Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress

Organisms have developed different mechanisms to respond to stresses. However, the roles of small ORF–encoded peptides (SEPs) in these regulatory systems remain elusive, which is partially because of the lack of comprehensive knowledge regarding these biomolecules. We chose the extremophile Deinococcus radiodurans R1 as a model species and conducted large-scale profiling of the SEPs related to the stress response. The integrated workflow consisting of multiple omics approaches for SEP identification was streamlined, and an SEPome of D. radiodurans containing 109 novel and high-confidence SEPs was drafted. Forty-four percent of these SEPs were predicted to function as antimicrobial peptides. Quantitative peptidomics analysis indicated that the expression of SEP068184 was upregulated upon oxidative treatment and gamma irradiation of the bacteria. SEP068184 was conserved in Deinococcus and exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Further quantitative and interactive proteomics analyses suggested that SEP068184 might function through metabolic pathways and interact with cytoplasmic proteins. Collectively, our findings demonstrate that SEPs are involved in the regulation of oxidative resistance, and the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms.     

Studies on the binding of 5-N-methylated quindoline derivative to human telomeric G-quadruplex

Quindoline derivatives as telomeric quadruplex ligands have shown good biological activity for telomerase inhibition. In the present study, we used spectroscopic and calorimetric methods to investigate the interactions between a quindoline derivative (5-methyl-11-(2-morpholinoethylamino)-10-H-indolo-[3,2-b]quinolin-5-ium iodide, compound 1) and human telomeric G-quadruplex. The thermodynamic studies using isothermal titration calorimetry (ITC) indicated that their binding process was temperature-dependent and enthalpy–entropy co-driven. The significant negative heat capacity was obtained experimentally from the temperature dependence of enthalpy changes, which was consistent with that from theoretical calculation, and all suggesting significant hydrophobic contribution to the molecular recognition process. Based on the results from UV–vis, ITC, steady-state and time-resolved fluorescence, their binding mode was determined as two ligand molecules stacking on the quartets on both ends of the quadruplex. These results shed light on rational design and development of quindoline derivatives as G-quadruplex binding ligands.     

Deer Carrying Capacity in Mid-Rotation Pine Plantations of Mississippi

ABSTRACT Herbicides, commonly used for vegetation management in intensively managed pine (Pinus spp.) forests of the southeastern United States, with and without fire, may alter availability of quality forage for white-tailed deer (Odocoileus virginianus; deer), an economically and socially important game species in North America. Because greater forage quality yields greater deer growth and productivity and intensively managed pine forests are common in the southeastern United States, forest managers would benefit from an understanding of fire and herbicide effects on forage availability to improve habitat conditions for deer. Therefore, we evaluated independent and combined effects of fire and herbicide (i.e., imazapyr) on forage biomass and deer nutritional carrying capacity (CC) on land owned and managed by Weyerhaeuser NR Company in east-central Mississippi, USA. We used a randomized complete block design of 6 pine plantations (blocks) divided into 4 10-ha treatment plots to each of which we randomly assigned a treatment (burn-only, herbicide-only, burn + herbicide, and control). We estimated biomass (kg/ha) of moderate- and high-use deer forage plants during July of 1999–2008, then estimated CC for diets to support either body maintenance (6% crude protein) or lactation (14% crude protein) with a nutritional constraints model. Herbaceous forages responded positively to fire and herbicide application. In most years, CC estimates for maintenance and lactation were greater in burn + herbicide than in controls. Maintenance-level CC was always greater in burn + herbicide than in controls, except at 1 year posttreatment. Burn + herbicide was 2.6–8.3 times greater (x̄ = 4.0) than control for lactation-level CC in 8 of 9 years posttreatment. We recommend fire and selective herbicides to increase high-quality deer forage in mid-rotation, intensively managed pine plantations.     

Quantifying physical functional trajectory in hospitalized older adults using body worn inertial sensors

Acute medical illness requiring hospitalization usually is a critical event in the trajectory leading to disability in older adults. Functional decline frequently occurs during hospitalization, resulting in a loss of Independence in activities of daily living after discharge. The aim of the study was to assess the functional decline in different ADLs of hospitalized elderly patients in an Acute Care for Elderly (ACE) unit incorporating a body-worn inertial sensor and accompanying custom algorithms. 38 hospitalized older adults (age ≥ 75) were included. The patients completed different functional tasks, including a balance test, Gait Velocity Test (GVT), verbal and arithmetic dual-task gait, and a sit-to-stand ability test at admission and discharge. Movement-related parameters were acquired from a unique tri-axial inertial sensor unit. Maximal muscle strength and muscle power output endpoints were also assessed. The results indicated that significant improvements (p < 0.05) were found at discharge compared with the admission values for gait variability and spatiotemporal parameters in the 4- and 6-meter GVT. These significant gains were also obtained in the verbal GVT. In contrast, a significant reduction was found in the functional status measured with the Barthel Index scale. Regarding to the sit-to-stand ability, lower peak power was observed in the sit-to-stand phase of the task at discharge. In conclusion, inertial sensor unit and our custom, validated, algorithms represent a feasible tool for measuring and monitoring functional trajectory during hospitalization in older adults and they are sensitive to detect differences in movement pattern parameters in different ADLs such as walking and the ability to stand from a seated position.     

