A Fiji protocol for analyzing puncta is a robust tool for measuring GLR-1::GFP accumulation in the ventral nerve cord of C. elegans.

In C. elegans, DAF-7/TGF-beta signaling regulates development, metabolism, and behavior. In addition loss of daf-7 leads to an increase of the glutamate receptor GLR-1. In daf-7(e1372) mutants, GLR-1 tagged with GFP (GLR-1::GFP) accumulates in wide puncta along the ventral nerve cord of the animal. Previous automated analyses of GLR-1::GFP accumulation relied on the proprietary software, IgorPro, for measurement of GLR-1::GFP puncta size, intensity, and density. We did a side-by-side comparison of analyses by IgorPro and an open source macro written for Fiji to analyze images from animals expressing GLR-1::GFP in wild type and daf-7(e1372) backgrounds. Analyses by the two programs were in strong agreement and are in accordance with previously published data on the effects of daf-7(e1372) on GLR-1::GFP accumulation. Based on these data, we conclude that the Fiji platform is a robust method for analyzing the accumulation of a fluorescently-tagged neurotransmitter receptor and that the Fiji puncta plugin will be applicable for image analysis for other neural markers.

Comparison and agreement between two image analysis tools for quantifying GFP::SNB-1 puncta in fshr-1 mutants of C. elegans.

Quantitative imaging of synaptic vesicle localization and abundance using fluorescently labeled synaptic vesicle associated proteins like GFP::SNB-1 is a well-established method for measuring changes in synapse structure at neuromuscular junctions (NMJ) in C. elegans . To date, however, the ability to easily and reproducibly measure key parameters at the NMJ - maximum intensity, size of GFP::SNB-1 puncta, density of puncta - has relied on the use of expensive, customizable software that requires coding skills to modify, precluding widespread access and thus preventing standardization within the field. We carried out a comparative evaluation of a new, open-source Fiji puncta plugin versus traditional Igor-based analysis of GFP::SNB-1 imaging data taken of cholinergic motor neurons in the dorsal nerve cord of loss of function mutants in fshr-1 , which encodes a G protein-coupled receptor known to impact GFP::SNB-1 accumulation. We analyzed images taken on a widefield fluorescence microscope, as well as on a spinning disk confocal microscope. Our data demonstrate strong concordance between the differences in GFP::SNB-1 localization in fshr-1 mutants compared to wild type worms across both analysis platforms (Fiji and Igor), as well as across microscope types (widefield and confocal). These data also agree with previously published observations related to synapse number and GFP::SNB-1 intensity in fshr-1 and wild type worms. Based on these findings, we conclude that the Fiji platform is viable as a method for analyzing synaptic vesicle localization and abundance at cholinergic dorsal nerve cord motor NMJs and expect the Fiji puncta plugin to be of broad utility in imaging across a variety of imaging platforms and synaptic markers.

A Fiji process for quantifying fluorescent puncta in linear cellular structures.

Understanding the cell biology of protein trafficking and homeostasis requires reproducible methods for identifying and quantifying proteins within cells or cellular structures. Imaging protocols for measuring punctate protein accumulation in linear structures, for example the neurites of C. elegans, have relied on proprietary software for a full range of analysis capabilities. Here we describe a set of macros written for the NIH-supported imaging software ImageJ or Fiji (Fiji is Just ImageJ) that reliably identify protein puncta so that they can be analyzed with respect to intensity, density, and width at half-maximum intensity (Full-Width, Half-Maximum, FWHM). We provide an explanation of the workflow, data outputs, and limitations of the Fiji macro. As part of this integration, we also provide two independent data sets with side-by-side analyses using the proprietary IgorPro software and the Fiji macro (Hulsey-Vincent, et al. A, B., 2023 submitted). The Fiji macro is an important new tool because it provides robust, reproducible data analysis in a free, open-source format.

Repetition Is Important to Students and Their Understanding during Laboratory Courses That Include Research.

