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The selective removal of dysfunctional mitochondria, a process termed mitophagy, is critical for cellular health and impairments have been linked to aging, Parkinson disease, and other neurodegenerative conditions. A central mitophagy pathway is orchestrated by the ubiquitin (Ub) kinase PINK1 together with the E3 Ub ligase PRKN/Parkin. The decoration of damaged mitochondrial domains with phosphorylated Ub (p-S65-Ub) mediates their elimination though the autophagy system. As such p-S65-Ub has emerged as a highly specific and quantitative marker of mitochondrial damage with significant disease relevance. Existing p-S65-Ub antibodies have been successfully employed as research tools in a range of applications including western blot, immunocytochemistry, immunohistochemistry, and enzyme-linked immunosorbent assay. However, physiological levels of p-S65-Ub in the absence of exogenous stress are very low, therefore difficult to detect and require reliable and ultrasensitive methods. Here we generated and characterized a collection of novel recombinant, rabbit monoclonal p-S65-Ub antibodies with high specificity and affinity in certain applications that allow the field to better understand the molecular mechanisms and disease relevance of PINK1-PRKN signaling. These antibodies may also serve as novel diagnostic or prognostic tools to monitor mitochondrial damage in various clinical and pathological specimens. Abbreviations : AD: Alzheimer disease; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; ELISA: enzyme-linked immunosorbent assay; HEK293E cell: human embryonic kidney E cell; ICC: immunocytochemistry; IHC: immunohistochemistry: KO: knockout; LoB: limit of blank; LoD: limit of detection; LoQ: limit of quantification; MEF: mouse embryonic fibroblast; MSD: Meso Scale Discovery; n.s.: non-significant; nonTg: non-transgenic; PBMC: peripheral blood mononuclear cell; PD: Parkinson disease; p-S65-PRKN: phosphorylated PRKN at serine 65; p-S65-Ub: phosphorylated Ub at serine 65; Ub: ubiquitin; WT: wild-type.

Neurodegenerative diseases are commonly associated with the formation of aberrant protein aggregates within the brain, and ultrastructural analyses have revealed that the proteins within these inclusions often assemble into amyloid filaments. Cryoelectron microscopy (cryo-EM) has emerged as an effective method for determining the near-atomic structure of these disease-associated filamentous proteins, and the resulting structures have revolutionized the way we think about aberrant protein aggregation and propagation during disease progression. These structures have also revealed that individual fibril conformations may dictate different disease conditions, and this newfound knowledge has improved disease modeling in the lab and advanced the ongoing pursuit of clinical tools capable of distinguishing and targeting different pathogenic entities within living patients. In this review, we summarize some of the recently developed cryo-EM structures of ex vivo α-synuclein, tau, β-amyloid (Aβ), TAR DNA-binding protein 43 (TDP-43), and transmembrane protein 106B (TMEM106B) fibrils and discuss how these structures are being leveraged toward mechanistic research and therapeutic development., Competing Interests: Declaration of interests L.P. is a consultant for Expansion Therapeutics., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Honey bees are important organisms for research in many fields, including physiology, behavior, and ecology. Honey bee colonies are relatively easy and affordable to procure, manage, and replace. However, some difficulties still exist in honey bee research, specifically that honey bee colonies have a distinct seasonality, especially in temperate regions. Honey bee colonies transition from a large society in which workers have a strict temporal division of labor in the summer, to a group of behaviorally flexible workers who manage the colony over winter. Furthermore, opening colonies or collecting bees when they are outside has the potential to harm the colony because of the disruption in thermoregulation. Here, we present a simple and affordable indoor management method utilizing a mylar tent and controlled environmental conditions that allows bees to freely fly without access to outdoor space. This technique permits research labs to successfully keep several colonies persistently active during winter at higher latitudes. Having an extended research period is particularly important for training students, allowing preliminary experiments to be performed, and developing methods. However, we find distinct behavioral differences in honey bees managed in this situation. Specifically learning and thermoregulatory behaviors were diminished in the bees managed in the tent. Therefore, we recommend caution in utilizing these winter bees for full experiments until more is known. Overall, this method expands the research potential on honey bees, and calls attention to the additional research that is needed to understand how indoor management might affect honey bees., (© The Author(s) 2024. Published by Oxford University Press on behalf of Entomological Society of America.)

