Temporal coding in vision: coding by the spike arrival times leads to oscillations in the case of moving targets

The ‘oscillations’ which have been observed in the visual cortex of cats and monkeys in the case of moving targets are discussed in relation to a temporal coding based on the arrival times of spikes or bursts. A decoding process for this temporal coding is proposed in which neurons work in a correlator mode. In the case of motion analysis, periodic resetting is needed to avoid information jamming. This resetting is proposed to be responsible for the ‘oscillations’. Good initial synchronization is required for the decoding process to be performed efficiently. A diffusive process based on interdendritic ionic currents is proposed and shown to operate efficiently, without any loss of spatial and temporal resolving powers. Received: 2 June 1994 / Accepted in revised form: 23 January 1996     

Delimitation of a QTL region controlling cold tolerance at booting stage of a cultivar, ‘Lijiangxintuanheigu’, in rice, <Emphasis Type="Italic">Oryza sativa</Emphasis> L.

Low temperature at the booting stage of rice causes male sterility resulting in severe yield loss. Cold tolerance has long been an important objective in rice breeding. We identified a quantitative trait locus (QTL) for cold tolerance on the long arm of chromosome 3 from the cold-tolerant breeding line ‘Ukei 840’ by using F₂ and BC₁F₂ populations from crosses between ‘Ukei 840’ and ‘Hitomebore’. The cold tolerance of ‘Ukei 840’ is derived from the Chinese cultivar ‘Lijiangxintuanheigu’. The effect of this QTL on cold tolerance was confirmed by developing ‘Hitomebore’ chromosome segment substitution lines having ‘Lijiangxintuanheigu’ alleles on chromosome 3. By producing recombinants in chromosome 3, the QTL region for cold tolerance was delimited to the region of about 1.2-Mb region between RM3719 and RM7000. All lines heterozygous for the QTL showed seed fertilities as low as that of ‘Hitomebore’, suggesting that the ‘Lijiangxintuanheigu’ allele for cold tolerance in the QTL region is recessive. Determination of a 1.2-Mb nucleotide sequence of ‘Ukei 840’ and comparison with the published genomic sequence of ‘Nipponbare’ showed 254 SNPs, of which 11 were in coding regions of genes, seven in five genes being non-synonymous. SNPs were detected in the 5-kb upstream regions of 89 genes, but no differences of gene expression levels were detected between alleles of these genes. Although further delimitation is required to identify the gene responsible for cold tolerance of ‘Lijiangxintuanheigu’, SNP markers developed here will be useful for marker-assisted selection in a breeding program using ‘Lijiangxintuanheigu’ as a donor of cold tolerance.     

Inflammation,Aging, and Cancer: Tumoricidal Versus Tumorigenesis of Immunity

Acute inflammation is a highly regulated defense mechanism of immune system possessing two well-balanced and biologically opposing arms termed apoptosis (‘Yin’) and wound healing (‘Yang’) processes. Unresolved or chronic inflammation (oxidative stress) is perhaps the loss of balance between ‘Yin’ and ‘Yang’ that would induce co-expression of exaggerated or ‘mismatched’ apoptotic and wound healing factors in the microenvironment of tissues (‘immune meltdown’). Unresolved inflammation could initiate the genesis of many age-associated chronic illnesses such as autoimmune and neurodegenerative diseases or tumors/cancers. In this perspective ‘birds’ eye’ view of major interrelated co-morbidity risk factors that participate in biological shifts of growth-arresting (‘tumoricidal’) or growth-promoting (‘tumorigenic’) properties of immune cells and the genesis of chronic inflammatory diseases and cancer will be discussed. Persistent inflammation is perhaps a common denominator in the genesis of nearly all age-associated health problems or cancer. Future challenging opportunities for diagnosis, prevention, and/or therapy of chronic illnesses will require an integrated understanding and identification of developmental phases of inflammation-induced immune dysfunction and age-associated hormonal and physiological readjustments of organ systems. Designing suitable cohort studies to establish the oxido-redox status of adults may prove to be an effective strategy in assessing individual’s health toward developing personal medicine for healthy aging.     

