Characterization of an African Swine Fever Virus Field Isolate from Vietnam with Deletions in the Left Variable Multigene Family Region

In this paper, we report the characterization of a genetically modified live-attenuated African swine fever virus (ASFV) field strain isolated from Vietnam. The isolate, ASFV-GUS-Vietnam, belongs to p72 genotype II, has six multi-gene family (MGF) genes deleted, and an Escherichia coli GusA gene (GUS) inserted. When six 6-8-week-old pigs were inoculated with ASFV-GUS-Vietnam oro-nasally (2 × 105 TCID50/pig), they developed viremia, mild fever, lethargy, and inappetence, and shed the virus in their oral and nasal secretions and feces. One of the pigs developed severe clinical signs and was euthanized 12 days post-infection, while the remaining five pigs recovered. When ASFV-GUS-Vietnam was inoculated intramuscularly (2 × 103 TCID50/pig) into four 6-8 weeks old pigs, they also developed viremia, mild fever, lethargy, inappetence, and shed the virus in their oral and nasal secretions and feces. Two contact pigs housed together with the four intramuscularly inoculated pigs, started to develop fever, viremia, loss of appetite, and lethargy 12 days post-contact, confirming horizontal transmission of ASFV-GUS-Vietnam. One of the contact pigs died of ASF on day 23 post-contact, while the other one recovered. The pigs that survived the exposure to ASFV-GUS-Vietnam via the mucosal or parenteral route were fully protected against the highly virulent ASFV Georgia 2007/1 challenge. This study showed that ASFV-GUS-Vietnam field isolate is able to induce complete protection in the majority of the pigs against highly virulent homologous ASFV challenge, but has the potential for horizontal transmission, and can be fatal in some animals. This study highlights the need for proper monitoring and surveillance when ASFV live-attenuated virus-based vaccines are used in the field for ASF control in endemic countries.

Targeting mangiferin loaded N-succinyl chitosan-alginate grafted nanoparticles against atherosclerosis - A case study against diabetes mediated hyperlipidemia in rat

Mangiferin (MGF), from Mangifera indica is well reported for its hypoglycemic activity and hypolipidemic activity. However, MGF suffers therapeutic limitation due to poor solubility causing disparaging bioavailability. Herein to address this problem, we have incorporated MGF in alginate grafted N-succinylated chitosan (NSC) nanomatrix. Characterization by molecular docking, FT-IR and 2D-NMR (COSY) has revealed that MGF could reinforce interaction with NSC. The OH and CH₂OH groups of MGF may set interactions with pyranosic OH, CH₂OH, NH₂ (or NH-succinyl and COOH-succinyl) of NSC. The NSC-MGF nanoconjugate revealed a spherical particle geometry of 100 ∼ 200 nm size. The encapsulated MGF showed 100% release in vitro. In vivo, NSC-MGF nanoconjugate revealed blood glucose lowering from 300 mg/dL to ∼ 90 mg/dL as well as ∼ 37% lowering of total plasma cholesterol. This is well comparative to the earlier reports which acknowledged only 1 ∼ 36% lowering of plasma cholesterol with MGF. Furthermore, NSC-MGF lowered serum trigyceride to ∼ 61%, while in earlier studies, only 10 ∼ 40% serum triglycerides reduction was found with solitary MGF.

The African Swine Fever Virus with MGF360 and MGF505 Deleted Reduces the Apoptosis of Porcine Alveolar Macrophages by Inhibiting the NF-κB Signaling Pathway and Interleukin-1β

