iDVEIP: A computer-aided approach for the prediction of viral entry inhibitory peptides

With the notable surge in therapeutic peptide development, various peptides have emerged as potential agents against virus-induced diseases. Viral entry inhibitory peptides (VEIPs), a subset of antiviral peptides (AVPs), offer a promising avenue as entry inhibitors (EIs) with distinct advantages over chemical counterparts. Despite this, a comprehensive analytical platform for characterizing these peptides and their effectiveness in blocking viral entry remains lacking. In this study, we introduce a groundbreaking in silico approach that leverages bioinformatics analysis and machine learning to characterize and identify novel VEIPs. Cross-validation results demonstrate the efficacy of a model combining sequence-based features in predicting VEIPs with high accuracy, validated through independent testing. Additionally, an EI type model has been developed to distinguish peptides specifically acting as Eis from AVPs with alternative activities. Notably, we present iDVEIP, a web-based tool accessible at http://mer.hc.mmh.org.tw/iDVEIP/, designed for automatic analysis and prediction of VEIPs. Emphasizing its capabilities, the tool facilitates comprehensive analyses of peptide characteristics, providing detailed amino acid composition data for each prediction. Furthermore, we showcase the tool's utility in identifying EIs against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).

Microbiome analysis of maternal and neonatal microbial communities associated with the different delivery modes based on 16S rRNA gene amplicon sequencing

OBJECTIVE

With the rising number of cases of non-vaginal delivery worldwide, scientists have been concerned about the influence of the different delivery modes on maternal and neonatal microbiomes. Although the birth rate trend is decreasing rapidly in Taiwan, more than 30 percent of newborns are delivered by caesarean section every year. However, it remains unclear whether the different delivery modes could have a certain impact on the postpartum maternal microbiome and whether it affects the mother-to-newborn vertical transmission of bacteria at birth.

MATERIALS AND METHODS

To address this, we recruited 30 mother-newborn pairs to participate in this study, including 23 pairs of vaginal delivery (VD) and seven pairs of caesarean section (CS). We here investigate the development of the maternal prenatal and postnatal microbiomes across multiple body habitats. Moreover, we also explore the early acquisition of neonatal gut microbiome through a vertical multi-body site microbiome analysis.

RESULTS AND CONCLUSION

The results indicate that no matter the delivery mode, it only slightly affects the maternal microbiome in multiple body habitats from pregnancy to postpartum. On the other hand, about 95% of species in the meconium microbiome were derived from one of the maternal body habitats; notably, the infants born by caesarean section acquire bacterial communities resembling their mother's oral microbiome. Consequently, the delivery modes play a crucial role in the initial colonization of the neonatal gut microbiome, potentially impacting children's health and development.

iDVIP: identification and characterization of viral integrase inhibitory peptides

Antiretroviral peptides are a kind of bioactive peptides that present inhibitory activity against retroviruses through various mechanisms. Among them, viral integrase inhibitory peptides (VINIPs) are a class of antiretroviral peptides that have the ability to block the action of integrase proteins, which is essential for retroviral replication. As the number of experimentally verified bioactive peptides has increased significantly, the lack of in silico machine learning approaches can effectively predict the peptides with the integrase inhibitory activity. Here, we have developed the first prediction model for identifying the novel VINIPs using the sequence characteristics, and the hybrid feature set was considered to improve the predictive ability. The performance was evaluated by 5-fold cross-validation based on the training dataset, and the result indicates the proposed model is capable of predicting the VINIPs, with a sensitivity of 85.82%, a specificity of 88.81%, an accuracy of 88.37%, a balanced accuracy of 87.32% and a Matthews correlation coefficient value of 0.64. Most importantly, the model also consistently provides effective performance in independent testing. To sum up, we propose the first computational approach for identifying and characterizing the VINIPs, which can be considered novel antiretroviral therapy agents. Ultimately, to facilitate further research and development, iDVIP, an automatic computational tool that predicts the VINIPs has been developed, which is now freely available at http://mer.hc.mmh.org.tw/iDVIP/.

