Starter culture for the production of ‘soyiru’

Bacillus subtilis or licheniformis facilitated production of soyiru with the best results being given by using both together. Fermentation employing Streptococcus enterococcus was unsuccessful.H.A. Suberu is with the Department of Biological Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria. J.A. Akinyanju is with the Department of Biological Sciences, University of Ilorin, P.M.B. 1515, Ilorin, Nigeria.     

Comparison of ‘ignition’ and ‘extraction’ methods for the determination of organic phosphate in rocks and soils

Summary Ignition markedly increased the solubility in dilute acid of iron- and aluminium-bound inorganic phosphate in samples of weathered New Zealand greywacke rock. This observation supports the view that ignition methods may sometimes overestimate the total organic phosphate of soils.     

On ‘analytical models for the patchy spread of plant disease’

Epidemiologists are interested in using models that incorporate the effects of clustering in the spatial pattern of disease on epidemic dynamics. Bolker (1999, Bull. Math. Biol. 61, 849–874) has developed an approach to study such models based on a moment closure assumption. We show that the assumption works above a thre shold initial level of disease that depends on the spatial dispersal of the pathogen. We test an alternative assumption and show that it does not have this limitation. We examine the relation between lattice and continuous-medium implementations of the approach.     

A conformational rationale for the origin of the mechanism of nucleicacid-directed protein synthesis of ‘living’ organisms

The physical basis for the natural evolution of a primitive decoding system is presented using the concepts of molecular interactions. Oligoribonucleotides of five residues havingU at the 5-end, a purine at the 3-end and any combination of three bases in the middle is taken as a primitive tRNA (PIT). From conformational considerations PIT is expected to haveU-turn conformation wherein, N₃–H₃ of baseU hydrogen-bonds with phosphate, three residues ahead leaving triplet bases called primitive anticodons (PAC) into a helical conformation, and this creates a cleft betweenU and PAC. An amino acid can be comfortably nestled into the cleft with the amide hydrogens and carboxyl oxygen hydrogen-bonded to the last purine and the first uridine, while the side-chain can interact with the cleft side of PAC. The other side of PAC is free to base-pair with triplet codons on a longer RNA. Also two PACs can recognize consecutive triplet codons, and this leads to a dynamic interaction in which the amino and carboxyl ends are brought into proximity, making the formation of peptide bond feasible.The cleft formed by different anticodon triplets, broadly speaking, shows preferences for the corresponding amino acids of the presently known codon assignment.Thus the nucleicacid-directed protein synthesis, which is a unique feature of all living organisms is shown to be a natural consequence of a particular way of favourable interaction between nucleic acids and amino acids, and our model provides the missing link between the chemical evolution of small organic molecules and biological evolution through the process of mutations in nucleicacids and nucleicacid-directed protein synthesis.Contribution No. 507 from this department.     

Viral phylodynamics and the search for an ‘effective number of infections’

Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.     

On the ‘transmission sense of information’

In order to illuminate the role of information in biology, Bergstrom and Rosvall (Biol Philos 26:159–176, 2011a; Biol Philos 26:195–200, 2011b) propose a ‘transmission sense of information’ which builds on Shannon’s theory. At the core of the transmission sense is an appeal to the reduction in uncertainty in receivers and to etiological function. I explore several ways of cashing out uncertainty reduction as well as the consequences of appealing to function.     

On the correct use of ‘data’

Acknowledgement  Thanks are due to Drs. Paul Johnston (P.Johnston@ exeter.ac.uk) and E. William Beese (ebeese@t-online.de) for kindly providing dictionary definitions and for sharing their thoughts about the correct use of ‘data’.     

No evidence for an ‘evolution of increased competitive ability’ for the invasive Lepidium draba

