%) may be less desirable because of high C:N, high bulk density, swelling associated with water absorption, and low volumetric water content, whereas a mixture of 75% peat and 25% pellets had enhanced hydraulic conductivity and greater water availability at lower (<−10 kPa) matric potentials. Adding pellets to substrates used to grow plants in nurseries has potential to add value to biochar and thereby improve economic viability of pyrolysis. Moreover, biochar-amended substrates offer opportunity to sequester carbon as part of the normal outplanting process. [Copyright &y& Elsevier]

This paper investigates differences in gene expression among the two Thlaspi caerulescens ecotypes La Calamine (LC) and Lellingen (LE) that have been shown to differ in metal tolerance and metal uptake. LC originates from a metalliferous soil and tolerates higher metal concentrations than LE which originates from a non-metalliferous soil. The two ecotypes were treated with different levels of zinc in solution culture, and differences in gene expression were assessed through application of a cDNA microarray consisting of 1,700 root and 2,700 shoot cDNAs. Hybridisation of root and shoot cDNA from the two ecotypes revealed a total of 257 differentially expressed genes. The regulation of selected genes was verified by quantitative reverse transcriptase polymerase chain reaction. Comparison of the expression profiles of the two ecotypes suggests that LC has a higher capacity to cope with reactive oxygen species and to avoid the formation of peroxynitrite. Furthermore, increased transcripts for the genes encoding for water channel proteins could explain the higher Zn tolerance of LC compared to LE. The higher Zn tolerance of LC was reflected by a lower expression of the genes involved in disease and defence mechanisms. The results of this study provide a valuable set of data that may help to improve our understanding of the mechanisms employed by plants to tolerate toxic concentrations of metal in the soil.

Human papillomaviruses (HPV) are implicated in the multistep process of cervical carcinogenesis. Transforming growth factor beta(TGF-beta) inhibits the proliferation of epithelial cells, and it has also been found to inhibit HPV gene expression in nontumorigenic epithelial cell lines. In the present study, we examined the expression of TGF-beta 1 and TGF-beta 2 protein immunohistochemically (IHC) in a series of 95 HPV-positive and HPV-negative lesions of the uterine cervix, with special emphasis on HPV type, grade of cervical intraepithelial neoplasia (CIN), and the clinical course of the disease. Expression of TGF-beta 1 was found in 56/95 (59%) and that of TGF-beta 2 in 87/95 (92%) of the specimens. Cytoplasmic TGF-beta 2 staining was localized in the epithelial layers higher than that of TGF-beta 1, which showed also some nuclear staining and was located in the basal cells of the epithelium as well. TGF-beta 1 was expressed in 36/68 (53%) of HPV-positive samples and in 16/21 (76%) of HPV-negative samples; TGF-beta 2 expression was detectable in 63/68 (93%) and 18/21 (86%), respectively. TGF-beta 1 was present slightly more frequently in HPV-CIN lesions (23/41, 56%) than in HPV-NCIN (HPV without CIN) specimens (13/27, 48%). TGF-beta 2 expression was detected in 39/41 (95%) of HPV-CIN and in 24/27 (89%) of HPV-NCIN specimens. TGF-beta 2 expression was not related to the clinical course of the disease. TGF-beta 1 expression was most frequent in regressed and persistent lesions (> 60%), compared to 45% in progressed and 33% in the recurred lesions. The results suggest that TGF-beta (especially TGF-beta 2) expression is common in CIN lesions, but the pattern and intensity of TGF-beta expression examined by IHC are not clearly related to the grade of the lesions or their clinical course. Assessment of the biological activity of TGF-beta s and their influence on HPV genes may shed more light on HPV-associated carcinogenesis.

Human papillomavirus (HPV) is frequently associated with cervical carcinoma. Inactivation of the p53 tumor suppressor gene product by binding to the HPV encoded E6 protein is considered as an important pathway for malignant progress in HPV-infected cells. In contrast, mutations of the p53 gene have been found in HPV-negative cervical carcinoma cells. To evaluate the involvement of p53 inactivation for the development of genital carcinoma, we determined the state of the p53 gene in 20 genital precancer lesions and carcinomas, which had been previously studied for the expression of p53 protein and the presence of HPV DNA. Exons 5 through 9 of the p53 gene were analyzed by single-strand conformation polymorphism analysis of polymerase chain reaction (PCR)-amplified DNA fragments, and the results obtained by the PCR-SSCP analysis were confirmed by DNA sequencing. No mutations were detected in any of the specimens, including the three HPV-negative cases. The present results suggest that the functional inactivation of p53 is not invariably required for the induction of malignant transformation in the genital tract, and thus other genetic events can also significantly participate in genital carcinogenesis.

