Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

Background

Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting.

Results

In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail.

Conclusions

The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08510-y.

Modular prosthetic reconstruction for primary bone tumours of the distal tibia in ten patients

BACKGROUND: Below-knee amputation (BKA) is the safest treatment for benign aggressive and malignant bone tumours of the distal tibia, yielding good oncological and functional results. However, in selected patients where limb salvage is feasible and amputation unacceptable to the patient, limb salvage using a distal tibial replacement (DTR) can be considered. This study aims to present the oncological and functional results of the use of the latter treatment method in our unit. METHODS: A retrospective folder review was performed for all ten patients who received a modular DTR between 1 January 2005 and 31 January 2019 for a primary bone tumour, either benign aggressive or malignant. Six were female and the mean age was 31 (12-75) years. There were five patients with giant cell tumour of bone, four with osteosarcoma and one with a low-grade chondrosarcoma. The patients with osteosarcoma had neoadjuvant chemotherapy before surgery. Function was assessed by the Musculoskeletal Tumor Society (MSTS) score. RESULTS: Two patients had local recurrence treated with a BKA and one other patient died of metastases three years postoperatively. At a mean follow-up of three years, the remaining eight patients had a mean MSTS score of 83% (67-93%). There were no radiological signs of loosening, and no revision surgeries. CONCLUSION: Endoprosthetic replacement of the distal tibia for primary bone tumours can be a safe treatment option in very selected cases. Level of evidence: Level 4

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university-based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping-by-sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo-autosomal sexing marker (zinc-finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.

Sex differences in stress and immune responses during confinement in Antarctica

Background

Antarctica challenges human explorers by its extreme environment. The effects of these unique conditions on the human physiology need to be understood to best mitigate health problems in Antarctic expedition crews. Moreover, Antarctica is an adequate Earth-bound analogue for long-term space missions. To date, its effects on human physiology have been studied mainly in male cohorts though more female expeditioners and applicants in astronaut training programs are selected. Therefore, the identification of sex differences in stress and immune reactions are becoming an even more essential aim to provide a more individualized risk management.

Methods

Ten female and 16 male subjects participated in three 1-year expeditions to the German Antarctic Research Station Neumayer III. Blood, saliva, and urine samples were taken 1–2 months prior to departure, subsequently every month during their expedition, and 3–4 months after return from Antarctica. Analyses included cortisol, catecholamine and endocannabinoid measurements; psychological evaluation; differential blood count; and recall antigen- and mitogen-stimulated cytokine profiles.

Results

Cortisol showed significantly higher concentrations in females than males during winter whereas no enhanced psychological stress was detected in both sexes. Catecholamine excretion was higher in males than females but never showed significant increases compared to baseline. Endocannabinoids and N-acylethanolamides increased significantly in both sexes and stayed consistently elevated during the confinement. Cytokine profiles after in vitro stimulation revealed no sex differences but resulted in significant time-dependent changes. Hemoglobin and hematocrit were significantly higher in males than females, and hemoglobin increased significantly in both sexes compared to baseline. Platelet counts were significantly higher in females than males. Leukocytes and granulocyte concentrations increased during confinement with a dip for both sexes in winter whereas lymphocytes were significantly elevated in both sexes during the confinement.

Conclusions

The extreme environment of Antarctica seems to trigger some distinct stress and immune responses but—with the exception of cortisol and blood cell counts—without any major relevant sex-specific differences. Stated sex differences were shown to be independent of enhanced psychological stress and seem to be related to the environmental conditions. However, sources and consequences of these sex differences have to be further elucidated.

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo)

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

The blood-tendon barrier: identification and characterisation of a novel tissue barrier in tendon blood vessels

Tissue barriers function as "gate keepers" between different compartments (usually blood and tissue) and are formed by specialised membrane-associated proteins, localising to the apicolateral plasma membrane domain of epithelial and endothelial cells. By sealing the paracellular space, the free diffusion of solutes and molecules across epithelia and endothelia is impeded. Thereby, tissue barriers contribute to the establishment and maintenance of a distinct internal and external environment, which is crucial during organ development and allows maintenance of an organ-specific homeostatic milieu. So far, various epithelial and endothelial tissue barriers have been described, including the blood-brain barrier, the blood-retina barrier, the blood-testis barrier, the blood-placenta barrier, and the cerebrospinal fluid (CSF)-brain barrier, which are vital for physiological function and any disturbance of these barriers can result in severe organ damage or even death. Here, we describe the identification of a novel barrier, located in the vascular bed of tendons, which we term the blood-tendon barrier (BTB). By using immunohistochemistry, transmission electron microscopy, and tracer studies we demonstrate the presence of a functional endothelial barrier within tendons restricting the passage of large blood-borne molecules into the surrounding tendon tissue. We further provide in vitro evidence that the BTB potentially contributes to the creation of a distinct internal tissue environment impacting upon the proliferation and differentiation of tendon-resident cells, effects which might be fundamental for the onset of tendon pathologies.

