Peptide-oligonucleotide conjugates form stable and selective complexes with antibody and DNA

The present work demonstrates that the relatively low molecular weight synthetic peptide-oligonucleotide conjugates are capable of stable and selective three-component complex formation with complementary 72-100mer DNA oligonucleotides and a cardiac troponin I monoclonal antibody. Neither the Watson-Crick-type interaction between peptide-oligonucleotide conjugate and DNA nor the conjugate-antibody interaction dramatically hampers the other. These interactions remain selective and specific in the presence of several other conjugates not specific to cardiac troponin I monoclonal antibody as well as in the presence of control 100mer DNA oligonucleotides. The data herein demonstrate the feasibility of the synthetic peptide-oligonucleotide conjugates as convenient molecular tools, e.g., for antibody epitope mapping.     

Quantification of 1H NMR spectra of human cerebrospinal fluid: a protocol based on constrained total-line-shape analysis

A protocol for quantitative ¹H NMR analysis of human cerebrospinal fluid (hCSF) was built up and assessed as based on Constrained Total-Line-Shape (CTLS) fitting. In this method, linear constraints were applied to spectral structures. The ¹H NMR spectra of 45 human CSF samples were measured and quantified using the CTLS method. The quantification strategies based on total-line-shape fitting are discussed. The metabolic model for CTLS includes 31 metabolites covering 85% of the total spectral intensity, excluding the protein contribution. Prior to data analysis, the data was divided into patients with no Alzheimer’s disease (AD), but with a normal AD marker profile (the peptide β-amyloid₄₂ and tau protein) present in CSF, and into controls that do not have an AD marker profile in CSF. Unexpectedly large variations in metabolite concentrations within the two patient groups were detected, but an analysis of variance revealed a significant (P = 0.027) difference only in the concentration of creatinine which was higher in patients that had a normal AD marker profile. Multivariate classification tools such as self-organizing maps (SOM) failed in separation of the two classes.     

Monitoring for the Management of Disease Risk in Animal Translocation Programmes

Monitoring is best viewed as a component of some larger programme focused on science or conservation. The value of monitoring is determined by the extent to which it informs the parent process. Animal translocation programmes are typically designed to augment or establish viable animal populations without changing the local community in any detrimental way. Such programmes seek to minimize disease risk to local wild animals, to translocated animals, and in some cases to humans. Disease monitoring can inform translocation decisions by (1) providing information for state-dependent decisions, (2) assessing progress towards programme objectives, and (3) permitting learning in order to make better decisions in the future. Here we discuss specific decisions that can be informed by both pre-release and post-release disease monitoring programmes. We specify state variables and vital rates needed to inform these decisions. We then discuss monitoring data and analytic methods that can be used to estimate these state variables and vital rates. Our discussion is necessarily general, but hopefully provides a basis for tailoring disease monitoring approaches to specific translocation programmes.     

MicroRNA and protein profiles in invasive versus non-invasive oral tongue squamous cell carcinoma cells in vitro

Complex molecular pathways regulate cancer invasion. This study overviewed proteins and microRNAs (miRNAs) involved in oral tongue squamous cell carcinoma (OTSCC) invasion. The human highly aggressive OTSCC cell line HSC-3 was examined in a 3D organotypic human leiomyoma model. Non-invasive and invasive cells were laser-captured and protein expression was analyzed using mass spectrometry-based proteomics and miRNA expression by microarray. In functional studies the 3D invasion assay was replicated after silencing candidate miRNAs, miR-498 and miR-940, in invasive OTSCC cell lines (HSC-3 and SCC-15). Cell migration, proliferation and viability were also studied in the silenced cells. In HSC-3 cells, 67 proteins and 53 miRNAs showed significant fold-changes between non-invasive vs. invasive cells. Pathway enrichment analyses allocated “Focal adhesion” and “ECM-receptor interaction” as most important for invasion. Significantly, in HSC-3 cells, miR-498 silencing decreased the invasion area and miR-940 silencing reduced invasion area and depth. Viability, proliferation and migration weren’t significantly affected. In SCC-15 cells, down-regulation of miR-498 significantly reduced invasion and migration. This study shows HSC-3 specific miRNA and protein expression in invasion, and suggests that miR-498 and miR-940 affect invasion in vitro, the process being more influenced by mir-940 silencing in aggressive HSC-3 cells than in the less invasive SCC-15.     

Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome,global protein secretion,and T cells

Introduction: The immune system is our defense system against microbial infections and tissue injury, and understanding how it works in detail is essential for developing drugs for different diseases. Mass spectrometry-based proteomics can provide in-depth information on the molecular mechanisms involved in immune responses.