Stereological estimation of the surface area and oxygen diffusing capacity of the respiratory stomach of the air‐breathing armored catfish Pterygoplichthys anisitsi (Teleostei: Loricariidae)

The stomach of Pterygoplichthys anisitsi has a thin, translucent wall and a simple squamous epithelium with an underlying dense capillary network. In the cardiac and pyloric regions, most cells have short microvilli distributed throughout the cell surface and their edges are characterized by short, densely packed microvilli. The mucosal layer of the stomach has two types of pavement epithelial cells that are similar to those in the aerial respiratory organs. Type 1 pavement epithelial cells, resembling the Type I pneumocyte in mammal lungs, are flat, with a large nucleus, and extend a thin sheet of cytoplasm on the underlying capillary. Type 2 cells, resembling the Type II pneumocyte, possess numerous mitochondria, a well‐developed Golgi complex, rough endoplasmic reticulum, and numerous lamellar bodies in different stages of maturation. The gastric glands, distributed throughout the mucosal layer, also have several cells with many lamellar bodies. The total volume (air + tissue), tissue, and air capacity of the stomach when inflated, increase along with body mass. The surface‐to‐tissue‐volume ratio of stomach varies from 108 cm^?1 in the smallest fish (0.084 kg) to 59 cm^?1 in the largest fish (0.60 kg). The total stomach surface area shows a low correlation to body mass. Nevertheless, the body‐mass‐specific surface area varied from 281.40 cm² kg^?1 in the smallest fish to 68.08 cm² kg^?1 in the largest fish, indicating a negative correlation to body mass (b = ?0.76). The arithmetic mean barrier thickness between air and blood was 1.52 ± 0.07 μm, whereas the harmonic mean thickness (τ_h) of the diffusion barrier ranged from 0.40 to 0.74 μm. The anatomical diffusion factor (ADF = cm² μm^?1 kg^?1) and the morphological O₂ diffusion capacity (D_morpholO₂ = cm³ min^?1 mmHg^?1 kg^?1) are higher in the smallest specimen and lower in the largest one. In conclusion, the structure and morphometric data of P. anisitsi stomach indicate that this organ is adapted for oxygen uptake from air. J. Morphol. 2009. © 2008 Wiley‐Liss, Inc.     

Critical water contents at leaf,stem and root level leading to irreversible drought-induced damage in two woody and one herbaceous species

Plant water content is a simple and promising parameter for monitoring drought-driven plant mortality risk. However, critical water content thresholds leading to cell damage and plant failure are still unknown. Moreover, it is unclear whether whole-plant or a specific organ water content is the most reliable indicator of mortality risk. We assessed differences in dehydration thresholds in leaf, stem and root samples, hampering the organ-specific rehydration capacity and increasing the mortality risk. We also tested eventual differences between a fast experimental dehydration of uprooted plants, compared to long-term water stress induced by withholding irrigation in potted plants. We investigated three species with different growth forms and leaf habits i.e., Helianthus annuus (herbaceous), Populus nigra (deciduous tree) and Quercus ilex (evergreen tree). Results obtained by the two dehydration treatments largely overlapped, thus validating bench dehydration as a fast but reliable method to assess species-specific critical water content thresholds. Regardless of the organ considered, a relative water content value of 60% induced significant cell membrane damage and loss of rehydration capacity, thus leading to irreversible plant failure and death.     

Proliferative capacity of cell cultures derived from the human placenta

Summary The placenta consists largely of fetal tissue, yet at term it displays histological signs of deterioration not apparent in the fetus. To determine whether the apparent degeneration of the placenta is genetically determined, the life-spans of placental cell cultures and the proportion of placental cells capable of incorporating [³H]thymidine for replicative DNA synthesis in vitro were measured. Under the culture conditions employed, the placental cells were removed from the influence of many extrinsic factors thought to play a role in the degeneration of the placenta in vivo. Cultures of fibroblast-like cells derived from the placenta exhibited a reduced life-span and correspondingly reduced proportion of cells able to incorporate [³H]thymidine for DNA synthesis in comparison to cultures derived from the fetal skin and the maternal decidua. These results suggest that intrinsic cellular processes may be involved in the apparent degeneration of the placenta. This work was supported by an NIH postdoctoral fellowship (R. A. V.) and grants from the National Institutes of Health, and the National Foundation/March of Dimes.