Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

Sperm Cyst "Looping": A Developmental Novelty Enabling Extreme Male Ornament Evolution

Postcopulatory sexual selection is credited as a principal force behind the rapid evolution of reproductive characters, often generating a pattern of correlated evolution between interacting, sex-specific traits. Because the female reproductive tract is the selective environment for sperm, one taxonomically widespread example of this pattern is the co-diversification of sperm length and female sperm-storage organ dimension. In Drosophila, having testes that are longer than the sperm they manufacture was believed to be a universal physiological constraint. Further, the energetic and time costs of developing long testes have been credited with underlying the steep evolutionary allometry of sperm length and constraining sperm length evolution in Drosophila. Here, we report on the discovery of a novel spermatogenic mechanism—sperm cyst looping—that enables males to produce relatively long sperm in short testis. This phenomenon (restricted to members of the saltans and willistoni species groups) begins early during spermatogenesis and is potentially attributable to heterochronic evolution, resulting in growth asynchrony between spermatid tails and the surrounding spermatid and somatic cyst cell membranes. By removing the allometric constraint on sperm length, this evolutionary innovation appears to have enabled males to evolve extremely long sperm for their body mass while evading delays in reproductive maturation time. On the other hand, sperm cyst looping was found to exact a cost by requiring greater total energetic investment in testes and a pronounced reduction in male lifespan. We speculate on the ecological selection pressures underlying the evolutionary origin and maintenance of this unique adaptation.

No apparent cost of evolved immune response in Drosophila melanogaster

Maintenance and deployment of the immune system are costly and are hence predicted to trade-off with other resource-demanding traits, such as reproduction. We subjected this longstanding idea to test using laboratory experimental evolution approach. In the present study, replicate populations of Drosophila melanogaster were subjected to three selection regimes-I (Infection with Pseudomonas entomophila), S (Sham-infection with MgSO4 ), and U (Unhandled Control). After 30 generations of selection flies from the I regime had evolved better survivorship upon infection with P. entomophila compared to flies from U and S regimes. However, contrary to expectations and previous reports, we did not find any evidence of trade-offs between immunity and other life history related traits, such as longevity, fecundity, egg hatchability, or development time. After 45 generations of selection, the selection was relaxed for a set of populations. Even after 15 generations, the postinfection survivorship of populations under relaxed selection regime did not decline. We speculate that either there is a negligible cost to the evolved immune response or that trade-offs occur on traits such as reproductive behavior or other immune mechanisms that we have not investigated in this study. Our research suggests that at least under certain conditions, life-history trade-offs might play little role in maintaining variation in immunity.

Prevalence of primary multidrug resistance to anti-tuberculosis drugs in Pakistan

SETTING

Pakistan ranks sixth in the world in terms of tuberculosis (TB) burden, with a World Health Organization estimated incidence of 181 per 100000, or 286000 new cases annually. Hospital-based data indicate a significant problem of multidrug-resistant TB (MDR-TB) in the country and highlight the need to assess its extent at community level. In this cross-sectional study, sputum samples from 742 untreated newly diagnosed pulmonary TB patients from all over the country were used.

OBJECTIVE

To assess the prevalence of primary drug resistance in Pakistan.

RESULTS

Of 672 culture-positive patients, 76 (11.3%) showed resistance to one or more drugs. Resistance to streptomycin (10 microg/ml) was found in 36 (5.4%) patients, isoniazid (INH) (1 microg/ml) in 51 (7.6%), rifampicin (RMP) (5 microg/ml) in 15 (2.2%), ethambutol (10 microg/ml) in 12 (1.8%) and pyrazinamide in 22 (3.3%) samples. Forty-six (6.8%) of the isolates tested were resistant to a single drug, 10 (1.5%) to two drugs, 12 (1.8%) to three drugs, and 6 (0.9%) to four drugs, while 2 (0.3%) isolates were resistant to all five first-line agents. Primary MDR-TB was 1.8% (n=12) (INH 1 microg/ml, RMP 5 microg/ml).

CONCLUSION

The results of this study show a prevalence of primary MDR-TB in Pakistan of <2%, which needs to be addressed through an effective DOTS strategy.

Harmonic scalpel tonsillectomy versus electrocautery tonsillectomy: a comparative pilot study

OBJECTIVE

Using quality of life criteria, this pilot study prospectively evaluates if the ultrasonic dissector coagulator's (Harmonic Scalpel [HS], Ethicon Endo-Surgery, Inc, Cincinnati, OH) unique properties offer advantages over traditional electrocautery (EC) tonsillectomies with respect to return to regular diet, activity, and complications such as bleeding and dehydration.

METHODS

Over a 13-month period, 316 tonsillectomies (161 EC and 155 HS) were evaluated. Return to regular diet, regular activity, and the use of postoperative pain medications were monitored via a brief questionnaire. Complications, such as increased perioperative and postoperative bleeding, were monitored by chart review. Statistical analysis of the questionnaire data was performed.

RESULTS

Seventy-five (46.6%) of the patients in the EC group responded versus 97 (62.6%) in the HS group. The ages ranged from 1 to 19 years old. Return to regular diet in 24 hours was statistically significant when comparing HS and EC questionnaire responders, 44.3% versus 22.7%, respectively; as was 72 hours, HS (74.2%) and EC (46.7%). Twenty-eight percent of the HS questionnaire responders versus 12% of EC resumed normal activity within 24 hours. The perioperative blood loss was equal in the 2 groups. There were 14 late bleeds; 9 were EC patients and 5 HS patients. Two HS patients and 4 EC patients had readmissions for dehydration.

