The Slowing Rate of CpG Depletion in SARS-CoV-2 Genomes Is Consistent with Adaptations to the Human Host

Depletion of CpG dinucleotides in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes has been linked to virus evolution, host-switching, virus replication, and innate immune responses. Temporal variations, if any, in the rate of CpG depletion during virus evolution in the host remain poorly understood. Here, we analyzed the CpG content of over 1.4 million full-length SARS-CoV-2 genomes representing over 170 million documented infections during the first 17 months of the pandemic. Our findings suggest that the extent of CpG depletion in SARS-CoV-2 genomes is modest. Interestingly, the rate of CpG depletion is highest during early evolution in humans and it gradually tapers off, almost reaching an equilibrium; this is consistent with adaptations to the human host. Furthermore, within the coding regions, CpG depletion occurs predominantly at codon positions 2-3 and 3-1. Loss of ZAP (Zinc-finger antiviral protein)-binding motifs in SARS-CoV-2 genomes is primarily driven by the loss of the terminal CpG within the motifs. Nonetheless, majority of the CpG depletion in SARS-CoV-2 genomes occurs outside ZAP-binding motifs. SARS-CoV-2 genomes selectively lose CpGs-motifs from a U-rich context; this may help avoid immune recognition by TLR7. SARS-CoV-2 alpha-, beta-, and delta-variants of concern have reduced CpG content compared to sequences from the beginning of the pandemic. In sum, we provide evidence that the rate of CpG depletion in virus genomes is not uniform and it greatly varies over time and during adaptations to the host. This work highlights how temporal variations in selection pressures during virus adaption may impact the rate and the extent of CpG depletion in virus genomes.     

Genomic architecture of autism from comprehensive whole-genome sequence annotation

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Incorporating intraspecific variation into species distribution models improves distribution predictions,but cannot predict species traits for a wide-spread plant species

The most common approach to predicting how species ranges and ecological functions will shift with climate change is to construct correlative species distribution models (SDMs). These models use a species’ climatic distribution to determine currently suitable areas for the species and project its potential distribution under future climate scenarios. A core, rarely tested, assumption of SDMs is that all populations will respond equivalently to climate. Few studies have examined this assumption, and those that have rarely dissect the reasons for intraspecific differences. Focusing on the arctic-alpine cushion plant Silene acaulis, we compared predictive accuracy from SDMs constructed using the species’ full global distribution with composite predictions from separate SDMs constructed using subpopulations defined either by genetic or habitat differences. This is one of the first studies to compare multiple ways of constructing intraspecific-level SDMs with a species-level SDM. We also examine the contested relationship between relative probability of occurrence and species performance or ecological function, testing if SDM output can predict individual performance (plant size) and biotic interactions (facilitation). We found that both genetic- and habitat-informed SDMs are considerably more accurate than a species-level SDM, and that the genetic model substantially differs from and outperforms the habitat model. While SDMs have been used to infer population performance and possibly even biotic interactions, in our system these relationships were extremely weak. Our results indicate that individual subpopulations may respond differently to climate, although we discuss and explore several alternative explanations for the superior performance of intraspecific-level SDMs. We emphasize the need to carefully examine how to best define intraspecific-level SDMs as well as how potential genetic, environmental, or sampling variation within species ranges can critically affect SDM predictions. We urge caution in inferring population performance or biotic interactions from SDM predictions, as these often-assumed relationships are not supported in our study.     

Landscape,soil and meteorological influences on canopy dynamics of northern flooding Pampa grasslands,Argentina

Question: How do meteorological variations at seasonal, interannual scales differentially affect the canopy dynamics of four contrasting landscape units within a region? Location: Flooding Pampa, Buenos Aires, Argentina. 5000 km². Central point: 35°15′S, 57°45′W. Methods: We used a 19‐year series of the normalized difference vegetation index (NDVI) derived from NOAA‐AVHRR PAL (Pathfinder AVHRR Land) images and meteorological data provided by a nearby weather station. The NDVI was used as surrogate of canopy photosynthetic status. The relationship between annually integrated NDVI and meteorological conditions was explored by stepwise multiple regressions for each defined unit. PC A was performed to compare units and growing seasons on a multivariate basis. Results: Mean seasonal NDVI curve was similarly shaped among landscapes. However, the absolute values differed widely. There was high interannual variation so that the mean seasonal pattern was seldom observed in any particular year. Annually integrated NDVI of all landscapes was negatively associated with summer temperature and positively with previous year precipitation. It was also directly related with current year winter precipitation in two landscapes and with summer precipitation in the others. NDVI response to September and March precipitation accounted for some of the differences in interannual variation among landscapes. Conclusions: Our results revealed a strong intra‐regional variation of canopy dynamics, closely linked to landscape (vegetation‐soil) and water availability (mainly in summer and during the previous year). These links may be used to predict forage production rates for livestock.     

