A computational model of the human thyroid

The thyroid, the largest gland in the endocrine system, secretes hormones that help promote bodily growth and development. This gland regulates hormonal secretion rate in spite of changes in dietary iodine which is a key ingredient in the hormone's biosynthesis. The thyroid relies on several feedback mechanisms for this regulation, and in this paper we use recent molecular-level and clinical observations to engineer a computational thyroid model. We use simulation and analysis to show that this models captures known aspects of thyroid physiology. We identify features in the model that are responsible for hormonal regulation, and use the model to identify and evaluate competing hypotheses associated with Wolff-Chaikoff escape.     

Molecular dynamics study of the interaction between fatty acid binding proteins with palmitate mini-micelles

The fatty acid binding proteins (FAPBs) function as intracellular carriers of fatty acid (FA) and related compounds. During the digestion of lipids, the local concentration of FA exceeds their critical micellar concentration; the excess ratio of FA/FABP can be as high as ~1,000/1, consequently building micelles. Considering that the micelle formation is a rapid process, the FABP must be able to remove the mini-micelle. In this study, we describe the results of molecular dynamics simulations of liver basic FABP (Lb-FABP), carried out in the presence of ~20 mM palmitate ions, all in the presence of explicit water and at ionic strength of ~100 mM, approximating physiological conditions. The Lb-FABP appears to react, along with a free FA, with mini-micelle creating a stable complex (on the time scale of the simulations), which is attached to the anti-portal domain of the protein. The complex may be formed by the stepwise addition of free FA or through the interaction of a pre-formed mini-micelle with the free protein. The driving force of the mini-micelle-FABP complex is a combination of electrostatic attraction between the negative carboxylates of the mini-micelle with the positive charge of the N terminal amine residues and Lennard-Jones FA–protein interactions. The preferred tendency of the mini-micelle to react with the anti-portal domain retains the α-helixes of the portal region free for its electrostatic interaction with the membrane, ensuring a rapid unloading of the cargo on the membrane.     

How Can Dolphins Recognize Fish According to Their Echoes? A Statistical Analysis of Fish Echoes

Echo-based object classification is a fundamental task of animals that use a biosonar system. Dolphins and porpoises should be able to rely on echoes to discriminate a predator from a prey or to select a desired prey from an undesired object. Many studies have shown that dolphins and porpoises can discriminate between objects according to their echoes. All of these studies however, used unnatural objects that can be easily characterized in human terminologies (e.g., metallic spheres, disks, cylinders). In this work, we collected real fish echoes from many angles of acquisition using a sonar system that mimics the emission properties of dolphins and porpoises. We then tested two alternative statistical approaches in classifying these echoes. Our results suggest that fish species can be classified according to echoes returning from porpoise- and dolphin-like signals. These results suggest how dolphins and porpoises can classify fish based on their echoes and provide some insight as to which features might enable the classification.     

Telomerase Activity in the Various Regions of Mouse Brain: Non-Radioactive Telomerase Repeat Amplification Protocol (TRAP) Assay

Telomerase, a ribonucleoprotein, is responsible for maintaining the telomere length and therefore promoting genomic integrity, proliferation, and lifespan. In addition, telomerase protects the mitochondria from oxidative stress and confers resistance to apoptosis, suggesting its possible importance for the surviving of non-mitotic, highly active cells such as neurons. We previously demonstrated the ability of novel telomerase activators to increase telomerase activity and expression in the various mouse brain regions and to protect motor neurons cells from oxidative stress. These results strengthen the notion that telomerase is involved in the protection of neurons from various lesions. To underline the role of telomerase in the brain, we here compare the activity of telomerase in male and female mouse brain and its dependence on age. TRAP assay is a standard method for detecting telomerase activity in various tissues or cell lines. Here we demonstrate the analysis of telomerase activity in three regions of the mouse brain by non-denaturing protein extraction using CHAPS lysis buffer followed by modification of the standard TRAP assay.In this 2-step assay, endogenous telomerase elongates a specific telomerase substrate (TS primer) by adding TTAGGG 6 bp repeats (telomerase reaction). The telomerase reaction products are amplified by PCR reaction creating a DNA ladder of 6 bp increments. The analysis of the DNA ladder is made by 4.5% high resolution agarose gel electrophoresis followed by staining with highly sensitive nucleic acid stain.Compared to the traditional TRAP assay that utilize ³²P labeled radioactive dCTP''s for DNA detection and polyacrylamide gel electrophoresis for resolving the DNA ladder, this protocol offers a non-toxic time saving TRAP assay for evaluating telomerase activity in the mouse brain, demonstrating the ability to detect differences in telomerase activity in the various female and male mouse brain region.     

