Facilitation stabilizes moisture-controlled alpine juniper shrublines in the central Tibetan Plateau

The Tibetan Plateau hosts one of the world's highest undisturbed alpine juniper shrublines. However, little is known about the dynamics of these shrublines in response to climate warming and shrub-to-shrub interactions. Since growth of shrubline junipers is limited more by moisture availability than by low temperatures, we tested if upslope advancement of alpine juniper shrublines was constrained by warmer temperatures and related recent droughts. We also evaluated whether facilitation among neighboring shrubs, as inferred from spatial analyses, influenced shrubline dynamics. Three rectangular plots crossing the Juniperus pingii var. wilsonii shrubline were sampled at elevations from 4810 to 4917. m. a.s.l. near the Nam Co Lake, central Tibetan Plateau. Location of each stem and its diameter at the root collar and age were measured. We reconstructed the spatial and temporal shrubline dynamics during the past 350. years using standard dendrochronological methods. Independent, long-term summer temperature reconstructions also were associated with shrub recruitment. Point-pattern analyses were used to characterize spatial patterns of different size classes of shrubs. The three shrublines showed little long-term changes despite ongoing warming; no upward shift has occurred in the past 100. years. Recruitment was negatively associated with summer temperatures and drought occurrence since the 1920s. Spatial patterns were characterized by clustering at local scales and attraction between the different size classes, suggesting facilitation. We conclude that moisture availability limits the recruitment and elevational advance of junipers in this area of the Tibetan Plateau. Dynamics of alpine shrublines are more contingent on positive interactions and local environmental factors than on regional climatic variability. © 2015 Elsevier B.V.This work was supported by the National Natural Science Foundation of China (41471158), the National Basic Research Program of China (2012FY111400), and the Action Plan for West Development of the Chinese Academy of Science (KZCX2-XB3-08-02). J.J.C. acknowledges funding by ARAID. We appreciate the great support from the Nam Co Monitoring and Research Station for Multisphere Interactions, Chinese Academy of SciencePeer Reviewe

Strain Relief in Cu-Pd Heteroepitaxy

We present experimental and theoretical studies of Pd/Cu(100) and Cu/Pd(100) heterostructures in order to explore their structure and misfit strain relaxation. Ultrathin Pd and Cu films are grown by pulsed laser deposition at room temperature. For Pd/Cu, compressive strain is released by networks of misfit dislocations running in the [100] and [010] directions, which appear after a few monolayers (ML) already. In striking contrast, for Cu/Pd the tensile overlayer remains coherent up to about 9 ML, after which multilayer growth occurs. The strong asymmetry between tensile and compressive cases is in contradiction with continuum elasticity theory and is also evident in the structural parameters of the strained films. Molecular dynamics calculations based on classical many-body potentials confirm the pronounced tensile-compressive asymmetry and are in good agreement with the experimental data.Peer reviewe

Molecular biomarkers in glioblastoma : a systematic review and meta-analysis

BACKGROUND: Glioblastoma (GBM) is a highly aggressive cancer with poor prognosis that needs better treatment modalities. Moreover, there is a lack of reliable biomarkers to predict the response and outcome of current or newly designed therapies. While several molecular markers have been proposed as potential biomarkers for GBM, their uptake into clinical settings is slow and impeded by marker heterogeneity. Detailed assessment of prognostic and predictive value for biomarkers in well-defined clinical trial settings, if available, is scattered throughout the literature. Here we conducted a systematic review and meta-analysis to evaluate the prognostic and predictive significance of clinically relevant molecular biomarkers in GBM patients. MATERIAL AND METHODS: A comprehensive literature search was conducted to retrieve publications from 3 databases (Pubmed, Cochrane and Embase) from January 2010 to December 2021, using specific terms. The combined hazard ratios (HR) and confidence intervals (95% CI) were used to evaluate the association of biomarkers with overall survival (OS) in GBM patients. RESULTS: Twenty-six out of 1831 screened articles were included in this review. Nineteen articles were included in the meta-analyses, and 7 articles were quantitatively summarised. Fourteen studies with 1231 GBM patients showed a significant association of MGMT methylation with better OS with the pooled HR of 1.66 (95% CI 1.32-2.09, p < 0.0001, random effect). Five studies including 541 GBM patients analysed for the prognostic significance of IDH1 mutation showed significantly better OS in patients with IDH1 mutation with a pooled HR of 2.37 (95% CI 1.81-3.12; p < 0.00001]. Meta-analysis performed on 5 studies including 575 GBM patients presenting with either amplification or high expression of EGFR gene did not reveal any prognostic significance with a pooled HR of 1.31 (95% CI 0.96-1.79; p = 0.08). CONCLUSIONS: MGMT promoter methylation and IDH1 mutation are significantly associated with better OS in GBM patients. No significant associations were found between EGFR amplification or overexpression with OS

Fire facilitates warming-induced upward shifts of alpine treelines by altering interspecific interactions

