We measured suspended sediment and chlorophyll-a fluxes between San Francisco Bay and the coastal ocean for two days in March 2002, October/November 2002, and June 2003, one day during neap tide and one during spring tide. We applied a harmonic analysis to velocity and chlorophyll-a data to model scalar and velocity fields during a spring-neap cycle. We then integrated these modeled data over the fortnightly period to calculate net dispersive fluxes. The net flux consisted of an advective and a dispersive component. Dispersive flux was decomposed into physical mechanisms such as tidal pumping, steady circulation and unsteady circulation.

Net flux of both sediment and chlorophyll changed seasonally. The net chlorophyll flux was out of the bay during spring and fall, but in during summer. The net flux of suspended sediment was large and in during the fall and out during spring and summer. The direction of advective flux was always out of the estuary and the magnitude depended on advective speed and mean scalar concentration. Dispersive flux was of similar magnitude as advective flux each season and changed direction seasonally. The dispersive flux was larger than the advective flux, contributing over 63% to the net flux of both scalars across season. Tidal pumping was the dominant dispersive process year round.

The dominance of tidal pumping implies that seasonal variability of ocean-estuary exchange is set almost entirely by variation in the east-west gradient of scalar concentrations between the ocean and the estuary. If concentrations are higher during flood tide compared to ebb tide, the tidal pumping flux will be into the estuary, whereas the converse is true if the concentration is higher on ebb tide.

The average chlorophyll and sediment concentrations are governed by different processes. During the summer while coastal upwelling occurs, chlorophyll concentration is higher in the ocean than in the estuary creating a gradient driven dispersive flux of coastal phytoplankton into the estuary. The opposite is true during spring when estuarine concentration is higher and the dispersive flux is driven out of the estuary. During fall there were relatively low gradients and the net dispersive chlorophyll flux was relatively small. The seasonal direction of chlorophyll fluxes measured in this study are consistent with physical and biological processes of a typical year, though, the magnitude and timing of these fluxes may change annually or inter-annually depending on the specific physical and biological conditions.

While the spatial and temporal distribution of favorable growth conditions determines the direction of the chlorophyll flux, growth within Central Bay plays a relatively small role in the local chlorophyll balance. Blooms or the accumulation of phytoplankton within Central Bay are limited by the large dispersive transport rates.

We assessed the success of Green Valley River Restoration Project, specifically assessing sedimentation and channel stability. The major objectives of the restoration were to provide flood control by constructing a two terraced channel, re-plant riparian corridor with native species, and mitigate for 1.89 acres of seasonal wetland lost to development. We attempted to compare project conditions after a major flow event in 1995 (second year after project completion) with those of the most recent (2002) surveys. Surveying methods were inconsistent from year to year making direct comparison of surveys difficult. In general, the two-terrace channel has remained relatively stable and successfully conveyed flood waters downstream. Erosion and deposition within the channel are less stable because of excessive sediment loading from upper watershed. Severe sedimentation along Hennessey Creek, a tributary to Green Valley Creek, caused damage to private property within the project reach during flood events. Litigation ensued and one of the outcomes was the development of new watershed scale management strategies. Some of these new strategies included improving farming techniques in the upper watershed to minimize sedimentation, conducting more scientific studies to assess sources of sediment, continuing monitoring creeks throughout the watershed, and consistently revising requirements developers must meet to build within the river corridor. Overall we see Greek Valley Creek as a successful project, one where the shortcomings of the project (sediment transport considerations) will provide useful learning tools for future management.

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Mitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD) in transcriptomic, proteomic, and metabolomic studies. Several mutations in mitochondrial DNA (mtDNA) sequence have been reported in SZ and BD patients.

Dorsolateral prefrontal cortex (DLPFC) from a cohort of 77 SZ, BD, and MDD subjects and age-matched controls (C) was studied for mtDNA sequence variations and heteroplasmy levels using Affymetrix mtDNA resequencing arrays. Heteroplasmy levels by microarray were compared to levels obtained with SNaPshot and allele specific real-time PCR. This study examined the association between brain pH and mtDNA alleles. The microarray resequencing of mtDNA was 100% concordant with conventional sequencing results for 103 mtDNA variants. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome was 22% higher (p = 0.0017) in DLPFC of individuals with SZ compared to controls. The association of brain pH and super haplogroup (U, K, UK) was significant (p = 0.004) and independent of postmortem interval time.

Focusing on haplogroup and individual susceptibility factors in psychiatric disorders by considering mtDNA variants may lead to innovative treatments to improve mitochondrial health and brain function.