Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs.

In the ciliated protozoan Paramecium tetraurelia, Piwi-associated small RNAs are generated upon the elimination of tens of thousands of short transposon-derived DNA segments as part of development. These RNAs then target complementary DNA for elimination in a positive feedback process, contributing to germline defense and genome stability. In this work, we investigate the formation of these RNAs, which we show to be transcribed directly from the short (length mode 27 bp) excised DNA segments. Our data support a mechanism whereby the concatenation and circularization of excised DNA segments provides a template for RNA production. This process allows the generation of a double-stranded RNA for Dicer-like protein cleavage to give rise to a population of small regulatory RNAs that precisely match the excised DNA sequences. VIDEO ABSTRACT.

Versatile CRISPR/Cas9-mediated mosaic analysis by gRNA-induced crossing-over for unmodified genomes.

Mosaic animals have provided the platform for many fundamental discoveries in developmental biology, cell biology, and other fields. Techniques to produce mosaic animals by mitotic recombination have been extensively developed in Drosophila melanogaster but are less common for other laboratory organisms. Here, we report mosaic analysis by gRNA-induced crossing-over (MAGIC), a new technique for generating mosaic animals based on DNA double-strand breaks produced by CRISPR/Cas9. MAGIC efficiently produces mosaic clones in both somatic tissues and the germline of Drosophila. Further, by developing a MAGIC toolkit for 1 chromosome arm, we demonstrate the method's application in characterizing gene function in neural development and in generating fluorescently marked clones in wild-derived Drosophila strains. Eliminating the need to introduce recombinase-recognition sites into the genome, this simple and versatile system simplifies mosaic analysis in Drosophila and can in principle be applied in any organism that is compatible with CRISPR/Cas9.

Alternative treatments of adenomyosis - an update in procedural management and clinical outcomes.

PURPOSE OF REVIEW: Adenomyosis is a common cause of abnormal uterine bleeding (AUB), dysmenorrhea, and pelvic pain. Definitive diagnosis and treatment have historically been by uterine histopathology at time of hysterectomy; however, advances in imaging have supported earlier diagnosis and subsequent conservative treatment. This review aims to update the evidence supporting the uterine-sparing, procedural management options with a focus on clinical outcomes. RECENT FINDINGS: Uterine artery embolization (UAE), radiofrequency ablation (RFA), high-intensity focused ultrasound (HIFU), percutaneous microwave ablation (PMWA), and adenomyomectomy are minimally invasive interventions proven to be effective in reducing AUB and dysmenorrhea due to adenomyosis. Symptom improvement is associated with a decrease in uterine volume. Studies support the use of alternative treatment options given the overall low rates of symptom recurrence and reintervention. Combination therapy may be more effective than monotherapy. SUMMARY: This review provides the current evidence for use of alternative treatment options for adenomyosis. Access to ablative therapies in the USA is limited and primarily off label, given lack of FDA approval. High-quality prospective and randomized controlled trials are needed in order to further delineate treatment comparisons, efficacy, safety, and ideal patient selection for these treatments. More data are needed to assess safety and utility in those desiring future fertility.

Upgraded CRISPR/Cas9 tools for tissue-specific mutagenesis in Drosophila.

CRISPR/Cas9 has emerged as a powerful technology for tissue-specific mutagenesis. However, tissue-specific CRISPR/Cas9 tools currently available in Drosophila remain deficient in three significant ways. First, many existing gRNAs are inefficient, such that further improvements of gRNA expression constructs are needed for more efficient and predictable mutagenesis in both somatic and germline tissues. Second, it has been difficult to label mutant cells in target tissues with current methods. Lastly, application of tissue-specific mutagenesis at present often relies on Gal4-driven Cas9, which hampers the flexibility and effectiveness of the system. Here, we tackle these deficiencies by building upon our previous CRISPR-mediated tissue-restricted mutagenesis (CRISPR-TRiM) tools. First, we significantly improved gRNA efficiency in somatic tissues by optimizing multiplexed gRNA design. Similarly, we also designed efficient dual-gRNA vectors for the germline. Second, we developed methods to positively and negatively label mutant cells in tissue-specific mutagenesis by incorporating co-CRISPR reporters into gRNA expression vectors. Lastly, we generated genetic reagents for convenient conversion of existing Gal4 drivers into tissue-specific Cas9 lines based on homology-assisted CRISPR knock-in. In this way, we expand the choices of Cas9 for CRISPR-TRiM analysis to broader tissues and developmental stages. Overall, our upgraded CRISPR/Cas9 tools make tissue-specific mutagenesis more versatile, reliable, and effective in Drosophila These improvements may be also applied to other model systems.

