S1 Classes Research Articles

Acidic and Neutral Polar NSO Compounds in Heavily Biodegraded Oils Characterized by Negative-Ion ESI FT-ICR MS

Five heavily biodegraded tar sand bitumens from an oil column were separated into maltene and asphaltene fractions for analysis by negative-ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). These bitumens have an identical source, which have experienced a natural sequence of biodegradation. The polar NSO compounds in maltene fractions contain O1, S1O1, O2, S1O2, S2O2, O3, S1O3, O4, S1O4, N1, N1O1, N1O2, N1S1, and S1 classes, while the polar NSO compounds in asphaltene fractions contain O1, S1O1, S2O1, O2, S1O2, S2O2, O3, S1O3, S2O3, O4, S1O4, S2O4, O5, S1O5, S2O5, O6, N1, N1O1, N1O2, N1O3, N1S1, and N2 classes. Polar NSO compounds with stronger molecular polarity and larger molecular weight are readily fractionated into asphaltene fractions. The O2 class is prevalent in polar NSO compounds of both maltene and asphaltene fractions of all bitumen samples. The N1 class in maltene fractions is dominated by compounds with DBE values of 9, 10, 12 and 13, while the N...

Impacts of Soil and Water Conservation on Land Suitability to Crops: The Case of Anjeni Watershed, Northwest Ethiopia

Soil loss in Ethiopia due to water erosion is a serious economic and environmental problem. Soil and water conservation (SWC) practices provide multiple onsite and offsite benefits. Thus, the present study was carried out to examine the long-term impacts of SWC measures in improving ecosystem services in general and land suitability to crop production in particular. Land suitability classes (LSC) were accounted using the multi-criteria analysis (MCA) on bio-physical variables of the environment. LSC were sorted by combining the FAO framework of land evaluation with GIS tools. Thus, LSC for teff (Eragrostis teff), maize (Zea mays L.), barley (Hordeum vulgaris L.), and wheat (Triticum aestivum L.) were found S2 and S3 in 1984 and 1997 whereas in 2010, some areas were transformed to S1 classes for wheat and teff. Suitable land allocation for these crops was made and 50% of the watershed is found to be S1 class for wheat while about 40% is in S2 class for all crops. In 1997 barley and teff covered 29.2% and 28.9%, respectively. While in 2010, 19% of the area was covered by teff, 18.9% by maize, 16.9% by barley and 15.6% by wheat. Wheat and maize showed significant spatial expansions that are best indicator crops for the betterment of the land quality or soil improvement.

Spatial Based Assessment of Land Suitability and Availability for Maize (<i>Zea mays</i> L.) Development in Maros Region, South Sulawesi, Indonesia

Recently, South Sulawesi Provincial government has launched the “gong” program with the main objective to optimize all the resources (land, infrastructures, and farmers) in agriculture areas for maize production in the province. This study is aimed at identifying the suitability and availability of land areas for maize development in Maros Regionthe regency having the most extensive agriculture production in South Sulawesi province. This study employed land evaluation method in geographic information system (GIS) based on the FAO Framework for Land Evaluation. Land availability was assessed from overlaying information on land use (obtained from available land use map and SPOT XS image interpretation) and suitability classes based on the FAO Framework, as well as administration boundary map. The results indicated that the S1 (highly suitable) class comprises a total area of approximately 34,468 ha, or about 24% from the total area. The limiting factors for S2 (moderately suitable) and S3 (marginally suitable) classes are slope and nutrient availability, but with the advanced management efforts (moderately input) such sub-classes can actually promote S3 class to S2 level. It was also found that from a total of 144,085 ha of the study area, potential maize development area (for extensification) covers approximately 24,716 ha (or 35.6%). Tanralili, Bantimurung, and Simbang sub-districts cover the largest suitable area, where no significant limiting factors exist. Surprisingly, potential development area for maize in Camba, Mallawa, and Tompobulu sub-districts denotes minus values. This implies the facts that maize cultivation is still practiced on the land that is ecologically not suitable, where steep slope is the dominant limiting factor.

