Chalfie M J Neurogenet "A touching story."

Chalfie M

[J Neurogenet]

A slide taped to a window at the Woods Hole Marine Biology Laboratory was my first introduction to the touch receptor neurons of the nematode <i>Caenorhabditis elegans</i>. Studying these cells as a postdoc with Sydney Brenner gave me a chance to work with John Sulston on a fascinating set of neurons. I would never have guessed then that 43 years later I would still be excited about learning their secrets.

Barger SR et al. (2023) J Cell Sci "Nuclear envelope assembly relies on CHMP-7 in the absence of BAF-LEM-mediated hole closure."

Bahmanyar S, Penfield L, Barger SR

[J Cell Sci, 2023]

Barrier-to-autointegration (BAF) is a DNA binding protein that crosslinks chromatin to allow mitotic nuclear envelope (NE) assembly. The Lap2b-Emerin-Man1(LEM)-domain protein LEMD2 and ESCRTII/III hybrid protein CHMP7 close NE holes surrounding spindle microtubules (MTs). BAF binds LEM-domain family proteins, which repairs NE ruptures in interphase, but whether BAF-LEM binding participates in NE hole closure around spindle MTs is not known. Here, we take advantage of the stereotypical event of NE formation in fertilized C. elegans oocytes to show that BAF-LEM binding and LEM-2LEMD2-CHMP-7 have distinct roles in NE closure around spindle MTs. LEM-2/EMR-1emerin function redundantly with BAF-1 in NE closure. Compromising BAF-LEM binding revealed an additional role for EMR-1emerin in maintenance of the NE permeability barrier. In the absence of BAF-LEM binding, LEM-2-CHMP-7 are required for NE assembly and embryo survival. The winged helix domain of LEM-2 recruits CHMP-7 to the NE in C. elegans and a LEM-2-independent nucleoplasmic pool of CHMP-7 also contributes to NE stability. Thus, NE hole closure surrounding spindle MTs requires redundant mechanisms that safeguard against failure in NE assembly to support embryogenesis.

Nah W et al. (2003) Lect N A I "Feature extraction for classification of Caenorhabditis elegans behavioral phenotypes."

Baek JH, Nah W, Hong SB

[Lect N A I, 2003]

Caenorhabditis (C.) elegans is often used in genetic analysis inneuroscience because it has simple model organisms; an adult hermaphroditecontains only 302 neurons. We use an automated tracking system, which makesit possible to measure the rate and direction of movement for each worm and tocompute the frequency of reversals in direction. In this paper, we propose newpreprocessing method using hole detection, and then we describe how to extractfeatures that are very useful for classification of C. elegans behaviouralphenotypes. We use 3 kinds of features (Large-scale movement, body size, andbody posture). For the experiments, we classify 9 mutant types of worms andanalyze their behavioural characteristics.

Bwambok DK et al. (2014) Anal Chem "Adaptive use of bubble wrap for storing liquid samples and performing analytical assays."

Christodouleas DC, Lange H, Morin SA, Bwambok DK, Phillips ST, Whitesides GM

[Anal Chem, 2014]

This paper demonstrates that the gas-filled compartments in the packing material commonly called &quot;bubble wrap&quot; can be repurposed in resource-limited regions as containers to store liquid samples, and to perform bioanalyses. The bubbles of bubble wrap are easily filled by injecting the samples into them using a syringe with a needle or a pipet tip, and then sealing the hole with nail hardener. The bubbles are transparent in the visible range of the spectrum, and can be used as &quot;cuvettes&quot; for absorbance and fluorescence measurements. The interiors of these bubbles are sterile and allow storage of samples without the need for expensive sterilization equipment. The bubbles are also permeable to gases, and can be used to culture and store micro-organisms. By incorporating carbon electrodes, these bubbles can be used as electrochemical cells. This paper demonstrates the capabilities of the bubbles by culturing E. coli, growing C. elegans, measuring glucose and hemoglobin spectrophotometrically, and measuring ferrocyanide electrochemically, all within the bubbles.

Schierenberg E et al. (1997) Zoology-Analysis of Complex Systems "Pattern formation and cell specification in nematode embryos: A theme with considerable variations."

