Structural Classification of Metal Complexes with Three-Coordinate Centres

Attempts to describe the geometry about three-coordinate silver(I) complexes have proven difficult because interatomic angles generally vary wildly and there is no adequate or readily available classification system found in the literature. A search of the Cambridge Structural Database shows that complexes formed between any metal centre and three non-metal donors (18001 examples) usually adopt geometries that are quite different than ideal ‘textbook’ extremes of either trigonal planar (∼4% with α = β = γ = 120 ± 2°), T-shaped (∼0.05% with α = 180 ± 2°, β = γ = 90 ± 2°), or trigonal pyramidal (∼0.3% with α = β = γ = 110 ± 2°). Moreover, there are multiple variations of “Y-type” and “other” shapes that require elaboration. Thus, to assist in future structural descriptions, we developed a classification system that spans all known and yet-to-be-discovered three-coordinate geometries. A spreadsheet has also been constructed that utilizes the “shape-space” approach to extract the structural description from a user input of three angles about a tri-coordinate centre and the number of atoms in a plane. The structures of two silver(I) complexes of new N-donor ligands p-NH2C6H4C6H4CH(pz = pyrazol-1-yl)2, L1, and 2-ferrocenyl-4,5-di(2-pyridyl)imidazole, L2, illustrate the utility of this classification system

Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations

BACKGROUND: Despite the widespread use of microarrays, much ambiguity regarding data analysis, interpretation and correlation of the different technologies exists. There is a considerable amount of interest in correlating results obtained between different microarray platforms. To date, only a few cross-platform evaluations have been published and unfortunately, no guidelines have been established on the best methods of making such correlations. To address this issue we conducted a thorough evaluation of two commercial microarray platforms to determine an appropriate methodology for making cross-platform correlations. RESULTS: In this study, expression measurements for 10,763 genes uniquely represented on Affymetrix U133A/B GeneChips(® )and Amersham CodeLink™ UniSet Human 20 K microarrays were compared. For each microarray platform, five technical replicates, derived from the same total RNA samples, were labeled, hybridized, and quantified according to each manufacturers' standard protocols. The correlation coefficient (r) of differential expression ratios for the entire set of 10,763 overlapping genes was 0.62 between platforms. However, the correlation improved significantly (r = 0.79) when genes within noise were excluded. In addition to levels of inter-platform correlation, we evaluated precision, statistical-significance profiles, power, and noise levels for each microarray platform. Accuracy of differential expression was measured against real-time PCR for 25 genes and both platforms correlated well with r values of 0.92 and 0.79 for CodeLink and GeneChip, respectively. CONCLUSIONS: As a result of this study, we recommend using only genes called 'present' in cross-platform correlations. However, as in this study, a large number of genes may be lost from the correlation due to differing levels of noise between platforms. This is an important consideration given the apparent difference in sensitivity of the two platforms. Data from microarray analysis need to be interpreted cautiously and therefore, we provide guidelines for making cross-platform correlations. In all, this study represents the most comprehensive and specifically designed comparison of short-oligonucleotide microarray platforms to date using the largest set of overlapping genes

Opinion piece: non-traditional practical work for traditional campuses

Traditional practical work for higher education in STEM subjects is under pressure from rising student numbers and adesired increase in active learning. Investing in more buildings and staff is financially challenging, while stretching existing resources affects outcomes, health, and participation. A more pragmatic approach is to embrace a less instrumentalist view of practical work in physical spaces and instead adopt a critical post-humanist approach which mixes both humanity and technology to achieve a sum greater than the parts, not bound by the limits of either. We share the experiences of leading UK exponents of non-traditional laboratories in the four main categories of simulation, virtual laboratories, real-asynchronous, and real- synchronous activities, as well as experts in scaling digital education initiatives for university-wide adoption. We foreshadow opportunities, challenges and potential solutions to increasing the opportunity for active learning by students studying at traditional campuses, via the complementary addition of non-traditional practical work

Local and distal effects of arbuscular mycorrhizal colonization on direct pathway Pi uptake and root growth in <i>Medicago truncatula</i>

Two pathways exist for plant Pi uptake from soil: via root epidermal cells (direct pathway) or via associations with arbuscular mycorrhizal (AM) fungi, and the two pathways interact in a complex manner. This study investigated dis - tal and local effects of AM colonization on direct root Pi uptake and root growth, at different soil P levels. Medicago truncatula was grown at three soil P levels in split-pots with or without AM fungal inoculation and where one root half grew into soil labelled with 33 P. Plant genotypes included the A17 wild type and the mtpt4 mutant. The mtpt4 mutant, colonized by AM fungi, but with no functional mycorrhizal pathway for Pi uptake, was included to better understand effects of AM colonization per se . Colonization by AM fungi decreased expression of direct Pi transporter genes locally, but not distally in the wild type. In mtpt4 mutant plants, direct Pi transporter genes and the Pi starvation- induced gene Mt4 were more highly expressed than in wild-type roots. In wild-type plants, less Pi was taken up via the direct pathway by non-colonized roots when the other root half was colonized by AM fungi, compared with non- mycorrhizal plants. Colonization by AM fungi strongly influenced root growth locally and distally, and direct root Pi uptake activity locally, but had only a weak influence on distal direct pathway activity. The responses to AM coloniza - tion in the mtpt4 mutant suggested that in the wild type, the increased P concentration of colonized roots was a major factor driving the effects of AM colonization on direct root Pi uptake.Stephanie J. Watts-Williams, Iver Jakobsen, Timothy R. Cavagnaro, and Mette Grønlun

Exposure to Environmental Radionuclides Associates With Tissue-Specific Impacts on Telomerase Expression and Telomere Length

Telomeres, the protective structures at the ends of chromosomes, can be shortened when individuals are exposed to stress. In some species, the enzyme telomerase is expressed in adult somatic tissues, and potentially protects or lengthens telomeres. Telomeres can be damaged by ionizing radiation and oxidative stress, although the effect of chronic exposure to elevated levels of radiation on telomere maintenance is unknown for natural populations. We quantified telomerase expression and telomere length (TL) in different tissues of the bank vole Myodes glareolus, collected from the Chernobyl Exclusion Zone, an environment heterogeneously contaminated with radionuclides, and from uncontaminated control sites elsewhere in Ukraine. Inhabiting the Chernobyl Exclusion Zone was associated with reduced TL in the liver and testis, and upregulation of telomerase in brain and liver. Thus upregulation of telomerase does not appear to associate with longer telomeres but may reflect protective functions other than telomere maintenance or an attempt to maintain shorter telomeres in a stressful environment. Tissue specific differences in the rate of telomere attrition and apparent radiosensitivity weaken the intra-individual correlation in telomere length among tissues in voles exposed to radionuclides. Our data show that ionizing radiation alters telomere homeostasis in wild animal populations in tissue specific ways