Resilience moderates the association between chronic pain and depressive symptoms in the elderly

BACKGROUND

Chronic pain is frequent in elderly people and, especially if widespread, associated with poor mental health. We investigated whether a resilient personality protects older adults against the adverse effects of chronic pain.

METHODS

Pain status [no pain, chronic local pain (CLP) and chronic widespread pain (CWP)] was determined using the American College of Rheumatologists' criteria for widespread pain in a cross-sectional sample of 724 participants aged 68-92 years drawn from the population-based KORA-Age study in Southern Germany. Depressive symptoms and resilience were assessed via the scales GDS-15 and RS-5. The relation between pain, resilience and depressive symptoms was modelled using logistic and quantile regression.

RESULTS

CLP prevalence and CWP prevalence were 57.5% and 12.3%, respectively. Confounder-adjusted logistic regression indicated a fourfold risk of depressed mood (GDS-15 ≥ 5) in CWP, vs. no pain (OR = 4.08, 95% CI 1.90-8.74). However, in quantile regression, the adverse effect of CWP was significantly attenuated by resilience when looking at the GDS-15 score lower quartile (p = 0.011) and median (p = 0.011). This effect appeared to be mainly driven by participants aged 75-84 years. Confounder adjustment reduced the effect of CLP on depressive symptoms to non-significance, and effect modification by resilience was undetectable in regression models of CLP.

CONCLUSIONS

Resilience was protective in the association of CWP with depressive symptoms in this analysis. Older adults with CWP may potentially benefit from interventions supporting resilience. Prospective research should investigate the protective role of resilience in the potentially self-perpetuating relation between chronic pain and depressed affect. WHAT DOES THIS STUDY ADD?: The association of chronic widespread pain with depressive symptoms in the elderly population is attenuated by resilience.

Resin-based Composite Light-cured Properties Assessed by Laboratory Standards and Simulated Clinical Conditions

The following parameters were varied: 1) irradiation technique: top and bottom polymerization according to the ISO standard, and polymerization from only the top, simulating clinical situations; 2) polymerization time: 5, 10, 20, and 40 seconds; 3) storage conditions: 24 hours in distilled water, thermocycling followed by storage for four weeks in artificial saliva or alcohol. Flexural strength (FS), flexural modulus (Eflexural), indentation modulus (E), Vickers hardness (HV), and degree of conversion (DC) were measured.

The laboratory results were similar to those measured by mimicking clinical conditions only at high polymerization times and mild storage conditions (20 seconds and 40 seconds and storage for 24 hours in water, and 40 seconds with aging and storing in saliva). Significantly higher DC values were measured on the top than on the bottom of a 2-mm layer for all polymerization times. Overall, 5-second and 10-second irradiation times induced significantly lower DC values compared to the currently recommended polymerization times of 20 and 40 seconds at both the top and bottom of the samples.

The initial DC differences as a function of irradiation time are leveled at 24 hours of storage but seem to do well in predicting long-term material behavior. A minimum irradiation time of 20 seconds is necessary clinically to achieve the best mechanical properties with modern high-intensity light emitting diode (LED) units.

[Surgical competence in the treatment of thoracic and abdominal injuries in rural hospitals]

The German S3 Guideline on Treatment of Polytrauma/Severely Injured Patients characterizes key recommendations on the current diagnostic and therapeutic approach in concomitant thoracic and abdominal trauma based on the available scientific data. The special requirements for appropriate basic treatment can be derived for rural hospitals, even though the particular grade of recommendation often is low because evidence-based studies are still lacking.The options for adequate basic treatment of thoracic and abdominal trauma in patients with multiple injuries treated in rural hospitals substantially depend on the dedication, the level of experience and training, and the willingness of the locally responsible team to cooperate.

[Perioperative nutrition - a nationwide web-based survey of German surgery departments]

BACKGROUND

Insufficient nutrition in surgical patients increases perioperative morbidity, mortality, length of stay and therapy costs. Therefore, guidelines declare the integration of nutrition into the overall management as one of the key aspects of perioperative care. This study was conducted to evaluate the current clinical practice of clinical nutrition in surgical departments in Germany.

METHODS

In 2009 German Surgical Society (DGCH) members in leading positions were surveyed with a standardised online questionnaire concerning their perioperative nutritional routines in elective surgery.

RESULTS

From the addressed physicians n = 156 (6.24 %) answered. Of those, 86.9 % consider the nutritional status of their patients. Only 6 % use standardised nutritional screening tools. Short preoperative fasting for solid and liquid food is practiced by 65 % and 40 %, respectively. After the operation, 65 % allow intake of clear fluids on the day of surgery and 78 % initiate solid food on the day of surgery or the first postoperative day. Oral nutritional supplements are given only "sometimes" or "rarely" by 53.9 % of the respondents.

CONCLUSION

The low response rate may imply the dilemma that the evidence-based benefit of perioperative nutrition does not meet sufficient interest. Even in case of a positive selection of "pro-nutrition respondents", standardised preoperative malnutrition screening is also rare. Aspects such as shorter perioperative fasting are already practiced more progressively. However, still greater efforts are needed to promote guideline-based clinical nutrition in surgical care in Germany.

