Biomedical subjects

Jianmin Ma

Publications and source records attributed to Jianmin Ma.

13 recordsLinked to original sources

PubMed2005

Tracking toxaphene in the North American Great Lakes basin. 1. Impact of toxaphene residues in United States soils.

A coupled atmospheric transport model was employed to study six scenarios to assess the contribution of reemission and long-range transport of toxaphene from different sources in the United States to its environmental fate in the Great Lakes ecosystem in the year 2000. Modeled air concentrations at the first model level (1.5 m) range from less than 5 pg m(-3) over the upper Great lakes (Lakes Superior and Huron) to several tens of picograms per cubic meter over the lower Great Lakes (Lakes Erie and Ontario) in the summer but drop off to the range from 0.05 to 2 pg m(-3) in the wintertime. The modeled toxaphene depositions to the lakes suggest a decreasing trend from the mid-1990s to 2000. Modeling results showed that, on an annual basis, for the Great Lakes basin as a whole, the southeast U.S. sources made the largest contribution to the toxaphene air concentrations and dry and wet depositions at 72%, 78%, and 88% respectively. The model results also showed that a significant proportion of these contributions occur during relatively short episodic events due primarily to the interseasonal changes in atmospheric circulation patterns.

Atmosphere↗

PubMed2005

Tracking toxaphene in the North American Great Lakes basin. 2. A strong episodic long-range transport event.

In this paper we examine the modeled daily toxaphene air concentrations from September 9 to 13, 2000, during which air concentration levels were 2-3 orders of magnitude higher than those derived from in situ measurements around the Great Lakes during the same year and during the 1990s. Meteorological conditions revealed that a typical deformation flow system associated with a high-pressure system extending from the east coast of Canada to the southern United States was one of the critical elements that enabled the transport of toxaphene to the Great Lakes. Cloud bands seen on satellite imagery and the rain band predicted by an atmospheric forecast model indicate that the system also delivered warm and humid air from the Gulf of Mexico and the southern United States to the Great Lakes. This resulted in strong wet deposition of toxaphene to the lakes. Substantial increase in the air concentration of toxaphene over the Great Lakes in this short period contributed greatly to raising the annual average daily air concentration for all of 2000. The results suggest that such an episodic event could be a major pathway for atmospheric transport of toxaphene from the southern United States to the Great Lakes.

Air Pollutants↗

PubMed2005

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses.

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Base Composition↗

PubMed2004

How do climate fluctuations affect persistent organic pollutant distribution in North America? Evidence from a decade of air monitoring.

Interannual variations of persistent organic pollutant (POP) air concentrations from the Great Lakes region and the Arctic during the 1990s are strongly associated with atmospheric low-frequency fluctuations, notably the North Atlantic Oscillation (NAO), the El Niño-Southern Oscillation (ENSO), and the Pacific North American (PNA) pattern. This suggests interactions between climate variation and the global distribution of POPs. Atmospheric concentrations of hexachlorocyclohexanes (HCHs), hexachlorobenzene (HCB), and several lighter polychlorinated biphenyls (PCBs) measured around the Great Lakes basin increased during the positive phases of NAO and ENSO in the spring. This implies that anomalous high air temperatures associated with NAO and ENSO enhance volatilization of POPs from reservoirs on the Earth's surface accumulated in the past. These compounds are then available for transport from source regions to more pristine regions such as the Arctic under favorable flow patterns associated with global climate variations.

Air Movements↗

PubMed2004

Impacts of lindane usage in the Canadian Prairies on the Great Lakes ecosystem. 2. Modeled fluxes and loadings to the Great Lakes.

Atmospheric loadings of gamma-hexachlorocyclohexane (gamma-HCH) from May 1, 1998, to April 30, 1999, to the Great Lakes simulated by a coupled soil-air and water-air atmospheric transport model are presented. Modeling results on an annual basis indicate that Lake Superior received the highest dry deposition load of 2.17 kg yr(-1). Dry deposition to the lower Great Lakes (Lakes Erie and Ontario) was 2-6 times lower as compared to the upper Great Lakes. Greater deposition in the upper Great Lakes is due mainly to their larger surface area and greater proximity to sources of gamma-HCH. Dry deposition fluxes (pg m(-2)) to lake surfaces were much lower than to land as a result of lower deposition velocities and lower air concentrations of gamma-HCH over the lakes. The highest gamma-HCH loading (kg yr(-1), in 1998-99) due to wet deposition occurred for Lake Ontario. This was mainly attributed to greater annual rainfall over Lake Ontario. An investigation of average seasonal fluxes predicted by the model shows that deposition fluxes to the Great Lakes are considerably higher in the summer than that in the autumn and winter seasons. The net direction of gas exchange also exhibits a seasonal dependence. Lakes Michigan, Huron, and Ontario show net absorption in the summer 1998 whereas at all other times net outgassing occurred at all of the lakes. Overall, gas exchange was the dominant process affecting loadings to the Great Lakes. Model-derived loadings and total deposition flows across the Great Lakes basin due to dry and wet depositions and net gas exchange agree reasonably well with the summer estimates compiled by the Integrated Atmospheric Deposition Network whereas autumn values show greater discrepancies. Better agreement was also observed for dry deposition as compared to wet deposition. Specifically, to improve short-term loading estimates (e.g., over days to months), the model results indicate the need for better spatially and temporally resolved information on concentrations in air and surface water and better estimates of precipitation and deposition velocities over the lakes.