Introduction: Acute liver failure (ALF) is defined as acute loss of liver function leading to hepatic encephalopathy associated with a high risk of patient death. Brain injury markers in serum and tissue can help detect and monitor ALF-associated brain injury. This study compares different brain injury parameters in plasma and tissue along with the progression of ALF., Method: ALF was induced by performing an 85% liver resection. Following the resection, animals were recovered and monitored for up to 48 h or until reaching the predefined endpoint of receiving standard medical therapy (SMT). Blood and serum samples were taken at T baseline , T 24 , and upon reaching the endpoint (T end ). Control animals were euthanized by exsanguination following plasma sampling. Postmortem brain tissue samples were collected from the frontal cortex (FCTx) and cerebellum (Cb) of all animals. Glial fibrillary acidic protein (GFAP) and tau protein and mRNA levels were quantified using ELISA and qRT-PCR in all plasma and brain samples. Plasma neurofilament light (NFL) was also measured using ELISA., Results: All ALF animals ( n  = 4) were euthanized upon showing signs of brain herniation. Evaluation of brain injury biomarkers revealed that GFAP was elevated in ALF animals at T 24h and T end , while Tau and NFL concentrations were unchanged. Moreover, plasma glial fibrillary acidic protein (GFAP) levels were negatively correlated with total protein and positively correlated with both aspartate transaminase (AST) and alkaline phosphatase (AP). Additionally, lower GFAP and tau RNA expressions were observed in the FCTx of the ALF group but not in the CB tissue., Conclusion: The current large animal study has identified a strong correlation between GFAP concentration in the blood and markers of ALF. Additionally, the protein and gene expression analyses in the FCTx revealed that this area appears to be susceptible, while the CB is protected from the detrimental impacts of ALF-associated brain swelling. These results warrant further studies to investigate the mechanisms behind this process., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Felgendreff, Hosseiniasl, Felgendreff, Amiot, Minshew, Ahmadzada, Qu, Wilken, Arribas Gomez, Nyberg and Cook.)

Background: Ileal-pouch-anal anastomosis is the operation of choice after proctocolectomy for ulcerative colitis; some patients will develop Crohn's disease. We aim to determine long-term behavior and outcomes of inflammatory bowel disease-ileal-pouch-anal anastomosis after colectomy, where a specialist gastrointestinal pathologist re-evaluated the initial colectomy specimen., Methods: Patients with inflammatory bowel disease-ileal-pouch-anal anastomosis were identified from a single-surgeon prospective database containing 1,165 patients accrued from 1991 to 2017 and invited to complete pouch-function and quality-of-life assessments. Medical records were used to obtain clinical outcomes and subjective functional assessments for those unable to be contacted. Data were compared between patients with and without histological assessment disagreement and subsequent inflammatory bowel disease behavior subgroups., Results: For 138 patients included in the analysis, the median follow-up was 22.5 (range: 5-39) years. A total of 39.1% of patients had histologic diagnostic change after gastrointestinal pathologist review, and 19% and 39% developed Crohn's disease-like disease behavior at 10- and 20-year follow-ups. Pouch function and quality-of-life scores were similar across diagnostic change subgroups. Pouch failure was higher in Crohn's-like disease (31.1 vs 13.0%, P < .05). Intestinal continuity was maintained in 68.9% of Crohn's disease-like patients, 57.9% required biologics. Gastrointestinal pathologist review did not alter the time to new diagnosis (P = .419) or time to pouch failure (P = .320), mean: 11.0 and 11.41 years, respectively., Conclusion: We describe equivocal patient-reported outcomes in patients with ileal-pouch-anal anastomosis and changing histologic and clinical diagnosis. Although pouch excision and biologic use rates are higher, many Crohn's disease-like patients maintain their pouch. Diagnostic change and pouch failure often occur >10 years after ileal-pouch-anal anastomosis creation. This supports the consideration of ileal-pouch-anal anastomosis after colectomy in carefully selected patients with inflammatory bowel disease, even those with ambiguous histology and the need for close long-term follow-up., (Copyright © 2023. Published by Elsevier Inc.)

Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.

Gut symbionts influence the physiology and behavior of their host, but the extent to which these effects scale to social behaviors is an emerging area of research. The use of the western honeybee (Apis mellifera) as a model enables researchers to investigate the gut microbiome and behavior at several levels of social organization. Insight into gut microbial effects at the societal level is critical for our understanding of how involved microbial symbionts are in host biology. In this Commentary, we discuss recent findings in honeybee gut microbiome research and synthesize these with knowledge of the physiology and behavior of other model organisms to hypothesize how host-microbe interactions at the individual level could shape societal dynamics and evolution., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

