Bathycamptus eckmani gen. et spec. nov. (Copepoda,Harpacticoida) with a review of the taxonomic status of certain other deepwater harpacticoids

Bathycamptus eckmani gen. et spec. nov., which is associated with mudballs produced by the. cirratulid Tharyx luticastellus, is described from bathyal muds in San Diego Trough, off California. ?Heteropsyllus minutus Wells from the Haden Ground, Scotland is considered to be its closest relative and is placed in the same genus. The genera Bathycamptus and Psammocamptus Mielke are regarded as sister groups on the basis of the shared sexual dimorphism shown by P3-P4. Relationships with other marine Canthocamptidae are discussed, and a re-evaluation of the genus Hemimesochra Sars is made. It is concluded that this genus should encompass only the type species H. clavularis Sars. ?Leimia dubia Wells and H. nympha Por are transferred to the new genus Boreolimella, which is closely related to Bathycamptus but not to Leimia Willey. The genus Perucamptus gen. nov. is established to include H. rapiens Becker and shows no clear relationship with the other genera. H. trisetosa Coull is assigned to Caroliiaicola gen. nov., which is regarded as being an advanced member of the Paranannopidae. H. secunda Wells is recognised as belonging to Mesopsyllus Por; whilst H. nixe Por is considered the type species of a new genus Pusillargillus.     

Metal ion coordination to 2′ functionality of guanosine mediates substrate-guanosine coupling in group I ribozymes: implications for conserved role of metal ions and for variability in RNA folding in ribozyme catalysis

Divalent metal ions are necessary in the self splicing reaction of group I introns, and we report that metal interaction to the 2′ position of guanosine for the Azoarcus ribozyme is required for catalysis. Moreover, this metal coordination promotes the guanosine-substrate coupled binding to the ribozyme, which is another conserved feature seen across phylogenetic boundaries. Typically there is a 4-9-fold difference in binding of G to E_free versus E · S. In the Tetrahymena ribozyme’s case this substrate-guanosine communication was attributed to conformational change(s) that lead to cooperative binding of the two cofactors which is almost nonexistent at low temperatures (4 °C). In the prokaryotic Azoarcus ribozyme we also see a 4-5-fold difference in binding of the guanosine/substrate to E_free versus E · G or E · S at 10 °C that is attributed to guanosine-substrate coupling. This coupling is diminished when the metal (Mg²⁺) coordination to the 2′ is disrupted with use of 2′-amino-2′-deoxyguanosine. The coupling is restored when softer Mn²⁺ ions are added to the buffer. This evidence generalizes a model for group I ribozyme catalysis that involves metal coordination to the 2′ position of guanosine. However, we see one striking difference in that the guanosine-substrate coupling is reversed. In the Azoarcus system (10 °C) the guanosine/substrate binds 5-fold more tightly to E_free than to E · S or E · G, which is the opposite for Tetrahymena even when the later is run at 4 °C. One implication for this difference in coupling is that the Azoarcus is in a folded state well accommodated for guanosine or substrate binding. This initial binding actually causes a conformational change that retards the subsequent binding of the second cofactor, which contrasts what was found for the Tetrahymena ribozyme. These results indicate that while the role for the metal ions in the chemical catalysis is conserved across phylogenetic boundaries, there is variability in the folding pattern of the ribozyme that leads to phosphoryl transfer.     

STUDIES ON THE METABOLISM OF THE AUTOTROPHIC BACTERIA : III. THE NATURE OF THE ENERGY STORAGE MATERIAL ACTIVE IN THE CHEMOSYNTHETIC PROCESS

In the autotrophic bacterium, Thiobacillus thiooxidans, the oxidation of sulfur is coupled to transfers of phosphate from the medium to the cells. CO₂ fixation is coupled to transfers of inorganic phosphate from the cells to the medium and is dependent, in the absence of concomitant sulfur oxidation, upon the amount of phosphate previously taken up during sulfur oxidation. The energy reservoir, which is formed by sulfur oxidation in the absence of CO₂ and which can be released for the fixation of CO₂ under conditions which do not permit sulfur oxidation, is a phosphorylated compound and the data suggest that the energy is stored in the cell as phosphate bond energy. It is possible to oxidize sulfur at a constant rate for hours in the absence of CO₂. The phosphate energy formed during this process is probably released by cell phosphotases. It is possible to inhibit these phosphotases by means of inorganic phosphate and thus to inhibit sulfur oxidation in the absence of CO₂. In the presence of CO₂, where alternative uses for the phosphate energy are available, the inhibition is relieved. Sulfur oxidation (energy input) is coupled, not to CO₂ fixation, but to phosphate esterification. CO₂ fixation (energy utilization) is coupled with phosphate release.     