Agriculture↗

PubMed2004

The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens.

The role of silent position in the codon on the protein structure is an interesting and yet unclear problem. In this paper, 563 Homo sapiens genes and 417 Escherichia coli genes coding for proteins with four different folding types have been analyzed using variance analysis, a multivariate analysis method newly used in codon usage analysis, to find the correlation between amino acid composition, synonymous codon, and protein structure in different organisms. It has been found that in E. coli, both amino acid compositions in differently folded proteins and synonymous codon usage in different gene classes coding for differently folded proteins are significantly different. It was also found that only amino acid composition is different in different protein classes in H. sapiens. There is no universal correlation between synonymous codon usage and protein structure in these two different organisms. Further analysis has shown that GC content on the second codon position can distinguish coding genes for different folded proteins in both organisms.

Amino Acid Sequence↗

PubMed2004

Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales.

In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Base Composition↗

PubMed2003

Evidence of the impact of ENSO events on temporal trends of hexachlorobenzene air concentrations over the Great Lakes.

This study presents an evidence for association of the air concentrations of HCB measured in the Great Lakes region with the El Niño-Southern Oscillation (ENSO) during the 1990s. The measured HCB concentrations in the atmosphere collected by the Integrated Atmospheric Deposition Network (IADN) program in the Great Lakes during the 1990s show strong correlations with the Multivariate ENSO index (MEI) during winter (December-February) and spring (March-May) seasons. These correlations are stronger in the western upper Great Lakes than in the eastern portion of the Great Lakes ecosystem (lake Ontario), and correspond well to the spatial variability of the surface air temperature in North America during El Niño years. Departures of HCB air concentrations for each winter during 1992-1999 from that averaged over all winters of 1992-1999, i.e. the anomaly, also show the same temporal trend as that of the MEI during the same period. In the same time period, it has been reported that direct HCB emissions from application of HCB in agriculture, from industrial sources in North America and in the rest of the world have decreased substantially compared to those in the 1970s and could not by themselves account for observed HCB air concentrations around the Great Lakes since the 1990s. Interannual fluctuations of HCB concentrations are caused most likely by reemission due to volatilization of HCB from the soil contaminated from past use, followed by long-range transport associated with ENSO events. In addition to the high correlation (R(2)=0.61) between winter HCB air concentrations averaged over the Great Lakes region and the MEI the atmospheric circulation patterns associated with ENSO events are conducive to the long-range transport of HCB into the Great Lakes region.

Agriculture↗

PubMed2003

Impacts of lindane usage in the Canadian prairies on the Great Lakes ecosystem. 1. Coupled atmospheric transport model and modeled concentrations in air and soil.

A coupled atmospheric transport, soil-air, water-air exchange model was developed to investigate the impacts of gamma-hexachlorocyclohexane (gamma-HCH or lindane) usage in the Canadian prairies over the Great Lakes region. The fate of gamma-HCH in air and soil is governed by atmospheric dynamics and physical and chemical processes that are described by the coupled model. These processes include transport and turbulent diffusion in the atmosphere, dry and wet deposition, exchange at the interfacial boundaries of air-water and soil-air, and removal processes from the soil such as diffusion, leaching, and degradation. Numerical experiments were conducted for the period of May 1, 1998-April 30, 1999, starting with application of lindane in the spring. The coupled model was executed with two lindane emission (usage) inventories in the model domain. The first scenario contained all known fresh emission sources in Canada-98% was usage in the prairies; the second excluded emission sources from Ontario and Quebec. The model showed that, in the absence of the reemission from past application of lindane, usage of lindane in Ontario and Quebec has a negligible impact on air concentrations in these regions and that the lindane budget in the Great Lakes ecosystem is mostly attributed to applications of lindane in the canola fields in Canadian prairie provinces. Model-predicted air concentrations and seasonal trends agreed well with measured data over the same time period for several background sites operated under the Integrated Atmospheric Deposition Network. Air temperature was shown to play a key role on surface-air exchange dynamics of gamma-HCH. A future paper will assess loadings to the Great Lakes based on these validated model results.