Anticancer peptide Q7 suppresses the growth and migration of human endometrial cancer by inhibiting DHCR24 expression and modulating the AKT-mediated pathway

Endometrial cancer is one of the most common malignancy affecting women in developed countries. Resection uterus or lesion area is usually the first option for a simple and efficient therapy. Therefore, it is necessary to find a new therapeutic drug to reduce surgery areas to preserve fertility. Anticancer peptides (ACP) are bioactive amino acids with lower toxicity and higher specificity than chemical drugs. This study is to address an ACP, herein named Q7, which could downregulate 24-Dehydrocholesterol Reductase (DHCR24) to disrupt lipid rafts formation, and sequentially affect the AKT signal pathway of HEC-1-A cells to suppress their tumorigenicity such as proliferation and migration. Moreover, lipo-PEI-PEG-complex (LPPC) was used to enhance Q7 anticancer activity in vitro and efficiently show its effects on HEC-1-A cells. Furthermore, LPPC-Q7 exhibited a synergistic effect in combination with doxorubicin or paclitaxel. To summarize, Q7 was firstly proved to exhibit an anticancer effect on endometrial cancer cells and combined with LPPC efficiently improved the cytotoxicity of Q7.

Source Apportionment of Volatile Organic Compounds (VOCs) by Positive Matrix Factorization (PMF) supported by Model Simulation and Source Markers - Using Petrochemical Emissions as a Showcase

This study demonstrates the use of positive matrix factorization (PMF) in a region with a major Petrochemical Complex, a prominent source of volatile organic compounds (VOCs), as a showcase of PMF applications. The PMF analysis fully exploited the quality and quantity of the observation data, sufficed by a cluster of 9 monitoring sites within a 20 km radius of the petro-complex. Each site provided continuous data of 54 speciated VOCs and meteorological variables. Wind characteristics were highly seasonal and played a decisive role in the source-receptor relationship, hence the dataset was divided into three sub-sets in accordance with the prevailing wind flows. A full year of real-time data were analyzed by PMF to resolve into various distinct source types including petrochemical, urban, evaporative, long-range air parcels, etc., with some sites receiving more petro-influence than others. To minimize subjectivity in the assignment of the PMF source factors, as commonly seen in some PMF works, this study attempted to solidify PMF results by supporting with two tools of spatially/temporally resolved air-quality model simulations and observation data. By exploiting the two supporting tools, the dynamic process of individual sources to a receptor were rationalized. Percent contributions from these sources to the receptor sites were calculated by summing over the occurrence of different source types. Interestingly, although the Petro-complex is the single largest local VOC source in the 20 km radius study domain, all monitoring sites in the region received far less influence from the Petro-complex than from other emission types within or outside the region, which together add up to more than 70% of the total VOC abundance.

Distribution of double-negative (CD4- CD8-, DN) T subsets in blood and synovial fluid from patients with rheumatoid arthritis

Double-negative (CD4- CD8-) T (DNT) cells have been postulated to be potentially autoreactive. However, the role of DNT cells in rheumatoid arthritis (RA) has received limited attention. We investigated the distribution of DNT subsets in peripheral blood (PB) and synovial fluid (SF) from patients with active RA to determine whether these cells have relevance to RA. Two-colour flow cytometric analysis was performed to detect DNT cells in PB from 35 RA patients, 26 healthy controls and in SF aspirated from 19 inflamed rheumatoid joints. The subsets of DNT cells, i.e those expressing T cell receptor alphabeta (alphabeta DNT) or gammadelta (gammadelta DNT) were simultaneously examined. Our results showed that DNT cells constituted a very minor subset of PB lymphocytes. When expressed as a percentage of total lymphocytes, alphabeta DNT levels in normal individuals ranged from 0.27 to 2.08% (average 0.76%), while those of gammadelta DNT ranged from 1.02 to 11.42% (average 3.23%). Compared with normal individuals, RA patients had a similar distribution of alphabeta DNT cells in both PB and SF. However, RA patients had significantly lower levels of gammadelta DNT cells in PB than control subjects (1.38 +/- 1.08% vs 3.23 +/- 2.12%, p<0.05), while the levels of gammadelta DNT cells in SF of RA patients were higher than those in PB from RA patients and normal controls. The difference between PB and SF in RA was statistically significant (3.90 +/- 1.88% vs 1.38 +/- 1.08%, p<0.05). A higher level of gammadelta DNT in SF than their paired PB was consistently noted from nine available paired samples. Our findings suggest that gammadelta NT cells, but not alphabeta DNT cells, are probably relevant to RA. The lower percentage of circulating gammadelta DNT cells might have resulted from migration from the circulation into the synovium, suggesting a role for gammadelta DNT cells in the pathogenesis of rheumatoid synovitis.

