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OBECTIVES: To examine magnetic resonance imaging-transrectal ultrasound (MRI-TRUS) fusion biopsies completed within Manitoba and evaluate their ability in detecting clinically significant prostate cancer. PATIENTS & METHODS: 200 cases from October 2021 and May 2022 that met the inclusion criteria were reviewed. Clinical and pathologic information was collected for each case. The cancer detection rate (CDR) and clinically significant CDR were calculated for systematic and targeted prostate biopsy cores for patients that underwent MRIs at Health Sciences Centre (HSC) or St. Boniface General Hospital (SBGH). Clinically significant prostate cancer was set as all cancers with a Gleason score ≥4+3/Grade Group ≥3 or Gleason score 3+4/Grade Group 2 with cribriform and/or intraductal carcinoma present. RESULTS: The overall CDR including both systematic and targeted biopsy cores was determined to be 75.0%, with an overall CDR for targeted biopsies of 70.5%. The targeted biopsy cores had an overall clinically significant CDR of 34.0%. Prostate cancer was detected in only the targeted biopsies in 38 of the 200 cases, with clinically significant prostate cancer detected in 12 of those cases compared to 9 cases that detected cancer in the systematic biopsies only, 3 of which were clinically significant. When stratified by MRI site, SBGH had a higher targeted biopsy CDR (76.1%) and clinically significant targeted biopsy CDR (35.1%) compared to HSC (59.1% and 31.8%). Nine of the 18 radical prostatectomies had no cancer detected in the systematic biopsies. CONCLUSIONS: This study has established that MRI-TRUS fusion biopsies are effective in detecting additional clinically significant prostate adenocarcinomas in Manitoba.

We describe a set of network analysis methods based on the rows of the Krylov subspace matrix computed from a network adjacency matrix via power iteration using a non-random initial vector. We refer to these node-specific row vectors as Krylov subspace trajectories. While power iteration using a random initial starting vector is commonly applied to the network adjacency matrix to compute eigenvector centrality values, this application only uses the final vector generated after numerical convergence. Importantly, use of a random initial vector means that the intermediate results of power iteration are also random and lack a clear interpretation. To the best of our knowledge, use of intermediate power iteration results for network analysis has been limited to techniques that leverage just a single pre-convergence solution, e.g., Power Iteration Clustering. In this paper, we explore methods that apply power iteration with a non-random inital vector to the network adjacency matrix to generate Krylov subspace trajectories for each node. These non-random trajectories provide important information regarding network structure, node importance, and response to perturbations. We have created this short preprint in part to generate feedback from others in the network analysis community who might be aware of similar existing work.

Recessive gene mutations underlie many developmental disorders and often lead to disabling neurological problems. Here, we report identification of a homozygous c.170G>A (p.Cys57Tyr or C57Y) mutation in the gene coding for protein disulfide isomerase A3 (PDIA3, also known as ERp57), an enzyme that catalyzes formation of disulfide bonds in the endoplasmic reticulum, to be associated with syndromic intellectual disability. Experiments in zebrafish embryos show that PDIA3C57Y expression is pathogenic and causes developmental defects such as axonal disorganization as well as skeletal abnormalities. Expression of PDIA3C57Y in the mouse hippocampus results in impaired synaptic plasticity and memory consolidation. Proteomic and functional analyses reveal that PDIA3C57Y expression leads to dysregulation of cell adhesion and actin cytoskeleton dynamics, associated with altered integrin biogenesis and reduced neuritogenesis. Biochemical studies show that PDIA3C57Y has decreased catalytic activity and forms disulfide-crosslinked aggregates that abnormally interact with chaperones in the endoplasmic reticulum. Thus, rare disease gene variant can provide insight into how perturbations of neuronal proteostasis can affect the function of the nervous system.

We describe a family of iterative algorithms that involve the repeated execution of discrete and inverse discrete Fourier transforms. One interesting member of this family is motivated by the discrete Fourier transform uncertainty principle and involves the application of a sparsification operation to both the real domain and frequency domain data with convergence obtained when real domain sparsity hits a stable pattern. This sparsification variant has practical utility for signal denoising, in particular the recovery of a periodic spike signal in the presence of Gaussian noise. General convergence properties and denoising performance relative to existing methods are demonstrated using simulation studies. An R package implementing this technique and related resources can be found at https://hrfrost.host.dartmouth.edu/IterativeFT.

Cell identity is characterized by a distinct combination of gene expression, cell morphology, and cellular function established as progenitor cells divide and differentiate. Following establishment, cell identities can be unstable and require active and continuous maintenance throughout the remaining life of a cell. Mechanisms underlying the maintenance of cell identities are incompletely understood. Here, we show that the gene ctbp-1, which encodes the transcriptional corepressor C-terminal binding protein-1 (CTBP-1), is essential for the maintenance of the identities of the two AIA interneurons in the nematode Caenorhabditis elegans. ctbp-1 is not required for the establishment of the AIA cell fate but rather functions cell-autonomously and can act in later larval stage and adult worms to maintain proper AIA gene expression, morphology and function. From a screen for suppressors of the ctbp-1 mutant phenotype, we identified the gene egl-13, which encodes a SOX family transcription factor. We found that egl-13 regulates AIA function and aspects of AIA gene expression, but not AIA morphology. We conclude that the CTBP-1 protein maintains AIA cell identity in part by utilizing EGL-13 to repress transcriptional activity in the AIAs. More generally, we propose that transcriptional corepressors like CTBP-1 might be critical factors in the maintenance of cell identities, harnessing the DNA-binding specificity of transcription factors like EGL-13 to selectively regulate gene expression in a cell-specific manner.

