The impact of over 80 years of land cover changes on bee and wasp pollinator communities in England

Change in land cover is thought to be one of the key drivers of pollinator declines, and yet there is a dearth of studies exploring the relationships between historical changes in land cover and shifts in pollinator communities. Here, we explore, for the first time, land cover changes in England over more than 80 years, and relate them to concurrent shifts in bee and wasp species richness and community composition. Using historical data from 14 sites across four counties, we quantify the key land cover changes within and around these sites and estimate the changes in richness and composition of pollinators. Land cover changes within sites, as well as changes within a 1 km radius outside the sites, have significant effects on richness and composition of bee and wasp species, with changes in edge habitats between major land classes also having a key influence. Our results highlight not just the land cover changes that may be detrimental to pollinator communities, but also provide an insight into how increases in habitat diversity may benefit species diversity, and could thus help inform policy and practice for future land management.     

Multicriteria Design of Plastic Recycling Based on Quality Information and Environmental Impacts

In this study, we develop a framework for the multicriteria design of plastic recycling based on quality information and environmental impacts for the purpose of supporting collaborative decision making among consumers, municipalities, and recyclers. The subject of this article is the mechanical recycling of postconsumer polyethylene terephthalate (PET) bottles. We present a “quality conversion matrix,” which links the quality of recycled PET resin to the quality of waste PET bottles and operational conditions, described in terms of the functions of modules constituting the entire recycling process. We estimate the quality of recycled PET resin and simulate the applicability to the intended products as the primary criterion by confirming whether the estimated quality of recycled resin satisfies the quality demands of PET resin users. The amounts of carbon dioxide (CO₂) emissions and fossil resource consumption are also estimated as the secondary criteria. An approach to collaborative decision making utilizing mixed‐integer linear programming (MILP) and Monte Carlo simulation is proposed on the premise of different objectives of various stakeholders, where all the feasible optimal solutions for achieving the quality demands are obtained. The quality requirements of waste bottles, along with the CO₂ emissions and fossil resource consumption estimated for each solution, contribute to the collaborative multicriteria design of plastic recycling.     

Laser-capture Microdissection of Human Prostatic Epithelium for RNA Analysis

The prostate gland contains a heterogeneous milieu of stromal, epithelial, neuroendocrine and immune cell types. Healthy prostate is comprised of fibromuscular stroma surrounding discrete epithelial-lined secretory lumens and a very small population of immune and neuroendocrine cells. In contrast, areas of prostate cancer have increased dysplastic luminal epithelium with greatly reduced or absent stromal population. Given the profound difference between stromal and epithelial cell types, it is imperative to separate the cell types for any type of downstream molecular analysis. Despite this knowledge, the bulk of gene expression studies compare benign prostate to cancer without micro-dissection, leading to stromal bias in the benign samples. Laser-capture micro-dissection (LCM) is an effective method to physically separate different cell types from a specimen section. The goal of this protocol is to show that RNA can be successfully isolated from LCM-collected human prostatic epithelium and used for downstream gene expression studies such as RT-qPCR and RNAseq.     

激光捕获显微切割在肿瘤多组学研究中的应用进展

当今社会,肿瘤因其高发病率和高死亡率成为威胁人类健康的重要疾病,研究者们对其发病机制及治疗手段的研究和探索也在不断深入。随着单细胞多组学测序技术的发展,肿瘤组织的异质性问题逐渐被研究人员所认识。为了解决这一问题,激光捕获显微切割（laser capture microdissection,LCM）技术应运而生。LCM技术是一种在显微镜直视下从器官或组织中准确获取某种特定的细胞群或单个细胞的样本收集技术。LCM技术结合多种分子生物学手段可以对异质性组织进行多组学研究,丰富了现有的肿瘤蛋白质组学、基因组学以及转录组学图谱,因此,LCM技术成为研究特异性表达及分子机制的有力工具,在肿瘤学领域得到广泛应用。基于此,对LCM的原理、优势及其在肿瘤多组学研究中的应用进行了综述,并对其未来可能的发展方向进行了展望,以期为肿瘤的研究和治疗提供新的思路。     

Advances in proteomic prostate cancer biomarker discovery

Prostate cancer is the most common non-cutaneous cancer in men in the United States. For reasons largely unknown, the incidence of prostate cancer has increased in the last two decades, in spite or perhaps because of a concomitant increase in serum prostate-specific antigen (PSA) screening. While PSA is acknowledged not to be an ideal biomarker for prostate cancer detection, it is however widely used by physicians due to lack of an alternative. Thus, the identification of a biomarker(s) that can complement or replace PSA represents a major goal for prostate cancer research. Screening complex biological specimens such as blood, urine, and tissue to identify protein biomarkers has become increasingly popular over the last decade thanks to advances in proteomic discovery methods. The completion of human genome sequence together with new development in mass spectrometry instrumentation and bioinformatics has been a major driving force in biomarker discovery research. Here we review the current state of proteomic applications as applied to various sample sources including blood, urine, tissue, and “secretome” for the purpose of prostate cancer biomarker discovery. Additionally, we review recent developments in validation of putative markers, efforts at systems biology approach, and current challenges of proteomics in biomarker discovery.     

