The new problem of genetics: A response to Gifford

Recently, Fred Gifford attempted to explicate the meaning of the term genetic as applied to phenotypic traits. He takes as his primary goal the explication of how the term is used and tries to avoid conclusions about how it should be used. He proposes two independent criteria (DF and PI) which together capture much of what biologists mean when they describe traits as genetic. Although Gifford's approach is extremely insightful in many ways, I argue that his analysis is not sufficiently critical concerning the adequacy of common usage.In particular, while DF is a perfectly legitimate and useful measure of heritability in populations, it is not necessarily a genetic one and should not be labeled as such. PI on the other hand, although very intuitive, depends on an extremely problematic distinction between causes and mere conditions (e.g., genes and epigenetic factors). Both criteria will be highly relative and both, via what I term the new problem of genetics, will inspire contradictory analyses based on the same data.Fortunately, as Gifford recognizes, it is not necessary to make sense of genetic at all in order to do biology. Quantitative genetics can do the kind of (heritability) analysis that DF embodies without making questionable claims about genes. Causal-mechanical or bottom-up biology can proceed perfectly well without postulating the priveleged role for genetic causes that PI entails. In short, talk of genetic traits, under either criteria, is unnecessary and misleading.     

Observations on the fine structure of the cercaria of Notocotylus attenuatus and formation of the cyst wall of the metacercaria

Summary The dorsal tegument of the mature cercaria of Notocotylus attenuatus is a syncytial, cytoplasmic layer, containing two types of secretory granule which are identifiable ultrastructurally. The type 1 secretory bodies are electron lucid, whereas most type 2 granules have a banded appearance. The ventral tegument contains granules which are secreted from the type 3 cells; the type 3 granules are membrane bound, electron dense, and consist of both an amorphous and a finely striated zone. The type 4 cells mainly contain cigar-shaped granules consisting of an amorphous core surrounded by concentric striations. The granules exhibit structural variability in shape and content. The type 4 cells undergo a cellular migration to the tegument during encystment. The structure of the posterior-lateral glands and mode of secretion of the granules are described. Possible functions of microtubules are discussed for each cell type. Details of some secretory processes involved in the formation of the hemispherical cyst wall are described. The layers of the cyst wall may be related to the granular contents of the various parenchymal cells of the cercaria. The tegument of the metacercaria originates primarily from the cytoplasm of the type 1, type 2, type 3 and type 4 cells.     

The effect of monoterpenes on astaxanthin production by a mutant ofPhaffia rhodozyma

Summary The total pigment and astaxanthin content ofPhaffia rhodozyma increased with increasing concentrations -pinene up to 500 l -pinene/l. Above this concentration the total pigment and astaxanthin content as well as the biomass production decreased. The addition of 500 l -pinene/l increased the total pigment content from 1652 g/g to 2201 g/g and the astaxanthin content from 1554 g/g to 1883 g/g. A sharp decrease in maximum specific growth rate occurred above 150 l -pinene/l.     

Flexibility on the karyotype evolution in bitterlings (Pisces, Cyprinidae)

In bitterlings (Acheilognathinae) C- and Ag-banding karyotypes of 6 species-subspecies collected in China and South Korea were analyzed. The chromosomal constitution of 2n=46 (4SM+42ST) in Rhodeus atremius fangi was quite different from that of 2n=48 (8M+20SM+20ST) in other species-subspecies in Rhodeus. It was concluded from the analysis of banded chromosomes that the increase in number of ST during the karyotype change from 2n=48 to 2n=46 was achieved by a series of pericentric inversions from 24 M-SM to 24 ST, and the decrease in the diploid number was caused by an additional tandem fusion of 4 ST chromosomes, forming a new ST pair in the 2n=46 karyotype. The karyotype of Tanakia koreensis, T. signifer, and Acheilognathus macropterus is 2n=48 (8M+20SM+20ST), 2n=48 (8M+20SM+14–16ST+4–6 A), 2n=44 (14M+16SM+14ST), respectively. In R. ocellatus ocellatus, T. koreensis, T. signifer and A. macropterus, karyotype changes from 2n=48 to 2n=44 due to centric fusion and inversion have also been estimated. It was suggested that C-banding heterochromatin was greatly concerned with the karyotype evolution in bitterlings.     

