Fundamental properties of intensity, form, and motion perception in the visual nervous systems of Calliphora phaenicia and Musca domestica

Several classes of interneurons in the optic lobes and brain of the insects, Musca domestica and Calliphora phaenicia, have been studied in detail. Visual stimuli have been categorized on the basis of the properties of intensity, form, and motion. Response characteristics of the classes of neural units are described with respect to these three classes of visual stimuli. While those units that detect motion in select directions have a tonic response, form detection units have a phasic response only. Through correlation of the responses of these classes with visual stimuli, it is shown that these units integrate the responses of other units which have very small visual fields. The small-field units are presumed to integrate the output of a small group of adjacent retinula cells and to respond differentially to intensity, form, and motion. It is shown that the response of both form and motion detection units is independent of the direction of pattern intensity gradation. As a consequence of this independence, it is further shown that failure to detect motion properly must start at a spatial wavelength four times the effective sampling station spacing rather than twice as has been predicted previously.     

Exploring overlapping functional units with various structure in protein interaction networks

Revealing functional units in protein-protein interaction (PPI) networks are important for understanding cellular functional organization. Current algorithms for identifying functional units mainly focus on cohesive protein complexes which have more internal interactions than external interactions. Most of these approaches do not handle overlaps among complexes since they usually allow a protein to belong to only one complex. Moreover, recent studies have shown that other non-cohesive structural functional units beyond complexes also exist in PPI networks. Thus previous algorithms that just focus on non-overlapping cohesive complexes are not able to present the biological reality fully. Here, we develop a new regularized sparse random graph model (RSRGM) to explore overlapping and various structural functional units in PPI networks. RSRGM is principally dominated by two model parameters. One is used to define the functional units as groups of proteins that have similar patterns of connections to others, which allows RSRGM to detect non-cohesive structural functional units. The other one is used to represent the degree of proteins belonging to the units, which supports a protein belonging to more than one revealed unit. We also propose a regularizer to control the smoothness between the estimators of these two parameters. Experimental results on four S. cerevisiae PPI networks show that the performance of RSRGM on detecting cohesive complexes and overlapping complexes is superior to that of previous competing algorithms. Moreover, RSRGM has the ability to discover biological significant functional units besides complexes.     

Chemical and genomic evolution of enzyme-catalyzed reaction networks

There is a tendency that a unit of enzyme genes in an operon-like structure in the prokaryotic genome encodes enzymes that catalyze a series of consecutive reactions in a metabolic pathway. Our recent analysis shows that this and other genomic units correspond to chemical units reflecting chemical logic of organic reactions. From all known metabolic pathways in the KEGG database we identified chemical units, called reaction modules, as the conserved sequences of chemical structure transformation patterns of small molecules. The extracted patterns suggest co-evolution of genomic units and chemical units. While the core of the metabolic network may have evolved with mechanisms involving individual enzymes and reactions, its extension may have been driven by modular units of enzymes and reactions.     

Babesia bovis, Babesia bigemina, Babesia canis, Babesia microti and Babesia rodhaini: comparison of ribosomal RNA gene organization.

The three ribosomal DNA (rDNA) units have been cloned from an Australian isolate of Babesia bigemina. The organization of the units is very similar to that reported for a Mexican isolate of B. bigemina. In Babesia canis four rDNA units have been identified. Both Babesia rodhaini and Babesia microti contain two different rDNA units. A small number of different rDNA units appears to be a common feature of this group of Protozoa. Restriction enzyme analysis of the rDNA units form these species and B. bovis suggests that the genus Babesia as currently defined does indeed include two distinct groups of organisms namely, B. bovis, B. bigemina and B. canis and B. rodhaini and B. microti.     

Mechanisms underlying the regulation of motor unit contraction in the skeletal muscle.

