Light activation of Russian wheat aphid-elicited physiological responses in susceptible wheat

The impact of light and its role in Russian wheat aphid, Diuraphis noxia (Mordvilko), damage symptom formation, and photosynthetic capacity in 'Arapahoe' wheat (Triticum aestivum L.) were examined. After 72 h under continuous dark or continuous light regimes, the number of aphids (nymphs), leaf rolling and chlorosis ratings, fresh leaf weight, and chlorophyll contents were recorded. Photosynthetic rates, chlorophyll a, kinetics and chlorophyll extractions also were determined. Aphid infestation caused significant reductions in plant height, fresh weight, gas exchange, and chlorophyll fluorescence only under continuous light. Under the 72 h continuous dark regime, aphid infestation did not cause either damage symptom formation or reduction in plant growth or metabolism (photosynthesis). Furthermore, significantly more D. noxia nymphs were produced under continuous light condition than continuous dark. Our results demonstrate that the development of D. noxia feeding damage symptoms (i.e., leaf rolling and chlorotic streaks) on susceptible wheat seedlings is a light-activated process, even though the elicitor of the plant damage symptoms is aphid feeding.     

Creatine kinase isoenzyme activity during and after an ultra-distance (200 km) run

It is commonly assumed that creatine kinase (CK) activity in plasma is related to the state of an inflammatory response at 24-48 h, and also it has shown biphasic patterns after a marathon run. No information is available on CK isoenzymes after an ultra-marathon run. The purpose of the present study is to examine the CK isoenzymes after a 200 km ultra-marathon run and during the subsequent recovery. Blood samples were obtained during registration 1 2 h before the 200-km race and during the race at 100 km, 150 km and at the end of 200 km, as well as after a 24 h period of recovery. Thirty-two male ultra-distance runners participated in the study. Serum CPK showed a marked increase throughout the race and 24 h recovery period (p < 0.001). Serum CK during the race occurs mostly in the CK-MM isoform and only minutely in the CK-MB isoform and is unchanged in the CK-BB isoform. High-sensitivity C-reactive protein (hs-CRP), oestradiol, AST and ALT increased significantly from the pre-race value at 100 km and a further increase took place by the end of the 200 km run. The results of our study demonstrate a different release pattern of creatine kinase after an ultra-distance (200 km) run compared to the studies of marathon running and intense eccentric exercise, and changes in several biomarkers, indicative of muscle damage during the race, were much more pronounced during the latter half (100–200 km) of the race. However, the increases in plasma concentration of muscle enzymes may reflect not only structural damage, but also their rate of clearance.     

Motif kernel generated by genetic programming improves remote homology and fold detection

Background  

Protein remote homology detection is a central problem in computational biology. Most recent methods train support vector machines to discriminate between related and unrelated sequences and these studies have introduced several types of kernels. One successful approach is to base a kernel on shared occurrences of discrete sequence motifs. Still, many protein sequences fail to be classified correctly for a lack of a suitable set of motifs for these sequences.     

Rituximab treatment in rheumatoid arthritis: how does it work?

Treatment with the chimerical monoclonal antibody rituximab results in CD20-directed B cell depletion. Although this depletion is almost complete in the peripheral blood of nearly all patients with rheumatoid arthritis, a proportion of patients does not exhibit a clinical response. The paper by Nakou and colleagues suggests that a decrease in CD19+CD27+ memory B cells in both peripheral blood and bone marrow precedes the clinical response to rituximab. This finding adds to the emerging evidence that lack of response to rituximab is associated with persistence of B lineage cells in specific body compartments.     

COMPARATIVE MEASURES OF DESICCATION-TOLERANCE IN THE TORTULA RURALIS COMPLEX. I. VARIATION IN DAMAGE CONTROL AND REPAIR

A mechanism for desiccation-tolerance in bryophytes based on carbon balance, damage limitation, and cellular repair is proposed. These criteria are incorporated into an experimental framework to measure desiccation-tolerance comparatively. In this report we utilize measures of damage control and damage repair to determine relative differences in tolerance between populations of three tolerant moss species: Tortula caninervis, T. ruralis, and T. norvegica. The measurement of damage control by electrolyte leakage alone was demonstrated not to be useful in determining levels of tolerance by traditional criteria in these closely related and highly tolerant species. Measurement of protein synthetic differences between hydrated and desiccated-rehydrated treatments was used to distinguish between the capabilities of the three moss species to repair cellular damage and to formulate a measure of tolerance. The overall ranking of the three species in descending order of tolerance is calculated to be: Tortula caninervis, T. ruralis, and T. norvegica. However, individual populations of each of these species exhibit variation in tolerance levels that span this broader classification. These rankings correlate well with the perceived ranking of water stress in the species' natural habitat.     

Molecular docking of alkaloid compounds with the matrix metalloproteinase 2

Matrix metalloproteinase protein-2 (MMP-2) is linked to the human oral squamous cell carcinoma. Therefore, it is of interest to design new inhibitors for MMP-2 to combat the disease. Thus, we document the molecular docking features of Aristolochic acid, Cryptopleurine, Epipodophyllotoxin, and Fagaronine with MMP-2 for further consideration.     

OntologyWidget – a reusable,embeddable widget for easily locating ontology terms

Background  

Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form.     