Course-based undergraduate research experiences (CUREs) provide students with opportunities for the same gains that apprenticed research with faculty members offers. As their popularity increases, it is important that critical elements of CUREs be supported by thoughtful design. Student experiences in CUREs can provide important insights into why CUREs are so effective. We present evidence from students who participated in CUREs at the introductory, intermediate, and advanced levels, as well as from graduate teaching assistants for an introductory lab course that included a CURE. Students and teaching assistants describe repetition as a valuable element in CUREs and other laboratory experiences. We used student work and open-ended interviews to identify which of five previously described elements of CUREs students found important. Because repetition was particularly salient, we characterized how students described repetition as they experienced it in courses that contained full-length CUREs or "micro-CUREs." In prompted interviews, students described how repetition in CUREs provided cognitive (learning concepts) and practical (learning technical skills) value. Recent graduates who had participated in CUREs at each level of their biology education were particularly aware that they placed value on repetition and acknowledged it as motivational in their own learning. Many students described repetition in metacognitive terms, which also suggests that as students advance through laboratory and CURE curricula, their understanding of how repetition supports their learning becomes more sophisticated. Finally, we integrated student descriptions to suggest ways in which repetition can be designed into CUREs or other laboratory courses to support scientific learning and enhance students' sense of scientific identity.

Building a laboratory at a Primarily Undergraduate Institution (PUI).

Scientists who are interested in building research programs at primarily-undergraduate institutions (PUIs) have unique considerations compared to colleagues at research-intensive (R1) institutions. Maintaining a research program at a PUI holds unique challenges that should be considered before prospective faculty go on the job market, as they negotiate a job offer, and after they begin a new position. In this article we describe some of the considerations that aspiring and newly hired faculty should keep in mind as they plan out how they will set up a laboratory as a new Principle Investigator (PI) at a PUI.Anyone hoping to start a research program at a PUI should understand both the timeframe of interviews, job offers, and negotiations and the challenges and rewards of working with undergraduate researchers. Once a job is offered, candidates should be aware of the range of negotiable terms that can be part of a start-up package. Space and equipment considerations are also important, and making the most of shared spaces, existing infrastructure, and deals can extend the purchasing power of start-up funds as a new PIs builds their lab. PUIs' focus on undergraduate education and mentorship leads to important opportunities for collaboration, funding, and bringing research projects directly into undergraduate teaching laboratories.A major focus of any new laboratory leader must be on building a productive, equitable, and supportive laboratory community. Equitable onboarding, mentorship plans, and formalized expectations, can all help build a productive and sustainable laboratory research program. However, important considerations about safety, inclusion, student schedules, and a PI's own professional commitments are also extremely important concerns when working with undergraduates in research. A successful research program at a PUI will bring students into meaningful scientific inquiry and requires insights and skills that are often not the focus of scientific training. This article aims to describe the scope of setting up a new laboratory as a way to alleviate some of the burden that new and prospective faculty often feel.

Obtaining a faculty position at a primarily undergraduate institution (PUI).

Scientists who hope to obtain a faculty position at a primarily undergraduate institution (PUI) need a distinct skill set and outlook on their future teaching and research career. To obtain a position at a PUI, candidates should 1) design a strategy for obtaining a faculty position that suits each individual's career goals and aspirations, 2) prepare for the application process, on-campus interview, and contract negotiations, and 3) plan a strategy for the probationary period leading up to tenure and promotion. Given the different types of PUIs, candidates need to consider whether they seek a position that consists of all or mostly all teaching, or both teaching and research. Candidates should educate themselves on the expectations at PUI's, including current thought, practice, and aspirations for science pedagogy, and gain teaching experience prior to seeking a suitable position. If the candidate's goal is a position with both teaching and research, it is important to discuss with the current research mentor what projects the candidate can take with them to their new position. The candidate should also consider what types of projects will be successful with undergraduate student researchers in a PUI research environment. Importantly, candidates should clearly demonstrate a commitment to diversity and inclusion in their teaching, research, and outreach, and application materials should demonstrate this. On interviews, candidates should be knowledgeable about the mission, values, and resources of the institution and how the candidate will contribute to that mission. Once hired, new faculty should discuss a formal or informal mentoring plan during the probationary period that includes peer evaluations on a regular basis, and maintain communication with the department chair or designated mentor regarding teaching, research, and service activities.

