A suitable method for localization of IAA oxidase

The method for histochemical detection of IAA oxidase proposed by Sagi was tested, based on colour reaction of natural products of IAA oxidation with Ehrlich-like reagent.     

A hypothetical explanation of congenital nystagmus

Congenital nystagmus (CN) is a conjugate, rhythmic, eye movement disorder characterized by a wide variety of waveforms ranging from jerk to pendular types. No detailed mechanisms have been proposed to explain the generation of the CN wave-form This paper proposes a hypothetical mechanism for CN, and shows with computer simulations that a model based on this hypothesis can account for a variety of disparate waveforms. The basis of this model is a gaze-holding network, or neural integrator, that has both position and velocity feedback loops. The signals carried in these loops could arise from either afference or efference. In normal subjects, the position feedback would be positive and the velocity feedback would be negative. Both would help to increase the time constant of an imperfect neural integrator in the brain stem. We propose that in patients with CN the sign of the velocity pathway is reversed, making the neural integrator unstable. This instability could manifest as many different CN waveforms, depending on the direction and velocity of post-saccadic ocular drift and actions of nonlinearities within the position and velocity feedback loops. Thus a single underlying abnormality may be responsible for a variety of CN waveforms.     

Diffusion-enhanced bioreactions: A hypothetical mechanism for plant cell aggregation

We show that the existence of diffusional resistance due to the presence of a solid phase can have a positive effect on the metabolic reactions of plant cells. In this case the efficiency of metabolic reactions, defined as the ratio of rate of production of biomass of aggregated cells/rate of production of biomass of dispersed cells, can be greater than unity for a certain range of aggregate sizes for both solid spheres (common plant cell aggregates) and hollow spheres (e.g.Volvox aggregates). This means that, under appropriate conditions, plant cells tend to stay in the aggregated form to improve the efficiency of their metabolic reactions. The result of the present analysis provides an explanation as to why aggregates of plant cells are observed under typical culture conditions.     

A route for prion neuroinvasion

The astonishing recognition that self-propagating changes in protein structure may be at the basis of spongiform encephalopathies is changing our views of transmissible diseases. Infectious agents consisting of abnormally folded proteins (i.e., the prion) can propagate in host organisms using previously unrecognized routes and invade the brain after a dangerous liaison with the immune system. The identification of the nodal points of neuroinvasion and new techniques to amplify minute amounts of misfolded proteins may open the possibility for post exposure prophylaxis.     

A hypothetical synaptic-neural-behavioral model of operant learning

Biological Cybernetics -     

A role for IAA in the infection of Arabidopsis thaliana by Orobanche aegyptiaca

BACKGROUND: Vascular continuity is established between a host plant and the root parasite broomrape. It is generally accepted that the direction of vascular continuity results from polar flow of auxin. Our hypothesis was that chemical disruptions of auxin transport and activity could influence the infection of the host by the parasite. METHODS: A sterile system for the routine infection of Arabidopsis thaliana seedlings in Nunc cell culture plates by germinated seeds of Orobanche aegyptiaca was developed. This method permitted a quantitative assay of the rate of host infection. The three-dimensional structure of the vascular contacts was followed in cleared tissue. IAA (indole acetic acid) or substances that influence its activity and transport were applied locally to the host root. RESULTS: The orientation of the xylem contacts showed that broomrape grafts itself upon the host by acting hormonally as a root rather than a shoot. Local applications of IAA, PCIB (p-chlorophenoxyisobutyric acid) or NPA (naphthylphthalamic acid) all resulted in drastic reductions of Orobanche infection CONCLUSIONS: Broomrape manipulates the host by acting as a sink for auxin. Disruption of auxin action or auxin flow at the contact site could be a novel basis for controlling infection by Orobanche.     

A new route for polar navigation

Placement of motility structures at the poles of rod‐shaped bacteria is a common engineering problem with a variety of potential solutions. While investigating the mechanisms for positioning of the single polar flagellum of Pseudomonas aeruginosa, Cowles and colleagues discovered a new membrane‐bound three‐component system related to TonB–ExbB–ExbD that they named ‘Poc’ for p olar o rganelle c o‐ordinator, which controls polar localization of both the flagellum and type IV pili. The Poc complex itself is not found at the poles, and is required for increased expression of pilus genes upon surface association, suggesting a new paradigm of localization control.     