Areas covered: Summarized are the key immunology findings obtained with MS-based proteomics in the past five years, with a focus on inflammasome activation, global protein secretion, mucosal immunology, immunopeptidome and T cells. Special focus is on extracellular vesicle-mediated protein secretion and its role in immune responses.

Expert commentary: Proteomics is an essential part of modern omics-scale immunology research. To date, MS-based proteomics has been used in immunology to study protein expression levels, their subcellular localization, secretion, post-translational modifications, and interactions in immune cells upon activation by different stimuli. These studies have made major contributions to understanding the molecular mechanisms involved in innate and adaptive immune responses. New developments in proteomics offer constantly novel possibilities for exploring the immune system. Examples of these techniques include mass cytometry and different MS-based imaging approaches which can be widely used in immunology.     

Ecotype-dependent control of growth,dormancy and freezing tolerance under seasonal changes in <Emphasis Type="Italic">Betula pendula</Emphasis> Roth

Woody plants in the temperate and boreal zone undergo annual cycle of growth and dormancy under seasonal changes. Growth cessation and dormancy induction in autumn are prerequisites for the development of substantial cold hardiness in winter. During evolution, woody plants have developed different ecotypes that are closely adapted to the local climatic conditions. In this study, we employed distinct photoperiodic ecotypes of silver birch (Betula pendula Roth) to elucidate differences in these adaptive responses under seasonal changes. In all ecotypes, short day photoperiod (SD) initiated growth cessation and dormancy development, and induced cold acclimation. Subsequent low temperature (LT) exposure significantly enhanced freezing tolerance but removed bud dormancy. Our results suggested that dormancy and freezing tolerance might partially overlap under SD, but these two processes were regulated by different mechanisms and pathways under LT. Endogenous abscisic acid (ABA) levels were also altered under seasonal changes; the ABA level was low during the growing season, then increased in autumn, and decreased in winter. Compared with the southern ecotype, the northern ecotype was more responsive to seasonal changes, resulting in earlier growth cessation, cold acclimation and dormancy development in autumn, higher freezing tolerance and faster dormancy release in winter, and earlier bud flush and growth initiation in spring. In addition, although there was no significant ecotypic difference in ABA level during growing season, the rates and degrees of ABA alterations were different between the ecotypes in autumn and winter, and could be related to ecotypic differences in dormancy and freezing tolerance.     

The effect of an emergent macrophyte (Typha angustifolia) on sediment resuspension in a shallow north temperate lake

1. The effects of emergent macrophytes on water turbidity and sediment resuspension in the shallow Kirkkojärvi basin of Lake Hiidenvesi were studied with sediment traps, and concomitant sediment and water samples. The study was conducted during May–August in three different zones of a stand of the emergent Typha angustifolia .
2. Within the stand (5 m from the edge), both the concentration of suspended solids and the rate of sediment resuspension were significantly lower than at the edge and outside the stand (5 m from the edge). The differences between the zones increased towards the end of summer together with the growing stem density. During the study period (82 days), 2210 g dw m⁻² of sediment was resuspended in the outer zone. At the edge and in the inner zone, the corresponding numbers were 1414 and 858 g dw m⁻², respectively.
3. With the resuspended sediment, 39.4 mg P  m⁻² day⁻¹ was brought to the water column outside the stand, 22.4 mg P  m⁻² day⁻¹ at the edge and 13.4 mg P  m⁻² day⁻¹ within the stand.
4. In early summer, the concentration of suspended solids had a highly significant positive effect on soluble reactive phosphorus (SRP) concentration in the water, whereas in late summer no effect was found. During the study period, phosphorus retention by emergent macrophyte stands corresponded to 3–5% of the present annual external phosphorus loading of the Kirkkojärvi basin.     

A critical thermal transition driving spring phenology of Northern Hemisphere conifers

Despite growing interest in predicting plant phenological shifts, advanced spring phenology by global climate change remains debated. Evidence documenting either small or large advancement of spring phenology to rising temperature over the spatio-temporal scales implies a potential existence of a thermal threshold in the responses of forests to global warming. We collected a unique data set of xylem cell-wall-thickening onset dates in 20 coniferous species covering a broad mean annual temperature (MAT) gradient (−3.05 to 22.9°C) across the Northern Hemisphere (latitudes 23°–66° N). Along the MAT gradient, we identified a threshold temperature (using segmented regression) of 4.9 ± 1.1°C, above which the response of xylem phenology to rising temperatures significantly decline. This threshold separates the Northern Hemisphere conifers into cold and warm thermal niches, with MAT and spring forcing being the primary drivers for the onset dates (estimated by linear and Bayesian mixed-effect models), respectively. The identified thermal threshold should be integrated into the Earth-System-Models for a better understanding of spring phenology in response to global warming and an improved prediction of global climate-carbon feedbacks.