福建柏开花与结实物候期的研究

福建柏1年2次花期,春花期4—5月,果期当年10月,种子无生活力;秋花期9～10月,果期翌年10月,种子有生活力,有效花期在秋季。开花结实的生物学及物候学特性与适生区的地点、地类、海拔、温度等地理气候因子紧密相关,总体变异规律：秋花期、球果成熟期、种子散落期山区比半山区早,半山区比丘陵区早,高海拔地区比低海拔地区早．发芽率山区〉半山区〉丘陵区。     

Recent advances in barley transformation

Barley, an important member of the cereals, has been successfully transformed through various methods such as particle bombardment, Agrobacterium tumefaciens, DNA uptake, and electroporation. Initially, the transformation in barley concentrated on developing protocols using marker genes such as gus, bar, and hpt. Immature embryos and callus derived from immature embryos were targeted for transformation. Subsequently, genes of agronomic and malting importance have been deployed in barley. Particle bombardment appears to be the preferred choice for barley transformation in the majority of the reports, although Agrobacterium-mediated transformation is being used more often. The current review focuses on the challenges encountered in barley transformation such as somaclonal variation, development of transformation systems for commercial cultivars, gene expression, stability and inheritance, and gene flow. Newer markers such as the green fluorescent protein (gfp), firefly luciferase, and phosphomannose isomerase were found to be useful in the selection of transgenic plants. Tissue-specific promoters such as those for B1-hordein and D-hordein genes, and spike-specific promoters, are increasingly used to drive gene expression. The review also describes recent research on gene-tagging through transformation, insertion of disease resistance, and abiotic stress resistance genes, transformation with genes for improved malting quality, nutrient content, feed quality, and the production of feed enzymes and pharmaceutical compounds.     

Butterfly seed predation: effects of landscape characteristics,plant ploidy level and population structure

Polyploidization has been suggested as one of the most common mechanisms for plant diversification. It is often associated with changes in several morphological, phenological and ecological plant traits, and therefore has the potential to alter insect–plant interactions. Nevertheless, studies evaluating the effect of plant polyploidy on interspecific interactions are still few. We investigated pre-dispersal seed predation by the butterfly Anthocharis cardamines in 195 populations of two ploidy levels of the herb Cardamine pratensis (tetraploid ssp. pratensis, 2n = 30 vs. octoploid ssp. paludosa, 2n = 56–64). We asked if differences in incidence and intensity of predation among populations were related to landscape characteristics, plant ploidy level and population structure. The incidence of the seed predator increased with increasing plant population size and decreasing distance to nearest population occupied by A. cardamines. The intensity of predation decreased with increasing plant population size and was not affected by isolation. Probability of attack decreased with increasing shading, and intensity of predation was higher in grazed than in non-grazed habitats. The attack intensity increased with increasing mean flower number of plant population, but was not affected by flowering phenology. Individuals in tetraploid populations suffered on average from higher levels of seed predation, had higher mean flower number, were less shaded and occurred more often in grazed habitats than octoploid populations. When accounting for differences in habitat preferences between ploidy levels there was no longer a difference in intensity of predation, suggesting that the observed differences in attack rates among populations of the two ploidy levels are mediated by the habitat. Overall, our results suggest that polyploidization is associated with differentiation in habitat preferences and phenotypic traits leading to differences in interspecific interaction among plant populations. This, in turn, may facilitate further divergence of ploidy levels.     

N-glycome profiling of Bothrops jararaca newborn and adult venoms

Glycosylation is an important post-translational modification of snake venom proteins and contributes to venom proteome complexity. Many snake venom components are known to be glycosylated, however, very little is known about the carbohydrate structures present in venom glycoproteins. Previous studies showed that the ontogenetic shift in diet, from ectothermic prey in early life to endothermic prey in adulthood, and shift in animal size are associated with changes in the venom proteome of the snake Bothrops jararaca. In this study we explored the composition of the N-glycome released from newborn and adult B. jararaca venom proteins. We used an ion trap mass spectrometer (IT-MS) to disassemble glycan structures based on the use of several pathways of MS (MSn) and demonstrate the presence of some structural isomers in both newborn and adult venom B. jararaca N-glycans. The main N-glycans identified in both venoms are of the hybrid/complex type however some mannose-rich type structures were also detected. The N-glycan composition of newborn and adult venoms did not vary indicating that differences in the utilization of the N-glycosylation motif could be the explanation for the differences in the glycosylation levels indicated by the differential electrophoretic profiles previously reported for B. jararaca newborn and adult venoms.