A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS

A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQ-FT MS mass spectrometer (or other high-resolution mass spectrometers, such as a Q-TOF MS). The strategy, termed "cross-assignment", is introduced to increase substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC-MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of Escherichia coli samples spiked with known amounts of non-E. coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC-MS data sets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication.     

Species richness of mussel assemblages and trait guilds in relation to environment and fish diversity in streams of Illinois,the USA

Hydrobiologia - Fish hosts are critical for freshwater mussels. However, correlation between mussel and fish species richness (SR) is variable. Here, we examine how the environment affects this...     

Discovering Candidate Chromosomal Regions Linked to Kernel Size-Related Traits via QTL Mapping and Bulked Sample Analysis in Maize

Kernel size-related traits, including kernel length, kernel width, and kernel thickness, are critical components in determining yield and kernel quality in maize (Zea mays L.). Dissecting the phenotypic characteristics of these traits, and discovering the candidate chromosomal regions for these traits, are of potential importance for maize yield and quality improvement. In this study, a total of 139 F2:3 family lines derived from EHel and B73, a distinct line with extremely low ear height (EHel), was used for phenotyping and QTL mapping of three kernel size-related traits, including 10-kernel length (KL), 10-kernel width (KWid), and 10-kernel thickness (KT). The results showed that only one QTL for KWid, i.e., qKWid9 on Chr9, with a phenotypic variation explained (PVE) of 13.4% was detected between SNPs of AX-86298371 and AX-86298372, while no QTLs were detected for KL and KT across all 10 chromosomes. Four bulked groups of family lines, i.e., Groups I to IV, were constructed with F2:3 family lines according to the phenotypic comparisons of KWid between EHel and B73. Among these four groups, Group I possessed a significantly lower KWid than EHel (P = 0.0455), Group II was similar to EHel (P = 0.34), while both Group III and Group IV were statistically higher than EHel (P < 0.05). Besides, except Group IV exhibited a similar KWid to B73 (P = 0.11), KWid of Groups I to III were statistically lower than B73 (P < 0.00). By comparing the bulked genotypes of the four groups to EHel and B73, a stable chromosomal region on Chr9 between SNPs of AX-86298372 to AX-86263154, entirely covered by qKWid9, was identified to link KWid with the positive allele of increasing phenotypic effect to KWid from B73, similar to that of qKWid9. A large amount of enzyme activity and macromolecule binding-related genes were annotated within this chromosomal region, suggesting qKWid9 as a potential QTL for KWid in maize.     

Comprehensive insights into the influence of supplemental green light on the photosynthesis of ginger (Zingiber officinale Roscoe)

Although green light is not considered to contribute to the photosynthesis of plants, the photosynthesis of ginger, a dual-purpose vegetable used as a medicine and food, is affected by the green wave band. In this study, the supplementary green band of sunlight (SG) increased the net photosynthetic rate (Pn), maximal photochemical efficiency of PSII (Fv/Fm), and actual photochemical efficiency of PSII (Y(II)) compared with the sunlight treatment (S). The Pn and Fv/Fm of the SG treatment were higher than those of the white light (W) treatment, while the Pn and Fv/Fm of the green light (G) treatment alone were lower than those of the W treatment. Further analysis found that the minimal fluorescence (Fo) of the S treatment increased, especially at noon, while the Fo of the SG treatment decreased. Similarly, the Fo of the W treatment increased significantly, while the Fo of the white–green mixed light (WG) treatment decreased. The relative fluorescence values of the K-J-I bands in the SG and WG treatments were lower than those in the S and W treatments, respectively. The photochemical quenching (qP) of the WG treatment was higher than that of the W treatment, while the primary thermal losses corresponded to the sum of nonregulated heat dissipation and fluorescence emission (Y(NO)) of the WG treatment was lower than that of the W treatment. The SG treatment reduced the accumulation of plastoglobules but increased the accumulation of starch granules and leaf thickness. Moreover, the green band supplemented with white light significantly increased the biomass of the aboveground plant parts and promoted the active growth of the aboveground parts. Supplementing green light plays a regulatory role in ginger based on the following four points. First, it effectively promotes the transfer of electrons between the acceptor side of photosystem II; second, it optimizes ginger photosynthesis; third, it alleviates strong light stress by reducing the accumulation of reactive oxygen species; and fourth, it promotes heat dissipation and reduces the rapid burst of active oxygen in the chloroplast caused by excess energy. In summary, green light can significantly optimize the photosynthetic characteristics of ginger.

     

TRAF6 Contributes to CFA-Induced Spinal Microglial Activation and Chronic Inflammatory Pain in Mice

Cellular and Molecular Neurobiology - Tumor necrosis factor receptor-associated factor 6 (TRAF6) has been reported to be expressed in spinal astrocytes and is involved in neuropathic pain. In this...     

SAHA Inhibits Somatic Hyperalgesia Induced by Stress Combined with Orofacial Inflammation Through Targeting Different Spinal 5-HT Receptor Subtypes

Neurochemical Research - Epigenetic regulation of gene expression has been implicated in the development of chronic pain. However, little is known about whether this regulation is involved in the...     

Palynological evidence for the temporal stability of the plant community in the Yellow River Source Area over the last 7,400 years

Vegetation History and Archaeobotany - The terrestrial ecosystem in the Yellow River Source Area (YRSA) is sensitive to climate change and human impacts, although past vegetation change and the...