Viruses are constantly subject to natural selection to enrich beneficial mutations and weed out deleterious ones. However, it remains unresolved as to how the phenotypic gains or losses brought about by these mutations cause the viral genomes carrying the very mutations to become more or less numerous. Previous investigations by us and others suggest that viruses with plus strand (+) RNA genomes may compel such selection by bottlenecking the replicating genome copies in each cell to low single digits. Nevertheless, it is unclear if similarly stringent reproductive bottlenecks also occur in cells invaded by DNA viruses. Here we investigated whether tomato yellow leaf curl virus (TYLCV), a small virus with a single-stranded DNA genome, underwent population bottlenecking in cells of its host plants. We engineered a TYLCV genome to produce two replicons that express green fluorescent protein and mCherry, respectively, in a replication-dependent manner. We found that among the cells entered by both replicons, less than 65% replicated both, whereas at least 35% replicated either of them alone. Further probability computation concluded that replication in an average cell was unlikely to have been initiated with more than three replicon genome copies. Furthermore, sequential inoculations unveiled strong mutual exclusions of these two replicons at the intracellular level. In conclusion, the intracellular population of the small DNA virus TYLCV is actively bottlenecked, and such bottlenecking may be a virus-encoded, evolutionarily conserved trait that assures timely selection of new mutations emerging through error-prone replication.
This content will become publicly available on February 1, 2025
- Award ID(s):
- 1948874
- NSF-PAR ID:
- 10487184
- Publisher / Repository:
- Elsevier
- Date Published:
- Journal Name:
- Computers & Geosciences
- Volume:
- 184
- Issue:
- C
- ISSN:
- 0098-3004
- Page Range / eLocation ID:
- 105518
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract We address a problem that extends a fundamental classical result of continuum mechanics from the time of its inception, as well as answers a fundamental question in the recent, modern nonlinear elastic theory of dislocations. Interestingly, the implication of our result in the latter case is qualitatively different from its well-established analog in the linear elastic theory of dislocations. It is a classical result that if $$u\in C^2({\mathbb {R}}^n;{\mathbb {R}}^n)$$ u ∈ C 2 ( R n ; R n ) and $$\nabla u \in SO(n)$$ ∇ u ∈ S O ( n ) , it follows that u is rigid. In this article this result is generalized to matrix fields with non-vanishing $${\text {curl }}$$ curl . It is shown that every matrix field $$R\in C^2(\varOmega ;SO(3))$$ R ∈ C 2 ( Ω ; S O ( 3 ) ) such that $${\text {curl }}R = constant$$ curl R = c o n s t a n t is necessarily constant. Moreover, it is proved in arbitrary dimensions that a measurable rotation field is as regular as its distributional $${\text {curl }}$$ curl allows. In particular, a measurable matrix field $$R: \varOmega \rightarrow SO(n)$$ R : Ω → S O ( n ) , whose $${\text {curl }}$$ curl in the sense of distributions is smooth, is also smooth.more » « less
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This dataset includes multiple fields: (i) files for monthly and annual fields for the max curl line and the zero curl line at 0.1 degree longitudinal resolutions; (ii) files for monthly and annual GS path obtained from Altimetry and originally processed by Andres (2016) at 0.1 degree longitudinal resolution. The maximum curl line (MCL) and the zero curl line (ZCL) calculations are briefly described here and are based on the original wind data (at 1.25 x 1.25 degree) provided by the Japanese reanalysis (JRA-55; Kobayashi et al., 2015) and available at https://zenodo.org/record/8200832 (Gifford et al. 2023). For details see Gifford, 2023.
The wind stress curl (WSC) fields used for the MCL and ZCL calculations extend from 80W to 45W and 30N to 45N at the 1.25 by 1.25-degree resolution. The MCL is defined as the maximum WSC values greater than zero within the domain per 1.25 degree longitude. As such, it is a function of longitude and is not a constant WSC value unlike the zero contour. High wind stress curl values that occurred near the coast were not included within this calculation. After MCL at the 1.25 resolution was obtained the line was smoothed with a gaussian smoothing and interpolated on to a 0.1 longitudinal resolution. The smoothed MCL lines at 0.1 degree resolution are provided in separate files for monthly and annual averages (2 files). Similarly, 2 other files (monthly and annual) are provided for the ZCL.
Like the MCL, the ZCL is a line derived from 1.25 degree longitude throughout the domain under the condition that it's the line of zero WSC. The ZCL is constant at 0 and does not vary spatially like the MCL. If there are more than one location of zero curl for a given longitude the first location south of the MCL is selected. Similar to the MCL, the ZCL was smoothed with a gaussian smoothing and interpolated on to a 0.1 longitudinal resolution.
The above files span the years from 1980 through 2019. So, the monthly files have 480 months starting January 1980, and the annual files have 40 years of data. The files are organized with each row being a new time step and each column being a different longitude. Therefore, the monthly MCL and ZCL files are each 480 x 351 for the 0.1 resolution data. Similarly, the annual files are 40 x 351 for the 0.1 degree resolution data.
Note that the monthly MCLs and ZCLs are obtained from the monthly wind-stress curl fields. The annual MCLs and ZCLs are obtained from the annual wind-stress curl fields.
Since the monthly curl fields preserves more atmospheric mesoscales than the annual curl fields, the 12-month average of the monthly MCLs and ZCLs will not match with the annual MCLs and ZCLs derived from the annual curl field. The annual MCLs and ZCLs provided here are obtained from the annual curl fields and representative metrics of the wind forcing on an annual time-scale.
Furthermore, the monthly Gulf Stream axis path (25 cm isoheight from Altimeter, reprocessed by Andres (2016) technique) from 1993 through 2019 have been made available here. A total of 324 monthly paths of the Gulf Stream are tabulated. In addition, the annual GS paths for these 27 years (1993-2019) of altimetry era have been put together for ease of use. The monthly Gulf Stream paths have been resampled and reprocessed for uniqueness at every 0.1 degree longitude from 75W to 50W and smoothed with a 100 km (10 point) running average via matlab. The uniqueness has been achieved by using Consolidator algorithm (D’Errico, 2023).
Each monthly or annual GS path has 251 points between 75W to 50W at 0.1 degree resolution.
Please contact igifford@earth.miami.edu for any queries. {"references": ["Andres, M., 2016. On the recent destabilization of the Gulf Stream path downstream of Cape Hatteras. Geophysical Research Letters, 43(18), 9836-9842.", "D'Errico, J., 2023. Consolidator (https://www.mathworks.com/matlabcentral/fileexchange/ 8354-consolidator), MATLAB Central File Exchange. Retrieved June 17, 2023.", "Gifford, Ian. H., 2023. The Synchronicity of the Gulf Stream Free Jet and the Wind Induced Cyclonic Vorticity Pool. MS Thesis, University of Massachusetts Dartmouth. 75pp.", "Gifford, Ian, H., Avijit Gangopadhyay, Magdalena Andres, Glen Gawarkiewicz, Hilde Oliver, Adrienne Silver, 2023. Wind Stress, Wind Stress Curl, and Upwelling Velocities in the Northwest Atlantic (80-45W, 30-45N) during 1980-2019, https://zenodo.org/record/8200832.", "Kobayashi, S., Ota, Y., Harada, Y., Ebita, A., Moriya, M., Onoda, H., Onogi, K., Kamahori, H., Kobayashi, C., Endo, H. and Miyaoka, K., 2015. The JRA-55 reanalysis: General specifications and basic characteristics.\u202fJournal of the Meteorological Society of Japan. Ser. II,\u202f93(1), pp.5-48. Kobayashi, S., Ota, Y., Harada, Y., Ebita, A., Moriya, M., Onoda, H., Onogi, K., Kamahori, H., Kobayashi, C., Endo, H. and Miyaoka, K., 2015. The JRA-55 reanalysis: General specifications and basic characteristics.\u202fJournal of the Meteorological Society of Japan. Ser. II,\u202f93(1), pp.5-48."]} -
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This dataset contains three netcdf files that pertain to monthly, seasonal, and annual fields of surface wind stress, wind stress curl, and curl-derived upwelling velocities over the Northwest Atlantic (80-45W, 30-45N) covering a forty year period from 1980 to 2019. Six-hourly surface (10 m) wind speed components from the Japanese 55-year reanalysis (JRA-55; Kobayashi et al., 2015) were processed from 1980 to 2019 over a larger North Atlantic domain of 100W to 10E and 10N to 80N. Wind stress was computed using a modified step-wise formulation, originally based on (Gill, 1982) and a non-linear drag coefficient (Large and Pond, 1981), and later modified for low speeds (Trenberth et al., 1989). See Gifford (2023) for more details.
