Intra-subspecies sequence variability of the MACPPE12 gene in Mycobacterium avium subsp. hominissuis

The PE (Pro-Glu) and PPE (Pro-Pro-Glu) multigene families are unique to mycobacteria, and are highly expanded in the pathogenic members of this genus. We determined the intra-subspecies genetic variability of the MACPPE12 gene, which is a specific PPE gene in Mycobacterium avium subsp. hominissuis (MAH), using 334 MAH isolates obtained from different isolation sources (222 human isolates, 145 Japanese and 77 Korean; 37 bathroom isolates; and 75 pig isolates). In total, 31 single-nucleotide polymorphisms (SNPs), which consisted of 16 synonymous SNPs and 15 nonsynonymous SNPs, were determined through comparison with the MACPPE12 gene sequence of MAH strain 104 as a reference. As the result, the 334 MAH isolates were classified into 19 and 13 different sequevars at the nucleic acid level (NA types) and amino acid level (AA types), respectively. Among the 13 AA types, only one type, the AA02 type, presented various NA types (7 different types) with synonymous SNPs, whereas all other AA types had a one-to-one correspondence with the NA types. This finding suggests that AA02 is a longer discernible lineage than the other AA types. Therefore, AA02 was classified as an ancestral type of the MACPPE12 gene, whereas the other AA types were classified as modern types. The ubiquitous presence of AA02 in all of the isolation sources and all different sequevars classified by the hsp65 genotype further supports this classification. In contrast to the ancestral type, the modern types showed remarkable differences in distribution between human isolates and pig isolates, and between Japanese isolates and Korean isolates. Divergence of the MACPPE12 gene may thus be a good indicator to characterize MAH strains in certain areas and/or hosts.     

Increased genetic diversity of the Mycobacterium tuberculosis W-Beijing genotype that predominates in eastern China

ObjectivesTo determine the genetic diversity of Mycobacterium tuberculosis (M. tuberculosis) strains in a Chinese population predominately infected with strains of the W-Beijing family.MethodsA cross-sectional study was conducted in three counties of eastern China. M. tuberculosis strains were collected at TB clinics, and patients were interviewed by trained physicians at the time of TB diagnosis. RD105 and RD181 were used to identify W-Beijing and modern W-Beijing strains, respectively, while seven-locus variable numbers of tandem repeat–mycobacterial interspersed repetitive unit (VNTR–MIRU) analysis was employed to differentiate the genotypes of these strains.ResultsOf 441 strains studied, 394 (89.3%) were identified as W-Beijing family strains; of them, 299 were modern W-Beijing strains. VNTR–MIRU identified 409 genotypes from 426 strains, including 395 unique patterns and 14 clusters. Ancestral W-Beijing strains were more likely to be clustered (OR = 1.32, 95%CI: 0.58–2.97) compared to modern W-Beijing strains. The proportions of clustered strains were 14.6%, 4.2% and 0% at sites Funing (FN), Deqing (DQ) and Yinzhou (YZ), respectively. Of the seven MIRU loci, VNTR3820 was found to have the highest discriminatory power and allelic diversity.ConclusionsVNTR–MIRU typing appears to be a reliable method for analyzing M. tuberculosis transmission in relatively closed populations. The low clustering proportions indicate that endogenous relapse may be a main source of TB cases in eastern China. Furthermore, our results indicate that migration has played may play an important role in the recent transmission of the W-Beijing family of M. tuberculosis.     

山西省农田生境复杂程度对小型啮齿动物多样性的影响

目的探索山西省不同地区农田小型啮齿动物的多样性与环境因子的关系,为制定山西省农田小型啮齿动物区域性综合治理措施提供主要依据。方法在山西省南部的临汾市隰县、中部的太原市娄烦县和北部的忻州市五台县设立研究区,在3-11月采用夹日法调查各研究区农田小型啮齿动物的多样性,以调查期内7月中旬的植被异质性指数来判定研究区的生境复杂程度,探讨山西省农田的生境复杂程度对小型啮齿动物多样性的影响。结果山西省农田小型啮齿动物的丰富度与其多样性指数和植被异质性指数的相关系数为0．998,呈显著的正相关;物种优势度指数与植被异质性指数的相关系数达-1．000,呈极显著负相关关系;而捕获率及均匀度指数和植被异质性指数只有0．404和0．994,其相关性并不显著。结论栖息环境的复杂程度是影响小型啮齿动物群落丰富度和多样性的关键因子,而农田中各植被类型盖度的均匀程度可能与小型啮齿动物群落的均匀度指数有关。     