Land Suitability Assessment for Rice Cultivation Based on GIS Modeling

The main objective of this study was to develop a spatial model for land suitability assessment for rice (Oryza sativa L.) cultivation using geographic information system (GIS) techniques. The land mapping units, resulting from the overlay of the selected theme layers, have unique land quality information, on which land suitability is based. Results showed that 55.5% of the study area is highly or moderately suitable for rice cultivation, whereas 34% of that area is unsuitable for rice cultivation due to soil and topographic conditions. The model was also validated with field studies. According to the statistical analysis, there was a significant, positive relationship between land suitability classes and grain yields. Grain yield was significantly affected by land suitability class at the level of P < 0.001. The highest grain yield was obtained from rice plots in the S1 class (7287 kg ha-1), followed by S2 (6872 kg ha-1) and S3 (3928 kg ha-1) classes.

DRAINAGE WATER QUALITY AND ITS EFFECTS ON SOIL PROPERTIES AND CHEMICAL COMPOSITION OF PLANTS

The present study was carried out on Meraga drain located in EL-Gamalia district, Dakahlia Governorate(Middle Nile Delta) to evaluate the effect of drainage water quality on soil properties and chemical composition of plants. Meraga drain passes many villages dotted along it receiving their agriculutral drainage water, house waste waters and industrial effluents. Water samples were seasonally collected from 6 sites along this drain ( EL-Gamalia city (0),1.5, 3.0, 4.5, 6 and 7.5 km.). Water samples were seasonally collected during June 2009 to March 2011. Also, soil samples and plant were collected seasonally from the distance of 1.5 to 6 km. The main obtained results are presented as follows: Electrical Conductivity (EC) values increased slightly with northward direction. Also, Sodium Absorption Ratio (SAR) took the same trend, the quality of studied drainage water belong to C3 S1 and C4 S1 classes and could be re-use in irrigation purpose under special management. Boron (B) concentration, at most of locations have low concentration (B1) < 3 mg L-1 which less than the critical limit indicating (slight to moderate for restriction on use). Nitrate –N concentrations was ranged from 5-30 ppm in the Meraga drains in two summer seasonally 2009 and 2010 whereas, the other seasonally was higher than the critical limits. Micronutrients and heavy metal ions concentrations (Fe+2, Mn2+, Zn2+ Pb2+) were less than permissible levelsat all selected water samples. Using drainage water for irrigation, caused an increase in soil content of available micronutrients (Fe, Mn and Zn) whereas, heavy metals (Pb) was less than the permissible limits (500 mg kg-1). Concentrations of heavy metal and micronutrients (Fe, Mn, Zn and Pb) in straw and grains of wheat and rice grown in the most locations were under the permissible limits except Pb and Fe concentration exceeds the critical levels in all locations.The concentration in straw of wheat and rice crops were higher than in the grain at all location. Zn and Mn concentrations were less than critical limits at all locations in shoot of clover plants and Pb and Fe concentrations were higher than critical limit at all locations. Finally, the rice crop had better effect on water quality than cotton then wheat and finally clover.

Phylogenetic relationships among diploid Aegilops species inferred from 5S rDNA units

Relationships among the currently recognized 11 diploid species within the genus Aegilops have been investigated. Sequence similarity analysis, based upon 363 sequenced 5S rDNA clones from 44 accessions plus 15 sequences retrieved from GenBank, depicted two unit classes labeled the long AE1 and short AE1. Several different analytical methods were applied to infer relationships within haplomes, between haplomes and among the species, including maximum parsimony and maximum likelihood analyses of consensus sequences, “total evidence” phylogeny analysis and “matrix representation with parsimony” analysis. None were able to depict suites of markers or unit classes that could discern among the seven haplomes as is observed among established haplomes in other genera within the tribe Triticeae; however, most species could be separated when displayed on gene trees. These results suggest that the haplomes currently recognized are so refined that they may be relegated as sub-haplomes or haplome variants. Amblyopyrum shares the same 5S rDNA unit classes with the diploid Aegilops species suggesting that it belongs within the latter. Comparisons of the Aegilops sequences with those of Triticum showed that the long AE1 unit class of Ae. tauschii shared the clade with the equivalent long D1 unit class, i.e., the putative D haplome donor, but the short AE1 unit class did not. The long AE1 unit class but not the short, of Ae. speltoides and Ae. searsii both share the clade with the previously identified long {S1 and long G1 unit classes meaning that both Aegilops species can be equally considered putative B haplome donors to tetraploid Triticum species. The semiconserved nature of the nontranscribed spacer in Aegilops and in Triticeae in general is discussed in view that it may have originated by processes of incomplete gene conversion or biased gene conversion or birth-and-death evolution.