In 2010, the introduction of other effective area-based conservation measures (OECMs) into international policy caused a paradigm shift in area-based conservation, which included consideration of areas outside formal protected areas and places where biodiversity conservation may not be a management objective for the site. Despite the importance of this shift for global conservation, conservation science and policy have been slow to engage with the concept of OECMs. As the world moves toward protecting 30% of the Earth by 2030, it is imperative to develop evidence-based guidance for how to identify effective conservation measures, especially tools to help evaluate and monitor the biodiversity outcomes associated with potential OECMs. To understand the current progress in developing the concept of OECMs, I evaluated the peer-reviewed literature to consolidate and synthesize current knowledge. I conducted a thematic analysis of papers to identify the types of challenges and opportunities being discussed and lessons from studies evaluating the effectiveness of OECMs. Only 105 studies mentioned OECMs, and those that did rarely move beyond superficial mention of OECMs as part of area-based conservation. Around one-half of studies listed potential risks or benefits of OECMs but none provided evidence these issues have materialized. Twenty-three studies attempted to identify potential OECMs, although specific case studies were rare. The 7 studies that evaluated existing OECMs were highly critical of how they had been implemented to date. Studies that evaluated conservation outcomes were extremely rare, and suggested effectiveness must be judged on a case-by-case basis. The current literature not only leaves many gaps in the science required to operationalize the concept of OECMs, but also often raises additional questions that need to be addressed. If these gaps are not filled by robust science, the promised benefits for biodiversity from OECMs may never be realized., (© 2023 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Genetic variation at the transmembrane protein 106B gene ( TMEM106B) has been linked to risk of frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) through an unknown mechanism. We found that presence of the TMEM106B rs3173615 protective genotype was associated with longer survival after symptom onset in a postmortem FTLD-TDP cohort, suggesting a slower disease course. The seminal discovery that filaments derived from TMEM106B is a common feature in aging and, across a range of neurodegenerative disorders, suggests that genetic variants in TMEM106B could modulate disease risk and progression through modulating TMEM106B aggregation. To explore this possibility and assess the pathological relevance of TMEM106B accumulation, we generated a new antibody targeting the TMEM106B filament core sequence. Analysis of postmortem samples revealed that the TMEM106B rs3173615 risk allele was associated with higher TMEM106B core accumulation in patients with FTLD-TDP. In contrast, minimal TMEM106B core deposition was detected in carriers of the protective allele. Although the abundance of monomeric full-length TMEM106B was unchanged, carriers of the protective genotype exhibited an increase in dimeric full-length TMEM106B. Increased TMEM106B core deposition was also associated with enhanced TDP-43 dysfunction, and interactome data suggested a role for TMEM106B core filaments in impaired RNA transport, local translation, and endolysosomal function in FTLD-TDP. Overall, these findings suggest that prevention of TMEM106B core accumulation is central to the mechanism by which the TMEM106B protective haplotype reduces disease risk and slows progression.

The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)

Treatments for neurodegenerative disease, including Frontotemporal dementia (FTD) and Amyotrophic lateral sclerosis (ALS), remain rather limited, underscoring the need for greater mechanistic insight and disease-relevant models. Our ability to develop novel disease models of genetic risk factors, disease modifiers, and other FTD/ALS-relevant targets is impeded by the significant amount of time and capital required to develop conventional knockout and transgenic mice. To overcome these limitations, we have generated a novel CRISPRi interference (CRISPRi) knockin mouse. CRISPRi uses a catalytically dead form of Cas9, fused to a transcriptional repressor to knockdown protein expression, following the introduction of single guide RNA against the gene of interest. To validate the utility of this model we have selected the TAR DNA binding protein (TDP-43) splicing target, stathmin-2 ( STMN2 ). STMN2 RNA is downregulated in FTD/ALS due to loss of TDP-43 activity and STMN2 loss is suggested to play a role in ALS pathogenesis. The involvement of STMN2 loss of function in FTD has yet to be determined. We find that STMN2 protein levels in familial FTD cases are significantly reduced compared to controls, supporting that STMN2 depletion may be involved in the pathogenesis of FTD. Here, we provide proof-of-concept that we can simultaneously knock down Stmn2 and express the expanded repeat in the Chromosome 9 open reading frame 72 ( C9ORF72 ) gene, successfully replicating features of C9-associated pathology. Of interest, depletion of Stmn2 had no effect on expression or deposition of dipeptide repeat proteins (DPRs), but significantly decreased the number of phosphorylated Tdp-43 (pTdp-43) inclusions. We submit that our novel CRISPRi mouse provides a versatile and rapid method to silence gene expression in vivo and propose this model will be useful to understand gene function in isolation or in the context of other neurodegenerative disease models., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Pickles, Zanetti Alepuz, Koike, Yue, Tong, Liu, Zhou, Jansen-West, Daughrity, Song, DeTure, Oskarsson, Graff-Radford, Boeve, Petersen, Josephs, Dickson, Ward, Dong, Prudencio, Cook and Petrucelli.)

Introduction: Vaccination with Vi capsular polysaccharide (Vi-PS) or protein-Vi typhoid conjugate vaccine (TCV) can protect adults against Salmonella Typhi infections. TCVs offer better protection than Vi-PS in infants and may offer better protection in adults. Potential reasons for why TCV may be superior in adults are not fully understood., Methods and Results: Here, we immunized wild-type (WT) mice and mice deficient in IgG or IgM with Vi-PS or TCVs (Vi conjugated to tetanus toxoid or CRM197) for up to seven months, with and without subsequent challenge with Vi-expressing Salmonella Typhimurium. Unexpectedly, IgM or IgG alone were similarly able to reduce bacterial burdens in tissues, and this was observed in response to conjugated or unconjugated Vi vaccines and was independent of antibody being of high affinity. Only in the longer-term after immunization (>5 months) were differences observed in tissue bacterial burdens of mice immunized with Vi-PS or TCV. These differences related to the maintenance of antibody responses at higher levels in mice boosted with TCV, with the rate of fall in IgG titres induced to Vi-PS being greater than for TCV., Discussion: Therefore, Vi-specific IgM or IgG are independently capable of protecting from infection and any superior protection from vaccination with TCV in adults may relate to responses being able to persist better rather than from differences in the antibody isotypes induced. These findings suggest that enhancing our understanding of how responses to vaccines are maintained may inform on how to maximize protection afforded by conjugate vaccines against encapsulated pathogens such as S . Typhi., Competing Interests: GSK Vaccines Institute for Global Health SRL is an affiliate of GlaxoSmithKline Biologicals SA. FM and RD are employees of the GSK group of companies. SJ and EP participate in a postgraduate studentship program at GSK. MA participated in a postgraduate studentship at GSK at the time of the study. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jossi, Arcuri, Alshayea, Persaud, Marcial-Juárez, Palmieri, Di Benedetto, Pérez-Toledo, Pillaye, Channell, Schager, Lamerton, Cook, Goodall, Haneda, Bäumler, Jackson-Jones, Toellner, MacLennan, Henderson, Micoli and Cunningham.)

