bluuebunny/crossref_metadata_2025 huggingface dataset:
Widespread convergent morphological evolution within the largest family of songbirds
Authors: Demery Amelia-Juliette , Burns Kevin J
Published: March 2023

Although convergence is a common evolutionary phenomenon, few studies have quantified its prevalence across a large, densely sampled clade. Large-scale phylogenies and the advent of novel computational methods facilitate more robust identification of convergent events and their statistical significance. The tanagers (Aves: Thraupidae), the largest family of songbirds, offer an excellent opportunity to study the extent of phenotypic convergence in response to similar ecological pressures on a continental scale. To investigate convergence in the group, we used the largest phylogenetic and multivariate morphological dataset to date for the clade. First, we used phylogenetic comparative analyses to show a correlation between diet and aspects of bill shape. We then investigated our dataset for the presence and magnitude of convergent events and assessed significance through simulations and modeling analyses. Overall, we found that around half (45.3%) of species and clades we tested have converged in morphological space more than would be expected by chance alone. Our study shows that across Thraupidae, various bill shapes have evolved convergently to fill multiple distinct sections of ecological niche space, reflecting a signal of ecological opportunity and structural constraints.
City of Fury: Urban Violence, Dystopia and Anti-Utopia in Nuevo orden and Era Uma Vez Brasília
Authors: Paz Mariano
Published: March 2023

In the twenty-first century Latin America has become the most urbanized region on the planet and, at the same time, the one that has the highest level of inequality. This article discusses how this tension is expressed in cinema, an eminently urban art, through two case studies: the Mexican Nuevo orden (dir. by Michel Franco, 2020) and the Brazilian film Era uma vez Brasília (dir. by Adirley Queirós, 2017). Both works are independent films that deal with issues of urban violence and authoritarianism through a distinct style that combines the techniques of realist representation with fictional elements borrowed from dystopian and science fiction genres. While the two show a preoccupation with the economic and racialized inequality that characterizes urban space in the capital cities of Mexico and Brazil, they ultimately evoke two modes of utopian discourse. Whereas the first film can be considered anti-utopian, criticizing the impulse to seek social change, the second one, though pessimistic, retains a utopian call for political action.
Trans-dimensional inversion of multimode seismic surface wave data from a trenched distributed acoustic sensing survey
Authors: Qu Luping , Dettmer Jan , Hall Kevin , Innanen Kristopher A , Macquet Marie , Lawton Donald C
Published: March 2023

Seismic data acquired from surface-deployed distributed acoustic sensing (DAS) fibre are broad band and typically dense spatially sampled. Corresponding to these features, compared with geophone data, the low-frequency components in DAS data show higher signal-to-noise ratio and multimode dispersion curves by broad-band DAS data exhibit a higher resolution, which increases the investigation depth of near-surface structures and enhances identification and picking of dispersion curves, respectively. Therefore, DAS data are ideal for the estimates of reliable and highly resolved near-surface velocity profiles. As surface-wave dispersion inversion (SWD) is a natural scheme for near-surface investigation, in this study we have formulated a DAS-SWD inversion in which multiple SWD modes are extracted from the DAS data, and are used as input to a trans-dimensional (TD) inversion procedure, in which the number of subsurface layers is treated as an unknown. Vibroseis data with a minimum frequency of 1 Hz were sensed along a horizontal surface trench as part of a baseline seismic survey carried out by the University of Calgary at the Containment and Monitoring Institute Field Research Station in Newell County, Alberta, Canada. These surface DAS data readily permit the picking of multimode dispersion curves, which are observed to enhance velocity profile resolution in both shallow and deep regions of the near-surface simultaneously, with the TD algorithm adapting the model to reflect this improved resolution. To avoid collecting abnormal model samples with thin-interleaved high- and low-velocity layers based on the known geological information of the field site, we employed constraints that preclude the structures that have velocity drops over 100 m s−1 along depth. Data errors are estimated via a non-parametric iterative process in terms of covariance matrices that include off-diagonal elements. Synthetic examples show that SWD with higher-order modes provides additional constraints on the structure and accurate noise estimation. Inversion of the field data resulted in high-resolution estimates of shear wave velocity as a function of depth throughout the top 120 m of the subsurface. The inferred structure is consistent with existing estimates of the regional lithology but resolves additional layers between 1- and 50-m depth.
Cross-cancer pleiotropic analysis identifies three novel genetic risk loci for colorectal cancer
Authors: Sun Jing , Wang Lijuan , Zhou Xuan , Hu Lidan , Yuan Shuai , Bian Zilong , Chen Jie , Zhu Yingshuang , Farrington Susan M , Campbell Harry , Ding Kefeng , Zhang Dongfeng , Dunlop Malcolm G , Theodoratou Evropi , Li Xue
Published: March 2023

Background

To understand the shared genetic basis between colorectal cancer (CRC) and other cancers and identify potential pleiotropic loci for compensating the missing genetic heritability of CRC.

Methods

We conducted a systematic genome-wide pleiotropy scan to appraise associations between cancer-related genetic variants and CRC risk among European populations. Single nucleotide polymorphism (SNP)-set analysis was performed using data from the UK Biobank and the Study of Colorectal Cancer in Scotland (10 039 CRC cases and 30 277 controls) to evaluate the overlapped genetic regions for susceptibility of CRC and other cancers. The variant-level pleiotropic associations between CRC and other cancers were examined by CRC genome-wide association study meta-analysis and the pleiotropic analysis under composite null hypothesis (PLACO) pleiotropy test. Gene-based, co-expression and pathway enrichment analyses were performed to explore potential shared biological pathways. The interaction between novel genetic variants and common environmental factors was further examined for their effects on CRC.

