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1.
Dev Dyn ; 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38924277

ABSTRACT

BACKGROUND: Sex-specific morphogenesis occurs in Caenorhabditis elegans in the vulva of the hermaphrodite and in the male tail during the last larval stage. Temporal progression of vulva morphogenesis has been described in fine detail. However, a similar precise description of male tail morphogenesis was lacking. RESULTS: We here describe morphogenesis of the male tail at time points matching vulva development with special focus on morphogenesis of the tail tip. Using fluorescent reporters, we follow changes in cell shapes, cell fusions, nuclear migration, modifications in the basement membrane, and formation of a new apical extracellular matrix at the end of the tail. CONCLUSION: Our analysis answers two open questions about tail tip morphogenesis (TTM) by showing that one of the four tail tip cells, hyp11, remains largely separate, while the other cells fully fuse with each other and with two additional tail cells to form a ventral tail syncytium. This merger of cells begins at the apical surface early during TTM but is only completed toward the end of the process. This work provides a framework for future investigations of cell biological factors that drive male tail morphogenesis.

2.
bioRxiv ; 2024 Jan 15.
Article in English | MEDLINE | ID: mdl-38293029

ABSTRACT

Background: Sex-specific morphogenesis occurs in C. elegans in the vulva of the hermaphrodite and in the male tail during the last larval stage. Temporal progression of vulva morphogenesis has been described in fine detail. However, a similar precise description of male tail morphogenesis was lacking. Results: We here describe morphogenesis of the male tail at time points matching vulva development with special focus on morphogenesis of the tail tip. Using fluorescent reporters, we follow changes in cell shapes, cell fusions, nuclear migration, modifications in the basement membrane and formation of a new apical extracellular matrix at the end of the tail. Conclusion: Our analysis answers two open questions about tail tip morphogenesis (TTM) by showing that one of the four tail tip cells, hyp11, remains separate while the other cells fuse with each other and with two additional tail cells to form a ventral tail syncytium. This fusion begins early during TTM but is only completed towards the end of the process. This work provides a framework for future investigations of cell-biological factors that drive male tail morphogenesis.

3.
bioRxiv ; 2024 Jan 12.
Article in English | MEDLINE | ID: mdl-38260477

ABSTRACT

Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs. dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the UPR (unfolded protein response) pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.

4.
bioRxiv ; 2023 Nov 22.
Article in English | MEDLINE | ID: mdl-38045386

ABSTRACT

A major question in evolutionary biology is how often the same developmental events, mechanisms and genes are reused in the recurrent evolution of similar phenotypes. If this happens frequently, it would suggest that evolution is often constrained by developmental genetic mechanisms. To help address this question, we used adherens junction staining and laser ablation to analyze the development underlying several features of nematode male tails have evolved recurrently. We find that recurrent evolution has sometimes employed similar developmental events (parallel evolution) and sometimes different events (convergent evolution). Specifically, phasmid position changed four times via cell migration and never by switches in cell lineage polarity; different genital papillae are missing in species with less than nine; and tail tip morphogenesis was gained at least twice (once with tail tip cell fusions and once without) and lost at least twice. As in previous analyses, we also find that genital papilla positions have shifted differently in different lineages relative to their conserved positions of origin in the lateral hypodermis. In particular, the v1 papilla homolog in diplogastrids has moved dorsally relative to the other v-papillae and lies posterior to the v2 papilla. The prevalence of recurrently evolved characters (homoplasy) suggests that caution should be exercised when using these characters for phylogenetic inference. On the other hand, because of their recurrent evolution, these characters provide good models for investigating how developmental and genetic systems may bias, constrain or allow phenotypic evolution.

