Feature-weight based measurement of cancerous transcriptome using cohort-wide and sample-specific information.

Identifying cancerous samples or cells using transcriptomic data is critical for cancer related basic research, early diagnosis, and targeted therapy. However, the high transcriptional heterogeneity of cancers still hinders people from accurately recognizing cancerous transcriptome using bulk, single-cell, or spatial RNA-seq data. Here, we present a novel method named FWP (Feature Weight Pro) that helps measure cancerous transcriptome using transcriptomic data.

Phage-Derived Depolymerase: Its Possible Role for Secondary Bacterial Infections in COVID-19 Patients.

As of 29 July 2022, there had been a cumulative 572,239,451 confirmed cases of COVID-19 worldwide, including 6,390,401 fatalities. COVID-19 patients with severe symptoms are usually treated with a combination of virus- and drug-induced immuno-suppression medicines. Critical clinical complications of the respiratory system due to secondary bacterial infections (SBIs) could be the reason for the high mortality rate in COVID-19 patients.

Disarm The Bacteria: What Temperate Phages Can Do.

In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation.

Phage Engineering for Targeted Multidrug-Resistant .

The lytic bacteriophages have potential application value in the treatment of bacterial infections. However, the narrow host spectrum of these phages limits their range of clinical application. Here, we demonstrate the use of scarless Cas9-assisted recombination (no-SCAR) gene-editing technology to regulate phage-host range.

Specific Integration of Temperate Phage Decreases the Pathogenicity of Host Bacteria.

Temperate phages are considered as natural vectors for gene transmission among bacteria due to the ability to integrate their genomes into a host chromosome, therefore, affect the fitness and phenotype of host bacteria. Many virulence genes of pathogenic bacteria were identified in temperate phage genomes, supporting the concept that temperate phages play important roles in increasing the bacterial pathogenicity through delivery of the virulence genes. However, little is known about the roles of temperate phages in attenuation of bacterial virulence.

A Novel Tail-Associated O91-Specific Polysaccharide Depolymerase from a Podophage Reveals Lytic Efficacy of Shiga Toxin-Producing Escherichia coli.

Shiga toxin-producing (STEC) strains are important zoonotic foodborne pathogens, causing diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome (HUS) in humans. However, antibiotic treatment of STEC infection is associated with an increased risk of HUS. Therefore, there is an urgent need for early and effective therapeutic strategies.

Isolation and characterization of a novel temperate bacteriophage from gut-associated Escherichia within black soldier fly larvae (Hermetia illucens L. [Diptera: Stratiomyidae]).

To gain insight into the presence and nature of prophages in the black soldier fly (BSF; Hermetia illucens L. [Diptera: Stratiomyidae]) gut, we isolated and characterized a novel, temperate Escherichia bacteriophage designated vB_EcoS_PHB10 (PHB10). Electron microscopy analysis revealed that phage PHB10 has a long, flexible, non-contractile tail and belongs to the family Siphoviridae.

Isolation of a T7-Like Lytic Bacteriophage vB_PmuP_PHB01 and Its Potential Use in Therapy against Infections.

A lytic bacteriophage PHB01 specific for type D was isolated from the sewage water collected from a pig farm. This phage had the typical morphology of the family , order , presenting an isometric polyhedral head and a short noncontractile tail. PHB01 was able to infect most of the non-toxigenic type D strains tested, but not toxigenic type D strains and those belonging to other capsular types.

Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine.

A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed different efficiency of plating values and lytic spectra within the same strains at 25 °C and 37 °C. High-throughput sequencing revealed that vB_BbrM_PHB04 has a linear double-stranded DNA genome with 124 putative open reading frames.

Therapeutic Application of Bacteriophage PHB02 and Its Putative Depolymerase Against Capsular Type A in Mice.

Phage PHB02 specifically infects capsular serogroup A strains. In this study, we found that capsule deletion mutants were not lysed by PHB02, suggesting that the capsule of serogroup A strains might be the primary receptor. Based on sequence analysis, a gene encoding a phage-associated putative depolymerase was identified.

Three Salmonella enterica serovar Enteritidis bacteriophages from the Siphoviridae family are promising candidates for phage therapy.

Salmonella is a common and widely distributed foodborne pathogen that is frequently implicated in gastrointestinal infections. The emergence and spread of Salmonella strains resistant to multiple antibiotics poses a significant health threat, highlighting the urgent need for early and effective therapeutic strategies. We isolated a total of 32 phages from water samples and anal swabs from pigs.

Complete Genome Sequence of a Novel T7-Like Bacteriophage from a Pasteurella multocida Capsular Type A Isolate.

A novel virulent bacteriophage, vB_PmuP_PHB02 (phage PHB02), infecting Pasteurella multocida capsular type A strains, was isolated from wastewater from a swine farm in China. Phage PHB02 has a linear double-stranded DNA genome consisting of 38,670 base pairs (bp), with a G+C content of 40.8% and a 127-bp terminal redundancy.

Theoretical analysis on the tuning dynamics of the waveguide-grating structures.

We investigate theoretically the tuning properties of the resonant mode of the waveguide-grating structures (WGS). This intends to understand how tuning mechanisms of the waveguide resonance mode depend on the structural and the geometric parameters of the WGS device, which can be used as guidance for the design of biosensors and other optoelectronic devices. The device parameters studied here include the angle of incidence, the thickness and refractive index of the waveguide, the period of the grating, and the refractive indices of the substrate and the medium on top of the grating.

Optical polarizers based on gold nanowires fabricated using colloidal gold nanoparticles.

We demonstrate optical polarization devices, consisting of gold nanowires, which are based on the strong polarization dependence of the particle plasmon resonance of the gold nanowires and the resonance of the waveguided grating structures. Using a layer of indium tin oxide underneath the gold nanowires as the waveguide, we achieved tunable polarization band-pass and band-suppression filters in the transmission and reflection configuration with a bandwidth less than 20 nm at full width at half maximum (FWHM) in the visible spectral range. Then, using side-input geometry for multiplying the absorption by the particle plasmon resonance, we achieved a strong band-suppression polarizer with an extinction ratio of up to 145.