Results

Genome-wide pleiotropic analysis identified three novel SNPs (rs2230469, rs9277378 and rs143190905) and three mapped genes (PIP4K2A, HLA-DPB1 and RTEL1) to be associated with CRC. These genetic variants were significant expressions quantitative trait loci in colon tissue, influencing the expression of their mapped genes. Significant interactions of PIP4K2A and HLA-DPB1 with environmental factors, including smoking and alcohol drinking, were observed. All mapped genes and their co-expressed genes were significantly enriched in pathways involved in carcinogenesis.

Conclusion

Our findings provide an important insight into the shared genetic basis between CRC and other cancers. We revealed several novel CRC susceptibility loci to help understand the genetic architecture of CRC.
The Office on Missing Persons in Sri Lanka: Why Truth Is a Radical Proposition
Authors: Kodikara Chulani
Published: March 2023

ABSTRACT∞

In 2016, the Sri Lanka Parliament passed the Office on Missing Persons Act (OMP) ‘to search for and trace missing persons.’ At the time, Sinhala Buddhist nationalist leaders strongly objected to it. In this article, I read their resistance as resistance to a truth-seeking mechanism. Locating my analysis within a global paradigm of ‘dealing with the past’ through truth-seeking that assumes that ‘truth is easier than justice,’ I show that nationalist resistance to the OMP flies in the face of this assumption. In postwar Sri Lanka, truth is not just a second-best option to justice but an equally radical demand. However, I also show that those same resistors have maintained the OMP on returning to power for several different reasons. Finally, I explore the response of relatives of the disappeared to the OMP and their increasing demand for an international truth and justice mechanism.
Nirsevimab: review of pharmacology, antiviral activity and emerging clinical experience for respiratory syncytial virus infection in infants
Authors: Jorgensen Sarah C J
Published: March 2023

Respiratory syncytial virus (RSV) is a leading cause of hospitalization and infant mortality worldwide. There are currently no approved vaccines against RSV, and immunoprophylaxis with the mAb palivizumab is limited to extremely vulnerable infants in resource-rich settings due to its high cost and the need for monthly injections throughout the RSV season. Nirsevimab (formerly MEDI8897) is a highly potent, long-acting, human, recombinant mAb that received approval for the prevention of RSV infection in newborns and infants during their first RSV season from the EMA and the UK’s Medicines and Healthcare products Regulatory Agency in November 2022 based on positive results in Phase 2b and 3 clinical trials. Nirsevimab targets the highly conserved site Ø of the prefusion conformation of the RSV fusion (F) protein and contains a triple amino acid substitution in the Fc domain that extends its half-life, allowing for a single dose to cover a typical RSV season in regions with temperate climates. In this article I review key attributes of nirsevimab with an emphasis on pharmacology, pharmacokinetics, antiviral activity, and the potential for resistance and escape variants. I also summarize current progress in clinical trials and consider future research priorities.
Association between antimicrobial consumption and resistance rate ofEscherichia coliin hospital settings
Authors: Abdullah Sabahat , Rahman Sajjad ur , Muhammad Faqir , Mohsin Mashkoor
Published: March 2023

Aims

This study aims to quantify antimicrobial consumption (AMC) and antimicrobial resistance (AMR) in tertiary care hospitals in Pakistan.

Methods and results

This observational study was conducted at two tertiary care hospitals of Pakistan over a 1-year period. The AMC and resistance patterns of Escherichia coli isolates collected from hospitals were observed and analysed using the pearson correlation coefficient. AMC in hospitals varied between 0.00186 and 0.72 (Mean = 0.12 ± 0.191) Defined Daily Dose (DDDs)/1000 patient-days. Fluoroquinolones were the most consumed antimicrobial followed by penicillins, cephalosporins, carbapenems, and aminoglycosides. Antimicrobial-resistant rates in hospitals varied between 92.2% and 34.6%. The highest resistance rate was observed for moxifloxacin, followed by ampicillin, cefotaxime, amoxicillin, ceftriaxone, ciprofloxacin, amoxiclav, and amikacin. Statistically significant association was found between AMC and resistance rate for ampicillin (r = 0.78, P = 0.032), cefotaxime (r = 0.87, P = 0.012), ceftriaxone (r = 0.67, P = 0.042), and ciprofloxacin (r = 0.63, P = 0.031). Additionally, there was a significant association between fluoroquinolone consumption and the resistance rate of third generation cephalosporins (r = 0.61, P = 0.032), and significance was also found when all antimicrobials were combined into 1 analysis (r = 0.721, P = 0.032).

Conclusion

This data documented a significant association between AMC and resistant rates for multiple antimicrobial agents.
Transcriptome analysis ofAurantiochytrium limacinumunder low salt conditions
Authors: Kubo Yuki , Morimoto Daichi , Kato Shuri , Shiroi Mai , Ohara Kanta , Higashine Tokuhiro , Mori Yuki , Yoshimi Toru , Takeuchi Masato , Sawayama Shigeki
Published: March 2023

Aurantiochytrium limacinum can accumulate high amounts of omega-3 polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). Although salinity affects the DHA content, its impact on the metabolic pathway responsible for DHA production in A. limacinum is not completely understood. To address this issue, we investigated the transcriptional profile of A. limacinum under hypoosmotic stress. We first cultured A. limacinum under typical and low salinity for RNA sequencing, respectively. Transcriptome analyses revealed that 933 genes exhibited significant changes in expression under hypoosmotic conditions, of which 81.4% were downregulated. Strikingly, A. limacinum downregulated genes related to polyketide synthesis and fatty acid synthase pathways, while upregulating β-oxidation-related genes. In accordance with this, DHA production significantly decreased under hypoosmotic conditions, while antioxidant-related genes were significantly upregulated. Considering that β-oxidation of fatty acids generates energy and reactive oxygen species (ROS), our results suggest that A. limacinum utilizes fatty acids for energy to survive under hypoosmotic conditions and detoxifies ROS using antioxidant systems.
Determination of safety status and probiotic properties ofEnterococcusstrains isolated from traditional cheeses in Turkey
Authors: Kanak Eda Kiliç , Yilmaz Suzan Öztürk , Altindiş Mustafa , Tanriverdi Elif Seren , Otlu Barış
Published: March 2023

Aims

This study aimed to evaluate the probiotic properties of Enterococcus strains isolated from Turkish traditional cheeses.

Methods and results

Fifty-two Enterococcus spp. were taxonomically determined as follows: Enterococcus faecium (26), Enterococcus faecalis (18), Enterococcus durans (6), and Enterococcus italicus (2). The ability of isolates/strains to survive the harsh conditions (acidity and in-vitro gastric solution) of the gastrointestinal tract was established. They also showed auto-aggregation, hydrophobicity, and co-aggregation ability. Hydrophobicities of the strains were found between 0.8%–21%, 0.7%–56%, and 2%–63% for xylene, chloroform, and ethyl acetate, respectively. Autoaggregation values of the Enterococcus strains were 4%–20%, 7%–30%, and 36%–98% after 2, 4, and 24-h incubation, respectively. In this study, the Enterococcus strains tested showed co-aggregation ability with the Escherichia coli ATCC 25922, Salmonella Typhimurium ATCC 14028, and Staphylococcus aureus ATCC 25923. The results of PCR amplification revealed that only five strains possess virulence factor genes (gelE,asa1,cyl A,esp). We determined antibiotic resistance, biofilm forming abilities, and hemolytic activity for safety evaluation of strains.

Conclusions

In this large and comprehensive study, we found that only few of Enterococcus strains have promising probiotic potential, among which E. faecalis ES1 and E. faecium EM1 showed the best probiotic properties (are the most promising probiotic candidates).
Characterization ofl-fucose isomerase fromPaenibacillus rhizosphaeraeto producel-fuculose from hydrolyzed fucoidan and commercial fucose
Authors: Iqbal Muhammad Waheed , Riaz Tahreem , Mu Wanmeng , Mahmood Shahid , Qi Xianghui , Ni Dawei , Zhang Wenli
Published: March 2023

Aims

l-Fuculose is a valuable rare sugar that is used to treat a variety of ailments, including HIV, cancer, Hepatitis B, human lysosomal disease (fucosidosis), and cardio-protective medications. The enzymatic approach for the production of l-fuculose using l-fucose as a substrate would be an advantageous method with a wide range of industrial applications. The objective of this study is the characterization of recombinant l-fucose isomerase from Paenibacillus rhizosphaerae (Pa-LFI) for the production of l-fuculose from an inexpensive and natural source (fucoidan) as well as its comparison with commercial l-fucose (Sigma-Aldrich).

Methods and results

Fucoidan, a fucose-containing polysaccharide (FPs), was isolated from Undaria pinnatifida, subsequently hydrolyzed, and characterized before the enzymatic production of l-fuculose. The results elaborate that FPs contain 35.9% of fucose along with other kinds of monosaccharides. The purified Pa-LFI exhibited a single band at 65 kDa and showed it as a hexamer with a native molecular mass of 396 kDa. The highest activity of 104.5 U mg−1 of Pa-LFI was perceived at a temperature of 50°C and pH 6.5 in the presence of 1 mM of Mn2+. The Pa-LFI revealed a melting temperature (Tm) of 75°C and a half-life of 12.6 h at 50°C. It exhibited that Pa-LFI with aldose substrate (l-fucose), has a stronger isomerizing activity, disclosing Km,kcat, and kcat/Km 86.2 mM, 32 831 min−1, and 335 min−1 mM−1, respectively. After reaching equilibrium, Pa-LFI efficiently catalyzed the reaction to convert l-fucose into l-fuculose and the conversion ratios of l-fuculose from 100 g L−1 of FPs and commercial fucose were around 6% (5.6 g L−1) and 30% (30.2 g L−1), respectively.

Conclusions

According to the findings of the current study, the Pa-LFI will be useful in the manufacturing of l-fuculose using an effective and easy approach that produces no by-products.
Comparison of N2O-reducing abilities and genome features of twonosZ-containing denitrifying bacteria,Pseudomonas veroniiDM15 andPseudomonas frederiksbergensisDM22
Authors: Liu Chunmei , Sheng Rong , Chen Xing , Liu Yi , Wei Wenxue
Published: March 2023

Aim

The study systematically compared the N2O-reducing functional performances and the genomic features of two N2O-reducing isolates, aimed to screen out effective N2O-reducing bacteria with strong environmental adaption, and explore the possible regulation.

Methods and Results

Two N2O reducers, namely, Pseudomonas veronii DM15 (DM15) and Pseudomonas frederiksbergensis DM22 (DM22), isolated from paddy soil were selected. Their N2O-reducing abilities, and nosZ gene transcript abundance were determined under different temperatures (20°C, 30°C, 40°C) and oxygen concentrations (0%, 10%, 21%), and the whole genomes were sequenced by Illumina sequencing. The results showed that both DM15 and DM22 exhibited the strongest N2O reducing activity at 30°C and under anaerobic conditions. In comparison, DM15 generally exhibited significantly higher N2O reducing abilities and nosZ gene expression than DM22 under all tested conditions. In addition, DM15 possessed obviously higher expression potentials (codon adaptation index (CAI) value) of nos genes than DM22, and the nos cluster of the former contained a transcriptional regulator gene of dnr, while the latter did not.