We present a novel approach for computing a variant of eigenvector centrality for multilayer networks with inter-layer constraints on node importance. Specifically, we consider a multilayer network defined by multiple edge-weighted, potentially directed, graphs over the same set of nodes with each graph representing one layer of the network and no inter-layer edges. As in the standard eigenvector centrality construction, the importance of each node in a given layer is based on the weighted sum of the importance of adjacent nodes in that same layer. Unlike standard eigenvector centrality, we assume that the adjacency relationship and the importance of adjacent nodes may be based on distinct layers. Importantly, this type of centrality constraint is only partially supported by existing frameworks for multilayer eigenvector centrality that use edges between nodes in different layers to capture inter-layer dependencies. For our model, constrained, layer-specific eigenvector centrality values are defined by a system of independent eigenvalue problems and dependent pseudo-eigenvalue problems, whose solution can be efficiently realized using an interleaved power iteration algorithm.

Neural control of muscle function is fundamental to animal behavior. Many muscles can generate multiple distinct behaviors. Nonetheless, individual muscle cells are generally regarded as the smallest units of motor control. We report that muscle cells can alter behavior by contracting subcellularly. We previously discovered that noxious tastes reverse the net flow of particles through the C. elegans pharynx, a neuromuscular pump, resulting in spitting. We now show that spitting results from the subcellular contraction of the anterior region of the pm3 muscle cell. Subcellularly localized calcium increases accompany this contraction. Spitting is controlled by an ‘hourglass’ circuit motif: parallel neural pathways converge onto a single motor neuron that differentially controls multiple muscles and the critical subcellular muscle compartment. We conclude that subcellular muscle units enable modulatory motor control and propose that subcellular muscle contraction is a fundamental mechanism by which neurons can reshape behavior.

Today, in an era of taxpayer revolts, lack of clarity in values, and changing family structure, children need advocates in the political arena as well as in the schools. This pamphlet suggests that administrators are in an excellent position to defend the rights of children on all fronts. It focuses on what administrators have done and specific things they can do to champion the causes of children and youth--who are often forgotten in the political process. (Author/LD)

© 2020 Elsevier Inc. Burkhart et al. show that mutants lacking components of H3.3 assembly complexes have pleiotropic defects that manifest near the onset of adulthood. Mitochondrial stress likely contributes to these late-onset defects. The late-onset defects of H3.3 assembly mutants can be maternally rescued.

Neural control of muscle function is fundamental to animal behavior. Many muscles can generate multiple distinct behaviors. Nonetheless, individual muscle cells are generally regarded as the smallest units of motor control. We report that muscle cells can alter behavior by contracting subcellularly. We previously discovered that noxious tastes reverse the net flow of particles through the C. elegans pharynx, a neuromuscular pump, resulting in spitting. We now show that spitting results from the subcellular contraction of the anterior region of the pm3 muscle cell. Subcellularly localized calcium increases accompany this contraction. Spitting is controlled by an ‘hourglass’ circuit motif: parallel neural pathways converge onto a single motor neuron that differentially controls multiple muscles and the critical subcellular muscle compartment. We conclude that subcellular muscle units enable modulatory motor control and propose that subcellular muscle contraction is a fundamental mechanism by which neurons can reshape behavior.

Heart attacks kill more Americans than all cancers combined. Fatal heart attack victims have no symptoms until minutes before they die, hence early detection of high-risk asymptomatic individuals is needed. Even though heart attacks kill and cost more than cancers, as a nation we spend over 20 times more on screening for asymptomatic cancer than for asymptomatic atherosclerotic cardiovascular disease (ASCVD), the underlying cause of heart attacks. Currently, payers only cover screening for risk factors of ASCVD such as blood pressure and blood cholesterol. This approach tends to miss high-risk and over-treat low-risk individuals. Although treadmill stress testing with ECG is not indicated for ASCVD detection in asymptomatic individuals, it is done often, and frequently leads to misleading conclusions or unnecessary downstream diagnostic procedures. For example, former President Clinton had passed his treadmill stress tests for several years during his presidential annual checkup but had a heart attack shortly after his presidency. This common practice is a waste of our limited resources. Instead, a more accurate risk assessment using coronary artery calcium (CAC) testing is available; and has just been adopted by ACC/AHA guidelines, however payers do not cover it. CAC is measured non-invasively with a 5-minute CT-scan of the heart, and costs less than $200, whereas cancer screening with colonoscopy and mammography costs over $3000. There is an opportunity to save lives and dollars if CAC testing is covered for appropriately selected individuals. Texas has already passed HB1290 to mandate CAC coverage. Other states must step up and take actions.

Oral history interview with Robert “Herb” Williams conducted by Tom Carr at Robert H. Williams’ home. Robert Williams was the former Director of WMU Physical Plant. He recalls his early education in Kentucky, enlisting in the ROTC reserve, and coming to Kalamazoo for the 1941 home game on WMU campus against Western Kentucky State Teachers College. He also recalls serving in Europe during World War II, transferring back to Michigan, and being hired in construction by the State Building Division out of Lansing in 1946. He describes his job, role on a construction site, and other building projects in Kalamazoo. In 1948, he was hired by John Goldsworth as a maintenance supervisor. He describes how McCracken Hall was built, how the West Campus (later, Main Campus) was developed through the 60s, the trolley system on East Campus, the presidents he worked for, hiring of Ed Powless to run the first bus route between East and West campuses, building of the University Student Center, and other memorable faculty. He retired after 34 years at WMU in January 1980. He passed away in 2016., Transcript unavailable.