Air Movements↗

PubMed2003

Folding type specific secondary structure propensities of synonymous codons.

We have proposed new amino acid secondary structure propensities in proteins with different folding types based on synonymous codons. They have been derived from 200 all alpha, all beta, alpha/beta, and alpha + beta proteins of known structures and their coding genes. The secondary structure propensities of the same codon in gene coding for different folding type proteins are not the same. For instance, amino acid Ile coded by AUU is indifferent to form the alpha unit in the alpha + beta protein class, but it is a former and a breaker for the alpha unit in the all alpha protein class and the alpha/beta class, respectively. On the other hand, the secondary structure propensities of different synonymous codons in the coding genes with the same folding type are also not all the same. As an example, CGU, CGG, and AGA, which are synonymous codons of Arg, are preferential to form the alpha unit in all alpha proteins, while CGA is an alpha unit breaker and the other two synonymous codons, CGC and AGG, are indifferent to form or break the alpha unit. As a result, protein secondary structure information contained both in mRNA sequences and in amino acid sequences has been introduced in these codon-based amino acid secondary structure propensities. These codon-based amino acid secondary structure propensities are helpful to in vitro protein design and protein secondary structure prediction.

Amino Acid Sequence↗

PubMed2003

[Effects of rehabilitation of submerged macrophytes on nutrient level of a eutrophic lake].

The effects of rehabilitation of submerged aquatic vegetation on nutrient level of eutrophic waters were investigated by using large-scale enclosure system installed in a hyper-eutrophicated lake, Lake Donghu of Wuhan. The concentrations of total nitrogen (TN) and total phosphorus (TP) of the enclosures with artificially recovered submerged macrophytes were significantly lower than those of the macrophyte-free control enclosure and the lake water, and the TP of macrophyte enclosure was found to be around 0.1 mg.L-1 and relatively stable. The concentration of ammonia and nitrite of the macrophyte enclosures were lower than those of the control and the lake water. However, the nitrate concentrations did not differ among the various water bodies. It was demonstrated that re-establishment of submerged macrophytes could efficiently reduce the nutrient level and thus control the overgrowth of the undesirable algae and improve water quality in the eutrophic lakes.

Ecosystem↗

PubMed2002

[Hygienic investigation of indoor environment in air-conditioned passenger trains].

OBJECTIVE: Explore the hygienic status of indoor environment in railway air-conditioned passenger trains. METHODS: We carried out a hygienic investigation of various air-conditioned passenger trains on total 10 railway lines in Shanghai, Chengtu, Kunming, Harbin, Urumchi and Guangzhou railway bureaus for two years between July, 1997 and Oct., 1999. The monitoring was conducted on difference train cars at different time, different railway status. The control groups were selected in the same condition. RESULTS: The results of temperature and wind speed in air-conditioned trains both meet with the national standards GB 9673-1996 in summer and winter. The humidity in summer exceeded the national standards. Of different railways the status, the noise in four different cars except dining cars exceeded the national standards. The results of shock demonstrated that all measure up to the standards of ISO 2631/1-85. As to indoor air quality, the concentration of CO in air-conditioned trains in difference seasons(summer, autumn, winter) all met with the national standards, the ratio was 100%. In summer, the concentrations of CO2 in hard seat cars and soft berth car exceeded the national standard with a statistic significance(P < 0.01). In winter, the concentrations of CO2 in soft berth and hard berth cars both exceeded the same standard. The results of inhalable particulate matter(IP) and total count of bacteria all satisfied the standards, meanwhile the natural lighting and artificial illumination in air-conditioned train cars all were superior to that in ordinary trains. CONCLUSION: Humidity in summer and noise in dining car exceeded the standards, the concentration of CO2 in different cars in summer and winter exceeded the standards in some degrees.

Air Conditioning↗

PubMedDate not supplied

Cluster analysis of the codon use frequency of MHC genes from different species.

The relative synonymous codon use frequency of 135 MHC genes from four mammal species (Homo sapiens, Pan troglodyte, Macaca mulanta and Rattus norvegicus) is analyzed using a hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions. The conclusion may be useful in gene classification and gene function prediction.

Animals↗