­­Systematic estimation of cystic fibrosis prevalence in Chinese and genetic spectrum comparison to Caucasians

Background Cystic fibrosis (CF) is a common, life-threatening genetic disease in Caucasians but rarely reported in Chinese population. The prevalence and population-specific genetic spectrum of CF in China needs to be systematically estimated and compared with Caucasians. Materials & Methods We reviewed 30,951 exome-sequencing samples, including 20,909 children samples and 10,042 parent samples, from Chinese Children's Rare Disease Genetic Testing Clinical Collaboration System (CCGT). After the in-lab filtration process, 477 candidate variants of CFTR gene were left and 56 variants were manually curated as pathogenic/likely-pathogenic (P/LP). These P/LP variants were adopted to estimate CF prevalence in three methods: the carrier frequency method, the permutation-combinations method and the Bayesian framework method. Allele frequencies of the 477 CFTR variants were compared with non-Finland European (NFE) and East Asian (EAS) from gnomAD database. To investigate the haplotype structure difference of CFTR, another 2,067 whole-genome-sequencing samples from CCGT and 195 NFE from 1000 genome project were analyzed by Shapeit4 software. Result With the 56 manually curated P/LP variants in CFTR gene, the estimated Chinese CF prevalence is approximately 1/106,400. Only 21 (37.5%) of the 56 variants were included in Caucasian specific CF screening panels, resulting in significantly under-estimation of CF prevalence in our children cohort (1/114,659 vs. 1/1,121,017, P=9e-27) and parents’ cohort (1/96,968 vs. 1/797,207, P=1e-10). The allele frequencies of six pathogenic variants (G970D, D979A, M469V, G622D, L88X, c.1766+5G>T) were significantly higher in our cohorts compared with gnomAD-NFE population (all P-value<0.1). Haplotype analysis showed more haplotype diversity in Chinese compared to Caucasians. In addition, G970D and F508del were founder mutation of Chinese and Caucasians with two SNPs (rs213950-rs1042077) identified as related genotype in exon region. Conclusions Chinese population showed significantly different genetic spectrum pattern in CFTR gene compared with Caucasian population, and thus a Chinese-specific CF screening panel is needed.

Detection and Molecular Characterization of Orientia tsutsugamushi from Suspected Scrub Typhus Patients in Mizoram, India

Serologic and molecular tests were performed for the diagnosis and to detect O. tsutsugamushi genotypes that are circulating in the state of Mizoram, India. Blood samples from scrub typhus-suspected patients were collected from Synod Hospital, Durtlang, Mizoram. Weil-Felix and immunochromatographic test (ICT) were performed from the serum samples. Nested PCR (nPCR) amplification of 47kDa outer membrane protein antigen gene and 56kDa type-specific antigen gene were done from the whole blood. 141/177 (79.66%) and 134/177 (75.7%) cases showed the presence of antibody against scrub typhus by Weil-Felix and ICT assays respectively. 76/177 (42.93%) patients showed the presence of 47kDa OMP antigen gene by nPCR while 55/177 (31.07%) showed the presence of 56kDa TSA gene by nPCR. Phylogenetic analysis of 56kDa TSA gene sequence revealed that Karp-related genotype was the most common genotype in the study area followed by Kato-related genotype. In this study, a high degree of diversity of O. tsutsugamushi was observed similar to the observations reported from other parts of India. Nested PCR of 47kDa OMP antigen gene showed higher sensitivity as compared to nPCR amplification of 56kDa TSA gene suggesting it as the assay of choice for diagnosis of scrub typhus disease.

Dopamine-Related Genotype Predicts Trajectories of Gait Reserve in Older Adults

The capacity to increase one’s gait speed is critical for maintaining safe community ambulation. There is limited work on the longitudinal changes in this capacity and its predictors. Because lower dopamine is associated with lower task adaptation and motivation, we hypothesized that lower dopamine would predict more decline in rapid gait speed. Catechol-O-methyltransferase (COMT) polymorphism and at least 3 repeated rapid and usual pace gait speed assessments were obtained over 10 years in 1,261 older adults (mean age=75.2, 867 White, 659 women). Linear mixed models computed person-specific rapid and usual pace gait speed trajectories. Regression models adjusted for usual gait trajectory tested whether COMT predicted rapid gait trajectory; covariates included, demographic, psychological, cognitive, and physical factors. Val/Val carriers (lower dopamine) declined more in rapid gait compared to Met/Met carriers (higher dopamine; adjusted b=-.002, SE=.001, p=.042). Modifying dopamine may positively influence the ability to maintain rapid gait over time.