Student Annotations of Published Data as a Collaboration between an Online Laboratory Course and the C. elegans Database, WormBase.

Course-based undergraduate research experiences (CUREs) provide the same benefits as individual, mentored faculty research while expanding the availability of research opportunities. One important aspect of CUREs is students' engagement in collaboration. The shift to online learning during the COVID-19 pandemic created an immediate need for meaningful, collaborative experiences in CUREs. We developed a partnership with the Caenorhabditis elegans (C. elegans) database, WormBase, in which students submitted annotations of published manuscripts to the website. Due to the stress on students during this time of crisis, qualitative data were collected in lieu of quantitative pre- and postanalyses. Most students reported on cognitive processes that represent mid-level Bloom's categories. By partnering with WormBase, students gained insight into the scientific community and contributed as community members. We describe possible modifications for future courses, potential expansion of the WormBase collaboration, and future directions for quantitative analysis.

The WD40-Repeat Protein WDR-20 and the Deubiquitinating Enzyme USP-46 Promote Cell Surface Levels of Glutamate Receptors.

Reversible modification of AMPA receptors (AMPARs) with ubiquitin regulates receptor levels at synapses and controls synaptic strength. The conserved deubiquitinating enzyme (DUB) ubiquitin-specific protease-46 (USP-46) removes ubiquitin from AMPARs and protects them from degradation in both Caenorhabditis elegans and mammals. Although DUBs are critical for diverse physiological processes, the mechanisms that regulate DUBs, especially in the nervous system, are not well understood. We and others previously showed that the WD40-repeat proteins WDR-48 and WDR-20 bind to and stimulate the catalytic activity of USP-46. Here, we identify an activity-dependent mechanism that regulates WDR-20 expression and show that WDR-20 works together with USP-46 and WDR-48 to promote surface levels of the C. elegans AMPAR GLR-1. usp-46, wdr-48, and wdr-20 loss-of-function mutants exhibit reduced levels of GLR-1 at the neuronal surface and corresponding defects in GLR-1-mediated behavior. Increased expression of WDR-20, but not WDR-48, is sufficient to increase GLR-1 surface levels in an usp-46-dependent manner. Loss of usp-46, wdr-48, and wdr-20 function reduces the rate of local GLR-1 insertion in neurites, whereas overexpression of wdr-20 is sufficient to increase the rate of GLR-1 insertion. Genetic manipulations that chronically reduce or increase glutamate signaling result in reciprocal alterations in wdr-20 transcription and homeostatic compensatory changes in surface GLR-1 levels that are dependent on wdr-20 This study identifies wdr-20 as a novel activity-regulated gene that couples chronic changes in synaptic activity with increased local insertion and surface levels of GLR-1 via the DUB USP-46.SIGNIFICANCE STATEMENT Deubiquitinating enzymes (DUBs) are critical regulators of synapse development and function; however, the regulatory mechanisms that control their various physiological functions are not well understood. This study identifies a novel role for the DUB ubiquitin-specific protease-46 (USP-46) and its associated regulatory protein WD40-repeat protein-20 (WDR-20) in regulating local insertion of glutamate receptors into the neuronal cell surface. This work also identifies WDR-20 as an activity-regulated gene that couples chronic changes in synaptic activity with homeostatic compensatory increases in surface levels of GLR-1 via USP-46. Given that 35% of USP family DUBs associate with WDR proteins, understanding the mechanisms by which WDR proteins regulate USP-46 could have implications for a large number of DUBs in other cell types.

The WD40-repeat protein WDR-48 promotes the stability of the deubiquitinating enzyme USP-46 by inhibiting its ubiquitination and degradation.