Conclusions

The results indicate that DM15 showed obviously stronger N2O-reducing abilities than DM22 under various conditions, which might be closely associated with its dnr transcriptional regulator, and thus promoting the higher transcriptional activities of nos genes. Although anaerobic conditions were the optimal conditions for N2O reduction in both strains, DM15 still reduced a certain amount of N2O even under aerobic conditions.
The use of phage display systems to combat infectious diseases in poultry: diagnostic, vaccine, and therapeutic approaches
Authors: Grabowski Łukasz , Pierzynowska Karolina , Gaffke Lidia , Cyske Zuzanna , Mincewicz Grzegorz , Węgrzyn Grzegorz
Published: March 2023

Development of molecular biology and understanding structures and functions of various biological molecules and entities allowed to construct various sophisticated tools for different biotechnological, medical, and veterinary applications. One of them is the phage display technology, based on the possibility to create specific bacteriophages bearing fusion genes, which code for fusion proteins consisting of a phage coat protein and a peptide of any amino acid sequence. Such proteins retain their biological functions as structural elements of phage virions while exposing foreign peptide sequences on their surfaces. Genetic manipulations allow to construct phage display libraries composed of billions of variants of exposed peptides; such libraries can be used to select peptides of desired features. Although the phage display technology has been widely used in biotechnology and medicine, its applications in veterinary and especially in poultry science were significantly less frequent. Nevertheless, many interesting discoveries have been reported also in the latter field, providing evidence for a possibility of effective applications of phage display-related methods in developing novel diagnostic tools, new vaccines, and innovative potential therapies dedicated to poultry. Especially, infectious diseases caused by avian viruses, bacteria, and unicellular eukaryotic parasites were investigated in this field. These studies are summarized and discussed in this review, with presentation of various possibilities provided by different phage display systems in development of useful and effective products facilitating management of the problem of infectious diseases of poultry.
Not just passengers, but co-pilots! Non-rhizobial nodule-associated bacteria promote cowpea growth and symbiosis with (brady)rhizobia
Authors: da Silva Thaíse Rosa , Rodrigues Ruth Terezinha , Jovino Raphael Silva , Carvalho Jackson Rafael de Sá , Leite Jakson , Hoffman Andreas , Fischer Doreen , Ribeiro Paula Rose de Almeida , Rouws Luc Felicianus Marie , Radl Viviane , Fernandes-Júnior Paulo Ivan
Published: March 2023

Aims

To isolate and characterize non-rhizobial nodule-associated bacteria (NAB) from cowpea root-nodules regarding their performance of plant-growth-promoting mechanisms and their ability to enhance cowpea growth and symbiosis when co-inoculated with bradyrhizobia.

Methods and Results

Sixteen NAB were isolated, identified, and in vitro evaluated for plant growth promotion traits. The ability to promote cowpea growth was analyzed when co-inoculated with Bradyrhizobium pachyrhizi BR 3262 in sterile and non-sterile substrates. The 16S rRNA gene sequences analysis revealed that NAB belonged to the genera Chryseobacterium (4), Bacillus (3), Microbacterium (3), Agrobacterium (1), Escherichia (1), Delftia (1), Pelomonas (1), Sphingomonas (1), and Staphylococcus (1). All strains produced different amounts of auxin siderophores and formed biofilms. Twelve out of the 16 strains carried the nifH, a gene associated with nitrogen fixation. Co-inoculation of NAB (ESA 424 and ESA 29) with Bradyrhizobium pachyrhizi BR 3262 significantly promoted cowpea growth, especially after simultaneous inoculation with the three strains.

Conclusions

NAB are efficient cowpea growth promoters and can improve the efficiency of the symbiosis between cowpea and the N2-fixing microsymbiont B. pachyrhizi BR 3262, mainly under a specific triple microbial association.
The critical role of gut microbiota dysbiosis in skeletal muscle wasting: a systematic review
Authors: Nikkhah Amirabbas , Ejtahed Hanieh-Sadat , Ettehad Marvasti Fateme , Taghavi MinaSadat , Pakmehr Azin , Hajipour Firouzeh , Larijani Bagher
Published: March 2023

Aims

Skeletal muscle wasting is affected by the gut microbiota dysbiosis through multiple pathways, including inflammatory process, defected immune system, and anabolic resistance. We aimed to systematically review the studies investigating the gut microbiota composition in sarcopenic and cachexic humans and animals.

Methods

We carried out a comprehensively systematic search using relevant keywords on PubMed, Web of Science, and Scopus databases until July 2021. Original human observational research and animal studies related to our research topics published in English were selected.

Results

Seven human studies and five animal studies were included. Three human studies were case-control, whereas the other four were cross-sectional studies that investigated three different conditions, including age-related sarcopenia, as well as liver cirrhosis and cancer cachexia. The principal alteration in age-related sarcopenia and liver cirrhosis-induced sarcopenia was a reduction in short-chain fatty acids (SCFAs) -producing bacteria. Lachnospiraceae family, consisting of Lachnospira, Fusicatenibacter, Roseburia, and Lachnoclostridium, significantly decreased in age-related sarcopenia, while in liver cirrhosis-induced sarcopenia, the alpha diversity of gut microbiota decreased compared with the control group. Moreover, Enterobacteriaceae, which has a pro-inflammatory effect increased in muscle-wasted animals.

