A phylogenetic examination of host use evolution in the quinaria and testacea groups of Drosophila.

Adaptive radiations provide an opportunity to examine complex evolutionary processes such as ecological specialization and speciation. While a well-resolved phylogenetic hypothesis is critical to completing such studies, the rapid rates of evolution in these groups can impede phylogenetic studies. Here we study the quinaria and testacea species groups of the immigrans-tripunctata radiation of Drosophila, which represent a recent adaptive radiation and are a developing model system for ecological genetics. We were especially interested in understanding host use evolution in these species. In order to infer a phylogenetic hypothesis for this group we sampled loci from both the nuclear genome and the mitochondrial DNA to develop a dataset of 43 protein-coding loci for these two groups along with their close relatives in the immigrans-tripunctata radiation. We used this dataset to examine their evolutionary relationships along with the evolution of feeding behavior. Our analysis recovers strong support for the monophyly of the testacea but not the quinaria group. Results from our ancestral state reconstruction analysis suggests that the ancestor of the testacea and quinaria groups exhibited mushroom-feeding. Within the quinaria group, we infer that transition to vegetative feeding occurred twice, and that this transition did not coincide with a genome-wide change in the rate of protein evolution.

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Microsurgical Clip Ligation of a Large Anterior Communicating Artery Aneurysm Previously Treated With Woven Endobridge Device: 2-Dimensional Operative Video.

The Woven Endobridge (WEB) intrasaccular flow diversion device (Microvention, Inc.) is commonly used to treat both unruptured and ruptured wide-necked bifurcation aneurysms.1 Despite its relative safety and comparable rates of aneurysm occlusion, the device may compress over time resulting in aneurysm recurrence.2 In this video, we demonstrate the microsurgical retreatment of a large anterior communicating artery (ACoA) aneurysm previously treated with WEB. A 53-year-old patient with hypertension and current tobacco use presented with a ruptured ACoA aneurysm measuring 8.4 mm × 8 mm × 7 mm. She was urgently treated with a 9 mm × 5 mm WEB SL and made a full recovery. At 6 months, cerebral angiography showed a significant recurrence secondary to WEB compression. We considered both endovascular and microsurgical approaches; however, the anatomy was unfavorable for endovascular treatment.3 Although previous reports have documented clipping as a retreatment strategy, a minority of these aneurysms were ACoA aneurysms.4-7 The patient consented to the surgical procedure. This operative video illustrates the in vivo appearance of the WEB device and the surgical technique used to treat this unusual situation. The WEB device was firm and not as compressible as previously reported, but clipping was still possible.4,6 We highlight the use of temporary clipping, fenestrated clips, and intraoperative angiography in treatment. The aneurysm was occluded, and the patient remained without deficits. In summary, clip ligation can be an excellent option for ACoA aneurysms in the setting of WEB recurrence. The patient consented to this report; Institutional Review Board/ethics committee approval was not required.

Neurosurgery at Baylor Scott & White Health: Recent History and a Decade of Neurosurgery Residency Training.

Neurosurgery at Baylor Scott & White Memorial Hospital in Temple, Texas began as a division in the Department of Surgery many decades ago. The hospital has long served as the flagship tertiary referral center for the Baylor Scott & White healthcare system, which merged in 2013 with Baylor University Medical Center, a hospital system based in Dallas. It is now the largest non-profit hospital system as well as the most awarded hospital system by the US News and World Report within the state of Texas. The Department of Neurosurgery was established at Baylor Scott & White Memorial Hospital in the 2006-2007 academic year. Between then and 2014, four neurosurgeons served as department chair or interim chair: Dr. Robert Buchanan, Dr. Gerhard Friehs, Dr. Ibrahim El Nihum, and Dr. David Garrett Jr. In 2014, Dr. Jason Huang was appointed chairman after a national search and established the neurosurgery residency program in 2015. The department has undergone tremendous growth under the leadership of Dr. Huang, and the residency program is a priority of the department. Surgical excellence is honed at primarily three campuses: Baylor Scott & White Memorial Hospital, Baylor Scott & White McLane Children's Medical Center, and Baylor Scott & White Medical Center - Hillcrest. In this editorial, we provide a brief history of the institution, a recent history of the neurosurgical presence at Baylor Scott & White Memorial Hospital in Temple, Texas, and briefly describe the program's future directions under the continued leadership of Dr. Jason Huang.