Biotic interactions between trees and other plants may modulate the responses of alpine treelines to climate. Moderate disturbances could, therefore, accelerate upward shifts of alpine treelines as the climate warms by reducing the coverage of competitor plants and resetting interspecific interactions. Larch (Larix potaninii var. macrocarpa) treelines disturbed by fire on the southeastern Tibetan Plateau are good locales for testing this hypothesis. We characterized treelines in five large rectangular plots spanning undisturbed and fire-disturbed fir (Abies georgei) and larch treelines. The fires in the 1960s caused gaps in the reconstructed age structures of the larches during the 1970s but did not lead to downslope shifts in treeline position. Recruitment has instead increased since the 1980s within the disturbed larch treelines, with treelines shifting upward by 11-44 m. In contrast, the undisturbed larch and fir treeline positions remained mostly unchanged. We hypothesize that upslope shifts of alpine treelines are likely a consequence of climatic warming, but fire disturbances can accelerate these dynamics by altering interspecific interactions

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling including optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we have reanalyzed six public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to >5% of the total number of peptides identified

DEqMS : A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

Quantitative proteomics by mass spectrometry is widely used in biomarker research and basic biology research for investigation of phenotype level cellular events. Despite the wide application, the methodology for statistical analysis of differentially expressed proteins has not been unified. Various methods such as t test, linear model and mixed effect models are used to define changes in proteomics experiments. However, none of these methods consider the specific structure of MS-data. Choices between methods, often originally developed for other types of data, are based on compromises between features such as statistical power, general applicability and user friendliness. Furthermore, whether to include proteins identified with one peptide in statistical analysis of differential protein expression varies between studies. Here we present DEqMS, a robust statistical method developed specifically for differential protein expression analysis in mass spectrometry data. In all data sets investigated there is a clear dependence of variance on the number of PSMs or peptides used for protein quantification. DEqMS takes this feature into account when assessing differential protein expression. This allows for a more accurate data-dependent estimation of protein variance and inclusion of single peptide identifications without increasing false discoveries. The method was tested in several data sets including E. coli proteome spike-in data, using both label-free and TMT-labeled quantification. Compared with previous statistical methods used in quantitative proteomics, DEqMS showed consistently better accuracy in detecting altered protein levels compared with other statistical methods in both label-free and labeled quantitative proteomics data. DEqMS is available as an R package in Bioconductor.Peer reviewe

Detecting Ecological Patterns Along Environmental Gradients: Alpine Treeline Ecotones

Everyone is familiar with that age-old adage: "a picture is worth a thousand words". Among ecologists, the word "picture" easily could be replaced with the word "pattern", although the significance remains the same: the pattern we observe in a single snapshot more than sums up what could be expressed if we tried to describe all the original events that led to the pattern. One particular class of patterns, spatial patterns, are the backbone of much contemporary ecological research. [...

Prognostic and predictive value of liquid biopsy-derived androgen receptor variant 7 (AR-V7) in prostate cancer : a systematic review and meta-analysis

In advanced prostate cancer, access to recent diagnostic tissue samples is restricted and this affects the analysis of the association of evolving biomarkers such as AR-V7 with metastatic castrate resistance. Liquid biopsies are emerging as alternative analytes. To clarify clinical value of AR-V7 detection from liquid biopsies, here we performed a meta-analysis on the prognostic and predictive value of androgen receptor variant 7 (AR-V7) detected from liquid biopsy for patients with prostate cancer (PC), three databases, the Embase, Medline, and Scopus were searched up to September 2021. A total of 37 studies were included. The effects of liquid biopsy AR-V7 status on overall survival (OS), radiographic progression-free survival (PFS), and prostate-specific antigen (PSA)-PFS were calculated with RevMan 5.3 software. AR-V7 positivity detected in liquid biopsy significantly associates with worse OS, PFS, and PSA-PFS (P <0.00001). A subgroup analysis of patients treated with androgen receptor signaling inhibitors (ARSi such as abiraterone and enzalutamide) showed a significant association of AR-V7 positivity with poorer OS, PFS, and PSA-PFS. A statistically significant association with OS was also found in taxane-treated patients (P = 0.04), but not for PFS (P = 0.21) or PSA-PFS (P = 0.93). For AR-V7 positive patients, taxane treatment has better OS outcomes than ARSi (P = 0.01). Study quality, publication bias and sensitivity analysis were integrated in the assessment. Our data show that liquid biopsy AR-V7 is a clinically useful biomarker that is associated with poor outcomes of ARSi-treated castrate resistant PC (CRPC) patients and thus has the potential to guide patient management and also to stratify patients for clinical trials. More studies on chemotherapy-treated patients are warranted. Systematic Review Registration: PROSPERO, CRD42021239353

The prospect of identifying resistance mechanisms for castrate-resistant prostate cancer using circulating tumor cells : is epithelial-to-mesenchymal transition a key player?

Prostate cancer (PCa) is initially driven by excessive androgen receptor (AR) signaling with androgen deprivation therapy (ADT) being a major therapeutic approach to its treatment. However, the development of drug resistance is a significant limitation on the effectiveness of both first-line and more recently developed second-line ADTs. There is a need then to study AR signaling within the context of other oncogenic signaling pathways that likely mediate this resistance. This review focuses on interactions between AR signaling, the well-known phosphatidylinositol-3-kinase/AKT pathway, and an emerging mediator of these pathways, the Hippo/YAP1 axis in metastatic castrate-resistant PCa, and their involvement in the regulation of epithelial-mesenchymal transition (EMT), a feature of disease progression and ADT resistance. Analysis of these pathways in circulating tumor cells (CTCs) may provide an opportunity to evaluate their utility as biomarkers and address their importance in the development of resistance to current ADT with potential to guide future therapies