Conclusion

This systematic review presents associations between the gut microbiota alterations and skeletal muscle wasting as a consequence of various pathologies, including aging sarcopenia, renal failure, and cancer cachexia in both human and animal studies.
Efficacy of chemical disinfectants against SARS-CoV-2 on high-touch surface materials
Authors: Hardison Rachael L , Nelson Sarah W , Limmer Rebecca , Marx Joel , Taylor Brian M , James Ryan R , Stewart Michael J , Lee Sang Don D , Calfee Michael Worth , Ryan Shawn P , Howard Megan W
Published: March 2023

Aims

This study aimed to provide operationally relevant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface disinfection efficacy information.

Methods and Results

Three EPA-registered disinfectants (Vital Oxide, Peroxide, and Clorox Total 360) and one antimicrobial formulation (CDC bleach) were evaluated against SARS-CoV-2 on material coupons and were tested using Spray (no touch with contact time) and Spray & Wipe (wipe immediately post-application) methods immediately and 2 h post-contamination. Efficacy was evaluated for infectious virus, with a subset tested for viral RNA (vRNA) recovery. Efficacy varied by method, disinfectant, and material. CDC bleach solution showed low efficacy against SARS-CoV-2 (log reduction < 1.7), unless applied via Spray & Wipe. Additionally, mechanical wiping increased the efficacy of treatments against SARS-CoV-2. The recovery of vRNA post-disinfection suggested that vRNA may overestimate infectious virus remaining.

Conclusions

Efficacy depends on surface material, chemical, and disinfection procedure, and suggests that mechanical wiping alone has some efficacy at removing SARS-CoV-2 from surfaces. We observed that disinfectant treatment biased the recovery of vRNA over infectious virus.

Significance and Impact of Study

These data are useful for developing effective, real-world disinfection procedures, and inform public health experts on the utility of PCR-based surveillance approaches.
Bacillus strains prevent lipopolysaccharide-induced inflammation in gut and blood of male mice
Authors: Pesarico Ana Paula , Jesus Gabriel Fernandes Alves , Córneo Emily , Borges Heloisa de Medeiros , Calixto Karen de Vasconcelos , Garcez Michelle Lima , Bellettini-Santos Tatiani , Voytena Ana Paula Lorenzen , Rossetto Marina , Ramlov Fernanda , Dal-Pizzol Felipe , Michels Monique
Published: March 2023

Aims

The protective effects of Bacillus amyloliquefaciens(CCT7935), Bacillus subtilis(CCT7935), Bacillus licheniformis (CCT 7836), and Bacillus coagulans (CCT 0199) against lipopolysaccharide (LPS)-induced intestinal inflammation were investigated.

Methods and results

Male Swiss mice were assigned into six groups: control group, LPS group, LPS + B. subtilis (CCT7935) group, LPS +   B. licheniformis (CCT 7836) group, LPS +   B. amyloliquefaciens (CCT7935) group, and LPS   + B. coagulans (CCT 0199) group. Each mouse of the groups Bacillus received 1 × 109 colony-forming units of Bacillus once daily by oral gavage during 30 days. Twenty-four hours after the last dose of Bacillus, all groups, except the control group, were intraperitoneally injected with LPS in the single dose of 15 mg kg−1. The mice were euthanized 24 h after the LPS administration. Histological alterations, myeloperoxidase activity, and nitrite levels were analyzed in the gut of mice and the inflammatory cytokines were analyzed in the gut and in the blood. The results demonstrate that the mice challenged with LPS presented the villi shortened and damaged, which were significantly protected by B. coagulans and B. amyloliquefaciens. Furthermore, all Bacillus tested were effective in preventing against the increase of myeloperoxidase activity, while B. amyloliquefaciens and B. subtilis prevented the increase of nitrite and IL-1β levels in the gut of mice induced with LPS was decreased only B. subtilis. LPS also elevated the IL-1 β, IL-6, and IL-10 levels in the blood, and these alterations were significantly suppressed by Bacillus, especially by B. subtilis.

Conclusions

The study suggests that the Bacillus investigated in this study might be effective therapeutic agents for preventing intestinal inflammation, because they decrease the inflammatory process an protect against tissue damage.
Anti-Candidaattributes andin-silicodrug-likeness properties of phenyl 2′β, 6′β-trimethyl cyclohexyl ketone and phenyl nonanyl ether produced byStreptomyces chrestomyceticusADP4
Authors: Singh Radha , Ali Mohd , Dubey Ashok K
Published: March 2023

Aim

To isolate and characterize anti-Candida compounds from soil actinobacterium Streptomyces chrestomyceticus ADP4 and to assess their drug likeness.

Methods and Results

Two anti-Candida compounds, Phenyl 2′α, 2′β, 6′β-trimethyl cyclohexyl ketone (1PB1) and Phenyl nonanyl ether (1PB2), were isolated from the metabolites produced by Streptomyces chrestomyceticus ADP4. Their structures were deduced by extensive analyses of spectral data obtained from liquid chromatography with tandem mass spectrometry (LCMS/MS), nuclear magnetic resonance (NMR), Fourier-transform infrared spectroscopy (FTIR) and ultraviolet (UV) spectroscopies. While both the compounds inhibited growth of the Candida spp., 1PB2 was effective in inhibiting biofilm formed by Candida albicans ATCC 10231. The compounds did not show any cytotoxicity against HepG2 cells and were found to be safe when predicted theoretically on rat model, bioaccumulation and mutagenicity by using the software: toxicity estimation software tool (TEST). The compounds displayed drug-like properties when analyzed by using SwissADME software.