Impact of sulfur on density of <Emphasis Type="Italic">Tetranychus pacificus</Emphasis> (Acari: Tetranychidae) and <Emphasis Type="Italic">Galendromus occidentalis</Emphasis> (Acari: Phytoseiidae) in a central California vineyard

Sulfur is the oldest and most widely used fungicide in the vineyards of California, where it is used for control of powdery mildew (Uncinula necator [Schw.] Burr). For decades, sulfur use has been associated with outbreaks of Tetranychus pacificus McGregor (Acari: Tetranychidae) on cultivated grapes in the San Joaquin Valley. I undertook large-scale field studies to test this association, to evaluate the impact of sulfur on Galendromus occidentalis (Nesbit) (Acari: Phytoseiidae), a major predator of T. pacificus, and to determine if timing of sulfur applications with respect to grape bloom has an impact on T. pacificus density. The studies took place in a 32 ha vineyard in Fresno County, and all fungicide applications were made with commercial-scale equipment. In 1998 a ‘high sulfur’ treatment, a combination of wettable sulfur and sulfur dust, was compared to ‘low sulfur,’ in which demethylation inhibitor (DMI) fungicides partially substituted for sulfur. In 1999 treatments were ‘sulfur,’ ‘DMI,’ ‘sulfur pre-bloom’ (here sulfur was applied prior to grape bloom, in late May, and then DMIs were applied until mid-season) and ‘sulfur post-bloom’ (the reverse of ‘sulfur pre-bloom’). In each year, the T. pacificus population increase came after the end of fungicide applications, and results clearly show a relationship between sulfur use and T. pacificus density. In 1998, mean T. pacificus density was 2.7 times higher and mean G. occidentalis density 2.5 times higher in ‘high sulfur’ compared to ‘low sulfur.’ In 1999, the highest T. pacificus counts were in the ‘sulfur’ and ‘sulfur pre-bloom’ treatments, 4.8 times higher than ‘sulfur post-bloom’ and 2 times higher than ‘DMIs.’ Density of G. occidentalis was 2.3 times as high in ‘sulfur’ or ‘sulfur pre-bloom’ than ‘DMIs.’ The predator/prey ratio was not significantly different among treatments in 1998, but in 1999 it was highest in the ‘sulfur pre-bloom’ treatment. In 1999, density of Homeopronematus anconai (Baker) (Acari: Tydeidae) was 2.7 times higher in ‘sulfur pre-bloom’ compared to ‘sulfur,’ and higher by 2.7 times in ‘DMI’ compared to ‘sulfur post-bloom,’ suggesting a negative effect of sulfur on this tydeid. These results do not support the hypotheses that the cause of the increase in T. pacificus density is due to negative effects of sulfur on phytoseiids or tydeids. Rather, it appears that a plant-based explanation is likely, first, because of the differences in pre-bloom versus post-bloom sulfuring, and second, because of the long lag time between the end of the sulfur applications and the corresponding increase in spider mite density.     

Strict paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in intraspecific crosses of kiwifruit

 Previous studies have established that chloroplasts are inherited paternally in Actinidia interspecific crosses. However, fertilisation problems in interspecific crosses may affect the transmission of organelles. Six female clones, i.e. ‘Abbott’, ‘Bruno’, ‘Greensill’, ‘Hayward’, ‘Jones’, ‘Monty’, and four male clones were used to identify cpDNA polymorphisms within the cultivated kiwifruit species A. deliciosa. The restriction patterns by HpaII of a chloroplast fragment amplified by PCR with a pair of universal primers revealed a polymorphism at the intraspecific level. The inheritance of cpDNA in 143 seedlings from three intraspecific crosses in kiwifruit (Actinidia deliciosa) was studied. All offspring displayed the restriction pattern of the paternal parent, indicating that maternal inheritance of cpDNA in kiwifruit is rare at best. Strict maternal inheritance of mtDNA was confirmed in the same crosses used to investigate cpDNA transmission. Studies of cytoplasmic inheritance in the Actinidia genus represent to date the best documented report of differential organelle inheritance of cpDNA and mtDNA in angiosperms. Received: 10 November 1998 / Accepted: 14 December 1998     

Why is ‘incommensurability’ a problem?

