GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan

Background

In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006–2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions. In this study, phenotypic data were collected in three separate regions of Kazakhstan and entire soybean sample was genotyped for identification of marker-trait associations (MTA).

Results

In this study, the collection of 113 accessions representing five different regions of the World was planted in 2015–2016 in northern, eastern, and south-eastern regions of Kazakhstan. It was observed that North American accessions showed the highest yield in four out of six trials especially in Northern Kazakhstan in both years. The entire sample was genotyped with 6 K SNP Illumina array. 4442 SNPs found to be polymorphic and were used for whole genome genotyping purposes. Obtained SNP markers data and field data were used for GWAS (genome-wide association study). 30 SNPs appear to be very significant in 42 MTAs in six studied environments.

Conclusions

The study confirms the efficiency of GWAS for the identification of molecular markers which tag important agronomic traits. Overall thirty SNP markers associated with time to flowering and maturation, plant height, number of fertile nodes, seeds per plant and yield were identified. Physical locations of 32 identified out of 42 total MTAs coincide well with positions of known analogous QTLs. This result indicates importance of revealed MTAs for soybean growing regions in Kazakhstan. Obtained results would serve as required prerequisite for forming and realization of specific breeding programs towards effective adaptation and increased productivity of soybean in three different regions of Kazakhstan.

     

Bacterial and Archaeal Community Structure in the Surface Diatom Sediments of Deep Freshwater Lake Baikal (Eastern Siberia)

Diatom sediment records of large lakes can be used to decipher the history of ancient phytoplankton. The upper layer of the sediment is an important area of remineralization of the sedimenting phytoplankton biomass. It hosts a bacterial community different from those of both the water column and deeper sediment layers. In this work, we analyzed the structure and diversity of the communities of Bacteria and Archaea in the surface sediment core containing valves of diatoms, the major producers in Lake Baikal. Pyrosequencing of the bacterial V3–V4 region of the 16 S ribosomal RNA (rRNA) and archaeal V1–V3 16 S rRNA gene regions yielded 29,168 and 36,997 reads, respectively. In total, we have identified 33 bacterial phyla; uncultured Actinobacteria were the most abundant in the upper layers, while lower sediment was dominated by Firmicutes and Alphaproteobacteria. The composition of the archaeal community changed with depth, but was generally dominated by Crenarchaeota from the classes Marine Group I and Miscellaneous Crenarchaeotic Group, as well as Euryarchaeota from the class Thermoplasmata. These dominant bacterial and archaeal taxa are presumed to participate in the destruction of buried organic matter, which eventually leads to degradation of the diatom valves.     

Detecting adherence to the recommended childhood vaccination schedule from user-generated content in a US parenting forum

Vaccine hesitancy is considered as one of the leading causes for the resurgence of vaccine preventable diseases. A non-negligible minority of parents does not fully adhere to the recommended vaccination schedule, leading their children to be partially immunized and at higher risk of contracting vaccine preventable diseases. Here, we leverage more than one million comments of 201,986 users posted from March 2008 to April 2019 on the public online forum BabyCenter US to learn more about such parents. For 32% with geographic location, we find the number of mapped users for each US state resembling the census population distribution with good agreement. We employ Natural Language Processing to identify 6884 and 10,131 users expressing their intention of following the recommended and alternative vaccination schedule, respectively RSUs and ASUs. From the analysis of their activity on the forum we find that ASUs have distinctly different interests and previous experiences with vaccination than RSUs. In particular, ASUs are more likely to follow groups focused on alternative medicine, are two times more likely to have experienced adverse events following immunization, and to mention more serious adverse reactions such as seizure or developmental regression. Content analysis of comments shows that the resources most frequently shared by both groups point to governmental domains (.gov). Finally, network analysis shows that RSUs and ASUs communicate between each other (indicating the absence of echo chambers), however with the latter group being more endogamic and favoring interactions with other ASUs. While our findings are limited to the specific platform analyzed, our approach may provide additional insights for the development of campaigns targeting parents on digital platforms.     

Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells

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The critical iron-oxygen intermediate in human aromatase

Aromatase (CYP19) is the target of several therapeutics used for breast cancer treatment and catalyzes the three-step conversion of androgens to estrogens, with an unusual C-C cleavage reaction in the third step. To better understand the CYP19 reaction, the oxy-ferrous complex of CYP19 with androstenedione substrate was cryotrapped, characterized by UV-vis spectroscopy, and cryoreduced to generate the next reaction cycle intermediate. EPR analysis revealed that the initial intermediate observed following cryoreduction is the unprotonated g₁ = 2.254 peroxo-ferric intermediate, which is stable up to 180 K. Upon gradual cryoannealing, the low-spin (g₁ = 2.39) product complex is formed, with no evidence for accumulation of the g₁ = 2.30 hydroperoxo-ferric intermediate. The relative stabilization of the peroxo-ferric heme and the lack of observed hydroperoxo-ferric heme distinguish CYP19 from other P450s, suggesting that the proton delivery pathway is more hindered in CYP19 than in most other P450s.     

Cortical PAR polarity proteins promote robust cytokinesis during asymmetric cell division

Cytokinesis, the physical division of one cell into two, is thought to be fundamentally similar in most animal cell divisions and driven by the constriction of a contractile ring positioned and controlled solely by the mitotic spindle. During asymmetric cell divisions, the core polarity machinery (partitioning defective [PAR] proteins) controls the unequal inheritance of key cell fate determinants. Here, we show that in asymmetrically dividing Caenorhabditis elegans embryos, the cortical PAR proteins (including the small guanosine triphosphatase CDC-42) have an active role in regulating recruitment of a critical component of the contractile ring, filamentous actin (F-actin). We found that the cortical PAR proteins are required for the retention of anillin and septin in the anterior pole, which are cytokinesis proteins that our genetic data suggest act as inhibitors of F-actin at the contractile ring. Collectively, our results suggest that the cortical PAR proteins coordinate the establishment of cell polarity with the physical process of cytokinesis during asymmetric cell division to ensure the fidelity of daughter cell formation.