Integrated Calendar

We studied both modern soils and buried paleosols in order to understand the relationship of temperature (T°C(47)) estimated from clumped isotope compositions (∆47) of soil carbonates to actual surface and burial temperatures. On average, T°C(47) exceeds mean annual temperature by 10-15°C due to summertime bias in soil carbonate formation, and to summertime ground heating by incident solar radiation. Secondary controls on T°C(47) are soil depth and shading. Site mean annual air temperature across a broad range (0-30°C) of site temperatures is highly correlated (r2 = 0.9) with T°C(47) from soils after accounting for variations in T°C(47) with soil depth and ground heating. The highly correlated relationship in this equation should now permit mean annual temperature in the past to be reconstructed from T°C(47) in paleosol carbonate
T°C(47) in soil and lake carbonates decreases systematically with elevation gain in the Himalaya, allowing us to to reconstruct paleoelevation from clumped isotope analysis of ancient carbonates. T°C(47) obtained from lacustrine carbonates from SW Tibet show that paleoelevations during late Miocene were similar to today.
We also measured T°C(47) from long sequences of deeply buried (≤5 km) paleosol carbonate in the Himalayan foreland in order to evaluate potential diagenetic resetting of clumped isotope composition. We found that paleosol carbonate faithfully records plausible soil T°C(47) down to 2.5-4 km burial depth, or ~90-125°C. Deeper than this and above this temperature, T°C(47) in paleosol carbonate is reset to temperatures >40C.

Bacterial biofilms are aggregates of cells that grow on surfaces and at interfaces. Unlike their motile state in solution, most cells in developing biofilms are encased in a network of biopolymers that is composed mainly of polysaccharides, proteins and nucleic acids - the extracellular matrix (ECM). In addition to acting as inter-cellular glue, the ECM protects cells within a biofilm from antibiotics, provides mechanical stability to biofilms, affects the hydrophobicity of the biofilm and mediates cell adhesion to surfaces. In this talk, I will describe the self-assembly process of a matrix protein component from oligomers to fibers that are highly resistant to degradation. In addition, while normally very stable, under external stress such as the lack of nutrients, the ECM is broken down to allow cells to leave the biofilm to search for available nutrient sources. I will describe a biofilm dispersal process that is achieved upon secretion of self–produced molecules that target the ECM exopolysaccharide. Understanding the conditions that are responsible for making the ECM as well as the conditions that lead to its collapse, offers control over biofilm development. Such a control will allow us to encourage the formation of beneficial biofilms but help to prevent the formation of detrimental biofilms or even eradicate them when already formed.

High-throughput ChIP-seq, HT-ChIP, and ChIP-exo measurements of protein-DNA binding preferences have challenged the understanding of transcriptional regulation in eukaryotic genomes. These measurements have demonstrated quite generally that transcription regulators bind thousands of active and inactive regions across the genome, and strikingly, in many cases few specific transcription factor binding sites can be identified in the Highly Occupied Target (HOT) regions. In my talk I will propose design principles of non-consensus protein-DNA binding. I will suggest that DNA exerts an effective protein localization potential that acts statistically on all DNA-binding proteins. This effective potential varies in each genomic location along the genome. I will also suggest that the predicted non-consensus protein-DNA binding mechanism provides a genome-wide background for specific promoter elements, such as transcription factor binding sites and TATA-like elements. I will discuss a number of examples, such as the genome-wide yeast transcription regulator and nucleosomal binding preferences, the yeast pre-initiation complex (PIC) binding preferences, and the human CTCF protein-DNA binding preferences.

Molecules in the gas or liquid phases are generally randomly distributed and isotropically oriented in space. Thus, the determination and the measurement of chemical reaction rates or of optical properties requires, by necessity, averaging over all orientations. Femtosecond laser pulses enable molecular manipulation on time scales faster than the internal rotational and vibrational degrees of freedom, opening the way to the direct addressing of aligned and oriented molecules.
In this talk I will review molecular alignment and control, and will discuss selective excitation of like species. Our recent observation of the creation of unidirectional molecular rotation by a sequence of laser pulses and its observation by the rotational Doppler Effect will be described. Time permitting, I will also present predictions for the formation of vortices driven by the laser induced rotational motion of the molecules.