Thelytokous Reproduction of Onion Thrips, Thrips tabaci Lindeman 1889, Infesting Welsh Onion and Genetic Variation among Their Subpopulations

Parthenogenesis is not uncommon in thrips. This asexual reproduction produces males (arrhenotokous) or female (thelytokous). Only females are found in the onion thrips (Thrips tabaci Lindeman 1889) infesting Welsh onion (Allium fistulosum) in several areas of Korea. To determine the reproduction mode of T. tabaci, thrips infesting Welsh onion were collected from different localities in Korea. Cytochrome oxidase I (COI) sequences were then assessed. Results showed that all test local populations had signature motif specific to a thelytokous type. These COI sequences were clustered with other thelytokous populations separated from arrhenotokous T. tabaci populations. In a laboratory test, individual rearing produced female progeny without any males. These results support that Korean onion thrips infesting Welsh onion have the thelytokous type of parthenogenesis. Local thrips populations exhibited significant variations in susceptibility to chemical and biological insecticides. Random amplified polymorphic DNA (RAPD) analysis indicated genetic variations of local populations. However, the genetic distance estimated from RAPD was independent of the actual distance among different local populations. These results suggest that genetic variations of T. tabaci are arisen from population subdivision due to asexual thelytokous reproductive mode.

The SARS-CoV-2 infection in Thailand: analysis of spike variants complemented by protein structure insights

Thailand was the first country outside China to officially report COVID-19 cases. Despite the strict regulations for international arrivals, up until February 2021, Thailand had been hit by two major outbreaks. With a large number of SARS-CoV-2 sequences collected from patients, the effects of many genetic variations, especially those unique to Thai strains, are yet to be elucidated. In this study, we analysed 439,197 sequences of the SARS-CoV-2 spike protein collected from NCBI and GISAID databases. 595 sequences were from Thailand and contained 52 variants, of which 6 had not been observed outside Thailand (p.T51N, p.P57T, p.I68R, p.S205T, p.K278T, p.G832C). These variants were not predicted to be of concern. We demonstrate that the p.D614G, although already present during the first Thai outbreak, became the prevalent strain during the second outbreak, similarly to what was described in other countries. Moreover, we show that the most common variants detected in Thailand (p.A829T, p.S459F and p.S939F) do not appear to cause any major structural change to the spike trimer or the spike-ACE2 interaction. Among the variants identified in Thailand was p.N501T. This variant, which involves an asparagine critical for spike-ACE2 binding, was not predicted to increase SARS-CoV-2 binding, thus in contrast to the variant of global concern p.N501Y. In conclusion, novel variants identified in Thailand are unlikely to increase the fitness of SARS-CoV-2. The insights obtained from this study could aid SARS-CoV-2 variants prioritisations and help molecular biologists and virologists working on strain surveillance.

Protein interaction analysis of Plasmodium falciparum circumsporozoite protein variants with human immunoproteins explains RTS,S vaccine efficacy in Ghana

The world's first malaria vaccine RTS,S provides only partial protection against Plasmodium falciparum infections. The explanation for such low efficacy is unclear. This study examined the associations of parasite genetic variations with binding affinity to human immunological proteins including human leukocyte antigen (HLA) and T cell receptors (TCR) involved in RTS,S-induced immune responses. Multiplicity of infections was determined by amplicon deep sequencing of merozoite surface protein 1 (PfMSP1). Genetic variations in the C-terminal of circumsporozoite protein (PfMSP1) gene were examined across 88 samples of P. falciparum collected from high and low transmission settings of Ghana. Binding interactions of PfMSP1 variants and HLA/TCR were analyzed using NetChop} and HADDOCK predictions. Anti-CSP IgG levels were measured by ELISA in a subset of 10 samples. High polyclonality was detected among P. falciparum infections. A total 27 CSP haplotypes were detected among samples. A significant correlation was detected between the CSP and MSP multiplicity of infection (MOI). No clear clustering of haplotypes was observed by geographic regions. The number of genetic differences in PfCSP between 3D7 and non-3D7 variants does not influence binding interactions to HLA/T cells nor anti-CSP IgG levels. Nevertheless, PfCSP peptide length significantly affects its molecular weight and binding affinity to the HLA. The presence of multiple non-3D7 strains among P. falciparum infections in Ghana impact the effectiveness of RTS,S. Longer PfCSP peptides may elicit a stronger immune response and should be considered in future version RTS,S. The molecular mechanisms of RTS,S cell-mediated immune responses related to longer CSP peptides warrants further investigations.

