Liu Z et al. (2017) Conf Proc IEEE Eng Med Biol Soc "NucleiNet: A convolutional encoder-decoder network for bio-image denoising."

Coquet P, Boudier T, Hu Y, Liu Z, Nasser L, Yu, H, Xu H

[Conf Proc IEEE Eng Med Biol Soc, 2017]

Generic and scalable data analysis procedures are highly demanded by the increasing number of multi-dimensional biomedical data. However, especially for time-lapse biological data, the high level of noise prevents for automated high-throughput analysis methods. The rapid developing of machine-learning methods and particularly deep-learning methods provide new tools and methodologies that can help in the denoising of such data. Using a convolutional encoder-decoder network, one can provide a scalable bio-image platform, called NucleiNet, to automatically segment, classify and track cell nuclei. The proposed method can achieve 0.99 F-score and 0.99 pixel-wise accuracy on C. elegans dataset, which means that over 99% of nuclei can be successfully detected with no merging nuclei found.

Pohl C et al. (2010) Dev Cell "Chiral forces organize left-right patterning in C. elegans by uncoupling midline and anteroposterior axis."

Pohl C, Bao Z

[Dev Cell, 2010]

Left-right (LR) patterning is an intriguing but poorly understood process of bilaterian embryogenesis. We report a mechanism for LR patterning in C. elegans in which the embryo uncouples its midline from the anteroposterior (AP) axis. Specifically, the eight-cell embryo establishes a midline that is tilted rightward from the AP axis and positions more cells on the left, allowing subsequent differential LR fate inductions. To establish the tilted midline, cells exhibit LR asymmetric protrusions and a handed collective movement. This process, termed chiral morphogenesis, involves differential regulation of cortical contractility between a pair of sister cells that are bilateral counterparts fate-wise and is activated by noncanonical Wnt signaling. Chiral morphogenesis is timed by the cytokinetic furrow of a neighbor of the sister pair, providing a developmental clock and an unexpected signaling interaction between the contractile ring and the adjacent cells.

Pan X et al. (2010) Biochem Biophys Res Commun "Torque generation by one of the motor subunits of heterotrimeric kinesin-2."

Scholey JM, Acar S, Pan X

[Biochem Biophys Res Commun, 2010]

Heterotrimeric kinesin-2 motors transport intraflagellar transport (IFT)-particles from the base to the tip of the axoneme to assemble and maintain cilia. These motors are distinct in containing two non-identical motor subunits together with an accessory subunit. We evaluated the significance of this organization by comparing purified wild type kinesin-2 holoenzymes that support IFT in vivo, with mutant trimers containing only one type of motor domain that do not support IFT in vivo. In motility assays, wild type kinesin-2 moved microtubules (MTs) at a rate intermediate between the rates supported by the two mutants. Interestingly, one of the mutants, but not the other mutant or the wild type protein, was observed to drive a persistent counter-clock-wise rotation of the gliding MTs. Thus one of the two motor domains of heterotrimeric kinesin-2 exerts torque as well as axial force as it moves along a MT, which may allow kinesin-2 to control its circumferential position around a MT doublet within the cilium.

Bianchi S et al. (2018) Mol Biol Cell "Interaction between the C. elegans centriolar protein SAS-5 and microtubules facilitates organelle assembly."

Bianchi S, Vakonakis I, Gonczy P, Steinmetz MO, Hilbert M, Dynes NJ, Rogala KB, Leidel SA

[Mol Biol Cell, 2018]

Centrioles are microtubule-based organelles that organise the microtubule network and seed the formation of cilia and flagella. New centrioles assemble through a step-wise process dependent notably on the centriolar protein SAS-5 in Caenorhabditis elegans SAS-5 and its functional homologues in other species form oligomers that bind the centriolar proteins SAS-6 and SAS-4, thereby forming an evolutionarily conserved structural core at the onset of organelle assembly. Here, we report a novel interaction of SAS-5 with microtubules. Microtubule binding requires SAS-5 oligomerisation and a disordered protein segment that overlaps with the SAS-4 binding site. Combined in vitro and in vivo analysis of select mutants reveals that the SAS-5-microtubule interaction facilitates centriole assembly in C. elegans embryos. Our findings lead us to propose that the interdependence of SAS-5 oligomerisation and microtubule binding reflects an avidity mechanism that strengthens SAS-5 associations with other centriole components and, thus, promotes organelle assembly.

