Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Length-weight relationship and the diets of Clarias lazera (Cuvier and Valenciennes), family Clariidae (Osteichthyes: Siluriformes) in Zaria, Nigeria

The length-weight relationship and the diets of Clarias lazera were investigated between July 1981 and June 1982. About 450 specimens were examined. The standard lengths of the fish ranged from 8.5 cm to 42.2 cm. Significant differences were found between the standard lengths of the males and females with the latter slightly shorter. Somatic weights varied between 10 g to 502 g. Length-weight regression analysis gave a "b" value of 3.02 for both males and females combined; thus indicating an isometric growth. Analysis of the food in the stomachs showed that the fish is an omnivore although, it fed more on insects and fish than other food items

Triploidy induction in Heterobranchus longifilis (Family: Clariidae) by cold shock

Triploid was induced in African Catfish (Heterobranchus longifilis) by cold shocking activated eggs at 5 degree C for forty minutes starting 3-4 minutes after fertilization. Triploidy was confirmed from mitotic chromosomes prepared from embryo which showed 100% triploidy in the cold shocking treatment and 100% diploidy in the control treatment

Effects of some environmental factors on the fecundity of Tilapia species (Family Cichlidae) in Kigera Reservoir, New Bussa

The effects of some environmental factors on the fecundity of Tilapia species (Family Cichilidae) was carried out at the Kigera dam. Four Tilapia species caught were Tilapia zilli, Hemichromis fasciatus, Sarotherodon galilaeus and Oreochromis niloticus while the environmental factors considered were water temperature, Dissolved Oxygen, pH value, level of rainfall and rate of sunshine and range of time. 43 fish comprising of 25 male with (58.1%) and 18 females having (41.9%) were studied with 74.42% been sexually matured. Both high levels of rainfall and dissolved oxygen favoured fecundity. The spawning peak occurred in (July), environmental factors monitored indicated that dissolved oxygen ranges from 3.7 to 4.45mg/lit rainfall ranges from (34.90mm to 237.80mm) sunshine ranges from (5hrs-8hrs) and pH ranges from (7.35-7.45). The spawning of these species in their natural or hatchery condition is therefore best achieved during the peak of raining season

Multiplexed DNA-mediated electrochemistry

The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of π-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the π-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA π-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.

First, Methylene Blue (MB′) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB′ was reduced through DNA-mediated charge transport. The redox signal intensity for MB′-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB′ on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.

Next, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening π-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA. Further gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.

Finally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Structure of the limbs and its significance for the ecology and systematics of the family Chydoridae. [Translation of: Voprosy Gidrobiologii, p385, 1965]

For an explanation of the dynamics of numbers of chydorids, appearing a massive group in the littoral of fresh water bodies, the structure of the limbs of 29 species was studied.

Key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae of the fauna of the USSR. [Translation from: Larvae and pupae of midges of the subfamily Orthocladiinae of the fauna of the USSR (Diptera, Chironomidae = Tendipedidae) (ed. Pankratova V.Ya.), 51-55. Leningrad, Nauka, 1970. ]

A key to the larvae of the genera of the sub-family Orthocladiinae from Larvae and Pupae of midges of the sub-family Orthocladiinae. Parts of the key refer to the rest of the publication which is not included in this partial translation.

Family: Cladophora Kutzing 1843. identification key. [ Translation from: Flora Slodkowodna Polski 10, 227-263, 1972.]

A description of the algal genus Cladophora from Vol 10 of the ”Freshwater Flora of Poland”. Illustrations are included.

The family of chironomids or midges - Chironomidae. Keys to larvae and pupae [Translation from: Guide to the freshwater invertebrates of the European area of the USSR (Plankton and benthos) (ed. L. A. Kutikova and Ya. I. Starobogatov), p.371-431. Leningrad, Gidrometeoizdat, 1977]

The translation of this section of the larger publication ”Opredelitel' presnovodnykh bespozvonochnykh evropeiskoi chasti SSSR. (Plankton i bentos)” provides identification keys to the larvae and pupae of chironomids that occur in the Soviet Union. The morphology of the larvae of Chironomidae is described in the introductory part.

Diasporization and family relations in Nella Larsens Quicksand and Jamaica Kincaids Lucy: the construction of female identity

O principal objetivo desta dissertação é investigar e analisar como os movimentos diaspóricos e as relações familiares exercem influência na construção das identidades das mulheres em Quicksand, de Nella Larsen, e Lucy, de Jamaica Kincaid. As questões a que pretendo responder são: Como as personagens principais, Helga Crane e Lucy, lidam com as diferentes culturas que encontram nas suas trajetórias ? ; Como essas diferentes culturas lidam com essas mesmas personagens?; e Como o encontro entre essas diferentes culturas e as relações familiares são descritos e influenciam na construção da identidade feminina nessas obras?. Minha hipótese é que encontraremos nas obras selecionadas duas jornadas, portadoras tanto de aspectos comuns quanto distintos, que começam com o desejo das personagens principais de escapar da opressão patriarcal. Isto é, Helga Crane e Lucy passam por um período de muitas descobertas sobre elas mesmas e as sociedades com que têm que lidar, o que determina dois produtos diferentes: a construção das identidades híbridas de Lucy, em meio a sua solidão, na obra de Kincaid, e a construção e o sufocamento das identidades de Helga pela religião, o patriarcado e as relações familiares, na obra de Larsen

Development of larval and early juvenile penpoint gunnel (Apodichthys flavidus) (family: Pholidae)

The penpoint gunnel (Apodichthys flavidus) is a member of the perciform family Pholidae. Pholids, commonly referred to as gunnels, are eel-like fishes that inhabit the rocky intertidal and subtidal regions of the northern oceans and are often associated with macroalgae, such as Fucus spp. or kelp (Watson, 1996). Gunnels are ecologically important forage fishes that form part of the diet of birds and commercially important groundfish species (Hobson and Sealy, 1985; NMFS1; Golet et al., 2000). The diet of A. flavidus and other pholids comprises primarily harpactacoid copepods, gammarid amphipods, isopods, and other crustaceans (Cross, 1981). Apodichthys flavidus ranges along the west coast of North America from southern California to the Gulf of Alaska (Mecklenburg et al., 2002). Adult A. flavidus are distinguished from other pholids by their total vertebral counts, the presence of a thick and grooved first anal spine, a preanal length that is approximately 60% standard length (SL), and a dark green to light olive coloration (Yatsu, 1981). It is one of the largest pholids (up to 46 cm) and is important in the live fish trade for both home and public aquaria (Froese and Pauly2).