Shortest-Path Network Analysis Is a Useful Approach toward Identifying Genetic Determinants of Longevity

Background Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. Methodology/Principal Findings We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein–protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. Conclusions/Significance This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of network analysis of aging to be extensively validated in a biological system. The novel longevity genes identified in this study are likely to yield further insight into the molecular mechanisms of aging and age-associated disease

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

CropPol: a dynamic, open and global database on crop pollination

Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e. berry weight, number of fruits and kg per hectare, among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), Northern America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-05 (21 studies), 2006-10 (40), 2011-15 (88), and 2016-20 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA). This article is protected by copyright. All rights reserved

CropPol: a dynamic, open and global database on crop pollination

This is the final version. Available from Wiley via the DOI in this record The original dataset (v1.1.0) of the CropPol database can be accessed from the ECOLOGY repository. Main upgrades of these datasets will be versioned and deposited in Zenodo (DOI: 10.5281/zenodo.5546600)Data availability. V.C. Computer programs and data-processing algorithms: The algorithms used in deriving, processing, or transforming data can be accessed in the DataS1.zip file and the Zenodo repository (DOI: 10.5281/zenodo.5546600). V.D. Archiving: The data is archived for long-term storage and access in Zenodo (DOI: 10.5281/zenodo.5546600)Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e. berry weight, number of fruits and kg per hectare, among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), Northern America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-05 (21 studies), 2006-10 (40), 2011-15 (88), and 2016-20 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA). This article is protected by copyright. All rights reserved.OBServ Projec

Susceptibility of adult Phlyctinus (Coleoptera: Curculionidae) to entomopathogens: A first look at potential differences in a newly revised species complex

The data that support the findings of this study are openly available in Mendeley Data at DOI: 10.17632/tckvm6hcwd.1 (Appendix S1) and DOI: 10.17632/fn2d8phjnm.1 (Appendix S2).International audiencePhlyctinus callosus and P. xerophilus (Coleoptera: Curculionidae) are two cryptic species of native entimine weevils, previously grouped together under the P. callosus sensu lato concept, that are pests of economic importance to the deciduous fruit and vine industry in the Western Cape province of South Africa. Laboratory bioassays were conducted using entomopathogenic fungi (EPF) isolates of Beauveria and entomopathogenic nematodes (EPNs), Heterorhabditis indica and Steinernema yirgalemense , to determine differences in susceptibility of adult P. callosus and P. xerophilus to potential biological control agents. The test arena used was 24‐well bioassay plates with an inoculation rate of 200 infective juveniles (IJs)/insect for EPNs and 5 × 10 5 conidia/insect for EPF. Insects were inoculated using a 12.7 mm filter paper impregnated with 50 μL of entomopathogen suspension. Infection was determined after 96 h incubation for EPNs through dissection of cadavers. Insects inoculated with EPF were incubated in the wells for 18 days and mortality recorded daily. Cadavers were surface sterilized and observed for overt mycosis. Differential susceptibility between P. callosus and P. xerophilus was observed in EPF but not in EPN bioassays. Differential susceptibility to EPF could be due to methodology. Low adult weevil pathogenicity was found for all entomopathogens, with variable results obtained from different bioassay batches

Steinernema yirgalemense (Steinernematidae) to control Phlyctinus callosus and Phlyctinus xerophilus (Curculionidae)

Weevils were collected under Cape-Nature permit no. CN35-28-13395 and with permission from the above-mentioned landowners.International audienceConsiderable progress has been made in the surveying, taxonomy, screening, mass production and formulation of entomopathogenic nematodes (EPN) and their associated symbiotic bacteria in South Africa. Steinernema yirgalemense isolate 157-C is one of the most promising native EPN candidates with regards to virulence, its broad insect-host spectrum, and can be readily mass-produced and formulated into a commercial product. The banded fruit weevils, Phlyctinus callosus sensu stricto and Phlyctinus xerophilus , previously grouped together under the Phlyctinus callosus sensu lato species concept, are native entimine weevils of economic importance to deciduous fruit, grapevine and berries in the Western Cape province of South Africa. This study investigated potential differences in baseline susceptibility of larvae and pupae of the two weevil species to S. yirgalemense in laboratory screenings. The test arena used was 24-well bioassay plates, with an inoculation concentration of 200 infective juveniles (IJ) insect −1 for larvae and 100 IJ insect −1 for pupae. Infection was determined 48 h and 96 h after inoculation. Field-efficacy of S. yirgalemense , applied at a concentration of 60 IJ cm −2 , against larvae of the two weevil species was determined in an ecologically relevant semi-field trial. In all cases in vitro mass-produced IJ of S. yirgalemense were used. No baseline differential susceptibility between P. callosus and P. xerophilus larvae was obtained in laboratory screenings. Phlyctinus pupae were approximately twice as susceptible compared to larvae, with significant differences between bioassay batches. Approximately 45% control of P. xerophilus larvae was obtained after 96 h of exposure to S. yirgalemense in the field, differing significantly from the control and P. callosus treatment. Low levels of Phlyctinus larval infection by native EPN (confirmed as Heterorhabditis bacteriophora from one P. xerophilus cadaver) occurred in both control and EPN treatment groups under field conditions

New data on an old pest complex: The status of Phlyctinus callosus Schönherr and Phlyctinus xerophilus Haran (Coleoptera: Curculionidae) in South Africa

Material was collected under Cape Nature Permits Numbers CN35-28-13395 and CN44-30-4229, and with permission from private landowners.International audiencePhlyctinus is an endemic weevil genus of the Cape Floristic Region that comprises eight to ten species, previously classified under the monotypic P. callosus sensu lato concept. Two species of this genus, Phlyctinus callosus and P. xerophilus, are of economic concern to the deciduous fruit and grapevine industry in the Western Cape province of South Africa, causing primary damages and being of phytosanitary concern at the adult stage. The taxonomic revision conducted in 2020 raised doubts whether one of the two species was a newly emerging pest and/or what species was considered in studies before the clarification of species boundaries. Also unclear is whether these species can be controlled similarly using current control measures. The aim of this study therefore is to review the pest status of the two species over time based on museum records, field collections and historical publications, and to clarify how control measure(s) are impacted. We infer that neither species appear to be emerging pests in the region, both being of agricultural significance for at least 80 years. Phlyctinus callosus is mostly distributed along the southern coast, while P. xerophilus is distributed in inland valleys. The two species show similar biology, physiology and ecology in agro-ecosystems, and can be excluded from the host plant canopy using stem-barriers, adults being flightless. As such, it is shown that the naming of P. xerophilus as a pest is mainly a taxonomical clarification within a pre-existing species complex