An invasive tree facilitates the persistence of native rodents on an over‐grazed floodplain in tropical Australia

In an ecosystem under simultaneous threat from multiple alien species, one invader may buffer the impact of another. Our surveys on a remote floodplain in the Kimberley region of north western Australia show that invasive chinee apple trees (Ziziphus mauritiana) provide critical refuge habitat for native rodents (pale field rats, Rattus tunneyi). Feral horses (Equus caballus) have trampled most of the remaining floodplain, but are excluded from the area around each chinee apple tree by thorny foliage. Although chinee apple trees constituted <10% of trees along our transects, they represented >50% of trees that harboured rat burrows. The mean number of burrows under each chinee apple tree was twice as high as under most other tree species, and we trapped more than seven times as many rats under chinee apple trees as under other types of trees. The extensive burrow systems under chinee apple trees contained female as well as male rats, whereas we only captured males around the smaller burrow systems under other tree species. Our data suggest that this invasive tree plays a critical role in the persistence of pale field rat populations in this degraded ecosystem, and that managers should maintain these trees (despite their alien origins) at least until feral horses have been removed.     

Secretion of cartilage oligomeric matrix protein is affected by the signal peptide

Cartilage oligomeric matrix protein (COMP) is a secreted glycoprotein found in the extracellular matrices of skeletal tissues. Mutations associated with two human skeletal dysplasias, pseudoachondroplasia and multiple epiphyseal dysplasia, disturb COMP secretion leading to intracellular accumulation of mutant COMP, especially in chondrocytes. Here we show that the manifestation of this secretory defect is dramatically influenced by the signal peptide that targets COMP for secretion. The comparison of wild type and mutant COMP secretion directed by the COMP or BM40 signal peptide in HEK-293 cells and rat chondrosarcoma cells revealed that the BM40 signal peptide substantially enhances secretion of mutant COMP that accumulates in endoplasmic reticulum-like structures when targeted by its own signal peptide. Additionally, we demonstrate that mutant COMP forms mixed pentamers with wild type COMP. Our findings suggest that the secretory defect in pseudoachondroplasia and multiple epiphyseal dysplasia is not specific for chondrocytes, nor does it require interaction of mutant COMP with other matrix proteins prior to transport from the cell. They also imply a previously unappreciated role for the signal peptide in the regulation of protein secretion beyond targeting to the endoplasmic reticulum.     

Peptide YY and neuropeptide Y induce villin expression, reduce adhesion, and enhance migration in small intestinal cells through the regulation of CD63, matrix metalloproteinase-3, and Cdc42 activity

Peptide YY (PYY) and neuropeptide Y (NPY) are regulatory peptides synthesized in the intestine and brain, respectively, that modify physiological functions affecting nutrient assimilation and feeding behavior. Because PYY and NPY also alter the expression of intestine-specific differentiation marker proteins and the tetraspanin CD63, which is involved in cell adhesion, we investigated whether intestinal cell differentiation could be linked to mucosal cell adhesion and migration through these peptides. PYY and NPY significantly decreased cell adhesion and increased cell migration in a dose-dependent manner prior to cell confluency in our model system, non-tumorigenic small intestinal hBRIE 380i cells. Both peptides reduced CD63 expression and CD63-dependent cell adhesion. CD63 overexpression increased and antisense CD63 cDNA decreased intestinal cell adhesion. In parallel, both PYY and NPY increased expression of matrix metalloproteinase-3 (MMP-3) to a level sufficient to induce cell migration by activating the Rho GTPase Cdc42. The effects of both peptides on cell migration were blocked in cells constitutively overexpressing dominant-negative Cdc42. PYY and NPY also significantly induced the expression of the differentiation marker villin, which could be eliminated by an MMP inhibitor at a concentration that inhibits cell migration. Increased MMP-3 activity, which enhanced cell migration, also induced villin mRNA levels. Therefore, these data indicate that the alteration of adhesion and migration by PYY and NPY occurs in part by synchronous modulation of three proteins that are involved in extracellular matrix-basolateral membrane interactions, CD63, MMP-3 and Cdc42, and that PYY/NPY regulation of expression of mucosal proteins such as villin is linked to the process of cell migration and adhesion.     

Seaweed processing using industrial single-mode cavity microwave heating: a preliminary investigation

A single-cavity microwave heating system has been designed and fabricated for microwave-assisted extraction of carrageenans from seaweed. The system comprises a single mode (TE101) waveguide fitted with power and temperature controls, together with a continuous-flow-recycle reactor operating at atmospheric pressure. The system has been tested by extraction of E. cottonii and E. spinosum in aqueous organic solvents. Even without purification, the extraction products were found to have virtually identical FTIR and 13C and 1H NMR spectra to the reference samples of kappa- and iota-carrageenan, respectively. The principal advantages of the microwave system are substantial reduction of extraction time and low consumption of organic solvents.     

