Crosstalk between the HpArsRS two-component system and HpNikR is necessary for maximal activation of urease transcription

Helicobacter pylori NikR (HpNikR) is a nickel dependent transcription factor that directly regulates a number of genes in this important gastric pathogen. One key gene that is regulated by HpNikR is ureA, which encodes for the urease enzyme. In vitro DNA binding studies of HpNikR with the ureA promoter (P-ureA) previously identified a recognition site that is required for high affinity protein/DNA binding. As a means to determine the in vivo significance of this recognition site and to identify the key DNA sequence determinants required for ureA transcription, herein, we have translated these in vitro results to analysis directly within H. pylori. Using a series of GFP reporter constructs in which the P-ureA DNA target was altered, in combination with mutant H. pylori strains deficient in key regulatory proteins, we confirmed the importance of the previously identified HpNikR recognition sequence for HpNikR-dependent ureA transcription. Moreover, we identified a second factor, the HpArsRS two-component system that was required for maximum transcription of ureA. While HpArsRS is known to regulate ureA in response to acid shock, it was previously thought to function independently of HpNikR and to have no role at neutral pH. However, our qPCR analysis of ureA expression in wildtype, Delta nikR and Delta arsS single mutants as well as a Delta arsS/nikR double mutant strain background showed reduced basal level expression of ureA when arsS was absent. Additionally, we determined that both HpNikR and HpArsRS were necessary for maximal expression of ureA under nickel, low pH and combined nickel and low pH stresses. In vitro studies of HpArsR-P with the P-ureA DNA target using florescence anisotropy confirmed a direct protein/DNA binding interaction. Together, these data support a model in which HpArsRS and HpNikR cooperatively interact to regulate ureA transcription under various environmental conditions. This is the first time that direct cross-talk between HpArsRS and HpNikR at neutral pH has been demonstrated

Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World

We have collated and reviewed published records of the genera Panicum and Setaria (Poaceae), including the domesticated millets Panicum miliaceum L. (broomcorn millet) and Setaria italica (L.) P. Beauv. (foxtail millet) in pre-5000 cal b.c. sites across the Old World. Details of these sites, which span China, central-eastern Europe including the Caucasus, Iran, Syria and Egypt, are presented with associated calibrated radiocarbon dates. Forty-one sites have records of Panicum (P. miliaceum, P. cf. miliaceum, Panicum sp., Panicum type, P. capillare (?) and P. turgidum) and 33 of Setaria (S. italica, S. viridis, S. viridis/verticillata, Setaria sp., Setaria type). We identify problems of taphonomy, identification criteria and reporting, and inference of domesticated/wild and crop/weed status of finds. Both broomcorn and foxtail millet occur in northern China prior to 5000 cal b.c.; P. miliaceum occurs contemporaneously in Europe, but its significance is unclear. Further work is needed to resolve the above issues before the status of these taxa in this period can be fully evaluated

Cassava genome from a wild ancestor to cultivated varieties

Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology

A Comparative Study of Problem-Based Learning and Traditional Approaches in College English Classrooms: Analyzing Pedagogical Behaviors Via Classroom Observation

In this study, we described and compared an English as a foreign language (EFL) teacher’s pedagogical behaviors in traditional and problem-based learning (PBL) classroom settings in a Chinese university. In spring 2019, we collected six 45-min videos, three in each condition, covering three modules: (a) warm-up and vocabulary, (b) essay structure, and (c) writing. The analyses of the teacher’s pedagogical behaviors and her interaction with students indicated that the instructor spent most of the instructional time delivering higher-order thinking content in both traditional and PBL classes. The teacher’s activity structure influenced students’ communication mode. Although the instructor provided students with more group discussion activities in the PBL classroom, lecturing was observed to be the primary delivery method in both classes. These results suggest that the application of PBL strategies in the EFL classroom did not significantly restructure the teacher’s pedagogical behaviors, and thus, failed to achieve the goal of providing students with more opportunities for improving their expressive English language proficiency. These findings underscore the need to develop an effective PBL-related curriculum and professional development opportunities for EFL teachers to effectively implement the PBL approach in the classroom