Are species lists derived from modeled species range maps appropriate for macroecological studies? A case study on data from BIEN

Because survey-based species lists for fine-scale areas are generally lacking, ecologists have been using species lists derived from modeled range maps in macroecological studies. Here I evaluate whether it is appropriate to use species lists derived from modeled range maps in macroecological studies. I compared species lists derived from about 90,000 range maps in the Botanical Information and Ecology Network (BIEN) for over 180 geographic regions (12 broad regions covering the whole of the New World; 172 smaller regions, i.e. Taxonomic Databases Working Group units) with those representing complete or nearly complete species lists obtained from the literature for the regions. I determined the completeness of native species composition and proportion of false presences and exotic (non-native) species in species lists derived from range maps in BIEN. I determined whether errors in species lists derived from modeled range maps affect macroecological inferences by comparing the relationships of α- and β-diversity with geographic and climatic variables between different datasets (i.e. species lists derived from range maps versus complete or nearly complete species lists derived from the literature). The completeness for native species lists derived from range maps was 60–74%, depending on spatial scale. On average, 65% of the species in a species list derived from BIEN for a geographic area are false presences or non-native species to the area. The relationships of α- and β-diversity derived from the BIEN dataset with geographic and climatic variables differ significantly from those derived from complete species lists. This study shows that the results of a macroecological study based on species lists derived from modeled range maps may be substantially incorrect due to high percentages of missing native species, and high numbers of non-native species and false presences. Thus, it may not be appropriate to use species lists derived from modeled range maps in the macroecological studies that require complete or nearly complete species lists.     

A case of primary amenorrhea with 46+XY genotype from Kashmir Valley

Primary amenorrhea is one of the common reproductive disorder affecting females. It leads to the absence of menarche in the reproductive age group in females and/or complete absence of reproductive organs. There are many causes which lead to PA, including genetic aberrations which are the leading factors.     

Bacterial pathogen evolution: breaking news

The immense social and economic impact of bacterial pathogens, from drug-resistant infections in hospitals to the devastation of agricultural resources, has resulted in major investment to understand the causes and consequences of pathogen evolution. Recent genome sequencing projects have provided insight into the evolution of bacterial genome structures; revealing the impact of mobile DNA on genome restructuring and pathogenicity. Sequencing of multiple genomes of related strains has enabled the delineation of pathogen evolution and facilitated the tracking of bacterial pathogens globally. Other recent theoretical and empirical studies have shown that pathogen evolution is significantly influenced by ecological factors, such as the distribution of hosts within the environment and the effects of co-infection. We suggest that the time is ripe for experimentalists to use genomics in conjunction with evolutionary ecology experiments to further understanding of how bacterial pathogens evolve.     

Entomopathogenic fungi against South American tick species

Ticks are parasites of serious concern for humans, domesticated animals and wild animals. Despite scientific advances, in South America the principal control method for ticks is the use of chemical acaricides. Indiscriminate use of these products causes environmental pollution, food contamination and development of tick resistance to acaricides. In vitro studies and field trials have demonstrated that pathogenic fungal isolates not only cause mortality of many tick species, but also reduce subsequent generations due to effects on their reproductive efficacy. Accordingly, this review presents results of several studies which were conducted in South America. Furthermore, it outlines current information on fungal pathogens of ticks and discusses the need to develop and implement effective strategies for use of entomopathogenic fungi to control ticks in the near future.     

Maximized virulence in a sterilizing pathogen: the anther-smut fungus and its co-evolved hosts