The ‘evolution of increased competitive ability’ (EICA) hypothesis states that reduced herbivory in the introduced range causes an evolutionary shift in resource allocation from herbivore defense to growth. Therefore, according to EICA, introduced genotypes are expected to grow more vigorously than conspecific native genotypes when cultivated under common standardized conditions. The EICA hypothesis also assumes that herbivores will perform better on introduced genotypes compared to native genotypes, because they are less well defended. However, selection for either defense or growth will depend on the type of defense (quantitative or qualitative) employed by the plant, and whether the plant is released from generalist or specialist herbivores. The predictions of the EICA hypothesis might be reversed if a plant experiences increased generalist herbivore pressure in the introduced range, and therefore invests more in qualitative defense. We examined this idea with the invasive perennial mustard, Lepidium draba. We grew a total of 16 populations of L. draba from both its native European and introduced western US ranges under common conditions in a greenhouse. We also tested for differences in plant resistance to the specialist herbivore, Psylliodes wrasei, by conducting a leaf disc feeding bioassay with native and introduced L. draba genotypes. Furthermore, we quantified the generalist herbivore load on L. draba in both ranges in order to assess the selection pressure for increased qualitative defense. Contrary to the original EICA prediction, all plant traits (biomass, number of shoots, length and diameter of longest leaf) tended to be greater for the native, rather than introduced L. draba genotypes. There was no significant difference in the proportion of leaf area consumed by the specialist herbivore between native and introduced genotypes. The generalist herbivore load on L. draba was significantly greater in the introduced range. Our data suggest that the EICA hypothesis does not explain the invasion success of L. draba in the US. Instead, we propose that the reduced vigor of introduced genotypes may be due to selection for increased defense against generalist herbivores in the introduced range.     

Assessing the efficacy of spray-delivered ‘eco-friendly’ chemicals for the control and eradication of marine fouling pests

Despite its frequent use in terrestrial and freshwater systems, there is a lack of published experimental research examining the effectiveness of spray-delivered chemicals for the management of non-indigenous and/or unwanted pests in marine habitats. This study tested the efficacy of spraying acetic acid, hydrated lime and sodium hypochlorite for the control of marine fouling assemblages. The chemicals are considered relatively ‘eco-friendly’ due to their low toxicity and reduced environmental persistence compared to synthetic biocides, and they were effective in controlling a wide range of organisms. Pilot trials highlighted acetic acid as the most effective chemical at removing fouling cover, therefore it was selected for more comprehensive full-scale trials. A single spray of 5% acetic acid with an exposure time of 1 min effectively removed up to 55% of the invertebrate species present and 65% of the cover on fouled experimental plates, while one application of 10% acetic acid over 30 min removed up to 78% of species present and 95% of cover. Single-spray treatments of 5% acetic acid reduced cover of the tunicate pest species Didemnum vexillum by up to 100% depending on the exposure duration, while repeat-spraying ensured that even short exposure times (1 min) achieved ～99% mortality. Both 5 and 10% acetic acid solutions appeared equally effective at removing the majority of algal species. This technique could be used for controlling the introduction of unwanted species or preventing the spread of pests, and is applicable to use on a variety of natural and artificial substrata, or for the treatment of structures that can be removed from the water.     

‘Ancestral’ neural mechanisms of electrolocation suggest a substrate for the evolution of the jamming avoidance response

Summary The genusSternopygus, believed to reflect ancestral traits of gymnotiform electric fish, is closely related to the more modern genusEigenmannia (Mago-Leccia 1978; Fink and Fink 1981).Sternopygus is the only known genus of electric fish that does not perform a jamming avoidance response (JAR) to minimize the potentially detrimental effects of signal interference between discharging neighbors (Bullock et al. 1972, 1975), and its ability to electrolocate objects is rather immune to jamming (Matsubara and Heiligenberg 1978).By studying the responses of midbrain neurons to stimulus regimes effective in eliciting the JAR inEigenmannia, we found thatSternopygus has neurons capable of discriminating the sign of the difference frequency between interfering electric organ discharges (EODs). These sign-selective neurons, which are believed to be important elements in the control of the JAR inEigenmannia, may, therefore, fulfill a more general function in the detection of moving objects and conspecifics but could potentially be assembled for the evolution of a JAR inSternopygus. The relative immunity to jamming in this genus may result, in part, from a stronger reliance upon the ampullary electrosensory system which operates in the DC and low-frequency range, outside the EOD spectrum of these fish.Abbreviations AM amplitude modulation - Df frequency difference - EOD electric organ discharge - JAR jamming avoidance response     

Making sense of ‘mixture’: states and the classification of ‘mixed’ people

Caribbean diaspora intellectuals have contributed significantly to African-American political struggles over the years, despite arguments by some African-American intellectuals about what they discern as West Indian negativism, extremism, and divisiveness in American political life. This essay examines the legacy of a representative sample of diasporic Caribbean intellectuals since the time of the Harlem Renaissance in the 1920s and culminating in the 1970s, notably, Garvey, members of the African Blood Brotherhood [ABB], C.L.R. James, and Walter Rodney, to demonstrate the phenomenal ideological vision, organizational capability, and political activism they have brought into fostering solidarity with African Americans in the struggle for fundamental change. The focus here is on their respective contributions to the debate on the relationship between class and race in America and the black diaspora generally, which has helped to shape the form, and orient the direction of African-American and Caribbean diasporic struggles for the better part of the twentieth century.     