The control of movements is made posible thanks to the activity of motor units in skeletal muscles. In the present paper the influence of frequency and pattern of motoneuronal firing on the tension of contraction and the tension-time area is presented and discussed. The most resistant to fatigue slow-twitch motor units are low susceptible to changes in a pattern of impulses and therefore they are well prepared to participate in long-lasting movements at low but rather stable levels of tension. Moreover, their contraction is very effective and it is performed at a low metabolic charge. Fast-twitch units have lower resistance to fatigue and they have higher tension but they have high susceptibility to a pattern of pulses and their tension can be effectively regulated by an increase or a decrease in the interpulse interval. Therefore, fast motor units are specialized to participate in the regulation of the movement force. The existence of different functional groups of motor units in skeletal muscles enables the performance of different motor tasks very effectively and at possibly low metabolic costs.     

Coding of envelope modulation in the auditory nerve and anteroventral cochlear nucleus.

We have investigated responses of the auditory nerve fibres (ANFS) and anteroventral cochlear nucleus (AVCN) units to narrowband 'single-formant' stimuli (SFSS). We found that low and medium spontaneous rate (SR) ANFS maintain greater amplitude modulation (AM) in their responses at high sound levels than do high SR units when sound level is considered in dB SPL. However, this partitioning of high and low SR units disappears if sound level is considered in dB relative to unit threshold. Stimuli with carrier frequencies away from unit best frequency (BF) were found to generate higher AM in responses at high sound levels than that observed even in most low and medium SR units for stimuli with carrier frequencies near BF. AVCN units were shown to have increased modulation depth in their responses when compared with high SR ANFS with similar BFS and to have increased or comparable modulation depth when compared with low SR ANFS. At sound levels where AM almost completely disappears in high SR ANFS, most AVCN units we studied still show significant AM in their responses. Using a dendritic model, we investigated possible mechanisms of enhanced AM in AVCN units, including the convergence of inputs from different SR groups of ANFS and a postsynaptic threshold mechanism in the soma.     

A structure for amplified DNA

We have employed gene transfer to generate cell lines in which a chromosomal region consisting solely of defined DNA sequences has undergone gene amplification. We have analyzed recombinant clones from the amplified array to determine the physical structure of amplified DNA in the cell lines. The amplified DNA we have analyzed consists of a tandem array of at least 20 individual repeating units. The individual units are contiguous, and are joined to one another by homologous recombination between repeated sequences. At first approximation, all homologous recombinations are permitted such that crossing-over may occur between any two repeated sequences. Since individual units contain multiple repeated elements, the array is not a regularly repeating structure. The individual units within the array are heterogeneous, both in size and in sequence content. These observations suggest models of gene amplification which involve multiple cycles of unscheduled DNA replication at a single locus, followed by multiple recombination events which serve to link individual units to one another and ultimately to the chromosome.     

Thermal stability of homologous functional units of Helix pomatia hemocyanin does not correlate with carbohydrate content

The thermal stability of the eight functional units of beta-hemocyanin of the gastropodan mollusc Helix pomatia was investigated by FTIR spectroscopy. Molluscan hemocyanin functional units have a molecular mass of approximately 50 kDa and generally contain three disulfide bridges: two in the mainly alpha-helical N-terminal domain and one in the C-terminal beta-sheet domain. They show more than 50% sequence homology and it is assumed that they adopt a similar conformation. However, the functional units of H. pomatiabeta-hemocyanin, designated HpH-a to HpH-h, differ considerably in their carbohydrate content (0-18 wt%). Most functional units are exceptionally stable with a melting temperature in the range 77-83 degrees C. Two functional units, HpH-b and HpH-c, however, have a reduced stability with melting temperature values of 73 degrees C and 64 degrees C, respectively. Although the most glycosylated functional unit (HpH-g) has the highest temperature stability, there is no linear correlation between the degree of glycosylation of the functional units and the unfolding temperature. This is ascribed to variations in secondary structure as well as in glycan attachment sites. Moreover, the disulfide bonds might play an important role in the conformational stability of the functional units. Sequence comparison of molluscan hemocyanins suggests that the less stable functional units, HpH-b and HpH-c, similar to most of their paralogous counterparts, lack the disulfide bond in the C-terminal domain.     

