The nature of “internal sensations” of higher brain functions may be derived from the design rules for artificial machines that can produce them

Modeling various neuronal functions in search of emergent properties may achieve success when the gold standard of replicating the models in physical systems starts exhibiting some of these properties. Since very large number of functions can be modeled and need testing, we suggest an alternate method of examining higher brain functions: seeing them as internal sensations formed from their hypothetical basic units. Here, we explain the need to replicate the natural mechanism using electronic circuits, discuss some of the technical aspects and introduce some concepts for searching for properties of internal sensations evolving from them.     

Transgenic Inhibitors of RNA Interference in Drosophila

RNA silencing functions as an adaptive antiviral defense in both plants and animals. In turn, viruses commonly encode suppressors of RNA silencing, which enable them to mount productive infection. These inhibitor proteins may be exploited as reagents with which to probe mechanisms and functions of RNA silencing pathways. In this report, we describe transgenic Drosophila strains that allow inducible expression of the viral RNA silencing inhibitors Flock House virus-B2, Nodamura virus-B2, vaccinia virus-E3L, influenza A virus-NS1 and tombusvirus P19. Some of these, especially the B2 proteins, are effective transgenic inhibitors of double strand RNA-induced gene silencing in flies. On the other hand, none of them is effective against the Drosophila microRNA pathway. Their functional selectivity makes these viral silencing proteins useful reagents with which to study biological functions of the Drosophila RNA interference pathway.     

Transgenic inhibitors of RNA interference in Drosophila

RNA silencing functions as an adaptive antiviral defense in both plants and animals. In turn, viruses commonly encode suppressors of RNA silencing, which enable them to mount productive infection. These inhibitor proteins may be exploited as reagents with which to probe mechanisms and functions of RNA silencing pathways. In this report, we describe transgenic Drosophila strains that allow inducible expression of the viral RNA silencing inhibitors Flock House virus-B2, Nodamura virus-B2, vaccinia virus-E3L, influenza A virus-NS1 and tombusvirus P19. Some of these, especially the B2 proteins, are effective transgenic inhibitors of double strand RNA-induced gene silencing in flies. On the other hand, none of them is effective against the Drosophila microRNA pathway. Their functional selectivity makes these viral silencing proteins useful reagents with which to study biological functions of the Drosophila RNA interference pathway.     

Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae

The endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome‐to‐Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.     

Role of transposable elements in trypanosomatids

Transposable elements constitute 2-5% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.     

Identifying cancer genes from cancer mutation profiles by cancer functions

It is of great importance to identify new cancer genes from the data of large scale genome screenings of gene mutations in cancers. Considering the alternations of some essential functions are indispensable for oncogenesis, we define them as cancer functions and select, as their approximations, a group of detailed functions in GO (Gene Ontology) highly enriched with known cancer genes. To evaluate the efficiency of using cancer functions as features to identify cancer genes, we define, in the screened genes, the known protein kinase cancer genes as gold standard positives and the other kinase genes as gold standard negatives. The results show that cancer associated functions are more efficient in identifying cancer genes than the selection pressure feature. Furthermore, combining cancer functions with the number of non-silent mutations can generate more reliable positive predictions. Finally, with precision 0.42, we suggest a list of 46 kinase genes as candidate cancer genes which are annotated to cancer functions and carry at least 3 non-silent mutations.     

On the Interrelationship of Speech Functioning and Manual Motor Activity in Aphasia

Clinicians, physiologists, and psychologists are familiar with cases of simultaneous disturbance of various functions in localized cerebral lesions. These phenomena have been studied and described repeatedly, but continue to be of substantial interest, as analysis of them may make a contribution to the study of localization of functions in the cerebral cortex, substitution and restoration of functions, and the nature of their interrelationships. Our attention was attracted by a case of simultaneous disturbance of motor function and the power of speech in a lesion of the left (dominant) hemisphere. We began by investigating motor functions in aphasia and in the normal state, with a view to subsequent comparison of the motor and verbal functions in the normal state and in aphasia.     

Polarized sorting of GPI-linked proteins in epithelia and membrane microdomains.

Taken together, our results with endogenous and transfected GPI-anchored proteins (summarized in Table 6) suggest that covalent attachment to GPI functions as an apical transport signal in polarized epithelial cells. This is the first example of a well-defined targeting signal for the post-Golgi sorting of plasma membrane proteins in polarized epithelia; the only other known post-Golgi targeting signal is mannose-6-phosphate, which functions in the recognition of lysosomal hydrolases and directs them to lysosomes.     

