Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11?kb), single molecule,real-time sequencing

The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.     

A model for mechanistic and system assessments of biochar effects on soils and crops and trade‐offs

We developed a biochar model within the Agricultural Production Systems sIMulator (APSIM) software that integrates biochar knowledge and enables simulation of biochar effects within cropping systems. The model has algorithms that mechanistically connect biochar to soil organic carbon (SOC), soil water, bulk density (BD), pH, cation exchange capacity, and organic and mineral nitrogen. Soil moisture (SW)–temperature–nitrogen limitations on the rate of biochar decomposition were included as well as biochar‐induced priming effect on SOC mineralization. The model has 10 parameters that capture the diversity of biochar types, 15 parameters that address biochar‐soil interactions and 4 constants. The range of values and their sensitivity is reported. The biochar model was connected to APSIM's maize and wheat crop models to investigate long‐term (30 years) biochar effects on US maize and Australia wheat in various soils. Results from this sensitivity analysis showed that the effect of biochar was the largest in a sandy soil (Australian wheat) and the smallest in clay loam soil (US maize). On average across cropping systems and soils the order of sensitivity and the magnitude of the response of biochar to various soil‐plant processes was (from high to low): SOC (11% to 86%) > N₂O emissions (?10% to 43%43%) > plant available water content (0.6% to 12.9%) > BD (?6.5% to ?1.7%) > pH (?0.8% to 6.3%) > net N mineralization (?19% to 10%) > CO₂ emissions (?2.0% to 4.3%) > water filled pore space (?3.7% to 3.4%) > grain yield (?3.3% to 1.8%) > biomass (?1.6% to 1.4%). Our analysis showed that biochar has a larger impact on environmental outcomes rather than agricultural production. The mechanistic model has the potential to optimize biochar application strategies to enhance environmental and agronomic outcomes but more work is needed to fill knowledge gaps identified in this work.     

Abnormalities in the central cholinergic transmitter system of the genetically epilepsy-prone rat

Seizure-experienced Genetically Epilepsy-prone Rats (GEPRs) have increased acetylcholine content and choline acetyltransferase activity in the thalamus and striatum. These cholinergic differences are accompanied by a slight but statistically significant reduction in acetylcholinesterase activity in the midbrain. In addition, no abnormalities were found in the numbers of specific 3H-QNB binding sites in the striatum, hippocampus, inferior colliculi or cortex. Other work has shown no difference in muscarinic receptor function as measured by carbachol-stimulated inositol-1-phosphate formation. These data suggest a possible presynaptic defect in the striatal and thalamic cholinergic system which may play some role in the seizure-prone state of the GEPR. However, caution must be used in interpreting these cholinergic derangements since more recent findings show no differences in thalamic acetylcholine content in seizure-naive GEPRs. Thus, the original cholinergic abnormalities detected in the seizure-experienced GEPR may be an enduring response to seizure activity.     

Guinea-pig casein A cDNA. Nucleotide sequence analysis and comparison of the deduced protein sequence with that of bovine alpha s2 casein

The nucleotide sequence (1036 bases) of guinea-pig casein A mRNA has been determined. Two cDNA recombinant plasmids contained a total of 993 base pairs, including part of the 5' noncoding region, and the complete coding and 3' noncoding region. The remaining 5' noncoding sequence was obtained by primer extension. The deduced 223-amino-acid-coding sequence of guinea-pig pre-casein A exhibited 30% homology with bovine alpha s2 casein, the most striking similarities being in the locations of potential phosphorylation sites.