Antecedent moisture and seasonal precipitation influence the response of canopy-scale carbon and water exchange to rainfall pulses in a semi-arid grassland

The influences of prior monsoon-season drought (PMSD) and the seasonal timing of episodic rainfall ('pulses') on carbon and water exchange in water-limited ecosystems are poorly quantified. *In the present study, we estimated net ecosystem exchange of CO(2) (NEE) and evapotranspiration (ET) before, and for 15 d following, experimental irrigation in a semi-arid grassland during June and August 2003. Rainout shelters near Tucson, Arizona, USA, were positioned on contrasting soils (clay and sand) and planted with native (Heteropogon contortus) or non-native invasive (Eragrostis lehmanniana) C4 bunchgrasses. Plots received increased ('wet') or decreased ('dry') monsoon-season (July-September) rainfall during 2002 and 2003. Following a June 2003 39-mm pulse, species treatments had similar NEE and ET dynamics including 15-d integrated NEE (NEE(pulse)). Contrary to predictions, PMSD increased net C uptake during June in plots of both species. Greater flux rates after an August 2003 39-mm pulse reflected biotic activity associated with the North American Monsoon. Furthermore, August NEE(pulse) and ecosystem pulse-use efficiency (PUE(e) = NEE(pulse)/ET(pulse)) was greatest in Heteropogon plots. PMSD and rainfall seasonal timing may interact with bunchgrass invasions to alter NEE and ET dynamics with consequences for PUE(e) in water-limited ecosystems.     

High level of soluble HLA-G in the female genital tract of Beninese commercial sex workers is associated with HIV-1 infection

Background

Most HIV infections are transmitted across mucosal epithelium. Understanding the role of innate and specific mucosal immunity in susceptibility or protection against HIV infection, as well as the effect of HIV infection on mucosal immunity, are of fundamental importance. HLA-G is a powerful modulator of the immune response. The aim of this study was to investigate whether soluble HLA-G (sHLA-G) expression in the female genital tract is associated with HIV-1 infection.

Methods and Findings

Genital levels of sHLA-G were determined in 52 HIV-1-uninfected and 44 antiretroviral naïve HIV-1-infected female commercial sex workers (CSWs), as well as 71 HIV-1-uninfected non-CSW women at low risk of exposure, recruited in Cotonou, Benin. HIV-1-infected CSWs had higher genital levels of sHLA-G compared with those in both the HIV-1-uninfected CSW (P = 0.009) and non-CSW groups (P = 0.0006). The presence of bacterial vaginosis (P = 0.008), and HLA-G*01:01:02 genotype (P = 0.002) were associated with higher genital levels of sHLA-G in the HIV-1-infected CSWs, whereas the HLA-G*01:04:04 genotype was also associated with higher genital level of sHLA-G in the overall population (P = 0.038). When adjustment was made for all significant variables, the increased expression of sHLA-G in the genital mucosa remained significantly associated with both HIV-1 infection (P = 0.02) and bacterial vaginosis (P = 0.03).

Conclusion

This study demonstrates that high level of sHLA-G in the genital mucosa is independently associated with both HIV-1 infection and bacterial vaginosis.     

Mites associated with stored grain commodities in Benin, West Africa

After insects, mites are the major arthropod pests that inhabit stored agricultural products worldwide. To determine the acarofauna that infests cowpea, maize, paddy rice and sorghum in Benin (West Africa), surveys were conducted in some principal markets (Dantokpa, Glazoue and Parakou) of this country. A total of 555 samples of grains and debris were collected in May and September 2011. More than 56 species belonging to 24 mite families were recorded in the four products. These mite species included predators, parasites, fungivorous, phytophagous and other groups whose feeding habits are not well known. The family Cheyletidae was the most prevalent and the most diverse predatory mite family encountered, in which Cheyletus malaccensis Oudemans was the most abundant species. Several families of mite pests and mites responsible for allergies (Acaridae, Glycyphagidae, Pyroglyphidae, Pyemotidae and Saproglyphidae) were also detected. The three most dominant and frequent species were C. malaccensis, Suidasia nesbitti (Hughes) and Suidasia sp. Statistical analysis showed that densities of these three mite species were higher in Parakou than in Glazoue and Dantokpa, on one hand, and higher in debris than in grains, on the other hand. The densities of S. nesbitti and Suidasia sp. decreased significantly during the dry season, whereas C. malaccensis remained stable throughout the two samplings. Of all grains, sorghum was the least infested with mites. This study shows that in Benin mites are present in stored agricultural products to which they cause serious damage, and may cause various allergies to people.     