The origins of the ‘incommensurability problem’ and its central aspect, the ‘meaning variance thesis’ are traced to the successive collapse of several distinctions maintained by the standard empiricist account of meaning in scientific theories. The crucial distinction is that between a conceptual structure and a theory. The ‘thesis’ and the ‘problem’ follow from critiques of this distinction by Duhem, Quine and Feyerabend. It is maintained that, rather than revealing the ‘problem’, the arguments leading to it simply show the inadequacy of the reductionist theory of meaning. The genuine remaining problem is that of the development of a new theory of meaning in science. This paper was written while I was Visiting Fulbright Research Scholar at the University of Leiden and the Museum Boerhaave, Leiden.     

Genomes were forged by massive bombardments with retroelements and retrosequences

Retroposition is an efficient route to move coding regions around the genome ‘in search’ of novel regulatory elements and to shotgun regulatory elements into the genome ‘in search’ of new target genes. The templates for such retrogenes are mRNAs, and for regulatory retronuons (nuon=any definable nucleic acid sequence) usually small non-mRNAs. An example in support of the ‘master gene’ model for SINEs (short interspersed repetive elements) is provided with neuronal BC1 RNA. Furthermore, an alternative explanation of LINE (long interspersed repetive elements) involvement in the generation of SINEs is given. I will also argue that the status of transposable elements with respect to the host resembles more symbiosis than parasitiasis and that host defense is often lenient as if even to ‘tolerate or support’ retronuons. Finally the paradox of evolution's lack of foresight and the future exaptive use of retronuons is being dealt with by referring to W.F. Doolittle's ‘Hierarchical Approaches to Genome Evolution’. This revised version was published online in July 2006 with corrections to the Cover Date.     

Selection of Highly Informative Microsatellite Markers to Identify Pollen Donors in ‘Hass’ Avocado Orchards

‘Hass’ is the most popular avocado (Persea americana Mill.) cultivar in the world. It has been characterized as a crop requiring cross-pollination. However, the potential extent of self-pollination and the most effective pollen donors (best cross-pollinizing cultivars) have not been determined. In this study, 56 markers were screened against ‘Hass’ and nine commonly used pollinizing cultivars grown in southern California: ‘Bacon,’ ‘Ettinger,’ ‘Fuerte,’ ‘Harvest,’ ‘Lamb Hass,’ ‘Marvel,’ ‘Nobel,’ ‘Sir Prize,’ and ‘Zutano.’ Seventeen microsatellite, i.e., simple sequence repeat (SSR) markers, were found to be very promising for paternity analysis. Four highly informative SSR markers were selected to accurately and unequivocally identify pollen parents of ‘Hass’ fruit from an orchard interplanted with these pollinizing cultivars. From 2003 to 2006, 7,984 ‘Hass’ fruit were analyzed for their paternity. Overall, the pollen parents of 99.55% of the analyzed fruit could be unequivocally identified with a single multiplex polymerase chain reaction (PCR). Only 36 fruits (<0.45%) required a second PCR reaction to reach unequivocal identification of the pollen parents.     

Isolation and characterization of dominant dwarf mutants, <Emphasis Type="Italic">Slr1-d</Emphasis>, in rice

sd1 is known as the ‘green revolution’ gene in rice because its application in rice breeding has dramatically increased rice yield. Since the ‘green revolution,’ sd1 has been extensively used to produce modern semi-dwarf varieties. The extensive use of limited dwarfing sources may, however, cause a bottleneck effect in the genetic background of rice varieties. To circumvent this problem, novel and useful sources of dwarf genes must be identified. In this study, we identified three semi-dominant dwarf mutants. These mutants were categorized as dn-type dwarf mutants according to the elongation pattern of internodes. Gibberellin (GA) response tests showed that the mutants were still responsive to GA, although at a reduced rate. Map-based cloning revealed that the dwarf phenotype in these mutants was caused by gain-of-function mutations in the N-terminal region of SLR1. Degradation of the SLR1 protein in these mutants occurred later than in the wild type. Reduced interaction abilities of the SLR1 protein in these mutants with GID1 were also observed using the yeast two-hybrid system. Crossing experiments indicated that with the use of an appropriate genetic background, the semi-dominant dwarf alleles identified in this study could be used to alleviate the deficiency of dwarfing genes for breeding applications.     

