Motion: the long and short of it

Several authors have proposed that motion is analyzed by two separate processes: short-range and long-range. We claim that the differences between short-range and long-range motion phenomena are a direct consequence of the stimuli used in the two paradigms and are not evidence for the existence of two qualitatively different motion processes. We propose that a single style of motion analysis, similar to the well known Reichardt and Marr-Ullman motion detectors, underlies all motion phenomena. Although there are different detectors of this type specialized for different visual attributes (namely first-order and second-order stimuli), they all share the same mode of operation. We review the studies of second-order motion stimuli to show that they share the basic phenomena observed for first-order stimuli. The similarity across stimulus types suggests, not parallel streams of motion extraction, one short-range and passive and the other long-range and intelligent, but a concatenation of a common mode of initial motion extraction followed by a general inference process.     

Phloem: the long and the short of it

The structure of phloem sieve-element-companion-cell complexes reflects a duality of function: to conduct photoassimilates throughout the plant, and to exchange solutes between the phloem and surrounding tissues. The conceptual integration of these long- and short-distance functions requires the abandonment of a long-cherished concept in phloem physicochemistry, that source-sink turgor differentials control flow. The manifest inability of decentralized organisms such as plants to control phloem translocation centrally disqualifies such differentials as control variables; besides, the phloem is maximally efficient if the pressure differentials are small. Testing this hypothesis and whether turgor differentials are small will require a significant recommitment to studying the quantitative anatomy of phloem.     

Olfactory memory: the long and short of it

It has been proposed that memory for odors does not have a short-term (orworking) memory system. The distinction between short- and long- termmemory in other sensory modalities has been generally supported by threemain lines of evidence: capacity differences between the proposed systems,evidence of differential coding, and differential memory losses inneuropsychological patients. The present paper examines these issues in aneffort to establish a similar distinction for the memory of olfactorystimuli. Each of these lines of evidence is examined in relation to theliterature on olfactory memory. Based on this examination, it seems thatthere is at least preliminary support from each of these lines of evidenceto advocate a distinction between a long- and short-term memory forolfactory stimuli. Emphasis is placed upon the qualitative similarity ofolfactory memory to other memory systems. This similarity is furtherhighlighted through an examination of the literature pertinent to serialposition effects in memory for olfactory stimuli.     

Mitochondrial fusion and fission in the control of apoptosis

Mitochondrial outer membrane permeabilization (MOMP) determines the point-of-no-return of most if not all signal-transduction cascades leading to cell death. It has been postulated that the molecular mechanism leading to MOMP could depend on the activation of the mitochondrial fission machinery mediated by proteins from the dynamin superfamily. However, recent work suggests that, depending on the specific apoptosis induction pathway, mitochondrial fission can occur independently or downstream from MOMP. Moreover, fragmentation of the mitochondrial network can inhibit MOMP and apoptosis in response to a particular range of lethal stimuli, namely those relying on Ca(2+) waves. Failure to transmit the Ca(2+) wave through disconnected mitochondria then interrupts the propagation of the pro-apoptotic signal. Thus, mitochondrial fission can either enhance or reduce the probability of MOMP and consequent cell death, depending on the initial lethal stimulus.     

The long and short of it

It can take twice as long to get a PhD in biomedical sciences in the US as it does in other countries such as the UK and Australia. Are US PhDs worth more, or are there advantages to a speedier system?     

RNA structure: the long and the short of it

The database of RNA structure has grown tremendously since the crystal structure analyses of ribosomal subunits in 2000-2001. During the past year, the trend toward determining the structure of large, complex biological RNAs has accelerated, with the analysis of three intact group I introns, A- and B-type ribonuclease P RNAs, a riboswitch-substrate complex and other structures. The growing database of RNA structures, coupled with efforts directed at the standardization of nomenclature and classification of motifs, has resulted in the identification and characterization of numerous RNA secondary and tertiary structure motifs. Because a large proportion of RNA structure can now be shown to be composed of these recurring structural motifs, a view of RNA as a modular structure built from a combination of these building blocks and tertiary linkers is beginning to emerge. At the same time, however, more detailed analysis of water, metal, ligand and protein binding to RNA is revealing the effect of these moieties on folding and structure formation. The balance between the views of RNA structure either as strictly a construct of preformed building blocks linked in a limited number of ways or as a flexible polymer assuming a global fold influenced by its environment will be the focus of current and future RNA structural biology.     

Anti-malarial humoral immunity: the long and short of it

Humoral immunity is critical for limiting Plasmodium parasite infections and the severity of malaria. Naturally acquired immunity against malaria occurs inefficiently and protection is relatively short-lived. Here we review recent advances and explore emerging hypotheses regarding the molecular and cellular pathways that regulate Plasmodium parasite-specific B cell responses and durable anti-malarial humoral immunity.     

Mitochondrial fusion and fission in cell life and death

Mitochondria are dynamic organelles that constantly fuse and divide. These processes (collectively termed mitochondrial dynamics) are important for mitochondrial inheritance and for the maintenance of mitochondrial functions. The core components of the evolutionarily conserved fusion and fission machineries have now been identified, and mechanistic studies have revealed the first secrets of the complex processes that govern fusion and fission of a double membrane-bound organelle. Mitochondrial dynamics was recently recognized as an important constituent of cellular quality control. Defects have detrimental consequences on bioenergetic supply and contribute to the pathogenesis of neurodegenerative diseases. These findings open exciting new directions to explore mitochondrial biology.     

Plant peptide hormones: The long and the short of it

A polypeptide from tobacco has been found to be processed into multiple functional peptides, each with independent hormone-like activities. This adds to a growing set of small peptides known to function as signal molecules in plants.     

Embryonic axes: the long and short of it in the mouse

Contrary to conventional wisdom, recent studies indicate that, during mouse development, the embryo's anterior-posterior axis shifts from the shorter transverse axis to the orthogonal longer one as the shape of the pre-gastrula-stage embryo is remodelled.     

Mhox and vertebrate skeletogenesis: The long and the short of it

The development of the vertebrate skeleton is under complex genetic control, and good progress is being made towards identifying the genes responsible. A recent paper⁽¹⁾ contributes to this progress by describing transgenic mice in which the homeobox-containing MHox gene has been disrupted. MHox(?/?) mice have a range of skeletal defects, involving loss or shortening of structures in the skull, face and limb. Puzzling features of the MHox(?/?) mutation, which has similar effects on bones with very different embryological origins and yet spares other bones completely, may hold clues to the mechanisms that shape the skeleton. MHox(?/?) mice, used in conjunction with other skeletal mutants, will be important tools for exploring these mechanisms further.     

Comparing de novo genome assembly: the long and short of it

Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers--both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies--are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing "next-generation" assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium.