Effect of Larval Nutrition on Maternal mRNA Contribution to the Drosophila Egg.

Embryonic development begins under the control of maternal gene products, mRNAs and proteins that the mother deposits into the egg; the zygotic genome is activated some time later. Maternal control of early development is conserved across metazoans. Gene products contributed by mothers are critical to many early developmental processes, and set up trajectories for the rest of development. Maternal deposition of these factors is an often-overlooked aspect of parental investment. If the mother experiences challenging environmental conditions, such as poor nutrition, previous studies in Drosophila melanogaster have demonstrated a plastic response wherein these mothers may produce larger eggs to buffer the offspring against the same difficult environment. This additional investment can produce offspring that are more fit in the challenging environment. With this study, we ask whether D. melanogaster mothers who experience poor nutrition during their own development change their gene product contribution to the egg. We perform mRNA-Seq on eggs at a stage where all mRNAs are maternally derived, from mothers with different degrees of nutritional limitation. We find that nutritional limitation produces similar transcript changes at all degrees of limitation tested. Genes that have lower transcript abundance in nutritionally limited mothers are those involved in translation, which is likely one of the most energetically costly processes occurring in the early embryo. We find an increase in transcripts for transport and localization of macromolecules, and for the electron transport chain. The eggs produced by nutrition-limited mothers show a plastic response in mRNA deposition, which may better prepare the future embryo for development in a nutrition-limited environment

Analytic Torsion on Hyperbolic Manifolds and the Semiclassical Approximation for Chern-Simons Theory

The invariant integration method for Chern-Simons theory for gauge group SU(2) and manifold \Gamma\H^3 is verified in the semiclassical approximation. The semiclassical limit for the partition function associated with a connected sum of hyperbolic 3-manifolds is presented. We discuss briefly L^2 - analytical and topological torsions of a manifold with boundary.Comment: 12 pages, LaTeX fil

Mean curvature flow in a Ricci flow background

Following work of Ecker, we consider a weighted Gibbons-Hawking-York functional on a Riemannian manifold-with-boundary. We compute its variational properties and its time derivative under Perelman's modified Ricci flow. The answer has a boundary term which involves an extension of Hamilton's Harnack expression for the mean curvature flow in Euclidean space. We also derive the evolution equations for the second fundamental form and the mean curvature, under a mean curvature flow in a Ricci flow background. In the case of a gradient Ricci soliton background, we discuss mean curvature solitons and Huisken monotonicity.Comment: final versio

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expressionComment: 7 figures, 20 supplementary figures, 6 supplementary tables Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, et al. (2013) Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression. PLoS Genet 9(9): e1003748. doi:10.1371/journal.pgen.100374

On Minimum Violations Ranking in Paired Comparisons

Ranking a set of objects from the most dominant one to the least, based on the results of paired comparisons, proves to be useful in many contexts. Using the rankings of teams or individuals players in sports to seed tournaments is an example. The quality of a ranking is often evaluated by the number of violations, cases in which an object is ranked lower than another that it has dominated in a comparison, that it contains. A minimum violations ranking (MVR) method, as its name suggests, searches specifically for rankings that have the minimum possible number of violations which may or may not be zero. In this paper, we present a method based on statistical physics that overcomes conceptual and practical difficulties faced by earlier studies of the problem.Comment: 10 pages, 10 figures; typos corrected (v2

The HABP2 G534E polymorphism does not increase nonmedullary thyroid cancer risk in Hispanics.

Familial nonmedullary thyroid cancer (NMTC) has not been clearly linked to causal germline variants, despite the large role that genetic factors play in risk. Recently, HABP2 G534E (rs7080536A) has been implicated as a causal variant in NMTC. We have previously shown that the HABP2 G534E variant is not associated with TC risk in patients from the British Isles. Hispanics are the largest and the youngest minority in the United States and NMTC is now the second most common malignancy in women from this population. In order to determine if the HABP2 G534E variant played a role in NMTC risk among Hispanic populations, we analyzed 281 cases and 1105 population-matched controls from a multicenter study in Colombia, evaluating the association through logistic regression. We found that the HABP2 G534E variant was not significantly associated with NMTC risk (P=0.843) in this Hispanic group. We also stratified available clinical data by multiple available clinicopathological variables and further analyzed the effect of HABP2 on NMTC presentation. However, we failed to detect associations between HABP2 G534E and NMTC risk, regardless of disease presentation (P≥0.273 for all cases). Therefore, without any significant associations between the HABP2 G534E variant and NMTC risk, we conclude that the variant is not causal of NMTC in this Hispanic population

A network-based ranking system for American college football

American college football faces a conflict created by the desire to stage national championship games between the best teams of a season when there is no conventional playoff system to decide which those teams are. Instead, ranking of teams is based on their record of wins and losses during the season, but each team plays only a small fraction of eligible opponents, making the system underdetermined or contradictory or both. It is an interesting challenge to create a ranking system that at once is mathematically well-founded, gives results in general accord with received wisdom concerning the relative strengths of the teams, and is based upon intuitive principles, allowing it to be accepted readily by fans and experts alike. Here we introduce a one-parameter ranking method that satisfies all of these requirements and is based on a network representation of college football schedules.Comment: 15 pages, 3 figure

The deep distributions of helium isotopes, radiocarbon, and noble gases along the U.S. GEOTRACES East Pacific Zonal Transect (GP16)

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Chemistry 201 (2018): 167-182, doi:10.1016/j.marchem.2017.03.009.We report the deep distributions of noble gases, helium isotopes, and radiocarbon measured during the U.S. GEOTRACES GP16 East Pacific Zonal Transect between 152 and 77°W at 12- 15°S in the South Pacific. The dominant feature is an intense tongue of hydrothermal effluent that extends more than 4,000 km westward from the East Pacific Rise (EPR) at ~2500m depth. The patterns reveal significant “downstream” variations in water mass structure, advection, and mixing that belie the simple perception of a continuous plume extending westward from the EPR. For example, one feature observed at 120°W, 14°S has tracer signatures that are consistent with a water mass originating from an area as much as 2,000 km south of this section, suggesting a quasi-permanent northward flow on the western flank of the EPR. Helium isotope variations in the plume show a uniquely high 3He/4He source in the tongue compared with typical mid-ocean ridge basalts (MORB), consistent with the anomalously high ratios observed in MORB glasses from the EPR segment just south of this transect. The water column data also reveal that the background 3He/4He east of the EPR is significantly lower than values characteristic of MORB, suggesting an additional, more geographically distributed radiogenic 4He flux of order 107 mol/y into the deep Pacific. In the western end of the section, incoming bottom waters have relatively less hydrothermal hydrothermal helium, more radiocarbon, and more oxygen, as well as negative saturation anomalies for the heavy noble gases (Ar, Kr, and Xe). During the basin-scale upwelling of this water, diapycnal mixing serves to erase these negative anomalies. The relative magnitudes of the increases for the heavy noble gases (Ar, Kr, and Xe) are quantitatively consistent with this process. This leads us to estimate the relatively smaller effects on He and Ne saturations, which range from near zero to 0.2% and 0.3% respectively. With this information, we are able to refine our estimates of the magnitude of 3He and 4He excesses and the absolute 3He/4He ratio of non-atmospheric helium introduced into deep Pacific waters.The work was funded under National Science Foundation grant number OCE-1232991 for WJJ and OCE-1130870 for CRG