β-Glucuronidase activity in human T and B lymphocytes and the Tμ and Tγ subpopulations

Summary The -glucuronidase staining characteristics of isolated T cell populations and the T and T enriched fractions derived of them were studied. T lymphocytes were obtained from purified T lymphocytes by ox-IgG rosette sedimentation. The rosette-forming cells in the pellet were referred to as T lymphocytes, whereas the lymphocytes in the interface were referred to as T depleted or T lymphocytes. B cells were studied on rosetted mononuclear cells with either mouse erythrocytes or with Staphylococcus Aureus (Cowan I) bacteria, after a preceeding polyvalent anti-human Ig treatment of the cells. While B cells showed mostly no reactivity, T and T cells were respectively characterised by a dot-like and granular pattern of reactivity. These findings are in agreement with those observed by others after -naphthyl-acetate esterase or acid phosphatase staining. Within the T lymphocyte fraction, the T non-, non lymphocytes seemed to have a granular pattern of reactivity. The same staining pattern was found in non-B, non-T lymphocytes.     

Extent and high frequency of a short conversion between the human Aγ and Gγ fetal globin genes

Summary Southern blotting and DNA sequencing after polymerase chain reaction (PCR) amplification provide evidence for the frequent occurrence (in 7 out of 24 chromosomes) of a short conversion GA in the 3 end of the human fetal A globin gene. This short conversion is characterized by the presence, 3 nucleotides downstream from the termination codon of the A gene, of the TCAC sequence that is normally present at the equivalent position at the 3 end of the G gene; it is therefore identical to a conversion already described. Interestingly, we have found that this conversion is associated with the presence of theHindIII polymorphic restriction site in the A IVS2, occuppying an equivalent position in both the G and A genes. Our observations strengthen the hypothesis that the presence of the HindIII polymorphic restriction site in A IVS2 and the presence of the sequence TCAC at the 3 end of the A gene might be the result of a single conversion event.     

Memorization and delayed expression of regulatory messages in plants

Plantlets of Bidens pilosus L., considered to be basically symmetrical, can be lateralized (A/B) by being administered a symmetry-breaking signal such as puncturing one of the plant cotyledons. The induced asymmetry remains latent as long as the plants have not been made permissive, i.e. as long as the plant apex is left functioning. When the apex has been removed (plant decapitation), the latent asymmetry is expressed by one of the cotyledonary buds (a/b) statistically beginning to elongate before the other. The interval of time between delivering the symmetry-breaking signal and making the plant permissive is the memorization-time, t. Memorization can be quantified by using a precedence index, q, the values of which range from 0 (no detectable asymmetry with regard to bud growth) to ±1 (bud growth perfectly asymmetric in favour of either bud b or a). Even for memorization times, t, up to 14 d, q-values up to 0.4 (or even larger) are observed. Various experimental characteristics (e.g. light, temperature, presence or absence of the root system) but not the plant age can affect the q-values, at the moment when the treatments are performed, at least in the range of 6 to 25 d. Combining several puncturing treatments either increases or decreases the q-values, depending on the nature of these treatments and the time-intervals, t, between them. Symmetrically removing both cotyledons in the minutes following the puncturing of one of them does not significantly alter the results, which means that the symmetry-breaking message is rapidly transported and memorized within the plant. Non-traumatic asymmetrical treatments (droplets of saline solutions, light-gradients) can also act as symmetry-breaking signals and be memorized. Plants other than Bidens are likely to possess similar memorization ability, although the q-values observed up to now have not been very large.     

Sequential fractionation of sediment phosphate

By means of sequential extractions with Ca-NTA and EDTA, a separation was performed between Fe(OOH) P and CaC0₃P in a few sediments; the remaining fraction, considered to be organic phosphate, was quantified as well. We found that with the commonly used method of extraction with NaOH and H₂S0₄, less Fe(OOH) P and much more CaC0₃ P was found than with the chelating extractants. The organic phosphate pool in live and dead algal material and in some mud samples was partly hydrolysed and therefore recovered as inorganic phosphates with classical extractions. The difference between chelating extractants and the classical ones is discussed.Abbreviations o-P: ortho phosphate (or its concentration) - org-P: organic phosphate - extr-P: extractable sediment bound phosphate - extr-Fe: extractable sediment bound iron - Fe(OOH) P: iron bound, sediment phosphate - CaCO₃ P: calcium bound, sediment phosphate - org-C: organic sediment bound carbon     

Regional specialization of the sperm membrane in the tick Amblyomma hebraeum koch (Acari: Ixodidae)