A major function of TAR DNA-binding protein-43 (TDP-43) is to repress the inclusion of cryptic exons during RNA splicing. One of these cryptic exons is in UNC13A, a genetic risk factor for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The accumulation of cryptic UNC13A in disease is heightened by the presence of a risk haplotype located within the cryptic exon itself. Here, we revealed that TDP-43 extreme N-terminus is important to repress UNC13A cryptic exon inclusion. Further, we found hnRNP L, hnRNP A1, and hnRNP A2B1 bind UNC13A RNA and repress cryptic exon inclusion, independently of TDP-43. Finally, higher levels of hnRNP L protein associate with lower burden of UNC13A cryptic RNA in ALS/FTD brains. Our findings suggest that while TDP-43 is the main repressor of UNC13A cryptic exon inclusion, other hnRNPs contribute to its regulation and may potentially function as disease modifiers., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: LP serves as a Consultant for Expansion Therapeutics., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Foresight science is a systematic approach to generate future predictions for planning and management by drawing upon analytical and predictive tools to understand the past and present, while providing insights about the future. To illustrate the application of foresight science in conservation, we present three case studies: identification of emerging risks to conservation, conservation of at-risk species, and aid in the development of management strategies for multiple stressors. We highlight barriers to mainstreaming foresight science in conservation including knowledge accessibility/organization, communication across diverse stakeholders/decision makers, and organizational capacity. Finally, we investigate opportunities for mainstreaming foresight science including continued advocacy to showcase its application, incorporating emerging technologies (i.e., artificial intelligence) to increase capacity/decrease costs, and increasing education/training in foresight science via specialized courses and curricula for trainees and practicing professionals. We argue that failure to mainstream foresight science will hinder the ability to achieve future conservation objectives in the Anthropocene., (© 2022. The Author(s) under exclusive licence to Royal Swedish Academy of Sciences.)

Background: Chronic inflammation is a key feature of obesity and a hallmark of colon cancer (CC). The obesity-related hormones leptin and adiponectin alter inflammatory gene profiles in cancer, but their specific role in CC is unclear. We have previously studied the effects of leptin and the macrophage-specific mediator itaconate on M2-like macrophages. This current study evaluates their effects on CC cells., Methods: HT-29 CC cells (derived from a young patient, stage III CC) were treated with either leptin, adiponectin, 4-octyl itaconate (OI) or dimethyl itaconate (DI). Gene expression after treatment was analyzed at four time points (3, 6, 18, and 24 h)., Results: CCL22 was upregulated after treatment with adiponectin (at 18 h [FC 16.3, p < 0.001]). IL-8 expression increased following both adiponectin (at 3 h [FC 68.1, p < 0.001]) and leptin treatments (at 6 h [FC 7.3, p < 0.001]), while OI induced downregulation of IL-8 (at 24 h [FC -5.0, p < 0.001]). CXCL10 was upregulated after adiponectin treatment (at 6 h [FC 3.0, p = 0.025]) and downregulated by both OI and DI at 24 h, respectively (OI [FC -10.0, p < 0.001]; DI [FC -10.0, p < 0.001]). IL-1β was upregulated after adiponectin treatment (at 3 h [FC 10.6, p < 0.001]) and downregulated by DI (at 24 h [FC -5.0, p < 0.001]). TNF-α expression was induced following adiponectin (at 6 h [FC 110.7, p < 0.001]), leptin (at 18 h [FC 5.8, p = 0.027]) and OI (at 3 h [FC 91.1, p = 0.001]). PPARγ was affected by both OI (at 3 h [FC 10.1, p = 0.031], at 24 h [FC -10.0, p = 0.031]) and DI (at 18 h [FC -1.7, p = 0.033])., Conclusions: Obesity hormones directly affect inflammatory gene expression in HT29 CC cells, potentially enhancing cancer progression. Itaconate affects the prognostic marker PPARγ in HT29 CC cells. Leptin, adiponectin and itaconate may represent a link between obesity and CC., Competing Interests: The authors declare no competing interests., (© 2023 The Authors.)

