Ubc13 and COOH terminus of Hsp70-interacting protein (CHIP) are required for growth hormone receptor endocytosis

Growth hormone receptor (GHR) endocytosis is a highly regulated process that depends on the binding and activity of the multimeric ubiquitin ligase, SCF(βTrCP) (Skp Cullin F-box). Despite a specific interaction between β-transducin repeat-containing protein (βTrCP) and the GHR, and a strict requirement for ubiquitination activity, the receptor is not an obligatory target for SCF(βTrCP)-directed Lys(48) polyubiquitination. We now show that also Lys(63)-linked ubiquitin chain formation is required for GHR endocytosis. We identified both the ubiquitin-conjugating enzyme Ubc13 and the ubiquitin ligase COOH terminus of Hsp70 interacting protein (CHIP) as being connected to this process. Ubc13 activity and its interaction with CHIP precede endocytosis of GHR. In addition to βTrCP, CHIP interacts specifically with the cytosolic tails of the dimeric GHR, identifying both Ubc13 and CHIP as novel factors in the regulation of cell surface availability of GHR.     

Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity

Most autosomal genetic causes of childhood-onset hypogammaglobulinemia are currently not well understood. Most affected individuals are simplex cases, but both autosomal-dominant and autosomal-recessive inheritance have been described. We performed genetic linkage analysis in consanguineous families affected by hypogammaglobulinemia. Four consanguineous families with childhood-onset humoral immune deficiency and features of autoimmunity shared genotype evidence for a linkage interval on chromosome 4q. Sequencing of positional candidate genes revealed that in each family, affected individuals had a distinct homozygous mutation in LRBA (lipopolysaccharide responsive beige-like anchor protein). All LRBA mutations segregated with the disease because homozygous individuals showed hypogammaglobulinemia and autoimmunity, whereas heterozygous individuals were healthy. These mutations were absent in healthy controls. Individuals with homozygous LRBA mutations had no LRBA, had disturbed B cell development, defective in vitro B cell activation, plasmablast formation, and immunoglobulin secretion, and had low proliferative responses. We conclude that mutations in LRBA cause an immune deficiency characterized by defects in B cell activation and autophagy and by susceptibility to apoptosis, all of which are associated with a clinical phenotype of hypogammaglobulinemia and autoimmunity.     

Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment

Cancer is known to be a complex disease and its therapy is difficult. Much information is available on molecules and pathways involved in cancer onset and progression and this data provides a valuable resource for the development of predictive computer models that can help to identify new potential drug targets or to improve therapies. Modeling cancer treatment has to take into account many cellular pathways usually leading to the construction of large mathematical models. The development of such models is complicated by the fact that relevant parameters are either completely unknown, or can at best be measured under highly artificial conditions. Here we propose an approach for constructing predictive models of such complex biological networks in the absence of accurate knowledge on parameter values, and apply this strategy to predict the effects of perturbations induced by anti-cancer drug target inhibitions on an epidermal growth factor (EGF) signaling network. The strategy is based on a Monte Carlo approach, in which the kinetic parameters are repeatedly sampled from specific probability distributions and used for multiple parallel simulations. Simulation results from different forms of the model (e.g., a model that expresses a certain mutation or mutation pattern or the treatment by a certain drug or drug combination) can be compared with the unperturbed control model and used for the prediction of the perturbation effects. This framework opens the way to experiment with complex biological networks in the computer, likely to save costs in drug development and to improve patient therapy.     

Plasticity as a plastic response: how submergence-induced leaf elongation in Rumex palustris depends on light and nutrient availability in its early life stage

Plants may experience different environmental cues throughout their development which interact in determining their phenotype. This paper tests the hypothesis that environmental conditions experienced early during ontogeny affect the phenotypic response to subsequent environmental cues. This hypothesis was tested by exposing different accessions of Rumex palustris to different light and nutrient conditions, followed by subsequent complete submergence. Final leaf length and submergence-induced plasticity were affected by the environmental conditions experienced at early developmental stages. In developmentally older leaves, submergence-induced elongation was lower in plants previously subjected to high-light conditions. Submergence-induced elongation of developmentally younger leaves, however, was larger when pregrown in high light. High-light and low-nutrient conditions led to an increase of nonstructural carbohydrates in the plants. There was a positive correlation between submergence-induced leaf elongation and carbohydrate concentration and content in roots and shoots, but not with root and shoot biomass before submergence. These results show that conditions experienced by young plants modulate the responses to subsequent environmental conditions, in both magnitude and direction. Internal resource status interacts with cues perceived at different developmental stages in determining plastic responses to the environment.     