Kutzowitz M, Wiegner O, Schierenberg E, Skiba F, Bossinger O

[Zoology-Analysis of Complex Systems, 1997]

The pattern of cellular development of the free-living nematode Caenorhabditis elegans has been described completely. For comparison we have begun to study the early embryogenesis of other nematodes to ask how much variation occurs in a group of animals, all with a very similar phenotype. We found one family, Cephalobidae, with a number of specific features, indicating that even for closely related taxa a similar terminal structure does not necessarily imply the same developmental strategies. In particular, we looked for mechanisms of cell specification. Besides studying cell lineages, spatial pattern formation and tissue-specific differentiation, we manipulated embryos with the help of a laser microbeam coupled to a microscope; through a hole shot in the eggshell we added drugs or removed blastomeres. On the one hand C. elegans embryogenesis makes use to a large extent of maternal gene products unequally segregated into early blastomeres. On the other hand early cell-cell interactions in the form of receptor/ligand-mediated inductions play an important role. In contrast, in Cephalobus, the best studied representative of Cephalobid nematodes, embryogenesis appears to rely to a much lesser extent on maternal inheritance but requires massive early transcription, and in addition, inhibitory interactions between blastomeres of similar developmental potential seem to be involved.

Yamazoe-Umemoto A et al. (2018) Bio Protoc "Measuring Spatiotemporal Dynamics of Odor Gradient for Small Animals by Gas Chromatography."

Kimura KD, Iwasaki Y, Yamazoe-Umemoto A

[Bio Protoc, 2018]

Odor is the most fundamental chemical stimulus that delivers information regarding food, mating partners, enemies, and danger in the surrounding environment. Research on odor response in animals is widespread, although studies on experimental systems in which the gradient of odor concentration is quantitatively measured has been quite limited. Here, we describe a method for measuring a gradient of odor concentration established by volatilization and diffusion in a relatively small enclosed space, which has been used widely in laboratories to analyze small model animals such as the nematode <i>Caenorhabditis elegans</i> and the fruit fly <i>Drosophila melanogaster</i>. We first vaporized known amounts of a liquid odorant 2-nonanone in a tank and subjected them to gas chromatographic analysis to obtain a calibration curve. Then, we aspirated a small amount of gas phase from a small hole on an agar plate and measured the odor concentration. By repeating this at different spatial and temporal points, we were able to detect a gradient of the odor concentration that increased over time. Furthermore, by applying these measured values to mathematical models of volatilization and diffusion, we were able to visualize an estimated dynamic change in odor concentration over an agar plate. Combining monitoring of odor concentration change in an agar plate with behavioral monitoring by machine vision will allow us to estimate how the brain computes information regarding odor concentration change in order to regulate behavior.

Attix, Haley et al. (2021) MicroPubl Biol

Cortez, Angel, Hastie, Eric, Attix, Haley, Zarilla, Kathy, Cho, Martin, George, Alex, Panchal, Henali

[MicroPubl Biol, 2021]

Research experiences in community college lead to increased retention in science, technology, engineering, and mathematics (STEM) (Nerio et al., 2019). This two week undergraduate research experience (URE) was designed to enhance laboratory skills in students with limited prior exposure, introduce developmental biology and genetics in a model organism system (C. elegans), and encourage participation in generation of data for a micropublication. The University of North Carolina at Chapel Hill and Durham Technical Community College partnered to host the URE for two weeks, for two hours, 4 days a week to limit lab time for students who work full time jobs. Here, we report our findings comparing early developmental cell division of wild type N2 embryos and a wild caught strain that was obtained from soil outside of Loeb Hall in Woods Hole, MA in 2017. The strain, originally called WH strain, was grown on OP50 and survived, suggesting it is a bacteriovore. The WH nematode lays embryos at the one cell stage, making early divisions observable without the dissection or bleaching required for the N2 strain. Students used primers to amplify the 18S ribosomal subunit geneused in phylogenetic analysis of taxafrom extracted genomic DNA and sent the product for sequencing (Floyd et al., 2005). The hairpin 17 region was selected to display a comparison because of high conservation (Nyaku et al., 2013). BLAST results for the N2 strain matched N2 and results for the wild caught WH strain matched with the nematode strain Acrobeloides sp. LKC 27 (a match of 99.7% and E value of 0), available from the Caenorhabditis Genetics Center. LKC 27 was isolated from a western corn rootworm from a Brookings, SD insectary in 2003 (personal communication with Dr. Lynn Carta, USDA-ARS). Students concluded that additional loci need to be examined to determine the relationship of the WH strain to LKC 27.

