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Ted Johnson

Publications and source records attributed to Ted Johnson.

8 recordsLinked to original sources
PubMed2005

The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.

The let-7 microRNA is phylogenetically conserved and temporally expressed in many animals. C. elegans let-7 controls terminal differentiation in a stem cell-like lineage in the hypodermis, while human let-7 has been implicated in lung cancer. To elucidate let-7's role in temporal control of nematode development, we used sequence analysis and reverse genetics to identify candidate let-7 target genes. We show that the nuclear hormone receptor daf-12 is a let-7 target in seam cells, while the forkhead transcription factor pha-4 is a target in the intestine. Additional likely targets are the zinc finger protein die-1 and the putative chromatin remodeling factor lss-4. Together with the previous identification of the hunchback ortholog hbl-1 as a let-7 target in the ventral nerve cord, our findings show that let-7 acts in at least three tissues to regulate different transcription factors, raising the possibility of let-7 as a master temporal regulator.

Animals↗
PubMed2005

Determining the frequency of open windows in residences: a pilot study in Durham, North Carolina during varying temperature conditions.

Air pollution exposures in the residential microenvironment can be significantly affected by air exchange rate (AER). A number of studies have shown that AER in residences is significantly affected by the number and location of open windows and doors. A pilot study was conducted in Durham, North Carolina, to determine whether useful data on open windows and doors could be acquired through a visual survey. The study consisted of 72 2-h survey sessions conducted between October 24, 2001 and March 13, 2003. During the first hour of each session, a technician selected a set of corner residences in one of 48 census tracts and completed a survey form and meteorological measurements for each residence. During the second hour, the technician revisited each residence surveyed during the first hour. The resulting database included data on 2200 "residential visits" (1100 residences times two visits per residence). The technician observed one or more open windows during 20.0 percent of the residential visits. One or more open doors were observed during 13.4 percent of the residential visits; 28.2 percent of the residential visits were associated with at least one open window or door. A series of stepwise linear regression analyses were performed on the data to identify factors associated with open windows and doors. Results of these analyses indicated that the likelihood of one or more windows being opened tended to increase under the following conditions: occupancy at time of visit; session during April, May, or June; high population or housing density; window air conditioning (AC) units; absence of AC; large number of doors; and wind speed above 2 mph. The likelihood of open doors tended to increase under the following conditions: occupancy at time of visit; residence within city limits; session during April, May, or June; detached one-story residence; large number of doors; high housing density; school out; and residence within 10 m of road. Transition probabilities (closed to open and open to closed) were determined for windows and doors by time of day.

Air Conditioning↗
PubMed2004

A pilot study using scripted ventilation conditions to identify key factors affecting indoor pollutant concentration and air exchange rate in a residence.

A pilot study was conducted using an occupied, single-family test house in Columbus, OH, to determine whether a script-based protocol could be used to obtain data useful in identifying the key factors affecting air-exchange rate (AER) and the relationship between indoor and outdoor concentrations of selected traffic-related air pollutants. The test script called for hourly changes to elements of the test house considered likely to influence air flow and AER, including the position (open or closed) of each window and door and the operation (on/off) of the furnace, air conditioner, and ceiling fans. The script was implemented over a 3-day period (January 30-February 1, 2002) during which technicians collected hourly-average data for AER, indoor, and outdoor air concentrations for six pollutants (benzene, formaldehyde (HCHO), polycyclic aromatic hydrocarbons (PAH), carbon monoxide (CO), nitric oxide (NO), and nitrogen oxides (NO(x))), and selected meteorological variables. Consistent with expectations, AER tended to increase with the number of open exterior windows and doors. The 39 AER values measured during the study when all exterior doors and windows were closed varied from 0.36 to 2.29 h(-1) with a geometric mean (GM) of 0.77 h(-1) and a geometric standard deviation (GSD) of 1.435. The 27 AER values measured when at least one exterior door or window was opened varied from 0.50 to 15.8 h(-1) with a GM of 1.98 h(-1) and a GSD of 1.902. AER was also affected by temperature and wind speed, most noticeably when exterior windows and doors were closed. Results of a series of stepwise linear regression analyses suggest that (1) outdoor pollutant concentration and (2) indoor pollutant concentration during the preceding hour were the "variables of choice" for predicting indoor pollutant concentration in the test house under the conditions of this study. Depending on the pollutant and ventilation conditions, one or more of the following variables produced a small, but significant increase in the explained variance (R(2)-value) of the regression equations: AER, number and location of apertures, wind speed, air-conditioning operation, indoor temperature, outdoor temperature, and relative humidity. The indoor concentrations of CO, PAH, NO, and NO(x) were highly correlated with the corresponding outdoor concentrations. The indoor benzene concentrations showed only moderate correlation with outdoor benzene levels, possibly due to a weak indoor source. Indoor formaldehyde concentrations always exceeded outdoor levels, and the correlation between indoor and outdoor concentrations was not statistically significant, indicating the presence of a strong indoor source.

Air Pollution, Indoor↗
PubMed2004

Frequency of open windows in motor vehicles under varying temperature conditions: a videotape survey in Central North Carolina during 2001.

Air pollution exposures in the motor vehicle cabin are significantly affected by air exchange rate, a function of vehicle speed, window position, vent status, fan speed, and air conditioning use. A pilot study conducted in Houston, Texas, during September 2000 demonstrated that useful information concerning the position of windows, sunroofs, and convertible tops as a function of temperature and vehicle speed could be obtained through the use of video recorders. To obtain similar data representing a wide range of temperature and traffic conditions, a follow-up study was conducted in and around Chapel Hill, North Carolina at five sites representing a central business district, an arterial road, a low-income commercial district, an interstate highway, and a rural road. Each site permitted an elevated view of vehicles as they proceeded through a turn, thereby exposing all windows to the stationary camcorder. A total of 32 videotaping sessions were conducted between February and October 2001, in which temperature varied from 41 degrees F to 93 degrees F and average vehicle speed varied from 21 to 77 mph. The resulting video tapes were processed to create a vehicle-specific database that included site location, date, time, vehicle type, vehicle color, vehicle age, window configuration, number of windows in each of three position categories (fully open, partially open, and closed), meteorological factors, and vehicle speed. Of the 4715 vehicles included in the database, 1905 (40.4%) were labeled as "open," indicating a window, sunroof, or convertible top was fully or partially open. Stepwise linear regression analyses indicated that "open" window status was affected by wind speed, relative humidity, vehicle speed, cloud cover, apparent temperature, day of week, time of day, vehicle type, vehicle age, vehicle color, number of windows, sunroofs, location, and air quality season. Open windows tended to occur less frequently when relative humidity was high, apparent temperature (a parameter incorporating wind chill and heat index) was below 50 degrees F, or the vehicle was relatively new. Although the effects of the identified parameters were relatively weak, they are statistically significant and should be considered by researchers attempting to model vehicle air exchange rates.

Air Movements↗
PubMed2002

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.

BACKGROUND: The sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. Through the analysis of such inventories, it has been shown that different genomes have very different usage of parts; for example, the common folds in the worm are very different from those in Escherichia coli. RESULTS: Despite these differences, we find that the genomic occurrence of generalized parts follows a well-known mathematical framework called the power law, with a few parts occurring many times and most occurring only a few times. This observation is true in a wide variety of genomic contexts. Earlier studies found power laws in a few specific cases, such as the occurrence of protein families. Here, we find many further cases of power-law behavior, for example in the occurrence of pseudogenes and in levels of gene expression. We show comprehensively that this behavior applies across many different genomes, for many different types of parts (DNA words, InterPro families, protein superfamilies and folds, pseudogene families and pseudomotifs), and for the many disparate attributes associated with these parts (their functions, interactions and expression levels). CONCLUSIONS: Power-law behavior provides a concise mathematical description of an important biological feature: the sheer dominance of a few members over the overall population. We present this behavior in a unified framework and propose that all these observations are connected to an underlying DNA duplication process as genomes evolved to their current state.

Animals↗
PubMed2002

Determining the frequency of open windows in motor vehicles: a pilot study using a video camera in Houston, Texas during high temperature conditions.