Robert J. H., handwritten letters including request to send no more magazines (1962)

Robert H., letter requesting sample and asking about Councils of Friends in other major cities, with a response from Robert Gregory (1966-1967)

Robert H., letters (1969)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged student-submitted from PDF version of thesis. Vita., Includes bibliographical references., The transcriptional response controlling adaptation to internal and environmental hypoxia is broadly conserved in animals. The key mediator of this response is the transcription factor HIF (hypoxia-inducible factor), which is active only in hypoxia due to the function of its negative regulators, the prolyl hydroxylase EGLN and the E3 ubiquitin ligase complex recognition subunit pVHL. HIF drives transcription of hundreds of targets that promote hypoxia adaptation. Recent work has also described important and broad roles for HIF outside of the traditional hypoxia response, including functions in immunity, oxidative and other stress responses, and behavior; how HIF targets drive these aspects of animal physiology is poorly understood. In this dissertation, I describe genetic analyses of the nematode C. elegans that have provided insight into the function of HIF targets in regulating animal physiology and behavior. The EGLN family was defined by the C. elegans homolog, EGL-9. Prior to the identification of EGL-9 as a HIF hydroxylase, our laboratory discovered the egl-9 gene from studies of egg-laying behavior. egl-9 loss-of-function mutants, in which HIF is constitutively active, are egg-laying defective; the mechanism regulating egg laying downstream of HIF has been unknown. From a screen for suppressors of the egl-9(lf) egg-laying defect, we identified the gene cyp-36A1, which encodes a cytochrome P450 enzyme and is likely a direct transcriptional target of HIF. In addition to modulating egg-laying behavior downstream of HIF, CYP-36A1 controls expression of more than a third of HIF-upregulated genes and regulates multiple stress responses. A screen for suppressors of cyp-36A1(lf) identified the nuclear hormone receptor NHR-46. We propose that CYP-36A1 functions as a hormone biosynthetic enzyme for the ligand of this receptor, thus mediating gene expression changes that alter stress physiology and behavior. We also found site-of-action and genetic evidence for at least, by Corinne L. Pender., Ph. D.

The paper defines a new coordinate system that was developed in 1977-78 for the world's first digital synthetic aperture radar (SAR) ground processor for images from the Seasat-A satellite. The coordinate system is for the range-Doppler paradigm in the context of a spaceborne platform orbiting a rotating planet. The mathematical expressions for the azimuth FM rate, isodoppler lines, target illumination trajectories and antenna attitude determination from Doppler centroid measurements are derived. The method for transforming the SAR images from that SAR digital signal processor that used these parametric inputs is also presented. The paper concludes with a report of the measurement of the map accuracy of the resulting images.

To better understand the tissue-specific regulation of chromatin state in cell-fate determination and animal development, we defined the tissue-specific expression of all 36 C. elegans presumptive lysine methyltransferase (KMT) genes using single-molecule fluorescence in situ hybridization (smFISH). Most KMTs were expressed in only one or two tissues. The germline was the tissue with the broadest KMT expression. We found that the germline-expressed C. elegans protein SET-17, which has a SET domain similar to that of the PRDM9 and PRDM7 SET-domain proteins, promotes fertility by regulating gene expression in primary spermatocytes. SET-17 drives the transcription of spermatocyte-specific genes from four genomic clusters to promote spermatid development. SET-17 is concentrated in stable chromatin-associated nuclear foci at actively transcribed msp (major sperm protein) gene clusters, which we term msp locus bodies. Our results reveal the function of a PRDM9/7-family SET-domain protein in spermatocyte transcription. We propose that the spatial intranuclear organization of chromatin factors might be a conserved mechanism in tissue-specific control of transcription.

Thing-to-thing payments are a key enabler in the Internet of Things (IoT) era, to ubiquitously allow for devices to pay each other for services without any human interaction. Traditional credit card-based systems are not able to handle this new paradigm, however blockchain technology is a promising payment candidate in this context. The prominent example of blockchain technology is Bitcoin, with its decentralized structure and ease of account creation. This paper presents a proof-of-concept implementation of a smart cable that connects to a smart socket and without any human interaction pays for electricity. In this paper, we identify several obstacles for the widespread use of bitcoins in thing-to-thing payments. A critical problem is the high transaction fees in the Bitcoin network when doing micro transactions. To reduce this impact, we present a single-fee micro-payment protocol that aggregates multiple smaller payments incrementally into one larger transaction needing only one transaction fee. The proof-of concept shows that trustless, autonomous, and ubiquitous thing-to-thing micro-payments is no longer a future technology.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2017., Cataloged from PDF version of thesis., Includes bibliographical references., From the 4th century BC until the late 19th century AD philosophers and biologists ranging from Hippocrates to Charles Darwin hypothesized that information about the environment could be passed from parents to progeny. However, in 1893, German biologist August Weismann tested these hypotheses and based on his observations concluded that information about the environment could not be transmitted from parents to progeny. Weismann's hypothesis became known as the Weismann barrier and served as one of the founding pillars of modern evolutionary synthesis, which postulates that genetic and phenotypic variability in plant and animal populations are brought about by genetic recombination resulting from sexual reproduction and random mutations. Nonetheless, throughout the 20th century there have been several observations of plants and animals where parental exposure to environmental stress modified offspring physiology. These changes in progeny physiology sometimes enhanced progeny survival in response to repeated environmental stress, suggesting that information about the environment might be passed from parent to progeny. The mechanisms by which parental environment can alter progeny physiology to enhance survival remain unknown. To explore such mechanisms I investigated how parental exposure of the nematode C. elegans to osmotic stress affects its progeny's response to continued osmotic stress. First, I found that C. elegans arrests its development during periods of osmotic stress to enhance survival and that this developmental arrest is caused by a loss of insulin-like signaling to the intestine. I then discovered that exposure of parents to mild osmotic stress enhances progeny resistance to osmotic stress and determined that this adaptation is the result of a loss of insulin-like signaling to the maternal germline, which results in increased expression of the glycerol biosynthetic enzyme GPDH-2 in embryos; the increased GPDH-2 expression results in increased glycerol p, by Nicholas O. Burton., Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2017., Cataloged from PDF version of thesis., Includes bibliographical references., To better understand the tissue-specific regulation of chromatin state in cell-fate determination and development, we defined the tissue-specific expression of all 36 lysine methyltransferase (KMT) genes by endogenous mRNA detection in C. elegans. We found that most KMTs are expressed in only one or two tissues and that the germline is the tissue with the most general KMT expression. We discovered that the germline-expressed C. elegans ortholog of mammalian PRDM9, SET-1 7, promotes fertility through gene regulation in primary spermatocytes. SET-17 drives transcription of spermatocyte-specific genes from four genomic clusters to promote spermatid production. SET-1 7 is concentrated in stable, chromatin-associated nuclear foci at actively transcribed gene clusters, which we term spermatocyte transcription bodies. Our results identify the spatially restricted function of a PRDM9 ortholog in spermatocyte transcription and we propose that the spatial organization of chromatin factors might be a conserved mechanism in tissue-specific control of transcription., by Christoph G. Engert., Ph. D.