Host sterilization is a common feature of sexually transmitted diseases (STDs). Because host reproductive failure may free up resources for pathogen reproduction and transmission, theory predicts that selection on sterilizing pathogens will favour maximum virulence (i.e. complete sterilization). We examined patterns of infection in sexually transmitted anther-smut fungi (Microbotryum) on four of their host species in the Caryophyllaceae. Using controlled fungal matings and experimental inoculations, we compared disease expression in inoculations ranging from host-specific pathogens to hybrids and cross-species treatments. Our data support the existence of host-specific sibling species within the genus Microbotryum based on a low infection rate from cross-inoculations and reduced fitness for hybrid pathogens. These patterns of host specificity and reproductive isolation, however, were not absolute. We did observe some successful cross-species and hybrid infections, but the expression of disease was frequently incomplete, including only partial host sterilization and the failed dehiscence of pathogen spores. The prevalence of these maladapted disease phenotypes may greatly inhibit the emergence of novel host pathogen combinations. Infections by hybrid pathogen genotypes were intermediate, in terms of both infection rate and the normality of disease symptoms, between host-specific and cross-inoculated pathogens. In addition, the frequency with which hybrid and cross-inoculated anther-smut pathogens were able to infect but not sterilize new hosts supports the prediction that sterilizing STDs are under selection to maximize virulence in natural populations.     

Retrospective study of morbidity and mortality of captive jaguars (Panthera onca) in North America: 1982–2002

One hundred seventy‐two medical records of captive jaguars (Panthera onca) were examined from 30 American Zoo and Aquarium Association (AZA) institutions housing jaguars between 1982–2002. The study determined common causes of morbidity and mortality, and the influence of age, gender, and melengestrol‐acetate (MGA) exposure on these rates. The most common causes of morbidity in captive jaguars were found to be dental, gastrointestinal, integumentary, and musculoskeletal diseases. Prevalence of types of disease varied with age, with older animals experiencing a higher prevalence of multiple types of disease. Females developed reproductive disease more frequently than males, and the data suggest that MGA exposure increased the risk of developing female reproductive disease. The most common causes of mortality were reproductive diseases in females and musculoskeletal diseases in males. There was a high rate of neonate and pediatric mortality, primarily due to stillbirths or unexplained neonatal death, trauma, and pneumonia. Other diseases or clinical signs that seemed remarkable were a high prevalence of episodes of epistaxis among young, as well as old, jaguars. Based on these findings, management suggestions for the captive jaguar population are presented. Zoo Biol 0:1–12, 2006. © 2006 Wiley‐Liss, Inc.     

Relationships among seminal culture, seminal white blood cells, and the percentage of primary sperm abnormalities in bulls evaluated prior to the breeding season

Semen samples from 100 beef breed bulls were evaluated for sperm morphology (phased contrast microscopy), seminal white blood cells, and the presence of potential reproductive pathogens. Eligibility required visualization of the glans penis throughout semen collection. Based on clinical spermiograms, bulls were grouped into normal, marginal, or unsatisfactory morphology classifications. The 3 experimental groups were similar in age and scrotal circumference and differed significantly in the percentage of primary sperm abnormalities. Most semen samples (94%) contained one or more potential reproductive pathogens (Hemophilus somnus. Mycoplasma bovigenitalium, Arcanobacterium pyogenes and Ureaplasma diversum). No significant relationship could be demonstrated between primary abnormalities and the assigned culture score. Our experimental results suggest that clinicians should interpret clinical semen culture results with great care. No significant relationship could be demonstrated between primary abnormalities and assigned white blood cell (WBC) score, although, only 1% of the samples was scored >5 WBC per high power field. The use of seminal WBC score may be valid adjunct to routine semen evaluation when that threshold is the basis for clinical decisions.     

Reduced selection leads to accelerated gene loss in <Emphasis Type="Italic">Shigella</Emphasis>

Background  

Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given to the causes of increased gene loss in facultative pathogens.     

Sex hormone modulation of human uterine epithelial cell immune responses

Sexually transmitted infections are a major worldwide publichealth problem affecting millions of people. A number of bacteria,fungi, viruses, and protozoa can infect reproductive tissues,resulting in varying degrees of pathology ranging from littlediscomfort to death. The female reproductive tract has evolvedinnate and adaptive immune mechanisms that protect from microbialinfection, thereby reducing infection and disease. Central tothis protection are the epithelial cells that line the femalereproductive tract. In the uterus, columnar epithelial cellsprovide a physical barrier to microbial infection, possess toll-likereceptors that detect pathogens and secrete a number of constitutiveand induced factors that directly or indirectly hinder infection.For example, uterine epithelial cells secrete peptides thatdestroy pathogenic microbes. In addition, epithelial cells producechemokines and cytokines that attract and activate innate immunecells and serve as a link to the adaptive immune system. Further,uterine epithelial cells serve as a conduit for secretory antibodiesto enter the lumen and can present antigen to T cells. Theseprotective mechanisms contribute to an environment in the uterusthat is generally considered sterile, unlike the environmentin the lower female reproductive tract. The uterine environmentis in constant flux due to the concentration changes in sexhormones that occur in preparation for reproduction. The sexhormones estrogen and progesterone alter the local immune systemto prepare for conception, influence how well the immune systemwill tolerate antigenic sperm and a semi-allogeneic fetus andyet provide a network of protective immune mechanisms againstmicrobial pathogens. Understanding how sex hormones influenceuterine epithelial cell function will provide a basis for immuneprotection in the uterus.     