THE ORIENTATION OF ANIMALS BY OPPOSED BEAMS OF LIGHT

When orientation is attained under the influence of beams of parallel light opposed at 180° the deflection θ from a path at right angles to the beams is given by tan See PDF for Equation, where I ₁ and I ₂ are the photic intensities and H is the average angle between the photoreceptive surfaces. This expression is independent of the units in which I is measured, and holds whether the primary photosensory effect is proportional to I or to log I. When photokinetic side-to-side motions of the head occur, H decreases with increasing total acting light intensity, but increases if higher total light intensity restricts the amplitude of random movements; in each case, H is very nearly proportional to log I ₁ I ₂. For beams of light at 90°, See PDF for Equation. The application of these equations to some particular instances is discussed, and it is shown why certain simpler empirical formulæ previously found by others yield fair concordance with the experimental data. The result is thus in complete accord with the tropism theory, since the equations are based simply on the assumption that when orientation is attained photic excitation is the same on the two sides.     

Regulation of Escherichia coli IscS desulfurase activity by ferrous iron and cysteine

IscS plays a principal role in the synthesis of sulfur-containing biomolecules. It is known that the expression of iscS can be negatively regulated by IscR, the first gene product of iscRSUA-hscBA-fdx. What governs the regulation of cysteine desulfurase activity, however, is unknown. Here, we report that IscS from Escherichia coli is able to bind iron with an association constant of 1.6 × 10¹⁷ M⁻¹ to form an IscS-iron complex. IscS is also capable of binding both iron and sulfide to form an IscS-iron-sulfide complex with a higher affinity. The desulfurase activity is gradually inhibited as the amount of iron and sulfide bound to IscS increases. When 2Fe-2S binds IscS, about 20% of the activity is inhibited; when 8Fe-8S adheres to IscS, about 70% of the activity is inhibited. Thus, the cell is able to modulate its desulfurase activity with the formation of an IscS-iron-sulfide complex.     

Structural Analysis of a Trimer of β2-Microgloblin Fragment by Molecular Dynamics Simulations

A peptide ${\beta }_2$-${\text{m}}_{21?31}$, which is a fragment from residue 21 to residue 31 of ${\beta }_2$-microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to understand the mechanism of amyloid fibril formations, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of ${\beta }_2$-${\text{m}}_{21?31}$. From the analyses on the temperature dependence, we found that there is a clear phase transition temperature in which the peptides aggregate with each other. Moreover, we found by the free energy analyses that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates.     

An S-Curve-Based Approach of Identifying Biological Sequences

The main idea of S-curve diagram is to assign different angle values (from 0° to 180°) to different nucleotide acid residues or to different protein amino acids, and then according to cos α _j and sin α _j , the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences—the degree of similarity—is put forward on the basis of the S-curve diagram. To put it in detail, the least square approach is first adopted to obtain a straight line equation according to the S-curve diagram, then according to the distance formula of the point to the straight line, the average ratio of square sum for the distance between the S-curve and the straight line is calculated, and finally, the similarity of the biological sequences is presented by the new standard—the degree of similarity. As is shown by the experimental results, the S-curve diagram can better represent biological sequences (such as protein’s) within Cartesian coordinate system, and the mutation point of biological sequence. Thus, it turns out that the new standard—the degree of similarity is of obviously great advantage.     

Applications of matrix algebra to communication nets

A “generic” problem amenable to matrix algebraic treatment is outlined. Several examples are given and one, a communication system, is studied in some detail. A typical structure matrix is used to describe the channels of communication and a “status” matrix is used to describe the distribution of information in the system at any time. A theorem is proved relating the status matrix at any timet to thetth power of the structure matrix. The elements of the communication system are interpreted as individuals who can send messages to each other. For the individuals attempting to solve a “group problem” certain relations are derived between the structure and status matrices and time of solution. The structure of the communication system is permitted to vary with time. A general theorem is proved relating the status matrix to the matrix product of the series of structure matrices representing the changing structure of the system. Some suggestions are made for further generalizations. In particular, it is suggested that so-called “higher order” information transmission can be similarly treated.     