A parentage study of closely related Ukrainian wine grape varieties using microsatellite markers

Four bred grapevine varieties released for commercial cultivation in Ukraine, namely ‘Antey Magarachskii’, ‘Rubinovyi Magaracha’, ‘Granatovyi Magaracha’ and ‘Rubin Golodrigi’, and their putative parental forms were genotyped using six microsatellite loci. Genotypes were compared with breeding records to verify genetic relationships among varieties. Results of the analysis confirmed four of six parent-offspring relationships. Results of the analysis allow to assume that genotype ‘Seyve Villard 20347’ is the direct parent of ‘Antey Magarachskii’ instead of its grandparent. The first-studied accession believed to be that of ‘Granatovyi Magaracha’ was identified as impurity. In order to verify the parentage of ‘Granatovyi Magaracha’, rest accessions of that variety and its putative parent ‘Antey Magarachskii’ were additionally genotyped at 13 nuclear loci and at three chloroplast loci. The parent-offspring relationship was confirmed, as all ‘Granatovyi Magaracha’ accessions had a common allele with the parent variety ‘Antey Magarachskii’ at each locus and the same chlorotype A. Different ‘Granatovyi Magaracha’ accessions could have been obtained via vegetative propagation of two seedlings which arose from one crossing.     

Where does heteroclisis come from? Evidence from Romanian dialects

This study examines some cases of heteroclisis in the history of Romanian dialects, and concludes that the data call for a reconsideration of Stump’s distinction (Language 82:279–322, 2006) between ‘cloven’ heteroclisis, where the intraparadigmatic ‘split’ is aligned with some morphosyntactic feature distinction, and ‘fractured’ heteroclisis, where this is not the case and the pattern of heteroclisis is purely morphological. Stump’s account creates the impression that the ‘cloven’ variety is universally predominant, and that the ‘fractured’ variety tends to follow very closely the available ‘cloven’ patterns of the language. I shall suggest, instead, that the ‘fractured-only’ situation may in fact underlie heteroclisis cross-linguistically, the phenomenon being in general sensitive not directly to morphosyntactic content, but rather to characteristic, and often purely ‘morphomic’, patterns of stem-allomorphy. Research for this paper was undertaken as part of the Arts and Humantities Research Council-funded project Autonomous Morphology in Diachrony: comparative evidence from the Romance Languages, currently being conducted at Oxford University.     

Expression of an engineered cysteine proteinase inhibitor (Oryzacystatin-IΔD86) for nematode resistance in transgenic rice plants

 We have used a genotype-independent transformation system involving particle gun bombardment of immature embryos to genetically engineer rice as part of a programme to develop resistance to nematodes. Efficient tissue culture, regeneration, DNA delivery and selection methodologies have been established for elite African varieties (‘ITA212’, ‘IDSA6’, ‘LAC23’, ‘WAB56-104’). Twenty-five transformed clones containing genes coding for an engineered cysteine proteinase inhibitor (oryzacystatin-IΔD86, OC-IΔD86), hygromycin resistance (aphIV) and β-glucuronidase (gusA) were recovered from the four varieties. Transformed plants were regenerated from all clones and analysed by PCR, Southern and western blot. Detectable levels of OC-IΔD86 (up to 0.2% total soluble protein) in plant roots were measured in 12 out of 25 transformed rice lines. This level of expression resulted in a significant 55% reduction in egg production by Meloidogyne incognita. Received: 4 August 1997 / Accepted: 22 August 1997     