Researchers have developed a variety of computer-based models to estimate population exposure to air pollution. These models typically estimate exposures by simulating the movement of specific population groups through defined microenvironments. Exposures in the motor vehicle microenvironment are significantly affected by air exchange rate, which in turn is affected by vehicle speed, window position, vent status, and air conditioning use. A pilot study was conducted in Houston, Texas, during September 2000 for a specific set of weather, vehicle speed, and road type conditions to determine whether useful information on the position of windows, sunroofs, and convertible tops could be obtained through the use of video cameras. Monitoring was conducted at three sites (two arterial roads and one interstate highway) on the perimeter of Harris County located in or near areas not subject to mandated Inspection and Maintenance programs. Each site permitted an elevated view of vehicles as they proceeded through a turn, thereby exposing all windows to the stationary video camera. Five videotaping sessions were conducted over a two-day period in which the Heat Index (HI)-a function of temperature and humidity-varied from 80 to 101 degrees F and vehicle speed varied from 30 to 74 mph. The resulting videotapes were processed to create a master database listing vehicle-specific data for site location, date, time, vehicle type (e.g., minivan), color, window configuration (e.g., four windows and sunroof), number of windows in each of three position categories (fully open, partially open, and closed), HI, and speed. Of the 758 vehicles included in the database, 140 (18.5 percent) were labeled as "open," indicating a window, sunroof, or convertible top was fully or partially open. The results of a series of stepwise linear regression analyses indicated that the probability of a vehicle in the master database being "open" was weakly affected by time of day, vehicle type, vehicle color, vehicle speed, and HI. In particular, open windows occurred more frequently when vehicle speed was less than 50 mph during periods when HI exceeded 99.9 degrees F and the vehicle was a minivan or passenger van. Overall, the pilot study demonstrated that data on factors affecting vehicle window position could be acquired through a relatively simple experimental protocol using a single video camera. Limitations of the study requiring further research include the inability to determine the status of the vehicle air conditioning system; lack of a wide range of weather, vehicle speed, and road type conditions; and the need to exclude some vehicles from statistical analyses due to ambiguous window positions.

Air Movements↗
PubMed2002

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.

We have developed an initial approach for annotating and surveying pseudogenes in the human genome. We search human genomic DNA for regions that are similar to known protein sequences and contain obvious disablements (i.e., mid-sequence stop codons or frameshifts), while ensuring minimal overlap with annotations of known genes. Pseudogenes can be divided into "processed" and "nonprocessed"; the former are reverse transcribed from mRNA (and therefore have no intron structure), whereas the latter presumably arise from genomic duplications. We annotate putative processed pseudogenes based on whether there is a continuous span of homology that is >70% of the length of the closest matching human protein (i.e., with introns removed), or whether there is evidence of polyadenylation. We have applied our approach to chromosomes 21 and 22, the first parts of the human genome completely sequenced, finding 190 new pseudogene annotations beyond the 264 reported by the sequencing centers. In total, on chromosomes 21 and 22, there are 189 processed pseudogenes, 195 nonprocessed pseudogenes, and, additionally, 70 pseudogenic immunoglobulin gene segments. (Detailed assignments are available at http://bioinfo.mbb.yale.edu/genome/pseudogene or http://genecensus.org/pseudogene.) By extrapolation, we predict that there could be up to approximately 20,000 pseudogenes in the whole human genome, with a little more than half of them processed. We have determined the main populations and clusters of pseudogenes on chromosomes 21 and 22. There are notable excesses of pseudogenes relative to genes near the centromeres of both chromosomes, indicating the existence of pseudogenic "hot-spots" in the genome. We have looked at the distribution of InterPro families and Gene Ontology (GO) functional categories in our pseudogenes. Overall, the families in both processed and nonprocessed pseudogene populations occur according to a similar power-law distribution as that found for the occurrence of gene families, with a few big families and many small ones. The processed population is, in particular, enriched in highly expressed ribosomal-protein sequences (approximately 20%), which appear fairly evenly distributed across the chromosomes. We compared processed pseudogenes of different evolutionary ages, observing a high degree of similarity between "ancient" and "modern" subpopulations. This may be attributable to the consistently high expression of ribosomal proteins over evolutionary time. Finally, we find that chromosome 22 pseudogene population is dominated by immunoglobulin segments, which have a greater rate of disablement per amino acid than the other pseudogene populations and are also substantially more diverged.

Chromosome Mapping↗