An Augmented Sample Selection Framework for Prediction of Anticancer Peptides.

Anticancer peptides (ACPs) have promising prospects for cancer treatment. Traditional ACP identification experiments have the limitations of low efficiency and high cost. In recent years, data-driven deep learning techniques have shown significant potential for ACP prediction. However, data-driven prediction models rely heavily on extensive training data. Furthermore, the current publicly accessible ACP dataset is limited in size, leading to inadequate model generalization. While data augmentation effectively expands dataset size, existing techniques for augmenting ACP data often generate noisy samples, adversely affecting prediction performance. Therefore, this paper proposes a novel augmented sample selection framework for the prediction of anticancer peptides (ACPs-ASSF). First, the prediction model is trained using raw data. Then, the augmented samples generated using the data augmentation technique are fed into the trained model to compute pseudo-labels and estimate the uncertainty of the model prediction. Finally, samples with low uncertainty, high confidence, and pseudo-labels consistent with the original labels are selected and incorporated into the training set to retrain the model. The evaluation results for the ACP240 and ACP740 datasets show that ACPs-ASSF achieved accuracy improvements of up to 5.41% and 5.68%, respectively, compared to the traditional data augmentation method.

Sex-biased, but not plumage color-based, prevalence of haemosporidian parasites in free-range chickens.

Previous studies found a relationship between blood parasite infection and bird gender, with higher prevalence in males. Some studies also found a relationship between host plumage color and parasitic infection, while others did not. Here, we investigated the blood parasite prevalence in correlation with sex and plumage color in free-range chickens (Gallus gallus domesticus) in China. We analyzed a total of 297 blood samples, out of which 234 chickens tested positive for haemosporidian parasites, with 78.5% parasite prevalence. Out of 139 males, 118 tested positive with 84.8% parasite prevalence while 116 of 158 female samples tested positive (73.4%). Leucocytotozoon was the most frequent genus isolated (193 infected individuals /234 birds), followed by Plasmodium (41 infected individuals/234 birds), with no Haemoproteus parasites being detected. There were no significant differences in the body parameters and chicken color plumages with regards to the infection status. Our study indicated that blood parasite infection was significantly different between male and female chickens, with infection prevalent in males.

Effect of Breeding Season on Haemosporidian Infections in Domestic Chickens.

Reproduction is believed to contribute to the frequently observed seasonal cycles in parasite loads in many organisms, as an investment in reproduction by the host could result in a higher susceptibility to parasites. In this study, we examined the impact of breeding season on haemosporidian infection in free-range chickens (Gallus gallus domesticus). We sampled a total of 122 chickens (66 chickens during the breeding season of April 2017 and 56 chickens during the non-breeding season of January 2017) to test for haemosporidian infections. The result showed that 56 out of 66 chickens examined during the breeding season tested positive for parasites (84.8% parasite prevalence), whereas 39 out of 56 chickens tested positive for parasites during the non-breeding season (69.6% parasite prevalence). Moreover, among the 11 Leucocytozoon lineages and 2 Plasmodium lineages identified, the parasite lineages that infected chickens during the breeding season were more diversified than those that affected chickens during the non-breeding season. This study indicated that chickens have a higher incidence of haemosporidian infection and a greater diversity of haemosporidian parasite lineages during the breeding season relative to the non-breeding season.

Characteristics of the enzyme-induced release of bitter peptides from wheat gluten hydrolysates.