Oocyte development in four species of scyphomedusa in the northern Adriatic Sea

Oocyte development was followed in 4 species of Scyphomedusae. In Pelagia noctiluca a centrifugal maturity gradient is present. Vitellogenesis may be related first to exogenous endodermal production and later to oocyte endogenous activity. Simultaneously, the paraovular body (POB) develops from the secondary endoderm; it is connected to the oocyte and controls secretion of mucus, which envelops the oocyte during spawning. In Aurelia aurita, there is no maturity gradient, nor any differentiated structures of endodermal origin, associated with oocytes. In Discomedusa lobata a maturity gradient is absent. Its vitellogenesis is similar to that in P. noctiluca, and is associated with structural modification of the secondary endoderm in the area contacting the oocyte. This structure is cytologically similar to the POB of P. noctiluca, though less differentiated. Spawning is similar to that of P. noctiluca, with fenestration of the surrounding endodermal cells as the oocyte passes from the ovary to the genital sinus. In Rhizostoma pulmo a maturity gradient is absent. An early and fairly evident development of the vitelline membrane was observed.     

Succession in zooplankton and hydrophytes of a seasonal water on the west coast of South Africa

Paramesochra mielkei sp.n. is described and figured from the interstices of subtidal sandy sediments off the SW Dutch coast. Kunz' (1981) phylogenetic scheme of the Paramesochridae Lang, 1948 is re-examined and it is suggested that the family comprises two phyletic lines which originated early in paramesochrid evolution. Translation into Linnean hierarchies implies the establishment of two new sub-families. Within the primitive Diarthrodellinae subfam. n., Tisbisoma Bozic, 1964 is ancestral to Diarthrodella Klie, 1949 s.l. and Rossopsyllus Soyer, 1975. Remanea Klie, 1929 is transferred to the Paramesochrinae subfam. n. which comprises the genera of both the Scottopsyllus- and the Paramesochra-group. The aberrant genus Caligopsyllus Kunz, 1975, standing close to Apodopsyllus, is removed from the Paramesochra-group. P. brevifurca Galhano, 1970 is splitted into two subspecies and replaced in the genus Paramesochra. An attempt is made to assess the phyletic interrelationships of the Paramesochra-species and the resulting cladogram splits the genus into four species-groups. P. mielkei sp.n. is referred to the dubia-group and seems to be closely related to P. borealis Geddes, 1981. Finally, an amended diagnosis and a revised key to the species of the genus Paramesochra are presented.     

The Q-cycle reviewed: How well does a monomeric mechanism of the bc1 complex account for the function of a dimeric complex?

Recent progress in understanding the Q-cycle mechanism of the bc₁ complex is reviewed. The data strongly support a mechanism in which the Q_o-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron–sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe–2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q_o-site, and the reduced iron–sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c₁ and liberate the H⁺. When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O₂ is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b_L to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b_L to enhance the rate constant. The acceptor reactions at the Q_i-site are still controversial, but likely involve a “two-electron gate” in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b₁₅₀ phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed.The mechanism discussed is applicable to a monomeric bc₁ complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b_L hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.     

A new genus of Entiminae from North Africa,supported by a phylogenetic analysis (Coleoptera: Curculionidae: Entiminae)

The genus Holcophloeus gen. nov. is here proposed to include Trachyphloeus cruciatus Seidlitz, 1868, and two new species native to North Africa, based on a phylogenetic analysis and an evaluation of the diagnostic characters. The taxonomic position of Holcophloeus in relation to the tribes Trachyphloeini Lacordaire, 1863, and Holcorhinini Desbrochers, 1898, is discussed, and the new genus is attributed to the Holcorhinini. Holcophloeus laurae sp. nov. from south‐eastern Morocco and Holcophloeus weilli sp. nov. from northern Libya are described and illustrated and a key to the species of the new genus is given. The lectotype of Trachyphloeus cruciatus Seidlitz, 1868, is designated. The genus Massimiellus Borovec, 2009, is transferred from Trachyphloeini to Holcorhinini. © 2013 The Linnean Society of London     

New skull of Lesothosaurus (Dinosauria: Ornithischia) from the Upper Elliot Formation (Lower Jurassic) of southern Africa

A new ornithischian skull from the Elliot Formation of southern Africa is described. The specimen is compared in detail with the fabrosaurid Lesothosaurus diagnosticus. It actually shares many characters with specimens of the syntypes of this species or specimens referred to it. It is nevertheless not identical to any of these specimens and it is, moreover, remarkably larger than them. The possibility of attributing this specimen to a so far undescribed ‘large fabrosaur’ from the same formation is discussed. It is concluded that the specimen in question in this paper, while being ascribable to the genus Lesothosaurus, cannot be determined to a specific level until the existence of two fabrosaurid species in the ‘Stormberg Group’ is demonstrated and their range of morphological and size variation is properly appraised.     

