Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches: 15 isolates from the early epidemic (March 12–April 1 2020) and 31 from later time-points ( 25–27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades: 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5–99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana.     

Craft Beers Fermented by Potential Probiotic Yeast or Lacticaseibacilli Strains Promote Antidepressant-Like Behavior in Swiss Webster Mice

Probiotics and Antimicrobial Proteins - This study aimed to produce a probiotic-containing functional wheat beer (PWB) by an axenic culture system with potential probiotic Saccharomyces cerevisiae...     

Shorter leukocyte telomere length is associated with severity of COVID-19 infection.

The infection by COVID-19 is a serious global public health problem. An efficient way to improve this disease's clinical management would be to characterize patients at higher risk of progressing to critically severe infection using prognostic biomarkers. The telomere length could be used for this purpose. Telomeres are responsible for controlling the number of maximum cell divisions. The telomere length is a biomarker of aging and several diseases. We aimed to compare leukocyte telomere length (LTL) between patients without COVID-19 and patients with different clinical severity of the infection. Were included 53 patients who underwent SARS-CoV-2 PCR divided in four groups. The first group was composed by patients with a negative diagnosis for COVID-19 (n = 12). The other three groups consisted of patients with a confirmed diagnosis of COVID-19 divided according to the severity of the disease: mild (n = 15), moderate (n = 17) and severe (n = 9). The LTL was determined by Q-PCR. The severe group had the shortest LTL, followed by the moderate group. The negative and mild groups showed no differences. There is an increase of patients with hypertension (p = 0.0099) and diabetes (p = 0.0067) in moderate and severe groups. Severe group was composed by older patients in comparison with the other three groups (p = 0.0083). Regarding sex, there was no significant difference between groups (p = 0.6279). In an ordinal regression model, only LTL and diabetes were significantly associated with disease severity. Shorter telomere length was significantly associated with the severity of COVID-19 infection, which can be useful as a biomarker or to better understand the SARS-CoV-2 pathophysiology.     

Mechanical scale and load cell underwater weighing: a comparison of simultaneous measurements and the reliability of methods

Both load cell and mechanical scale-based hydrostatic weighing (HW) systems are used for the measurement of underwater weight. However, there has been no direct comparison of the 2 methods. The purpose of the current investigation was to simultaneously compare a load cell and mechanical scale for use in HW. Twenty-seven men and women (mean ± SD, age: 22 ± 2 years) participated in the 2-day investigation. Each subject completed 2 HW assessments 24 hours apart. Single-day comparisons of all trials for both days revealed no significant difference between the mechanical scale and the load cell (mean difference < 0.016 kg, p > 0.05). True underwater weight values were not significantly different between methods for either days (mean difference < 0.014 kg, p > 0.05) and accounted for a mean difference in percent fat (%FAT) of <0.108%. The 95% limits of agreement indicated a maximum difference between methods of 0.53% FAT. Both methods produced similar reliability SEM values (mechanical SEM < 0.72%FAT, load cell SEM < 0.75%FAT). In conclusion, there was no difference between mechanical scale and load cell measurements of underwater weights and the added precision of the load cell only marginally (<0.16%FAT) improved day-to-day reliability. Either a mechanical scale or load cell can be used for HW with similar accuracy and reliability in young adults with a body mass index of 18.7-34.4 (5-25%FAT).     

Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane

Diversity Arrays Technology (DArT) provides whole genome profiling for hundreds to thousands of polymorphic markers in a single assay using a high-throughput microarray platform. The presented work aimed to establish DArT genotyping for the genetically challenging genome of sugarcane. Due to the genome complexity of this sugar-producing crop of high economic importance, an application of DArT genotyping to this species required extensive testing and optimization. As the method of genome complexity reduction determines the efficiency of polymorphism identification in DArT, various approaches and several methods were tested, in order to establish the most optimal. The sugarcane DArT markers generated with these established methods identified high genetic differentiation of sugarcane ancestral species from modern cultivars, in agreement with the data available for other types of molecular markers for this crop. The majority of sugarcane DArT markers segregated in a Mendelian fashion and were readily incorporated into the framework genetic map. As the DArT markers are sequence-ready genomic clones, we sequenced 384 clones and found that one-third of sequenced markers came from the transcribed portion of the sugarcane genome. The presented results further validate the potential of DArT technology in providing cost-effective genetic profiles for plants, irrespective of their genome complexity, for effective applications in molecular-assisted breeding, diversity analysis or genetic identity testing.     