Tuning the cochlea: wave-mediated positive feedback between cells

Frequency analysis by the mammalian cochlea is traditionally thought to occur via a hydrodynamically coupled ‘travelling wave’ along the basilar membrane. A persistent difficulty with this picture is how sharp tuning can emerge. This paper proposes, and models, a supplementary or alternative mechanism: it supposes that the cochlea analyses sound by setting up standing waves between parallel rows of outer hair cells. In this scheme, multiple cells mutually interact through positive feedback of wave-borne energy. Analytical modelling and numerical evaluation presented here demonstrate that this can provide narrow-band frequency analysis. Graded cochlear tuning will then rely on the distance between rows becoming greater as distance from the base increases (as exhibited by the actual cochlea) and on the wave’s phase velocity becoming slower. In effect, tuning is now a case of varying the feedback delay between the rows, and a prime candidate for a wave exhibiting suitably graded phase velocity—a short-wavelength ‘squirting wave’—is identified and used in the modelling. In this way, resonance between rows could supply both amplification and high Q, characteristics underlying the ‘cochlear amplifier’—the device whose action has long been evident to auditory science but whose anatomical basis and mode of operation are still obscure.     

Darwin without borders? Looking at ‘generalised Darwinism’ through the prism of the ‘hourglass model’

This article critically analyzes the arguments of the ‘generalized Darwinism’ recently proposed for the analysis of social-economical systems. We argue that ‘generalized Darwinism’ is both restrictive and empty. It is restrictive because it excludes alternative (non-selectionist) evolutionary mechanisms such as orthogenesis, saltationism and mutationism without any examination of their suitability for modeling socio-economic processes and ignoring their important roles in the development of contemporary evolutionary theory. It is empty, because it reduces Darwinism to an abstract triple-principle scheme (variation, selection and inheritance) thus ignoring the actual structure of Darwinism as a complex and dynamic theoretical structure inseparable from a very detailed system of theoretical constraints. Arguing against ‘generalised Darwinism’ we present our vision of the history of evolutionary biology with the help of the ‘hourglass model’ reflecting the internal dynamic of competing theories of evolution.     

Small plot mating disruption trials for tufted apple bud moth,Platynota idaeusalis, in Pennsylvania apple orchards

Mating disruption treatments for the tufted apple bud moth (TABM),Platynota idaeusalis (Walker), were tested in small plot trials in apple orchards in Pennsylvania. Treatments were evaluated by fruit injury and by capture of male TABM in traps baited with synthetic pheromone sources or virgin females. The TABM pheromone is a two component isomeric blend ofE-11-tetradecen-1-ol (E11-14:OH) andE-11-tetradecenyl acetate (E11-14:Ac). A 50∶50 ratio of these two components was used in standard monitoring septa and in mating disruption treatments released from either hollow fibers (‘fiber’) or PVC tubes (‘PVC’). Other pheromone blends tested included a 90∶10 ratio of E11-14: Ac and E11-14:OH (‘EAc’) and its reverse (‘EOH’), mixture ‘EAc’ with 30% of the Z-isomers (‘low AEc’), and a blend similar to the preceding with 2% Z9-12:Ac (‘generic’). These other blends were released from multi tube tape (‘tape’) or Shin-Etsu type rope (‘rope’) dispensers. Seasonal dispenser release rate in mg ha⁻¹ h⁻¹ was ca. 30 for the ‘rope’ dispensers, 14 for ‘PVC’ and 6 for ‘fiber’. ‘EAc-tape’ and ‘EOH-tape’ were equally effective in reducing catches of males in traps baited with synthetic lures and in traps baited with virgin females. Both treatments also reduced fruit injury. ‘EAc-rope’, ‘fiber’ and ‘PVC’ also were generally effective; whereas, the ‘low EAc’ and ‘generic’ treatments reduced trap capture less than 90% and did not reduce fruit injury. Dispenser density was positively correlated with reduction in trap capture for the ‘low EAc-rope’ and ‘genericrope’ treatments. Traps loaded with ‘fiber’ dispensers captured more male TABM than the other treatments in non-pheromone permeated environments. Trap capture of other tortricids was reduced in pheromone treatments. ‘EAc-rope’ and the ‘TABM’ treatments provided mean (s.e.) percent reduction in trap catch of 99.5 (0.4) and 42.9 (10.1), respectively, for the redbanded leafroller,Argyrotaenia velutinana (Walker), and 90.4 (6.8) and 90.4 (1.3), respectively, for the obliquebanded leafroller,Choristoneura rosaceana (Harris).     