In today's datacenters, there is an increasing demand for more network traffic capacity. The majority of the increase in traffic is internal to the datacenter, i.e., it flows between different servers within the datacenter. This category of traffic is often referred to as east-west traffic and traditional hierarchical architectures are not well equipped to handle this type of traffic. Instead, they are better suited for the north-southbound traffic between hosts and the Internet. One suggested solution for this capacity problem is to adopt a folded CLOS topology, also known as spine-leaf, which often relies on software defined network (SDN) controllers to manage traffic. This paper shows that it is possible to implement a spine-leaf network using commodity-ofthe-shelf switches and thus improve the east-west traffic capacity. This can be obtained using low complexity configuration and edgerouting for load balancing, eliminating the need for a centralized SDN controller.

INTRODUCTION:The AARR task force on suicidal ideation and behavior (SI/SB) in dementia conducted an online survey on the extent of SI/SB in individuals diagnosed with mild cognitive impairment (MCI) or dementia who were participating in clinical trials. METHODS:Investigators with experience in conducting SI/SB assessments in clinical trial subjects with MCI or dementia were invited to complete a global 19-item online survey. RESULTS:A total of 204 evaluable responses were collected with the majority from North America and Europe (83.4%) and the remainder from Asia, Latin America, and Mideast/Africa. The mean (SD) number of subjects personally assessed by the respondents in the past year with MCI, mild-moderate dementia, or severe dementia was 12.8 (26.2), 31.2 (39.6), and 10.1 (34.7), respectively. The mean number of subjects in each diagnostic group with suicidal ideation (SI), suicidal behavior (SB), or completed suicide (CS) was on average quite low (0.3 to 1.1 for SI, 0.1 to 0.2 for SB, and 0.0 to 0.2 for CS). Confidence in subject self-reports of SI/SB over different time periods declined with increasing severity of cognitive impairment and with increasing duration of the recall time period assessed. Of respondents, 56% and 75% had low confidence in self-ratings of SI/SB from subjects with severe dementia over the past 24 hours and the past week to 1 month, respectively. Ratings of the reliability of information collected on SI/SB also decreased with increasing severity of cognitive impairment. Approximately 70% of respondents rated the reliability of the information they obtained from all sources (patient, caregiver, and others) for subjects with MCI as high, but only about half (42.0% to 55.3%) and less than a quarter (17.4% to 24.3%) rated the reliability of information obtained for subjects with mild to moderate dementia or severe dementia as high, respectively. DISCUSSION:These results support the usefulness of prospective SI/SB assessments in MCI and mild