Motor unit number estimation--a Bayesian approach

All muscle contractions are dependent on the functioning of motor units. In diseases such as amyotrophic lateral sclerosis (ALS), progressive loss of motor units leads to gradual paralysis. A major difficulty in the search for a treatment for these diseases has been the lack of a reliable measure of disease progression. One possible measure would be an estimate of the number of surviving motor units. Despite over 30 years of motor unit number estimation (MUNE), all proposed methods have been met with practical and theoretical objections. Our aim is to develop a method of MUNE that overcomes these objections. We record the compound muscle action potential (CMAP) from a selected muscle in response to a graded electrical stimulation applied to the nerve. As the stimulus increases, the threshold of each motor unit is exceeded, and the size of the CMAP increases until a maximum response is obtained. However, the threshold potential required to excite an axon is not a precise value but fluctuates over a small range leading to probabilistic activation of motor units in response to a given stimulus. When the threshold ranges of motor units overlap, there may be alternation where the number of motor units that fire in response to the stimulus is variable. This means that increments in the value of the CMAP correspond to the firing of different combinations of motor units. At a fixed stimulus, variability in the CMAP, measured as variance, can be used to conduct MUNE using the "statistical" or the "Poisson" method. However, this method relies on the assumptions that the numbers of motor units that are firing probabilistically have the Poisson distribution and that all single motor unit action potentials (MUAP) have a fixed and identical size. These assumptions are not necessarily correct. We propose to develop a Bayesian statistical methodology to analyze electrophysiological data to provide an estimate of motor unit numbers. Our method of MUNE incorporates the variability of the threshold, the variability between and within single MUAPs, and baseline variability. Our model not only gives the most probable number of motor units but also provides information about both the population of units and individual units. We use Markov chain Monte Carlo to obtain information about the characteristics of individual motor units and about the population of motor units and the Bayesian information criterion for MUNE. We test our method of MUNE on three subjects. Our method provides a reproducible estimate for a patient with stable but severe ALS. In a serial study, we demonstrate a decline in the number of motor unit numbers with a patient with rapidly advancing disease. Finally, with our last patient, we show that our method has the capacity to estimate a larger number of motor units.     

The spread of sequence variants in Rattus satellite DNAs

The genus Rattus has two related families of satellite DNA: Satellite I consists of tandem arrays of a 370 base pair repeat unit which is a dimer of two 185 base pair portions (a, b) which are about 60% homologous. Satellite I' consists of tandem arrays of a 185 base pair repeat unit (a') which is about 85% homologous to a and 60% homologous to b. R. norvegicus contains only satellite I but R. rattus contains both satellites I and I'. We examined certain aspects of satellite DNA evolution by comparing the spacing at which variant repeat units of each satellite have spread among non-variant repeat units in these two species. With but one exception, in R. rattus, 15 different variant repeat units have spread among non-variant repeat units of satellite I, with a spacing equal to the length of the (a,b) dimer. Similarly, fourteen different variant repeat units of the monomeric satellite I' have mixed among non-variant repeat units with a spacing equal to the length of the (a') monomer. These results suggest that a mechanism involving homologous interaction among satellite sequences could account for the spread of variant family members. We also found that a sequence variant present in certain portions of the dimeric repeat unit of satellite I is more efficiently amplified (or less efficiently corrected) than variants occurring in other regions. This was not true for the monomeric repeat unit of satellite I'.     