[Quality of life of German surgeons: results of a survey of 3,652 attendees of the annual meetings of the German Surgical Societies ]

BACKGROUND AND OBJECTIVE

Quality of life is of vital importance for patients undergoing surgery. However, little is known about the quality of life of surgeons who are facing a stressful and dramatically changing working environment. For this reason, this large scale study investigated the quality of life (QL) of surgeons in Germany in the context of occupational, private, and system-related risk factors with a standardized QL measurement instrument.

METHODS

The study population consisted of attendees (surgeons, non-surgical physicians, medical students) of the nine major annual conferences of the German Society of Surgery between 2008 and 2009. Participants filled in a single questionnaire including study-specific questions (demographic variables, professional position, and occupational situation) and a standardized quality of life instrument. Surgeons' responses with regard to their professional situation and their quality of life were contrasted with those of the two controls (non-surgical physicians, i. e. orthopedics, pediatrics, gastroenterologists and medical students). Furthermore, QL scores were compared with German population reference data and with reference data of several patient groups.

RESULTS

3652 individuals (2991 surgeons, 561 non-surgical physicians, 100 medical students) participated in this study. 68 % of the surgeons but only 39 % of the non-surgeons worked more than 60 hours per week on average. Surgeons reported restrictions on their private and family life due to work overload, more so than non-surgeons (74 % vs. 59 %). Responses to the PLC quality of life questionnaire confirmed these results, showing score values lower than those of the German population reference data and of several patient groups.

CONCLUSION

The time has come for surgeons to consider their own quality of life, as this is a main issue in their scientific and clinical work with patients.

[Organizational forms of emergency medicine from the perspective of DGCH and BDC. Discipline-specific or interdisciplinary?]

Due to logistic, organizational and economic advantages, interdisciplinary emergency centers are gaining more and more acceptance compared to established, discipline-specific and independent emergency rooms. Organizational concepts for interdisciplinary emergency centers need to consider the mandate for comprehensive patient care and the consequential performance spectrum. Thus, the implementation of generally accepted guidelines and specifications is demanding.Currently developed concepts of the accordant interdisciplinary working groups try to fulfill these premises. Further fundamental criteria to be met are the quality and education of medical and nursing staff, which are predominantly doing their jobs within the interdisciplinary emergency centers. The concept of the German surgical societies and connected organizations is not the implementation of a new definition of the role of emergency specialized physicians but rather a substantial advancement of the existing and established regulations for further education. Therefore, a further advanced-training program for clinical emergency medicine has to be implemented in addition to the existing emergency education within the common trunk, which every physician has to pass through during discipline-specific education. Furthermore, this program should complement the existing pre-clinical emergency education, which can be acquired after specialization.The accordant criteria to be developed and the coordination with the German Medical Association (Bundesärztekammer) are currently prioritized on the agenda of the interdisciplinary working group. Due to reasons of compatibility with the regulations for further education, specific management skills for future heads and directors of such interdisciplinary emergency centers should not be stipulated within the advanced-training program for clinical emergency medicine but should be gained through specific course concepts beyond this program.

TISSUE MAST CELLS AND ACUTE INFLAMMATION IN EXPERIMENTAL CUTANEOUS MUCORMYCOSIS OF NORMAL, 48/80-TREATED, AND DIABETIC RATS

The role of the tissue mast cells in relation to the acute inflammatory reaction to experimental cutaneous mucormycosis was studied histologically in normal rats, in animals whose tissue mast cells had been depleted of their cytoplasmic granules prior to infection by the administration of compound 48/80 and in others in whom acute alloxan diabetes with acidosis had been produced before injection of the fungus. The discharge of the tissue mast cell granules in normal rats occurred within minutes at the site of infection and appeared to initiate the rapid onset of acute inflammation. The degranulation of the tissue mast cells subsided in a short time and the cells reassumed a normal histologic appearance while inflammation progressed with the formation of circumscribed lesions. In animals pretreated with compound 48/80 in which the tissue mast cells contained no granules, the onset of inflammation was briefly delayed, the intensity of the process was somewhat decreased, fibroblastic proliferation was retarded, and the fungus growth in the early lesions was increased. However, the infection did not spread and the lesions were well localized. The tissue mast cells in the diabetic and acidotic rats completely failed to discharge their cytoplasmic granules, the onset and intensity of the acute inflammatory response were markedly delayed and decreased and the infection progressed rapidly with massive fungus growth invading adjacent tissues. A relationship between the discharged tissue mast cell granules and eosinophilic granulocytes was noted since the latter were numerous among the inflammatory cell exudate in normal rats and scarce in the lesions of the diabetic animals. It is concluded that a function of the tissue mast cells in the normal rat is the rapid initiation of acute inflammation at the site of injury and that degranulation of these cells prior to infection somewhat delays the inflammatory response and therefore slightly diminishes host resistance. Furthermore, a severe metabolic disorder such as acute alloxan diabetes with acidosis, inhibits the normal function of the tissue mast cells, delays and decreases inflammation, and in this manner contributes to the greatly increased susceptibility of the host to infection.