Evidences for an Alternative Genealogy of ‘Sangiovese’

Two different hypothesis for the parentage of ‘Sangiovese’, the most important and widespread Italian winegrape, have been proposed by some previous studies. We screened our grapevine collection, mostly comprising south Italian cultivars collected to preserve biodiversity, to asses kinships. Surprisingly we found two previously unreported candidate parents for ‘Sangiovese’. The first putative parent is ‘Ciliegiolo’ a well know variety already addressed as relative of ‘Sangiovese’; the second putative parent is ‘Negrodolce’, an old local variety we recovered and was considered lost during the last century. In order to obtain a stronger statistical support for this new kinship, we tested seventy different microsatellite markers but only 57 were found reliable. The new proposed parentage stood well even with such a in depth molecular analysis whereas only one discrepancy was found in one of the 57 microsatellite marker analyzed. This discrepancy is certainly due to a null-allele and therefore it should not impair our hypothesis but it points out limits of the microsatellites profiling as a pedigree research method considering that this is the third different kinship proposed so far for ‘Sangiovese’. Thus in this article, by means of detailed molecular fingerprinting, we provide a completely new strong evidence for a south Italian origin of ‘Sangiovese’ and we discuss our findings comparing our data with those previously reported by other authors.     

Taxonomy and chemically semi-defined media for the analysis of the tacrolimus producer ‘Streptomyces tsukubaensis’

‘Streptomyces tsukubaensis’ was the first tacrolimus producer strain identified. Although it has been included in the Streptomyces genus, its taxonomic position has not been rigorously determined. By using a polyphasic approach, we have established that the tacrolimus producer strain ‘S. tsukubaensis’ NRRL 18488 represents a unique species in the Streptomyces genus, which is phylogenetically distant from other subsequently described producers. This fact means a horizontal transference of the tacrolimus-producing gene cluster. Physiology, nutrient requirement, and molecular genetics analyses of tacrolimus biosynthesis in ‘S. tsukubaensis’ necessitate chemically defined or semi-defined media, which work as a jigsaw puzzle and allow for pieces (nutrients) exchange. To date, studies related to ‘S. tsukubaensis’ have been mainly focused in the improvement of tacrolimus production using complex industrial fermentation media, which difficulty allows testing of tacrolimus overproduction enhancers or inhibitors because of the presence of non‐defined substances. In the present work, two semi-defined media were developed in order to study the main factors involved in tacrolimus production in ‘S. tsukubaensis’.     

Testing Predictions of the ‘Evolution of Increased Competitive Ability’ Hypothesis for an Invasive Crucifer

The successful spread of invasive plants may result from an evolutionary shift in resource allocation from defence to growth due to release from enemies, as proposed by the ‘evolution of increased competitive ability’ hypothesis (EICA). The crucifer Lepidium draba was used to test this hypothesis, measuring growth and levels of glucosinolates and myrosinase of leaves as constitutive defence parameters. Individuals from 21 populations of the native (Europe) and the invasive range (North-America) were grown under common greenhouse conditions. According to the EICA hypothesis it was predicted that plants from the invasive range might show stronger growth and have lower levels of defence as a result of selection favouring such genotypes. There was significant variation between populations in shoot, root, total biomass, and number of ramets of 3-month-old plants but no difference due to origin from both continents. The main glucosinolate p-hydroxybenzyl glucosinolate was significantly higher in seedlings of the invasive range while myrosinase activity was higher in old plants of the invasive range. Therefore, the EICA hypothesis does not hold, however, alternatively there is evidence for selection favouring stronger defence in the invasive range. The binary defence system of this crucifer is discussed with respect to the degree of specialisation of potential herbivores.