Induction of embryogenic mango cultures as affected by genotype,explanting, 2,4-D and embryogenic nurse culture

The nucellus was removed from immature seeds of 4 mango genotypes, andcultured under different induction conditions. The mango genotypes includedpolyembryonic ‘Hindi’ and ‘Nam Doc Mai’ and monoembryonic ‘Lippens’ and’Tommy Atkins‘. Nucellar explants were cultured on modified B5 basal mediumunder the following inductive conditions: 1) 4.52 μM 2,4-D; 2) nogrowth regulator (control); 3) 4.52 μM 2,4-D + embryogenic ‘Parris‘nurse culture; 4) no growth regulator + embryogenic ‘Parris’ nurse culture.Induction of embryogenic competence was mediated by 4 factors: genotype,explanting, 2,4-D and the presence of a highly embryogenic nurse culture,although there was considerable difference in genotype response. ‘Hindi’ hadthe greatest embryogenic potential, followed by ‘Lippens’, ‘Tommy Atkins‘and ‘Nam Doc Mai’, respectively. Induction of embryogenic cultures of allgenotypes at low frequency occurred as a result of explanting excisednucellus onto control medium. The most effective treatment for inducingembryogenic cultures was 2,4-D + embryogenic ‘Parris’ nurse culture with’Hindi’, ‘Lippens’ and ‘Nam doc Mai’, with the exception of ‘Tommy Atkins’,in which the treatment with 2,4-D alone was most effective. This revised version was published online in June 2006 with corrections to the Cover Date.     

A chimeric <Emphasis Type="Italic">Rfo</Emphasis> gene generated by intergenic recombination cosegregates with the fertility restorer phenotype for cytoplasmic male sterility in radish

In this work, we have identified a chimeric pentatricopeptide repeat (PPR)-encoding gene cosegregating with the fertility restorer phenotype for cytoplasmic male sterility (CMS) in radish. We have constructed a CMS-Rf system consisting of sterile line ‘9802A2’, maintainer line ‘9802B2’ and restorer line ‘2007H’. F₂ segregating population analysis indicated that male fertility is restored by a single dominant gene in the CMS-Rf system described above. A PPR gene named Rfoc was found in the restorer line ‘2007H’. It cosegregated with the fertility restorer in the F₂ segregating population which is composed of 613 fertile plants and 187 sterile plants. The Rfoc gene encodes a predicted protein 687 amino acids in length, comprising 16 PPR domains and with a putative mitochondrial targeting signal. Sequence alignment showed that recombination between the 5′ region of Rfob (EU163282) and the 3′ region of PPR24 (AY285675) resulted in Rfoc, indicating a recent unequal crossing-over event between Rfo and PPR24 loci at a distance of 5.5 kb. The sterile line ‘9802A2’ contains the rfob gene. In the F₂ population, Rfoc and rfob were observed to fit a segregation ratio 1:2:1 showing that Rfoc was allelic to Rfo. Previously we have reported that a fertile line ‘2006H’, which carries the recessive rfob gene, is able to restore the male fertility of CMS line ‘9802A1’ (Wang et al. in Theor Appl Genet 117:313–320, 2008). However, here when conducting a cross between the fertile line ‘2006H’ and CMS line ‘9802A2, the resulting plants were male sterile, which shows that sterile line ‘9802A2’ possesses a different nuclear background compared to ‘9802A1’. Based on these results, the genetic model of fertility restoration for radish CMS is also discussed.     

Microbiology and the species problem

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept.