Environmental DNA (eDNA) techniques have only recently been applied in the marine environment to detect the presence of marine species. Species-specific primers and probes were designed to detect the ...eDNA of the endangered Maugean skate (Zearaja maugeana) from as little as 1 L of water collected at depth (10-15 m) in Macquarie Harbour (MH), Tasmania. The identity of the eDNA was confirmed as Z. maugeana by sequencing the qPCR products and aligning these with the target sequence for a 100% match. This result has validated the use of this eDNA technique for detecting a rare species, Z. maugeana, in the wild. Being able to investigate the presence, and possibly the abundance, of Z. maugeana in MH and Bathurst harbour (BH), would be addressing a conservation imperative for the endangered Z. maugeana. For future application of this technique in the field, the rate of decay was determined for Z. maugeana eDNA under ambient dissolved oxygen (DO) levels (55% saturation) and lower DO (20% saturation) levels, revealing that the eDNA can be detected for 4 and 16 hours respectively, after which eDNA concentration drops below the detection threshold of the assay. With the rate of decay being influenced by starting eDNA concentrations, it is recommended that samples be filtered as soon as possible after collection to minimize further loss of eDNA prior to and during sample processing.
The preparation of polymeric composites from recycled thermoplastic with natural fibers is an interesting alternative that contribute for preservation of natural resources, decrease of pollutant ...waste and production of low cost materials. Low-density polyethylene waste (LDPEW) from packaging films presents low index of mechanical recycling, generating several environmental problems and for their management after discard. On the other hand, wood waste as such as pine wood waste (PWW) are also produced in large scale and their recycling potential is not very explored. The aim of this study was the preparation of LDPEW/PWW composites in presence of coupling agent maleic anhydride grafted polyethylene (PE-g-MA) and to evaluate their mechanical, morphological and thermal properties. LDPEW/PWW composites were prepared by extrusion processing and specimens obtained by injection molding for after characterization by tensile testing, impact testing, scan electronic microscopy and thermal analysis. The mechanical properties of the LDPEW/PWW composites are depending of the PWW content in the material, allowing the adjustment of the composition according to the potential for practical application, while the thermal stability of the composites is compatible with the required conditions for thermomechanical processing. The preparation of LDPEW/PWW composites showed viability for production of low cost materials from recycled waste.
Cellodextrins are non-digestible oligosaccharides that have attracted interest from the food industry as potential prebiotics. They are typically produced through the partial hydrolysis of cellulose, ...resulting in a complex mixture of oligosaccharides with a varying degree of polymerisation (DP). Here, we explore the defined synthesis of cellotriose as product since this oligosaccharide is believed to be the most potent prebiotic in the mixture. To that end, the cellobiose phosphorylase (CBP) from
Cellulomonas uda
and the cellodextrin phosphorylase (CDP) from
Clostridium cellulosi
were evaluated as biocatalysts, starting from cellobiose and α-
d
-glucose 1-phosphate as acceptor and donor substrate, respectively. The CDP enzyme was shown to rapidly elongate the chains towards higher DPs, even after extensive mutagenesis. In contrast, an optimised variant of CBP was found to convert cellobiose to cellotriose with a molar yield of 73%. The share of cellotriose within the final soluble cellodextrin mixture (DP2-5) was 82%, resulting in a cellotriose product with the highest purity reported to date. Interestingly, the reaction could even be initiated from glucose as acceptor substrate, which should further decrease the production costs.
Key points
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Cellobiose phosphorylase is engineered for the production of cellotriose.
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Cellotriose is synthesised with the highest purity and yield to date.
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Both cellobiose and glucose can be used as acceptor for cellotriose production.
Global forest restoration targets have been set, yet policy makers and land managers lack guiding principles on how to invest limited resources to achieve them. We conducted a meta-analysis of 166 ...studies in naturally regenerating and actively restored forests worldwide to answer: (1) To what extent do floral and faunal abundance and diversity and biogeochemical functions recover? (2) Does recovery vary as a function of past land use, time since restoration, forest region, or precipitation? (3) Does active restoration result in more complete or faster recovery than passive restoration? Overall, forests showed a high level of recovery, but the time to recovery depended on the metric type measured, past land use, and region. Abundance recovered quickly and completely, whereas diversity recovered slower in tropical than in temperate forests. Biogeochemical functions recovered more slowly after agriculture than after logging or mining. Formerly logged sites were mostly passively restored and generally recovered quickly. Mined sites were nearly always actively restored using a combination of planting and either soil amendments or recontouring topography, which resulted in rapid recovery of the metrics evaluated. Actively restoring former agricultural land, primarily by planting trees, did not result in consistently faster or more complete recovery than passively restored sites. Our results suggest that simply ending the land use is sufficient for forests to recover in many cases, but more studies are needed that directly compare the value added of active versus passive restoration strategies in the same system. Investments in active restoration should be evaluated relative to the past land use, the natural resilience of the system, and the specific objectives of each project.
Cell migration is a key procedure involved in many biological processes including embryological development, tissue formation, immune defense or inflammation, and cancer progression. How physical, ...chemical, and molecular aspects can affect cell motility is a challenge to understand migratory cells behavior.
assays are excellent approaches to extrapolate to
situations and study live cells behavior. Here we present four
protocols that describe step-by-step cell migration, invasion and adhesion strategies and their corresponding image data quantification. These current protocols are based on
wound healing assays (comparing traditional pipette tip-scratch assay vs. culture insert assay), 2D individual cell-tracking experiments by live cell imaging and
spreading and transwell assays. All together, they cover different phenotypes and hallmarks of cell motility and adhesion, providing orthogonal information that can be used either individually or collectively in many different experimental setups. These optimized protocols will facilitate physiological and cellular characterization of these processes, which may be used for fast screening of specific therapeutic cancer drugs for migratory function, novel strategies in cancer diagnosis, and for assaying new molecules involved in adhesion and invasion metastatic properties of cancer cells.
Summary
Ecological and evolutionary research increasingly uses quantitative synthesis of primary research studies (meta‐analysis) for answering fundamental questions, informing environmental policy ...and summarizing results for decision makers.
Knowing how meta‐analysis works is important for researchers so that their research can have broader impact. Meta‐analytic thinking encourages scientists to see single primary research studies as substantial contributions to a larger picture.
To facilitate inclusion in a meta‐analysis, relevant primary research studies must be found and basic information about the methods and results must be thoroughly, clearly and transparently reported. While many published papers provide this information, it is common for essential data to be omitted, leading to study exclusion from meta‐analyses.
We provide guidelines for correctly reporting basic data needed from primary studies in ecology and evolutionary biology so that they can be included in meta‐analyses, together with examples that show how data should be reported to enable calculation and analysis of effect sizes, and how data should be made accessible.
These guidelines are important for reporting research results in general, whether or not results are included in subsequent meta‐analyses, because they are necessary for the interpretation and assessment of study outcomes. Increased implementation of these guidelines by authors, editors and publishers, and reinforcement by funders, will foster higher quality and more inclusive syntheses, further the goals of transparency and reproducibility in science, and improve the quality and value of primary research studies.
Background
The Geriatric Depression Scale (GDS) is a widely used instrument to assess depression in older adults. The short GDS versions that have four (GDS-4) and five items (GDS-5) represent ...alternatives for depression screening in limited-resource settings. However, their accuracy remains uncertain.
Objective
To assess the accuracy of the GDS-4 and GDS-5 versions for depression screening in older adults.
Methods
Until May 2020, we systematically searched PubMed, PsycINFO, Scopus, and Google Scholar; for studies that have assessed the sensitivity and specificity of GDS-4 and GDS-5 for depression screening in older adults. We conducted meta-analyses of the sensitivity and specificity of those studies that used the Diagnostic and Statistical Manual of Mental Disorders (DSM) or the International Classification of Diseases-10 (ICD-10) as reference standard. Study quality was assessed with the QUADAS-2 tool. We performed bivariate random-effects meta-analyses to calculate the pooled sensitivity and specificity with their 95% confidence intervals (95% CI) at each reported common cut-off. For the overall meta-analyses, we evaluated each GDS-4 version or GDS-5 version separately by each cut-off, and for investigations of heterogeneity, we assessed altogether across similar GDS versions by each cut-off. Also, we assessed the certainty of evidence using the GRADE methodology.
Results
Twenty-three studies were included and meta-analyzed, assessing eleven different GDS versions. The number of participants included was 5048. When including all versions together, at a cut-off 2, GDS-4 had a pooled sensitivity of 0.77 (95% CI: 0.70–0.82) and a pooled specificity of 0.75 (0.68–0.81); while GDS-5 had a pooled sensitivity of 0.85 (0.80–0.90) and a pooled specificity of 0.75 (0.69–0.81). We found results for more than one GDS-4 version at cut-off points 1, 2, and 3; and for more than one GDS-5 version at cut-off points 1, 2, 3, and 4. Mostly, significant subgroup differences at different test thresholds across versions were found. The accuracy of the different GDS-4 and GDS-5 versions showed a high heterogeneity. There was high risk of bias in the index test domain. Also, the certainty of the evidence was low or very low for most of the GDS versions.
Conclusions
We found several GDS-4 and GDS-5 versions that showed great heterogeneity in estimates of sensitivity and specificity, mostly with a low or very low certainty of the evidence. Altogether, our results indicate the need for more well-designed studies that compare different GDS versions.
Aging is characterized by the progressive decline of physiology at the cell, tissue and organism level, leading to an increased risk of mortality. Proteotoxic stress, mitochondrial dysfunction and ...genomic instability are considered major universal drivers of cell aging, and accumulating evidence establishes clear biunivocal relationships among these key hallmarks. In this regard, the finite lifespan of the budding yeast, together with the extensive armamentarium of available analytical tools, has made this single cell eukaryote a key model to study aging at molecular and cellular levels. Here we review the current data that link proteostasis to cell cycle progression in the budding yeast, focusing on senescence as an inherent phenotype displayed by aged cells. Recent advances in high-throughput systems to study yeast mother cells while they replicate are providing crucial information on aging-related processes and their temporal interdependencies at a systems level. In our view, the available data point to the existence of multiple feedback mechanisms among the major causal factors of aging, which would converge into the loss of proteostasis as a nodal driver of cell senescence and death.
Aging is a complex phenomenon of functional decay in a biological organism. Although the effects of aging are readily recognizable in a wide range of organisms, the cause(s) of aging are ill defined ...and poorly understood. Experimental methods on model organisms have driven significant insight into aging as a process, but have not provided a complete model of aging. Computational biology offers a unique opportunity to resolve this gap in our knowledge by generating extensive and testable models that can help us understand the fundamental nature of aging, identify the presence and characteristics of unaccounted aging factor(s), demonstrate the mechanics of particular factor(s) in driving aging, and understand the secondary effects of aging on biological function. In this review, we will address each of the above roles for computational biology in aging research. Concurrently, we will explore the different applications of computational biology to aging in single-celled versus multicellular organisms. Given the long history of computational biogerontological research on lower eukaryotes, we emphasize the key future goals of gradually integrating prior models into a holistic map of aging and translating successful models to higher-complexity organisms.
In order to produce rejuvenated daughters, dividing budding yeast cells confine aging factors, including protein aggregates, to the aging mother cell. The asymmetric inheritance of these protein ...deposits is mediated by organelle and cytoskeletal attachment and by cell geometry. Yet it remains unclear how deposit formation is restricted to the aging lineage. Here, we show that selective membrane anchoring and the compartmentalization of the endoplasmic reticulum (ER) membrane confine protein deposit formation to aging cells during division. Supporting the idea that the age-dependent deposit forms through coalescence of smaller aggregates, two deposits rapidly merged when placed in the same cell by cell-cell fusion. The deposits localized to the ER membrane, primarily to the nuclear envelope (NE). Strikingly, weakening the diffusion barriers that separate the ER membrane into mother and bud compartments caused premature formation of deposits in the daughter cells. Detachment of the Hsp40 protein Ydj1 from the ER membrane elicited a similar phenotype, suggesting that the diffusion barriers and farnesylated Ydj1 functioned together to confine protein deposit formation to mother cells during division. Accordingly, fluorescence correlation spectroscopy measurements in dividing cells indicated that a slow-diffusing, possibly client-bound Ydj1 fraction was asymmetrically enriched in the mother compartment. This asymmetric distribution depended on Ydj1 farnesylation and intact diffusion barriers. Taking these findings together, we propose that ER-anchored Ydj1 binds deposit precursors and prevents them from spreading into daughter cells during division by subjecting them to the ER diffusion barriers. This ensures that the coalescence of precursors into a single deposit is restricted to the aging lineage.
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•Protein deposits that form during aging associate with the endoplasmic reticulum (ER)•ER serves as a platform for deposit coalescence•Deposit precursors are anchored to ER via farnesylated Hsp40 (Ydj1FS)•ER diffusion barriers ensure the asymmetric partitioning of Ydj1FS during division
Saarikangas et al. report that confinement of age-associated protein deposit formation to the aging lineage in yeast involves a two-tiered mechanism. Deposit precursors are captured by ER-membrane-bound chaperone Ydj1. The compartmentalization of the ER by diffusion barriers then facilitates their asymmetric segregation during cell division.
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