The E6 protein of the high-risk human papillomavirus (HPV) types 16 and 18 is capable of complexing with the wild-type p53 tumor suppressor gene product, leading to loss of the normal p53 function as an anti-oncogene, whereas the low-risk HPV types 6 and 11 lack this binding property. The malignant potential of HPV 16 and 18 has been ascribed to this complexing of E6 with p53, which regularly leads to undetectable expression of the latter in HPV-positive lesions. To assess the role of p53 in HPV-associated genital carcinogenesis, the expression of p53 protein was studied immunohistochemically in 22 genital carcinomas and precancer lesions; 8 vulvar carcinomas, 1 VIN (vulvar intraepithelial neoplasia), 5 cervical carcinomas and 8 CIN (cervical intraepithelial neoplasia) using monoclonal antibody PAb 1801. Presence of HPV was demonstrated by PCR using HPV consensus primers, and amplified HPV-DNA was digested with the restriction enzymes giving distinct patterns for various HPV-types in gel electrophoresis. HPV-typing was confirmed by in situ hybridization with biotinylated DNA probes. Altogether, 17 of the 22 specimens (77%) showed p53 expression: 67% of the precancer lesions and 83% of carcinomas. Expression was more frequent (89%) in the vulvar than (70%) in cervical lesions. Using PCR,HPV DNA was detected in 19/22(86%) of the samples. The following HPV types were identified: HPV 6 (2 samples), HPV 11 (3 cases), HPV 16 (5 cases), HPV 33 (3 cases), and 6 contained unidentified HPV types. All HPV DNA-negative specimens showed p53 expression. Of the 19 HPV DNA-positive lesions, 5 were p53-negative, three of these being HPV 16 positive CIN lesions. The remaining two HPV 16 lesions were invasive carcinomas with a weak p53 expression. HPV 6 and 11-positive lesions showed a weak p53 expression more frequently than HPV-negative cases and HPV 33 lesions. The results indicate that p53 expression is detectable, but it is less frequent and less intense in HPV DNA-positive genital precancer lesions and carcinomas (particularly those with HPV 16 DNA) as compared with HPV DNA-negative lesions.

The assessment of oncogene expression at cellular level is important in understanding the role of those genes in carcinogenesis. Using in situ hybridization and immunohistochemistry, the expression of oncogenes can be visualized in topographic relation to tissue morphology. In the present study, c-myc overexpression was studied in ten carcinomas of different origin (6 mammary adenocarcinomas, 2 vulvar and 2 bronchial squamous cell carcinomas) by in situ hybridization (ISH) with 35S-labeled RNA probes and by immunohistochemistry (IHC). DNA amplification and transcription of c-myc oncogene were also studied with polymerase chain reaction (PCR) using beta-globin as an intrinsic standard for DNA amplification. The effect of formalin fixation of c-myc expression was simultaneously studied. Half of the tumours (5/10) demonstrated c-myc mRNA overexpression by ISH performed on frozen sections and two of the samples were shown to over-express c-myc protein by IHC. Only two samples fixed in formalin showed positive signals for c-myc mRNA. None of the biopsies showed DNA amplifications either with ISH or PCR. The present results suggest that ISH with RNA probes is a useful method for detecting the transcription of activated oncogenes in malignant tissues, especially when applied on frozen sections. The results also indicate that in some cases, c-myc gene may be adequately transcribed to mRNA but the latter is not translated to the appropriate oncoprotein.

A simple method of processing formalin-fixed, paraffin-embedded tissue sections for DNA amplification by polymerase chain reaction (PCR) is described. In this procedure, deparaffinized sections are readily subjected to DNA isolation simply by boiling and the released DNA can be directly employed for PCR. The method allows analysis of single-copy genes or viral sequences at least up to 300 base pairs long in one working day. This method is particularly useful in analysing retrospective materials when the simplicity and low cost of the assay are preferable. Furthermore, the simplicity of the procedure reduces the risk of contamination.

Formalin-fixed, paraffin-embedded specimens from 91 primary transitional cell cancers (TCC) of the urinary bladder were stained with a monoclonal antibody to c-erb B-2 oncoprotein. Twelve percent (11/91) of the TCC stained for c-erb b-2 oncoprotein, and in 4% (4/91) of cases, the expression was graded as moderate or heavy. The expression of c-erb B-2 was significantly (p = 0.072) related to the WHO grade, whereas no significant difference in its expression was found between (a) the superficial and invasive TCC and (b) between the papillary and nonpapillary TCC. One of the tumours had a verified metastasis at the time of diagnosis and it exhibited heavy expression of c-erb B-2. The expression of c-erb B-2 was significantly related to the number of nucleolar organiser regions/TCC nucleus (p = 0.003). Aneuploid TCC were more frequently associated with moderate or heavy expression of c-erb B-2 than the diploid ones. Recurrence and progression of TCC could not be significantly related to expression of c-erb B-2 oncoprotein. In survival analysis, moderate and heavy expression of c-erb B-2 were related to poor prognosis (p = 0.032) during a mean follow-up time of 14 years. In conclusion, moderate and heavy expression of c-erb B-2 oncoprotein in TCC seems to be related to more aggressive behaviour whereas low expression of this oncoprotein had no predictive value. No evidence was obtained, however, that the expression of c-erb B-2 concoprotein alone would determine the biological behaviour of TCC.