Effects of cortisol implants on the PKX myxosporean causing proliferative kidney disease in rainbow trout, Salmo gairdneri

The myxosporean (PKX) that causes proliferative kidney disease in salmonid fishes is found primarily in the kidney interstitium of clinically affected fish, where it invokes a severe inflammatory response. Incomplete spores are observed in the lumen of kidney tubules in recovering fish. PKX-infected rainbow trout, Salmo gairdneri, were immunosuppressed with cortisol implants to determine if a reduction in renal interstitial inflammation would enhance the development of the parasite. Immunosuppression of these fish was indicated by high plasma cortisol levels, chronic mortality due to opportunistic pathogens, and depressed leucocrits when compared to infected fish not receiving cortisol implants. Cortisol-treated PKX-infected fish had 20 times the density of interstitial PKX compared with nontreated fish, but showed less interstitial inflammation. All of the former group examined at 4 wk postimplantation exhibited intraluminal sporogonic forms of PKX, whereas no sporogonic forms were detected in the nontreated fish. Suppression of the inflammatory response clearly enhanced the parasite's ability to reach the sporogonic stage, but did not induce complete development of the spore. Possibly the kidney tubules of rainbow trout do not provide the proper physiological environment for complete sporulation of PKX and a nonsalmonid fish may be the primary host.     

The changing face of pediatric respiratory tract infections: how human metapneumovirus and human bocavirus fit into the overall etiology of respiratory tract infections in young children

Lower respiratory tract infections are one of the leading causes of morbidity and mortality in children worldwide. Recent technological advances in the field of molecular biology have allowed virologists to detect many previously undetected viral pathogens. Two of these, human metapneumovirus (hMPV) and human bocavirus (HBoV), are of particular clinical interest to pediatric health care providers. This review discusses the most common viral respiratory infections in children, explores the role of newly discovered respiratory pathogens, and describes techniques for the diagnosis of viral respiratory infections.     

Infectious causes of reproductive loss in camelids

Reproductive losses in camelids are due to infertility, pregnancy loss, udder diseases and neonatal mortality caused by a variety of infectious diseases. Uterine infection and abortion represent the major complaint in camelid veterinary practice. The major infectious organisms in endometritis and metritis are E. coli and Streptococcus equi subspecies zooepidemicus. Abortion rates due to infectious diseases vary from 10% to more than 70% in some areas. Leptospirosis, toxoplasmosis and chlamydiosis have been diagnosed as the major causes of abortion in llamas and alpacas. In camels, brucellosis and trypanosomiasis represent the major causes of infectious abortion in the Middle East and Africa. Mastitis is rare in South American camelids. The prevalence of subclinical udder infection in camels can reach very high proportions in dairy camels. Udder infections are primarily due to Streptococcus agalactiae and Staphylococcus aureus. Neonatal mortality is primarily due to diarrhea following failure of passive transfer and exposure to E. coli, rotavirus, coronavirus, Coccidia and Salmonella. This paper reviews the etio-pathogenesis of these causes of reproductive losses, as well as the major risk factors and strategies to prevent their occurrence.     