INTRODUCTION:Better understanding of suicide risk and its management in older adults with cognitive impairment and/or dementia remain significant unmet public health needs. Urgency to address them derives from concern that CNS treatments for dementia may impact suicide risk. Regulatory guidances requiring assessment of emergent suicidal ideation and behavior (SI/SB) at every clinical trial visit emphasize the need for understanding their prevalence. METHODS:The literature regarding SI/SB in older persons with cognitive impairment or dementia was reviewed by an Alzheimer's Association Taskforce with emphasis on epidemiology, classification, assessment, and regulatory requirements. RESULTS:Gaps in our knowledge were identified, challenges discussed and recommendations for future work provided. DISCUSSION:Currently available SI/SB data from geriatric persons with dementia do not provide adequate understanding of its epidemiology, identification, assessment, or management. The growing public health burden of this population requires greater attention from clinicians and researchers on tactics and assessment tools to meet these needs.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016., Cataloged from PDF version of thesis., Includes bibliographical references., Apoptosis or programmed cell death was originally defined by evolutionarily conserved morphological characteristics that include shrinkage of cell volume and chromatin condensation. Apoptosis functions as a highly controlled mechanism for the elimination of unwanted or damaged cells and is essential for disease prevention. Apoptotic cell death is a cell-autonomous process driven by the caspase family of cysteine proteases. The discovery of the CED-3 caspase in C. elegans led to the paradigm that caspase cleavage of substrates drives cell death and promotes engulfment. While many caspase substrates have been identified, it is not well understood how caspase substrates act to promote cell death and engulfment. The control of caspase activation in C. elegans is conserved among metazoans and involves the interplay of pro and anti-apoptotic BCL-2 and BH3-only family proteins. In C. elegans an increase in apoptotic cell refractility observed by Nomarski optics is one of the hallmark morphological characteristics of apoptosis. We found that the presumptive TRP channel CED-1 1 acts downstream of caspase activation in apoptotic cells to drive the increase in refractility. We discovered that CED-1 1 is also required for a decrease in cell volume and increase in nuclear permeability of apoptotic cells. We showed that CED-1 1 is required for efficient degradation of apoptotic cells and facilitates the death process, suggesting that the decrease in cell volume and/or increase in nuclear permeability could promote the death and degradation of the cell. We conclude that CED-1 1 acts downstream of caspase activation to effect multiple observed changes to apoptotic cells and to facilitate death and degradation. In addition we investigated the anti-apoptotic function of the generally pro-apoptotic BCL-2 homolog CED-9., by Kaitlin B. Driscoll., Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student-submitted PDF version of thesis., Includes bibliographical references., Programmed cell death is an evolutionarily conserved process that plays critical roles in normal animal development and has been extensively studied in C. elegans. During programmed cell death, caspases are activated in the dying cell. The cell corpse is engulfed by a neighboring cell and degraded. Almost all cell deaths in C. elegans are "suicides"-they are caspase-dependent and apparently cell-autonomous, and do not require engulfment. During development of the C. elegans male, the cells B.alapaav and B.arapaav are generated during the late third-larval stage. During the early fourth-larval stage one of these cells undergoes programmed cell death, and the other survives. These two cells form an equivalence group; the decision of which cell dies and which survives is stochastic. The cell that dies is engulfed by the neighboring cell P12.pa and was speculated to be an engulfment-dependent cell "murder" or an "induced suicide." I have discovered that B.al/rapaav instead represents an "assisted suicide" that requires both the core apoptosis pathway and the engulfment pathway. egl-1 and ced-3 are expressed in the dying or undead cell in wild-type and engulfment-defective animals, and these genes are required for the B.al/rapaav cell death. In engulfment mutants the B.al/rapaav death process fails at a point after caspase activation, suggesting that the core cell-death pathway is necessary but not sufficient for this cell death. Previous genetic screens have not been designed to systematically identify essential genes with a role in cell death. Most somatic cell deaths in C. elegans occur during early development, but several male-specific cell deaths occur during the fourth larval stage. These late cell deaths provide an opportunity to examine essential genes for a role in programmed cell death, as RNAi treatment after hatching can eliminate gene function before these deaths occur but after embryogenesis. I performed an RNAi screen for 1,132 essential genes and assayed, by Holly L. Johnsen., Ph. D.

Background Programmed cell deaths in the nematode Caenorhabditis elegans are generally considered suicides. Dying cells are engulfed by neighboring cells in a process of phagocytosis. To better understand the interaction between the engulfment and death processes, we analyzed B.al/rapaav cell death, which has been previously described as engulfment-dependent and hence as a possible murder. Results We found that B.al/rapaav is resistant to caspase-pathway activation: the caspase-mediated suicide pathway initiates the cell-death process but is insufficient to cause B.al/rapaav death without the subsequent assistance of engulfment. When the engulfing cell P12.pa is absent, other typically non-phagocytic cells can display cryptic engulfment potential and facilitate this death. Conclusions We term this death an “assisted suicide” and propose that assisted suicides likely occur in other organisms. The study of assisted suicides might provide insight into non-cell autonomous influences on cell death. Understanding the mechanism that causes B.al/rapaav to be resistant to activation of the caspase pathway might reveal the basis of differences in the sensitivity to apoptotic stimuli of tumor and normal cells, a key issue in the field of cancer therapeutics., Howard Hughes Medical Institute, National Institutes of Health (U.S.) (Pre-Doctoral Training Grant T32GM007287)

Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development., Funding Agencies|Cancer fund, Swedish Medical Research Council [K2013-61X-22310-01-04, 2012-3168]; Academy of Finland Centre of Excellence in Molecular Systems Immunology and Physiology Research [250114]; Sigrid Juselius Foundation; Generalitat de Catalunya AGAUR [2014-SGR364]; Spanish Association Against Cancer; Spanish Ministry of Health ISCIII FIS [PI12/01528]; RTICC [RD12/0036/0008]

Cells adapt to temperature shifts by adjusting levels of lipid desaturation and membrane fluidity. This fundamental process occurs in nearly all forms of life, but its mechanism in eukaryotes is unknown. We discovered that the evolutionarily conserved Caenorhabditis elegans gene acdh-11 (acyl-CoA dehydrogenase [ACDH]) facilitates heat adaptation by regulating the lipid desaturase FAT-7. Human ACDH deficiency causes the most common inherited disorders of fatty acid oxidation, with syndromes that are exacerbated by hyperthermia. Heat upregulates acdh-11 expression to decrease fat-7 expression. We solved the high-resolution crystal structure of ACDH-11 and established the molecular basis of its selective and high-affinity binding to C11/C12-chain fatty acids. ACDH-11 sequesters C11/C12-chain fatty acids and prevents these fatty acids from activating nuclear hormone receptors and driving fat-7 expression. Thus, the ACDH-11 pathway drives heat adaptation by linking temperature shifts to regulation of lipid desaturase levels and membrane fluidity via an unprecedented mode of fatty acid signaling.