Genotyping of Acantamoeba spp. from rhisophere in Hungary

The protista Acanthamoeba is a free-living amoeba existing in various environments. A number of species among protista are recognized as human pathogens, potentially causing Acanthamoeba keratitis (AK), granulomatous amoebic encephalitis (GAE), and chronic granulomatous lesions. In this study, 10 rhizosphere samples were collected from maize and alfalfa plants in experimental station at Institute of Genetics, Microbiology and Biotechnology, Szent István University. We detected Acanthamoeba based on the quantitative real-time PCR assay and sequence analysis of the 18S rRNA gene. All studied molecular biological methods are suitable for the detection of Acanthamoeba infection in humans. The quantitative real-time PCR-based methods are more sensitive, simple, and easy to perform; moreover, these are opening avenue to detect the effect of number of parasites on human disease. Acanthamoeba species were detected in five (5/10; 50%) samples. All Acanthamoeba strains belonged to T4 genotype, the main AK-related genotype worldwide. Our result confirmed Acanthamoeba strains in rhizosphere that should be considered as a potential health risk associated with human activities in the environment.

Genetic Diversity of Hepatic/Non-Hepatic Cystic Echinococ-cosis in Baqiyatallah Hospital, Tehran, Iran

Background: Cystic echinococcosis (CE) is a worldwide zoonotic helminthic disease caused by the larval stage of Echinococcus granulosus. The infection is particularly important in terms of economic and medico-veterinary aspects in endemic areas including Iran. Considering the possibility of organ-tropism in E. granulosus strains, the present study was aimed to identify the genotypes of E. granulosus in different organs involved in patients, undergone surgery in Baqiyatallah Hospital, Tehran, Iran from 2005-2015. Methods: Overall, 29 formalin-fixed paraffin-embedded tissues (FFPT) from patients with histologically confirmed CE including liver (N: 14) lungs (N: 6) abdomen (N: 2), pancreas (N: 2) and each of spleen, gallbladder and, muscles (N: 1) plus unknown organs (N: 2) were used and genetically characterized using polymerase chain reaction, followed by partial sequencing of mitochondrial cytochrome c oxidase gene subunit 1(cox1) and analyzed. Results: Nineteen out of 29 isolates including liver (N: 6) lungs (N: 4) abdomen (N: 2), pancreas (N: 2) and each of spleen, gallbladder, and muscle (N: 1), unknown organs (N: 2) obtained from paraffin-embedded blocks of human CE created an acceptable sequence in two directions. All 19 isolates regardless of the organ involved were recognized as E. granulosus sensu stricto (G1). Conclusion: The sequence alignments of the isolates displayed two profiles. All sequenced samples showed E. granulosus sensu stricto (G1) with no organ-related genotype.

Sustainability as a basic property of the phenomenon of life organized in supraorganismal systems

The phenomenon of life is organized in supraorganismal systems, populations and ecosystems. The main mechanisms of sustainability of these systems are: 1) the influence of limiting factors on population growth and ecosystem development; 2) the allocation of plant and animal species into ecological niches; 3) co-adaptation of plants and animals; 4) species genetic integration; 5) biocommunications. Limiting factors inhibit populations’ growth and distribution of organisms, so that populations obey the logistic growth, reaching a relatively stable climax stage. The space of limiting factors restricted by the tolerance limits of organisms forms an ecological niche of species. During long-joint evolution (co-evolution), species form co-adaptations (mutual adaptations). As a result of species genetic integrity, each new generation inherits not only adaptations for its specific ecological niche, but also a determined physical space including all the environmental factors to which the species is adapted. Consolidation of individuals with a related genotype is supported by intraspecific communication processes. Means of communication are genetically determined. Humankind is the only species on Earth that has subjugated limiting factors. As a result the population of humans shows an unlimited exponential growth, population explosion. It is a basic factor in the instability of the Nature - Society system.