Application of mechanoregulatory models to simulate peri-implant tissue formation in an in vivo bone chamber

Several mechanoregulatory tissue differentiation models have been proposed over the last decade. Corroboration of these models by comparison with experimental data is necessary to determine their predictive power. So far, models have been applied with various success rates to different experimental set-ups investigating mainly secondary fracture healing. In this study, the mechanoregulatory models are applied to simulate the implant osseointegration process in a repeated sampling in vivo bone chamber, placed in a rabbit tibia. This bone chamber provides a mechanically isolated environment to study tissue differentiation around titanium implants loaded in a controlled manner. For the purpose of this study, bone formation around loaded cylindrical and screw-shaped implants was investigated. Histologically, no differences were found between the two implant geometries for the global amount of bone formation in the entire chamber. However, a significantly larger amount of bone-to-implant contact was observed for the screw-shaped implant compared to the cylindrical implant. In the simulations, a larger amount of bone was also predicted to be in contact with the screw-shaped implant. However, other experimental observations could not be predicted. The simulation results showed a distribution of cartilage, fibrous tissue and (im)mature bone, depending on the mechanoregulatory model that was applied. In reality, no cartilage was observed. Adaptations to the differentiation models did not lead to a better correlation between experimentally observed and numerically predicted tissue distribution patterns. The hypothesis that the existing mechanoregulatory models were able to predict the patterns of tissue formation in the in vivo bone chamber could not be fully sustained.     

Comparison of predicted scaffold-compatible sequence variation in the triple-hairpin structure of human imunodeficiency virus type 1 gp41 with patient data

It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well.     

Consistency matrices: quantified structure alignments for sets of related proteins

Comparing two remotely similar structures is a difficult problem: more often than not, resulting structure alignments will show ambiguities and a unique answer usually does not even exist. In addition, alignments in general have a limited information content because every aligned residue is considered equally important. To solve these issues to a certain extent, one can take the perspective of a whole group of similar structures and then evaluate common structural features. Here, we describe a consistency approach that, although not actually performing a multiple structure alignment, does produce the information that one would conceivably want from such an experiment: the key structural features of the group, e.g., a fold, which in this case are projected onto either a pair of proteins or a single protein. Both representations are useful for a number of applications, ranging from the detection of (partially) wrong structure alignments to protein structure classification and fold recognition. To demonstrate some of these applications, the procedure was applied to 195 SCOP folds containing a total of 1802 domains sharing very low sequence similarity.     

Photoexcitation of tryptophan groups induces reduction of two disulfide bonds in goat alpha-lactalbumin

Illumination of goat alpha-lactalbumin (GLA) with 280 or 295 nm light results in tryptophan-mediated photolysis of disulfide bonds within the protein. The photolysis is not dependent on the absence or presence of Ca(2+) and is observed as well on illumination of native and of partially unfolded GLA. However, photolysis of native GLA results in a partial unfolding of the protein. The latter phenomenon is most clearly observed on fluorescence measurements at low temperatures (near 3 degrees C). The photolysis induces some dimerization and oligomerization, but most GLA molecules remain monomeric. To obtain more information about the reaction products, the illuminated protein is treated with iodoacetamide to label the free thiol groups, it is fragmented with trypsin, and the fragments are analyzed by mass spectrometry. Via this approach, we observe that the cleavage of disulfide bonds is restricted to Cys6-Cys120 and Cys73-Cys91 bonds. The photolytic cleavage of either of these disulfide bonds results in the formation of a single free thiol, a phenomenon restricted to Cys120 and Cys91, respectively. We also found indications that a thioether linkage is formed between Cys73 and Trp60. The alkylsulfenylation of Trp60 presumably results from a combination of primary thiyl and tryptyl radicals.     