In civil society we expect that policy and management decisions will be made using the best available evidence. Yet, it is widely known that there are many barriers that limit the extent to which that occurs. One way to overcome these barriers is via robust, comprehensive, transparent and repeatable evidence syntheses (such as systematic reviews) that attempt to minimize various forms of bias to present a summary of existing knowledge for decision-making purposes. Relative to other disciplines (e.g., health care, education), such evidence-based decision-making remains relatively nascent for environment management despite major threats to humanity, such as the climate, pollution and biodiversity crises demonstrating that human well-being is inextricably linked to the biophysical environment. Fortunately, there are a growing number of environmental evidence syntheses being produced that can be used by decision makers. It is therefore an opportune time to reflect on the science and practice of evidence-based decision-making in environment management to understand the extent to which evidence syntheses are embraced and applied in practice. Here we outline a number of key questions related to the use of environmental evidence that need to be explored in an effort to enhance evidence-based decision-making. There is an urgent need for research involving methods from social science, behavioural sciences, and public policy to understand the basis for patterns and trends in environmental evidence use (or misuse or ignorance). There is also a need for those who commission and produce evidence syntheses, as well as the end users of these syntheses to reflect on their experiences and share them with the broader evidence-based practice community to identify needs and opportunities for advancing the entire process of evidence-based practice. It is our hope that the ideas shared here will serve as a roadmap for additional scholarship that will collectively enhance evidence-based decision-making and ultimately benefit the environment and humanity., Competing Interests: Competing interestsThe majority of authors are involved in some capacity with the Collaboration for Environmental Evidence. Several of the authors are on the editorial team for Environmental Evidence. Indeed, this paper is very much a product of the editorial board and is intended to signal our interest in receiving content related to the topic of this article., (© The Author(s) 2023.)

Performance thresholds are an important tool for determining successful conservation outcomes. They provide an objective means of defining good ecological condition and have been endorsed as an essential part of best practice in protected area (PA) management within the International Union for the Conservation of Nature Green List of Protected and Conserved Areas Standard. With a growing number of PAs attaining Green List status globally, thresholds developed by PAs on the Green List present an excellent resource with which to identify the attributes of well-defined performance thresholds. We examined 349 thresholds associated with PAs on the Green List to determine whether they were specific and measurable (i.e., factors recognized as essential for setting well-defined targets). We assessed whether thresholds were defined quantitatively and whether definitions included ambiguous terms (e.g., stable numbers). We identified six different ways thresholds were expressed and found that many thresholds were expressed as management objectives, rather than ecological condition thresholds, although this trend improved over time. Approximately one-half of the performance thresholds lacked the necessary specificity to delineate successful outcomes. Our results enabled us to develop a checklist of information required to set robust performance thresholds. Recommendations include that thresholds should be quantitatively defined, including quantitative estimates of the limits of acceptable change (LAC) around the target condition. To ensure transparency, a rationale and associated evidence should be provided to support the threshold and the LAC. When accompanied by a rationale and quantitative estimate of the current condition of the value, unambiguously defined thresholds with a quantitative LAC provide an objective means of demonstrating that successful conservation outcomes have been achieved. These recommendations will help conservation managers apply the Green List Standard and improve the measurement of conservation outcomes more broadly., (© 2022 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Blood neurofilament light chain (NFL) is proposed to serve as an estimate of disease severity in hospitalized patients with coronavirus disease 2019 (COVID-19). We show that NFL concentrations in plasma collected from 880 patients with COVID-19 within 5 days of hospital admission were elevated compared to controls. Higher plasma NFL associated with worse clinical outcomes including the need for mechanical ventilation, intensive care, prolonged hospitalization, and greater functional disability at discharge. No difference in the studied clinical outcomes between black/African American and white patients was found. Finally, vaccination associated with less disability at time of hospital discharge. In aggregate, our findings support the utility of measuring NFL shortly after hospital admission to estimate disease severity and show that race does not influence clinical outcomes caused by COVID-19 assuming equivalent access to care, and that vaccination may lessen the degree of COVID-19-caused disability., Competing Interests: B.O. has consulted for Biogen, MediciNova, Mitsubishi, Amylyx, and Tsumura. K.A.N. has performed consulting for Alector, AI Therapeutics, Biogen, MT Pharma, Avanir Pharmaceuticals, and Biohaven. J.B.H. is the CLIA director for the Lung Bioengineering facility at Mayo Clinic Florida campus, a non-Mayo corporation. Z.K.W. also serves as PI or Co-PI on Biohaven Pharmaceuticals, Inc. (BHV4157-206 and BHV3241-301), Neuraly, Inc. (NLY01-PD-1), and Vigil Neuroscience, Inc. (VGL101-01.001 and VGL101-01.002) grants; as well as a Co-PI of the Mayo Clinic APDA Center for Advanced Research and as an external advisory board member for the Vigil Neuroscience, Inc. L.P. is a consultant for Expansion Therapeutics. The other authors declare that they have no competing interests., (© 2022 The Author(s).)

