Differential modification of seawater carbonate chemistry by major coral reef benthic communities

Ocean acidification (OA) resulting from uptake of anthropogenic CO₂ may negatively affect coral reefs by causing decreased rates of biogenic calcification and increased rates of CaCO₃ dissolution and bioerosion. However, in addition to the gradual decrease in seawater pH and Ω _a resulting from anthropogenic activities, seawater carbonate chemistry in these coastal ecosystems is also strongly influenced by the benthic metabolism which can either exacerbate or alleviate OA through net community calcification (NCC = calcification – CaCO₃ dissolution) and net community organic carbon production (NCP = primary production ? respiration). Therefore, to project OA on coral reefs, it is necessary to understand how different benthic communities modify the reef seawater carbonate chemistry. In this study, we used flow-through mesocosms to investigate the modification of seawater carbonate chemistry by benthic metabolism of five distinct reef communities [carbonate sand, crustose coralline algae (CCA), corals, fleshy algae, and a mixed community] under ambient and acidified conditions during summer and winter. The results showed that different communities had distinct influences on carbonate chemistry related to the relative importance of NCC and NCP. Sand, CCA, and corals exerted relatively small influences on seawater pH and Ω _a over diel cycles due to closely balanced NCC and NCP rates, whereas fleshy algae and mixed communities strongly elevated daytime pH and Ω _a due to high NCP rates. Interestingly, the influence on seawater pH at night was relatively small and quite similar across communities. NCC and NCP rates were not significantly affected by short-term acidification, but larger diel variability in pH was observed due to decreased seawater buffering capacity. Except for corals, increased net dissolution was observed at night for all communities under OA, partially buffering against nighttime acidification. Thus, algal-dominated areas of coral reefs and increased net CaCO₃ dissolution may partially counteract reductions in seawater pH associated with anthropogenic OA at the local scale.     

Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain

JC virus is a member of the Polyomavirus family of DNA tumor viruses and the causative agent of progressive multifocal leukoencephalopathy (PML). PML is a disease that occurs primarily in people who are immunocompromised and is usually fatal. As with other Polyomavirus family members, the replication of JC virus (JCV) DNA is dependent upon the virally encoded protein T-antigen. To further our understanding of JCV replication, we have determined the crystal structure of the origin-binding domain (OBD) of JCV T-antigen. This structure provides the first molecular understanding of JCV T-ag replication functions; for example, it suggests how the JCV T-ag OBD site-specifically binds to the major groove of GAGGC sequences in the origin. Furthermore, these studies suggest how the JCV OBDs interact during subsequent oligomerization events. We also report that the OBD contains a novel “pocket”; which sequesters the A1 & B2 loops of neighboring molecules. Mutagenesis of a residue in the pocket associated with the JCV T-ag OBD interfered with viral replication. Finally, we report that relative to the SV40 OBD, the surface of the JCV OBD contains one hemisphere that is highly conserved and one that is highly variable.     

PHYSIOLOGICAL ACCLIMATION OF MARINE PHYTOPLANKTON TO DIFFERENT NITROGEN SOURCES1

We examined the energetic dependency of the biochemical and physiological responses of Thalassiosira pseudonana Hasle and Heimdal. Chaetoceros gracilis Schütt, Dunaliella tertiolecta Butcher, and Gymnodinium sanguineum Hirasaka to NH₄⁺, NO₃^?, and urea by growing them at subsaturating and saturating photon flux (PF). At subsaturating PF, when energy was limiting, NO₃^? and NH₄⁺ grown cells had similar growth rates and C and X quotas. Therefore, NO₃^? grown cells used up to 48% more energy than NH₄⁺ grown cells to assimilate carbon and nitrogen. Based on our measurements of pigments, chlorophyll-a-specific in vivo absorption cross-section, and fluorescence-chlorophyll a^?1, we suggest that NO₃^?, grown cells do not compensate for the greater energy requirements of NO₃^? reduction by trapping more light energy. At saturating PF, when energy is not limiting, the utilization of NO₃^?, compared to NH₄⁺ resulted in lower growth rates and N quotas in Thalassiosira pseudonana and lower N quotas in Chaetoceros gracilis, suggesting enzymatic rather than energetic limitations to growth. The utilization of urea compared to Nh₄⁺ resulted in lower growth rates in Chaetoceros gracilis and Gymnodinium sanguineum (saturating PF) and in lower N quotas in all species tested at both subsaturating and saturating PF. The high C:N ratios observed in all urea-grown species suggest that nitrogen assimilation may be limited by urea uptake or deamination and that symptoms of N limitation in microalgae may be induced by the nature of the N source in addition to the N supply rate. Our results provide new eridence that the maximum growth rates of microalgae may be limited by enzymatic processes associated with the assimilation of NO₃^?, or urea.     