Scaling effects of grazing in a semi-arid grassland

Abstract. Previous studies have demonstrated relationships between spatial scale and spatial pattern and developed general hypotheses of scaling effects. Few studies, however, have examined the interactive relationship between scale and pattern-driving processes such as grazing. The goal of this study is to evaluate scale-dependent patterns across three spatial scales for three grazing intensities over 45 yr and to identify some mechanisms that may be associated with scale related differences. Correlation analysis and analysis of the coefficients of variation indicate that the relationships between units are dependent upon spatial scale and treatment. Across all grazing treatments, the relationship between units of the same scale becomes stronger as the spatial scale is increased. However, the rate of increase in the correlation coefficient is different for each treatment. The coefficient of variation responded inversely across scales with the greatest variation between small-scale units and little difference between the intermediate- and large scales. In addition to different relationships between units at each scale, differences in heterogeneity within treatments over time is illustrated by the relationship between small-scale units within each treatment and their associated larger scale units. The strongest relationship occurred in the heavily grazed treatments where correlation coefficients of small-scale units with intermediate- and large-scale units were ca. 0.60, indicating similar dynamics across scales. For the moderately grazed and ungrazed treatments this relationship varied from 0.40 to 0.47. Results from this study suggest that grazing alters scaling effects. Variability between small-scale units was greatest in the ungrazed treatment which had greater heterogeneity and less predictability than grazed treatments because of the influence of grazing on plant morphology, demography and composition. At the intermediate scale, relationships between units were fairly similar with the least variation occurring in the moderately grazed treatment. Alternatively, variation between large-scale units was greatest in the moderately grazed treatment because of the relationship between rest cycles, weather patterns, and patch grazing. Therefore, grazing can have a positive, a negative, or no influence on heterogeneity between units depending upon the scale of observation. Evaluation of long-term dynamics across these treatments at the same small spatial scale results in different variances within each treatment which may violate assumptions of some statistical and experimental designs. Therefore, evaluations of temporal dynamics should consider scale relative to the relationship between plant size, density and longevity (relative scale).     

A discrete fully recurrent network of max product units for associative memory and classification

This paper defines the truncated normalized max product operation for the transformation of states of a network and provides a method for solving a set of equations based on this operation. The operation serves as the transformation for the set of fully connected units in a recurrent network that otherwise might consist of linear threshold units. Component values of the state vector and outputs of the units take on the values in the set [0, 0.1,..., 0.9, 1]. The result is a much larger state space given a particular number of units and size of connection matrix than for a network based on threshold units. Since the operation defined here can form the basis of transformations in a recurrent network with a finite number of states, fixed points or cycles are possible and the network based on this operation for transformations can be used as an associative memory or pattern classifier with fixed points taking on the role of prototypes. Discrete fully recurrent networks have proven themselves to be very useful as associative memories and as classifiers. However they are often based on units that have binary states. The effect of this is that the data to be processed consisting of vectors in R(n) have to be converted to vectors in [0, 1]m with m much larger than n since binary encoding based on positional notation is not feasible. This implies a large increase in the number of components. The effect can be lessened by allowing more states for each unit in our network. The network proposed demonstrates those properties that are desirable in an associative memory very well as the simulations show.     

First report on polysaccharides of Asterochloris and their potential role in the lichen symbiosis

A structural study of the carbohydrates from the aposymbiotically cultured Asterochloris sp., the algal symbiont of the lichen Cladina confusa was carried out for the first time. A xylorhamnogalactofuranan was purified and was predominated by (1-->3)-linked galactofuranosyl units with sidechains in position 6 on approximately 6.4% of the units. The sidechains have galactofuranosyl units 5-O and 6-O-substituted, as well rhamnopyranosyl units 2-O, 3-O and 2,3-di-O-substituted. Xylose was detected only as nonreducing end units, together with galactofuranosyl units. Amylose and a beta-(1-->4)-xylan were also present. These polysaccharides have not been found in the symbiotic thallus of C. confusa, which contained only glucans, galactomannoglucan and galactoglucomannan. A potential role of these carbohydrates in lichen recognition proccess is also discussed.     