Huang Y et al. (2007) BMC Genomics "A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs."

Gu X, Huang Y

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: Phylogenetically related miRNAs (miRNA families) convey important information of the function and evolution of miRNAs. Due to the special sequence features of miRNAs, pair-wise sequence identity between miRNA precursors alone is often inadequate for unequivocally judging the phylogenetic relationships between miRNAs. Most of the current methods for miRNA classification rely heavily on manual inspection and lack measurements of the reliability of the results. RESULTS: In this study, we designed an analysis pipeline (the Phylogeny-Bootstrap-Cluster (PBC) pipeline) to identify miRNA families based on branch stability in the bootstrap trees derived from overlapping genome-wide miRNA sequence sets. We tested the PBC analysis pipeline with the miRNAs from six animal species, H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, and C. elegans. The resulting classification was compared with the miRNA families defined in miRBase. The two classifications were largely consistent. CONCLUSIONS: The PBC analysis pipeline is an efficient method for classifying large numbers of heterogeneous miRNA sequences. It requires minimum human involvement and provides measurements of the reliability of the classification results.

Smith HE et al. (2017) PLoS One "Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing."

Yun S, Smith HE

[PLoS One, 2017]

Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria. Although success is predicated upon the sensitive and accurate detection of candidate alleles, relatively little effort has been invested in evaluating the underlying software components that are required for mutation identification. Therefore, we have benchmarked a number of commonly used tools for sequence alignment and variant calling, in all pair-wise combinations, against both simulated and actual datasets. We compared the accuracy of those pipelines for mutation identification in C. elegans, and found that the combination of BBMap for alignment plus FreeBayes for variant calling offers the most robust performance.

Krishna NR et al. (2011) Protein Expr Purif "Expression, purification and characterization of refolded rBm-33 (pepsin inhibitor homolog) from Brugia malayi: a human Lymphatic Filarial parasite."

Krushna NS, Rajan SS, Narayanan RB, Gunasekaran K, Krishna NR

[Protein Expr Purif, 2011]

Bm-33 (pepsin inhibitor homolog) produced by the human filarial parasite Brugia malayi, was expressed in Escherichia coli. Expression of rBm33 in BL21 (DE3), Rosetta-2 gami (DE3) pLysS and GJ1158 bacterial strains, results in the accumulation of a 33 kDa protein in inclusion bodies. Inactive rBm-33 was purified under the denaturing conditions and refolded by step wise dialysis using buffers of pH ranging from 11 to 7. Size exclusion chromatography of rBm-33 (refolded) reveals that nearly 83% of the recombinant protein exhibits pepsin inhibition activity. Circular dichroism studies indicate that the protein is predominantly composed of 85% -helix. rBm-33 (refolded) was assessed for its pepsin inhibition activity using casein agar plate method, UV-spectroscopy and zymogram analysis. These findings suggest that rBm-33 (refolded) has affinity for human pepsin and completely inhibits the proteolytic activity with the gradual increase in rBm-33 (refolded) concentration. Size exclusion chromatography reveals the formation of rBm-33-pepsin complex and was cross checked using immunoblot with glutaraldehyde cross linking. These findings reveal that rBm-33 (refolded) is in native fold to exhibit pepsin inhibition.

van Schendel R et al. (2016) PLoS Genet "Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining."

van Heteren J, Welten R, van Schendel R, Tijsterman M

[PLoS Genet, 2016]

