Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Information processing and higher psychological functions in the disconnected hemispheres of human commissurotomy patients

Several patients of P. J. Vogel who had undergone cerebral commissurotomy for the control of intractable epilepsy were tested on a variety of tasks to measure aspects of cerebral organization concerned with lateralization in hemispheric function. From tests involving identification of shapes it was inferred that in the absence of the neocortical commissures, the left hemisphere still has access to certain types of information from the ipsilateral field. The major hemisphere can still make crude differentiations between various left-field stimuli, but is unable to specify exact stimulus properties. Most of the time the major hemisphere, having access to some ipsilateral stimuli, dominated the minor hemisphere in control of the body.

Competition for control of the body between the hemispheres is seen most clearly in tests of minor hemisphere language competency, in which it was determined that though the minor hemisphere does possess some minimal ability to express language, the major hemisphere prevented its expression much of the time. The right hemisphere was superior to the left in tests of perceptual visualization, and the two hemispheres appeared to use different strategies in attempting to solve the problems, namely, analysis for the left hemisphere and synthesis for the right hemisphere.

Analysis of the patients' verbal and performance I.Q.'s, as well as observations made throughout testing, suggest that the corpus callosum plays a critical role in activities that involve functions in which the minor hemisphere normally excels, that the motor expression of these functions may normally come through the major hemisphere by way of the corpus callosum.

Lateral specialization is thought to be an evolutionary adaptation which overcame problems of a functional antagonism between the abilities normally associated with the two hemispheres. The tests of perception suggested that this function lateralized into the mute hemisphere because of an active counteraction by language. This latter idea was confirmed by the finding that left-handers, in whom there is likely to be bilateral language centers, are greatly deficient on tests of perception.

Metallogenic Provinces of the Southwestern United States and Northern Mexico

Some of the metallogenic provinces of the southwestern United States and northern Mexico are defined by the geographic distribution of trace elements in the primary sulfide minerals chalcopyrite and sphalerite. The elements investigated include antimony, arsenic, bismuth, cadmium, cobalt, gallium, germanium, indium, manganese, molybdenum, nickel, silver, tellurium, thallium, and tin. Of these elements, cobalt, gallium, germanium, indium, nickel, silver, and tin exhibit the best defined geographic distribution.

The data indicate that chalcopyrite is the preferred host for tin and perhaps molybdenum; sphalerite is the preferred host for cadmium, gallium, germanium, indium, and manganese; galena is the preferred host for antimony, bismuth, silver, tellurium, and thallium; and pyrite is the preferred host for cobalt, nickel, and perhaps arsenic. With respect to the two minerals chalcopyrite and sphalerite, antimony, arsenic, molybdenum, nickel, silver, and tin prefer chalcopyrite; and bismuth, cadmium, cobalt, gallium, germanium, indium, manganese, and thallium prefer sphalerite. This distribution probably is the result of the interaction of several factors, among which are these: the various radii of the elements, the association due to chemical similarities of the major and trace elements, and the degree of ionic versus covalent and metallic character of the metal-sulfur bonds in chalcopyrite and sphalerite. The type of deposit, according to a temperature classification, appears to be of minor importance in determining the trace element content of chalcopyrite and sphalerite.

A preliminary investigation of large single crystals of sphalerite and chalcopyrite indicates that the distribution within a single crystal of some elements such as cadmium in sphalerite and indium and silver in chalcopyrite is relatively uniform, whereas the distribution of some other elements such as cobalt and manganese in sphalerite is somewhat less uniform and the distribution of tin in sphalerite is extremely erratic. The variations in trace element content probably are due largely to variations in the composition of the fluids during the growth of the crystals, but the erratic behavior of tin in sphalerite perhaps is related to the presence of numerous cavities and inclusions in the crystal studied.

Maps of the geographic distribution of trace elements in chalcopyrite and sphalerite exhibit three main belts of greater than average trace element content, which are called the Eastern, Central, and Western belts. These belts are consistent in trend and position with a beltlike distribution of copper, gold, lead, zinc, silver, and tungsten deposits and with most of the major tectonic features. However, there appear to be no definite time relationships, for as many as four metallogenic epochs, from Precambrian to late Tertiary, are represented by ore deposits within the Central belt.

The evidence suggests that the beltlike features have a deep seated origin, perhaps in the sub-crust or outer parts of the mantle, and that the deposits within each belt might be genetically related through a beltlike compositional heterogeneity in the source regions of the ores. Hence, the belts are regarded as metallogenic provinces.