Vampire squid: detritivores in the oxygen minimum zone

Vampire squid (Vampyroteuthis infernalis) are considered phylogenetic relics with cephalopod features of both octopods and squids. They lack feeding tentacles, but in addition to their eight arms, they have two retractile filaments, the exact functions of which have puzzled scientists for years. We present the results of investigations on the feeding ecology and behaviour of Vampyroteuthis, which include extensive in situ, deep-sea video recordings from MBARI''s remotely operated vehicles (ROVs), laboratory feeding experiments, diet studies and morphological examinations of the retractile filaments, the arm suckers and cirri. Vampire squid were found to feed on detrital matter of various sizes, from small particles to larger marine aggregates. Ingested items included the remains of gelatinous zooplankton, discarded larvacean houses, crustacean remains, diatoms and faecal pellets. Both ROV observations and laboratory experiments led to the conclusion that vampire squid use their retractile filaments for the capture of food, supporting the hypothesis that the filaments are homologous to cephalopod arms. Vampyroteuthis'' feeding behaviour is unlike any other cephalopod, and reveals a unique adaptation that allows these animals to spend most of their life at depths where oxygen concentrations are very low, but where predators are few and typical cephalopod food is scarce.     

Season of sampling and season of birth influence serotonin metabolite levels in human cerebrospinal fluid

Background

Animal studies have revealed seasonal patterns in cerebrospinal fluid (CSF) monoamine (MA) turnover. In humans, no study had systematically assessed seasonal patterns in CSF MA turnover in a large set of healthy adults.

Methodology/Principal Findings

Standardized amounts of CSF were prospectively collected from 223 healthy individuals undergoing spinal anesthesia for minor surgical procedures. The metabolites of serotonin (5-hydroxyindoleacetic acid, 5-HIAA), dopamine (homovanillic acid, HVA) and norepinephrine (3-methoxy-4-hydroxyphenylglycol, MPHG) were measured using high performance liquid chromatography (HPLC). Concentration measurements by sampling and birth dates were modeled using a non-linear quantile cosine function and locally weighted scatterplot smoothing (LOESS, span = 0.75). The cosine model showed a unimodal season of sampling 5-HIAA zenith in April and a nadir in October (p-value of the amplitude of the cosine = 0.00050), with predicted maximum (PC_max) and minimum (PC_min) concentrations of 173 and 108 nmol/L, respectively, implying a 60% increase from trough to peak. Season of birth showed a unimodal 5-HIAA zenith in May and a nadir in November (p = 0.00339; PC_max = 172 and PC_min = 126). The non-parametric LOESS showed a similar pattern to the cosine in both season of sampling and season of birth models, validating the cosine model. A final model including both sampling and birth months demonstrated that both sampling and birth seasons were independent predictors of 5-HIAA concentrations.

Conclusion

In subjects without mental illness, 5-HT turnover shows circannual variation by season of sampling as well as season of birth, with peaks in spring and troughs in fall.     

Production of high amounts of 3-hydroxypropionaldehyde from glycerol by Lactobacillus reuteri with strongly increased biocatalyst lifetime and productivity

