Determining the relative roles of species replacement and species richness differences in generating beta‐diversity patterns

Aim To determine the relative contribution of species replacement and species richness differences to the emergence of beta‐diversity patterns. Innovation A novel method that disentangles all compositional differences (β_cc, overall beta diversity) in its two components, species replacement (β_‐3) and species richness differences (β_rich) is proposed. The performance of the method was studied with ternary plots, which allow visualization of the influence of the relative proportions of shared and unique species of two sites over each metric. The method was also tested in different hypothetical gradients and with real datasets. The novel method was compared with a previous proposal based on the partitioning of overall compositional differences (β_sor) in replacement (β_sim) and nestedness (β_nes). The linear response of β_cc contrasts with the curvilinear response of β_sor to linear gradients of dissimilarity. When two sites did not share any species, β_sim was always 1 and β_‐3 only reached 1 when the number of exclusive species of both sites was equal. β_‐3 remained constant along gradients of richness differences with constant replacement, while β_sim decreased. β_rich had a linear response to a linear gradient of richness differences with constant species replacement, whereas β_nes exhibited a hump‐shaped response. Moreover, β_sim > β_nes when clearly almost all species of one site were lost, whereas β_‐3 < β_rich in the same circumstances. Main conclusions The behaviour of the partition of β_cc into β_‐3 and β_rich is consistent with the variation of replacement and richness differences. The partitioning of β_sor into β_sim and β_nes overestimates the replacement component and underestimates richness differences. The novel methodology allows the discrimination of different causes of beta‐diversity patterns along latitudinal, biogeographic or ecological gradients, by estimating correctly the relative contributions of replacement and richness differences.     

Body Mass Index and Serum Proteomic Profile in Breast Cancer and Healthy Women: A Prospective Study

Epidemiological studies suggest a possible association between BMI, diagnosis and clinical-pathological breast cancer characteristics but biological bases for this relationship still remain to be ascertained. Several biological mechanisms play a role in the genesis and progression of breast cancer. This study aimed to investigate relationships between BMI and breast cancer diagnosis/progression in a Southern Italian population and to try to interpret results according to the serum proteomic profile of healthy and breast cancer patients.BMI, presence or absence of breast cancer and its clinical-pathological characteristics were analyzed in a series of 300 breast cancer women and compared with those of 300 healthy women prospectively. To investigate whether obesity is associated with alterations in serum protein profile, SELDI-ToF approach was applied.Alcohol consumption (22.7% vs 11.3%; p<0.001) and postmenopausal status (65.7% vs 52%; p<0.001) but not BMI resulted significantly different in patients vs controls. Conversely, BMI was significantly associated with a larger-tumour size (BMI> = 30 respect to normal weight: OR = 2.49, 95% CI 1.25–4.99, p = 0.0098) and a higher probability of having positive axillary lymph node (OR = 3.67, CI 95% 2.16–6.23, p<0.0001). Multivariate analysis confirmed the association of breast cancer diagnosis with alcohol consumption (OR = 2.28;CI 1.36–3.83; p<0.0018). Serum protein profile revealed the presence of significant (p-value <0,01) differentially expressed peaks m/z 6934, m/z 5066 in high BMI breast cancer patients vs healthy subjects and m/z 6934, m/z 3346 in high vs low BMI breast cancer patients.The analysis of pathological features of cancer indicates that normal weight women have a significantly higher probability of having a smaller breast cancer at time of diagnosis and negative axillary lymph nodes while increased BMI is associated with an altered protein profile in breast cancer patients. Further studies to identify specific proteins found in the serum and their role in breast cancerogenesis and progression are in progress.     