Relationship between the tension-time area and the frequency of stimulation in motor units of the rat medial gastrocnemius muscle.

The tension-time area is an estimation of the work performed by contracting motor units. The relationship between tension and frequency of stimulation and between tension-time area and frequency have been studied on 148 single motor units of the rat medial gastrocnemius muscle, under isometric conditions. Motor units were classified as fast fatigable (FF), fast resistant to fatigue (FR) or slow (S). Trains of stimuli of increasing frequency and constant duration were used. For all motor units a half of the maximum tetanic tension corresponded to lower frequencies compared to frequencies at a half of the maximum tension-time area. Moreover, the slopes of tension-frequency and area-frequency curves (change of tension or area per 1 Hz rise in frequency) were higher for slow than for fast motor units. The tension-time area per one pulse was calculated for different frequencies of stimulation. For slow units the maximum area per pulse corresponded to significantly lower frequencies than for fast ones, especially of FF type. However, for all three types of motor units this optimal frequency corresponded to sub-fused tetani with a tension of about 75% of the maximum tension, and with the fusion index slightly over 0.90. The absolute values of the maximum tension-time area per pulse revealed that in one contraction within the tetanus, slow units are generating greater work than FR units. The work performed by FF units is nearly two times larger than for S units, although the tension of slow units is over eight times lower. The presented results reveal that the contraction of slow motor units is much more effective than was suggested based on their low tension.     

Managing the risk of comparing estimated breeding values across flocks or herds through connectedness: a review and application

Comparing predicted breeding values (BV) among animals in different management units (e.g. flocks, herds) is challenging if units have different genetic means. Unbiased estimates of differences in BV may be obtained by assigning base animals to genetic groups according to their unit of origin, but units must be connected to estimate group effects. If many small groups exist, error of BV prediction may be increased. Alternatively, genetic groups can be excluded from the statistical model, which may bias BV predictions. If adequate genetic connections exist among units, bias is reduced. Several measures of connectedness have been proposed, but their relationships to potential bias in BV predictions are not well defined. This study compares alternative strategies to connect small units and assesses the ability of different connectedness statistics to quantify potential bias in BV prediction. Connections established using common sires across units were most effective in reducing bias. The coefficient of determination of the mean difference in predicted BV was a perfect indicator of potential bias remaining when comparing individuals in separate units. However, this measure is difficult to calculate; correlated measures such as prediction errors of differences in unit means and correlations among prediction errors are suggested as practical alternatives.     

Sensory responses and movement-related activities in extrinsic neurons of the cockroach mushroom bodies

We have previously reported that most units in the input regions of the cockroach mushroom bodies have activities related to sensory inputs, while the majority of units in the output regions are related to movements of the animal. In the present study, we were able to attain a more satisfactory isolation of single units by using thinner wires and further characterize the activities of units in the mushroom body output regions. Forty-one units recorded here were classified into three types: sensory, movement-related, and sensori-motor units. Different units from each group exhibited a great variety in activities. Some movement-related and sensori-motor units exhibited activity preceding the onset of movements. We propose that the mushroom body participates in the integration of a variety of sensory and motor signals, possibly for initiating and maintaining motor action. While different neurons displayed a great diversity of responses, the activities of multiple neurons recorded simultaneously exhibited similar, but not identical, responses. These neurons appeared to locate adjacent to each other and may represent a cluster of extrinsic neurons that act synergistically to transmit a specific set of mushroom body output signals. Accepted: 5 May 1999     

Heterogeneity of pumpkin ribosomal DNA

The ribosomal DNA (rDNA) of Cucurbita pepo L. has been found to consist of tandemly arrayed repeat units, most of which are 10 kilobases in length. Thirty-six repeat units, cloned into the HindIII site of pACYC 177, fall into seven classes which differ from each other in length and/or nucleotide sequence. Most of the heterogeneity occurs in noncoding portions of the repeat unit although there is some nucleotide sequence variation in the coding portion as well. Heterogeneity of base modification was observed in genomic rDNA of which two examples are: (a) all of the repeat units have three BamHI sites, one of which is unavailable for restriction in about half of the units and (b) all of the CCGG sites except one are methylated at the internal cytidine in many of the units; a second site is unmethylated in some of the units and in a very few units a third site remains unmethylated.     