African swine fever virus (ASFV) poses serious threats to the swine industry. The mortality rate of African swine fever (ASF) is 100%, and there is no effective vaccine currently available. Complex immune escape strategies of ASFV are crucial factors affecting immune prevention and vaccine development. CD2v and MGF360-505R genes have been implicated in the modulation of the immune response. The molecular mechanisms contributing to innate immunity are poorly understood. In this study, we discover the cytopathic effect and apoptosis of ΔCD2v/ΔMGF360-505R-ASFV after infection in porcine alveolar macrophages (PAMs) was significantly less than wild-type ASFV. We demonstrated that CD2v- and MGF360-505R-deficient ASFV decrease the level of apoptosis by inhibiting the NF-κB signaling pathway and IL-1β mRNA transcription. Compared with wild-type ASFV infection, the levels of phospho-NF-κB p65 and p-IκB protein decreased in CD2v- and MGF360-505R-deficient ASFV. Moreover, CD2v- and MGF360-505R-deficient ASFV induced less IL-1β production than wild-type ASFV and was attenuated in replication compared with wild-type ASFV. We further found that MGF360-12L, MGF360-13L, and MGF-505-2R suppress the promoter activity of NF-κB by reporter assays, and CD2v activates the NF-κB signaling pathway. These findings suggested that CD2v- and MGF360-505R-deficient ASFV could reduce the level of ASFV p30 and the apoptosis of PAMs by inhibiting the NF-κB signaling pathway and IL-1β mRNA transcription, which might reveal a novel strategy for ASFV to maintain the replication of the virus in the host.

An Alternative Statistical Characterization of TWDP Fading Model

Two-wave with diffuse power (TWDP) is one of the most promising models for the description of small-scale fading effects in 5G networks, which employs mmWave band, and in wireless sensor networks deployed in different cavity environments. However, its current statistical characterization has several fundamental issues. Primarily, conventional TWDP parameterization is not in accordance with the model’s underlying physical mechanisms. In addition, available TWDP expressions for PDF, CDF, and MGF are given either in integral or approximate forms, or as mathematically untractable closed-form expressions. Consequently, the existing TWDP statistical characterization does not allow accurate evaluation of system performance in all fading conditions for most modulation and diversity techniques. In this regard, physically justified TWDP parameterization is proposed and used for further calculations. Additionally, exact infinite-series PDF and CDF are introduced. Based on these expressions, the exact MGF of the SNR is derived in a form suitable for mathematical manipulations. The applicability of the proposed MGF for derivation of the exact average symbol error probability (ASEP) is demonstrated with the example of M-ary PSK modulation. The derived M-ary PSK ASEP expression is further simplified for large SNR values in order to obtain a closed-form asymptotic ASEP, which is shown to be applicable for SNR > 20 dB. All proposed expressions are verified by Monte Carlo simulation in a variety of TWDP fading conditions.

Classification and characterization of multigene family proteins of African swine fever viruses

African swine fever virus (ASFV) poses serious threats to the pig industry. The multigene family (MGF) proteins are extensively distributed in ASFVs and are generally classified into five families, including MGF-100, MGF-110, MGF-300, MGF-360 and MGF-505. Most MGF proteins, however, have not been well characterized and classified within each family. To bridge this gap, this study first classified MGF proteins into 31 groups based on protein sequence homology and network clustering. A web server for classifying MGF proteins was established and kept available for free at http://www.computationalbiology.cn/MGF/home.html. Results showed that MGF groups of the same family were most similar to each other and had conserved sequence motifs; the genetic diversity of MGF groups varied widely, mainly due to the occurrence of indels. In addition, the MGF proteins were predicted to have large structural and functional diversity, and MGF proteins of the same MGF family tended to have similar structure, location and function. Reconstruction of the ancestral states of MGF groups along the ASFV phylogeny showed that most MGF groups experienced either the copy number variations or the gain-or-loss changes, and most of these changes happened within strains of the same genotype. It is found that the copy number decrease and the loss of MGF groups were much larger than the copy number increase and the gain of MGF groups, respectively, suggesting the ASFV tended to lose MGF proteins in the evolution. Overall, the work provides a detailed classification for MGF proteins and would facilitate further research on MGF proteins.

Increased expression of IGF-1Ec with increasing colonic polyp dysplasia and colorectal cancer

PURPOSE

IGF-1Ec is an isoform of Insulin-like growth factor 1 (IGF-1) and has recently been identified to be overexpressed in cancers including prostate and neuroendocrine tumours. The aim of this paper is to investigate the expression of IGF-1Ec in colorectal cancer and polyps compared to normal colon tissues and its association with recurrent disease using semi-quantitative immunohistochemistry.

METHODS

Immunohistochemistry for IGF-1Ec expression was performed for colorectal cancer, colorectal polyps and normal colonic tissues. The quantification of IGF-1Ec expression was performed with the use of Image J software and the IHC profiler plugin. Following ethics approval from the National Research Ethics Service (Reference 11/LO/1521), clinical information including recurrent disease on follow-up was collected for patients with colorectal cancer.