Frontotemporal dementia and amyotrophic lateral sclerosis (FTD-ALS) are associated with both a repeat expansion in the C9orf72 gene and mutations in the TANK-binding kinase 1 ( TBK1 ) gene. We found that TBK1 is phosphorylated in response to C9orf72 poly(Gly-Ala) [poly(GA)] aggregation and sequestered into inclusions, which leads to a loss of TBK1 activity and contributes to neurodegeneration. When we reduced TBK1 activity using a TBK1-R228H (Arg 228 →His) mutation in mice, poly(GA)-induced phenotypes were exacerbated. These phenotypes included an increase in TAR DNA binding protein 43 (TDP-43) pathology and the accumulation of defective endosomes in poly(GA)-positive neurons. Inhibiting the endosomal pathway induced TDP-43 aggregation, which highlights the importance of this pathway and TBK1 activity in pathogenesis. This interplay between C9orf72 , TBK1 , and TDP-43 connects three different facets of FTD-ALS into one coherent pathway.

Frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP) is a neurodegenerative disease primarily affecting the frontal and/or temporal cortices. However, a growing body of evidence suggests that the cerebellum contributes to biochemical, cognitive, and behavioral changes in FTLD-TDP. To evaluate cerebellar TDP-43 expression and function in FTLD-TDP, we analyzed TDP-43 protein levels and the splicing of a TDP-43 target, STMN2, in the cerebellum of 95 FTLD-TDP cases and 25 non-neurological disease controls. Soluble TDP-43 was decreased in the cerebellum of FTLD-TDP cases but a concomitant increase in insoluble TDP-43 was not seen. Truncated STMN2 transcripts, an indicator of TDP-43 dysfunction, were elevated in the cerebellum of FTLD-TDP cases and inversely associated with TDP-43 levels. Additionally, lower cerebellar TDP-43 associated with a younger age at disease onset. We provide evidence of TDP-43 loss of function in the cerebellum in FTLD-TDP, supporting further investigation into this understudied brain region., (© 2022. The Author(s).)

Misfolding and aggregation of disease-specific proteins, resulting in the formation of filamentous cellular inclusions, is a hallmark of neurodegenerative disease with characteristic filament structures, or conformers, defining each proteinopathy. Here we show that a previously unsolved amyloid fibril composed of a 135 amino acid C-terminal fragment of TMEM106B is a common finding in distinct human neurodegenerative diseases, including cases characterized by abnormal aggregation of TDP-43, tau, or α-synuclein protein. A combination of cryoelectron microscopy and mass spectrometry was used to solve the structures of TMEM106B fibrils at a resolution of 2.7 Å from postmortem human brain tissue afflicted with frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP, n = 8), progressive supranuclear palsy (PSP, n = 2), or dementia with Lewy bodies (DLB, n = 1). The commonality of abundant amyloid fibrils composed of TMEM106B, a lysosomal/endosomal protein, to a broad range of debilitating human disorders indicates a shared fibrillization pathway that may initiate or accelerate neurodegeneration., Competing Interests: Declaration of interests The authors declare no competing interests., (Published by Elsevier Inc.)

Animals are constantly bombarded with stimuli, which presents a fundamental problem of sorting among pervasive uninformative stimuli and novel, possibly meaningful stimuli. We evaluated novelty detection behaviorally in honey bees as they position their antennae differentially in an air stream carrying familiar or novel odors. We then characterized neuronal responses to familiar and novel odors in the first synaptic integration center in the brain-the antennal lobes. We found that the neurons that exhibited stronger initial responses to the odor that was to be familiarized are the same units that later distinguish familiar and novel odors, independently of chemical identities. These units, including both tentative projection neurons and local neurons, showed a decreased response to the familiar odor but an increased response to the novel odor. Our results suggest that the antennal lobe may represent familiarity or novelty to an odor stimulus in addition to its chemical identity code. Therefore, the mechanisms for novelty detection may be present in early sensory processing, either as a result of local synaptic interaction or via feedback from higher brain centers., Competing Interests: The authors have declared that no competing interests exist.