Electronic properties of some nitrobenzo[<Emphasis Type="Italic">a</Emphasis>]pyrene isomers: a possible relationship to mutagenic activity

Ionization potential (IP), electron affinity (EA), dipole moment (μ) and electronic polarizability (α) of 1-, 3- and 6-nitrobenzo[a]pyrene isomers (1-NBaP, 3-NBaP, 6-NBaP) were determined by using density functional theory (DFT) and recent semiempirical PM6 methods. Calculated IP value remains almost constant along the series of isomers, while EA value depends on the nitro group position, increasing by ca. 0.2 eV on passing from 6- to 1-NBaP (or 3-NBaP) isomer. Stability, μ and α values decrease in the order 6-NBaP < 1-NBa ∼ 3-NBaP, the largest μ variation being predicted to be 1.5 D (30%) by DFT computations. The results obtained herein are consistent with the observed greater mutagenic activity of 3- and 1-NBaP in comparison to 6-NBaP isomer, suggesting that both binding to enzyme, which depends on electric properties, and reduction process, which is related to EA value may be crucial steps in the mutagenic mechanism of this series of isomers. Figure Structure and dipole moment vector of nitrobenzo[a]pyrene isomers     

Overstimulation of Glutamate Signals Leads to Hippocampal Transcriptional Plasticity in Hamsters

It’s known that neurons in mammalian hibernators are more tolerant to hypoxia than those in non-hibernating species and as a consequence animals are capable of awakening from the arousal state without exhibiting cerebral damages. In addition, evidences have suggested that euthermic hamster neurons display protective adaptations against hypoxia, while those of rats are not capable, even though molecular mechanisms involved in similar neuroprotective strategies have not been yet fully studied. In the present work, overstimulation of glutamatergic receptors NMDA recognized as one of the major death-promoting element in hypoxia, accounted for altered network complexity consistent with a moderate reduction of hippocampal neuronal survival (p < 0.05) in hamsters. These alterations appeared to be featured concomitantly with altered glutamatergic signaling as indicated by significant down-regulation (p < 0.01) of NMDAergic (NR2A) and AMPAergic (GluR1, R2) receptor subtypes together with the metabotropic mGluR5 subtype. Diminished mRNA levels were also reported for NMDA receptor binding factors and namely PSD95 plus DREAM, which exert positive and negative regulatory properties, respectively, on receptor trafficking events. Conversely, involvement of glutamatergic signaling systems on neuronal excitotoxicity was strengthened by the co-activation of GABA_AR-mediated effects as indicated by toxic morphological effects being notably reduced along with up-regulated GluR1, GluR2, mGluR5, DREAM, and Homer1c scaffold proteins when muscimol was added. Overall, these results point to a neuroprotective role of the GABAergic system against excitotoxicity episodes via DREAM-dependent inhibition of NMDA receptor and activation of AMPA receptor plus mGluR5, respectively, thus proposing them as novel therapeutic targets against cerebral ischemic damages in humans.     

A panel of the most suitable reference genes for RT-qPCR expression studies of coffee: screening their stability under different conditions

The reliability of analyses using real-time quantitative polymerase chain reaction (RT-qPCR) depends on the selection of appropriate reference genes to correct for sample-to-sample and run-to-run variations. The aim of the present study was to select the most suitable reference genes for gene expression analyses in tissue samples from coffee, Coffea arabica L. (Arabica) grown under well-watered (WW) and water-deficit (WD) conditions and C. canephora Pierre ex A. Froehner (Robusta) grown under WW conditions. Expression profiles and stabilities were evaluated for 12 reference genes in different tissues from C. arabica and for 8 genes in tissues from C. canephora. The web-based RefFinder tool, which combines the geNorm, NormFinder, Bestkeeper, and Delta-Ct algorithms, was employed to assess the stability of the tested genes. The most stable reference genes identified for all tissues grouped (WW/WD) of C. arabica were clathrin adaptor protein medium subunit (AP47), ubiquitin (UBQ), 60S ribosomal protein L39 (RPL39), and elongation factor 1α (EF1α), while class III alcohol dehydrogenase (ADH2), β-actin (ACT), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and ubiquitin (UBQ) genes were the most stable for all tissues grouped (WW) of C. canephora tissues. Validation by the expression level analysis of CaACO-like demonstrated that the use of the best and the worst set of reference genes produced different expression results. The results reinforce the general assumption that there is no universal reference gene and that it is essential to select the most appropriate gene for each individual experiment to apply adequate normalization procedures of RT-qPCR data.     