Bitter peptides in the enzymatic hydrolysates were prepared and purified from wheat gluten using aqueous ethanol solutions and macroporous resin, which has opened a new road for the extraction and separation of bitter peptides. This report contains the release regularity of bitter peptides and the factors affecting the change of bitter intensity during enzymatic hydrolysis, providing a scientific basis for the research on debitterizing method. In this study, the effects of different degrees of hydrolysis (DH) and enzyme active sites on the bitter peptide content and bitter taste thresholds were discussed. The relationship between amino acid composition, molecular weight distribution, surface hydrophobicity and bitter taste thresholds was extensively researched. The results showed the exposure of hydrophobic amino acids and the bitterness intensity of the hydrolysates increased as the DH increased, and the bitterness of wheat gluten hydrolysates (WGHs) hydrolyzed by Alcalase was stronger than that of Trypsin. According to correlation analysis, the proportion of total hydrophobic amino acid is the first factor that affects the sensory properties of bitter peptide, and the release content of bitter peptides and the content of total bitter amino acids are the second, following by the content of peptide in the molecular weight range of 500-1,000 Da and the surface hydrophobicity. The amino acid sequence of bitter peptides from WGHs were identified and predicted using high performance liquid chromatography-mass spectrometry (HPLC-MS/MS) and bioinformatics. It was found that the molecular weight of most of the peptides was below 1,500 Da, and the Q value was higher than 5.86 kJ/mol.

Review on the release mechanism and debittering technology of bitter peptides from protein hydrolysates.

Recent scientific evidence indicates that protein hydrolysates contain bioactive peptides that have potential benefits for human health. However, the bitter-tasting hydrophobic peptides in protein hydrolysates negatively affect the sensory quality of resulting products and limit their utilization in food and pharmaceutical industries. The approaches to reduce, mask, and remove bitter taste from protein hydrolysates have been extensively reported. This review paper focuses on the advances in the knowledge regarding the structure-bitterness relationship of peptides, the release mechanism of bitter peptides, and the debittering methods for protein hydrolysates. Bitter tastes generating with enzymatic hydrolysis of protein is influenced by the type, concentration, and bitter taste threshold of bitterness peptides. A "bell-shaped curve" is used to describe the relationship between the bitterness intensity of the hydrolysates and the degree of hydrolysis. The bitter receptor perceives bitter potencies of bitter peptides by the hydrophobicity recognition zone. The intensity of bitterness is influenced by hydrophobic and electronic properties of amino acids and the critical spatial structure of peptides. Compared to physicochemical debittering (i.e., selective separation, masking of bitter taste, encapsulation, Maillard reaction, and encapsulation) and other biological debittering (i.e., enzymatic hydrolysis, enzymatic deamidation, plastein reaction), enzymatic hydrolysis is a promising debittering approach as it combines protein hydrolyzation and debittering into a one-step process, but more work should be done to advance the knowledge on debittering mechanism of enzymatic hydrolysis and screening of suitable proteases. Further study can focus on combining physicochemical and biological approaches to achieve high debittering efficiency and produce high-quality products.

Revisiting the multisite phosphorylation that produces the M-phase supershift of key mitotic regulators.

The term M-phase supershift denotes the phosphorylation-dependent substantial increase in the apparent molecular weight of numerous proteins of varied biological functions during M-phase induction. Although the M-phase supershift of multiple key mitotic regulators has been attributed to the multisite phosphorylation catalyzed by the Cdk1/cyclin B/Cks complex, this view is challenged by multiple lines of paradoxical observations. To solve this problem, we reconstituted the M-phase supershift of Xenopus Cdc25C, Myt1, Wee1A, APC3, and Greatwall in Xenopus egg extracts and characterized the supershift-producing phosphorylations. Our results demonstrate that their M-phase supershifts are each due to simultaneous phosphorylation of a considerable portion of S/T/Y residues in a long intrinsically disordered region that is enriched in both S/T residues and S/TP motifs. Although the major mitotic kinases in Xenopus egg extracts, Cdk1, MAPK, Plx1, and RSK2, are able to phosphorylate the five mitotic regulators, they are neither sufficient nor required to produce the M-phase supershift. Accordingly, inhibition of the four major mitotic kinase activities in Xenopus oocytes did not inhibit the M-phase supershift in okadaic acid-induced oocyte maturation. These findings indicate that the M-phase supershift is produced by a previously unrecognized category of mitotic phosphorylation that likely plays important roles in M-phase induction.