Aspock G et al. (2001) Dev Dyn "The Caenorhabditis elegans distal-less ortholog ceh-43 is required for development of the anterior hypodermis."

Burglin TR, Aspock G

[Dev Dyn, 2001]

Homeobox genes of the Distal-less (Dll) class are expressed in developing appendages as well as in the central nervous system in invertebrates and vertebrates. Mutant analyses in mice and Drosophila have implicated these genes in outgrowth of structures, cell adhesion, cell migration, and cell fate decisions. We have investigated the expression and function of ceh-43, the Dll ortholog from the nematode Caenorhabditis elegans, by using gfp reporter constructs and double-stranded RNA-mediated interference (RNAi). Our results show that, as in the fly, the C. elegans Dll ortholog seems to play a role in cell adhesion. An antibody against the butterfly Distal-less homeodomain stains the nervous system of C. elegans embryos (Panganiban et al. [1997] Proc Natl Acad Sci USA. 94:5162-5166). GFP expression under the control of the ceh-43 promoter looks similar, although strong expression is primarily confined to the head hypodermis and to neuronal support cells. ceh43(RNAi) results in 100% lethality at embryonic or early larval stages. At the beginning of morphogenesis, ceh-43(RNAi) embryos start to lose cells through a hole in the head hypodermis. They either rupture interiorly as elongation proceeds, or they elongate normally to threefold egg length with the pharynx not connected to the mouth. Elongated ceh-43(RNAi) animals die before or soon after hatching with a fluid-filled pseudocoel and large vacuoles. These phenotypes suggest a role for ceh-43 in development of adhesive properties in the head hypodermis that connects the epithelia of the skin and the digestive tract. Furthermore, possible defects in the excretory system may result at least in part from a requirement for ceh-43 in the CAN neurons where ceh-43::gfp is also expressed.

French JB et al. (2010) Biochemistry "Characterization of nicotinamidases: steady state kinetic parameters, classwide inhibition by nicotinaldehydes, and catalytic mechanism."

Vrablik TL, Xu P, French JB, Hanna-Rose W, Allen E, Sauve AA, Cen Y

[Biochemistry, 2010]

Nicotinamidases are metabolic enzymes that hydrolyze nicotinamide to nicotinic acid. These enzymes are widely distributed across biology, with examples found encoded in the genomes of Mycobacteria, Archaea, Eubacteria, Protozoa, yeast, and invertebrates, but there are none found in mammals. Although recent structural work has improved our understanding of these enzymes, their catalytic mechanism is still not well understood. Recent data show that nicotinamidases are required for the growth and virulence of several pathogenic microbes. The enzymes of Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans regulate life span in their respective organisms, consistent with proposed roles in the regulation of NAD(+) metabolism and organismal aging. In this work, the steady state kinetic parameters of nicotinamidase enzymes from C. elegans, Sa. cerevisiae, Streptococcus pneumoniae (a pathogen responsible for human pneumonia), Borrelia burgdorferi (the pathogen that causes Lyme disease), and Plasmodium falciparum (responsible for most human malaria) are reported. Nicotinamidases are generally efficient catalysts with steady state k(cat) values typically exceeding 1 s(-1). The K(m) values for nicotinamide are low and in the range of 2 -110 M. Nicotinaldehyde was determined to be a potent competitive inhibitor of these enzymes, binding in the low micromolar to low nanomolar range for all nicotinamidases tested. A variety of nicotinaldehyde derivatives were synthesized and evaluated as inhibitors in kinetic assays. Inhibitions are consistent with reaction of the universally conserved catalytic Cys on each enzyme with the aldehyde carbonyl carbon to form a thiohemiacetal complex that is stabilized by a conserved oxyanion hole. The S. pneumoniae nicotinamidase can catalyze exchange of (18)O into the carboxy oxygens of nicotinic acid with H(2)(18)O. The collected data, along with kinetic analysis of several mutants, allowed us to propose a catalytic mechanism that explains nicotinamidase and nicotinic acid (18)O exchange chemistry for the S. pneumoniae enzyme involving key catalytic residues, a catalytic transition metal ion, and the intermediacy of a thioester intermediate.