Conclusions

1PB1 and 1PB2 are being reported for the first time from any natural source along with their anti-Candida properties. In-silico studies revealed their druggability and suitability to take up further work on the compounds for their possible application in treating Candida-associated infections.

Significance and impact of the study

The increasing prevalence of Candidiasis associated with drug-resistant strains of Candida spp. highlighted the urgent need for discovery of new compounds with anti-Candida properties that could hold promise as potential drug candidate.
Genomic features and heat resistance profiles ofEscherichia coliisolated from Brazilian beef
Authors: Machado Maxsueli Aparecida Moura , Castro Vinicius Silva , da Cunha Neto Adelino , Carvalho Ricardo César Tavares , Stanford Kim , Conte-Junior Carlos Adam , Figueiredo Eduardo Eustáquio de Souza
Published: March 2023

Aims

Characterize Escherichia coli and E. coli -producing (STEC) isolates from Brazilian beef to determine heat resistance and the presence of the transmissible locus of stress tolerance (tLST).

Methods and results

Twenty-two STEC previously isolated from beef and characterized as STEC by PCR were subjected to different heat survival challenges (60°C and 71°C). Furthermore, the three tLST-positive isolates and one tLST-negative isolate by PCR were selected for WGS analysis. Phenotypic results indicated that 3/22 (13.64%) were heat resistant, 12/22 (54.54%) were moderately resistant, and 7/22 (31.82%) were sensitive to heat treatments. WGS analyses showed that three isolates with heat resistance showed tLST with up to 80% and 42% of similarity by BLAST analysis, with the major tLST genes being responsible for the homeostasis module. However, WGS showed the absence of stx genes associated with tLST-positive isolates, albeit with virulence and resistance genes found in extraintestinal pathogenic E. coli (ExPEC).

Conclusion

Our findings demonstrate the presence of heat-resistant E. coli as well as confirm some tLST genes in E. coli isolated from Brazilian beef.
Potentially probioticLimosilactobacillus reuterifrom human milk strengthens the gut barrier in T84 cells and a murine enteroid model
Authors: Anjum Jasia , Quach Andrew , Wongkrasant Preedajit , Nazir Shahid , Tariq Muhammad , Barrett Kim E , Zaidi Arsalan
Published: March 2023

Aims

At conception, the infant gut barrier is immature, gradually developing with regular intake of maternal milk. This study addressed whether the barrier-strengthening effect of breast feeding might be attributable, at least in part, to autochthonous beneficial human milk bacteria.

Methods and results

Twelve bacterial strains from the breast milk of Pakistani mothers who underwent cesarean delivery (NPL-88, NPL-157, NPL-179, NPL-181, NPL-388 (Limosilactobacillus reuteri), NPL-76, NPL-495, NPL-504 (Limosilactobacillus fermentum), NPL-415 (Lactobacillus pentosus), NPL-412, NPL-416 (Lactiplantibacilllus plantarum) and NPL-374 (Bifidobacterium longum) were shortlisted based on their tolerance to acidic pH (2.8–4.2) and bile (0.1–0.3%). The effect of these bacteria on gut barrier function in the presence and absence of pathogens was assessed as changes in transepithelial electrical resistance (TEER) in the human T84 colonic epithelial cell line and in murine enteroid-derived monolayers (EDMs). The TEER of T84 cells monolayers rose in the presence of most of the human milk strains, being most pronounced in case of L. reuteri NPL-88 (34% within five h), exceeding the effect of the well-known probiotic L. acidophilus (20%). qRT-PCR, western blot and immunofluorescent staining associated the increase in TEER with enhanced expression of tight junction proteins. Pretreatment of murine EDMs with NPL-88 also largely prevented the ability of the pathogen, Salmonella, to decrease TEER (87 ± 1.50%; P < 0.0001, n = 4).

Conclusions

Human milk lactic acid bacteria are potential probiotics that can strengthen gut barrier function and protect breastfed neonates against enteric infections.
Lactiplantibacillus plantarumP101 alleviates alcoholic liver injury by modulating the Nrf2/HO-1 pathway in mice
Authors: Liu Shanji , Zhao Yu , Xu Xiaowei , Wang Mengqi , Tao Xueying , Xu Hengyi
Published: March 2023

Aims

The occurrence of alcoholic liver injury is related to the oxidative stress. Bacteria for alleviating alcoholic related liver injury have received widespread attention. Study aims to investigate the alleviated efficacy of Lactiplantibacillus plantarum (L. plantarum) P101 on alcohol-induced liver injury and its potential mechanism.

Methods and results

The model of alcoholic liver injury was obtained according to the NIAAA method and the mice were treated with L. plantarum P101 (108 CFU.mice−1). Results showed that treatment of L. plantarum P101 could significantly improve liver function and antioxidant capacity. Furthermore, L. plantarum P101 significantly up-regulated Nuclear factor erythroid 2-related factor (Nrf2) and its target molecule, Hemeoxygenase 1 (HO-1), by promoting nuclear translocation of Nrf2. Moreover, inflammatory factors and pro-apoptotic protein (Caspase3) levels were significantly decreased in mice treated with L. plantarum P101.

