Phospholipid methyltransferase phosphorylation by intact hepatocytes: effect of glucagon

We have obtained a rabbit antiserum that specifically immunoprecipitates the 50K and 25K proteins of rat liver phospholipid methyltransferase. Exposure of intact rat hepatocytes preincubated with [32P]phosphate to glucagon induces a time-dependent phosphorylation of the 50K protein of phospholipid methyltransferase. The incorporation of 32P into the 50K protein was only on phosphoserine. These data support the concept that the activation of rat liver phospholipid methyltransferase by glucagon is mediated by phosphorylation of the enzyme.     

Intercellular communication in the rat anterior pituitary gland: an in vivo and in vitro study

The concept of "stimulus-secretion coupling" suggested by Douglas and co-workers to explain the events related to monamine discharge by the adrenal medulla (5, 7) may be applied to other endocrine tissues, such as adrenal cortex (36), pancreatic islets (4), and magnocellular hypothalamic neurons (6), which exhibit a similar ion-dependent process of hormone elaboration. In addition, they share another feature, that of joining neighbor cells via membrane junctions (12, 26, and Fletcher, unpublished observation). Given this, and the reports that hormone secretion by the pars distalis also involves a secretagogue-induced decrease in membrane bioelectric potential accompanied by a rise in cellular [Ca++] (27, 34, 41), it was appropriate to test the possibility that cells of the anterior pituitary gland are united by junctions.     

Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.     

Two Steady‐Entrainment Phases and Graded Masking Effects by Light Generate Different Circadian Chronotypes in Octodon degus

Processes involved in the operation of the circadian pacemaker are well characterized; however; little is known about what mechanisms drive the overt diurnal, nocturnal, or crepuscular behavior in a species. In this context, dual‐phasing rodents, such as Octodon degus, emerge as a useful model to decipher these keys. Two main chronotypes, nocturnal and diurnal, have been traditionally described in laboratory‐housed degus based on the percentage of activity displayed by the animals during the scotophase or photophase. However, if one considers also the entrainment phase angle during the first days following a change from LD to DD conditions, a third chronotype (intermediate)—or more properly, a continuous grading of circadian expressions between diurnal and nocturnal chronotype—can be observed. Our experiments suggest the pacemaker of the diurnal animal is entrained to the photophase, and light does not exert a negative masking effect. The pacemaker of the nocturnal degus, on the other hand, is entrained to the scotophase, and light exerts a strong negative masking effect. Finally, the intermediate chronotype is characterized by variable negative masking effect of light overlapping a pacemaker entrained to the photophase. The phase shift inversion from diurnal to nocturnal chronotype is related to the availability of a wheel in the cage, and the effect may be located downstream from the clock. However, body temperature rhythm recordings, less affected by masking effects, point to an involvement of the circadian pacemaker in chronotype differentiation, as transient entrainment cycles, and not an abrupt phase shift, were detected after providing access to the wheel. The diurnality of degus seems to be the result of a variety of mechanisms, which may explain how different processes can lead to similar chronotypes.     

Global dynamics of two-compartment models for cell production systems with regulatory mechanisms

We present a global stability analysis of two-compartment models of a hierarchical cell production system with a nonlinear regulatory feedback loop. The models describe cell differentiation processes with the stem cell division rate or the self-renewal fraction regulated by the number of mature cells. The two-compartment systems constitute a basic version of the multicompartment models proposed recently by Marciniak-Czochra and collaborators [25] to investigate the dynamics of the hematopoietic system. Using global stability analysis, we compare different regulatory mechanisms. For both models, we show that there exists a unique positive equilibrium that is globally asymptotically stable if and only if the respective reproduction numbers exceed one. The proof is based on constructing Lyapunov functions, which are appropriate to handle the specific nonlinearities of the model. Additionally, we propose a new model to test biological hypothesis on the regulation of the fraction of differentiating cells. We show that such regulatory mechanism is incapable of maintaining homeostasis and leads to unbounded cell growth. Potential biological implications are discussed.     

Unraveling the Nexus: Exploring the Pathways to Combined Resource Use

In response to the unprecedented decline in global natural resource endowments, the so‐called nexus framework is gaining increasing influence on resource management practices. In this research, we approach the resource nexus through the concept of nexus pathways. Nexus pathways are configurations that resource flows follow along supply chains leading to the combined use of two or more resources. Three general types of pathways are identified: direct (on‐site use), dependent (one‐way supply chains), and interdependent (supply‐chain feedbacks). We quantify and compare each pathway by means of multiregional input‐output analysis and structural path analysis, and apply this approach to a comparative case study on the water‐energy nexus (WEN) in the United States and China. Interdependencies or feedbacks are generally thought to be relevant for the WEN, especially between water and energy sectors. Our economy‐wide analysis for both countries indicates, however, that feedbacks neither play an important role in the WEN nor substantially take place between water and energy sectors. The most important feedbacks contribute to less than 1% of total resource use, and these take place mostly between manufacturing sectors. Overall, the studied WEN is mostly driven by dependent pathways and, to a lesser degree, direct resource use. Comparative differences between the two countries are largely explained by differences in economic structure, technology, and resource endowments. Our findings call into question current research and policy focus and suggest greater attention to less complex, but more determining, pathways leading to absolute resource use.     

Interactive Visualization and Industrial Ecology: Applications,Challenges, and Opportunities

The emergence of increasingly complex data in industrial ecology (IE) has caused scholarly interest in interactive visualization (IV). IV allows users to interact with data, aiding in processing and interpreting complex datasets, processes, and simulations. Consequently, IV can help IE practitioners communicate the complexities of their methods and results, shed light on the underlying research assumptions, and enable more transparent monitoring of data quality and error. This can significantly increase the reach and impact of research, promote transparency, reproducibility, and open science, as well as improve the clarity and presentation of IE research. A review of current IV applications reveals that, while data exploration has received some attention among IE practitioners, IV applications in scientific communication are clearly lacking. With the help of a working example, we explore the value of IV, discuss its operationalization, and highlight challenges that the IE community must face during IV uptake. Such challenges include technical and knowledge limitations, limits on user interaction, and implementation strategies. With these challenges in mind, we outline key aspects needed to lift the IE field to the forefront of scientific communication in the coming years. Among these, we draft the basic principles of a “Hub for Interactive Visualization in Industrial Ecology” (HIVE), a point of encounter where IE practitioners could find an array of data visualization tools that are geared toward IE datasets. IV is here to stay, and its inceptive stage presents many opportunities to IE practitioners to shape its operationalization and benefit from early adoption.     

Classification and nomenclature of all human homeobox genes

Background

The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.

Results

We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.

Conclusion

We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.