Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer

Background: S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. Methodology/Principal Findings: This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces. Conclusions/Significance: This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene

Reassignment of the murine 3'TRDD1 recombination signal sequence.

T cell receptor genes are assembled in developing T lymphocytes from discrete V, D, and J genes by a site-specific somatic rearrangement mechanism. A flanking recombination signal, composed of a conserved heptamer and a semiconserved nonamer separated by 12 or 23 variable nucleotides, targets the activity of the rearrangement machinery to the adjoining V, D, and J genes. Following the rearrangement of V, D, or J genes, their respective recombination signals are ligated together. Although these signal joints are allegedly invariant, created by the head-to-head abuttal of the heptamers, some do exhibit junctional diversity. Recombination signals were initially identified by comparison and alignment of germ-line sequences with the sequence of rearranged genes. However, their overall low level of sequence conservation makes their characterization solely from sequence data difficult. Recently, computational analysis unraveled correlations between nucleotides at several positions scattered within the spacer and recombination activity, so that it is now possible to identify putative recombination signals and determine and predict their recombination efficiency. In this paper, we analyzed the variability introduced in signal joints generated after rearrangement of the TRDD1 and TRDD2 genes in murine thymocytes. The recurrent presence of identical nucleotides inserted in these signal joints led us to reconsider the location and sequence of the TRDD1 recombination signal. By combining molecular characterization and computational analysis, we show that the functional TRDD1 recombination signal is shifted inside the putative coding sequence of the TRDD1 gene and, consequently, that this gene is shorter than indicated in the databases

Trend to equilibrium for flows with random diffusion

Motivated by the possibility of noise to cure equations of finite-time blowup, recent work arXiv:2109.09892 by the second and third named authors showed that with quantifiable high probability, random diffusion restores global existence for a large class of active scalar equations in arbitrary dimension with possibly singular velocity fields. This class includes Hamiltonian flows, such as the SQG equation and its generalizations, and gradient flows, such as the Patlak-Keller-Segel equation. A question left open is the asymptotic behavior of the solutions, in particular, whether they converge to a steady state. We answer this question by showing that the solutions from arXiv:2109.09892 in the periodic setting converge in Gevrey norm exponentially fast to the uniform distribution as time $t\rightarrow\infty$.Comment: 17 pages. arXiv admin note: text overlap with arXiv:2109.0989

Adaptations for growing wheat in a drying climate

Declining rainfall in the winter months in southwest Australia could have large impacts on wheat production in the area, particularly in those parts where production is historically limited by water supply.It is expected that the climate in southwest Australia will become drier, particularly in the winter months. These months have historically received the most rainfall in southwest Australia and make an important contribution to the in-season water supply to spring wheat (Triticum aestivum). Published simulation studies of wheat yield in the medium rainfall (325 to 450 mm annual rainfall) parts of the southwest Australian wheatbelt suggested that reductions in winter rainfall after 1975 have not reduced grain yields because soil water supply during these months often exceeds crop demand. However, the effect of recent changes in rainfall distribution on wheat production in more water-limited production areas (≤ 325 mm annual rainfall) is not known. This study aims to investigate the effects of changes in rainfall distribution on wheat yield in marginal parts of the southwest Australian wheatbelt.Two field experiments were conducted at Merredin Research Station, Western Australia (31.50°S, 118.22°E, mean annual rainfall 313 mm) in 2008 and 2009. Water supply to ‘Rainfall Distribution’ treatments were partly controlled with the use of rainout shelters and irrigation. The experiments investigated the effects and interactions of rainfall distribution, row spacing (23 cm and 60 cm), genotype and timing of nitrogen on growth, water use and grain yield of spring wheat. Results from the experiments showed that wheat yields in out of season dominant rainfall varied according to water storage at sowing. Widening row spacing reduced biomass and slowed water use but did not increase grain yield due to increase evaporation in season and residual water left in the soil after maturity. Data from the 2009 experiment was used to calibrate the Agricultural Production Systems Simulator (APSIM) crop model, which in turn was used to investigate the effects of recent and projected climate change on wheat yield in marginal wheat growing areas of southwest Australia. Row spacing, nitrogen rates and timing, and phenology treatments were included in the simulations to test for interactions with changes in climate. The simulation was run for eight locations that span the fringe of the southwest Australian wheatbelt and compared the 35 years preceding 1975 with the 35 years following 1975.In northern parts there were large reductions in June and July rainfall after 1975 and the slight increase in out of season rainfall didn’t result in sufficient water storage before seeding to compensate for it. In central parts, the decrease in growing season rainfall after 1975 was almost equivalent to the increase in out of season rainfall but grain yield declined. In eastern parts there was little change to growing season rainfall and grain yield benefitted by having additional stored soil water at seeding from increased out of season rainfall. In southern parts there was little change in rainfall pre and post 1975 and subsequently little change in grain yield. Two climate change scenarios from the online climate change scenario generator OzClim were applied to historical climatic data to create two plausible future climates (‘optimistic’ and ‘pessimistic’) for the year 2030. Both future climates resulted in reduced grain yields for each location when compared to the 1975 to 2009 time period.The worrying thing for producers was that none of the strategies tested aided wheat yield in the predicted changing climate. It was hypothesised that widening row spacing would slow biomass accumulation and water use by the crop, which would result in more post-anthesis water use and grain yield when the crop was growing largely from stored soil water at seeding. The results showed that widening row spacing did indeed slow water use and provide more water post-anthesis, but wheat yields were consistently lower due to lack of head density, increased evaporation from the soil surface and the inability of the crop to use all the available water before maturity.Findings in this thesis suggest that there is scope to breed wheat genotypes that are better suited to wide rows, and would allow growers to exploit the practical advantages of wide rows while minimizing the disadvantages. Field experiments suggested that early vigour and tillering (and head density) were important to grain yield in wide rows and it is suggested that a genotype suited to wide rows would include early vigour to reduce evaporation and increase competition with weeds, heavy tillering so that grain yield isn’t limited by sink-size and a vigorous root system with a good lateral spread to access all available soil water.In addition to highlighting the sensitivity of wheat production to changes in climate in marginal southwest Australia, and identifying the potential for row spacing and genetic interactions to be exploited, this study has identified gaps in knowledge that will benefit wheat producers if filled. Firstly there are some key unknown factors about the effects of climate change on Australian wheat production such as the effect of the interaction between elevated atmospheric CO2, increased temperatures and water deficit on wheat growth and yield. Also, the likely effect of climate change on the frequency, timing and severity of frosts is unknown. Both of these are fundamental to the successful development of strategies to adapt to climate change, and maintain grain production in a region that is very important to the prosperity of Australia’s rural industries