Expression and localization of Tmie in adult rat cochlea

Loss-of function mutations in transmembrane inner ear expressed (Tmie/TMIE) gene have been shown to cause deafness in mice and humans (DFNB6). However, the functional roles of TMIE in the cochlea remain unclear. A primary step toward the understanding of the role of TMIE in hearing and its dysfunction is the documentation of its cellular and sub-cellular location within the cochlea, the auditory organ. In this study, we located and determined the cellular expression of Tmie within the rat cochlea using a polyclonal anti-Tmie antibody. The anti-Tmie antibody identified a specific band of 17 kDa in a variety of rat tissues by using Western blot analyses. The expression products of Tmie were also detected in the spiral limbus, spiral ligament, organ of Corti, and stria vascularis by immunohistochemistry analysis and RT-PCR. Our results point out the presence and localization of Tmie products in the cochlea of rat. Knowledge of spatial distribution of Tmie will provide important insight into the mechanisms that lead to deafness due to mutations in the TMIE gene.     

Life-Cycle based methods for sustainable product development

Sustainability-a term originating from silviculture, which was adopted by UNEP as the main political goal for the future development of humankind-is also the ultimate aim of product development. It comprises three components: environment, economy and social aspects which have to be properly assessed and balanced if a new product is to be designed or an existing one is to be improved. The responsibility of the researchers involved in the assessment is to provide appropriate and reliable instruments. For the environmental part there is already an internationally standardized tool: Life Cycle Assessment (LCA). Life Cycle Costing (LCC) is the logical counterpart of LCA for the economic assessment. LCC surpasses the purely economic cost calculation by taking into account hidden costs and potentially external costs over the life cycle of the product. It is a very important point that different life-cycle based methods (including Social Life Cycle Assessment) for sustainablity assessment use the same system boundaries.     

Molecular dissection of the amygdala and its relevance to autism

The limbic system, and in particular the amygdala, have been implicated in autism. The amygdala is a complex structure that in rodents consists of at least 12 different nuclei or subnuclei. A comparative analysis of amygdala neuroanatomy in normal vs. autistic brains would be aided by the availability of molecular markers to unambiguously recognize these different amygdala substructures. Here we report on the development of methods to identify genes enriched in the central, lateral and medial nuclei of the rodent amygdala. Our results suggest that laser-capture microdissection of specific amygdala subnuclei, when combined with linear amplification of cRNA probes for oligonucleotide microarray hybridization, can efficiently identify genes whose expression is confined to these substructures. Importantly, many of these genes were missed in previous gene expression-profiling experiments using whole amygdala tissue. The isolation of human orthologs of these subnucleus-specific genes, and/or the application of these methods directly to human tissue, may provide useful markers for characterizing neuropathological correlates of autism, as well as for identifying molecular differences between normal and autistic brains.     

Selection and validation of microarray candidate genes from subregions and subnuclei of the brain

DNA array technology now allows an enormous amount of expression data to be obtained. For large-scale gene profiling enterprises, this is of course welcome. However, the scientist interested in follow-up studies of a handful of differentially expressed genes may find it hard to sift through the vast datasets to pinpoint genes with the most desirable and reliable behaviors. Here, we present the methodology we have employed to discover genes differentially expressed in the adult mouse brain. We first used Affymetrix microarrays to compare gene expression from five different brain regions: the amygdala, cerebellum, hippocampus, olfactory bulb, and periaqueductal gray. Second, we identified genes differentially expressed within three distinct amygdala subnuclei. In this case, the tissue was microdissected by laser-capture to minimize contamination from adjacent subnuclei, and extracted RNA was subjected to three rounds of linear amplification prior to hybridization to the microarrays. To select candidate genes, we developed a custom algorithm to identify those genes with the most robust changes in expression across different replicate samples. Confirmation of expression patterns with in situ hybridization uncovered further criteria to consider in the selection process.