Hemoglobin as a potential source of natural regulatory oligopeptides

Theoretical structure-function analysis of all possible hemoglobin molecule fragments was performed to determine sites that could be potential sources of regulatory oligopeptides. Known data on bovine hemoglobin primary structure and information of the EROP-Moscow database concerning structure and functions of natural oligopeptides were used along with a computer program complex. A total of 6750 natural non-hemoglobin oligopeptides with hemoglobin fragments of 2–14 amino acid residues were found. Structures of 20 of them were completely identical to hemoglobin fragments. Most of the revealed oligopeptides exhibit properties of neuropeptides, antimicrobial agents, and hormones. A number of them exhibit functions previously not known for hemoglobin fragments. The possibility of natural formation of regulatory oligopeptides from hemoglobin and other food protein molecules, generation of the exogenous oligopeptide pool, their participation in regulation processes as well as accordance of results obtained here with the oligopeptide continuum concepts are discussed.     

Extraribosomal functions of bacterial ribosomal proteins

Ribosomal proteins (r-proteins) constitute a considerable part of the cell proteome. Although their primary role in the cell is to serve as integral components of protein synthesis machinery, ribosomes, many of them have functions beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with other cell components. Extraribosomal activities of some ribosomal proteins were observed as early as the 1970s–1980s. In recent years, both the list of moonlighting r-proteins and the repertoire of their additional functions beyond the ribosome was greatly expanded, mainly owing to new techniques developed for dissecting RNA/DNA-protein or protein-protein interactions within functional complexes involved in various cell processes. The review surveys information on the extraribosomal functions demonstrated experimentally or presumed for bacterial r-proteins.     

Only one of the two signals required for initiation of the cell cycle is associated with cellular accumulation of ribosomal RNA

Two intracellular functions are elicited by the serum component in culture media in order to initiate the cell cycle: "competence" and "progression". Although both functions have to be present simultaneously for start of cell division, it is shown here for Swiss 3T3 cells that only one of them, the progression signal, is associated with reaccumulation of ribosomal RNA. This result points to the cellular complement of ribosomes as one of the limiting parameters for cell division.     

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or between species can give clues about phenotypic differences. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases.     

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.     

Cortical function: jump-starting the brain

Magnetic stimulation as used in studies of the human brain may not merely disrupt cognitive functions, but also enhance them. The direction of the effect may depend on the frequency of stimulation as much as the area of the brain that is stimulated.     

Statistical theories of functions and the problem of epidemic disease

Several decades ago, Christopher Boorse formulated an influential statistical theory of normative biological functions but it has often been claimed that his theory suffers from insuperable problems such as an inability to handle cases of epidemic and universal diseases. This paper develops a new statistical theory of normative functions that is capable of dealing with the notorious problem of epidemic and universal diseases. The theory is also more detailed than its predecessors and offers other important advantages over them. It is argued here that statistical theories of biological functions should not be so quickly dismissed.     

The moonlighting enzyme CD13: old and new functions to target

Aminopeptidase N (CD13) is a widely expressed ectoenzyme with functions that do not always depend on its enzymatic activity: an aspect that has been overlooked. Numerous CD13-targeting tools have been developed in the last few years. Several of them are already undergoing clinical trials, and there are promising reports on the effectiveness of others in animal models of disease. However, their efficacy might be obscured by their effects on unrecognized functions of CD13, resulting in unexpected complications. The purpose of this review is (i) to discuss the various functions ascribed to CD13 and the possible mechanisms behind them and (ii) to consider some of the questions that need to be answered to achieve a better understanding of the biological relevance of these functions, a more precise interpretation of the results obtained after their manipulation and a more rational design of CD13-targeting agents.     

Membrane traffic: editorial overview

The most outstanding feature of eukaryotic cells is compartmentalization by membranes, which enables them to achieve a broad spectrum of functions; some of them are common to all cell-types and others are specific to certain cell-types. Individual compartments, namely organelles, have unique sets of proteins that are specifically delivered from one compartment to another by membrane traffic. During the past several years, combinations of genomic, proteomic, structural and real-time imaging analyses with conventional genetical, biochemical and cell biological approaches have provided us with much new information not only about the intricate pathways and sophisticated regulatory mechanisms of membrane traffic but also about integration of membrane traffic with other cellular functions such as signaling and morphogenesis. This Minireview series composed of eight articles highlights the recent progress in this rapidly expanding research field.     

Signalling and functional diversity within the Axl subfamily of receptor tyrosine kinases

The related Axl, Sky and Mer receptor tyrosine kinases (RTKs) are increasingly being implicated in a host of discrete cellular responses including cell survival, proliferation, migration and phagocytosis. Furthermore, their ligands Gas6 and protein S are characteristically dependent on vitamin K for expression of their functions. The Gas6/Axl system is implicated in several types of human cancer as well as inflammatory, autoimmune, vascular and kidney diseases. Each member of the Axl RTK subfamily possesses distinct expression profiles as well as discrete functions. In this article, we review the knowledge so far on the intracellular signalling interactions and pathways concerning each of the Axl RTKs. In this way, we hope to gain a greater understanding of the mechanisms that set each of them apart, and that relay their associated functions.