Pneumocystis carinii,Toxoplasma gondii,Cytomegalovirus and the Compromised Host

Pneumocystis carinii and Toxoplasma gondii are the two major parasitic protozoan pathogens in the immunocompromised host. Both organisms cause latent infection in humans and many animals. Cats are the definitive hosts for toxoplasmosis; the animal vector for pneumocystis (if any) has not been defined. Toxoplasma is an obligate intracellular parasite, whereas the available evidence suggests that Pneumocystis carinii exists primarily extracellularly. In compromised hosts, pneumocystis infection usually involves only lungs, whereas toxoplasma causes a generalized infection with encephalitis being the principal clinical manifestation. Both types of infection are treated with combinations of folate antagonists (trimethoprim or pyrimethamine with sulfonamide). Both parasites are associated with cytomegalovirus infection in immunosuppressed hosts, an association which may be due to symbiosis between parasites, or to an additive immunosuppressive effect of dual infection on the hosts.     

Panorama de l’infertilité masculine

This paper reviews new epidemiological, etiological and therapeutic aspects of male infertility. Because of the great improvement in the efficacy of assisted reproductive techology due to ICSI, the recently discovered genetic causes of male infertility have to be considered. While studies concerning the role of xenobiotics in disrupting endocrine regulation of testicular functions are in progress, genetic causes of male infertility has been discovered. Microdeletions of the long arm of the Y chromosome account for a substantial part of unexplained spermatogenic failures. Mutations of CFTR gene are involved in bilateral agenesis of vas deferens. This condition might be considered as a mild form of cystic fibrosis. These genetic defects together with chromosmal abnormalities, which are known to be responsible for spermatogenic failures, should be considered as potential sources of reproductive abnormalities of more global pathology transmissible to children who can be obtained by ICSI with ejaculated, epididymal or testicular sperm.     

Amphibian decline and extinction: what we know and what we need to learn

For over 350 million yr, thousands of amphibian species have lived on Earth. Since the 1980s, amphibians have been disappearing at an alarming rate, in many cases quite suddenly. What is causing these declines and extinctions? In the modern era (post 1500) there are 6 leading causes of biodiversity loss in general, and all of these acting alone or together are responsible for modern amphibian declines: commercial use; introduced/exotic species that compete with, prey on, and parasitize native frogs and salamanders; land use change; contaminants; climate change; and infectious disease. The first 3 causes are historical in the sense that they have been operating for hundreds of years, although the rate of change due to each accelerated greatly after about the mid-20th century. Contaminants, climate change, and emerging infectious diseases are modern causes suspected of being responsible for the so-called 'enigmatic decline' of amphibians in protected areas. Introduced/exotic pathogens, land use change, and infectious disease are the 3 causes with a clear role in amphibian decline as well as extinction; thus far, the other 3 causes are only implicated in decline and not extinction. The present work is a review of the 6 causes with a focus on pathogens and suggested areas where new research is needed. Batrachochytrium dendrobatidis (Bd) is a chytrid fungus that is an emerging infectious disease causing amphibian population decline and species extinction. Historically, pathogens have not been seen as a major cause of extinction, but Bd is an exception, which is why it is such an interesting, important pathogen to understand. The late 20th and early 21st century global biodiversity loss is characterized as a sixth extinction event. Amphibians are a striking example of these losses as they disappear at a rate that greatly exceeds historical levels. Consequently, modern amphibian decline and extinction is a lens through which we can view the larger story of biodiversity loss and its consequences.     

分泌抗PRRSV抗体的猪源单克隆B细胞永生化方法的建立

猪繁殖与呼吸综合征(porcine reproductive and respiratory syndrome, PRRS)是由猪繁殖与呼吸综合征病毒(porcine reproductive and respiratory syndrome virus, PRRSV)引起的高度接触性传染疾病,对社会经济造成重大损失。目前并未获得有效的中和抗体应用于科研及治疗中,所以建立一种筛选具有中和活性的单克隆抗体的方法,对PRRSV防治及抗原位点筛选具有重要意义。单克隆抗体在人类和动物的众多疾病治疗及诊断中得到广泛应用,而针对不同病原如何筛选出有效的中和抗体是目前急需解决的问题。在单克隆抗体筛选的众多方法中,B细胞永生化方法是一种有效的且大概率能获得单克隆中和抗体的方法。通过将bcl-6和bcl-xl两个基因中间通过f2a序列连接后构建到一个载体上,进行逆转录病毒包装。包装成熟的逆转录病毒感染免疫PRRSV的猪源淋巴细胞,并使用加入CD40L和IL21细胞因子的完全培养基培养,然后使用CD21作为筛选标记通过磁珠法进行B细胞筛选,最后对筛选得到的B细胞单克隆化并进行检测,验证是否有抗体分泌。结果...     

Global patterns of fern species diversity: An evaluation of fern data in GBIF

Despite that several studies have shown that data derived from species lists generated from distribution occurrence records in the Global Biodiversity Information Facility (GBIF) are not appropriate for those ecological and biogeographic studies that require high sampling completeness, because species lists derived from GBIF are generally very incomplete, Suissa et al. (2021) generated fern species lists based on data with GBIF for 100 km × 100 km grid cells across the world, and used the data to determine fern diversity hotspots and species richness–climate relationships. We conduct an evaluation on the completeness of fern species lists derived from GBIF at the grid–cell scale and at a larger spatial scale, and determine whether fern data derived from GBIF are appropriate for studies on the relations of species composition and richness with climatic variables. We show that species sampling completeness of GBIF is low (<40%) for most of the grid cells examined, and such low sampling completeness can substantially bias the investigation of geographic and ecological patterns of species diversity and the identification of diversity hotspots. We conclude that fern species lists derived from GBIF are generally very incomplete across a wide range of spatial scales, and are not appropriate for studies that require data derived from species lists in high completeness. We present a map showing global patterns of fern species diversity based on complete or nearly complete regional fern species lists.     

Endotoxin-induced and prostaglandin-mediated effects on corpus luteum function in the mare

Intravenous administration of endotoxin to mares causes synthesis and release of PGF(2alpha); this process affects corpus luteum function, either causing a transient drop in progesterone levels or complete luteolysis with shortening of the estrous cycle. It seems likely that any disease associated with endotoxemia can cause important prostaglandin-mediated effects on reproductive function in the mare.     

Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus

Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of individual barriers and the degree of overall isolation between populations. We found almost complete isolation between the three populations mainly due to premating extrinsic barriers. Intrinsic genetic barriers were weak and variable among populations. There were asymmetries in some intrinsic barriers due to the origin of cytoplasm in hybrids. Overall, these results suggest that reproductive isolation between these three populations is almost complete despite the absence of geographic barriers, and that the main drivers of this isolation are ecologically based, consistent with the mechanisms underlying ecological speciation.     

Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach

Background

The increased sequencing of pathogen genomes and the subsequent availability of genome-scale functional datasets are expected to guide the experimental work necessary for target-based drug discovery. However, a major bottleneck in this has been the difficulty of capturing and integrating relevant information in an easily accessible format for identifying and prioritizing potential targets. The open-access resource TDRtargets.org facilitates drug target prioritization for major tropical disease pathogens such as the mycobacteria Mycobacterium leprae and Mycobacterium tuberculosis; the kinetoplastid protozoans Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi; the apicomplexan protozoans Plasmodium falciparum, Plasmodium vivax, and Toxoplasma gondii; and the helminths Brugia malayi and Schistosoma mansoni.

Methodology/Principal Findings

Here we present strategies to prioritize pathogen proteins based on whether their properties meet criteria considered desirable in a drug target. These criteria are based upon both sequence-derived information (e.g., molecular mass) and functional data on expression, essentiality, phenotypes, metabolic pathways, assayability, and druggability. This approach also highlights the fact that data for many relevant criteria are lacking in less-studied pathogens (e.g., helminths), and we demonstrate how this can be partially overcome by mapping data from homologous genes in well-studied organisms. We also show how individual users can easily upload external datasets and integrate them with existing data in TDRtargets.org to generate highly customized ranked lists of potential targets.

Conclusions/Significance

Using the datasets and the tools available in TDRtargets.org, we have generated illustrative lists of potential drug targets in seven tropical disease pathogens. While these lists are broadly consistent with the research community''s current interest in certain specific proteins, and suggest novel target candidates that may merit further study, the lists can easily be modified in a user-specific manner, either by adjusting the weights for chosen criteria or by changing the criteria that are included.