3-hydroxypropionaldehyde (3HPA) is a promising versatile substance derived from the renewable feedstock glycerol. It is a product of glycerol metabolism in Lactobacillus reuteri. Because of toxic effects, the biotechnological production is poor. In this work the biocatalyst lifetime and product formation could be drastically increased. In the established two-step process already applied, cells are grown in the first step under anaerobic conditions, and in the second step the immobilised or suspended biocatalyst is used for 3HPA-production under strict anaerobic conditions. In the first step it was possible to reach a biomass concentration of 5.5g CDW/L (OD(600)≈23.4). In the second step, normally, 3HPA accumulates to a toxic concentration and the reaction stops in less than 60min because of the interaction of 3HPA with cell components. To prevent this, the toxic product is bound to the newly found scavenger carbohydrazide to form the hydrazone. For the first time it was possible to recycle the immobilised biocatalyst for at least ten cycles (overall life time>33hours) in a repeated batch biotransformation with an overall production of 67g 3HPA. The optimal pH-value was between 6.8 and 7.2 at an optimal temperature of 40-45°C. In a single batch biotransformation with suspended resting cells it was possible to produce 150g/L 3HPA as carbohydrazone at an overall productivity of 10.7gL(-1)hours(-1). In a single fed-batch biotransformation at 45°C 138g/L glycerol was converted into 108g/L 3HPA with an overall productivity of 21.6gL(-1)hours(-1). This is the highest 3HPA concentration and productivities reported so far for the microbial production of 3HPA from glycerol.     

Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing

MicroRNAs (miRNAs), non-coding RNAs regulating gene expression, are frequently aberrantly expressed in human cancers. Next-generation deep sequencing technology enables genome-wide expression profiling of known miRNAs and discovery of novel miRNAs at unprecedented quantitative and qualitative accuracy. Deep sequencing was performed on 11 fresh frozen clear cell renal cell carcinoma (ccRCC) and adjacent non-tumoral renal cortex (NRC) pairs, 11 additional frozen ccRCC tissues, and 2 ccRCC cell lines (n?=?35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. those without disease recurrence, with recurrence and with metastatic disease at diagnosis. Thirty-two consecutive samples (16 ccRCC/NRC pairs) were used for stem-loop PCR validation. Novel miRNAs were predicted using 2 distinct bioinformatic pipelines. In total, 463 known miRNAs (expression frequency 1-150,000/million) were identified. We found that 100 miRNA were significantly differentially expressed between ccRCC and NRC. Differential expression of 5 miRNAs was confirmed by stem-loop PCR in the 32 ccRCC/NRC samples. With respect to RCC subgroups, 5 miRNAs discriminated between non-recurrent versus recurrent and metastatic disease, whereas 12 uniquely distinguished non-recurrent versus metastatic disease. Blocking overexpressed miR-210 or miR-27a in cell line SKCR-7 by transfecting specific antagomirs did not result in significant changes in proliferation or apoptosis. Twenty-three previously unknown miRNAs were predicted in silico. Quantitative genome-wide miRNA profiling accurately separated ccRCC from (benign) NRC. Individual differentially expressed miRNAs may potentially serve as diagnostic or prognostic markers or future therapeutic targets in ccRCC. The biological relevance of candidate novel miRNAs is unknown at present.     

A synopsis of the genus Cypholoba Chaudoir (Coleoptera, Carabidae, Anthiini) known to occur in the Republic of South Africa

Nearly one third of the described species of Cypholoba Chaudoir (Coleoptera: Carabidae) are known to inhabit the Republic of South Africa. A key and diagnostic notes are provided for their identification, as well as notes about way of life for some of the species based on observations in the Kruger National Park. Fifteen species and subspecies of the genus are recorded from the Republic of South Africa; adult specimens of each species and subspecies are illustrated and information about the distribution of each species in the Republic of South Africa is summarized and mapped: Cypholoba alstoni (Péringuey), Cypholoba alveolata (Brême), Cypholoba amatonga Péringuey, Cypholoba fritschi (Chaudoir), Cypholoba gracilis gracilis (Dejean), Cypholoba gracilis scrobiculata (Bertoloni), Cypholoba gracilis zuluana Basilewsky, Cypholoba graphipteroides graphipteroides (Guérin-Méneville), Cypholoba leucospilota semilaevis (Chaudoir), Cypholoba macilenta (Olivier), Cypholoba notata (Perroud), Cypholoba oberthueri seruana Strohmeyer, Cypholoba opulenta (Boheman), Cypholoba rutata (Péringuey), and Cypholoba tenuicollis aenigma (Dohrn).