The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas

In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.

Challenges That Face Behavioral Genetic Studies: Researchers Perspective from the MENA Region

Background: Behavioral genetic studies are important for the understanding of the contribution of genetic variations to human behavior. However, such studies might be associated with some ethical concerns. Methods: In the current study, ethical challenges related to studies of genetic variations contributing to human behavior were examined among researchers. To achieve the study purpose, the Middle East and North Africa (MENA) region researchers were taken as an example, where the aftermentioned ethical challenges were discussed among a group of researchers, who were the participants of an online forum. Discussions and responses of the participants were monitored and were later qualitatively analyzed. Results: Discussions revealed that several ethical challenges, including subjects’ recruitment, the difficulty of obtaining informed consents, and issues of privacy and confidentiality of obtained data as information leakage, in this case, will lead to social stigma and isolation of the participants and their immediate family members. Jordanian social and cultural norms, faith, and the tribal nature of the population were raised as a major challenge that might face conducting behavioral genetic studies in the Arab populations of the MENA. The lack of regulation related to the conduction of genetic studies, misunderstanding, and misuse of genetic information are other challenges. A full explanation of genetic research and the current and future possible benefits/risks of such research could be potential solutions. Conclusion: In conclusion, the MENA populations are tackled with major challenges in relation to conducting research studies in genetics/antisocial behavior field/s. Establishment of guidelines related to genetic studies, capacity building, increasing public awareness about the importance of genetic testing, and enhancing responsible conduct of research will facilitate the conduct of such sensitive studies in the future in the region.

CLOCK genetic variations are associated with age-related changes in sleep duration and brain volume

Background Although a connection between sleep disruption and brain aging has been documented, biological mechanisms need to be further clarified. Intriguingly, aging is associated with circadian rhythm and/or sleep dysfunction in a key gene regulating circadian rhythm, CLOCK, have been linked to both aging-related sleep disturbances and neurodegenerative diseases. This study aims to investigate how CLOCK genetic variation associates with sleep duration changes and/or volumetric brain alteration. Methods This population-based cross-sectional study used data from the Korean Genome Epidemiology Study (KoGES), and analyzed sleep characteristics and genetic and brain imaging data in 2,221 subjects (mean 58.8±6.8 years, 50.2% male). Eleven single-nucleotide polymorphisms (SNPs) in CLOCK were analyzed using PLINK software v1.09 to test for their association with sleep duration and brain volume. Haplotype analysis was performed by using pair-wise linkage disequilibrium (LD) of CLOCK polymorphisms, and multivariate analysis of covariance was for statistical analysis. Results Decreased sleep duration was associated with several SNPs in CLOCK intronic regions, with the highest significance for rs10002541 (P=1.58x10 -5). Five SNPs with the highest significance (rs10002541-rs6850524-rs4580704- rs3805151-rs3749474) revealed that CGTCT was the most prevalent. In the major CGTCT haplotype, decreased sleep duration over time was associated with lower cortical volumes predominantly in frontal and parietal regions. Less common haplotypes (GCCTC/CGTTC) had shorter sleep duration and more decreases in sleep duration over 8 years, which revealed smaller total and gray matter volumes, especially in frontal and temporal regions of the left hemisphere. Conclusion CLOCK genetic variations could be involved in age-related sleep and brain volume changes.

Difficulties of Prenatal Genetic Counseling for a Subsequent Child in a Family With Multiple Genetic Variations

Many parents with a disabled child caused by a genetic condition appreciate the option of prenatal genetic diagnosis to understand the chance of recurrence in a future pregnancy. Genome-wide tests, such as chromosomal microarray analysis and whole-exome sequencing, have been increasingly used for prenatal diagnosis, but prenatal counseling can be challenging due to the complexity of genomic data. This situation is further complicated by incidental findings of additional genetic variations in subsequent pregnancies. Here, we report the prenatal identification of a baby with a MECP2 missense variant and 15q11.2 microduplication in a family that has had a child with developmental and epileptic encephalopathy caused by a de novo KCNQ2 variant. An extended segregation analysis including extended relatives, in addition to the parents, was carried out to provide further information for genetic counseling. This case illustrates the challenges of prenatal counseling and highlights the need to understand the clinical and ethical implications of genome-wide tests.