5.
MicroPubl Biol ; 20232023.
Article in English | MEDLINE | ID: mdl-37927909

ABSTRACT

The development of the adult C. elegans male tail involves an extensive remodeling during the last larval stage where the pointed tail of the L4 male is converted into the blunt-ended adult tail with its collection of mechano-sensitive rays. The first step in this remodeling is the retraction of the four hypodermal cells of the tail tip to generate the blunt-ended tail. Male tail tip retraction is an excellent model for characterizing how upstream regulatory networks interact with the downstream cell biological effectors that drive morphogenetic changes in all animals. Previously, we've shown that two DM-domain transcription factors, MAB-3 and DMD-3 , are central regulators of male tail tip retraction. Using a microarray-based approach we have identified ~400 genes that are more highly expressed in the L4 male tail tip relative to the hermaphrodite L4 tail tip. The uncharacterized gene T05H10.3 , which we've named mtre-1 , was highly over-represented in the male tail tip vs. the hermaphrodite tail tip and was under-represented in mab-3 ; dmd-3 mutant male tail tips vs. wild-type male tail tips. A transcriptional reporter for mtre-1 shows clear expression in the male tail tip cells for a short period (~3 hours) at the end of retraction. This expression is dependent on the activity of MAB-3 and DMD-3 , since expression is reduced in dmd-3 single mutant males and absent in mab-3 ; dmd-3 mutant males. Finally, males homozygous for a putative null allele of mtre-1 display a phenotypically wild-type adult male tail, indicating that mtre-1 is not essential for male tail morphogenesis.

6.
PLoS One ; 18(9): e0288196, 2023.
Article in English | MEDLINE | ID: mdl-37672545

ABSTRACT

Recently, much attention has been focused on a group of rhabditid nematodes called Phasmarhabditis, a junior synonym of Pellioditis, as a promising source of biocontrol agents for invasive slugs. Pellioditis pelhamensis n. sp. was first isolated from earthworms near Pelham Bay Park in Bronx, New York, USA, in 1990 and has been found to be pathogenic to slugs as well as some earthworms. It has also been used in several comparative developmental studies. Here, we provide a description of this species, as well as a redescription of a similar earthworm-associated nematode, Pellioditis pellio Schneider, 1866, re-isolated from the type locality. Although P. pelhamensis n. sp. and P. pellio are morphologically similar, they are reproductively isolated. Molecular phylogenetic analysis places both species in a clade that includes all species previously described as Phasmarhabditis which are associated with gastropods. Phasmarhabditis Andrássy, 1976 is therefore a junior synonym of Pellioditis Dougherty, 1953. Also, Pellioditis bohemica Nermut', Puza, Mekete & Mrácek, 2017, described to be a facultative parasite of slugs, is found to be a junior synonym of Pellioditis pellio (Schneider, 1866), adding to evidence that P. pellio is associated with both slugs and earthworms. The earthworm-associated species P. pelhamensis n. sp. and P. pellio represent different subclades within Pellioditis, suggesting that Pellioditis species in general have a broader host range than just slugs. Because of this, caution is warranted in using these species as biological control agents until more is understood about their ecology.


Subject(s)
Gastropoda , Oligochaeta , Rhabditoidea , Animals , Humans , Phylogeny , Research Personnel , Biological Control Agents
7.
J Vis Exp ; (181)2022 03 31.
Article in English | MEDLINE | ID: mdl-35435919

ABSTRACT

Single-cell methodologies have revolutionized the analysis of the transcriptomes of specific cell types. However, they often require species-specific genetic "toolkits," such as promoters driving tissue-specific expression of fluorescent proteins. Further, protocols that disrupt tissues to isolate individual cells remove cells from their native environment (e.g., signaling from neighbors) and may result in stress responses or other differences from native gene expression states. In the present protocol, laser microdissection (LMD) is optimized to isolate individual nematode tail tips for the study of gene expression during male tail tip morphogenesis. LMD allows the isolation of a portion of the animal without the need for cellular disruption or species-specific toolkits and is thus applicable to any species. Subsequently, single-cell RNA-seq library preparation protocols such as CEL-Seq2 can be applied to LMD-isolated single tissues and analyzed using standard pipelines, given that a well-annotated genome or transcriptome is available for the species. Such data can be used to establish how conserved or different the transcriptomes are that underlie the development of that tissue in different species. Limitations include the ability to cut out the tissue of interest and the sample size. A power analysis shows that as few as 70 tail tips per condition are required for 80% power. Tight synchronization of development is needed to obtain this number of animals at the same developmental stage. Thus, a method to synchronize animals at 1 h intervals is also described.