RESULTS

Immunohistochemistry was performed in 16 patients with colorectal cancer and 11 patients with colonic polyps and compared to normal colon tissues and prostate adenocarcinoma (positive control) tissues. Significantly increased expression of IGF-1Ec was demonstrated in colorectal cancer (p < 0.001) and colorectal polyps (p < 0.05) compared to normal colonic tissues. Colonic adenomas with high-grade dysplasia had significantly higher expression of IGF-1Ec compared to low-grade dysplastic adenomas (p < 0.001). Colorectal cancers without lymph node metastases at the time of presentation had significantly higher IGF-1Ec expression compared to lymph node-positive disease (p < 0.05). No correlation with recurrent disease was identified with IGF-1Ec expression.

CONCLUSION

IGF-1Ec is significantly overexpressed in colorectal cancer and polyps compared to normal colon tissues offering a potential target to improve colonoscopic identification of colorectal polyps and cancer and intraoperative identification of colorectal tumours.

Splicing factor-modulated generation of mechano growth factor regulates physiological processes in osteoblasts under mechanical stimuli

Mechanical stimuli influence various physiological processes in osteoblasts. We previously showed that mechano-growth factor (MGF), a splicing variant of insulin-like growth factor 1, is highly expressed in osteoblasts in response to mechanical stimuli. This study aims to explore the systemic functions of MGF in osteoblasts, and the mechanisms by which mechanical stress regulates the alternative splicing of Igf1 to generate MGF. We found that MGF promoted the proliferation and migration of osteoblasts, while it inhibited their differentiation via Erk1/2 pathway. Furthermore, cyclic stretching upregulated the expression of ASF/SF2, which in turn regulated the expression of MGF. Our findings indicate that mechanical stimuli influence the physiological responses of osteoblasts by increasing the expression of MGF, which is regulated by splicing factors.

Impaired Skeletal Muscle Regeneration Induced by Macrophage Depletion Could Be Partly Ameliorated by MGF Injection

Skeletal muscle injury is one of the most common injuries in sports medicine. Our previous study found that macrophage depletion impairs muscle regeneration and that mechano growth factor (MGF) may play an important role in this process. However, whether injection of MGF protects against impaired muscle regeneration after macrophage depletion has not been explored. Therefore, we generated a muscle contusion and macrophage depletion mouse model and injected MGF into the damaged muscle. Comprehensive morphological and genetic analyses were performed on the injured skeletal muscle after macrophage depletion and MGF injection. The results showed that injection of MGF did not exert a protective effect on muscle fiber regeneration; however, it did decrease fibrosis in the contused skeletal muscle after macrophage depletion. Moreover, MGF injection decreased the expression of muscle inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and TGF-β), chemokines (CCL2, CCL5, and CXCR4), oxidative stress factors (gp91phox) and matrix metalloproteinases (MMP-1, MMP-2, MMP-9, MMP-10, and MMP-14). These results suggest that the impairment of skeletal muscle regeneration induced by macrophage depletion could be partly ameliorated by MGF injection and that inflammatory cytokines, oxidative stress factors, chemokines, and MMP may be involved in this process.

In vitro and in vivo degradation and mechanical properties of ZEK100 magnesium alloy coated with alginate, chitosan and mechano-growth factor

The biocompatibility, ultimate loading capacity and biodegradability of magnesium alloy make it an ideal candidate in biomedical fields. Fabrications of multilayered coatings carrying sodium alginate (ALG), chitosan (CHI) and mechano-growth factor (MGF) on fluoride-pretreated ZEK100 magnesium alloy have been obtained via layer by layer (LBL) to reduce the degradation rate of magnesium alloy in this study. The modified surfaces of ZEK100 substrates were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), Fourier transform infrared (FTIR) and CARE EUT-1020 tester. Results reveal that multilayer-coated magnesium alloy can be successfully obtained with smooth surface morphology, and the mechanical properties of coated samples are almost the same as those of uncoated samples. However, the fatigue life of coated ZEK100 is slightly larger than that of uncoated samples after 1 day of immersion. By comparing the degradation of uncoated and multilayer-coated ZEK100 samples in vitro and in vivo, respectively, it is found that the degradation rate of ZEK100 samples can be inhibited by LBL modification on the surface of the sample; and the corrosion rate in vivo is lower than that in vitro, which help solve the rapid degradation problem of magnesium alloy. In terms of the visible symptom of tissues in the left femur medullary cavity and material responses on the surface, multilayer-coated ZEK100 magnesium alloy has a good biocompatibility. These results indicate that multilayer-coated ZEK100 may be a promising material for bone tissue repair.