DNA MICROSPECTROPHOTOMETRY OF SHOOT APICAL MERISTEM CELL POPULATIONS IN CERATOPTERIS THALICTROIDES (FILICALES)

A microspectrophotometric analysis of the DNA content of cell populations in the shoot apical meristem of young and adult stages of the filicalean fern Ceratopteris thalictroides was conducted to determine if the previously reported uptake of labeled DNA precursors by the apical cell was a consequence of endomitotic DNA replication or of DNA synthesis preceeding mitosis. Results demonstrate that in both the young and adult plants the estimated DNA content of the apical cell nuclei parallels that of the other cells of the meristem. There was no evidence of an “apical zone” of endopolyploid cells.     

Autophagy is involved in nutritional stress response and differentiation in Trypanosoma cruzi

Autophagy is the major mechanism used by eukaryotic cells to degrade and recycle proteins and organelles. Bioinformatics analysis of the genome of the protozoan parasite Trypanosoma cruzi revealed the presence of all components of the Atg8 conjugation system, whereas Atg12, Atg5, and Atg10 as the major components of the Atg12 pathway could not be identified. The two TcATG4 (autophagin) homologs present in the genome were found to correctly process the two ATG8 homologs after the conserved Gly residue. Functional studies revealed that both ATG4 homologues but only one T. cruzi ATG8 homolog (TcATG8.1) complemented yeast deletion strains. During starvation of the parasite, TcAtg8.1, but not TcAtg8.2, was found by immunofluorescence to be located in autophagosome-like vesicles. This confirms its function as an Atg8/LC3 homolog and its potential to be used as an autophagosomal marker. Most importantly, autophagy is involved in differentiation between developmental stages of T. cruzi, a process that is essential for parasite maintenance and survival. These findings suggest that the autophagy pathway could represent a target for a novel chemotherapeutic strategy against Chagas disease.     

Intramolecularly quenched fluorogenic peptide substrates for human renin.

Six intramolecularly quenched fluorogenic peptides related to the sequences Phe8 to His13, His6 to His13, and Tyr4 to His13 of the human angiotensinogen, containing o-aminobenzoyl (Abz) and ethylenediamine dinitrophenyl (EDDnp) groups at amino- and carboxyl-terminal amino acids residues, were synthesized by classical solution methods. The Leu-Val is the only bond of all obtained peptides that was hydrolyzed by human renin with different degrees of purity and was resistant to hydrolysis by pig renin and cathepsin D. The hydrolysis of Abz-His-Pro-Phe-His-Leu-Val-Ile-His-EDDnp by human renin was inhibited by a highly specific transition-state analog of angiotensinogen (IC50 = 7.8 x 10(-9) M), described by K. Iizuka et al. (1990, J. Med. Chem. 33, 2707-2714). Therefore, specific and sensitive substrates for the continuous assay of human renin in which as little as 70 microGU of human renin could be detected by Abz-Phe-His-Leu-Val-Ile-His-EDDnp were described. The optimal pHs of hydrolysis of the substrates were in the range 4 to 6.     

Computer-aided comparison of protein electrophoretic patterns for grouping and identification of heterotrophic bacteria from mineral water

The microflora of a natural mineral water was studied immediately after bottling (T0) and after 7 d storage (T7) during 6 months, and isolates were clustered by SDS-PAGE of wholecell protein profiles. Isolates from each cluster were further characterized by API 20NE, fatty acid composition and quinone profiles. The numerical analysis of the electrophoregrams of all bacteria isolated from the mineral water formed 15 clusters and five unclustered strains. Except for five minor clusters, all clusters were composed of strains isolated over several months. The numerical analysis of the electrophoregrams of bacteria isolated immediately after bottling formed 15 clusters while after 7 d storage only four of these populations could be isolated, indicating that populations present in the mineral water were stable and that changes occurring after bottling probably resulted from a selection process. Only one unclustered strain was identified simultaneously by all the systems, as Sphingomonas paucimobilis. The monitoring of the aquifer and the bottling system, and the construction of a large database with bacteria of the autochthonous flora allows the detection of alterations in the aquifer by changes in the microflora.     

Correction to: Determining ecosystem functioning in Brazilian biomes through foliar carbon and nitrogen concentrations and stable isotope ratios

Biogeochemistry - The initial online publication contained typesetting mistakes in the author information. The original article has been corrected.