Characterization of Legacy Sediment variations in accretion and carbon dynamics following dam removal in a recently restored tidal freshwater wetland

Damming disrupts the natural flow of sediment to adjoining water bodies resulting in the accumulation of Legacy Sediments (LS). While the impact of LS inputs has been well investigated in lotic Mid-Atlantic piedmont stream restorations, (i.e. milldam removal 1,2,3,4,5,), there have been few studies investigating LS following dam removal in low-gradient coastal plain streams. The objectives of this study were to quantify spatial and temporal variations of LS characteristics in a low-gradient tidal stream restoration within the lower James River watershed. Secondary objectives were to assess the current temporal and spatial variability in sediment deposition within the recently restored Kimages Creek wetlands and adjacent, unaltered wetlands of Harris Creek to investigate current sedimentation processes in a restoration setting

Interactions between the oomycete Pythium arrhenomanes and the rice root-knot nematode Meloidogyne graminicola in aerobic Asian rice varieties

Background: Aerobic rice fields are frequently infested by pathogenic oomycetes (Pythium spp.) and the rice root-knot nematode Meloidogyne graminicola. Here, the interaction between Pythium arrhenomanes and Meloidogyne graminicola was studied in rice roots of two aerobic rice varieties. In different experimental set-ups and infection regimes, plant growth, rice yield, Pythium colonization, as well as establishment, development and reproduction of M. graminicola were studied. Results: In this study, it is shown that the presence of P. arrhenomanes delays the establishment, development and reproduction of M. graminicola compared to single nematode infected plants. The delay in establishment and development of M. graminicola becomes stronger with higher P. arrhenomanes infection pressure. Conclusions: Our data indicate that P. arrhenomanes antagonizes M. graminicola in the rice root and that the plant benefits from this antagonism as shown by the yield data, especially when either of the pathogens is present in high levels

Characterization of Current and Historical Variations in Sediment Accretion and Carbon Dynamics at the Rice Rivers Center Kimages Creek Wetland Restoration

Current research of freshwater wetland soils have assessed and reported smaller stocks of soil organic carbon in restored wetlands compared to reference natural wetlands. However, a majority of these studies focus on sites restored from agricultural draining of non-tidal depressional wetlands,whereas carbon and accretion dynamics in tidal freshwater wetlands restored via dam removal is poorly understood. The U.S. Army Corps of Engineers estimates over 80,000 dams greater than 6 feet and tens of thousands of smaller dams pepper the U.S., of which the majority are unsafe, old or no longer serve their intended purpose. Damming disrupts the natural flow of sediment to adjoining water bodies resulting in the accumulation of what are commonly referred to as Legacy Sediments (LS). These sediments have the ability to alter the biology, hydrology, geomorphology, and biogeochemistry of their river corridors and adjacent riparian ecosystems. While the effect of these sediment inputs on ecosystem function has been well investigated in non-tidal regions, particularly in the form of milldam removal, there has been little-to-no inquiry on how LS exist within and affect tidal wetlands and their biotic and abiotic processes. The objectives of this study are to uantify the current temporal and spatial variation in sediment deposition and soil carbon dynamics within KC and Harris Creek (HC) wetlands via sediment collection tiles (SCTs); assess the differences in LS characteristics along the tidal to non-tidal gradient and between different depositional areas through soil core sampling and radiocarbon dating; and, compare carbon sequestration and sediment accretion rates between the two historical environments: the pre-impoundment forested freshwater wetland & the Lake Charles environment (LS)

BLM and RMI1 alleviate RPA inhibition of topoIIIα decatenase activity

RPA is a single-stranded DNA binding protein that physically associates with the BLM complex. RPA stimulates BLM helicase activity as well as the double Holliday junction dissolution activity of the BLM-topoisomerase IIIα complex. We investigated the effect of RPA on the ssDNA decatenase activity of topoisomerase IIIα. We found that RPA and other ssDNA binding proteins inhibit decatenation by topoisomerase IIIα. Complex formation between BLM, TopoIIIα, and RMI1 ablates inhibition of decatenation by ssDNA binding proteins. Together, these data indicate that inhibition by RPA does not involve species-specific interactions between RPA and BLM-TopoIIIα-RMI1, which contrasts with RPA modulation of double Holliday junction dissolution. We propose that topoisomerase IIIα and RPA compete to bind to single-stranded regions of catenanes. Interactions with BLM and RMI1 enhance toposiomerase IIIα activity, promoting decatenation in the presence of RPA

Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions

BACKGROUND: Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria. RESULTS: We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs. CONCLUSION: This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1696-9) contains supplementary material, which is available to authorized users

Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing

The cyclin-dependent kinase inhibitor p21WAF1/CIP1 (p21) is a cell-cycle checkpoint effector and inducer of senescence, regulated by p53. Yet, evidence suggests that p21 could also be oncogenic, through a mechanism that has so far remained obscure. We report that a subset of atypical cancerous cells strongly expressing p21 showed proliferation features. This occurred predominantly in p53-mutant human cancers, suggesting p53-independent upregulation of p21 selectively in more aggressive tumour cells. Multifaceted phenotypic and genomic analyses of p21-inducible, p53-null, cancerous and near-normal cellular models showed that after an initial senescence-like phase, a subpopulation of p21-expressing proliferating cells emerged, featuring increased genomic instability, aggressiveness and chemoresistance. Mechanistically, sustained p21 accumulation inhibited mainly the CRL4–CDT2 ubiquitin ligase, leading to deregulated origin licensing and replication stress. Collectively, our data reveal the tumour-promoting ability of p21 through deregulation of DNA replication licensing machinery—an unorthodox role to be considered in cancer treatment, since p21 responds to various stimuli including some chemotherapy drugs

Prospective, randomized, fellow eye comparison of WaveLight® Allegretto Wave® Eye-Q versus VISX CustomVueTM STAR S4 IRTM in photorefractive keratectomy: analysis of visual outcomes and higher-order aberrations

Majid Moshirfar1, Daniel S Churgin2, Brent S Betts3, Maylon Hsu1, Shameema Sikder4, Marcus Neuffer1, Dane Church5, Mark D Mifflin11University of Utah, John A Moran Eye Center, Department of Ophthalmology and Visual Sciences, Salt Lake City, UT, USA; 2University of Arizona College of Medicine, Phoenix, AZ; 3Temple University School of Medicine, Philadelphia, PA, USA; 4Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA; 5Virginia Commonwealth University School of Medicine, Richmond, VA, USABackground: The purpose of this study was to compare differences in visual outcomes, higher-order aberrations, contrast sensitivity, and dry eye in patients undergoing photorefractive keratectomy using wavefront-guided VISX CustomVue™ and wavefront-optimized WaveLight® Allegretto platforms.Methods: In this randomized, prospective, single-masked, fellow-eye study, photorefractive keratectomy was performed on 46 eyes from 23 patients, with one eye randomized to WaveLight Allegretto, and the fellow eye receiving VISX CustomVue. Three-month postoperative outcome measures included uncorrected distance visual acuity, corrected distance visual acuity, refractive error, root mean square of total and grouped higher-order aberrations, contrast sensitivity, and Schirmer’s testing.Results: Mean values for uncorrected distance visual acuity (logMAR) were —0.03 ± 0.07 and —0.06 ± 0.09 in the wavefront-optimized and wavefront-guided groups, respectively (P = 0.121). Uncorrected distance visual acuity of 20/20 or better was achieved in 91% of eyes receiving wavefront-guided photorefractive keratectomy, and 87% of eyes receiving wavefront-optimized photorefractive keratectomy, whereas uncorrected distance visual acuity of 20/15 was achieved in 35% of the wavefront-optimized group and 64% of the wavefront-guided group (P ≥ 0.296). While root mean square of total higher-order aberration, coma, and trefoil tended to increase in the wavefront-optimized group (P = 0.091, P = 0.115, P = 0.459, respectively), only spherical aberration increased significantly (P = 0.014). Similar increases were found in wavefront-guided root mean square of total higher-order aberration (P = 0.113), coma (P = 0.403), trefoil (P = 0.603), and spherical aberration (P = 0.014). There was no significant difference in spherical aberration change when comparing the two platforms. The wavefront-guided group showed an increase in contrast sensitivity at 12 cycles per degree (P = 0.013).Conclusion: Both VISX CustomVue and WaveLight Allegretto platforms performed equally in terms of visual acuity, safety, and predictability in photorefractive keratectomy. The wavefront-guided group showed slightly improved contrast sensitivity. Both lasers induced a comparable degree of statistically significant spherical aberration, and tended to increase other higher-order aberration measures as well.Keywords: wavefront-guided, wavefront-optimized, photorefractive keratectom