Subject(s)
Proteins , Transcriptome , Animals , Laser Capture Microdissection/methods , Lasers , Male
8.
Genetics ; 219(3)2021 11 05.
Article in English | MEDLINE | ID: mdl-34740245

ABSTRACT

Specialized cells of the somatic gonad primordium of nematodes play important roles in the final form and function of the mature gonad. Caenorhabditis elegans hermaphrodites are somatic females that have a two-armed, U-shaped gonad that connects to the vulva at the midbody. The outgrowth of each gonad arm from the somatic gonad primordium is led by two female distal tip cells (fDTCs), while the anchor cell (AC) remains stationary and central to coordinate uterine and vulval development. The bHLH protein HLH-2 and its dimerization partners LIN-32 and HLH-12 had previously been shown to be required for fDTC specification. Here, we show that ectopic expression of both HLH-12 and LIN-32 in cells with AC potential transiently transforms them into fDTC-like cells. Furthermore, hlh-12 was known to be required for the fDTCs to sustain gonad arm outgrowth. Here, we show that ectopic expression of HLH-12 in the normally stationary AC causes displacement from its normal position and that displacement likely results from activation of the leader program of fDTCs because it requires genes necessary for gonad arm outgrowth. Thus, HLH-12 is both necessary and sufficient to promote gonadal regulatory cell migration. As differences in female gonadal morphology of different nematode species reflect differences in the fate or migratory properties of the fDTCs or of the AC, we hypothesized that evolutionary changes in the expression of hlh-12 may underlie the evolution of such morphological diversity. However, we were unable to identify an hlh-12 ortholog outside of Caenorhabditis. Instead, by performing a comprehensive phylogenetic analysis of all Class II bHLH proteins in multiple nematode species, we found that hlh-12 evolved within the Caenorhabditis clade, possibly by duplicative transposition of hlh-10. Our analysis suggests that control of gene regulatory hierarchies for gonadogenesis can be remarkably plastic during evolution without adverse phenotypic consequence.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors , Caenorhabditis elegans , Gonads , Sex Differentiation , Animals , Female , Male , Animals, Genetically Modified , Basic Helix-Loop-Helix Transcription Factors/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans/growth & development , Caenorhabditis elegans Proteins/metabolism , Evolution, Molecular , Gene Expression Regulation, Developmental , Gonads/cytology , Gonads/growth & development , Organogenesis/genetics , Phylogeny , Sex Differentiation/genetics , Transcription Factors/metabolism
9.
PLoS One ; 16(8): e0255417, 2021.
Article in English | MEDLINE | ID: mdl-34347828

ABSTRACT

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases there is a need for increased world-wide SARS-CoV-2 testing capability that is both efficient and effective. Having open and easy access to detailed information about these tests, their sensitivity, the types of samples they use, etc. would be highly useful to ensure their reproducibility, to help clients compare and decide which tests would be best suited for their applications, and to avoid costs of reinventing similar or identical tests. Additionally, this resource would provide a means of comparing the many innovative diagnostic tools that are currently being developed in order to provide a foundation of technologies and methods for the rapid development and deployment of tests for future emerging diseases. Such a resource might thus help to avert the delays in testing and screening that was observed in the early stages of the pandemic and plausibly led to more COVID-19-related deaths than necessary. We aim to address these needs via a relational database containing standardized ontology and curated data about COVID-19 diagnostic tests that have been granted Emergency Use Authorizations (EUAs) by the FDA (US Food and Drug Administration). Simple queries of this actively growing database demonstrate considerable variation among these tests with respect to sensitivity (limits of detection, LoD), controls and targets used, criteria used for calling results, sample types, reagents and instruments, and quality and amount of information provided.


Subject(s)
COVID-19 Testing , Databases, Factual , Emergencies , United States Food and Drug Administration/organization & administration , COVID-19/diagnosis , COVID-19 Testing/methods , COVID-19 Testing/standards , Data Management/organization & administration , Data Management/standards , Databases, Factual/supply & distribution , Emergencies/classification , Emergency Treatment/classification , Emergency Treatment/methods , Humans , Internet , Laboratories/standards , Reference Standards , Sensitivity and Specificity , United States , User-Computer Interface
10.
Article in English | MEDLINE | ID: mdl-33376929

ABSTRACT

A recent survey of orthopaedic surgeons asking about risk factors for nonunion following foot and ankle arthrodesis revealed that patient age is considered to be a relatively low risk factor, despite the potential for autologous graft quality to deteriorate with increasing age. The purpose of the current study was to evaluate the impact of patient age and graft type on fusion rates following hindfoot and ankle arthrodesis. METHODS: In this study, we analyzed data from a previously published clinical trial, comparing fusion success in 397 subjects who underwent hindfoot or ankle arthrodesis (597 joints) supplemented with either autograft or an osteoinductive autograft alternative, recombinant human platelet-derived growth factor-BB homodimer carried in beta-tricalcium phosphate (rhPDGF-BB/ß-TCP). The odds of fusion success were compared among subjects older or younger than age thresholds of 55, 60, 65, 70, and 75 years. The odds of fusion success were also compared between autograft and rhPDGF-BB/ß-TCP among subjects older than each age threshold. RESULTS: In the autograft group, the joints of subjects who were younger than the age thresholds of 60 and 65 years had >2 times the odds of successful fusion compared with those of older subjects. There was no significant difference in the odds of fusion success between the older and younger subjects at the age threshold of 55 years. In the rhPDGF-BB/ß-TCP group, there was no significant difference in the odds of successful fusion between older and younger subjects at any age threshold. When the odds of fusion success were compared between the 2 graft materials in subjects who were older than each age threshold, rhPDGF-BB/ß-TCP had approximately 2 times the odds of fusion success compared with autograft for all thresholds, except 55 years. CONCLUSIONS: The presented evidence suggests that age is an identifiable and concerning risk factor for hindfoot and ankle arthrodesis nonunion, a finding in contrast to the wider perception in the surgeon community. Notably, patients ≥60 years of age had significantly lower odds of fusion success with the use of autograft. The data reveal that use of rhPDGF-BB/ß-TCP as an alternative bone-healing adjunct may help mitigate the risk of nonunion when these procedures are performed in the elderly population. LEVEL OF EVIDENCE: Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.

11.
bioRxiv ; 2020 Aug 10.
Article in English | MEDLINE | ID: mdl-32766578

ABSTRACT

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases, the prevalence of asymptomatic cases and the fact that undocumented cases appear to be significant for transmission of the causal virus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), there is an urgent need for increased SARS-CoV-2 testing capability that is both efficient and effective1. In response to the growing threat of the COVID-19 pandemic in February, 2020, the FDA (US Food and Drug Administration) began issuing Emergency Use Authorizations (EUAs) to laboratories and commercial manufacturers for the development and implementation of diagnostic tests[1]. So far, the gold standard assay for SARS-CoV-2 detection is the RT-qPCR (real-time quantitative polymerase chain reaction) test[2]. However, the authorized RT-qPCR test protocols vary widely, not only in the reagents, controls, and instruments they use, but also in the SARS-CoV-2 genes they target, what results constitute a positive SARS-CoV-2 infection, and their limit of detection (LoD). The FDA has provided a web site that lists most of the tests that have been issued EUAs, along with links to the authorization letters and summary documents describing these tests[1]. However, it is very challenging to use this site to compare or replicate these tests for a variety of reasons. First, at least 12 of 18 tests for EUA submissions made prior to March 31, 2020, are not listed there. To our knowledge, no EUAs have been issued for these applications. Second, the data are not standardized and are only provided as longhand prose in the summary documents. Third, some details (e.g. primer sequences) are absent from several of the test descriptions. Fourth, for tests provided by commercial manufacturers, summary documents are completely missing. To address at least the first three issues, we have developed a database, EUAdb (EUAdb.org), that holds standardized information about EUA-issued tests and is focused on RT-qPCR diagnostic tests, or "high complexity molecular-based laboratory developed tests"[1]. By providing a standardized ontology and curated data in a relational architecture, we seek to facilitate comparability and reproducibility, with the ultimate goal of consistent, universal and high-quality testing nationwide. Here, we document the basics of the EUAdb data architecture and simple data queries. The source files can be provided to anyone who wants to modify the database for his/her own research purposes. We ask that the original source of the files be made clear and that the database not be used in its original or modified forms for commercial purposes.

12.
Foot Ankle Int ; 41(8): 911-915, 2020 08.
Article in English | MEDLINE | ID: mdl-32432488

ABSTRACT

BACKGROUND: Pain following autograft harvest has been studied; however, published literature has typically focused on the iliac crest with follow-up limited to only a few years. It remains unknown if pain continues or improves over time. The purpose of this study was to evaluate long-term pain associated with autograft harvest to supplement hindfoot or ankle arthrodesis. METHODS: Subjects in the control arm of a previously conducted trial comparing autograft with a synthetic bone graft for hindfoot or ankle arthrodesis were invited back for a single visit at a minimum of 5 years following their initial surgery. Harvest site, fusion site, and weight-bearing pain were evaluated using a 100-point visual analog scale (VAS). Of the 130 invited subjects, 60 (46.1%) returned for assessment, 58 of whom completed pain assessments. RESULTS: At a mean follow-up of 9.0 years (range, 7.8-10.5), more than a third (36.6%) of subjects had some level of harvest site pain. Using VAS greater than 20 mm as a threshold of clinical significance, pain remained clinically significant in 5.2% of subjects. There was a significant correlation between harvest site pain and both weight-bearing and fusion site pain. There was not a significant correlation between harvest site pain and volume of graft harvested. CONCLUSION: Autograft harvest can result in chronic, clinically significant pain that can last up to 10 years. In the era of shared decision making, this information will help surgeons and patients quantify the risks of chronic pain after arthrodesis procedures that include a secondary operative incision for graft harvest. LEVEL OF EVIDENCE: Level II, prospective comparative study.


Subject(s)
Arthrodesis , Autografts , Bone Transplantation/adverse effects , Chronic Pain/etiology , Pain, Postoperative , Adult , Aged , Arthrodesis/methods , Chronic Pain/diagnosis , Female , Follow-Up Studies , Humans , Male , Middle Aged , Pain Measurement
13.
J Orthop Surg Res ; 14(1): 376, 2019 Nov 21.
Article in English | MEDLINE | ID: mdl-31752951

ABSTRACT

BACKGROUND: The separate design concepts of dual-mobility cups and triple-taper femoral stems were developed to improve survivorship following total hip replacement (THR) by reducing instability/dislocation and enabling enhanced fixation. Successful outcomes at over two decades have been reported with earlier-generation devices based on these concepts. The current study aimed to provide the first long-term results with a unique pairing of later-generation dual-mobility cup and triple-taper cementless femoral stem after a decade of use in patients undergoing THR. METHODS: In this retrospective analysis, records were reviewed for all subjects implanted with this dual-mobility cup/cementless femoral stem combination at three centers between 2002 and 2005. Any subject who had not already had follow-up visit beyond 10 years, was not previously revised, and still living were invited for a single follow-up visit consisting of Merle d'Aubgine Scores, the Western Ontario and McMaster Universities Osteoarthritis (WOMAC) index, and standard radiographs. RESULTS: There were 244 THRs available for analysis. At a mean follow-up of 11.9 years, the Kaplan-Meier survivorship (endpoint: revision for any reason) was 99.1% (95% CI, 97.6-99.7) for the stem and 95.9% (95% CI, 93.1-97.6) for the cup. Merle d'Aubigne Scores were significantly improved from baseline and WOMAC scores were in the satisfactory range at the final follow-up. Radiographic analysis revealed no cases of stem subsidence, no cases of bone hypertrophy, 1 (0.4%) case of bone atrophy, and 3 (1.2%) cases of osteolysis around the stem. No subjects had radiolucent lines greater than 1 mm in any femoral Gruen zone. Evidence of cup migration was seen in 1 (0.4%) subject and 1 (0.4%) subject had evidence of osteolysis that was seen in Gruen zones I, II, IV, and V. CONCLUSIONS: This combination of a later-generation dual-mobility cup and cementless triple-taper stem was associated with excellent survivorship and satisfactory functional outcomes at over 10 years follow-up. TRIAL REGISTRATION: ClinicalTrials.gov, NCT02648152. Date of registration: January 6, 2016. Retrospectively registered.


Subject(s)
Arthroplasty, Replacement, Hip/instrumentation , Hip Prosthesis/statistics & numerical data , Adult , Aged , Aged, 80 and over , Female , Femur/surgery , Humans , Male , Middle Aged , Retrospective Studies , Treatment Outcome
14.
Elife ; 82019 07 02.
Article in English | MEDLINE | ID: mdl-31264582

ABSTRACT

Sexual maturation must occur on a controlled developmental schedule. In mammals, Makorin3 (MKRN3) and the miRNA regulators LIN28A/B are key regulators of this process, but how they act is unclear. In C. elegans, sexual maturation of the nervous system includes the functional remodeling of postmitotic neurons and the onset of adult-specific behaviors. Here, we find that the lin-28-let-7 axis (the 'heterochronic pathway') determines the timing of these events. Upstream of lin-28, the Makorin lep-2 and the lncRNA lep-5 regulate maturation cell-autonomously, indicating that distributed clocks, not a central timer, coordinate sexual differentiation of the C. elegans nervous system. Overexpression of human MKRN3 delays aspects of C. elegans sexual maturation, suggesting the conservation of Makorin function. These studies reveal roles for a Makorin and a lncRNA in timing of sexual differentiation; moreover, they demonstrate deep conservation of the lin-28-let-7 system in controlling the functional maturation of the nervous system.


Subject(s)
Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans/genetics , RNA, Long Noncoding/genetics , Repressor Proteins/genetics , Ribonucleoproteins/genetics , Animals , Caenorhabditis elegans/growth & development , Cell Differentiation , Gene Expression Regulation, Developmental , Humans , MicroRNAs , Mutation , Nervous System/growth & development , Sexual Maturation/genetics , Ubiquitin-Protein Ligases
15.
Dev Cell ; 49(4): 542-555.e9, 2019 05 20.
Article in English | MEDLINE | ID: mdl-30956008

ABSTRACT

Biological roles for most long non-coding RNAs (lncRNAs) remain mysterious. Here, using forward genetics, we identify lep-5, a lncRNA acting in the C. elegans heterochronic (developmental timing) pathway. Loss of lep-5 delays hypodermal maturation and male tail tip morphogenesis (TTM), hallmarks of the juvenile-to-adult transition. We find that lep-5 is a ∼600 nt cytoplasmic RNA that is conserved across Caenorhabditis and possesses three essential secondary structure motifs but no essential open reading frames. lep-5 expression is temporally controlled, peaking prior to TTM onset. Like the Makorin LEP-2, lep-5 facilitates the degradation of LIN-28, a conserved miRNA regulator specifying the juvenile state. Both LIN-28 and LEP-2 associate with lep-5 in vivo, suggesting that lep-5 directly regulates LIN-28 stability and may function as an RNA scaffold. These studies identify a key biological role for a lncRNA: by regulating protein stability, it provides a temporal cue to facilitate the juvenile-to-adult transition.


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/growth & development , RNA, Long Noncoding/metabolism , Repressor Proteins/metabolism , Amino Acid Sequence , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Morphogenesis/genetics , Morphogenesis/physiology , Mutation , Phenotype , RNA, Long Noncoding/genetics , Repressor Proteins/genetics , Ribonucleoproteins/genetics , Ribonucleoproteins/metabolism , Transcription Factors/metabolism
16.
Evol Lett ; 3(2): 217-236, 2019 Apr.
Article in English | MEDLINE | ID: mdl-31007946

ABSTRACT

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

17.
Genetics ; 210(2): 397-433, 2018 10.
Article in English | MEDLINE | ID: mdl-30287515

ABSTRACT

Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.