Anaerobic ammonia-oxidizing bacteria and related activity in Baltimore inner harbor sediment

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by (15)N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Planctomycetales-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related Plactomycetales are globally distributed.     

Light-dependent fluorescence in the coral Galaxea fascicularis

The concept of ecological stoichiometry has been useful for understanding nutrient dynamics in aquatic food webs; however, the majority of studies have focused on autotrophic systems, leaving detritus-based food webs largely understudied. In addition, most detritus-based studies have explored enrichment in high-gradient, low-nutrient systems, despite the fact that many of the streams most likely to face enrichment (those surrounded by agriculture) are low-gradient and contain inherently higher dissolved nutrient concentrations due to differences in soil type, geomorphology, and atmospheric deposition. Constraints on consumer growth due to consumer-resource imbalances have been documented in these low-nutrient streams, but the extent to which consumer growth may be limited in higher-nutrient, detritus-based streams is unknown. We investigated the impact of dissolved nutrients (N and P) on mayfly growth, using artificial streams simulating a high-nutrient detritus-based system. Mayflies were reared and sampled under two total nutrient concentrations, one meant to mimic a more natural undisturbed (ambient) watershed and one to mimic a disturbed (enriched) watershed. Under each of these conditions two N:P ratios (low and high) were tested. The low N:P treatments produced higher mayfly growth under both ambient and enriched conditions, showing that nutrient limitation can occur even in high-nutrient streams.     

Theme section on mesophotic coral ecosystems: advances in knowledge and future perspectives

The Second International Mesophotic Coral Ecosystems (MCEs) workshop was held in Eilat, Israel, October 26–31, 2014. Here we provide an account of: (1) advances in our knowledge of MCE ecology, including the central question of the potential vertical connectivity between MCEs and shallow-water reefs (SWRs), and that of the validity of the deep-reef refugia hypothesis (DRRH); (2) the contribution of the 2014 MCE workshop to the central question presented in (1), as well as its contribution to novel MCE studies on corals, sponges, fish, and crabs; and (3) gaps, priorities, and recommendations for future research stemming from the workshop. Despite their close proximity to well-studied SWRs, and the growing evidence of their importance, our scientific knowledge of MCEs is still in its infancy. During the last five years, we have witnessed an ever-increasing scientific interest in MCEs, expressed in the exponential increase in the number of publications studying this unique environment. The emerging consensus is that lower MCE benthic assemblages represent unique communities, either of separate species or genetically distinct individuals within species, and any significant support for the DRRH will be limited to upper MCEs. Determining the health and stability of MCEs, their biodiversity, and the degree of genetic connectivity among SWRs and MCEs, will ultimately indicate the ability of MCEs to contribute to the resilience of SWRs and help to guide future management and conservation strategies. MCEs deserve therefore management consideration in their own right. With the technological advancements taking place in recent years that facilitate access to MCEs, the prospects for exciting and innovative discoveries resulting from MCE research, spanning a wide variety of fields, are immense.     

<Emphasis Type="Italic">Euphyllia paradivisa</Emphasis>, a successful mesophotic coral in the northern Gulf of Eilat/Aqaba,Red Sea

Mesophotic coral ecosystems (MCEs) host a thriving community of biota that has remained virtually unexplored. Here we report for the first time on a large population of the endangered coral species Euphyllia paradivisa from the MCEs of the Gulf of Eilat/Aqaba (GOE/A), Red Sea. The mesophotic zone in some parts of the study site harbors a specialized coral community predominantly comprising E. paradivisa (73 % of the total coral cover), distributed from 36 to 72 m depth. Here we sought to elucidate the strict distribution but high abundance of E. paradivisa in the MCEs at the GOE/A. We present 4 yr of observations and experiments that provide insight into the physiological plasticity of E. paradivisa: its low mortality rates at high light intensities, high competitive abilities, successful symbiont adaptation to the shallow-water environment, and tolerance to bleaching conditions or survival during prolonged bleaching. Despite its ability to survive under high irradiance in shallow water, E. paradivisa is not found in the shallow reef of the GOE/A. We suggest several factors that may explain the high abundance and exclusivity of E. paradivisa in the MCE: its heterotrophic capabilities; its high competition abilities; the possibility of it finding a deep-reef refuge there from fish predation; and its concomitant adaptation to this environment.