Opioid Use After Laparoscopic Surgery for Endometriosis and Pelvic Pain.

STUDY OBJECTIVE: The primary objective was to quantify postoperative opioid use after laparoscopic surgery for endometriosis or pelvic pain. The secondary objective was to identify patient characteristics associated with greater postoperative opioid requirements. DESIGN: Prospective, survey-based study in which subjects completed 1 preoperative and 7 postoperative surveys within 28 days of surgery regarding medication usage and pain control. SETTING: Tertiary care, academic center. PATIENTS: A total of 100 women with endometriosis or pelvic pain. INTERVENTIONS: Laparoscopic same-day discharge surgery by fellowship-trained minimally invasive gynecologists. MEASUREMENTS AND MAIN RESULTS: A total of 100 patients were recruited and 8 excluded, for a final sample size of 92 patients. All patients completed the preoperative survey. Postoperative response rates ranged from 70.7% to 80%. The mean number of pills (5 mg oxycodone tablets) taken by day 28 was 6.8. The average number of pills prescribed was 10.2, with a minimum of 4 (n = 1) and maximum of 20 (n = 3). Previous laparoscopy for pelvic pain was associated with a significant increase in postoperative narcotic use (8.2 vs 5.6; p = .044). Hysterectomy was the only surgical procedure associated with a significant increase in postoperative narcotic use (9.7 vs 5.4; p = .013). There were no difference in number of pills taken by presence of deep endometriosis or pathology-confirmed endometriosis (all p >.36). There was a trend of greater opioid use in patients with diagnoses of self-reported chronic pelvic pain, anxiety, and depression (7.9 vs 5.7, p = .051; 7.7 vs 5.2, p = .155; 8.1 vs 5.6, p = .118). CONCLUSION: Most patients undergoing laparoscopic surgery for endometriosis and pelvic pain had a lower postoperative opioid requirement than prescribed, suggesting surgeons can prescribe fewer postoperative narcotics in this population. Patients with a previous surgery for pelvic pain, self-reported chronic pelvic pain syndrome, anxiety, and depression may represent a subset of patients with increased postoperative opioid requirements.

Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control.

Approximately half the mammalian genome is composed of repetitive sequences, and accumulating evidence suggests that some may have an impact on genome function. Here, we characterized a large array class of repeats of long-interspersed elements (LINE-1). Although widely distributed in mammals, locations of such arrays are species specific. Using targeted deletion, we asked whether a 170-kb LINE-1 array located at a mouse imprinted domain might function as a modulator of local transcriptional control. The LINE-1 array is lamina associated in differentiated ES cells consistent with its AT-richness, and although imprinting occurs both proximally and distally to the array, active LINE-1 transcripts within the tract are biallelically expressed. Upon deletion of the array, no perturbation of imprinting was observed, and abnormal phenotypes were not detected in maternal or paternal heterozygous or homozygous mutant mice. The array does not shield nonimprinted genes in the vicinity from local imprinting control. Reduced neural expression of protein-coding genes observed upon paternal transmission of the deletion is likely due to the removal of a brain-specific enhancer embedded within the LINE array. Our findings suggest that presence of a 170-kb LINE-1 array reflects the tolerance of the site for repeat insertion rather than an important genomic function in normal development.

Abdominal wall endometriosis: an update in diagnosis, perioperative considerations and management.

PURPOSE OF REVIEW: Abdominal wall endometriosis (AWE) is rare with limited evidence guiding diagnosis and treatment. The purpose of this review is to provide an update of the diagnosis, perioperative considerations, and treatment of AWE. RECENT FINDINGS: Recent studies further characterize presenting symptoms and locations of AWE. Prior abdominal surgery remains the greatest risk factor for the development of AWE. Newer evidence suggests that increasing BMI may also be a risk factor. Ultrasound is first-line imaging for diagnosis. Magnetic resonance image is preferred for surgical planning for deep or extensive lesions. Laparotomy with wide local excision is considered standard treatment for AWE with great success. Novel techniques in minimally invasive surgery have been described as effective for the treatment of AWE. A multidisciplinary surgical approach is often warranted for successful excision and reapproximation of skin and/or fascial defects. Noninvasive therapies including ultrasonic ablation or cryotherapy are also emerging as promising treatment strategies in select patients. SUMMARY: Recent studies provide further evidence to guide diagnosis through physical exam and imaging as well as pretreatment planning. Treatment options for AWE are rapidly expanding with novel approaches in minimally invasive and noninvasive therapies now available.

Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance.

Ciliates are a fascinating model system for the study of the interaction between eukaryotic germlines and somatic lines, especially with regard to the invasion and defence against transposable elements. They separate their germline and somatic line into two nuclei within the same cell, and they silence transposons and repetitive elements by way of deleting them from their somatic genome. This large-scale deletion event uses a series of intricate sequence targeting pathways involving small RNAs and transposases, part of which consists of a transnuclear comparison between maternal soma and daughter germline. We present recent progress in this dynamic field, and argue that these DNA targeting pathways provide an optimal system for the transgenerational inheritance of acquired traits. Ciliates thus also demonstrate the evolutionary value of transposable elements, both as sources of sequence diversity and also as drivers of adaptive evolution by necessitating defensive systems.

Social norm feedback reduces primary care antibiotic prescribing in a regression discontinuity study.

BACKGROUND: Reducing antibiotic prescribing is a priority for health authorities responsible for preventing antimicrobial resistance. Northern Ireland has high rates of antimicrobial use. We implemented a social norm feedback intervention and evaluated its impact. OBJECTIVES: To estimate the size and duration of the effect of a social norm feedback letter to GPs who worked in the 20% of practices with the highest antimicrobial prescribing. METHODS: The letter was sent in October 2017 to 221 GPs in 67 practices. To assess the effect of the intervention, we used a sharp non-parametric regression discontinuity (RD) design, with prescribing rates in the four calendar quarters following the intervention as the outcome variables. RESULTS: In the quarter following the intervention (October to December 2017) there was a change of -25.7 (95% CI = -42.5 to -8.8, P = 0.0028) antibiotic items per 1000 Specific Therapeutic group Age-sex Related Prescribing Units (STAR-PU). At 1 year, the coefficient was -58.7 (95% CI = -116.7 to -0.7, P = 0.047) antibiotic items per 1000 STAR-PU. The greatest change occurred soon after the intervention. Approximately 18900 fewer antibiotic items were prescribed than if the intervention had not been made (1% of Northern Ireland's annual primary care antibiotic prescribing). CONCLUSIONS: A social norm feedback intervention reduced antibiotic prescribing in the intervention practices. The diminishing effect over time suggests the need for more frequent feedback. The RD method allowed measurement of the effectiveness of an intervention that was delivered as part of normal business, without a randomized trial.

A trans-homologue interaction between reciprocally imprinted miR-127 and Rtl1 regulates placenta development.

The paternally expressed imprinted retrotransposon-like 1 (Rtl1) is a retrotransposon-derived gene that has evolved a function in eutherian placentation. Seven miRNAs, including miR-127, are processed from a maternally expressed antisense Rtl1 transcript (Rtl1as) and regulate Rtl1 levels through RNAi-mediated post-transcriptional degradation. To determine the relative functional role of Rtl1as miRNAs in Rtl1 dosage, we generated a mouse specifically deleted for miR-127. The miR-127 knockout mice exhibit placentomegaly with specific defects within the labyrinthine zone involved in maternal-fetal nutrient transfer. Although fetal weight is unaltered, specific Rtl1 transcripts and protein levels are increased in both the fetus and placenta. Phenotypic analysis of single (ΔmiR-127/Rtl1 or miR-127/ΔRtl1) and double (ΔmiR-127/ΔRtl1) heterozygous miR-127- and Rtl1-deficient mice indicate that Rtl1 is the main target gene of miR-127 in placental development. Our results demonstrate that miR-127 is an essential regulator of Rtl1, mediated by a trans-homologue interaction between reciprocally imprinted genes on the maternally and paternally inherited chromosomes.

Icacinaceae from the eocene of Western North America.

