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MicroRNAs (miRNAs) are small non-coding endogenous riboregulators that play significant roles in plant growth, development, metabolism, defense, and stress responses. Upland cotton is best known for its economic value as natural fiber and oil. It is also an important model for genome evolution, polyploidy effects, cell growth, and cell wall biosynthesis. The polyploid species, Gossypium hirsutum L. (2n = 52), evolved from two progenitors (2n = 26), one contributing an ancestral genome similar to A genomes of G. herbaceum and G. arboreum, and the other like the D genome of G. raimondii. There is much to be learned about Gossypium miRNAs and their gene targets, about the effects of polyploidy and their practical ramifications. In this study, small-RNA (sRNA) libraries from four Gossypium species and three tissue libraries (seed, seedling, and leaf) from G. hirsutum were constructed and analyzed using high-throughput sequencing with Illumina/MiSeq then computational prediction by MIREAP. Results showed 245 known miRNAs belonging to 67 miRNA families and 149 novel (non-redundant and redundant) miRNAs derived from 394 genomic loci. This unified study identified 21 and 33 conserved miRNA families across four Gossypium species and three tissue libraries, respectively. Similar to canonical miRNAs, the 5′ of novel miRNAs had the higher preference for U and A residues. In this study, 551 potential target genes were predicted in 45 conserved miRNA families, while 439 targets were associated with 113 novel miRNAs. The majority of the conserved (34%) and novel (22%) miRNA targets identified belonged to cellular processes and signaling. However, the functional diversity of novel miRNA targets is attributed to the tissue and species bias. Most of the identified targets were regulated by mRNA cleavage than by translational repression. These results provide a basis for better understanding regulatory networks in upland cotton (G. hirsutum) and its closest progenitors. Keywords: Cotton, Progenitor, Sequencing, Prediction, MIREAP, sRNA, miRNA, Family, Known, Novel, Gene regulation, Target

Water, soil/sediment, and 36 fish samples were collected at three major sites along Flint Creek in 2015-2016 and analyzed for total organic carbon (TOC), dissolved organic carbon (DOC), total mercury (tHg), and other water quality indicators. This study was a follow-up to a 2012 study that revealed elevated tHg levels in fish, resulting in a public health advisory. This study revealed tHg concentrations in water below the detection limit (0.0002 ppm); while, tHG in soil/sediment ranged from < 0.0133 ppm to 0.0682 ppm dry weight. No temporal trends existed, but tHG tended to increase with TOC. Mercury levels in sediment were below the threshold effects level suggested as a preliminary screening level by the National Oceanic and Atmospheric Administration (acute = 1.4, chronic = 0.77 ppb). In summary, tHg levels were low; posing little risk to drinking water. Soil/sediment levels were generally higher and could pose risk to aquatic species.

Total recoverable concentration of five elements of concern: Aluminum, Iron, Manganese, Arsenic and Lead (Al, Fe, Mn, As, Pb) were measured by inductively coupled plasma atomic emission spectrometry, and mass spectrometry. The results show that sediment texture plays a controlling role in the concentrations and their spatial distribution. Principal Component Analysis and Cluster Analysis were used to analyze the grain sizes of the sediments. Result of texture analysis classified the samples into three main components in percentages: sand, silt, and clay. Significant differences among the element concentrations in the three groups were observed, and the concentrations of the elements in each group are reported in this study. Most of the elements have their highest concentrations in the fine-grained samples with clay playing an important role, in comparison with the sand component of the soil/sediment samples. There appears to be a strong correlation between samples with high silt, and clay content with the areas of elevated concentrations for Al, Fe, and Mn. There was a strong correlation between aluminum and lead with clay; lead with silt; and sand with manganese, aluminum, and lead. However, there was no strong relationship between the soil textures and iron or arsenic. All elements measured were statistically significant (at P ≤ 0.05) by watershed. The upland areas, and depositional areas’ spatial variation of element concentrations in the sediments were also observed, which was in line with the spatial distribution of the grain size and was thought to be related to the watersheds hydrological dynamics.

The reniform nematode (RN), Rotylenchulus reniformis, is an agriculturally important pest with a broad host range that results in a large economic impact in tropical, subtropical and in warm temperate zones. In an initial effort to understand the transcriptome and gene expression in RN, we present EST results that reveal numerous putative parasitism-related genes some of which play roles in plant cell wall modification. The characterized contigs included 8362 (40.6%) matches to unique proteins. Coding contigs predicted were 10,656 (51.7%) or 3079 (14.9%), that was similar to those identified in Brugia malayi and Caenorhabditis elegans as reference organisms respectively. Specific transcripts studied in more detail include putative plant parasitism genes, prominent among them were several plant cell wall modification genes. Contigs matching 14 parasitism genes found in sedentary endoparasitic nematodes included expansins, hexosaminidase, glycosyl hydrolases family, 14-3-3 protein, xylanases, glutathione peroxidase, pectate lyase, β-1,4-endoglucanase, major sperm protein, aminopeptidase, c-type lectin, chitin synthase, FMR famide-like peptide, and calreticulin. These genes function in suppression of host defenses and development of feeding sites.

In recent years, water shortage is becoming one of the most serious problems in the Poyang Lake. In this paper, the long-term water balance items of the Poyang Lake have been analyzed to reveal the coupling effects of Three Gorges Dam (TGD) and droughts on the water balance of Poyang Lake. The results indicate that: (1) the water balance items of Poyang Lake vary greatly, e.g. lake precipitation and inflow decrease during the past several decades while evaporation and water consumption increase significantly; (2) the water balance of Poyang Lake has been affected by the operation of TGD. Negative lake water balance in recent years leads to a serious water shortage problem in the Poyang Lake. Moreover, the operation of TGD also changed the river–lake relationship in the lower Yangtze River basin; (3) the coupling effects of drought and TGD on the lake water balance has been analyzed by using composite analysis method and it can be found that the operation of TGD has significantly altered the lake water balance. But it is not the only factor that affects the lake water balance, and the droughts might cause their relations to be much more complicated.

Water pollution by microorganisms of fecal origin is a current world-wide public health concern. Total coliforms, fecal coliforms (Escherichia coli) and enterococci are indicators commonly used to assess the microbiological safety of water resources. In this study, influent water samples and treated water were collected seasonally from a water treatment plant and two major water wells in a Black Belt county of Alabama and evaluated for water quality indicator bacteria. Influent river water samples serving the treatment plant were positive for total coliforms, fecal coliforms (E. coli), and enterococci. The highest number of total coliform most probable number (MPN) was observed in the winter (847.5 MPN/100 mL) and the lowest number in the summer (385.6 MPN/100 mL). Similarly E. coli MPN was substantially higher in the winter (62.25 MPN/100 mL). Seasonal variation of E. coli MPN in influent river water samples was strongly correlated with color (R2 = 0.998) and turbidity (R2 = 0.992). Neither E. coli nor other coliform type bacteria were detected in effluent potable water from the treatment plant. The MPN of enterococci was the highest in the fall and the lowest in the winter. Approximately 99.7 and 51.5 enterococci MPN/100 mL were recorded in fall and winter seasons respectively. One-way ANOVA tests revealed significant differences in seasonal variation of total coliforms (P