Early Surgery for Moyamoya Is Not Associated with Worse Outcomes: Analysis of a North American Adult Cohort.

BACKGROUND: Patients with symptomatic moyamoya disease (MMD) or moyamoya syndrome (MMS) are at high risk of recurrent stroke. Surgical revascularization with either direct or indirect superficial temporal artery to middle cerebral artery bypass is a well-accepted treatment. However, the optimal timing and surgical technique for adult patients with MMD or MMS remain unknown. METHODS: We performed a retrospective medical record review of patients who had undergone superficial temporal artery to middle cerebral artery bypass for MMD or MMS from January 1, 2017, to January 1, 2022. The data collected included demographics, comorbidities, complications, as well as angiographic, and clinical outcomes. Early surgery was defined as surgery performed ≤2 weeks of the last stroke and delayed surgery as surgery performed >2 weeks after the last stroke. In the statistical analysis, we compared early versus delayed surgery and direct versus indirect bypass. RESULTS: Nineteen patients had undergone bypass surgery on 24 hemispheres. Of the 24 cases, 10 were early and 14 were delayed. In addition, 17 were direct, and 7 were indirect. No statistically significant difference was found in total complications between the early (3 of 10; 30%) and delayed (3 of 14; 21%; P = 0.67) groups. Five complications occurred in the direct group (5 of 17; 29%) and one in the indirect group (1 of 7; 14%; P = 0.63). No mortalities related to surgery occurred. Angiographic follow-up showed more extensive revascularization after early direct bypass than after delayed indirect bypass. CONCLUSIONS: In our population of North American adults who had undergone surgical revascularization for MMD or MMS, early surgery within 2 weeks of the last stroke did not differ from delayed surgery in terms of complications or clinical outcomes. Early direct bypass showed more revascularization on angiography than did delayed indirect surgery.

Quamdiu? Time to proficiency in endoscope-assisted minimally invasive clot evacuation.

INTRODUCTION: Spontaneous intraparenchymal brain hemorrhages are a devastating disease associated with significant disability or death. Minimally invasive clot evacuation (MICE) techniques can reduce mortality. We reviewed our experience with learning endoscope-assisted MICE to determine whether adequate results could be obtained in less than 10 cases. METHODS: We performed a retrospective chart review of patients undergoing endoscope-assisted MICE at a single institution by a single surgeon from January 1, 2018 to January 1, 2023 using a neuro-endoscope, a commercial clot evacuation device, and frameless stereotaxis. Demographic data was collected along with surgical results and complications. Image analysis using software determined the degree of clot removal. Hospital length of stay and functional outcomes were assessed using the Glasgow Coma Scale score (GCS) and Glasgow Outcome Score (extended) (GOS-E). RESULTS: Eleven patients were identified: average age 60.82 years old, 64 % male, all had hypertension. There was a clear improvement in IPH evacuation over the series. By case #7, greater than 80 % of clot volume was evacuated consistently. All patients remained neurologically stable or improved following surgery. In long-term follow-up, four patients (36.4 %) had good outcomes (GOS-E ≥ 6) and 2 patients had fair outcomes (GOS-E = 4) (18 %). There were no surgical mortalities, re-hemorrhages, or infections. CONCLUSIONS: With an experience of less than 10 cases, it is possible to obtain results comparable to most published series of endoscope-assisted MICE. Benchmarks such as greater than 80 % volume removal, less than 15 mL residual, and 40 % good functional outcomes can be obtained.

Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae.

Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma. However, the assembled portion of the Muller F element (orthologous to the fourth chromosome in Drosophila melanogaster) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to >18 Mb. Here, we present chromosome-level long-read genome assemblies for 4 Drosophila species with expanded F elements ranging in size from 2.3 to 20.5 Mb. Each Muller element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.

Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai , Drosophila takahashii , Drosophila bipectinata , and Drosophila ananassae.

Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma . However, the assembled portion of the Muller F Element (orthologous to the fourth chromosome in Drosophila melanogaster ) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to > 18 Mb. Here, we present chromosome-level long read genome assemblies for four Drosophila species with expanded F Elements ranging in size from 2.3 Mb to 20.5 Mb. Each Muller Element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.

Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy.

The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP's Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled Drosophila genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020-2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning environment, we provide four strategic lessons we infer toward democratizing science education. First, it appears that increasing access to scientific research and professional development opportunities by supporting virtual, cost-free attendance at national conferences attracts more faculty members to educational initiatives. Second, we observed that transitioning new member training to an online platform removed geographical barriers, reducing time and travel demands, and increased access for diverse faculty to join. Third, developing a Virtual Teaching Assistant program increased the availability of peer support, thereby improving the opportunities for student success. Finally, increasing access to web-based technology is critical for providing equitable opportunities for marginalized students to fully participate in research courses. Online CUREs have great potential for democratizing science education.

Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila.

Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila, many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila. First, we inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of them could develop on diet with toxin. Finally, we asked how α-amanitin tolerance might have evolved across the immigrans-tripunctata radiation, and inferred that toxin tolerance was ancestral in mushroom-feeding Drosophila and subsequently lost multiple times. Our findings expand our understanding of toxin tolerance across the immigrans-tripunctata radiation and emphasize the uniqueness of toxin tolerance in this adaptive radiation and the complexity of biochemical adaptations.

Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila.

Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila , many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila . We first inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of these species could develop on diet with toxin. Third, we examined fly development on a diet containing a natural mix of toxins extracted from the Death Cap Amanita phalloides mushroom. Both tolerant and susceptible species developed on diet with this mix, though tolerant species survived at significantly higher concentrations. Finally, we asked how cyclopeptide tolerance might have evolved across the immigrans-tripunctata radiation and inferred that toxin tolerance was ancestral and subsequently lost multiple times. Our results suggest the evolutionary history of cyclopeptide tolerance is complex, and simply describing this trait as present or absent does not fully capture the occurrence or impact on this adaptive radiation. More broadly, the evolution of novelty can be more complex than previously thought, and that accurate descriptions of such novelties are critical in studies examining their evolution.

The Genomics Education Partnership: First findings on genomics research in community colleges.

The Genomics Education Partnership (GEP), a consortium of diverse colleges/universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with internet access, may be particularly accessible for 2-year institutions with limited research capacity and significant budget constraints. To understand how GEP supports student research at CCs, we analyzed student knowledge and self-reported outcomes. We found that CC student gains are comparable to non-CC student gains, with improvements in attitudes toward science and thriving in science. Our early findings suggest that the GEP model of centralized support with flexible CURE implementation benefits CC students and may help mitigate barriers to implementing research at CCs.

Manual annotation of Drosophila genes: a Genomics Education Partnership protocol.

Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.

Neurovascular Syndromes.

Patients with cerebrovascular syndromes are at risk for additional concerns associated with their syndrome. A wide variety of syndromes are associated with cerebrovascular diseases. Multidisciplinary care is helpful to ensure comprehensive evaluation and management. Precise diagnosis and appreciation for the underlying syndrome is critical for effective cerebrovascular and broader care. This text focuses on these conditions with a focus on underlying pathophysiology and associated genetics, presentation, diagnosis, and management of each disease.

Safety of Contemporary Carotid Artery Stenting and Associated Risk Factors for Treatment of Carotid Artery Stenosis.