Many neurodegenerative disorders are associated with mitochondrial defects [1, 2 and 3]. Mitochondria can play an active role in degeneration by releasing reactive oxygen species and apoptotic factors [4, 5, 6 and 7]. Alternatively, mitochondria can protect axons from stress and insults, for example by buffering calcium [8]. Recent studies manipulating mitochondria lend support to both of these models [9, 10, 11, 12 and 13]. Here, we identify a C. elegans mutant, ric-7, in which mitochondria are unable to exit the neuron cell bodies, similar to the kinesin-1/unc-116 mutant. When axons lacking mitochondria are cut with a laser, they rapidly degenerate. Some neurons even spontaneously degenerate in ric-7 mutants. Degeneration can be suppressed by forcing mitochondria into the axons of the mutants. The protective effect of mitochondria is also observed in the wild-type: a majority of axon fragments containing a mitochondrion survive axotomy, whereas those lacking mitochondria degenerate. Thus, mitochondria are not required for axon degeneration and serve a protective role in C. elegans axons.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Biology, 1999., Includes bibliographical references., by Xiaowei Lu., Ph.D.

Thesis: Ph. D. in Neuroscience, Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2014., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student-submitted PDF version of thesis., Includes bibliographical references (pages 239-249)., The most fascinating function of the nervous system is its ability to generate consciousness, the subjective experience or qualia that distinguishes awake life from dreamless sleep. How consciousness is generated is an ancient philosophical question which has proven resistant to scientific analysis. While the human brain is known to generate consciousness, its complexity prevents acquisition of a mechanistic understanding of consciousness. Therefore, I chose to study the much simpler nervous system of the nematode Caenorhabditis elegans. I tested worms for a specific kind of learning, called trace conditioning, which correlates with conscious awareness in humans, under the assumption that if worms were able to trace condition, they might also be capable of conscious awareness. However, I was not able to show trace conditioning in worms, so the question of whether worms exhibit consciousness remains unresolved. In the process of using light in learning experiments, I noticed that worms stop feeding immediately after being exposed to short wavelength (UV) light. Curious about whether worms might actually have a subjective experience in response to light akin to primitive vision, I investigated the molecular and neural mechanisms that control this behavioral response. I identified the I2 pharyngeal neuron as a cellular light sensor required for the speed of feeding inhibition. Hydrogen peroxide elicited behavioral and cellular responses strikingly similar to those caused by light. The sensing of both light and hydrogen peroxide were mediated by the LITE-1 and GUR-3 proteins, both putative gustatory receptors, as well as by the conserved antioxidant enzyme peroxiredoxin PRDX-2. My results suggest that the LITE-1/GUR-3 family of receptors likely detects light through its generation of hydrogen peroxide or of another redox product. This is a novel mechanism by which light can be sensed. Additionally, by studying the worm's feeding response to light, I identified a pattern, by Nikhil Bhatla., Ph. D. in Neuroscience

Thesis: S.M., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, 2014., Cataloged from PDF version of thesis., Includes bibliographical references (pages 111-119)., Autonomous agents are increasingly being called upon to perform challenging tasks in complex settings with little information about underlying environment dynamics. To successfully complete such tasks the agent must learn from its interactions with the environment. Many existing techniques make assumptions about problem structure to remain tractable, such as limiting the class of possible models or specifying a fixed model expressive power. Complicating matters, there are many scenarios where the environment exhibits multiple underlying sets of dynamics; in these cases, most existing approaches assume the number of underlying models is known a priori, or ignore the possibility of multiple models altogether. Bayesian nonparametric (BNP) methods provide the flexibility to solve both of these problems, but have high inference complexity that has limited their adoption. This thesis provides several methods to tractably plan under uncertainty using BNPs. The first is Simultaneous Clustering on Representation Expansion (SCORE) for learning Markov Decision Processes (MDPs) that exhibit an underlying multiple-model structure. SCORE addresses the co-dependence between observation clustering and model expansion. The second contribution provides a realtime, non-myopic, risk-aware planning solution for use in camera surveillance scenarios where the number of underlying target behaviors and their parameterization are unknown. A BNP model is used to capture target behaviors, and a solution that reduces uncertainty only as needed to perform a mission is presented for allocating cameras. The final contribution is a reinforcement learning (RL) framework RLPy, a software package to promote collaboration and speed innovation in the RL community. RLPy provides a library of learning agents, function approximators, and problem domains for performing RL experiments. RLPy also provides a suite of tools that help automate tasks throughout the experiment pipeline, from initial prototyping th, by Robert H. Klein., S.M.

A better understanding of the molecular mechanisms of signaling by the neurotransmitter serotonin is required to assess the hypothesis that defects in serotonin signaling underlie depression in humans. Caenorhabditis elegans uses serotonin as a neurotransmitter to regulate locomotion, providing a genetic system to analyze serotonin signaling. From large-scale genetic screens we identified 36 mutants of C. elegans in which serotonin fails to have its normal effect of slowing locomotion, and we molecularly identified eight genes affected by 19 of the mutations. Two of the genes encode the serotonin-gated ion channel MOD-1 and the G-protein-coupled serotonin receptor SER-4. mod-1 is expressed in the neurons and muscles that directly control locomotion, while ser-4 is expressed in an almost entirely non-overlapping set of sensory and interneurons. The cells expressing the two receptors are largely not direct postsynaptic targets of serotonergic neurons. We analyzed animals lacking or overexpressing the receptors in various combinations using several assays for serotonin response. We found that the two receptors act in parallel to affect locomotion. Our results show that serotonin functions as an extrasynaptic signal that independently activates multiple receptors at a distance from its release sites and identify at least six additional proteins that appear to act with serotonin receptors to mediate serotonin response., National Institutes of Health (U.S.) (Grant GM24663)