Isolation and culture of rat superior mesenteric artery smooth muscle cells

Summary The structure and function of vascular smooth muscle cells have been extensively investigated with the aid of in vitro culture techniques. The majority of studies have utilized aortic tissue as the source of cells. We present here a method for isolating and culturing smooth muscle cells of the rat superior mesenteric artery, an elasto-muscular vessel that is structurally and functionally different from the aorta. Cells were isolated from partially digested explants and characterized by immunochemical and biochemical techniques. Unlike cultured fibroblasts, the cultured cells stained positive for smooth muscle specific actin. The cells also produced laminin and type IV collagen in culture. This method provides a means for the isolation of large numbers of viable smooth muscle cells from the superior mesenteric artery which can be propagated in culture for in vitro study.     

Fluid dynamics and microscale chemical movement in the chemosensory appendages of the lobster, Homarus americanus

Every chemosensory structure has a boundary layer surroundingit through which chemical signals must pass before contactingreceptor cells. Fluid motion in this boundary layer is slowand odor movement is mainly by diffusion. The boundary layerstructure depends upon external fluid velocities and the morphologyof the appendage. High-speed (10–200 Hz) electrochemicalrecordings from microchemical electrodes were used to quantifychemical transport in the microscale environment of three morphologicallydifferent chemosensory appendages of the lobster, Homarus americanus:lateral antennule, medial antennule and walking legs. Controlledpulses of the odor tracer (dopamine) were delivered to the threeappendages at three different flow speeds (0, 3, 6 cm/s). Theamplitudes of the pulses increased with increasing flow speed,indicating that boundary layer thickness decreased with increasingflow speed. Larger pulse amplitudes were measured in the walkinglegs than in the lateral or medial antennules at all flow speeds.In addition, larger amplitudes were recorded in the medial antennulethan the lateral antennule. Changes in pulse amplitude withincreasing flow speed were larger than changes in pulse duration.These results demonstrate that pulse amplitude is affected morethan pulse duration by boundary layer thickness and that themorphology of the receptor strucure helps determine the structureof signals arriving at receptor cells. This may explain whyanimals have adopted sampling strategies that reduce boundarylayer thickness.     

Tumor-suppressor Gene Promoter Hypermethylation in Saliva of Head and Neck Cancer Patients

Head and neck squamous cell carcinoma (HNSCC) accounts for a bulk of the oral and laryngeal cancers, the majority (70%) of which are associated with smoking and excessive drinking, major known risk factors for the development of HNSCC. In contrast to reports that suggest an inverse relationship between smoking and global DNA CpG methylation, hypermethylation of promoters of a number of genes was detected in saliva collected from patients with HNSCC. Using a sensitive methylation-specific polymerase chain reaction (MSP) assay to determine specific methylation events in the promoters of RASSF1A, DAPK1, and p16 genes, we demonstrate that we can detect tumor presence with an overall accuracy of 81% in the DNA isolated from saliva of patients with HNSCC (n = 143) when compared with the DNA isolated from the saliva of healthy nonsmoker controls (n = 31). The specificity for this MSP panel was 87% and the sensitivity was 80% (with a Fisher exact test P < .0001). In addition, the test panel performed extremely well in the detection of the early stages of HNSCCs, with a sensitivity of 94% and a specificity of 87%, and a high κ concordance value of 0.8, indicating an excellent overall agreement between the presence of HNSCC and a positive MSP panel result. In conclusion, we demonstrate that the promoter methylation of RASSF1A, DAPK1, and p16 MSP panel is useful in detecting hypermethylation events in a noninvasive manner in patients with HNSCC.     