Functional annotation of hypothetical proteins - A review

The complete human genome sequences in the public database provide ways to understand the blue print of life. As of June 29, 2006, 27 archaeal, 326 bacterial and 21 eukaryotes is complete genomes are available and the sequencing for 316 bacterial, 24 archaeal, 126 eukaryotic genomes are in progress. The traditional biochemical/molecular experiments can assign accurate functions for genes in these genomes. However, the process is time-consuming and costly. Despite several efforts, only 50-60 % of genes have been annotated in most completely sequenced genomes. Automated genome sequence analysis and annotation may provide ways to understand genomes. Thus, determination of protein function is one of the challenging problems of the post-genome era. This demands bioinformatics to predict functions of un-annotated protein sequences by developing efficient tools. Here, we discuss some of the recent and popular approaches developed in Bioinformatics to predict functions for hypothetical proteins.     

A new entry route for HIV

Identification of HIV-1 variants capable of entering T cells via the CD8 receptor suggests a new mode of viral pathogenesis. But are these variants rare, aberrant viruses or a real problem?     

Elisa determination of IAA using antibodies against ring-linked IAA

An enzyme-linked immunosorbent assay (ELISA) for indole-3-acetic acid (IAA) is described which uses antibodies raised against IAA conjugated to carrier protein on the indolic ring of IAA. As little as 0.5 pmol of IAA is detectable with the ELISA. There is no significant cross-reactivity with amide conjugates of IAA and samples do not need methylation, in contrast to an ELISA using antibodies raised against carboxyl-linked IAA. Affinity chromatography on IAA-agarose was used to purify antibody preparations. Measurements of IAA levels in crown gall tumour tissue lines were made using the assay.     

Ophioglossaceae: a hypothetical archetype for the angiosperm carpel

KATO, M., 1990.Ophioglossaceae: a hypothetical archetype for the angiosperm carpel. In the light of a recently proposed phylogenetic position of Ophioglossaceae as living progymnosperms, a new archetype model for the angiosperm carpel is proposed. The three-dimensional construction of ophioglossoid fertile leaves with epiphyllous sporophores may be comparable to angiosperm carpels with adaxial ovules. The orientation of erect sporangia on young sporophores dorsiventrally facing the trophophores resembles that of anatropous ovuleS. Glossopterid fructifications may be interpreted as having the same construction as ophioglossoid leaveS. In the present hypothesis, the adaxial position of the ovules arose prior to the evolutionary process leading from gymnospermy to angiospermy. Previous hypotheses involving origins from Caytonia and Glossopteris are criticized.     

The slow process: A hypothetical cognitive adaptation for distributed cognitive networks

Human cognitive evolution is characterized by two special features that are truly novel in the primate line. The first is the emergence of "mindsharing" cultures that perform cooperative cognitive work, and serve as distributed cognitive networks. The second is the emergence of a brain that is specifically adapted for functioning within those distributed networks, and cannot realize its design potential without them. This paper proposes a hypothetical neural process at the core of this brain adaptation, called the "slow process". It enables the human brain to comprehend social events of much longer duration and complexity than those that characterize primate social life. It runs in the background of human cognitive life, with the faster moving sensorimotor interface running in the foreground. Most mammals can integrate events in the shorter time zone that corresponds to working memory. However, very few can comprehend complex events that extend over several hours (for example, a game or conversation) in what may be called the "intermediate" time zone. Adult humans typically live, plan, and imagine their lives in this time range, which seems to exceed the capabilities of our closest relatives, bonobos and chimpanzees. In summary, human cognition has both an individual and a collective dimension. Individual brains and minds function within cognitive-cultural networks, or CCNs, that store and transmit knowledge. The human brain relies on cultural input even to develop the basic cognitive capacities needed to gain access to that knowledge in the first place. The postulated slow process is a top-down executive capacity that evolved specifically to manage the cultural connection, and handle the cognitive demands imposed by increasingly complex distributed systems.     