Loss-of-function mutations in the Caenorhabditis elegans gene sup-18 suppress the defects in muscle contraction conferred by a gain-of-function mutation in SUP-10, a presumptive regulatory subunit of the SUP-9 two-pore domain K+ channel associated with muscle membranes. We cloned sup-18 and found that it encodes the C. elegans ortholog of mammalian iodotyrosine deiodinase (IYD), an NADH oxidase/flavin reductase that functions in iodine recycling and is important for the biosynthesis of thyroid hormones that regulate metabolism. The FMN-binding site of mammalian IYD is conserved in SUP-18, which appears to require catalytic activity to function. Genetic analyses suggest that SUP-10 can function with SUP-18 to activate SUP-9 through a pathway that is independent of the presumptive SUP-9 regulatory subunit UNC-93. We identified a novel evolutionarily conserved serine-cysteine-rich region in the C-terminal cytoplasmic domain of SUP-9 required for its specific activation by SUP-10 and SUP-18 but not by UNC-93. Since two-pore domain K+ channels regulate the resting membrane potentials of numerous cell types, we suggest that the SUP-18 IYD regulates the activity of the SUP-9 channel using NADH as a coenzyme and thus couples the metabolic state of muscle cells to muscle membrane excitability., National Institutes of Health (U.S.) (NIH Grant GM24663), National Science Foundation (U.S.) (Graduate Research Fellowship by NSFC Grant 31371253), National Institutes of Health (U.S.) (NIH predoctoral training grant), Howard Hughes Medical Institute (Investigator)

Although replication-coupled chromatin assembly is known to be important for the maintenance of patterns of gene expression through sequential cell divisions, the role of replication-coupled chromatin assembly in controlling cell differentiation during animal development remains largely unexplored. Here we report that the CAF-1 protein complex, an evolutionarily conserved histone chaperone that deposits histone H3-H4 proteins onto replicating DNA, is required to generate a bilateral asymmetry in the C. elegans nervous system. A mutation in 1 of 24 C. elegans histone H3 genes specifically eliminates this aspect of neuronal asymmetry by causing a defect in the formation of a histone H3-H4 tetramer and the consequent inhibition of CAF-1-mediated nucleosome formation. Our results reveal that replication-coupled nucleosome assembly is necessary to generate a bilateral asymmetry in C. elegans neuroanatomy and suggest that left-right asymmetric epigenetic regulation can establish bilateral asymmetry in the nervous system., Howard Hughes Medical Institute, National Cancer Institute (U.S.) (Grant CA13106)

The decision of a cell to undergo programmed cell death is tightly regulated during animal development and tissue homeostasis. Here, we show that the Caenorhabditis elegans Six family homeodomain protein C. elegans homeobox (CEH-34) and the Eyes absent ortholog EYA-1 promote the programmed cell death of a specific pharyngeal neuron, the sister of the M4 motor neuron. Loss of either ceh-34 or eya-1 function causes survival of the M4 sister cell, which normally undergoes programmed cell death. CEH-34 physically interacts with the conserved EYA domain of EYA-1 in vitro. We identify an egl-1 5′ cis-regulatory element that controls the programmed cell death of the M4 sister cell and show that CEH-34 binds directly to this site. Expression of the proapoptotic gene egl-1 in the M4 sister cell requires ceh-34 and eya-1 function. We conclude that an evolutionarily conserved complex that includes CEH-34 and EYA-1 directly activates egl-1 expression through a 5′ cis-regulatory element to promote the programmed cell death of the M4 sister cell. We suggest that the regulation of apoptosis by Six and Eya family members is conserved in mammals and involved in human diseases caused by mutations in Six and Eya., Howard Hughes Medical Institute

Oxygen deprivation followed by reoxygenation causes pathological responses in many disorders, including ischemic stroke, heart attacks, and reperfusion injury. Key aspects of ischemia-reperfusion can be modeled by a Caenorhabditis elegans behavior, the O2-ON response, which is suppressed by hypoxic preconditioning or inactivation of the O[subscript 2]-sensing HIF (hypoxia-inducible factor) hydroxylase EGL-9. From a genetic screen, we found that the cytochrome P450 oxygenase CYP-13A12 acts in response to the EGL-9–HIF-1 pathway to facilitate the O2-ON response. CYP-13A12 promotes oxidation of polyunsaturated fatty acids into eicosanoids, signaling molecules that can strongly affect inflammatory pain and ischemia-reperfusion injury responses in mammals. We propose that roles of the EGL-9–HIF-1 pathway and cytochrome P450 in controlling responses to reoxygenation after anoxia are evolutionarily conserved., National Institutes of Health (U.S.) (Grant GM24663), National Science Foundation (U.S.). Graduate Research Fellowship Program, Massachusetts Institute of Technology. Undergraduate Research Opportunities Program, Helen Hay Whitney Foundation (Postdoctoral Fellowship)