Natural incidence of egg parasitoids of Edessa meditabunda (F.) (Hemiptera: Pentatomidae) on Crotalaria spectabilis in Campo Novo do Parecis, MT, Brazil

Egg parasitoids of the stink bug Edessa meditabunda (F) were studied on rattlepod Crotalaria spectabilis used in soybean crop rotation in Campo Novo do Parecis, Mato Grosso state, central western Brazil. Seven species of parasitoids were found: two Encyrtidae, one Eurytomidae, and four Platygastridae. The occurrence of Trissolcus euchisti (Ashmead) and Trissolcus elimatus Johnson (Platygastridae) on eggs of E. meditabunda is recorded for the first time. Moreover, this is the first record of T. elimatus and T. euchisti from Brazil.     

Synthesis and evaluation of the antiproliferative activity of novel isoindolo[2,1-a]quinoxaline and indolo[1,2-a]quinoxaline derivatives

A novel series of isoindolo[2,1-a]quinoxaline and indolo[1,2-a]quinoxaline derivatives was synthesized and evaluated in vitro against various human cancer cell lines for antiproliferative activity. These new compounds displayed activity against leukemia and breast cancer cell lines in the 3- to 18-μM concentration range.     

Efficient, non-toxic hybrid PPV-PAMAM dendrimer as a gene carrier for neuronal cells

A novel hybrid dendrimer (TRANSGEDEN) that combines a conjugated rigid polyphenylenevinylene (PPV) core with flexible polyamidoamine (PAMAM) branches at the surface was synthesized and characterized. The potential of this material as a nonviral gene delivery system was also examined, and it was observed that dendriplexes formed by TRANSGEDEN and small interfering ribonucleic acids (siRNAs) can be incorporated into >90% of neuronal cells without any toxicity up to a dendrimer concentration of 3 μM. TRANSGEDEN was used to deliver a specific siRNA to rat cerebellar granular neurons (CGNs) to knock down the cofilin-1 protein. Cofilin-1 removal partially protects CGNs from N-methyl D-aspartate (NMDA)-mediated neuronal death.     

Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy

The aim of this study was to determine, through a genome-wide association study (GWAS), the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis (SSc). We considered limited (lcSSc) and diffuse (dcSSc) cutaneous involvement, and the relationships with presence of the SSc-specific auto-antibodies, anti-centromere (ACA), and anti-topoisomerase I (ATA). Four GWAS cohorts, comprising 2,296 SSc patients and 5,171 healthy controls, were meta-analyzed looking for associations in the selected subgroups. Eighteen polymorphisms were further tested in nine independent cohorts comprising an additional 3,175 SSc patients and 4,971 controls. Conditional analysis for associated SNPs in the HLA region was performed to explore their independent association in antibody subgroups. Overall analysis showed that non-HLA polymorphism rs11642873 in IRF8 gene to be associated at GWAS level with lcSSc (P = 2.32×10⁻¹², OR = 0.75). Also, rs12540874 in GRB10 gene (P = 1.27 × 10⁻⁶, OR = 1.15) and rs11047102 in SOX5 gene (P = 1.39×10⁻⁷, OR = 1.36) showed a suggestive association with lcSSc and ACA subgroups respectively. In the HLA region, we observed highly associated allelic combinations in the HLA-DQB1 locus with ACA (P = 1.79×10⁻⁶¹, OR = 2.48), in the HLA-DPA1/B1 loci with ATA (P = 4.57×10⁻⁷⁶, OR = 8.84), and in NOTCH4 with ACA P = 8.84×10⁻²¹, OR = 0.55) and ATA (P = 1.14×10⁻⁸, OR = 0.54). We have identified three new non-HLA genes (IRF8, GRB10, and SOX5) associated with SSc clinical and auto-antibody subgroups. Within the HLA region, HLA-DQB1, HLA-DPA1/B1, and NOTCH4 associations with SSc are likely confined to specific auto-antibodies. These data emphasize the differential genetic components of subphenotypes of SSc.