Gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design

In the 20th century geneticists began to unravel some of the simpler aspects of the etiology of inherited diseases in humans. The theory of linkage analysis was developed and applied long before the advent of molecular biology, but only the technological advances of the second half of the 20th century made large-scale gene mapping with a dense genome-spanning set of markers a reality. More recently, the primary topic of interest has shifted from simple Mendelian diseases, for which genotypes of some gene are the cause of disease, to more complex diseases, for which genotypes of some set of genes together with environmental factors merely alter the probability that an individual gets the disease, although individual factors are typically insufficient to cause the disease outright. To this end, a great deal of dogma has evolved about the best way to skin this cat, although to date success has been minimal with any approach. We postulate that the main reason for this is a lack of attention to experimental design. Once the data have been ascertained, the most powerful statistical methods will not be able to salvage an inappropriately designed study (Andersen 1990). Each phenotype and/or population mandates its own individually tailored study design to maximize the chances of successful gene mapping. We suggest that careful consideration of the available data from real genotype-phenotype correlation studies (as opposed to oversimplified theoretically tractable models), and the practical feasibility of different ascertainment schemes dictate how one should proceed. In this review we review the theory and practice of gene mapping at the close of the 20th century, showing that most methods of linkage and linkage disequilibrium analysis are similar in a fundamental sense, with the differences being related more to study design and ascertainment than to technical details of the underlying statistical analysis. To this end, we propose a new focus in the field of statistical genetics that more explicitly highlights the primacy of study design as the means to increase power for gene mapping.     

Macrophage polarization: a key event in the secondary phase of acute spinal cord injury

Acute spinal cord injury (SCI) has become epidemic in modern society. Despite advances made in the understanding of the pathogenesis and improvements in early recognition and treatment, it remains a devastating event, often producing severe and permanent disability. SCI has two phases: acute and secondary. Although the acute phase is marked by severe local and systemic events such as tissue contusion, ischaemia, haemorrhage and vascular damage, the outcome of SCI are mainly influenced by the secondary phase. SCI causes inflammatory responses through the activation of innate immune responses that contribute to secondary injury, in which polarization‐based macrophage activation is a hallmarker. Macrophages accumulated within the epicentre and the haematoma of the injured spinal cord play a significant role in this inflammation. Depending on their phenotype and activation status, macrophages may initiate secondary injury mechanisms and/or promote CNS regeneration and repair. When it comes to therapies for SCI, very few can be performed in the acute phase. However, as macrophage activation and polarization switch are exquisitely sensitive to changes in microenvironment, some trials have been conducted to modulate macrophage polarization towards benefiting the recovery of SCI. Given this, it is important to understand how macrophages and SCI interrelate and interact on a molecular pathophysiological level. This review provides a comprehensive overview of the immuno‐pathophysiological features of acute SCI mainly from the following perspectives: (i) the overview of the pathophysiology of acute SCI, (ii) the roles of macrophage, especially its polarization switch in acute SCI, and (iii) newly developed neuroprotective therapies modulating macrophage polarization in acute SCI.     

Gondwana Link: connecting people,landscapes, and livelihoods across southwestern Australia

The Gondwana Link (GL) program spans some 1,000 km and includes organizations, businesses, and individuals working to improve ecological function across the most intact large areas of habitat remaining in southwestern Australia (SWA). Noncompetitive leadership plus a focus on tangible achievement have been critical to providing the cohesion and initial momentum needed to support and inspire increased effort from those involved. Ongoing success rests on the responses of people working together, having respect for the integrity of the collective effort and for the specific roles of others across differing but complementary roles. Significant achievements have been secured, with progress in scientific knowledge generally following initial implementation of key actions. Lasting improvements in ecological health and resilience will only occur through larger‐scale actions, which require more effort and time. The GL program has been an important initiative in strengthening the awareness of the distinctive ecological systems across SWA and the intertwined characteristics of resilience and fragility that characterize the region and its people. It has also had a role in inspiring and informing growth in large‐scale connectivity programs nationally and internationally.     

The Human Frontier Science Program: its aims and a proposal for its implementation

Reactions to the Human Frontier Science Program have been mixed. It has been welcomed as an important initiative in basic biological research yet regarded with suspicion by some outside Japan who see it as facilitating access to European and North American fundamental research. However, suspicion is clearing away and the governments concerned are looking forward to the Program's implementation. In this article, the Program's aims and the mechanisms for its execution are outlined as proposed in the light of a recent feasibility study.     