Klaus Hager,1 Alan S Baseman,2 Jeffrey S Nye,2 H Robert Brashear,2 John Han,2 Mary Sano,3 Bonnie Davis,4 Henry M Richards2 1Clinic for Medicine of the Elderly, Hannover, Germany; 2Janssen Research and Development, LLC, Raritan, NJ, USA; 3The Mount Sinai Medical Center, New York, NY, USA; 4Synaptec Inc., Palm Beach Gardens, FL, USA Background: Currently available treatments for Alzheimer's disease (AD) can produce mild improvements in cognitive function, behavior, and activities of daily living in patients, but their influence on long-term survival is not well established. This study was designed to assess patient survival and drug efficacy following a 2-year galantamine treatment in patients with mild to moderately severe AD. Methods: In this multicenter, double-blind study, patients were randomized 1:1 to receive galantamine or placebo. One primary end point was safety; mortality was assessed. An independent Data Safety Monitoring Board monitored mortality for the total deaths reaching prespecified numbers, using a time-to-event method and a Cox-regression model. The primary efficacy end point was cognitive change from baseline to month 24, as measured by the Mini-Mental State Examination (MMSE) score, analyzed using intent-to-treat analysis with the 'last observation carried forward' approach, in an analysis of covariance model. Results: In all, 1,024 galantamine- and 1,021 placebo-treated patients received study drug, with mean age ~73 years, and mean (standard deviation [SD]) baseline MMSE score of 19 (4.08). A total of 32% of patients (661/2,045) completed the study, 27% (554/2,045) withdrew, and 41% (830/2,045) did not complete the study and were discontinued due to a Data Safety Monitoring Board-recommended early study termination. The mortality rate was significantly lower in the galantamine group versus placebo (hazard ratio [HR] =0.58; 95% confidence interval [CI]: 0.37; 0.89) (P=0.011). Cognitive impairment, based on the mean (SD)

The life span of Caenorhabditis elegans is controlled by signaling between the germline and the soma. Germ cell removal extends life span by triggering the activation of the DAF-16/FOXO transcription factor in the intestine. Here we analyze microRNA function in C. elegans aging and show that the microRNA mir-71 functions to mediate the effects of germ cell loss on life span. mir-71 is required for the life span extension caused by germline removal, and overexpression of mir-71 further extends the life span of animals lacking germ cells. mir-71 functions in the nervous system to facilitate the localization and transcriptional activity of DAF-16 in the intestine. Our findings reveal a microRNA-dependent mechanism of life span regulation by the germline and indicate that signaling among the gonad, the nervous system, and the intestine coordinates the life span of the entire organism., Howard Hughes Medical Institute, European Molecular Biology Organization (Fellowship), Ellison Medical Foundation (Grant)

During animal development, the proper regulation of apoptosis requires the precise spatial and temporal execution of cell-death programs, which can include both caspase-dependent and caspase-independent pathways. Although the mechanisms of caspase-dependent and -independent cell killing have been examined extensively, how these pathways are coordinated within a single cell that is fated to die is unknown. Here we show that the Caenorhabditis elegans Sp1 transcription factor SPTF-3 specifies the programmed cell deaths of at least two cells—the sisters of the pharyngeal M4 motor neuron and the AQR sensory neuron—by transcriptionally activating both caspase-dependent and -independent apoptotic pathways. SPTF-3 directly drives the transcription of the gene egl-1, which encodes a BH3-only protein that promotes apoptosis through the activation of the CED-3 caspase. In addition, SPTF-3 directly drives the transcription of the AMP-activated protein kinase-related gene pig-1, which encodes a protein kinase and functions in apoptosis of the M4 sister and AQR sister independently of the pathway that activates CED-3. Thus, a single transcription factor controls two distinct cell-killing programs that act in parallel to drive apoptosis. Our findings reveal a bivalent regulatory node for caspase-dependent and -independent pathways in the regulation of cell-type-specific apoptosis. We propose that such nodes might act as features of a general mechanism for regulating cell-type-specific apoptosis and could be therapeutic targets for diseases involving the dysregulation of apoptosis through multiple cell-killing mechanisms., Howard Hughes Medical Institute

Biogenic amines such as serotonin and dopamine are intercellular signaling molecules that function widely as neurotransmitters and neuromodulators. We have identified in the nematode Caenorhabditis elegans three ligand-gated chloride channels that are receptors for biogenic amines: LGC-53 is a high-affinity dopamine receptor, LGC-55 is a high-affinity tyramine receptor, and LGC-40 is a low-affinity serotonin receptor that is also gated by choline and acetylcholine. lgc-55 mutants are defective in a behavior that requires endogenous tyramine, which indicates that this ionotropic tyramine receptor functions in tyramine signaling in vivo. Our studies suggest that direct activation of membrane chloride conductances is a general mechanism of action for biogenic amines in the modulation of C. elegans behavior., National Institutes of Health (U.S.) (Grant GM24663), Howard Hughes Medical Institute, Life Sciences Research Foundation, Medical Foundation, Inc.

DNA replication and its connection to M phase restraint are studied extensively at the level of single cells but rarely in the context of a developing animal. C. elegans lin-6 mutants lack DNA synthesis in postembryonic somatic cell lineages, while entry into mitosis continues. These mutants grow slowly and either die during larval development or develop into sterile adults. We found that lin-6 corresponds to mcm-4 and encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex. The MCM-4 protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase. Induction of cell cycle entry and differentiation continues in developing mcm-4 larvae, even in cells that went through abortive division. In contrast to somatic cells in mcm-4 mutants, the gonad continues DNA replication and cell division until late larval development. Expression of MCM-4 in the epidermis (also known as hypodermis) is sufficient to rescue the growth retardation and lethality of mcm-4 mutants. While the somatic gonad and germline show substantial ability to cope with lack of zygotic mcm-4 function, mcm-4 is specifically required in the epidermis for growth and survival of the whole organism. Thus, C. elegans mcm-4 has conserved functions in DNA replication and replication checkpoint control but also shows unexpected tissue-specific requirements.