Loss of 5S rDNA units in the evolution of Agropyron, Pseudoroegneria, and Douglasdeweya

We have investigated relationships among the three closely related genera Agropyron, Pseudoroegneria, and Douglasdeweya. Based upon grouping of 330 5S rDNA sequences into unit classes, we found that Douglasdeweya, with the genomic constitution PPStSt, has 2 unit classes, the long P1 and short S1, and Pseudoroegneria, with the genomic constitution StSt or StStStSt, has the long S1 and short S1 unit classes. In contrast, only the long P1 unit class was found in species of the genus Agropyron (PP). Having a single unit class is unique among all the genera of the tribe Triticeae investigated so far and may reflect gene loss or lineage sorting during its genesis. The presence of the short S1 and long P1 unit classes confirms the amphiploid origin of Douglasdeweya.

تقويم مدى صلاحية المياه الجوفية للري في قطاع غزة - فلسطين(بالغة الانجليزية).

The Gaza Strip is entirely dependent on groundwater resources. This Study aims at evaluating if groundwater in Gaza Strip ( the study area) for irrigation during the period 2002/2003. This paper discusses water quality considerations for irrigation and determines some chemical characteristics of waters used for irrigation in Gaza Strip. The study depends on 240 water samples collected from irrigation wells, and analyzed chemically by the water Department in the ministry of Agriculture where the values of electrical conductivity (EC) and cations (Ca , Mg , Na, and K) were measured. Some parameters were calculated by the researcher to determine the suitability of water for irrigation such as Soluble Sodium Percentage (SSP), and Sodium Adsorption Ratio ( SAR ). The suitability of irrigation water id classified according to the Wilcox diagram and the diagram by the U.S. Department of Agriculture. Excluding the Northern Governorate, the data obtained from the study shows that irrigation water used in Gaza Strip is of bad quality. According to the classification by Wilcox, more than 50 % ( including the samples which fall beyond the limits if the Wilcox classification) of total well water samples in Gaza Strip is considered unsuitable for irrigation, while 29.6 % of it is classified as good – to – permissible. As is shown in this paper, 13.3 % and 4.2 % of well water samples are classified as doubtful- to – unsuitable and permissible- to – doubtful respectively. Form the values of EC and SAR for the water samples obtained from the different governorates and using U.S. salinity diagram, it is clear that the majority of the water samples fall in the C4- S4 and C4 –S3 classes. They form 22.5 % and 14.2 % of the total samples respectively. C4-S4 class is considered unsuitable for irrigation. Also, more that 15 % of the total samples fall beyond the limits of the U.S. salinity diagrams and do not appear on them, and are not generally suitable for irrigation. About 26% of the total samples in Gaza Strip fall in the C3-S1 class. This class belongs to the low sodium and high salinity water group, which can be used for irrigation on almost all soils with good drainage but is not good for sodium – sensitive crops. A few samples were in the C2- S1 ( 1.7%), C2- S2 (0.4%), C3-S2 (8.3%), C3-S3 (1.7%), C4 – S1 (3.3%) , and C4- S2 (6.3%) classes. Due to the rapid expansion of irrigated agriculture, excrescent use of the salinity water in Gaza Strip is becoming more vital. However, water salinity is a major problem due to its negative influence in the area and yields of many crops. Gaza Strip suffers from a reduction of crop yields, especially those crops that are not tolerant to salt like citrus trees and other fruit trees. Keywords: Gaza Strip, water quality, irrigation, cations, electrical conductivity, sodium adsorption ratio.