Impacts of epidural electrical stimulation on Wnt signaling,FAAH, and BDNF following thoracic spinal cord injury in rat

Electrical stimulation (ES) has been shown to improve some of impairments after spinal cord injury (SCI), but the underlying mechanisms remain unclear. The Wnt signaling pathways and the endocannabinoid system appear to be modulated in response to SCI. This study aimed to investigate the effect of ES therapy on the activity of canonical/noncanonical Wnt signaling pathways, brain-derived neurotrophic factor (BDNF), and fatty-acid amide hydrolase (FAAH), which regulate endocannabinoids levels. Forty male Wistar rats were randomly divided into four groups: (a) Sham, (b) laminectomy + epidural subthreshold ES, (c) SCI, and (d) SCI + epidural subthreshold ES. A moderate contusion SCI was performed at the thoracic level (T10). Epidural subthreshold ES was delivered to upper the level of T10 segment every day (1 hr/rat) for 2 weeks. Then, animals were killed and immunoblotting was used to assess spinal cord parameters. Results revealed that ES intervention for 14 days could significantly increase wingless-type3 (Wnt3), Wnt7, β-catenin, Nestin, and cyclin D1 levels, as well as phosphorylation of glycogen synthase kinase 3β and Jun N-terminal kinase. Additionally, SCI reduced BDNF and FAAH levels, and ES increased BDNF and FAAH levels in the injury site. We propose that ES therapy may improve some of impairments after SCI through Wnt signaling pathways. Outcomes also suggest that BDNF and FAAH are important players in the beneficial impacts of ES therapy. However, the precise mechanism of BDNF, FAAH, and Wnt signaling pathways on SCI requires further investigation.     

肠道菌群与脊髓损伤并发症

脊髓损伤是严重的致残性神经系统疾病,脊髓损伤后产生的水肿、炎症反应和代谢紊乱等并发症是致使脊髓损伤继发性加重的主要原因。近年来,随着对肠道微生物的研究越来越深入,肠道菌群对神经系统疾病的影响得到广泛关注。肠道菌群可以通过调节机体能量代谢、炎症反应及作用于神经内分泌和脑-肠轴的途径影响中枢神经系统疾病。最近研究发现,肠道菌群与脊髓损伤并发症的关系非常紧密。脊髓损伤后肠道菌群的变化可能影响脊髓损伤后并发症发生以及加重。本文主要就肠道菌群对脊髓损伤后并发症的影响和可能的作用机制进行综述,为临床研究和治疗脊髓损伤提供新思路。     

Le recueil de sperme chez le blessé médullaire

Infertility is a major issue for men with spinal cord injury (SCI). Male infertility is due to a combination of ejaculatory dysfunction and abnormal sperm quantity and quality. The reported ability to ejaculate during sexual stimulation or masturbation is about 15%. Techniques to remediate ejaculation have vastly improved the fertility potential of men with SCI. Penile vibratory stimulation (PVS) to induce ejaculation is now recommended as first-line treatment due to its safety and relative efficacy. PVS can also be used at home for fertility purposes with success rates of more than 70%. Pharmacological treatments can be associated with PVS to enhance ejaculation. Midodrine, an alpha1-adrenergic agonist, has been recently used with success rates of 66% in SCI patients who failed PVS alone. PVS with midodrine can now be considered as second-line treatment for anejaculation, after PVS and before electroejaculation. It is a safe procedure, but requires cardiovascular monitoring. PVS with midodrine can also be effective in the treatment of retrograde ejaculation by inducing bladder neck closure.     

The contribution of vaccination to global health: past,present and future

Vaccination has made an enormous contribution to global health. Two major infections, smallpox and rinderpest, have been eradicated. Global coverage of vaccination against many important infectious diseases of childhood has been enhanced dramatically since the creation of WHO''s Expanded Programme of Immunization in 1974 and of the Global Alliance for Vaccination and Immunization in 2000. Polio has almost been eradicated and success in controlling measles makes this infection another potential target for eradication. Despite these successes, approximately 6.6 million children still die each year and about a half of these deaths are caused by infections, including pneumonia and diarrhoea, which could be prevented by vaccination. Enhanced deployment of recently developed pneumococcal conjugate and rotavirus vaccines should, therefore, result in a further decline in childhood mortality. Development of vaccines against more complex infections, such as malaria, tuberculosis and HIV, has been challenging and achievements so far have been modest. Final success against these infections may require combination vaccinations, each component stimulating a different arm of the immune system. In the longer term, vaccines are likely to be used to prevent or modulate the course of some non-infectious diseases. Progress has already been made with therapeutic cancer vaccines and future potential targets include addiction, diabetes, hypertension and Alzheimer''s disease.     