PREMISE OF THE STUDY: The Icacinaceae are a pantropical family of trees, shrubs, and climbers with an extensive Paleogene fossil record. Our improved understanding of phylogenetic relationships within the family provides an excellent context for investigating new fossil fruit and leaf material from the Eocene of western North America. METHODS: We examined fossils from early and middle Eocene sediments of western Wyoming, northeastern Utah, northwestern Colorado, and Oregon and compared them with extant species of Iodes and other icacinaceous genera as well as previously described fossils of the family. KEY RESULTS: Three new fossil species are described, including two based on endocarps (Iodes occidentalis sp. nov. and Icacinicaryites lottii sp. nov.) and one based on leaves (Goweria bluerimensis sp. nov.). The co-occurrence of I. occidentalis and G. bluerimensis suggests these might represent detached organs of a single species. A new genus, Biceratocarpum, is also established for morphologically distinct fossil fruits of Icacinaceae previously placed in Carpolithus. Biceratocarpum brownii gen. et comb. nov. resembles the London Clay species "Iodes" corniculata in possessing a pair of subapical protrusions. CONCLUSIONS: These fossils increase our knowledge of Icacinaceae in the Paleogene of North America and highlight the importance of the Northern Hemisphere in the early diversification of the family. They also document interchange with the Eocene flora of Europe and biogeographic connections with modern floras of Africa and Asia, where Icacinaceae are diverse today. The present-day restriction of this family to tropical regions offers ecological implications for the Eocene floras in which they occur.

Retrospective evaluation of the effects of a single intraoperative dose of dexamethasone in horses undergoing exploratory laparotomy for small intestinal lesions (2008-2019): 240 cases.

OBJECTIVE: To determine the effect of a single intraoperative dose of dexamethasone on the risk of postoperative reflux (POR) in horses undergoing small intestinal surgery and to investigate its association with incisional complications and short-term survival. DESIGN: Retrospective cohort study over an 11-year period (2008-2019). SETTING: UK-based private referral center. ANIMALS: Two hundred and forty client-owned horses >6 months of age undergoing exploratory laparotomy for treatment of a small intestinal lesion. INTERVENTIONS: Ninety-seven horses received a single intraoperative dose of dexamethasone (0.1 mg/kg, IV). MEASUREMENTS AND MAIN RESULTS: Of 97 horses that received dexamethasone, 52 (53.6%) required small intestinal resection. Of 143 horses that did not receive dexamethasone, small intestinal resection was performed in 78 (54.5%). A total of 70 horses (29%) developed POR. There was no difference in the risk of POR between horses that received dexamethasone (25/97; 26%) and those that did not (45/143; 31%, P = 0.34). Risk factors associated with the development of POR included small intestinal resection (odds ratio [OR]: 4.55, 95% confidence interval [CI]: 2.27-9.11, P < 0.001), a PCV >40% 24 hours postoperatively (OR: 4.11, 95% CI: 2-8.45, P < 0.001), and a WBC count >10 × 109/L on admission (OR: 3.29, 95% CI: 1.47-7.41, P = 0.004). Dexamethasone was not associated with the odds of POR. Horses undergoing repeat laparotomy had a higher risk of incisional infection (OR: 8.07, 95% CI: 1.98-32.81, P = 0.004). Dexamethasone administration was not associated with incisional infection. The development of POR was negatively associated with short-term survival (OR: 0.07, 95% CI: 0.03-0.17, P ≤ 0.001). Dexamethasone administration was not retained in the final multivariable model for survival. CONCLUSIONS: Intraoperative dexamethasone was not associated with the development of POR in this study population, nor did it have an effect on postoperative survival or incisional infection in horses undergoing surgical management of small intestinal disease.

Use of antimicrobials licensed for systemic administration in UK equine practice.