The mitogenome of common snipe, Gallinago gallinago gallinago Linnaeus, 1758 and evolutionary implications for the family Scolopacidae.

The mitochondrial genome (mitogenome) of Gallinago gallinago gallinago Linnaeus, 1758 was determined by the high-throughput data. The assembled mitogenome was 16,919 bp in length, with a 58.7% A + T content and GC skew of -0.3850. Among 13 PCGs, an unusual start codon (GTG) was identified for the COX1 gene, and incomplete stop codons (T-) were found in the COX3, ND2 and ND4 genes. The function of a cytosine insertion at site 174 in the ND3 gene and its phylogenetic significance are worthy of further scrutiny. In the control region (CR), thirteen 15-bp simple sequence repeats were found in G. g. gallinago. Phylogenetic analysis indicated that Gallinago was clustered at the basal position of the Scolopax clade and that the monophyly of Gallinago was also recovered. The mitogenome data of G. g. gallinago provides useful resources for further studying the evolution of Scolopacidae.

A new protocol for absolute quantification of haemosporidian parasites in raptors and comparison with current assays.

BACKGROUND: Accurate quantification of infection intensity is essential to estimate infection patterns of avian haemosporidian parasites in order to understand the evolution of host-parasite associations. Traditional microscopy is cost-effective but requires high-quality blood smears and considerable experience, while the widely used semi-quantitative qPCR methods are mostly employed with ideal, laboratory-based golden samples and standard curves, which may limit the comparison of parasitemia from different laboratories. METHODS: Here we present a digital droplet PCR (ddPCR) protocol for absolute quantification of avian haemosporidians in raptors. Novel primers were designed that target a conserved fragment of a rRNA region of the mitochondrial genome of the parasites. Sensitivity and repeatability were evaluated compared to qPCR and other assays. RESULTS: This ddPCR assay enables accurate quantification of haemosporidian parasites belonging to Plasmodium, Haemoproteus and Leucocytozoon with minimum infection quantities of 10-5 (i.e. one parasite copy in 105 host genomes) without the use of standard curves. Quantities assessed by ddPCR were more accurate than qPCR using the same primers through reduction of non-specific amplification in low-intensity samples. The ddPCR technique was more consistent among technical duplicates and reactions, especially when infection intensities were low, and this technique demonstrated equal sensitivity with high correspondence (R2 = 0.97) compared to the widely used qPCR assay. Both ddPCR and qPCR identified more positive samples than the standard nested PCR protocol for the cytb gene used for barcoding avian haemosporidians. CONCLUSIONS: We developed a novel ddPCR assay enabling accurate quantification of avian haemosporidians without golden samples or standard curves. This assay can be used as a robust method for investigating infection patterns in different host-parasite assemblages and can facilitate the comparison of results from different laboratories.

Peanut meal-based wood adhesives enhanced by urea and epichlorohydrin.

Peanut meal (PM) has recently emerged as a potential protein source for wood adhesives, owing to superior features such as high availability, renewability and eco-friendliness. However, the poor properties of unmodified PM-based wood adhesives, compared with their petroleum-derived counterparts, limit their use in high-performance applications. In order to promote the application of PM-based wood adhesives in plywood industry, urea (U) and epichlorohydrin (ECH) were used to enhance the properties of the adhesives and the modification mechanism was investigated. PM-based wood adhesives made with U and ECH were shown to possess sufficient water resistance and exhibited higher apparent viscosity and solid content than without. Fourier-transform infrared spectroscopy results suggested that U denatured PM protein and expose more reactive groups, allowing ECH to react better with U-treated PM protein to form a dense, cross-linked network which was the main reason for the improvement of the properties. The crystallinity increased from 2.7% to 11% compared with the control, indicating that the molecular structure of the resultant adhesive modified by U and ECH became more regular and compact owing to the cross-linked network structure. Thermogravimetry tests showed that decomposition temperature of the protein skeleton structure increased from 307°C to 314°C after U and ECH modification. Scanning electron microscopy images revealed that using U and ECH for adhesives resulted in a smooth protein surface which prevented moisture penetration and improved water resistance. PM-based adhesives thus represent potential candidates to replace petroleum-derived adhesives in the plywood industry, which will effectively promote the rapid development of eco-friendly adhesives and increase the added value of PM.