BACKGROUND: The prevalence of carotid artery atherosclerosis and stroke is increasing. Carotid artery stenting (CAS), which treats carotid artery stenosis and prevents strokes, has benefited from advances in techniques and technology. In this study, we aimed to identify significant risk factors for major complications following contemporary CAS. METHODS: Utilizing the National Surgical Quality Improvement Program registry, we investigated individuals who underwent CAS between the years 2015-2018. Multivariable logistic regression was performed to identify risk factors associated with stroke, myocardial infarction (MI), and death within 30 days of CAS. RESULTS: Of the 770 patients within the National Surgical Quality Improvement Program registry who met study criteria, 3.2% experienced strokes, 1.6% experienced MIs, and 2.2% died within 30 days of CAS. A total of 6.1% of patients experienced any of these major complications. Of the 395 asymptomatic patients, 3.5% suffered a stroke, 1.5% experienced an MI, and 1.0% died for a total of 5.6% patients suffering from any event. Of the 375 symptomatic patients, there were 2.9% strokes, 1.6% MIs, and 3.5% deaths with 6.7% suffering any event. Age, race, and hyponatremia were significantly associated with stroke, and hyponatremia was associated with MI. Age, anemia, hypoalbuminemia, international normalized ratio, and emergency case were associated with death. CONCLUSIONS: These results suggest that preoperative risk stratification of CAS patients may not be straightforward as each adverse event has its own risk factors, precluding a generalized CAS risk stratification scoring system from being created. This paper can aid in patient selection for CAS by highlighting risk factors in modern CAS.

Drosophila eugracilis - Akt.

Gene Model for Akt in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2).

PulseRider Treated Aneurysm with Significant Artifact on Postoperative Magnetic Resonance Angiography: A Case Report and Literature Review.

The PulseRider is a neuroendovascular adjunct for wide-necked intracranial aneurysms. The decreased metal burden of the PulseRider theoretically reduces artifact on radiologic imaging. However, we report here on a case of a patient who underwent PulseRider-assisted stent-coiling of a basilar tip aneurysm. He returned 19 months later for intermittent diplopia and darkening of vision but was neurologically intact on exam. Both contrast-enhanced and time-of-flight magnetic resonance angiography (MRA) demonstrated absence of signal in the basilar artery in the proximal anchors of the PulseRider. Given his lack of reproducible symptoms and high functional status, it is presumed that the imaging reflected artifact and not thrombosis/stenosis. Although the PulseRider is a useful treatment option for wide-necked intracranial aneurysms, the clinician should be aware that even contrast-enhanced MRA can produce artifact that resembles thrombosis/stenosis. Non-angiogram radiologic imaging modalities may be appropriate for evaluation for residual aneurysm but not patency of the parent artery.

Drosophila yakuba - Tsc1.

Gene Model for Tsc1 in the Drosophila yakuba's DyakCAF1 assembly (GCA_000005975.1).

Drosophila yakuba - Tsc1.

Gene Model for the ortholog of Tsc1 in the Drosophila yakuba DyakCAF1 assembly (GCA_000005975.1).

Novel Decompressive Hemicraniectomy Technique for Traumatic Brain Injury: Technical Note.

BACKGROUND: Traumatic brain injury (TBI) is a significant cause of morbidity and mortality across all age groups. Decompressive hemicraniectomy is the treatment for TBI-related refractory intracranial hypertension. The traditional technique for this procedure can result in wound complications due to injury of the scalp flap's vascular supply, namely the superficial temporal and postauricular arteries. METHODS: In this technical note we describe our experience using a novel technique that preserves both vascular territories by placing the inferior aspect of the incision posterior to the ear as opposed to anterior to it. This modification has the potential to reduce wound healing complications, especially in those at higher risk, while also reducing operative time by avoiding temporalis muscle incision and closure during procedure. RESULTS: After performing hospital chart review, a total of 7 patients were found who underwent this hemicraniectomy technique for severe TBI. Of these, 5 patients had this performed on the left side, and 2 patients had this performed on the right side. Six of the patients had an accompanying subdural hematoma, whereas 1 patient had no intracranial hemorrhage present. CONCLUSIONS: In each case, both the superficial temporal and postauricular arteries were preserved, and rapid healing of the scalp flap occurred. In addition to providing a large bone window to allow the brain to swell, this technique has the potential to reduce complications of wound healing by preserving the vascular supply of the scalp flap and reduce operative times by minimizing temporalis muscle dissection.