BACKGROUND: Judicious antimicrobial use (AMU) is important for preserving therapeutic effectiveness. Large-scale studies of antimicrobial prescribing can provide clinical benchmarks and help identify opportunities for improved stewardship. OBJECTIVES: To describe systemic AMU in UK equine practice and identify factors associated with systemic and Category B (third and fourth generation cephalosporins, quinolones and polymixins) AMU. STUDY DESIGN: Retrospective cohort. METHODS: Anonymised electronic patient records (EPRs) for all equids attended by 39 UK veterinary practices between 1 January and 31 December 2018 were collected via the VetCompass programme. Systemic antimicrobial prescriptions were identified using electronic keyword searches. Indications for AMU were determined through manual review of a randomly selected subset of EPRs. The types and frequency of systemic antimicrobials prescribed and indications were summarised using descriptive statistics. Mixed-effects logistic regression was used to evaluate practice- and horse-related risk factors. RESULTS: Systemic antimicrobials were prescribed to 12 538 (19.5%, 95% confidence interval [CI]: 19.2%-19.8%) of 64 322 equids attended in 2018. Category B antimicrobials were prescribed to 1.9% (95% CI: 1.8%-2.0%) of attended equids and in 8.9% (95% CI: 8.5%-9.4%) of antimicrobial courses. Bacteriological culture was performed in 19.1% (95% CI: 17.1%-21.3%) of Category B antimicrobial courses. The most commonly prescribed antimicrobial classes were potentiated sulphonamides (50.2% of equids receiving antimicrobials) and tetracyclines (33.5% of equids receiving antimicrobials). Integumentary disorders were the most common reason for systemic AMU (40.5% of courses). Urogenital disorders were the most common reason for Category B AMU (31.1% of courses). Increased odds of systemic and Category B AMU were observed in equids <1 year compared with those aged 5-14 years. Breed was associated with AMU, with odds of systemic and Category B AMU highest in Thoroughbreds and Thoroughbred crosses. MAIN LIMITATIONS: Convenience sample of practices may limit generalisability. CONCLUSIONS: Empirical use of Category B antimicrobials remains commonplace.

A study of the impact of the COVID-19 pandemic on equine veterinary care in the UK.

Background: During the COVID-19 pandemic, equine health care in the UK may have been adversely affected due to mandated changes in the delivery of veterinary healthcare and the potential for reduced health-seeking behaviour. Methods: Electronic patient records (EPRs) were analysed to describe veterinary activity for all equids under the active care of 20 veterinary practices in the UK in the 12 months before and after the introduction of the first UK lockdown. Pre-pandemic and pandemic levels of clinical activity were compared. Further comparisons of care, including immediate management and treatment, were made following a detailed review of EPRs from randomly selected subsets of equids under care in four time periods. Results: All measures of activity and face-to-face interaction were lower in the early pandemic period than in the equivalent pre-pandemic period. Compared to pre-pandemic, the early pandemic was associated with a decrease in prophylactic care and non-urgent diagnostic imaging and an increase in systemic non-steroid anti-inflammatory prescription. Convenience sampling of veterinary practices may have limited the generalisability of the findings. The quality of EPRs was variable. Conclusions: While equine veterinary activity was significantly disrupted in the early pandemic period, there was a rapid return to pre-pandemic levels of activity. Subsequent lockdowns appeared to have had little effect on veterinary care.

Primary cutaneous infection by Mycobacterium avium: a case report and literature review.

Nontuberculous mycobacteria (NTM) are becoming increasingly important cutaneous pathogens as the number of susceptible patients increases. Nevertheless, primary cutaneous infection by one particular species, Mycobacterium avium complex (MAC), remains relatively unusual, particularly in immunocompetent patients. We review the English-language literature on primary cutaneous MAC in patients who were neither immunocompromised nor pharmacologically immunosuppressed. We offer an additional report of a healthy patient who presented to our clinic with primary cutaneous MAC following seemingly innocuous trauma to the leg.

Climbing since the early Miocene: The fossil record of Paullinieae (Sapindaceae).