The use of correlation integrals in the study of localized muscle fatigue of elbow flexors during maximal efforts.

Innovative applications of non-linear time series analysis have recently been used to investigate physiological phenomena. In this study, we investigated the feasibility of using the correlation integral to monitor the localized muscle fatigue process in the biceps brachii during sustained maximal efforts. The subjects performed isometric maximum contractions until failure in elbow flexion (90 degrees from neutral). The median and the 70th percentile frequency of the Surface electromyography (SEMG) power spectrum, the integrated SEMG, and the Correlation Integral (CI) were evaluated during the trials. The linear correlation between these variables and the elbow torque production was used to quantify the ability of a parameter to follow the fatiguing process. The CI had the highest linear correlation with torque (0.77 (0.12SD)), while the spectral indices correlations with torque were much lower. The decreasing trend of the torque production was followed by the spectral indices for only the beginning part of the contraction, while the CI increased sharply after the torque production fell to about 0.60 of the MVC. This suggests that the CI is sensitive to different changes of the SEMG signal during fatigue than the spectral variables.     

Discovery of novel conformationally restricted diazocan peptidomimetics as inhibitors of interleukin-1beta synthesis

A novel diazocan containing dipeptide mimetic was synthesized via reductive N-N bond cleavage of a pyrazolidino-pyrazolidine using Raney-Ni and evaluated as an ICE inhibitor. This versatile 8-membered ring containing scaffold possesses an N-5 ring nitrogen that was used to explore structure-activity relationships in a cell-based assay measuring inhibition of interleukin-1beta.     

Biochemical specialization within Arabidopsis RNA silencing pathways

In plants, the RNA silencing machinery responds to numerous inputs, including viral infection, microRNAs, and endogenous siRNAs that may act both in trans and in cis. Additionally, the full spectrum of silencing outcomes has been demonstrated in plants, ranging from mRNA degradation to repression at the level of protein synthesis to chromatin remodeling. Genetic studies in Arabidopsis have indicated that individual response pathways are functionally compartmentalized. However, to date, no biochemical systems have been available to investigate the roles of specific proteins within silencing pathways or the effects of selected mutations on the biochemical activity of those components. Here, we describe the generation of Arabidopsis extracts that reproduce many aspects of RNA silencing reactions in vitro. We find that specific members of the Dicer and Argonaute families have distinct biochemical activities, which provides insight into their roles within RNA silencing pathways in Arabidopsis.     

Sensitive Detection of Gene Expression in Mycobacteria under Replicating and Non-Replicating Conditions Using Optimized Far-Red Reporters

Fluorescent reporter proteins have proven useful for imaging techniques in many organisms. We constructed optimized expression systems for several fluorescent proteins from the far-red region of the spectrum and analyzed their utility in several mycobacterial species. Plasmids expressing variants of the Discosoma Red fluorescent protein (DsRed) from the Mycobacterium bovis hsp60 promoter were unstable; in contrast expression from the Mycobacterium smegmatis rpsA promoter was stable. In Mycobacterium tuberculosis expression of several of the far-red reporters was readily visualised by eye and three reporters (mCherry, tdTomato, and Turbo-635) fluoresced at a high intensity. Strains expressing mCherry showed no fitness defects in vitro or in macrophages. Treatment of cells with antibiotics demonstrated that mCherry could also be used as a reporter for cell death, since fluorescence decreased in the presence of a bactericidal compound, but remained stable in the presence of a bacteriostatic compound. mCherry was functional under hypoxic conditions; using mCherry we demonstrated that the P_mtbB is expressed early in hypoxia and progressively down-regulated. mCherry and other far-red fluorescent proteins will have multiple uses in investigating the biology of mycobacteria, particularly under non-replicating, or low cell density conditions, as well as providing a novel means of detecting cell death rapidly.     

The prokaryotic selenoproteome

In the genetic code, the UGA codon has a dual function as it encodes selenocysteine (Sec) and serves as a stop signal. However, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. Here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. One method searched for selenoprotein genes by identifying RNA stem-loop structures, selenocysteine insertion sequence elements; the second approach identified Sec/Cys pairs in homologous sequences. These analyses identified all or almost all selenoproteins in completely sequenced bacterial and archaeal genomes and provided a view on the distribution and composition of prokaryotic selenoproteomes. In addition, lineage-specific and core selenoproteins were detected, which provided insights into the mechanisms of selenoprotein evolution. Characterization of selenoproteomes allows interpretation of other UGA codons in completed genomes of prokaryotes as terminators, addressing the UGA dual-function problem.