Summary The spermatozoon of Amblyomma hebraeum is about 200 m long and comprises: (1) a thick, club-shaped anterior part, about 20 m long bearing at its apex a tactile hemisphere, and (2) an elongated tail-like part, about 180 m long. The surface of the tactile hemisphere is covered by numerous bulbous expansions, attached to it by short stalks. The base of the hemisphere is surrounded by a fringe of thin motile processes; the remaining surface of the spermatozoon is covered with long cellular processes which run more or less parallel to one another.The membrane-associated particles found on the membrane beneath the cellular processes are regularly arranged as groups of parallel strands. The external surface of the so-called peripheral granules, as revealed by freeze-etching, is smooth with a very small number of particles. Internally the particles exhibit a regular hexagonal pattern which has not been observed, so far, on any other membrane of these sperm cells.The regional specialization of the spermatozoon surface membrane in relation to sperm motility is discussed. The results obtained indicate that processes of three types: (1) bulbous expansions, (2) motile processes, and (3) cellular processes are regional specializations, all engaged in aspects of sperm motility.The technical assistance of Mr. R. Haemmerle of Balzers Research Laboratories, Mrs. F. Seif and Miss C. Pugin, is gratefully acknowledged     

Problems in estimating growth rates of marine phytoplankton from short-term14C assays

Growth rate estimates () of phytoplankton populations that were sampled from nitrogen-limited continuous cultures and then incubated for short durations in batch culture with added¹⁴C-HCO₃ ^– were significantly different than steady-state growth rates () for 3 of 5 marine phytoplankton species. Two diatoms,Thalassiosira weissflogii andChaetoceros simplex, displayed virtually identical growth rates (=) over a wide range of, whereas for a third diatom,Phaeodactylum tricornutum, was overestimated by an average of 40% compared to. In contrast, was underestimated by the¹⁴C technique for the two remaining species: up to 40% at a steady-state of 1.0 day^–1 for the chlorophyteDunaliella tertiolecta and up to 100% at of 1.4 day^–1 for the haptophytePavlova lutheri. For the latter two species the divergence between and appeared to increase with increasing steady-state. A simple model of labeled and total carbon flow between the aqueous phase and cellular biomass was constructed to demonstrate that respiration was negligible when=, but was significant when>. In the cases in which<, a rapid physiological alteration presumably took place once the steady state was disturbed and cells were placed in the incubation chambers, which perhaps was related to the nutritional state of the cultures at the time of sampling. Questions thus are raised regarding our ability to measure accurately primary productivity from shipboard experiments with confined samples of phytoplankton from nutrient-impoverished waters that probably are less hardy than the laboratory cultures used in these studies.     

The structure of the incompatibility factors of Schizophyllum commune: Constitution of the three classes of B factors

Summary The B factors of Schizophyllum commune are of 3 classes: The high recombining class I has 7 alleles and 7 alleles; the low recombining classes are class II with 7 allels and probably 2 alleles and class III with probably 2 (or also 2) alleles and 7 allels. A fourth hypothetical class (-) was not found and either does not exist or is indistinguishable from class III by the tests employed. The and alleles differ from and by either (a) mutations affecting both mating specificity and recombination frequency, or (b) deletions involving most of the B region.The research was supported by a grant from the Atomic Energy Commission of the U.S. No. (30-1)-3875 and was performed at the Biological Laboratories, Harvard University, Cambridge, Mass., U.S.A.     

Existence and uniqueness of a sharp travelling wave in degenerate non-linear diffusion Fisher-KPP equations

In this paper we use a dynamical systems approach to prove the existence of a unique critical value c ^* of the speed c for which the degenerate density-dependent diffusion equation u _ct = [D(u)u _x ] _x + g(u) has: 1. no travelling wave solutions for 0 < c < c ^*, 2. a travelling wave solution u(x, t) = (x - c ^* t) of sharp type satisfying (– ) = 1, () = 0 ^*; '(^*–) = – c ^*/D'(0), '(^*+) = 0 and 3. a continuum of travelling wave solutions of monotone decreasing front type for each c > c ^*. These fronts satisfy the boundary conditions (– ) = 1, '(– ) = (+ ) = '(+ ) = 0. We illustrate our analytical results with some numerical solutions.     

Characterization of the effectors required for stable inheritance of Streptococcus pyogenes pSM19035-derived plasmids in Bacillus subtilis

The low-copy-number and broad-host-range pSM19035-derived plasmid pBT233 is stably inherited in Bacillus subtilis cells. Two distinct regions, segA and segB, enhance the segregational stability of the plasmid. Both regions function in a replicon-independent manner. The maximization of random plasmid segregation is accomplished by the recombination proficiency of the host or the presence of the pBT233 segA region. The segA region contains two open reading frames (or) [ and ]. Inactivation or deletion of or results in SegA^– plasmids. Better than random segregation requires an active segB region. The segB region contains two ors (or and or). Inactivation of either of the orfs does not lead to an increase in cell death, but or^– plasmids are randomly segregated. These results suggest that pBT233 stabilization relies on a complex system involving resolution of plasmid oligomers (segA) and on the function(s) encoded by the segB region.     