黄芩主要成分黄芩甙的测定及体外抑菌作用研究

目的 研究分析黄芩主要成分黄芩甙的测定方法及体外抑菌作用。方法 采用煎煮法、温浸法、超声波法、加碱温浸法、醇提法提取黄芩内的有效成分黄芩甙,对比黄芩甙提取率;采用滤纸片平板扩散法检测黄芩甙对不同菌群的抑菌活性;采用试管稀释法检测黄芩甙对不同菌群的最小抑菌浓度。结果 黄芩甙提取率由高到低的方法依次为加碱温浸法、醇提法、超声波法、煎煮法、温浸法;黄芩甙对不同细菌的抑菌活性由高到低依次为绿脓杆菌、金黄色葡萄球菌、大肠杆菌、枯草杆菌、嗜酸乳杆菌、沙门氏杆菌;黄芩甙对不同细菌的最小抑菌浓度由低到高依次为金黄色葡萄球菌、绿脓杆菌、枯草杆菌、大肠杆菌、嗜酸乳杆菌、沙门氏杆菌。结论 加碱温浸法是黄芩甙的最佳提取方法,黄芩甙对绿脓杆菌、金黄色葡萄球菌及大肠杆菌抑菌作用相对较强,对沙门氏杆菌抑菌作用相对较弱,具体作用机制有待进一步深入研究探讨。     

Clade extinction appears to balance species diversification in sister lineages of Afro-Oriental passerine birds

Recent analyses suggest that the number of species in a clade often increases rapidly at first, but that diversification subsequently slows, apparently as species fill ecological space. Support for diversity dependence comes largely from the failure of species richness to increase with clade age in some analyses of contemporary diversity. However, clades chosen for analysis generally are named taxa and thus are not selected at random. To avoid this potential bias, we analyzed the numbers of species and estimated ages of 150 pairs of sister clades established by dispersal of ancestral species between the Oriental and African biogeographic regions. The observed positive exponential relationship between clade size and age suggests that species diversify within clades without apparent limit. If this were true, the pattern of accumulation of sister-clade pairs with increasing age would be consistent with the random decline and extinction of entire clades, maintaining an overall balance in species richness. This “pulse” model of diversification is consistent with the fossil record of most groups and reconciles conflicting evidence concerning diversity dependence of clade growth.The close relationship between local species richness and characteristics of the physical environment supports the existence of ecological constraints on species coexistence mediated through competition and other interactions (1–3), although historical influences on diversity sometimes parallel gradients in the physical environment (4–6). If species richness were limited as ecological space filled, one would expect the net rate of species production to slow and the number of species in a clade to level off as species richness approached ecological constraints.Evidence for such “diversity-dependent diversification” consists mostly of (i) nonrandom concentrations of branch points (speciation events) toward the origin of a clade (7–12) and (ii) independence of the number of species and clade age in comparisons among clades (11–14). However, clades included in such analyses often are not randomly chosen. In particular, small clades may be ignored because they do not command interest, and large, older clades are often passed over because of incomplete sampling (15, 16). Moreover, most phylogenetic analyses of diversification include species in named higher taxa rather than clades that have diversified within particular regions.Further support for diversity limits comes from the fossil records of many higher taxa, which exhibit long-term stability in number of species (17–19). It is also clear that species and entire clades continually replace each other through time, and the dynamics of this process appear to include the decline and extinction of evolutionary groups as a component of the local and regional regulation of the number of coexisting species (20–25).We take advantage of the sister relationships of clades of passerine birds in two major biogeographic regions—tropical southern Asia [Oriental (OR)] and the continent of Africa [African (AF)]—to examine the independent diversification of sister clades of known stem ages, selected only because one of the ancestors had dispersed between the two continents at some time in the past. Movement of species between these regions occurred either over water across the Indian Ocean, possibly using island stepping-stones, or through the Arabian Peninsula during periods of suitable environment. Each dispersal event defines the origin of a pair of same-aged sister clades in the two regions.If each diversifying clade filled a certain part of ecological space to a carrying capacity for species, after which diversification slowed, the sizes of clades filling this space would level off over time (26). Furthermore, the number of species per sister clade, particularly among older clades that have filled ecological space, might be correlated between regions, with species richness reflecting the ecological space available to each of the sister lineages (27). Finally, for those dispersal events whose directionality can be inferred, the rate of diversification should be higher, leading to larger clade size compared between sister lineages, in the newly colonized region, which initially would have fewer close (and ecologically similar) relatives of the ancestral species.We include all species of passerine birds (Passeriformes) and, separately, species in nonpasserine orders, of small, terrestrial birds, in the Oriental and African biogeographic regions (SI Appendix, section S1). The passerine avifauna of these regions accumulated from several sources over most of the Cenozoic Era (28, 29), with an old Gondwanan clade of suboscine passerines diversifying in tropical Africa and southern Asia early in the Tertiary, followed by radiations of core corvoid and passerid oscine passerines out of Australia during the early to mid-Cenozoic, through Wallacea to southern Asia, or directly across the Indian Ocean to Africa (30, 31). Thus, the diversification of sister clades in the African and Oriental regions takes place against a background of an increasing number of lineages of modern passerine birds as a whole within the region. Nonpasserine orders of terrestrial birds are likely to have diversified earlier within these regions (32) and perhaps were replaced to some extent by the passerines.Characteristics of a sample of clades include the distribution of node ages and the relationship between clade size and stem age, as well as the distribution of clade sizes regardless of age, including the proportion of clades that contain a single species. Any process-based model of diversification should be judged by how well it reproduces these characteristics. We use these criteria to evaluate simulations in which we attempt to reconstruct the underlying diversification process.     

Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG)

Mycobacterium bovis bacillus Calmette-Guerin (BCG), the only vaccine currently used against tuberculosis, is an attenuated derivative of M. bovis that has been propagated in vitro for more than 40 years. We have previously reported that the experimentally-verified human T cell epitopes of the M. tuberculosis complex (MTBC) are the most conserved elements of the genome; whether immune recognition is the force driving the conservation of epitopes in the MTBC is unknown. Therefore, we sequenced the genomes of 12 BCG strains to determine whether T cell epitopes were under selection pressure during BCG in vitro evolution. We constructed a genome-wide phylogeny and refined the previously-determined BCG phylogeny. Notably, we identified a new cluster between BCG Japan and BCG Russia, and repositioned the relationships of several strains within the lineage. We also compared the sequence diversity of 1530 experimentally verified human T cell epitopes in the BCG vaccines with those in the MTBC. We found 23% of the known T cell epitopes are absent, and that the majority (82%) of the absent epitopes in BCG are contained in 6 proteins encoded in 2 regions of difference (RD) unique to BCG strains. We also found that T cell epitope sequences in BCG are more conserved than non-epitope sequences in the same gene. Finally, we find evidence that epitope sequence variation in BCG potentially affects human T cell recognition. These findings provide new insight into sequence variation in a slow-growing bacterium closely related to the MTBC that has been subjected to prolonged passage outside of a mammalian host, and indicate little difference in the extent of variation in vivo and in vitro.     

Implications of ideological bias in social psychology on clinical practice

Ideological bias is a worsening but often neglected concern for social and psychological sciences, affecting a range of professional activities and relationships, from self‐reported willingness to discriminate to the promotion of ideologically saturated and scientifically questionable research constructs. Though clinical psychologists co‐produce and apply social psychological research, little is known about its impact on the profession of clinical psychology. Following a brief review of relevant topics, such as “concept creep” and the significance of the psychotherapeutic relationship, the relevance of ideological bias to clinical psychology, counterarguments and a rebuttal, clinical applications, and potential solutions are presented. For providing empathic and multiculturally competent clinical services, in accordance with professional ethics, psychologists would benefit from treating ideological diversity as another professionally recognized diversity area.     

EAACI position paper on diet diversity in pregnancy,infancy and childhood: Novel concepts and implications for studies in allergy and asthma

To fully understand the role of diet diversity on allergy outcomes and to set standards for conducting research in this field, the European Academy of Allergy and Clinical Immunology Task Force on Diet and Immunomodulation has systematically explored the association between diet diversity and allergy outcomes. In addition, a detailed narrative review of information on diet quality and diet patterns as they pertain to allergic outcomes is presented. Overall, we recommend that infants of any risk category for allergic disease should have a diverse diet, given no evidence of harm and some potential association of benefit in the prevention of particular allergic outcomes. In order to harmonize methods for future data collection and reporting, the task force members propose relevant definitions and important factors for consideration, when measuring diet diversity in the context of allergy. Consensus was achieved on practice points through the Delphi method. It is hoped that the definitions and considerations described herein will also enable better comparison of future studies and improve mechanistic studies and pathway analysis to understand how diet diversity modulates allergic outcomes.     

Skeletons of the Eye: An Evolutionary and Developmental Perspective

The ocular skeleton, composed of the scleral cartilage and scleral ossicles, is present in many vertebrates. The morphology of the scleral cartilage and ossicles varies within different extant reptiles (including birds) and also varies dramatically from the morphology in extant teleosts. This incredible range of diverse morphologies is the result of millions of years of evolution. Both the position of these elements within the eye and the timing of development vary amongst different vertebrates. While the development of both the scleral cartilage and scleral ossicles is somewhat understood in reptiles and in teleosts, the functional advantage of these elements is still debated. Most reptiles have a multi-component scleral ossicle ring composed of a series of flat bone plates and a scleral cartilage cup lining the retina, some sharks have calcified cartilage plates, and some teleosts have two bones while most others only have a ring of scleral cartilage. The data presented shows that different vertebrates have adapted to similar selective pressures in different ways. However, the reason why sarcopterygians have a series of overlapping bones in the sclera remains unclear. A better understanding of the ocular skeletal diversity in Reptilia as well as a better understanding of the mechanisms of vision within different environments (i.e., air vs. water) and that used by secondarily aquatic organisms is needed. This review discusses the observed variation in morphology and development of the ocular skeleton in the context of evolution and highlights our knowledge gaps in these areas. Anat Rec, 2018. © 2018 American Association for Anatomy.