Response of net ecosystem gas exchange to a simulated precipitation pulse in a semi-arid grassland: the role of native versus non-native grasses and soil texture

Physiological activity and structural dynamics in arid and semi-arid ecosystems are driven by discrete inputs or pulses of growing season precipitation. Here we describe the short-term dynamics of ecosystem physiology in experimental stands of native (Heteropogon contortus) and invasive (Eragrostis lehmanniana) grasses to an irrigation pulse across two geomorphic surfaces with distinctly different soils: a Pleistocene-aged surface with high clay content in a strongly horizonated soil, and a Holocene-aged surface with low clay content in homogenously structured soils. We evaluated whole-ecosystem and leaf-level CO₂ and H₂O exchange, soil CO₂ efflux, along with plant and soil water status to understand potential constraints on whole-ecosystem carbon exchange during the initiation of the summer monsoon season. Prior to the irrigation pulse, both invasive and native grasses had less negative pre-dawn water potentials ( _pd), greater leaf photosynthetic rates (A _net) and stomatal conductance (g _s), and greater rates of net ecosystem carbon exchange (NEE) on the Pleistocene surface than on the Holocene. Twenty-four hours following the experimental application of a 39 mm irrigation pulse, soil CO₂ efflux increased leading to all plots losing CO₂ to the atmosphere over the course of a day. Invasive species stands had greater evapotranspiration rates (ET) immediately following the precipitation pulse than did native stands, while maximum instantaneous NEE increased for both species and surfaces at roughly the same rate. The differential ET patterns through time were correlated with an earlier decline in NEE in the invasive species as compared to the native species plots. Plots with invasive species accumulated between 5% and 33% of the carbon that plots with the native species accumulated over the 15-day pulse period. Taken together, these results indicate that system CO₂ efflux (both the physical displacement of soil CO₂ by water along with plant and microbial respiration) strongly controls whole-ecosystem carbon exchange during precipitation pulses. Since CO₂ and H₂O loss to the atmosphere was partially driven by species effects on soil microclimate, understanding the mechanistic relationships between the soil characteristics, plant ecophysiological responses, and canopy structural dynamics will be important for understanding the effects of shifting precipitation and vegetation patterns in semi-arid environments.     

Proteomic biomarkers predicting lymph node involvement in serum of cervical cancer patients. Limitations of SELDI-TOF MS

ABSTRACT: BACKGROUND: Lymph node status is not part of the staging system for cervical cancer, but provides important information for prognosis and treatment. We investigated whether lymph node status can be predicted with proteomic profiling. Material & methods Serum samples of 60 cervical cancer patients (FIGO I/II) were obtained before primary treatment. Samples were run through a HPLC depletion column, eliminating the 14 most abundant proteins ubiquitously present in serum. Unbound fractions were concentrated with spin filters. Fractions were spotted onto CM10 and IMAC30 surfaces and analyzed with surface-enhanced laser desorption time of flight (SELDI-TOF) mass spectrometry (MS). Unsupervised peak detection and peak clustering was performed using MASDA software. Leave-one-out (LOO) validation for weighted Least Squares Support Vector Machines (LSSVM) was used for prediction of lymph node involvement. Other outcomes were histological type, lymphvascular space involvement (LVSI) and recurrent disease. RESULTS: LSSVM models were able to determine LN status with a LOO area under the receiver operating characteristics curve (AUC) of 0.95, based on peaks with m/z values 2,698.9, 3,953.2, and 15,254.8. Furthermore, we were able to predict LVSI (AUC 0.81), to predict recurrence (AUC 0.92), and to differentiate between squamous carcinomas and adenocarcinomas (AUC 0.88), between squamous and adenosquamous carcinomas (AUC 0.85), and between adenocarcinomas and adenosquamous carcinomas (AUC 0.94). CONCLUSIONS: Potential markers related with lymph node involvement were detected, and protein/peptide profiling support differentiation between various subtypes of cervical cancer. However, identification of the potential biomarkers was hampered by the technical limitations of SELDI-TOF MS.