Hydrolysis ofγ-glutamyl linkages byFusobacterium nucleatum

The cell extracts of two human oral strains (FN2 and FN3) ofFusobacterium nucleatum displayed exceptionally high-glutamylpeptidase activity as determined withN--l-glutamyl-2-naphthylamine as substrate. This activity was so dominant that the hydrolysis of otherN-aminoacyl-2-naphthylamines progressed at a rate <10% of the former. Two major enzymes (I and II) were partially purified from FN2. I had a molecular weight of 115,000 and did not hydrolyze-glutamylcysteinylglycine (glutathione). II had a molecular weight of 70,000 and rapidly liberated only glutamic acid from glutathione. Strain FN3 contained several enzymes hydrolyzing-glu-2NA. Direct anion exchange chromatography of FN3 cell extracts separated one enzyme that liberated both glutamic acid and glycine from glutathione, one that was inactive against glutathione (but hydrolyzed-glu-2NA), and one that liberated only glutamic acid. Although-glu-2NA was a good synthetic substrate, glutathione was hydrolyzed at least 500 times faster by an enzyme present in both strains. These results indicate that the presence of-glutamylpeptidase activity is very characteristic of theseF. nucleatum strains.     

K-current fluctuations in inward-rectifying channels of frog skeletal muscle

Summary K currents and K-current fluctuations were recorded in inwardly rectifying K channels of frog skeletal muscle under voltage-clamp conditions. External application of 0.2 to 10mm Cs reduces the inward mean K current but produces a distinct increase of the spectral density of K-current fluctuations. The additional fluctuations arise from the random blocking by Cs ions. From the variance of current fluctuations, the steady-state current and the probability of the open unblocked channel an effective single-channel conductance ^* was calculated. ^* strongly depends on the external Cs concentration (7.8 pS at 0.2mm Cs, 2.1 pS at 10mm Cs). This dependence is interpreted in terms of a two-step blocking process: (1) a fast exchange of Cs ions between the external solution and a first binding site inside the channel which leads to the Cs-modulated effective single-channel conductance, and (2) a slow Cs binding to a second site deeper in the channel which produces the observed current fluctuations. With this hypothesis we obtained a real single-channel conductance of 10 pS and a real density ofn4 inwardly rectifying channels per m² of muscle surface area.     

Study ofO-sialylation of glycoproteins in C6 glioma cells treated with retinoic acid

When treated with retinoic acidin vivo, C6 glioma cells show an enhancement of CMP-Neu5Ac:Gal 1–3 GalNAc-R -2,3 sialyltransferase activity. A 300kDa glycoprotein was detected by lectin affinoblotting in retinoic acid-treated C6 cells which stained weakly or not at all in control cells. Comparative studies with different lectins demonstrated that this glycoprotein contains 2,3 Neu5Ac Gal-GalNAc O-glycan moieties. Cultures in the presence of an inhibitor of O-glycan synthesis (N-acetylgalactosaminide -O-benzyl) demonstrated that enhancement of staining of the 300 kDa glycoprotein was not due to the increase of the 2,3 sialyltransferase but to thede novo synthesis of the polypeptide chain of this glycoprotein.Abbreviations RA retinoic acid - Neu5Ac N-acetylneuraminic acid - CMP-Neu5Ac cytidine 5 monophosphosialate - 2,3 ST CMP-Neu5Ac:Gal 1–3 GalNAc-R -2,3 sialyltransferase - GalNAc-O-benzyl N-acetylgalactosaminide -O-benzyl - Gal1-3GalNAc-O-benzyl Galactosyl 1-3N-acetylgalactosaminide -O-benzyl - TBS Tris-HCl buffer 50mm pH 7.5 containing NaCl 0.15m and Tween 20 0.05% - B1 buffer TBS containing MgCl₂ 1mm, MnCl₂ 1mm and CaCl₂ 1mm     

Amplification and latency in photoreceptors: Integrated or separated phenomena?