Paullinieae are a diverse group of tropical and subtropical climbing plants that belong to the soapberry family (Sapindaceae). The six genera in this tribe make up approximately one-quarter of the species in the family, but a sparse fossil record limits our understanding of their diversification. Here, we provide the first description of anatomically preserved fossils of Paullinieae and we re-evaluate other macrofossils that have been attributed to the tribe. We identified permineralized fossil roots in collections from the lower Miocene Cucaracha Formation where it was exposed along the Culebra Cut of the Panama Canal. We prepared the fossils using the cellulose acetate peel technique and compared the anatomy with that of extant Paullinieae. The fossil roots preserve a combination of characters found only in Paullinieae, including peripheral secondary vascular strands, vessel dimorphism, alternate intervessel pitting with coalescent apertures, heterocellular rays, and axial parenchyma strands of 2-4 cells, often with prismatic crystals. We also searched the paleontological literature for other occurrences of the tribe. We re-evaluated leaf fossils from western North America that have been assigned to extant genera in the tribe by comparing their morphology to herbarium specimens and cleared leaves. The fossil leaves that were assigned to Cardiospermum and Serjania from the Paleogene of western North America are likely Sapindaceae; however, they lack diagnostic characters necessary for inclusion in Paullinieae and should be excluded from those genera. Therefore, the fossils described here as Ampelorhiza heteroxylon gen. et sp. nov. are the oldest macrofossil evidence of Paullinieae. They provide direct evidence of the development of a vascular cambial variant associated with the climbing habit in Sapindaceae and provide strong evidence of the diversification of crown-group Paullinieae in the tropics by 18.5-19 million years ago.

Preschoolers' crossmodal mappings of timbre.

Crossmodal correspondences have been of interest to researchers for nearly a century, although it is only more recently that interactions related to timbre have been examined systematically. Timbre is often described using crossmodal adjectives (e.g., bright, smooth). However, it is not clear whether these semantic conventions are primarily the result of low-level multisensory interactions or are more a product of associative learning and musical training. Do young children exhibit crossmodal correspondences involving timbre? The aim of this study was to investigate the effects of timbre, age, and sensory modality (visual and tactile) on the consistency and congruency of young children's patterns of crossmodal mappings. Preschool children (N = 69, M age = 4.51) completed a novel audio-visual and audio-tactile association task. Results indicate that children are moderately consistent in their associations; mappings are largely congruent with adult associations; and results suggest a possible developmental time course for the establishment of crossmodal correspondences between approximately ages 3 and 6. However, congruency is dependent on modality, with robust agreement in the tactile-auditory domain but a good deal more variance and a stronger developmental influence on visual-auditory associations. These results are the first to demonstrate that crossmodal correspondences are a feature of timbre perception early in development.

Roles of Noncoding RNAs in Ciliate Genome Architecture.

Ciliates are an interesting model system for investigating diverse functions of noncoding RNAs, especially in genome defence pathways. During sexual development, the ciliate somatic genome undergoes massive rearrangement and reduction through removal of transposable elements and other repetitive DNA. This is guided by a multitude of noncoding RNAs of different sizes and functions, the extent of which is only recently becoming clear. The genome rearrangement pathways evolved as a defence against parasitic DNA, but interestingly also use the transposable elements and transposases to execute their own removal. Thus, ciliates are also a good model for the coevolution of host and transposable element, and the mutual dependence between the two. In this review, we summarise the genome rearrangement pathways in three diverse species of ciliate, with focus on recent discoveries and the roles of noncoding RNAs.

The Drosophila seminal proteome and its role in postcopulatory sexual selection.

Postcopulatory sexual selection (PCSS), comprised of sperm competition and cryptic female choice, has emerged as a widespread evolutionary force among polyandrous animals. There is abundant evidence that PCSS can shape the evolution of sperm. However, sperm are not the whole story: they are accompanied by seminal fluid substances that play many roles, including influencing PCSS. Foremost among seminal fluid models is Drosophila melanogaster, which displays ubiquitous polyandry, and exhibits intraspecific variation in a number of seminal fluid proteins (Sfps) that appear to modulate paternity share. Here, we first consolidate current information on the identities of D. melanogaster Sfps. Comparing between D. melanogaster and human seminal proteomes, we find evidence of similarities between many protein classes and individual proteins, including some D. melanogaster Sfp genes linked to PCSS, suggesting evolutionary conservation of broad-scale functions. We then review experimental evidence for the functions of D. melanogaster Sfps in PCSS and sexual conflict. We identify gaps in our current knowledge and areas for future research, including an enhanced identification of PCSS-related Sfps, their interactions with rival sperm and with females, the role of qualitative changes in Sfps and mechanisms of ejaculate tailoring. This article is part of the theme issue 'Fifty years of sperm competition'.

The genome of a subterrestrial nematode reveals adaptations to heat.

The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. The expanded Hsp70 genes are transcriptionally induced upon growth under heat stress, and we find that positive selection is detectable in several members of this family. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic basis of heat tolerance in a complete subterrestrial eukaryotic genome.