The host-specificity of Theileria sp. (sable) and Theileria sp. (sable-like) in African Bovidae and detection of novel Theileria in antelope and giraffe

Tick-borne diseases caused by Theileria are of economic importance in domestic and wildlife ruminants. The majority of Theileria infects a limited number of host species, supporting the concept of host specificity. However, some Theileria seem to be generalists challenging the host specificity paradigm, such as Theileria sp. (sable) reported from various vertebrate hosts, including African buffalo, cattle, dogs and different antelope species. We tested the hypothesis that T. sp. (sable) uses Bovidae as hosts in general using a real-time polymerase chain reaction assay specific for T. sp. (sable) and a closely related genotype: T. sp. (sable-like). Various antelope species from the Tragelaphini (black wildebeest, blesbuck, blue wildebeest, gemsbuck, sable and waterbuck) tested positive for either T. sp. (sable) or T. sp. (sable-like). However, no African buffalo (n = 238) or cattle (n = 428) sampled in the current study tested positive, suggesting that these latter species are not carrier hosts. The results were confirmed using next-generation sequencing which also indicated at least 13 new genotypes or species found in various antelope and giraffes. Genotypes were found in single host species or in evolutionarily related hosts, suggesting that host specificity in Theileria may be a lineage specific phenomenon likely associated with tick-host-parasite co-evolution.

Assessing Impacts of Climate Change on Phenology and Quality Traits of Vitis vinifera L.: The Contribution of Local Knowledge

Developing adaptation strategies in Vitis vinifera, a crop sensitive to climate change, is crucial for resilience of traditional viticultural systems, especially in climate-vulnerable areas like the Mediterranean basin. A progressive warming is demonstrated to alter the geographical distribution of grapevine, reducing land capability for typical grapes and vine productions in most Southern European districts traditionally specialized in tree crops. Grapevine growth and reproduction under climate change require a continuous monitoring to adapt agronomic practices and strategies to global change. The present study illustrates an empirical approach grounded on a set of bio-physical indicators assessing the genotype-related response to climate variation. This approach was tested in Umbria, central Italy, to verify the response of some major international and local grapevine varieties to climate variation during a relatively long time interval (1995–2015). Long-term data for ripening time and berry quality collected in the study area were correlated to representative bioclimatic indices including Winkler, Huglin, and Cool night indicators. Results of this study highlighted the increase of air temperature (reflecting the inherent growth in thermal availability for maturation) and the alteration of precipitation patterns toward more intense precipitation. Climate variability exerted distinctive impacts on grapevine phenology depending on the related genotype. Empirical findings underline the usefulness of a permanent field monitoring of the relationship between selected climate variables and grape ripening with the aim to develop adaptive viticultural practices at farm’s scale.

Occurrence of Ehrlichia canis and Hepatozoon canis and probable exposure to Rickettsia amblyommatis in dogs and cats in Natal, RN

Occurrence of infection or exposure to Ehrlichia canis, Hepatozoon canis and Rickettsia spp. was detected in feral cats living in two fragments from Atlantic rainforest, in Natal, RN, Brazil, and in dogs living around the parks. While serum samples were collected from 155 animals (53 cats living in the parks; 29 dogs living in human homes around the parks; and 73 dogs living at an animal control center - ACC), spleen samples were collected from 20 dogs that were euthanized at ACC. Serum samples were analyzed to Rickettsia spp. and E. canis antibodies using the indirect immunofluorescence assay. Seventeen of the 102 dogs (17%) had E. canis antibodies and 13% (20/155) of all dogs and cats (i.e. 3% (3/102) of the dogs and 32% (17/53) of the cats) were seropositive for Rickettsia spp. antigens. The animals were therefore been exposed to R. amblyommatis or by a very closely related genotype. Among the 20 dog spleen samples analyzed, eight were PCR positive for E. canis and two for H. canis (GenBank accession number MG772657 and MG772658, respectively). In none of the spleen samples were obtained amplicons for Babesia spp. through PCR. This study provided the first evidence that Rickettsia of the spotted fever group is circulating among dogs and cats in Natal.

Anthocyanin Composition and MybA-related Genotype in Kyoho Grape and Its Derivatives

In this study, we measured the anthocyanin composition and content in the ‘Kyoho’ grape cultivar and its derivatives via ultra-performance liquid chromatography–mass spectrometry and characterized the MybA-related genes at the color locus via capillary electrophoresis and quantitative real-time polymerase chain reaction. A total of 30 anthocyanins (15 monoglucoside and 15 diglucoside) were detected. Peonidin-3-O-(t-6''-O-coumaroyl)-glucoside-5-O-glucoside was the most abundant component, and the content of malvidin-3-O-(c-6''-O-coumaroyl)-glucoside-5-O-glucoside was low in all cultivars. All 49 cultivars contained VvmybA1, VvmybA2, and VvmybA3, whereas only the black-skinned cultivars contained VlmybA2. The anthocyanin content in the cultivars that contained VlmybA2 was significantly higher than other cultivars. These results could provide information for future color breeding programs in grapes.