Conclusions

This study confirmed that the beneficial effect of L. plantarum P101 supplement was achieved via regulating Nrf2/HO-1 antioxidant pathway, and alleviated alcoholic liver injury.
A comprehensive assessment of the antimicrobial and immunomodulatory effects of frequently consumed fermented foods: insights in the management of COVID-19
Authors: Dhar Rinita , Chakraborty Megha , Dutta Tapan K
Published: March 2023

COVID-19, which is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), is the deadliest outbreak of this millennium. Despite adopting several precautionary strategies and guidelines, COVID-19 has spread rapidly, and the number of cases is still in escalation across the world. The various immune-boosting drugs with severe side effects and the vaccines approved after negotiated clinical trials have been struggling to cope with the emergence of new variants of the virus. Nevertheless, given a large number of asymptomatic cases, a high magnitude of recovery rate, and a relatively higher prevalence of morbidity and mortality among immunologically compromised individuals, those affected by an illness, and the elderly, it appears that a healthy microbiome and the associated immune responses are the key factors for survival. Incidentally, the consumption of traditionally popular and nutritious fermented foods, which are composed of biologically functional ingredients and several health-promoting probiotics, offers promising health benefits through the improvement of the immune system in general. Given the progress in functional food research, it has become crucial to understand the impact of a healthy microbiome and the immunomodulatory roles of fermented foods on the battles to combat infectious diseases. Based on the evidence of the impact of probiotics-based fermented foods, the beneficial roles of a few frequently consumed fermented foods in the management of various infections have been resolutely discussed in the present study, with a focus on their antagonistic and immune-modulating effects in the context of the current COVID-19 pandemic.
Cannabis as antivirals
Authors: Sea Yi Lin , Gee Yee Jing , Lal Sunil Kumar , Choo Wee Sim
Published: March 2023

Cannabis is a plant notorious for its psychoactive effect, but when used correctly, it provides a plethora of medicinal benefits. With more than 400 active compounds that have therapeutic properties, cannabis has been accepted widely as a medical treatment and for recreational purposes in several countries. The compounds exhibit various clinical benefits, which include, but are not limited to, anticancer, antimicrobial, and antioxidant properties. Among the vast range of compounds, multiple research papers have shown that cannabinoids, such as cannabidiol and delta-9-tetrahydrocannabinol, have antiviral effects. Recently, scientists found that both compounds can reduce severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) viral infection by downregulating ACE2 transcript levels and by exerting anti-inflammatory properties. These compounds also act as the SARS-CoV-2 main protease inhibitors that block viral replication. Apart from cannabinoids, terpenes in cannabis plants have also been widely explored for their antiviral properties. With particular emphasis on four different viruses, SARS-CoV-2, human immunodeficiency virus, hepatitis C virus, and herpes simplex virus-1, this review discussed the role of cannabis compounds in combating viral infections and the potential of both cannabinoids and terpenes as novel antiviral therapeutics.
Arcobacterspecies in milk contamination: a prevalence-based systematic review and meta-analysis
Authors: Ekundayo Temitope C , Itiolu Ibilola F , Ijabadeniyi Oluwatosin A
Published: March 2023

Aims

Milk is consumed raw or minimally processed and plays a role in the dissemination of pathogens of public health concerns. The present investigation is aimed at assessing the occurrence of pathogenic Arcobacter species in 2945 milk samples.

Methods and Results

Arcobacter data systematically retrieved from five repositories until 20 February 2022 according to PRISMA principles were logit transformed and fitted using a generalized linear mixed-effects model. The between-study heterogeneity was estimated as I2-value. Leave-one-out cross-validation and funnel plot with Egger’s tests were used to assess the hardiness and bias in the model. The global prevalence of Arcobacter genus in the milk was 12% [95% confidence interval (CI): 7–19%; I2 = 87.3%, 95% CI: 83.0–90.6%] and no publication bias observed (Egger’s test: P = 0.112). Arcobacter genus prevalence in milk was 13% (95% CI: 5–30%), 10% (95% CI: 1–46%), and 9% (95% CI: 4–19%) in Europe, South America, and Asia, respectively. Arcobacter butzleri was the most prevalent [8% (95% CI: 4–13%)], followed by A. cryaerophilus [0.6% (95% CI: 0.2–33.2%)] and A. skirrowii [0.19% (95% CI: 0.03–1.2%)]. Also, species-specific prevalence of A. butzleri, A. cryaerophilus, and A. skirrowii varied continentally, but the test for species-specific/continental differences was not significantly different (P > 0.5).
An update on possible alternative therapeutics for future periodontal disease management
Authors: Das Vishnu , Vinod Vivek , Biswas Lalitha , Kumar Anil , Biswas Raja
Published: March 2023

Periodontitis is an inflammatory disease caused by microbial infections of the gum. At an advanced stage, periodontitis can even destroy the alveolar bone. Fusobacterium nucleatum, Prevotella intermedia, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Capnocytophaga gingivalis, and Pr. nigrescens are the major pathogens in periodontitis. Scaling and root planning are used together with local or systemic antibiotics to treat periodontitis. The difficulty in complete eradication of periodontal pathogens frequently leads to the relapse of the disease. As not many new antibiotics are available in the market, many researchers are now focusing on developing alternative strategies against periodontal microbes. This review provides an overview of the possible use of bacteriophages, lysins, honey, plant extracts, metallic salts, nanoparticles, and vaccines as alternative therapeutic agents against periodontal infections. The information provided here could help in designing alternative therapeutics for the treatment of periodontal infections.
Efficient removal of heavy metals by endophytic bacteriaStaphylococcus succinusH3
Authors: Luo Hong , Yang Caiyun , Pang Mingmei , Wang Yuanyuan , Cheng Wenting , Jiang Kunling , Ling Lijun
Published: March 2023

Aims

Heavy metal pollution is a serious and difficult environmental problem. With increasing heavy metal content in industrial wastewater, an environmentally friendly and efficient treatment method must be identified.