A database of six eukaryotic hypothetical genes and proteins

Assigning functions to proteins of unknown function is of considerable interest to the proteomic researchers as the genes encoding them are conserved over various species. Here, we describe HypoDB, a database of hypothetical genes and proteins in six eukaryotes. The database was collected and organized based on the number of entries in each chromosome with few annotations. Hypothetical protein database contains information related to gene and protein sequences, chromosome number and location, secondary and tertiary structure related data. AVAILABILITY: The database is available for free at http://www.trimslabs.com/database/hypodb/index.html.     

A hypothetical anti-neoplastic mechanism associated to reserve cells

Reserve-stem cells, the permanent cells of body tissues, are thought to be the progenitor cells of cancer. This concept originates from the assumption that accumulation of somatic mutations necessary for malignant transformation can only take place in cellular targets with a prolonged life span. The progeny of reserve cells entering the differentiative pathway would be protected from potential critical mutations happening later than the reserve cell stage by normal cell population replacement unless possible targets would escape the replacement process by further mutations extending the cell's life span, impairment of physiological apoptosis. The existence of a mechanism for maintenance of genetic integrity in stem/reserve cells has previously been proposed. This mechanism differs from already identified DNA repair systems and, potentially, could prevent malignant transformation at the reserve cell stage, counteracting the expected high propensity of stem/reserve cells to neoplastic proliferation. Here, we show some histopathological observations suggesting that an anti-cancer mechanism might be associated to reserve/stem cells and that it could be responsible for huge differences in cancer incidence between closely related body sites. Furthermore, primary impairment of this protective mechanism might characterize the oncogenic pathway responsible for tumors of primitive cells. Several features of the histopathological observations presented lead us to propose that the underlying molecular mechanism may involve the telomere complex.     

A study of the hypothetical role of cytokinins in completion of tRNA

Summary It has been suggested that the effect of cytokinins in retarding leaf senescence comes about through their incorporation into tRNA. To test this hypothesis, kinetin-8-¹⁴C, 6-benzylaminopurine-benzyl-7-¹⁴C and adenine-8-³H were applied to detached tobacco leaves, and the nucleic acids were thereafter extracted and chromatographed on MAK columns. Kinetin-8-¹⁴C and adenine-8-³H were readily incorporated into RNA in a similar pattern. 6-Benzylaminopurine-benzyl-7-¹⁴C was effective in delaying chlorophyll loss but was not incorporated into any nucleic-acid fraction. It is concluded that the possibility of cytokinins retarding leaf senescence by completion of tRNA is not supported.     

Biochemical Bases for the Loss of Basipetal IAA Transport with Advancing Physiological Age in Etiolated Helianthus Hypocotyls: Changes in IAA Movement, Net IAA Uptake, and Phytotropin Binding

Basipetal transport of [¹⁴C]IAA in hypocotyl segments isolated from various regions of etiolated Helianthus annuus L. cv NK 265 seedlings declines with increasing physiological age. This decline was the result of a reduction in both transport capacity and apparent velocity. Net IAA uptake was greater and the abilities of auxin transport inhibitors to stimulate net IAA uptake were reduced in older tissues. Net IAA accumulation by microsomal vesicles exhibited a similar behavior with respect to age. Specific binding of [³H]N-1-naphthylphthalamic acid (NPA) to microsomes prepared from young and older hypocotyl regions was saturable and consistent with a single class of binding sites. The apparent affinity constants for NPA binding in microsomes prepared from young versus older tissues were 6.4 and 10.8 nanomolar, respectively, and the binding site densities for young versus old tissues were 7.44 and 3.29 picomoles/milligram protein, respectively. Specific binding of [³H]NPA in microsomes prepared from both tissues displayed similar sensitivities toward unlabeled flurenol and exhibited only slight differences in sensitivity toward 2,3,5-triiodobenzoic acid. These results demonstrate that the progressive loss of basipetal IAA transport capacity in etiolated Helianthus hypocotyls with advancing age is associated with substantial alterations in the phytotropin-sensitive, IAA efflux system and they suggest that these changes are, at least partially, responsible for the observed reduction of polar IAA transport with advancing tissue age.