A commentary on muscle unit properties in cat hindlimb muscles

A broad survey of muscle unit properties in 14 muscles of the cat hind limb is presented which emphasizes some general features of unit properties in mammalian muscles. A more detailed analysis of muscle unit properties in three muscles of the posterior compartment of the lower leg is then presented using Burke's tetrapartite (FF, FI or F (Int.), FR, and S) unit classification scheme. Our data on the properties of motor units in cat tibialis posterior (TP) have been compared to those generated by Burke and colleagues on units in flexor digitorum longus (FDL) and medial gastrocnemius (MG). In all three muscles, twitch contraction time was distinctly slower for type S units and specific tension outputs were substantially greater for type FF units than for type S units. The innervation ratios of type FR units were slightly lower than for type S units but the specific tension of the FR units was closer to FF units than to type S units. The FF units controlled 70–74% of the cumulative force output of each muscles, indicating a substantial capacity for powerful rapid contractions of all three of these muscles despite their differences in “size,” action, and force generation. Distinctive features of the three muscles included differences in the unit types' force producing capabilities and in the relative representation of “nonfatigable” type FR and S units in each muscle. In particular, TP is endowed with some unusually powerful type FF units and a high percentage (42%) of type S units. In contrast, FDL has units that develop relatively little force and an unusually high representation (56%) of type FR units. The possible relationships between these muscle features and their presumed role in posture and locomotion is discussed.     

Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.

Tandemly repeated DNA families appear to undergo concerted evolution, such that repeat units within a species have a higher degree of sequence similarity than repeat units from even closely related species. While intraspecies homogenization of repeat units can be explained satisfactorily by repeated rounds of genetic exchange processes such as unequal crossing over and/or gene conversion, the parameters controlling these processes remain largely unknown. Alpha satellite DNA is a noncoding tandemly repeated DNA family found at the centromeres of all human and primate chromosomes. We have used sequence analysis to investigate the molecular basis of 13 variant alpha satellite repeat units, allowing comparison of multiple independent recombination events in closely related DNA sequences. The distribution of these events within the 171-bp monomer is nonrandom and clusters in a distinct 20- to 25-bp region, suggesting possible effects of primary sequence and/or chromatin structure. The position of these recombination events may be associated with the location within the higher-order repeat unit of the binding site for the centromere-specific protein CENP-B. These studies have implications for the molecular nature of genetic recombination, mechanisms of concerted evolution, and higher-order structure of centromeric heterochromatin.     

Comparative structure and evolution of goat and sheep satellite I DNAs.

The satellite I DNAs of domestic goat (Capra hircus) and domestic sheep (Ovis aries) have been studied using molecular hybridisation and restriction enzyme analysis. Both satellite DNAs are composed of repeat units of 820 base pairs in length, but their restriction maps, although similar, differ in certain respects. Thus the majority of sheep satellite I repeat units have two EcoRI sites and one AluI site, whereas the majority of goat satellite I repeat units have one EcoRI site and two AluI sites. The sheep satellite I repeat units with the two EcoRI sites are much more homogeneous than the repeats forming the remainder of the satellite, as judged by the difference in the melting temperatures of native and reassociated molecules. DNAs from species of wild sheep and goats were screened for the presence of these repeat units, and they appear to have been amplified during the radiation of the Ovis genus. Goat satellite I is composed of a single sequence type which has changed through base substitution until the sequence now shows considerable heterogeneity. It is proposed that the major sequence types of these two satellite DNAs were amplified by different saltatory replication events at different times in the evolution of the group.