A modified SDS-based DNA extraction method from raw soybean.

Soybean is the most important genetically modified (GM) oilseed worldwide. Regulations relating to the approval of biotech soybean varieties and product labeling demand accurate and reliable detection techniques to screen for GM soya. High-quality extracted DNA is essential for DNA-based monitoring methods. Thus, four widely used protocols (SDS, CTAB, DP305, and DNeasy Plant Mini Kit) were compared in the present study to explore the most efficient DNA extraction method for raw soya matrix. The SDS-based method showed the highest applicability. Then crucial factors influencing DNA yield and purity, such as SDS lysis buffer component concentrations and organic compounds used to isolate DNA, were further investigated to improve the DNA obtained from raw soybean seeds, which accounts for the innovation of this work. As a result, lysis buffer (2% SDS (w/v), 150 mM NaCl, 50 mM Tris/HCl, 50 mM EDTA, pH 8.0) and organic reagents including chloroform/isoamyl alcohol (24:1, v/v) (C: I), isopropanol, and ethanol corresponding to the extraction and first and second precipitation procedures, respectively, were used in the optimized SDS method. The optimized method was verified by extracting approximately 2020-2444 ng DNA/mg soybean with A260/280 ratios of 1.862-1.954 from five biotech and non-biotech soybean varieties. Only 0.5 mg of soya was required to obtain enough DNA for PCR amplification using the optimized SDS-based method. These results indicate that the screening protocol in the present study achieves the highest suitability and efficiency for DNA isolation from raw soya seed flour.

High prevalence and narrow host range of haemosporidian parasites in Godlewski's bunting (Emberiza godlewskii) in northern China.

Avian haemosporidian parasites are highly diverse, have a wide range of host specificity, and reveal diverse compatibility with regard to host range and geographical distribution. Therefore, understanding haemosporidian parasite diversity in different host species and different regions is crucial. A survey of the haemosporidian parasite in 186 Godlewski's buntings in Beijing was conducted to compare infection patterns between Godlewski's bunting, local passerines and the global avian host. High prevalence (88.7%) was found in the bunting and displayed annual stability during the research period. Most of the infections were caused by four dominant lineages, three of which were clustered with lineages of morphological species. In comparison with other lineages in local passerines, the dominant lineages were relative specialists. The findings suggest that the compatibility of dominant lineages in the bunting hosts may play important roles in high haemosporidian prevalence, and the narrow host range of the dominant lineages may be due to coevolution between the parasites and host species.

Effect of deamidation-induced modification on umami and bitter taste of wheat gluten hydrolysates.

BACKGROUND: Bitter taste is the main limiting factor for various applications of protein hydrolysates. Frequently used physicochemical methods for debittering protein hydrolysates come with some undesired side effects. Deamidation-induced modification would be a very promising technique to improve the flavor of wheat gluten hydrolysates (WGHs). This study was designed to determine the effect of deamidation with certain enzymes or acid treatment on the chemical composition, bitterness and umami properties of WGHs. The difference between umami peptide and free glutamic acid on the suppression of bitterness is emphatically discussed. The optimal scheme is proposed based on the flavor of WGHs and the yield of peptides. RESULTS: The generation of umami substances suppressed bitter signal transduction. When the content of umami substances was relatively high, the umami-enhancing properties of umami peptides were obviously effective. The intensity of umami taste was high enough to further suppress bitter taste in the course of neurocognitive functioning. CONCLUSION: When WGHs were treated with Glutaminase for 180 min, the umami taste score increased from 1.62 to 4.27 and the bitter taste score decreased from 1.33 to 0.65. © 2016 Society of Chemical Industry.