Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia) drepanolobium

The Acacia drepanolobium (also known as Vachellia drepanolobium) ant-plant symbiosis is considered a classic case of species coexistence, in which four species of tree-defending ants compete for nesting space in a single host tree species. Coexistence in this system has been explained by trade-offs in the ability of the ant associates to compete with each other for occupied trees versus the ability to colonize unoccupied trees. We seek to understand the proximal reasons for how and why the ant species vary in competitive or colonizing abilities, which are largely unknown. In this study, we use RADseq-derived SNPs to identify relatedness of workers in colonies to test the hypothesis that competitively dominant ants reach large colony sizes due to polygyny, that is, the presence of multiple egg-laying queens in a single colony. We find that variation in polygyny is not associated with competitive ability; in fact, the most dominant species, unexpectedly, showed little evidence of polygyny. We also use these markers to investigate variation in mating behavior among the ant species and find that different species vary in the number of males fathering the offspring of each colony. Finally, we show that the nature of polygyny varies between the two commonly polygynous species, Crematogaster mimosae and Tetraponera penzigi: in C. mimosae, queens in the same colony are often related, while this is not the case for T. penzigi. These results shed light on factors influencing the evolution of species coexistence in an ant-plant mutualism, as well as demonstrating the effectiveness of RADseq-derived SNPs for parentage analysis.

239 INFLUENCE OF BREED PREDOMINANCE ON MATURATION COMPETENCE, FERTILIZATION, AND DEVELOPMENT IN VITRO OF BOVINE OOCYTES

The purpose of this research was to compare the competence of bovine oocytes of different breed predominance (Bos taurus v. Bos indicus) to mature and to be fertilized. This was done through the collection, selection, maturation, and fertilization of oocytes from slaughtered cows, predominantly either B. taurus or B. indicus. Only cows that were at least 5/8 B. taurus or 5/8 B. indicus, according to a series of phenotypic characteristics, such as the presence of a hump, dewlap, length of the ears, and others, were selected. To obtain cumulus–oocyte complexes, ovarian follicles (3 to 10 mm in diameter) were aspirated, and only oocytes with 2 or more layers of cumulus cells, an intact zona pellucida, and a homogeneous granular cytoplasm were selected. After selection, oocyte maturation [in vitro maturation (IVM)] and IVF were done. Frozen–thawed semen was used from one Brahman bull (B. indicus). For the evaluation of IVM as for IVF, oocytes were fixed for approximately 24 h at 4°C in a solution of ethanol : acetic acid (3 : 1). They were then stained with 1% acetic orcein. A chi-squared test was performed for all reported rates. The rate of maturation of oocytes from cows with a predominant B. indicus phenotype was 66.93%, whereas cows with a B. taurus phenotype reached 43.10% (P < 0.001). Regarding the fertilization rate, predominantly B. indicus females had 43.68% of oocytes normally fertilized and 41.74% of oocytes were abnormally penetrated. This category included polyspermic and asynchronic (abnormally developed pronucleus) oocytes. In cows with B. taurus predominance, 31.96% of oocytes were normally penetrated and 46.39% were abnormally penetrated by spermatozoa (no significant differences were found). The rate of non-fertilized oocytes was significantly different (P < 0.05) among B. indicus and B. taurus oocytes (6.79 and 17.52%, respectively). A small and nonsignificant proportion of degenerated oocytes resulted in both groups (7.79% for B. indicus and 4.14% for B. taurus). The cleavage rate was not different among phenotypic groups (36.12 and 32.30%, respectively, for B. indicus and B. taurus). In conclusion, the present results indicate that oocytes from predominantly B. indicus cows were more competent than oocytes from cows with a predominance of the B. taurus breed. Nonetheless, this superiority was not evident in terms of cleavage rates. Semen from other B. indicus and B. taurus breeds must be tested to clarify any breed interactions.

RESULTS AND COMPLICATIONS IN DORSAL AND VOLAR WRIST GANGLIA ARTHROSCOPIC RESECTION

The authors present the procedure and results of five years of arthroscopic treatment of wrist radiocarpal and midcarpal ganglia. Thirty cases of dorsal ganglia and seventeen cases of volar ganglia were operated on arthroscopically. The technique was easy to perform in all the radiocarpal ganglia, not easy in midcarpal dorsal ganglia and very difficult in midcarpal volar ganglia. The results were recorded with a mean follow-up of 15 months. Twenty-seven cases of dorsal ganglia and twelve cases of volar ganglia had excellent results with active motion recovery, no complications, absence of scars and no recurrence. Two cases had a recurrence. There were four complications: a case of injury of a radial artery branch, a case of extensive haematoma, and two cases of neuropraxia. In three cases the procedure was converted into open surgery: they had a longer time of healing and a residual scar. The arthroscopic resection has been in our experience effective and safe for the treatment of all radiocarpal ganglia. Good results have been obtained also in the treatment of dorsal midcarpal ganglia. Concerning the uncommon cases of volar midcarpal (STT) ganglia, an open approach seems still indicated.

ARTHROSCOPIC RESECTION OF WRIST GANGLIA

The arthroscopic resection of synovial cysts of the wrist is a simple technique which is comfortable for the patient. We report on a series of 96 patients with dorsal synovial cysts (75 women, 21 men). All patients had undergone preliminary treatment which had been unsuccessful. We operated on 32 patients with a volar cyst (27 women, five men). All the patients were operated on as outpatients under local regional anaesthesia. For the dorsal cysts, after having precisely located the cyst, it is then resected after having inserted a shaver directly through the wall of the cyst starting with the capsule. For the volar cysts the arthroscope was inserted through a 3-4 portal and the shaver was inserted through a 1-2 radiocarpal portal. In all cases, there was no immobilisation and a range of motion was started the same day. For the dorsal cysts, our average follow-up was 34 months (range 12–46 months). There were no complications. We had four recurrences. For the palmar cysts, our average follow-up was 26 months (range 12–39 months). There have been no recurrences to date.