New developments on the role of NMDA receptors in Alzheimer's disease

Since the initial findings that NMDA receptors play important roles in cellular models of learning as well as neurotoxicity, abnormal function of this receptor has been considered a potential mechanism in the pathophysiology underlying Alzheimer's disease. Treatment of Alzheimer's disease with an NMDA receptor antagonist began several years ago, with some limited success. More recent mechanistic studies have examined the role of NMDA receptors in the synaptic effects of beta amyloid (Aβ).     

Technique of Porcine Liver Procurement and Orthotopic Transplantation using an Active Porto-Caval Shunt

The success of liver transplantation has resulted in a dramatic organ shortage. Each year, a considerable number of patients on the liver transplantation waiting list die without receiving an organ transplant or are delisted due to disease progression. Even after a successful transplantation, rejection and side effects of immunosuppression remain major concerns for graft survival and patient morbidity. Experimental animal research has been essential to the success of liver transplantation and still plays a pivotal role in the development of clinical transplantation practice. In particular, the porcine orthotopic liver transplantation model (OLTx) is optimal for clinically oriented research for its close resemblance to human size, anatomy, and physiology. Decompression of intestinal congestion during the anhepatic phase of porcine OLTx is important to guarantee reliable animal survival. The use of an active porto-caval-jugular shunt achieves excellent intestinal decompression. The system can be used for short-term as well as long-term survival experiments. The following protocol contains all technical information for a stable and reproducible liver transplantation model in pigs including post-operative animal care.     

Porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory disease (PRRS) is an economically important disease around the globe; it has been estimated to cost the swine industry in USA approximately 560 million US dollars annually. It is well established that PRRS is caused by an enveloped, single-stranded positive-sense RNA virus known as porcine reproductive and respiratory syndrome virus (PRRSV). The inability to successfully control PRRS across farms via traditional methods (e.g. vaccine and animal flow) has led to a growing interest in area-based eradication. Important to such an initiative is information on PRRSV transmission within and between herds and intervention strategies to prevent its spread. This paper will review the current literature on selected areas of PRRS known to be important to the topic of pathogen elimination, including etiology, clinical manifestations, direct and indirect routes of transmission, as well as discuss measures for disease control, prevention and eradication.     

The web and the structure of taxonomy

An easily accessible taxonomic knowledge base is critically important for all biodiversity-related sciences. At present, taxonomic information is organized and regulated by a system of rules and conventions that date back to the introduction of binomial nomenclature by Linnaeus. The taxonomy of any particular group of organisms comprises the sum information in the taxonomic literature, supported by designated type specimens in major collections. In this article, the way modern means of disseminating information will change the practice of taxonomy, in particular the Internet, is explored. Basic taxonomic information, such as specimen-level data, location of types, and name catalogues are already available, at least for some groups, on the Web. Specialist taxonomic databases, key-construction programs, and other software useful for systematists are also increasingly available. There has also been a move towards Web-publishing of taxonomic hypotheses, though as yet this is not fully permitted by the Codes of Nomenclature. A further and more radical move would be to transfer taxonomy completely to the Web. A possible model of this is discussed, as well as a pilot project, the "CATE" initiative, which seeks to explore the advantages and disadvantages of such a move. It is argued that taxonomy needs to forge better links with its user-communities to maintain its funding base, and that an important part of this is making the products of its research more accessible through the Internet.     

Systems of Production and Social Discourse: The Skipper Effect Revisited

We have argued that differences in success in Icelandic fishing are statistically explained more by technical and ecological factors than by personal qualities of skippers, the "skipper effect." Research by other scholars has reopened the discussion of the skipper effect. We assess some of the statistical arguments, pointing out that while there may be a strong skipper effect in some societies, in other societies it is weak or negligible. We suggest that it is important to distinguish between the statistical reality of the skipper effect and its sociology and that the concept of skipper effect is of limited utility in comparative studies, since different researchers using it have not always been talking about the same phenomena and fishing success is conceived differently in different societies. The discussion of the skipper effect echoes debates on resource management and the authenticity of folk models, as well as larger debates in social theory on the relationship between the symbolic and the real and the role of history and agency. Folk theories of production, we argue, are best regarded as cultural accounts constructed in social discourse, in the context of production systems.     