CONCLUSIONS

It appears from this early pilot study that the Harmonic Scalpel tonsillectomy offers advantages of early return to diet and activity over standard electrocautery tonsillectomies. We report no difference in perioperative or postoperative bleeding.

Conversion of atrial fibrillation by the experimental antiarrhythmic drug tedisamil in two canine models

INTRODUCTION

Tedisamil is an experimental bradycardic agent possessing action potential-prolonging effects. It has been proven effective in terminating ventricular arrhythmias in several animal models and atrial flutter in a conscious dog model. There are no reports to date evaluating tedisamil's efficacy in terminating atrial fibrillation (AF).

METHODS AND RESULTS

Two different canine models of AF were used. One group of dogs (n = 6) was subjected to 28 days of chronic fibrillatory pacing at 50 Hz using an implantable neural stimulator. Sustained AF was achieved in all dogs within 14 days of initiating pacing. A second set of dogs (n = 5) had AF induced via bilateral vagal stimulation. Tedisamil 1 mg/kg was 100% effective in terminating AF in both models. Cardioversion was associated with a statistically significant prolongation of the fibrillatory cycle length immediately before return to normal sinus rhythm in both models. A dose-response trial was performed in the vagal AF group as well as in a second group of three dogs that underwent chronic fibrillatory pacing. The efficacy of tedisamil was dose dependent, with limited efficacy at 0.1 and 0.3 mg/kg intravenously in both models. Tedisamil was able to prevent reinduction of sustained AF 30 minutes after administration of 1 mg/kg in the chronic pacing model in all dogs. Side effects included minor hypersalivation in most dogs receiving the 1 mg/kg dose. No ventricular ectopy or arrhythmias were observed.

CONCLUSION

Tedisamil is effective for conversion of sustained AF to normal sinus rhythm in two different models of AF.

Effect of isoproterenol on QRS complex morphology during ventricular pacing: implications for pace mapping

Ventricular pace mapping may be used to identify the site of origin of idiopathic ventricular tachycardia. Isoproterenol is often required to induce this type of ventricular tachycardia, but its effect on QRS morphology during pace mapping is unknown. Therefore, this study was performed to evaluate the effect of isoproterenol on QRS morphology during ventricular pacing. The study population consisted of 20 patients (mean age 38 +/- 14 years) undergoing a clinically indicated electrophysiology procedure. Ventricular overdrive pacing was performed in trains of 12 stimuli at cycle lengths of 400, 350, 300, and 250 ms, first in the baseline state during an infusion of isoproterenol, and again after isoproterenol washout. Pacing was performed at the right ventricular apex in 10 patients, in the right ventricular outflow tract in 6 patients, and in the left ventricle in 4 patients. Visual evaluation revealed no apparent effects of isoproterenol on QRS morphology at any of the three pacing sites or at any of the pacing cycle lengths. It was concluded that QRS morphology during ventricular pacing is not affected by isoproterenol infusion. Therefore, in patients with idiopathic ventricular tachycardia, even if the induction of tachycardia requires infusion of isoproterenol, successful pace mapping may be performed in its absence.

Changes in cardiac repolarization following short periods of ventricular pacing

INTRODUCTION

"Cardiac memory" (primary T wave change) is thought to occur after 15 minutes to several hours of right ventricular (RV) pacing. The two components of the temporal change in repolarization are memory and accumulation. The purpose of this study was to examine quantitatively the effect of short periods of ventricular pacing on the human cardiac action potential, using monophasic action potential (MAP) recordings.

METHODS AND RESULTS

Thirty-one patients (ages 43+/-14 years) with structurally normal hearts undergoing a clinically indicated electrophysiologic procedure were enrolled. Catheters were placed in the right atrium (RA) and RV, and a MAP catheter was positioned at the RV septum. APD90 was calculated from digitized MAP recordings. MAP morphology comparisons were performed using the root mean square (RMS) of the difference between complexes. All pacing was at 500-msec cycle length. There were four pacing protocols: (1) RA pacing was performed for approximately 15 minutes to evaluate temporal stability of the MAP recordings (5 pts); (2) to evaluate the memory phenomenon, four successive 1-minute episodes of RV pacing were interspersed with 2 minutes of RA pacing (5 pts); (3) the accumulation phenomenon was evaluated by assessing the effects of 1, 5, 10, and 15 minutes of RV pacing on the MAP during RA pacing (16 pts); and (4) 20 minutes of RV pacing was followed by 10 minutes of RA pacing to correlate visually apparent T wave changes with changes in MAP recordings (5 pts). In the control patients, no changes in APD90 or RMS analysis were noted during 14.9+/-1.4 minutes of RA pacing. In the second protocol, RMS of the difference between the baseline MAP complexes and the signal average of the first 50 beats following each of four 1-minute RV pacing trains demonstrated progressively greater differences in morphology after successive episodes of RV pacing. In protocol 3, RMS analysis identified a progressively greater difference between the baseline MAP recording and the average of the first 50 beats after 1, 5, 10, and 15 minutes of RV pacing. In protocol 4, visually apparent changes in T waves occurred in parallel with the RMS of the difference between the baseline MAP recordings and the average of the first 50 beats after 20 minutes of RV pacing. Similar changes also were demonstrated by APD90 analysis.

CONCLUSION

This study is the first to demonstrate that episodes of abnormal ventricular activation as short as 1 minute in duration may exert lingering effects on the repolarization process once normal ventricular activation resumes.