TaqMan Real-Time PCR Assays for Single-Nucleotide Polymorphisms Which Identify Francisella tularensis and Its Subspecies and Subpopulations

Francisella tularensis, the etiologic agent of tularemia and a Class A Select Agent, is divided into three subspecies and multiple subpopulations that differ in virulence and geographic distribution. Given these differences, there is a need to rapidly and accurately determine if a strain is F. tularensis and, if it is, assign it to subspecies and subpopulation. We designed TaqMan real-time PCR genotyping assays using eleven single nucleotide polymorphisms (SNPs) that were potentially specific to closely related groups within the genus Francisella, including numerous subpopulations within F. tularensis species. We performed extensive validation studies to test the specificity of these SNPs to particular populations by screening the assays across a set of 565 genetically and geographically diverse F. tularensis isolates and an additional 21 genetic near-neighbor (outgroup) isolates. All eleven assays correctly determined the genetic groups of all 565 F. tularensis isolates. One assay differentiates F. tularensis, F. novicida, and F. hispaniensis from the more genetically distant F. philomiragia and Francisella-like endosymbionts. Another assay differentiates F. tularensis isolates from near neighbors. The remaining nine assays classify F. tularensis-confirmed isolates into F. tularensis subspecies and subpopulations. The genotyping accuracy of these nine assays diminished when tested on outgroup isolates (i.e. non F. tularensis), therefore a hierarchical approach of assay usage is recommended wherein the F. tularensis-specific assay is used before the nine downstream assays. Among F. tularensis isolates, all eleven assays were highly sensitive, consistently amplifying very low concentrations of DNA. Altogether, these eleven TaqMan real-time PCR assays represent a highly accurate, rapid, and sensitive means of identifying the species, subspecies, and subpopulation of any F. tularensis isolate if used in a step-wise hierarchical scheme. These assays would be very useful in clinical, epidemiological, and/or forensic investigations involving F. tularensis.     

QTLs for Tolerance of Drought and Breeding for Tolerance of Abiotic and Biotic Stress: An Integrated Approach

Background

The coupling of biotic and abiotic stresses leads to high yield losses in rainfed rice (Oryza sativa L.) growing areas. While several studies target these stresses independently, breeding strategies to combat multiple stresses seldom exist. This study reports an integrated strategy that combines QTL mapping and phenotypic selection to develop rice lines with high grain yield (GY) under drought stress and non-stress conditions, and tolerance of rice blast.

Methodology

A blast-tolerant BC₂F₃-derived population was developed from the cross of tropical japonica cultivar Moroberekan (blast- and drought-tolerant) and high-yielding indica variety Swarna (blast- and drought-susceptible) through phenotypic selection for blast tolerance at the BC₂F₂ generation. The population was studied for segregation distortion patterns and QTLs for GY under drought were identified along with study of epistatic interactions for the trait.

Results

Segregation distortion, in favour of Moroberekan, was observed at 50 of the 59 loci. Majority of these marker loci co-localized with known QTLs for blast tolerance or NBS-LRR disease resistance genes. Despite the presence of segregation distortion, high variation for DTF, PH and GY was observed and several QTLs were identified under drought stress and non-stress conditions for the three traits. Epistatic interactions were also detected for GY which explained a large proportion of phenotypic variance observed in the population.

Conclusions

This strategy allowed us to identify QTLs for GY along with rapid development of high-yielding purelines tolerant to blast and drought with considerably reduced efforts. Apart from this, it also allowed us to study the effects of the selection cycle for blast tolerance. The developed lines were screened at IRRI and in the target environment, and drought and blast tolerant lines with high yield were identified. With tolerance to two major stresses and high yield potential, these lines may provide yield stability in rainfed rice areas.