PMv Neuronal Firing May Be Driven by a Movement Command Trajectory within Multidimensional Gaussian Fields

The premotor cortex (PM) is known to be a site of visuo-somatosensory integration for the production of movement. We sought to better understand the ventral PM (PMv) by modeling its signal encoding in greater detail. Neuronal firing data was obtained from 110 PMv neurons in two male rhesus macaques executing four reach-grasp-manipulate tasks. We found that in the large majority of neurons (∼90%) the firing patterns across the four tasks could be explained by assuming that a high-dimensional position/configuration trajectory-like signal evolving ∼250 ms before movement was encoded within a multidimensional Gaussian field (MGF). Our findings are consistent with the possibility that PMv neurons process a visually specified reference command for the intended arm/hand position trajectory with respect to a proprioceptively or visually sensed initial configuration. The estimated MGF were (hyper) disc-like, such that each neuron's firing modulated strongly only with commands that evolved along a single direction within position/configuration space. Thus, many neurons appeared to be tuned to slices of this input signal space that as a collection appeared to well cover the space. The MGF encoding models appear to be consistent with the arm-referent, bell-shaped, visual target tuning curves and target selectivity patterns observed in PMV visual-motor neurons. These findings suggest that PMv may implement a lookup table-like mechanism that helps translate intended movement trajectory into time-varying patterns of activation in motor cortex and spinal cord. MGFs provide an improved nonlinear framework for potentially decoding visually specified, intended multijoint arm/hand trajectories well in advance of movement.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

Characterization of β-casein gene in Indian riverine buffalo

The study aimed at characterization of buffalo β-casein gene and its promoter by PCR-SSCP analysis. Complete β-casein exon VII region analysis revealed two SSCP band patterns, with pattern-I representing predominant allele B (85%) present in homozygous (genotype BB) condition and pattern-II representing a rare allele A1 present in heterozygous condition (genotype A1B). Sequencing of two patterns revealed three nucleotide substitutions at codon 68, 151 and 193 of exon VII. The cDNA sequence of buffalo β-casein gene indicated three further nucleotide substitutions between allele A1 and B at codon 10, 39, and 41. Analysis of β-casein proximal promoter region (-350 upstream to +32) revealed four SSCP band patterns. These SSCP patterns corresponded to nucleotide substitutions at seven locations within 382 bp 5' UTR region of β-casein gene. Haplotype analysis suggested pattern-I of exon VII (wild type) was associated with three types of promoters and pattern-II of exon VII (rare type) corresponded to one exclusive type of promoter. The study suggested two haplotypes of exon VII and four haplotypes of promoter for buffalo β-casein.

The plasma membrane proteome of maize roots grown under low and high iron conditions

Iron (Fe) homeostasis is essential for life and has been intensively investigated for dicots, while our knowledge for species in the Poaceae is fragmentary. This study presents the first proteome analysis (LC-MS/MS) of plasma membranes isolated from roots of 18-day old maize (Zea mays L.). Plants were grown under low and high Fe conditions in hydroponic culture. In total, 227 proteins were identified in control plants, whereas 204 proteins were identified in Fe deficient plants and 251 proteins in plants grown under high Fe conditions. Proteins were sorted by functional classes, and most of the identified proteins were classified as signaling proteins. A significant number of PM-bound redox proteins could be identified including quinone reductases, heme and copper-containing proteins. Most of these components were constitutive, and others could hint at an involvement of redox signaling and redox homeostasis by change in abundance. Energy metabolism and translation seem to be crucial in Fe homeostasis. The response to Fe deficiency includes proteins involved in development, whereas membrane remodeling and assembly and/or repair of Fe-S clusters is discussed for Fe toxicity. The general stress response appears to involve proteins related to oxidative stress, growth regulation, an increased rigidity and synthesis of cell walls and adaption of nutrient uptake and/or translocation. This article is part of a Special Issue entitled: Plant Proteomics in Europe.