Betulinic acid inhibits pyroptosis in spinal cord injury by augmenting autophagy via the AMPK-mTOR-TFEB signaling pathway

Spinal cord injury (SCI) results in a wide range of disabilities. Its complex pathophysiological process limits the effectiveness of many clinical treatments. Betulinic acid (BA) has been shown to be an effective treatment for some neurological diseases, but it has not been studied in SCI. In this study, we assessed the role of BA in SCI and investigated its underlying mechanism. We used a mouse model of SCI, and functional outcomes following injury were assessed. Western blotting, ELISA, and immunofluorescence techniques were employed to analyze levels of autophagy, mitophagy, pyroptosis, and AMPK-related signaling pathways were also examined. Our results showed that BA significantly improved functional recovery following SCI. Furthermore, autophagy, mitophagy, ROS level and pyroptosis were implicated in the mechanism of BA in the treatment of SCI. Specifically, our results suggest that BA restored autophagy flux following injury, which induced mitophagy to eliminate the accumulation of ROS and inhibits pyroptosis. Further mechanistic studies revealed that BA likely regulates autophagy and mitophagy via the AMPK-mTOR-TFEB signaling pathway. Those results showed that BA can significantly promote the recovery following SCI and that it may be a promising therapy for SCI.     

TRPA1 receptor modulation attenuates bladder overactivity induced by spinal cord injury

The ankyrin-repeat transient receptor potential 1 (TRPA1) has been implicated in pathological conditions of the bladder, but its role in overactive bladder (OAB) following spinal cord injury (SCI) remains unknown. In this study, using a rat SCI model, we assessed the relevance of TRPA1 in OAB induced by SCI. SCI resulted in tissue damage, inflammation, and changes in bladder contractility and in voiding behavior. Moreover, SCI caused upregulation of TRPA1 protein and mRNA levels, in bladder and in dorsal root ganglion (DRG; L6-S1), but not in corresponding segment of spinal cord. Alteration in bladder contractility following SCI was evidenced by enhancement in cinnamaldehyde-, capsaicin-, or carbachol-induced bladder contraction as well as in its spontaneous phasic activity. Of relevance to voiding behavior, SCI induced increase in the number of nonvoiding contractions (NVCs), an important parameter associated with the OAB etiology, besides alterations in other urodynamic parameters. HC-030031 (TRPA1 antagonist) treatment decreased the number and the amplitude of NVCs while the TRPA1 antisense oligodeoxynucleotide (AS-ODN) treatment normalized the spontaneous phasic activity, decreased the cinnamaldehyde-induced bladder contraction and the number of NVCs in SCI rats. In addition, the cinnamaldehyde-induced bladder contraction was reduced by exposure of the bladder preparations to HC-030031. The efficacy of TRPA1 AS-ODN treatment was confirmed by means of the reduction of TRPA1 expression in the DRG, in the corresponding segment of the spinal cord and in the bladder, specifically in detrusor muscle. The present data show that the TRPA1 activation and upregulation seem to exert an important role in OAB following SCI.     

Salidroside attenuates neuroinflammation and improves functional recovery after spinal cord injury through microglia polarization regulation

Spinal cord injury (SCI) is a severe neurological disease; however, few drugs have been proved to treat SCI effectively. Neuroinflammation is the major pathogenesis of SCI secondary injury and considered to be the therapeutic target of SCI. Salidroside (Sal) has been reported to exert anti‐inflammatory effects in airway, adipose and myocardial tissue; however, the role of Sal in SCI therapeutics has not been clarified. In this study, we showed that Sal could improve the functional recovery of spinal cord in rats as revealed by increased BBB locomotor rating scale, angle of incline, and decreased cavity of spinal cord injury and apoptosis of neurons in vivo. Immunofluorescence double staining of microglia marker and M1/M2 marker demonstrated that Sal could suppress M1 microglia polarization and activate M2 microglia polarization in vivo. To verify how Sal exerts its effects on microglia polarization and neuron protection, we performed the mechanism study in vitro in microglia cell line BV‐2 and neuron cell line PC12. The results showed that Sal prevents apoptosis of PC12 cells in coculture with LPS‐induced M1 BV‐2 microglia, also the inflammatory secretion phenotype of M1 BV‐2 microglia was suppressed by Sal, and further studies demonstrated that autophagic flux regulation through AMPK/mTOR pathway was involved in Sal regulated microglia polarization after SCI. Overall, our study illustrated that Sal could promote spinal cord injury functional recovery in rats, and the mechanism may relate to its microglia polarization modulation through AMPK‐/mTOR‐mediated autophagic flux stimulation.