17 FLOW CYTOMETRY ANALYSIS OF THE TURKEY SPERM GLYCOCALYX: EFFECTS OF NEURAMINIDASE TREATMENT

The surface of all eucaryotic cells consists of a carbohydrate-rich zone known as the glycocalyx which mediates a variety of specific cell-recognition processes, including sperm-egg interactions. Several carbohydrate residues are known to be necessary for poultry sperm to traverse the female reproductive tract and for sperm-egg recognition. Alteration of the sperm glycocalyx during semen storage could adversely impact fertility. Accordingly, the aim of this work was to elucidate the sugar residues existing in the surface of turkey spermatozoa as a first step in understanding the deleterious effects of semen storage on sperm physiology and function. Nine turkey toms were randomly assigned to 1 of 3 groups (3 males/group) and semen was pooled for each group. Seminal plasma was removed and isolated sperm were resuspended in Tris-NaCl buffer at either (1) pH 7.4 for immediate staining with 1 of 16 FITC-conjugated lectins (100 �g/mL; 30 min; 25�C; 100 � 106 cells/mL), or (2) pH 6.0 for neuraminidase treatment (30 min; 37�C; 1 IU/109 cells), followed by washing (700 g, 5 min; 4 times) and lectin staining. The control consisted of sperm cells incubated only in Tris-NaCl buffer. Stained and control samples were washed twice (700 g, 5 min) and counterstained with 12 �M propidium iodide (PI); the green fluorescence intensity of PI-negative cells was assessed using a Coulter EPICS XL-MCL" Flow Cytometer (Beckman Coulter, Inc., Fullerton, CA, USA) and single-parameter histogram analysis (6 replicates). Median fluorescence intensity (MdFI) was used to assess differences in the presence of sugar residues among the control, non-neuraminidase-treated, and neuraminidase-treated samples (Kruskal-Wallis test; Tukey's HSD test in post-hoc comparisons). Lectin staining occurred in the PI-positive subpopulation, or membrane-disrupted cells, of all samples. By contrast, only intact cells were labeled by LPA, ConA, RCA-I, and s-WGA lectins in the non-neuraminidase-treated samples, indicating that only residues of sialic acid, �-mannose/�-glucose, �-galactose, and N-acetylglucosamine oligomers were on the surface. As expected, removal of sialic acid significantly (P < 0.05) decreased the fluorescence intensity of LPA-labeled cells. This treatment significantly (P < 0.05) increased the affinity of ConA, RCA-I, and s-WGA lectins, and exposed sugar residues previously undetected using ECA (N-acetyllactosamine), GNA (�-mannose), GS-I (�-galactose), GS-II (N-acetylglucosamine monomers), LOTUS (�-l-fucose), PNA (�-galactose), SBA (�-N-acetylgalactosamine), and WFA (�-N-acetylgalactosamine) lectins. Low levels of MdFI were observed for cells labeled by JAC (�-galactose), PSA (�-mannose/�-glucose), STA (N-acetylglucosamine polymers) and UEA-I (�-l-fucose) irrespective of neuraminidase treatment (P > 0.05). These observations suggest that (1) the carbohydrate content of turkey sperm glycocalyx is extensively masked by sialic acid molecules, (2) it contains a diversity of sugar residues, and (3) discrimination between intact and damaged cells needs to be done in order to properly identify surface binding.

GM-CSF potentiated peripheral blood progenitor cell (PBPC) collection with or without bone marrow as hematologic support of high-dose chemotherapy: two protocols

High-dose chemotherapy with autologous bone marrow support (ABMS) achieves prolonged relapse-free survival in relapsed lymphomas and leukemias and has provided durable complete responses in certain solid tumors. The principal morbidity and mortality result from the infectious and bleeding complications during the 3-4 week aplasia until the bone marrow autograft can recover. Hematopoietic growth factors, alone or used after chemotherapy, increase the number of circulating progenitor cells in the peripheral blood compartment. In one trial, 12 patients with solid tumors were treated with high-dose chemotherapy and supported with both bone marrow and peripheral blood progenitor cells (PBPC) collected after GM-CSF administration. Reconstitution of bone marrow function occurred quickly (ANC greater than 500/microliters by day 17; platelet-transfusion independence by day 16), resulting in short hospital stays (median, 28 days). In a second study, 12 patients with metastatic breast cancer responding to induction chemotherapy (doxorubicin, 5-fluorouracil, and methotrexate) were given GM-CSF during induction to collect PBPCs during leukocyte recovery. These PBPCs were used as the sole hematopoietic support during high-dose chemotherapy with cyclophosphamide, thiotepa, and carboplatin. Granulocyte and platelet reconstitution were extremely rapid (median, 14 and 12 days, respectively). When compared with 29 patients undergoing the same intensification therapy using ABMT as sole support, time to hematopoietic recovery, transfusion requirements, and duration of hospital stay were all significantly improved for the patients receiving PBPC. PBPC with or without marrow may enhance the safety, tolerance, and cost of high-dose therapy. Moreover, PBPC may render multiple course combination, high-dose therapy feasible.