Maintained functional diversity in benthic communities in spite of diverging functional identities

Ecological studies based on time‐series often investigate community changes centered on species abundance or biomass but rarely expose the consequential functional aspects underlying such changes. Functional diversity measures have proven to be more accurate predictors for ecosystem functioning than traditional taxonomic approaches and hence gained much attention. There are only limited studies available that analyse the functional implications behind decadal changes of entire communities. We studied zoobenthic communities of two habitats, sheltered and exposed, of a coastal system subject to contrasting changes in community composition over the past four decades. Besides eutrophication and climate‐related impacts, the system has been invaded by a non‐native polycheate Marenzelleria spp., adding altered functional properties to the communities. The functional dispersion (FDis) metric was used as a measure for comparing the functional diversity of the contrasting habitats, with special focus on the role of Marenzelleria for the entire communities. We highlight changes in the functional identity of the communities, expressed as community‐weighted means of trait expression (CWM), using multivariate techniques, and investigate the relationship between taxonomic and functional changes. Despite contrasting community developments in the two habitats, with characteristics traditionally suggesting different environmental quality, we found that the FDis in both habitats remained similar and increased with the introduction of Marenzelleria. Although showing maintained functional diversity across time and space, the functional identity (CWM) of communities changed irrespective of taxonomical differences. Examples include inter alia alterations in palatability proxies, feeding position and sediment transportation types, indicating changed functionality of zoobenthos in coastal systems. We show, when focussing on qualitative functional changes of communities, it is important to evaluate the underlying functional identity, and not only rely on measures of the diversity of functions per se, as the quality indication of expressed functional traits can be concealed when using multi‐functionality approaches.     

Digital image analysis of AgNORs in cervical smears of women with premalignant and malignant lesions of the uterine cervix

We performed a hospital-based, unmatched case-control study to investigate the association between progressive stages of cervical neoplasia and digital analysis of cell proliferation by silver stained nucleolus organizer region associated proteins (AgNORs). We measured cell proliferation levels in the cervical epithelial cells of 10 women with low grade squamous intraepithelial lesions (LG-SIL), eight with high grade squamous intraepithelial lesions (HG-SIL), 11 with cervical cancer (CC) and eight with no cervical lesions (controls) using the AgNORs technique. Cell proliferation was measured by digital image analysis (DIA). DIA revealed increased total areas of AgNORs in HG-SIL and CC compared to LG-SIL and control patients. AgNORs with a kidney or cluster shape exhibited greater areas than those with a spherical or long shape. We propose a cut-off of 118 pixels to differentiate benign (control and LG-SIL) from malignant (HG-SIL and CC) lesions. DIA of AgNORs is a simple and inexpensive method for studying proliferation. The increased total area of AgNORs in malignant lesions provides information regarding cell behavior and may be related to cervical carcinogenesis; however, further validation studies are required to establish its usefulness in cytological analysis.     

Expression, processing, and glycosaminoglycan binding activity of the recombinant human 315-kDa hyaluronic acid receptor for endocytosis (HARE)

The hyaluronic acid (HA) receptor for endocytosis (HARE; also designated stabilin-2 and FEEL-2) mediates systemic clearance of glycosaminoglycans from the circulatory and lymphatic systems via coated pit-mediated uptake. HARE is primarily found as two isoforms (315- and 190-kDa) in sinusoidal endothelial cells of the liver, lymph node, and spleen. Here we characterize the ligand specificity and function of the large stably expressed 315-HARE isoform in Flp-In 293 cell lines. Like human spleen sinusoidal endothelial cells, Flp-In 293 cell lines transfected with a single cDNA encoding the full-length 315-HARE express both the 315-kDa and the proteolytically truncated 190-kDa isoforms in a ratio of approximately 3-4:1. The 190-kDa HARE isoform generated from the 315-kDa HARE and the 315-kDa HARE specifically bound 125I-HA. Like the 190-kDa HARE expressed alone (Harris, E. N., Weigel, J. A., and Weigel, P. H. (2004) J. Biol. Chem. 279, 36201-36209), the 190- and 315-kDa HARE isoforms expressed in 315-HARE cell lines were recognized by anti-HARE monoclonal antibodies 30, 154, and 159. All 315-HARE cell lines could endocytose and degrade 125I-HA. Competition studies with live cells indicate that 190-HARE and 315-HARE bind HA with higher apparent affinity (Kd approximately 10-20 nM) than chondroitin sulfate (CS) types A, C, D, or E. Only slight competition of HA endocytosis was observed with CS-B (dermatan sulfate) and chondroitin. Direct binding assays with the 315-HARE ectodomain revealed high affinity HA binding, and lower binding affinities for CS-C, CS-D, and CS-E. A majority of each HARE isoform was intracellular, within the endocytic system, suggesting transient surface residency typical of an active endocytic recycling receptor.     