Methods and results

Considering the ability of endophytic bacteria to adsorb metal ions, this paper explored the heavy metal resistance, adsorption, and adsorption mechanisms and performance of S. succinus H3, an endophytic bacterium. S. succinus H3 exhibited metal resistance at 4 mM Cu2+ and 5 mM Mg2+. The adsorption rate of Cu2+ and Mg2+ ions by the live/dead strain was approximately 70%, and the adsorption capacity was positively correlated with the metal ion concentration. The kinetics and isothermal models were used to study the process of S. succinus H3 adsorption on Cu2+. It exhibits a good correlation with the Freundlich isothermal model. The N-H group, protein C=O group, polysaccharide C-O group, O-H group and some lipids are the main functional groups in the cell wall. S. succinus H3 may bond with the amine group to adsorb Mg2+ through complexation/coordination and may form a copper complex after adsorbing Cu2+. S. succinus H3 has a live adsorption rate of 15% in eight mixed metal ion systems at a 50 mg/L concentration. The study results can lay a foundation for expanding the bacterial resource pool of pollutant treatment and improving the efficiency for sewage treatment. The high heavy metal adsorption capacity of microorganisms has a decisive role in industrial wastewater treatment by microorganisms. Such microorganisms with high metal resistance and adsorption capacity to heavy metals can thrive in industrial wastewater, remove heavy metals efficiently, and greatly improve the efficiency of wastewater treatment.

Conclusion

The study results can lay a theoretical foundation for the use of S. succinus H3 to biologically treat heavy metal wastewater in the future.
Cell wall polysaccharides of endophyticPseudomonas putidaelicit defense against rice blast disease
Authors: Ashajyothi Mushineni , Balamurugan Alexander , Patel Asharani , Krishnappa Charishma , Kumar Rajesh , Kumar Aundy
Published: March 2023

Aims

To characterize the functional role of extracellular polysaccharides and lipopolysaccharide (LPS) extracted from endophytic Pseudomonas putida BP25 (PpBP25) against rice blast.

Methods and Results

We profiled the transcriptome of endobacterized rice seedlings using RNA-seq. Fluorescence imaging of interaction between Magnaporthe:: gfp and P. putida:: mCherry was performed on rice phylloplane using confocal laser scanning microscopy (CLSM). Microbial polysaccharides, exopolysaccharide (EPS), and LPS extracted from PpBP25 were characterized using Fourier-transform infrared-spectroscopic analysis (FTIR). Biochemical assays and gene expression analysis were conducted on EPS- and LPS-treated rice seedlings. A detached-leaf assay was designed to test the blasticidal-effect of bacterial-endophyte, EPS, and LPS on rice phylloplane. PpBP25 elicited defense in rice with a consequently altered seedling phenotype. Rice cultivar, Pusa Basmati-1, colonized by PpBP25 showed an altered transcriptome profile displaying a total of 110-downregulated and 68-upregulated genes (P < 0.005) representing growth/development and defense pathways, respectively. CLSM of PpBP25 bacterized phylloplane showed reduced conidial-germination and mycelial-biomass of Magnaporthe oryzae. To decipher the elicitor role of polysaccharides, we purified and characterized EPS and LPS using FTIR. Rice treated with the EPS and LPS showed root-growth inhibition the phenotype of MAMP-triggered immunity. While the EPS showed blast suppressive activity at 1–20 mg mL−1 (79.80%–86.87% reduction over control), the LPS exhibited 78.0%–79.8% reduction at 20–200 μg mL−1on rice. Polysaccharides treated seedling showed elevated activities of peroxidase and polyphenol-oxidase activities, and total-phenols content. Treated plantlets showed up regulation of OsPR1.1,OsPR3, OsGLP3-3,OsZFP179, and Oshox24 as well as downregulation of OsACS6.

Conclusions

We showed that P. putida Bp25 and its cell wall-associated polysaccharides could elicit defense against rice blast
Big data in genomic research for big questions with examples from covid-19 and other zoonoses
Authors: Wassenaar Trudy M , Ussery David W , Rosel Adriana Cabal
Published: March 2023

Omics research inevitably involves the collection and analysis of big data, which can only be handled by automated approaches. Here we point out that the analysis of big data in the field of genomics dictates certain requirements, such as specialized software, quality control of input data, and simplification for visualization of the results. The latter results in a loss of information, as is exemplified for phylogenetic trees. Clear communication of big data analyses can be enhanced by novel visualization strategies. The interpretation of findings is sometimes hampered when dedicated analytical tools are not fully understood by microbiologists, while the researchers performing these analyses may not have a full overview of the biology of the microbes under study. These issues are illustrated here, using SARS-Cov-2 and Salmonella enterica as zoonotic examples. Whereas in scientific communications jargon should be avoided or explained, nomenclature to group similar organisms and distinguish these from more distant relatives is not only essential, but also influences the interpretation of results. Unfortunately, changes in taxonomically accepted names are now so frequent that they hamper rather than assist research, as is illustrated with difficulties of microbiome studies. Nomenclature to group viral isolates, as is done for SARS-Cov2, is also not without difficulties. Some weaknesses in current omics research stem from poor quality of data or biased databases, and problems can be magnified by machine learning approaches. Moreover, the overall opus of scientific publications can now be considered “big data”, as is illustrated by the avalanche of COVID-19-related publications. The peer-review model of scientific publishing is only barely coping with this novel situation, resulting in retractions and the publication of bogus works. The avalanche of scientific publications that originated from the current pandemic can obstruct literature searches, and this will unfortunately continue over time.