Differential expression and modulation of costimulatory molecules CD80 and CD86 on monocytes from patients with systemic lupus erythematosus

Patients with systemic lupus erythematosus (SLE) were recently shown to be defective in costimulatory molecule CD80 (B7-1) expression on antigen-presenting cells. This study was undertaken to further investigate the expression and cytokine regulation of both CD80 and CD86 (B7-2) on monocytes from patients with SLE. Freshly isolated and in vitro cytokine-stimulated peripheral blood mononuclear cells from 13 patients with SLE and 10 healthy subjects were analysed, cytometrically with dual-fluorescence staining, to detect expression of CD80 and CD86 in the CD14+ monocyte population. The results showed that, as in normal individuals, an overwhelming majority (95.62+/-3.54%) of monocytes from patients with SLE expressed the CD86 molecule, but only a few monocytes (5.54+/-4.36%) had detectable CD80 expression. The effects of interleukin-10 (IL-10) on the expression of CD80 and CD86 on monocytes from patients with SLE and normal controls were similar. IL-10 down-regulated the expression of CD86 while it slightly enhanced that of CD80. Interferon-gamma (IFN-gamma) increased both CD80 and CD86 expression on monocytes from both SLE patients and normal groups, albeit less significantly in the former than in the latter, i.e. CD80: 142.84+/-65.99% versus 226.08+/-78.90%, P<0.05; and CD86: 72.55+/-74.23% versus 153.99+/-94.14%, P<0.05, when expressed as percentage modulation. Granulocyte-macrophage colony-stimulating factor (GM-CSF) showed a capacity for up-regulation of CD80 and CD86 expression on monocytes, of a magnitude that was similar both in patients with SLE and in normal subjects. We concluded that CD80 and CD86 were differentially expressed and modulated on monocytes and the defective IFN-gamma-induced up-regulation of CD80 and CD86 expression on SLE monocytes might be a factor in the pathogenesis of SLE.

Clinical experience of 13 cases with severe pulmonary hemorrhage in systemic lupus erythematosus with active nephritis

Pulmonary hemorrhage is a rare, but serious manifestation of systemic lupus erythematosus (SLE). Herein, we report 13 cases of severe pulmonary hemorrhage in SLE. Hemoptysis was present in 11 patients. All thirteen patients had active nephritis and were in the stage of nephrotic syndrome. A majority of the patients had neuropsychiatric manifestations and coagulopathy including thrombocytopenia or lupus anticoagulant. All episodes of pulmonary hemorrhage occurred after large dose of corticosteroid had been administered in treating nephritis. Recurrent pulmonary hemorrhage was noted in four patients. Ten (77%) of the 13 patients finally died. Respiratory failure was the main cause of death. Our observation suggests that active nephritis with hypoalbuminemia is a major risk factor for severe pulmonary hemorrhage in SLE patients and that high dose corticosteroid use can not prevent the occurrence of severe pulmonary hemorrhage in SLE.

Double-negative (CD4-CD8-) TCRalphabeta+ cells in patients with systemic lupus erythematosus

Massive accumulation of CD4-CD8-TCRalphabeta+ cells in secondary lymphoid organs is characteristic of lupus-prone MRL/lpr mice. However, the role of these double negative T cells (DNT) in human lupus patients receive only limited attention. Herein, we investigate the frequency of DNT in the peripheral blood mononuclear cells of forty seven Chinese patients with systemic lupus erythematosus (SLE) and forty four normal individuals. DNT were measured with dual-fluorescence flow cytometry. The results showed that DNT only constituted a very minor subset of lymphocytes both in patients and normals, it normally did not exceed 2% of the lymphocyte population. Compared with normal subjects, patients with SLE had slightly increased levels of DNT within the total lymphocyte population (0.66+/-0.45% vs 0.51+/-0.33%) or within TCRalphabeta+ population (1.14+/-0.88% vs 0.88+/-0.54%). The difference, however, did not reach statistical significance. The levels of DNT correlated neither with the titers of anti-DNA antibodies in sera nor with the presence of active and severe lupus nephritis in SLE patients. Longitudinal follow-up of six patients at the stages of active and inactive nephritis revealed similar levels of DNT in the same individual. The preliminary results suggest that circulating DNT do not appear to play a critical role in Chinese patients with SLE.