Background: Along with the rising incidence of obesity, there has been an increase in patients diagnosed with early-onset colorectal cancer (<50 years old). In colorectal cancer, worse patient survival is associated with certain cytokine expression and downregulation of peroxisome proliferator activated receptor gamma expression. The effects of the obesity hormone leptin and macrophage-specific metabolite itaconate on these mechanisms are poorly understood. We investigated their impact on peroxisome proliferator activated receptor gamma and macrophage cytokine expression in vitro., Methods: M2-like macrophages were treated with either leptin, 4-octyl itaconate, or dimethyl itaconate in a dose- and time-dependent manner. Gene expression after treatment with 4 doses (D1-4) of each compound was analyzed at 4 time points (3, 6, 18, and 24 hours)., Results: Peroxisome proliferator activated receptor gamma was downregulated after 4-octyl itaconate treatment at 18 hours (FC -32.67, P ≤ .001). Interleukin-8 was upregulated after leptin and dimethyl itaconate treatment at 6 hours (FC 26.35 at D4, P ≤ .001, and FC 23.26 at D3, P = .006). Dimethyl itaconate upregulated IL-1β at 24 hours (FC 18.00 at D4, P ≤ .001). Tumor necrosis factor-α showed maximum downregulation after 4-octyl itaconate at 18 hours (FC -103.25 at D4, P ≤ .001)., Conclusions: Itaconate downregulates peroxisome proliferator activated receptor gamma as a tumor-suppressing factor and upregulates anti-inflammatory cytokines in M2-like macrophages. Itaconate provides a link between obesity and colorectal cancer and may be a key regulator in early-onset colorectal cancer., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Permanent protection of biodiversity on private lands is achieved through various mechanisms around the world. In Australia, conservation covenants are widely used to dedicate private lands to biodiversity conservation. The permanency of covenants necessitates similarly long-term commitment by landholders to meet and maintain the conservation obligations under the covenant. To better understand the effectiveness of conservation covenants as a tool for on-going environmental stewardship, we examined the relationship between landholders' initial motivations to covenant, their current perspectives on covenants and their management practices. We compared two groups of covenantors, those who initiated a covenant (original signees) and those who acquired a property with a covenant already in place (successive owners). We found the motivations and views of original signees and successive owners were similar overall, showing strong pro-environmental perspectives, and the majority of landholders were continuing to undertake management activities for the benefit of biodiversity. A small portion of respondents were dissatisfied with the covenant mechanism or covenant provider. This group tended to include successive owners and landholders who covenanted for regulatory reasons or financial incentives. Fewer dissatisfied landholders were actively managing the covenanted land compared to those who were satisfied. Considering the impending increase in successive owners as aging covenantors transfer ownership of their properties, the growing potential for covenants required under regulatory arrangements, and decreasing support within covenanting programs, this study identifies a risk that the satisfaction of landholders may decrease over time. Recognizing and addressing the challenges faced by landholders can bolster the commitment to covenant obligations and the longevity of covenants as a mechanism for positive conservation outcomes., (Copyright © 2021. Published by Elsevier Ltd.)

A hallmark pathological feature of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the depletion of RNA-binding protein TDP-43 from the nucleus of neurons in the brain and spinal cord 1 . A major function of TDP-43 is as a repressor of cryptic exon inclusion during RNA splicing 2-4 . Single nucleotide polymorphisms in UNC13A are among the strongest hits associated with FTD and ALS in human genome-wide association studies 5,6 , but how those variants increase risk for disease is unknown. Here we show that TDP-43 represses a cryptic exon-splicing event in UNC13A. Loss of TDP-43 from the nucleus in human brain, neuronal cell lines and motor neurons derived from induced pluripotent stem cells resulted in the inclusion of a cryptic exon in UNC13A mRNA and reduced UNC13A protein expression. The top variants associated with FTD or ALS risk in humans are located in the intron harbouring the cryptic exon, and we show that they increase UNC13A cryptic exon splicing in the face of TDP-43 dysfunction. Together, our data provide a direct functional link between one of the strongest genetic risk factors for FTD and ALS (UNC13A genetic variants), and loss of TDP-43 function., (© 2022. The Author(s).)

Individual variation in morphology, physiology, and behavior has been a topic of great interest in the biological sciences. While scientists realize the importance of understanding diversity in individual phenotypes, historically the "minority" results (i.e., outlier observations or rare events) of any given experiment have been dismissed from further analysis. We need to reframe how we view "outliers" to improve our understanding of biology. These rare events are often treated as problematic or spurious, when they can be real rare events or individuals driving evolution in a population. It is our perspective that to understand what outliers can tell us in our data, we need to: (1) Change how we think about our data philosophically, (2) Fund novel collaborations using science "weavers" in our national funding agencies, and (3) Bridge long-term field and lab studies to reveal these outliers in action. By doing so, we will improve our understanding of variation and evolution. We propose that this shift in culture towards more integrative science will incorporate diverse teams, citizen scientists and local naturalists, and change how we teach future students., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.)

Successful, state-dependent management, in which the goal of management is to maintain a system in a desired state, involves defining the boundaries between different states. Once these boundaries have been defined, managers require a strategic action plan with thresholds that initiate management interventions to either maintain or return the system to a desired state. This approach to management is widely used across diverse industries from agriculture, to medicine, to information technology, but it has only been adopted in conservation management relatively recently. Conservation practitioners have expressed a willingness to integrate this structured approach in their management systems, but they have also voiced concerns, including lack of a robust process for doing so. Given the widespread use of state-dependent management in other fields, we conducted an extensive review of the literature on threshold-based management to gain insight into how and where it is applied and identify potential lessons for conservation management. We identified 22 industries using 75 different methods for setting management thresholds in 843 studies. Methods spanned six broad approaches, including expert driven, statistical, predictive, optimization, experimental, and artificial intelligence methods. The objectives of each of these studies influenced the approaches used, including the methods for setting thresholds and selecting actions, and the number of thresholds set. The role of value judgments in setting thresholds was clear; studies across all industries frequently involved experts in setting thresholds, often accompanied by computational tools to simulate the consequences of proposed thresholds under different conditions. Of the 30 conservation studies examined, two-thirds used expert-driven methods, consistent with prior evidence that experience-based information often drives conservation management decisions. The methods we identified from other disciplines could help conservation decision makers set thresholds for management interventions in different contexts, linking monitoring to management actions and ensuring that conservation interventions are timely and effective., (© 2021 Society for Conservation Biology.)