The 5S rRNA gene diversity in the genus Secale and determination of its closest haplomes

We analyzed 127 rDNA sequences (5S DNA units) obtained from 23 seed accession samples from more or less 10 taxa in wild and cultivated rye, genus Secale L. The sequences fell into two known groups, here assigned to two unit classes, viz. long R1 and short R1 (designations to reflect on R haplome of rye). The different taxa could not be fully differentiated based on the 5S DNA units. We searched for 5S DNA sequences from known unit classes most closely similar to the long R1 and the short R1. One set with the long R1 unit class contained sequences of the long P1 unit class from Agropyron (P haplome) and from Kengyilia (StYP haplome), long J1 from Thinopyrum (J haplome), whereas the set with the short R1 included the long S1 from Pseudoroegneria (St haplome) and Kengyilia (StYP haplome), the short J1 from Thinopyrum (J haplome) and the short V1 from Dasypyrum (V haplome). Each of the two sets was analyzed separately by maximum likelihood (ML) phylogenetic analysis from which we were able to infer that the 5S DNA units of Secale differentiated in a non-clock fashion and followed the HKY substitution model in the gene tree with the long R1 unit class and the HKY + G in the gene tree with the short R1 unit class. A complementary Bayesian analysis yielded identical tree topologies to the ML ones for each of the two sequence sets. In the tree with the long R1 units the long P1 and long J1 unit classes were closest to the long R1 unit class, whereas in the tree with the short R1 units the long S1 and short J1 unit classes were closest to the short R1 unit class, indicating possibly a close relationship between the St, J and R haplomes.

Molecular diversity of the 5S rDNA units in theElymus dahuricuscomplex (Poaceae: Triticeae) supports the genomic constitution ofSt,Y, andHhaplomes

The phylogenetic analysis of 118 5S rRNA gene sequences cloned from members of the Elymus dahuricus complex containing the St, Y, and H haplomes, and of several related species containing at least one of these three haplomes, is reported. Differences in sequence pattern, primarily within the nontranscribed spacer, enabled the identification of six putative orthologous groups that we refer to as unit classes. In previous publications, we have been able to assign unit classes to haplomes. In addition to four unit classes previously identified in other genera, namely the long H1, long S1, long P1, and long {Y1, here we document two new unit classes called the long S2 and long W1. Most sequences of the E. dahuricus complex and related tetraploid species are classified as long S1 and assigned to the St haplome. Both long S1 and long S2 unit classes were identified in the diploid Pseudoroegneria spicata (Pursh) Á. Löve with the St haplome. The long S2 unit class was also identified in the hexaploid Elymus scabrus (R. Br.) Á. Löve with the St,Y,and W haplomes. The long P1 was known from the diploid Agropyron cristatum Gaertn. with the P haplome, and the long W1 was determined in Australopyrum retrofractum (Vickery) Á. Löve, known to contain the W haplome, but was not yet detected in E. scabrus, a hexaploid species with W being one of the three haplomes. The long H1 reported earlier from Hordeum was identified in several clones of the E. dahuricus complex. As previously reported, the long {Y1 unit class was found to be rare overall, but we identified it in a few clones of Elymus drobovii and in the E. dahuricus complex.Key words: 5S rDNA, unit classes, haplomes, concerted evolution.

Evidence that the KH RNA-binding Domains Influence the Action of the E. coli NusA Protein

The NusA transcription elongation protein, which binds RNA, contains sequences corresponding to the S1 and KH classes of identified RNA binding domains. An essential function in E.coli, NusA is also one of the host factors required for action of the N transcription antitermination protein of λ. Tandem KH domains have been identified downstream of the S1 domain. We changed the first Gly to Asp of the GXXG motif, a tetrapeptide diagnostic of KH domains, of both NusA KH domains. The change in the first, G253D, has a large effect, while the change in the second, G319D, has a small effect on NusA action. The changes in both KH domains interfere with NusA binding to RNA. A change of a highly conserved Arg in the S1 domain, R199A, has previously been reported to interfere with RNA binding while exerting a small effect on NusA action. However, a nusA allele with both the R199A and G319D changes encodes a functionally inactive NusA protein. These studies provide direct evidence that the both KH as well as the S1 RNA binding domains are important for NusA action in support of bacterial viability as well as transcription antitermination mediated by the λ N protein.

The 5S rRNA gene sequence variation in wheats and some polyploid wheat progenitors (Poaceae: Triticeae)

We have cloned and sequenced 115 repeat units of the 5S rDNA genes and spacers from wheat (Triticum) and the polyploid wheat progenitor, Aegilops, and analyzed them together with sequences available in GenBank® (National Center for Biotechnology Information, NCBI, NLM, NIH, Bethesda, Maryland, USA). We were able to assort the sequences into nine orthologous groups which we call unit classes. The following unit classes were assigned to haplomes, and labeled accordingly: long A1, short A1, short A2, long G1, short G1, long D1, short D1, long S1 and short S1. The AA-genome, DD-genome and SS-genome species were each found to contain a long and a short class. The AAGG-genome species T. timopheevii and the AAAtAtGG-genome species T. zhukovskyi, both contain the long A1, long G1 and short G1 unit classes. The AABB-genome species T. turgidum consists of the short A2, a unit class not yet found in T. monococcum, and the long S1 unit class found in the species of Aegilops section Sitopsis. The bread wheat AABBDD-genome contains the long A1, short A2, long D1, long S1 and short G1 unit classes. The presence of the long S1, also demonstrated to occur in both T. turgidum and T. aestivum, supports the hypothesis that the progenitor of the B-haplome in wheat originated in Aegilops section Sitopsis. The presence of the short G1 unit class, i.e. the G-haplome in bread wheat, is unexpected. These new findings are discussed in the light of published findings, especially those relating to 5S DNA loci and evolutionary hypotheses.

The 5S rDNA units in Kengyilia (Poaceae: Triticeae): diversity of the nontranscribed spacer and genomic relationships

The sequences of eighty 5S rDNA clones were obtained by polymerase chain reaction (PCR) amplification of DNA from 12 accessions representing eight species of Kengyilia. Orthologous sequences were grouped into five unit classes: long P1, long S1, long {Y1, short P1, and short S1. Both the long P1 and long S1 classes are prevalent in Kengyilia, whereas the rest are rare. The short S1 class has not been described previously in other Kengyilia species. Two clones represent the long {Y1 class, with only one clone reported previously in Kengyilia alatavica (Drobow) J.L. Yang, Yen &amp; Baum and a single clone found in this investigation. The long H1 unit class reported earlier for Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen &amp; Baum, but not for K. alatavica, was not found in any of the eight species investigated. Therefore, its presence in K. rigidula may be the result of introgression from Elymus nutans Grisebach, an HS-genome species containing the long H1 unit class; the two are often found growing together and are known to yield sterile hybrids in those populations. The specific 5S DNA unit classes, except for the ones that were found in very low frequency and in few samples, may have a potential not only as markers for the identification of haplomes but also of hybrids containing a combination of genomes. This investigation indicated, along with previous studies, that the 5S unit classes either form integral parts of haplomes or remain conserved and identifiable within haplomes originating from distant species, indicating that concerted evolution in the 5S gene plays only a partial role as an evolutionary force.Key words: 5S DNA gene, molecular diversity, Kengyilia, Triticeae, concerted evolution.

The 5S rDNA units in &lt;i&gt;Kengyilia&lt;/i&gt; (Poaceae: Triticeae): diversity of the nontranscribed spacer and genomic relationships

The sequences of eighty 5S rDNA clones were obtained by polymerase chain reaction (PCR) amplification of DNA from 12 accessions representing eight species of Kengyilia. Orthologous sequences were grouped into five unit classes: long P1, long S1, long {Y1, short P1, and short S1. Both the long P1 and long S1 classes are prevalent in Kengyilia, whereas the rest are rare. The short S1 class has not been described previously in other Kengyilia species. Two clones represent the long {Y1 class, with only one clone reported previously in Kengyilia alatavica (Drobow) J.L. Yang, Yen & Baum and a single clone found in this investigation. The long H1 unit class reported earlier for Kengyilia rigidula (Keng and S.L. Chen) J.L. Yang, Yen & Baum, but not for K. alatavica, was not found in any of the eight species investigated. Therefore, its presence in K. rigidula may be the result of introgression from Elymus nutans Grisebach, an HS-genome species containing the long H1 unit class; the two are often found growing tog...