Subject(s)
Caenorhabditis elegans/embryology , Evolution, Molecular , Morphogenesis , Animals , Caenorhabditis elegans/genetics , Gene Expression Regulation, Developmental
18.
Curr Biol ; 27(19): 2928-2939.e6, 2017 Oct 09.
Article in English | MEDLINE | ID: mdl-28943090

ABSTRACT

Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair. We show that this unichromosomal architecture is shared by a long-lived clade of asexual nematodes closely related to the genetic model organism Caenorhabditis elegans. Analysis of the genome assembly reveals that the unitary chromosome arose through fusion of six ancestral chromosomes, with extensive rearrangement among neighboring regions. Typical nematode telomeres and telomeric protection-encoding genes are lacking. Most regions show significant heterozygosity; homozygosity is largely concentrated to one region and attributed to gene conversion. Cell-biological and molecular evidence is consistent with the absence of key features of meiosis I, including synapsis and recombination. We propose that D. pachys preserves heterozygosity and produces diploid embryos without fertilization through a truncated meiosis. As a prelude to functional studies, we demonstrate that D. pachys is amenable to experimental manipulation by RNA interference.


Subject(s)
Evolution, Molecular , Genome, Helminth , Reproduction, Asexual , Rhabditoidea/genetics , Animals , Whole Genome Sequencing
19.
Int Orthop ; 41(6): 1119-1123, 2017 06.
Article in English | MEDLINE | ID: mdl-27838761

ABSTRACT

PURPOSE: The supercapsular percutaneously-assisted total hip (SuperPath) surgical technique for total hip replacement (THR) is a tissue-sparing approach that has been shown to improve key variables associated with the economic burden of THR (e.g., length of stay, readmissions). To date, no studies have examined the economic impact of using this technique in the United States. The objective of this study was to compare the in-hospital costs of this technique to all other THRs performed in a large hospital system in the United States. METHODS: The costing database for a large hospital system was retrospectively searched for all in-hospital costs associated with primary THRs performed between January 2013 and September 2015. Data for all SuperPath THRs (group A) were compared to that of all other THRs performed at centres within the hospital system (group B). RESULTS: Use of the SuperPath technique resulted in significant overall in-hospital cost reductions of 15.0 % (p < 0.000), including reductions in operating room costs of 17.3 % (p < 0.000), physical/occupational therapy costs of 26.8 % (p = 0.005), and pharmacy costs of 25.3 % (p < 0.000). Length of stay (1.2 vs. 2.6 days), transfusion rates (1.9 vs. 15.8 %), and 30-day readmission rates (0.4 vs. 2.9 %) were also lower in group A. CONCLUSIONS: The use of this tissue-sparing surgical technique resulted in reductions in in-hospital costs, length of stay, and readmissions when compared to all other THRs performed in a large hospital system in the United States.


Subject(s)
Arthroplasty, Replacement, Hip/economics , Hospital Costs/statistics & numerical data , Length of Stay/statistics & numerical data , Patient Readmission/statistics & numerical data , Adult , Aged , Aged, 80 and over , Arthroplasty, Replacement, Hip/methods , Databases, Factual , Female , Humans , Male , Middle Aged , Patient Readmission/economics , Retrospective Studies , United States , Young Adult
20.
Ann Transl Med ; 4(18): 339, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27761443

ABSTRACT

BACKGROUND: Patient dissatisfaction following total knee replacement (TKR) has been reported as high as 24%. Most previous studies have focused on satisfaction for TKR overall, with few reporting satisfaction for specific implant designs. The purpose of this study was to assess patient satisfaction for TKRs performed using a second generation medial-pivot system (EVOLUTION®, MicroPort Orthopedics Inc., Arlington, TN, USA). METHODS: Of a single surgeon's first 250 consecutive TKRs performed using the subject system, 224 completed a patient satisfaction assessment, the Knee Injury and Osteoarthritis Outcome Score (KOOS), range of motion, and radiographs at 2 months follow-up. RESULTS: The overall very satisfied/satisfied rate was 94.6% at 2 months. Following the first 50 TKRs, the satisfied rate improved to 99.4% suggesting a bias towards the initial cases potentially due to learning the system and instrumentation. Overall KOOS, range of motion, and radiographic outcomes were satisfactory at final follow-up. CONCLUSIONS: In conclusion, more subjects implanted with a second generation medial-pivot system were satisfied compared to previous reports for TKR.

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