The chromosomes of the Filariae

An understanding of the nature of the chromosomes of the filariae is expected to greatly assist the future interpretation of genome data. Filarial development is not eutelic, and there does not seem to be a fixed number of cell divisions in the way that there is in Caenorhabditis. It is not clear whether the chromosomes of the filariae have localized centromeres or whether they are holocentric. Sex determination is by a chromosomal "balance" X0 system in most filariae, but in some Onchocercidae there has been a chromosomal fusion to create a neo-XY system. It is presumed that the molecular basis of sex determination in filariae is similar to Caenorhabditis. The ancestral karyotype of the filariae is probably 5A+X0, but in some Onchocercidae this has been reduced to 4A+XY, and in O. volvulus and O. gibsoni it has been further reduced to 3A+XY. Onchocerca volvulus and O. gibsoni both have supernumary (B-) chromosomes and in O. volvulus there is a single active nucleolus organising region near the middle of the long autosome.     

Optimal patch use in a stochastic environment

This paper considers an animal foraging on prey which are distributed in well-defined patches. It is assumed that the environment may be stochastic and that the animal can gain information on patch type as it forages. The foraging policy which maximises mean reward rate for the environment is characterised in terms of a function of state called the potential function. This policy is shown to be given by the rule: continue foraging on the present patch while the potential is positive, when the potential falls to zero move on to the next patch. Let r denote the current reward rate on a patch and let γ denote the maximum mean reward rate for the environment. It is shown that r ? γ if it is optimal to leave. Conditions which ensure r < γ are also given. For a large class of environments the optimal policy is stated in terms of a revised reward rate r?, and is given by the rule: continue on the present patch while $\text{r}\text{?}\text{> γ}$, when r? falls to γ move on to the next patch. Finally, it is shown that the stay time on a patch is a decreasing function of γ.     

The effect of divalent cations on Na+ tolerance in Charophytes. II: Chara corallina

Abstract The freshwater Charophyte Chora corallina dies when subjected to 70 molm^?3 NaCl if the Ca²⁺ concentration is 0.1 mol m ^?3. This stress is accompanied by a depolarization of the cell to a membrane potential more positive than E_K, a net influx of Na⁺ into the vacuole, and a net loss of K⁺ from the vacuole. Raising the Ca²⁺ concentration to 7 mol m ^?3 in the presence of elevated Na⁺ restores the Na⁺ to Ca²⁺ ratio to 10: 1 as in the control solution, and results in enhanced survival even though turgor is not regulated. Mg²⁺ is not a good substitute for Ca²⁺. It is suggested that the main reason that C. corallina fails to occupy saline habitats is its failure to regulate turgor, not sensitivity to Na ⁺, since the latter is similar to that seen in C. buckellii, which is found in saline habitats.     

The nonenzymic hydrolysis of Δ2-thiazoline-2-carboxylate: The product of the suspected physiological reaction catalyzed by d-amino acid oxidase

Δ²-Thiazoline-2-carboxylate, the product of the suspected physiological reaction catalyzed by d-amino acid oxidase, is stable to hydrolysis at 37°C and pH 7 or above, but it hydrolyzes readily at pH 5 or below to give a mixture of N- and S-oxalylcysteamines; the N-oxalyl derivative predominates at pH's above 1 while the S-oxyalyl compound is the major product at high acidities. The pH-rate profile looks like the superposition of two bell-shaped curves. The initial increase in the rate as the pH is lowered is controlled by a pK_a of 3.95 and from pH 1 to 3 the rate is relatively constant (k = 6.7 × 10⁻⁴s⁻¹ at 37°C and ionic strength 0.5 m). Below pH 1 the rate increases again to a maximum in 1 m HCl and then decreases in more highly acidic solutions. The rate of conversion of S-oxalylcysteamine to N-oxalylcysteamine is inversely proportional to the hydrogen ion concentration from pH 3 to 5 but becomes largely independent of pH from pH 1 to 2. In the pH-independent region the rate is comparable with that observed by others for S-acetylcysteamine but in the pH-dependent region the rate is 20 to 25 times faster for the oxalyl derivative than for the acetyl compound. At pH 1, N-oxalylcysteamine is partially converted to the S-oxalyl derivative but the rate of hydrolysis (k = 1.0 × 10⁻⁵s⁻¹ at 37°C) to cysteamine and oxalate of this partially equilibrated system occurs at a comparable rate. The results of this investigation are rationalized in terms of what is known about other thiazoline hydrolyses and intramolecular S to N acyl migrations. The main differences in the present case are presumably due to the fact that thiazoline-2-carboxylate can undergo hydrolysis by two reaction manifolds, one with the carboxyl unprotonated and the other with it protonated. The relevance of these results to possible reactions of thiazoline-2-carboxylate in vivo is briefly considered.