After the six-hourly zonal and meridional wind stresses were calculated, the zonal change in meridional stress (curlx) and the negative meridional change in zonal stress (curly) were found using NumPy’s gradient function in Python (Harris et al., 2020) over the larger North Atlantic domain (100W-10E, 10-80N). The curl (curlx + curly) over the study domain (80-45W, 10-80N) is then extracted, which maintain a constant order of computational accuracy in the interior and along the boundaries for the smaller domain in a centered-difference gradient calculation.
The monthly averages of the 6-hour daily stresses and curls were then computed using the command line suite climate data operators (CDO, Schulzweida, 2022) monmean function. The seasonal (3-month average) and annual averages (12-month average) were calculated in Python using the monthly fields with NumPy (NumPy, Harris et al., 2020).
Corresponding upwelling velocities at different time-scales were obtained from the respective curl fields and zonal wind stress by using the Ekman pumping equation of the study by Risien and Chelton (2008; page 2393). Please see Gifford (2023) for more details.
The files each contain nine variables that include longitude, latitude, time, zonal wind stress, meridional wind stress, zonal change in meridional wind stress (curlx), the negative meridional change in zonal wind stress (curly), total curl, and upwelling. Units of time begin in 1980 and are months, seasons (JFM etc.), and years to 2019. The longitude variable extends from 80W to 45W and latitude is 30N to 45N with uniform 1.25 degree resolution.
Units of stress are in Pascals, units of curl are in Pascals per meter, and upwelling velocity is described by centimeters per day. The spatial grid is a 29 x 13 longitude x latitude array.
Filenames:
monthly_windstress_wsc_upwelling.nc: 480 time steps from 80W to 45W and 30N to 45N.
seasonal_windstress_wsc_upwelling.nc: 160 time steps from 80W to 45W and 30N to 45N.
annual_windstress_wsc_upwelling.nc: 40 time steps from 80W to 45W and 30N to 45N.
Please contact igifford@earth.miami.edu for any queries. {"references": ["Gifford, I.H., 2023. The Synchronicity of the Gulf Stream Free Jet and the Wind Induced Cyclonic Vorticity Pool. MS Thesis, University of Massachusetts Dartmouth. 75pp.", "Gill, A. E. (1982). Atmosphere-ocean dynamics (Vol. 30). Academic Press.", "Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357\u2013362 (2020). DOI: 10.1038/s41586-020-2649-2.", "Japan Meteorological Agency/Japan (2013), JRA-55: Japanese 55-year Reanalysis, Daily 3-Hourly and 6-Hourly Data, https://doi.org/10.5065/D6HH6H41, Research Data Archive at the National Center for Atmospheric Research, Computational and Information Systems Laboratory, Boulder, Colo. (Updated monthly.)", "Kobayashi, S., Ota, Y., Harada, Y., Ebita, A., Moriya, M., Onoda, H., Onogi, K., Kamahori, H., Kobayashi, C., Endo, H. and Miyaoka, K., 2015. The JRA-55 reanalysis: General specifications and basic characteristics.\u202fJournal of the Meteorological Society of Japan. Ser. II,\u202f93(1), pp.5-48.", "Large, W.G. and Pond, S., 1981. Open ocean momentum flux measurements in moderate to strong winds.\u202fJournal of physical oceanography,\u202f11(3), pp.324-336.", "Risien, C.M. and Chelton, D.B., 2008. A global climatology of surface wind and wind stress fields from eight years of QuikSCAT scatterometer data.\u202fJournal of Physical Oceanography,\u202f38(11), pp.2379-2413.", "Schulzweida, Uwe. (2022). CDO User Guide (2.1.0). Zenodo. https://doi.org/10.5281/zenodo.7112925.", "Trenberth, K.E., Large, W.G. and Olson, J.G., 1989. The effective drag coefficient for evaluating wind stress over the oceans.\u202fJournal of Climate,\u202f2(12), pp.1507-1516."]}