It is shown that the models for the transduction process in photoreceptors which treat latency and amplification as integrated phenomena (integrated models) yield time scales for single photon signals (quantum bumps) which distinctly conflict with the experimentally observed ones for the ventral nerve photoreceptor of Limulus: the ratio of bump duration/ latency t _B/t _lat is predicted by integrated models to be 3 in contrast to the experimental result of 0.5. Moreover, integrated models lead to a predicted value of an extinction rate of 50%, i.e., 50% of the absorbed photons should be expected to cause no signal in the dark adapted state of the cell. In this paper it is shown that separation of latency and amplification in such a way that the latency causing process precedes amplification in the transduction process eliminates these discrepancies. In addition, the separate modeling of latency and amplification resolves the rather large ambiguity in determining the exponent n of the initial signal current J(t) ⁿreported in the literature to be between n2 (from noise analysis) up to n17 (from flash experiments). Two alternative models for the latency part of transduction are suggested which give a qualitatively much better agreement with the experimental histograms of latencies.List of Symbols A quantum bump amplitude, maximum of quantum bump signal current - latency criterion as a fraction in terms of J _max - E energy of the stimulating flash - g conductance of a single light-regulated channel - I(t) light intensity of the stimulating flash as a function of time - J(t) response current of photoreceptors to light flashes under voltage clamp - J _max maximum signal current response signal - J _min minimum current above which the signal current becomes distinguishable from the base line noise - k rate constant in models separating latency from amplification - L ligand in ligand binding model - rate constant of exponential bump decay - m number of amplification steps following gainless latency process in models separating latency and amplification - n exponent in the initial behaviour J(t)t ⁿ - Q net charge transfer of quantum bump signal current - (t) first-passage time probability density - t _B duration of quantum bump response - t _lat latency time - t _max time to peak for quantum bumps - t _r rise time for quantum bumps - U U-U _L, U=clamp voltage, U _L=reversal potential of light-regulated channels - v amplification factor - X _k intermediate conformations in transduction models This work was supported by Deutsche Forschungsgemeinschaft (SFB 160)     

Transformation of dehydroepiandrosterone and pregnenolone by Mucor piriformis

The mode of transformation of dehydroepiandrosterone (I, 3-hydroxyandrost-5-en-17-one) and pregnenolone (II, 3-hydroxypregn-5-en-20-one) was studied using Mucor piriformis. Biotransformation products formed from I were 3,17-dihydroxyandrost-5-ene (Ia), 3-hydroxyandrost-5-ene-7,17-dione (Ib), 3,17-dihydroxyandrost-5-en-7-one (Ic), 3,7-dihydroxyandrost-5-en-17-one (Ie). Biotransformation products formed from compound II were 3,7-dihydroxypregn-5-en-20-one (IIa) and 3,7,11-trihydroxypregn-5-en-20-one (IIb). The organism did not carry out isomerization of the 5-en-3-ol to a 4-en-3-one system in the steroid molecules tested. In addition, it failed to carry out 14-hydroxylation possibly because of the lack of a 4-en-3-one system in I and II, and stereospecific hydroxylation at the C-7 position in I and II.     

Plastids of the yellow y-1 strain ofEuglena gracilis

Summary A yellow strain, called y-1, was isolated during heat-induced bleaching ofEuglena gracilis strain Z.The ultrastructure, growth, and carotenoid content of this strain were studied and compared with those of the wild-typeEuglena and the heat-bleached colourless strain.The yellow, xanthophyll-containing strain y-1 resembles in many respects the etiolated wild-typeEuglena which has lost the ability to form chloroplasts in the light. It represents a transitional stage in the process of progressive degradation of plastids induced by bleaching treatments between the wild-typeEuglena and the colourless strain.Both bleached strains differ mainly in their carotenoid content formed in the light and especially in the dark, and the size and distribution of undeveloped plastids. In the yellow bodies of both strains PLB structure appears in accordance with their plastid nature.Thus, as shown in the present paper, the structural changes, appearing in the plastids of bleachedEuglena, seem to be at least morphologically very similar to the structural changes occuring in transforming plastids of higher plants.     

Expression sites and developmental regulation of genes encoding (1→3,1→4)-β-glucanases in germinated barley

Expression sites of genes encoding (13,14)--glucan 4-glucanohydrolase (EC 3.2.1.73) have been mapped in germinated barley grains (Hordeum vulgare L.) by hybridization histochemistry. A³²P-labelled cDNA (copy DNA) probe was hybridized to cryosections of intact barley grains to localize complementary mRNAs. No mRNA encoding (13,14)--glucanase is detected in ungerminated grain. Expression of (13,14)--glucanase genes is first detected in the scutellum after 1 d and is confined to the epithelial layer. At this stage, no expression is apparent in the aleurone. After 2 d, levels of (13,14)--glucanase mRNA decrease in the scutellar epithelium but increase in the aleurone. In the aleurone layer, induction of (13,14)--glucanase gene expression, as measured by mRNA accumulation, progresses from the proximal to distal end of the grain as a front moving away from, and parallel to, the face of the scutellum.Abbreviations cDNA copy DNA - RNase ribonuclease