Ubiquitination is a reversible post-translational modification that has emerged as a critical regulator of synapse development and function. However, the mechanisms that regulate the deubiquitinating enzymes (DUBs) responsible for the removal of ubiquitin from target proteins are poorly understood. We have previously shown that the DUB ubiquitin-specific protease 46 (USP-46) removes ubiquitin from the glutamate receptor GLR-1 and regulates its trafficking and degradation in Caenorhabditis elegans We found that the WD40-repeat proteins WDR-20 and WDR-48 bind and stimulate the catalytic activity of USP-46. Here, we identified another mechanism by which WDR-48 regulates USP-46. We found that increased expression of WDR-48, but not WDR-20, promotes USP-46 abundance in mammalian cells in culture and in C. elegans neurons in vivo Inhibition of the proteasome increased USP-46 abundance, and this effect was nonadditive with increased WDR-48 expression. We found that USP-46 is ubiquitinated and that expression of WDR-48 reduces the levels of ubiquitin-USP-46 conjugates and increases the t1/2 of USP-46. A point-mutated WDR-48 variant that disrupts binding to USP-46 was unable to promote USP-46 abundance in vivo Finally, siRNA-mediated knockdown of wdr48 destabilizes USP46 in mammalian cells. Together, these results support a model in which WDR-48 binds and stabilizes USP-46 protein levels by preventing the ubiquitination and degradation of USP-46 in the proteasome. Given that a large number of USPs interact with WDR proteins, we propose that stabilization of DUBs by their interacting WDR proteins may be a conserved and widely used mechanism that controls DUB availability and function.

Function of the Deubiquitinating Enzyme USP46 in the Nervous System and Its Regulation by WD40-Repeat Proteins.

Posttranslational modification of proteins by ubiquitin regulates synapse development and synaptic transmission. Much progress has been made investigating the role of ubiquitin ligases at the synapse, however very little is known about the deubiquitinating enzymes (DUBs) which remove ubiquitin from target proteins. Although there are far fewer DUBs than ubiquitin ligases encoded by the human genome, it is becoming clear that DUBs have very specific physiological functions, suggesting that DUB activity is tightly regulated in vivo. Many DUBs function as part of larger protein complexes, and multiple regulatory mechanisms exist to control the expression, localization and catalytic activity of DUBs. In this review article, we focus on the role of the DUB USP46 in the nervous system, and illustrate potential mechanisms of regulating DUBs by describing how USP46 is regulated by two WD40-repeat (WDR) proteins, WDR48/UAF1 and WDR20, based on recent structural studies and genetic analyses in vivo.

The CaM Kinase CMK-1 Mediates a Negative Feedback Mechanism Coupling the C. elegans Glutamate Receptor GLR-1 with Its Own Transcription.

Regulation of synaptic AMPA receptor levels is a major mechanism underlying homeostatic synaptic scaling. While in vitro studies have implicated several molecules in synaptic scaling, the in vivo mechanisms linking chronic changes in synaptic activity to alterations in AMPA receptor expression are not well understood. Here we use a genetic approach in C. elegans to dissect a negative feedback pathway coupling levels of the AMPA receptor GLR-1 with its own transcription. GLR-1 trafficking mutants with decreased synaptic receptors in the ventral nerve cord (VNC) exhibit compensatory increases in glr-1 mRNA, which can be attributed to increased glr-1 transcription. Glutamatergic transmission mutants lacking presynaptic eat-4/VGLUT or postsynaptic glr-1, exhibit compensatory increases in glr-1 transcription, suggesting that loss of GLR-1 activity is sufficient to trigger the feedback pathway. Direct and specific inhibition of GLR-1-expressing neurons using a chemical genetic silencing approach also results in increased glr-1 transcription. Conversely, expression of a constitutively active version of GLR-1 results in decreased glr-1 transcription, suggesting that bidirectional changes in GLR-1 signaling results in reciprocal alterations in glr-1 transcription. We identify the CMK-1/CaMK signaling axis as a mediator of the glr-1 transcriptional feedback mechanism. Loss-of-function mutations in the upstream kinase ckk-1/CaMKK, the CaM kinase cmk-1/CaMK, or a downstream transcription factor crh-1/CREB, result in increased glr-1 transcription, suggesting that the CMK-1 signaling pathway functions to repress glr-1 transcription. Genetic double mutant analyses suggest that CMK-1 signaling is required for the glr-1 transcriptional feedback pathway. Furthermore, alterations in GLR-1 signaling that trigger the feedback mechanism also regulate the nucleocytoplasmic distribution of CMK-1, and activated, nuclear-localized CMK-1 blocks the feedback pathway. We propose a model in which synaptic activity regulates the nuclear localization of CMK-1 to mediate a negative feedback mechanism coupling GLR-1 activity with its own transcription.