ATP Synthase with Its �� Subunit Reduced to the N-terminal Helix Can Still Catalyze ATP Synthesis

ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. As part of the synthesis mechanism, the torque of the rotor has to be converted into conformational rearrangements of the catalytic binding sites on the stator to allow synthesis and release of ATP. The γ subunit of the rotor, which plays a central role in the energy conversion, consists of two long helices inside the central cavity of the stator cylinder plus a globular portion outside the cylinder. Here, we show that the N-terminal helix alone is able to fulfill the function of full-length γ in ATP synthesis as long as it connects to the rest of the rotor. This connection can occur via the ϵ subunit. No direct contact between γ and the c ring seems to be required. In addition, the results indicate that the ϵ subunit of the rotor exists in two different conformations during ATP synthesis and ATP hydrolysis.F₁F_o-ATP synthase is responsible for the bulk of ATP synthesis from ADP and P_i in most organisms. F₁F_o-ATP synthase consists of the membrane-embedded F_o subcomplex with, in most bacteria, a subunit composition of ab₂c_n (with n = 10–15) and the peripheral F₁ subcomplex, with a subunit composition of α₃β₃γδϵ. The energy necessary for ATP synthesis is derived from an electrochemical transmembrane proton (or, in some organisms, sodium ion) gradient. Proton flow, down the gradient, through F_o is coupled to ATP synthesis on F₁ by a unique rotary mechanism. The protons flow through channels at the interface of a and c subunits, which drives rotation of the ring of c subunits. The c_n ring, together with F₁ subunits γ and ϵ, forms the rotor. Rotation of γ leads to conformational changes in the catalytic nucleotide-binding sites on the β subunits, where ADP and P_i are bound. The conformational changes result in formation and release of ATP. Thus, ATP synthase converts electrochemical energy, the proton gradient, into mechanical energy in the form of subunit rotation and back into chemical energy as ATP. In bacteria, under certain physiological conditions, the process can run in reverse. ATP is hydrolyzed to generate a transmembrane proton gradient that the bacterium requires for such functions as nutrient import and locomotion (for reviews, see Refs. 1–6).F₁ (or “F₁-ATPase”) has three catalytic nucleotide-binding sites, located on the β subunits, at the interface with the adjacent α subunit. The catalytic sites have pronounced differences in their nucleotide-binding affinity. During rotational catalysis, the sites switch their affinities in a synchronized manner; the position of γ determines which catalytic site is the high affinity site (K_d1 in the nanomolar range), which site is the medium affinity site (K_d2 ≈ 1 μm), and which site is the low affinity site (K_d3 ≈ 30–100 μm; see Refs. 7, 8). Only the high affinity site is catalytically active (9). In the original crystal structure of bovine mitochondrial F₁ (10), one of the three catalytic sites was filled with the ATP analog AMPPNP,³ a second one with ADP (plus azide; see Ref. 11), and the third site was empty. Hence, the β subunits are referred to as β_TP, β_DP, and β_E, respectively. The high affinity site is located on the β_TP subunit (12).The coupling process between ATP synthesis or hydrolysis on β and rotation of γ is not yet fully understood on a residue level. A number of point mutations at the interfaces between α or β and γ and between γ, ϵ, and c have been described that result in varying degrees of uncoupling (13–17). Some mutations at these interfaces were found that abolish ATP synthesis or hydrolysis activity or both (18–20). Considering the pronounced effect of these point mutations, some of which were even conservative substitutions, it came as a surprise when it was recently shown that an “axle-less” γ, consisting just of the globular portion, with the portions of the N- and C-terminal helices that reach into the α₃β₃ cylinder removed, displayed ATP-driven rotation in the correct direction (21).Some reports have implicated the ϵ subunit (corresponding to the δ subunit in the mitochondrial enzyme) as being involved in coupling (15, 22–25). It was shown that ϵ exists in different conformations that vary in the folding and positioning of the C-terminal domain. The x-ray structure of the mitochondrial enzyme (26) shows the two helices of the C-terminal domain folded back on each other like a hairpin and positioned close to the interface between γ and the c ring (“down” conformation). In the crystal structure of a γϵ complex from Escherichia coli the hairpin is unfolded (27); when integrated into F₁ or F₁F_o, the C terminus would reach “up,” coming close to the DELSEED-loop of the α and/or β subunits. While in this up conformation the angle between both helices of the C-terminal domain of ϵ is ∼90°, it has been postulated that this domain might also exist in a fully extended up conformation, stretching close to the N terminus of γ, with helical regions replacing the turn between the two helices (28). Fixing ϵ in either up conformation by cross-linking to γ has been shown to impair ATP hydrolysis but not synthesis. Freezing ϵ in the down position inhibited neither reaction (29, 30).Here, we report a finding that is arguably just as surprising as the rotation of an axle-less γ. In ATP synthase from the thermophilic bacterium Bacillus PS3, enzymes with γ subunit constructs where the globular domain and the C-terminal helix were eliminated, consisting of just the N-terminal 35 or 42 residues, TF₁F_o(γQ36stop)⁴ and TF₁F_o(γP43stop), were able to catalyze significant rates of ATP synthesis. According to the crystal structure (26), the shorter of the two γ constructs should not make any contact either with c or with ϵ in the down conformation. Thus, the fact that ATP synthesis was observed suggests that ϵ in an up conformation forms a complex with the truncated γ, which is able to catalyze ATP synthesis. Indeed, when the γQ36stop truncation was combined with an ϵ truncation where the C-terminal domain was removed, ATP synthesis was abolished. The functions of the γ and ϵ subunits will be discussed in light of the new findings.     

Solution-based targeted genomic enrichment for precious DNA samples

ABSTRACT: BACKGROUND: Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible. RESULTS: We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. CONCLUSIONS: This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.