The aberrant translation of a repeat expansion in chromosome 9 open reading frame 72 ( C9orf72 ), the most common cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), results in the accumulation of toxic dipeptide repeat (DPR) proteins in the central nervous system We have found that, among the sense DPR proteins, HDAC6 specifically interacts with the poly (GA) and co-localizes with inclusions in both patient tissue and a mouse model of this disease (c9FTD/ALS). Overexpression of HDAC6 increased poly (GA) levels in cultured cells independently of HDAC6 deacetylase activity, suggesting that HDAC6 can modulate poly (GA) pathology through a mechanism that depends upon their physical interaction. Moreover, decreasing HDAC6 expression by stereotaxic injection of antisense oligonucleotides significantly reduced the number of poly (GA) inclusions in c9FTD/ALS mice. These findings suggest that pharmacologically reducing HDAC6 levels could be of therapeutic value in c9FTD/ALS., Competing Interests: Authors KL and FR were employed by Ionis Pharmaceuticals. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 del Rosso, Carlomagno, Todd, Jones, Prudencio, Daughrity, Yue, Jansen-West, Tong, Shao, Wu, Castanedes-Casey, Tabassian, Oskarsson, Ling, Rigo, Dickson, Yao, Petrucelli, Cook and Zhang.)

Brain imaging studies of patients with COVID-19 show evidence of macro- and microhemorrhagic lesions, multifocal white matter hyperintensities, and lesions consistent with posterior reversible leukoencephalopathy. Imaging studies, however, are subject to selection bias, and prospective studies are challenging to scale. Here, we evaluated whether serum neurofilament light chain (NFL), a neuroaxonal injury marker, could predict the extent of neuronal damage in a cohort of 142 hospitalized patients with COVID-19. NFL was elevated in the serum of patients with COVID-19 compared to healthy controls, including those without overt neurological manifestations. Higher NFL serum concentrations were associated with worse clinical outcomes. In 100 hospitalized patients with COVID-19 treated with remdesivir, a trend toward lower NFL serum concentrations was observed. These data suggest that patients with COVID-19 may experience neuroaxonal injury and may be at risk for long-term neurological sequelae. Neuroaxonal injury should be considered as an outcome in acute pharmacotherapeutic trials for COVID-19., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).)

There is an imperative for conservation practitioners to help biodiversity adapt to accelerating environmental change. Evolutionary biologists are well-positioned to inform the development of evidence-based management strategies that support the adaptive capacity of species and ecosystems. Conservation practitioners increasingly accept that management practices must accommodate rapid environmental change, but harbour concerns about how to apply recommended changes to their management contexts. Given the interest from both conservation practitioners and evolutionary biologists in adjusting management practices, we believe there is an opportunity to accelerate the required changes by promoting closer collaboration between these two groups. We highlight how evolutionary biologists can harness lessons from other disciplines about how to foster effective knowledge exchange to make a substantive contribution to the development of effective conservation practices. These lessons include the following: (1) recognizing why practitioners do and do not use scientific evidence; (2) building an evidence base that will influence management decisions; (3) translating theory into a format that conservation practitioners can use to inform management practices; and (4) developing strategies for effective knowledge exchange. Although efforts will be required on both sides, we believe there are rewards for both practitioners and evolutionary biologists, not least of which is fostering practices to help support the long-term persistence of species., Competing Interests: None declared., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Learning and attention allow animals to better navigate complex environments. While foraging, honey bees ( Apis mellifera L.) learn several aspects of their foraging environment, such as color and odor of flowers, which likely begins to happen before they evaluate the quality of the food. If bees begin to evaluate quality before they taste food, and then learn the food is depleted, this may create a conflict in what the bee learns and remembers. Individual honey bees differ in their sensitivity to information, thus creating variation in how they learn or do not learn certain environmental stimuli. For example, foraging honey bees exhibit differences in latent inhibition (LI), a learning process through which regular encounter with a stimulus without a consequence such as food can later reduce conditioning to that stimulus. Here, we test whether bees from distinct selected LI genotypes learn differently if reinforced via just antennae or via both antennae + proboscis. We also evaluate whether learned information goes extinct at different rates in these distinct LI genetic lines. We find that high LI bees learned significantly better when they were reinforced both antenna + proboscis, while low LI and control bees learned similarly with the two reinforcement pathways. We also find no differences in the acquisition and extinction of learned information in high LI and low LI bees. Our work provides insight into how underlying cognition may influence how honey bees learn and value information, which may lead to differences in how individuals and colonies make foraging decisions., (© The Author(s) 2021. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)