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.Subject terms: Microbial ecology, Plant ecology     

The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal expression in meristems and young primordia

The Arabidopsis thaliana MERISTEM LAYER 1 (ATML1) gene is expressed in the epidermis of developing embryos and shoot meristems. To identify regulatory sequences necessary for epidermis-specific expression, three fusions of overlapping ATML1 genomic sequences to the GUS reporter gene were introduced into Arabidopsis plants. All fusion genes conferred epidermis-specific expression of both GUS mRNA and protein activity but varied in both the timing and relative levels of expression, suggesting partial redundancy of ATML1 regulatory elements. This study defines L1-specific regulatory sequences that are sufficient to direct foreign gene expression in a layer-specific manner.     

Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes

Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.     

Plastocyanin is indispensable for photosynthetic electron flow in Arabidopsis thaliana

Plastocyanin is a soluble copper-containing protein present in the thylakoid lumen, which transfers electrons to photosystem I. In the chloroplast of the flowering plant Arabidopsis thaliana, a cytochrome c6-like protein is present, which was recently suggested to function as an alternative electron carrier to plastocyanin. We show that Arabidopsis plants mutated in both of the two plastocyanin-coding genes and with a functional cytochrome c6 cannot grow photoautotrophically because of a complete block in light-driven electron transport. Even increased dosage of the gene encoding the cytochrome c6-like protein cannot complement the double mutant phenotype. This demonstrates that in Arabidopsis only plastocyanin can donate electrons to photosystem I in vivo.     

Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana

We have mapped quantitative trait loci (QTL) responsible for natural variation in light and hormone response between the Cape Verde Islands (Cvi) and Landsberg erecta (Ler) accessions of Arabidopsis thaliana using recombinant inbred lines (RILs). Hypocotyl length was measured in four light environments: white, blue, red, and far-red light and in the dark. In addition, white light plus gibberellin (GA) and dark plus the brassinosteroid biosynthesis inhibitor brassinazole (BRZ) were used to detect hormone effects. Twelve QTL were identified that map to loci not previously known to affect light response, as well as loci where candidate genes have been identified from known mutations. Some QTL act in all environments while others show genotype-by-environment interaction. A global threshold was established to identify a significant epistatic interaction between two loci that have few main effects of their own. LIGHT1, a major QTL, has been confirmed in a near isogenic line (NIL) and maps to a new locus with effects in all light environments. The erecta mutation can explain the effect of the HYP2 QTL in the blue, BRZ, and dark environments, but not in far-red. LIGHT2, also confirmed in an NIL, has effects in white and red light and shows interaction with GA. The phenotype and map position of LIGHT2 suggest the photoreceptor PHYB as a candidate gene. Natural variation in light and hormone response thus defines both new genes and known genes that control light response in wild accessions.     

Needle track seeding of papillary thyroid carcinoma from fine needle aspiration biopsy. A case report

BACKGROUND: Dissemination of tumor cells from needle biopsy has been observed in a wide range of tumor types. Fine needle aspiration (FNA) biopsy has become accepted as the first-line test in the evaluation of thyroid nodules. Local recurrence of thyroid cancer from needle track seeding is an extremely rare complication of thyroid FNA. CASE: A 59-year-old woman developed local recurrence of papillary thyroid carcinoma three years after FNA of the primary cancer. Local metastases developed in the skin and sternocleidomastoid muscle. The location of the recurrent cancer and the linear relationship of the metastases indicated that local recurrence was due to needle track seeding at the time of FNA. CONCLUSION: Needle track seeding has been recognized as a possible, albeit rare, complication of FNA of thyroid cancer. Although proper FNA technique can reduce the potential for needle track seeding, its occurrence is an unavoidable complication of FNA evaluation of thyroid malignancies.