For more than half a century, genotoxic agents have been used to induce mutations in the genome of model organisms to establish genotype-phenotype relationships. While inaccurate replication across damaged bases can explain the formation of single nucleotide variants, it remained unknown how DNA damage induces more severe genomic alterations. Here, we demonstrate for two of the most widely used mutagens, i.e. ethyl methanesulfonate (EMS) and photo-activated trimethylpsoralen (UV/TMP), that deletion mutagenesis is the result of polymerase Theta (POLQ)-mediated end joining (TMEJ) of double strand breaks (DSBs). This discovery allowed us to survey many thousands of available C. elegans deletion alleles to address the biology of this alternative end-joining repair mechanism. Analysis of ~7,000 deletion breakpoints and their cognate junctions reveals a distinct order of events. We found that nascent strands blocked at sites of DNA damage can engage in one or more cycles of primer extension using a more downstream located break end as a template. Resolution is accomplished when 3' overhangs have matching ends. Our study provides a step-wise and versatile model for the in vivo mechanism of POLQ action, which explains the molecular nature of mutagen-induced deletion alleles.

Kale OO (1981) J Helminthol "The effect of drug treatment on the pattern of emergence of Onchocerca volvulus microfilariae from skin snips."

Kale OO

[J Helminthol, 1981]

A controlled study was carried out to determine the effect of some known anti-filarial drugs on the pattern of emergence of Onchocerca volvulus microfilariae from skin snips into saline. The results show that before treatment, 81.7 to 92.1% of microfilariae emerge in all the groups within 24 hours. The differences between the groups were not significant. After treatment with oral diethylcarbamazine, metrifonate and topical diethylcarbamazine (DEC) the percentage of microfilariae emerging from the snips dropped significantly to 48.4, 56.0 and 60.1 respectively, whereas no significant change occurred following treatment with levamisole (88.1%) and yeast tablets (89.1%). A pair-wise comparison of the post-treatment microfilarial emergence in all the groups showed statistically significant differences when (i) oral DEC is compared to levamisole, topical DEC and yeast, (ii) metrifonate is compared to levamisole and yeast and (iii) topical DEC is compared to yeast. It is suggested that microfilariae which fail to emerge from snips after treatment are those that have been killed or paralysed by the action of the drugs. The study has thus established that drug action in vivo is one of the factors which affects the proportion of microfilariae which emerge from skin snips and provides an additional parameter for measuring the antimicrofilarial potential of drugs in clinical chemotherapeutic trials.

Coux O (2003) Biochem Soc Trans "An interaction map of proteasome subunits."

Coux O

[Biochem Soc Trans, 2003]

Despite the central role of the 26 S proteasome in eukaryotic cells, many facets of its structural organization and functioning are still poorly understood. To learn more about the interactions between its different subunits, as well as its possible functional partners in cells, we performed, with Marc Vidal's laboratory (Dana-Farber Cancer Institute, Boston, MA, U.S.A.), a systematic two-hybrid analysis using Caenorhaditis elegans 26 S proteasome subunits as baits (Davy, Bello, Thierry-Mieg, Vaglio, Hitti, Doucette-Stamm, Thierry-Mieg, Reboul, Boulton, Walhout et al. (2001) EMBO Rep. 2, 821-828). A pair-wise matrix of all subunit combinations allowed us to detect numerous possible intra-complex interactions, among which some had already been reported by others and eight were novel. Interestingly, four new interactions were detected between two ATPases of the 19 S regulatory complex and three alpha-subunits of the 20 S proteolytic core. Possibly, these interactions participate in the association of these two complexes to form the 26 S proteasome. Proteasome subunit sequences were also used to screen a cDNA library to identify new interactors of the complex. Among the interactors found, most (58) have no clear connection to the proteasome, and could be either substrates or potential cofactors of this complex. Few interactors (7) could be directly or indirectly linked to proteolysis. The others (12) interacted with more than one proteasome subunit, forming 'interaction clusters' of