Effect of helix length on the stability of the Lac repressor antiparallel coiled coil.

The helix length dependence of the stability of antiparallel four-chain coiled coils is investigated using eight synthetic peptides (Lac21-Lac28) whose sequences are derived from the tetramerization domain of the Lac repressor protein. Previous studies using analytical ultracentrifugation sedimentation equilibrium experiments to characterize Lac21 and Lac28 justifies the use of a two state model to describe the unfolding behavior of these two peptides. Using circular dichroism spectropolarimetry as a measure of tetramer assembly, both chemical and thermal denaturation experiments were carried out to determine thermodynamic parameters. We found that the hydrophobic core residues provide the greatest impact on stability and, as a consequence, must reorganize the register of the antiparallel helices to accommodate the burial of the nonpolar amino acids. Addition of noncore residues appears to have only a minor effect on stability, and in some cases, show a slight destabilization.

The WD40-repeat proteins WDR-20 and WDR-48 bind and activate the deubiquitinating enzyme USP-46 to promote the abundance of the glutamate receptor GLR-1 in the ventral nerve cord of Caenorhabditis elegans.

Ubiquitin-mediated endocytosis and degradation of glutamate receptors controls their synaptic abundance and is implicated in modulating synaptic strength. The deubiquitinating enzymes (DUBs) that function in the nervous system are beginning to be defined, but the mechanisms that control DUB activity in vivo are understood poorly. We found previously that the DUB USP-46 deubiquitinates the Caenorhabditis elegans glutamate receptor GLR-1 and prevents its degradation in the lysosome. The WD40-repeat (WDR) proteins WDR20 and WDR48/UAF1 have been shown to bind to USP46 and stimulate its catalytic activity in other systems. Here we identify the C. elegans homologs of these WDR proteins and show that C. elegans WDR-20 and WDR-48 can bind and stimulate USP-46 catalytic activity in vitro. Overexpression of these activator proteins in vivo increases the abundance of GLR-1 in the ventral nerve cord, and this effect is further enhanced by coexpression of USP-46. Biochemical characterization indicates that this increase in GLR-1 abundance correlates with decreased levels of ubiquitin-GLR-1 conjugates, suggesting that WDR-20, WDR-48, and USP-46 function together to deubiquitinate and stabilize GLR-1 in neurons. Overexpression of WDR-20 and WDR-48 results in alterations in locomotion behavior consistent with increased glutamatergic signaling, and this effect is blocked in usp-46 loss-of-function mutants. Conversely, wdr-20 and wdr-48 loss-of-function mutants exhibit changes in locomotion behavior that are consistent with decreased glutamatergic signaling. We propose that WDR-20 and WDR-48 form a complex with USP-46 and stimulate the DUB to deubiquitinate and stabilize GLR-1 in vivo.

Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis.

OBJECTIVE: Several studies have suggested an increased frequency of variants in the gene encoding angiogenin (ANG) in patients with amyotrophic lateral sclerosis (ALS). Interestingly, a few ALS patients carrying ANG variants also showed signs of Parkinson disease (PD). Furthermore, relatives of ALS patients have an increased risk to develop PD, and the prevalence of concomitant motor neuron disease in PD is higher than expected based on chance occurrence. We therefore investigated whether ANG variants could predispose to both ALS and PD. METHODS: We reviewed all previous studies on ANG in ALS and performed sequence experiments on additional samples, which allowed us to analyze data from 6,471 ALS patients and 7,668 controls from 15 centers (13 from Europe and 2 from the USA). We sequenced DNA samples from 3,146 PD patients from 6 centers (5 from Europe and 1 from the USA). Statistical analysis was performed using the variable threshold test, and the Mantel-Haenszel procedure was used to estimate odds ratios. RESULTS: Analysis of sequence data from 17,258 individuals demonstrated a significantly higher frequency of ANG variants in both ALS and PD patients compared to control subjects (p = 9.3 × 10(-6) for ALS and p = 4.3 × 10(-5) for PD). The odds ratio for any ANG variant in patients versus controls was 9.2 for ALS and 6.7 for PD. INTERPRETATION: The data from this multicenter study demonstrate that there is a strong association between PD, ALS, and ANG variants. ANG is a genetic link between ALS and PD.

The deubiquitinating enzyme USP-46 negatively regulates the degradation of glutamate receptors to control their abundance in the ventral nerve cord of Caenorhabditis elegans.

Ubiquitin-mediated endocytosis and post-endocytic trafficking of glutamate receptors control their synaptic abundance and are implicated in modulating synaptic strength. Ubiquitination is a reversible modification, but the identities and specific functions of deubiquitinating enzymes in the nervous system are lacking. Here, we show that the deubiquitinating enzyme ubiquitin-specific protease-46 (USP-46) regulates the abundance of the glutamate receptor GLR-1 in the ventral nerve cord of Caenorhabditis elegans. Mutants lacking usp-46 have decreased GLR-1 in the ventral nerve cord and corresponding defects in GLR-1-dependent behaviors. The amount of ubiquitinated GLR-1 is increased in usp-46 mutants. Mutations that block GLR-1 ubiquitination or receptor degradation in the multi-vesicular body/lysosome prevent the decrease in GLR-1 observed in usp-46 mutants. These data support a model in which USP-46 promotes GLR-1 abundance at synapses by deubiquitinating GLR-1 and preventing its degradation in the lysosome. This work suggests that the balance between the addition and removal of ubiquitin is important for glutamate receptor trafficking.

Large-scale SOD1 mutation screening provides evidence for genetic heterogeneity in amyotrophic lateral sclerosis.

OBJECTIVE: To estimate the frequency of SOD1 mutations in a large referral cohort of familial amyotrophic lateral sclerosis (FALS) and sporadic amyotrophic lateral sclerosis (SALS) patients from The Netherlands and to compare this frequency with that of other developed countries. METHODS: A total of 451 sporadic and 55 FALS patients were screened for SOD1 mutations. The authors performed PCR amplification of all five coding exons of SOD1 followed by direct DNA sequencing using forward and reverse primers. RESULTS: One novel mutation (p.I99V) and a homozygous p.D90A mutation were identified in SALS patients. In a pedigree with Mendelian dominant FALS, one patient was found to be heterozygous for the p.D90A mutation. SOD1 mutation frequency was found to be significantly lower in The Netherlands compared with other countries with p=0.0004 for FALS (21.9% vs 2.5%) and p=0.005 for SALS (2.5% vs 0.44%). CONCLUSIONS: The authors demonstrate that SOD1 mutations are rare in The Netherlands in familial and SALS. This observation suggests that the genetic background of amyotrophic lateral sclerosis differs between different populations, countries and regions. This may have consequences for the interpretation of association studies and explain why replication of association studies has proven difficult in amyotrophic lateral sclerosis.

Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis.

We conducted a genome-wide association study among 2,323 individuals with sporadic amyotrophic lateral sclerosis (ALS) and 9,013 control subjects and evaluated all SNPs with P < 1.0 x 10(-4) in a second, independent cohort of 2,532 affected individuals and 5,940 controls. Analysis of the genome-wide data revealed genome-wide significance for one SNP, rs12608932, with P = 1.30 x 10(-9). This SNP showed robust replication in the second cohort (P = 1.86 x 10(-6)), and a combined analysis over the two stages yielded P = 2.53 x 10(-14). The rs12608932 SNP is located at 19p13.3 and maps to a haplotype block within the boundaries of UNC13A, which regulates the release of neurotransmitters such as glutamate at neuromuscular synapses. Follow-up of additional SNPs showed genome-wide significance for two further SNPs (rs2814707, with P = 7.45 x 10(-9), and rs3849942, with P = 1.01 x 10(-8)) in the combined analysis of both stages. These SNPs are located at chromosome 9p21.2, in a linkage region for familial ALS with frontotemporal dementia found previously in several large pedigrees.