Identification of a genomic DNA sequence that quantitatively modulates KLF1 expression in differentiating human hematopoietic cells

Expression of the β-like globin genes is under strict developmental control, with both direct and indirect inputs responsible for this effect. One of the major players regulating their transition is KLF1/EKLF, where even a two-fold difference in its level alters the regulation of globin switching. We have reproduced this change in KLF1 expression in both cell lines and primary human cells, thus demonstrating that directed, quantitative control of KLF1 expression can be attained by genomic manipulation, and suggest a new way in which modulation of transcription factor levels may be used for clinical benefit.

The PsMYB12L/PsDFR Module is Involved in Double-Color Formation in Paeonia Suffruticosa ‘Shima Nishiki’

Background: Paeonia suffruticosa ‘Shima Nishiki’ is a extremely precious double-color cultivar in the world because of its unique and attractive flower color. However, the underlying molecular mechanisms of its double-color formation have not been completely unravelled until now. In the present study, firstly, the full-length cDNA sequence, genomic DNA sequence, promoter region sequence of the PsDFR gene in the red and pink petals of the ‘Shima Nishiki’ cultivar were cloned and analyzed, respectively. Meanwhile, the methylation level of CpG island and promoter region of this gene in the red and pink petals was also measured. Moreover, the identification of regulatory effect of PsMYB114L/PsMYB12L and PsDFR was performed. Results: Here, we found that the full-length cDNA sequence, genomic DNA sequence, promoter region sequence of PsDFR were identical in the red and pink petals, respectively. There were some differences for the methylation level of this gene in the red and pink petals, but these differences were little and didn’t show obvious regularity. In addition, the regulatory effect of PsMYB12L and PsDFR was successfully identified. Conclusions: Based on these above results, we concluded that PsMYB12L regulating the differential expression of PsDFR may be a key reason for the double-color formation. These results will advance our understanding of the molecular regulatory mechanisms of double-color formation in P. suffruticosa ‘Shima Nishiki’.

Isolation and characterization of yeast from different sources

Four strains of yeasts isolated from some mare’s fermented milk, whey and fruit were identified using their morphology, biochemistry and phylogenetic characteristics. These yeasts belonged to four genera viz: Candida (one strain), Pichia (one strain), Saccharomyces (one strain) and Kluyveromyces (one strain). The physiological and biochemical tests of the yeasts carried out showed all isolates to ferment glucose for their growth. All isolates showed elliptical to round spores. Pichia kudriavzevii was able to ferment xylose of the four isolates. The assimilation and fermentation of most sugars by the isolates was variable. The blast sequence query showed that Saccharomyces cerevisiae and Pichia kudriavzevii had maximum identity (100%) with the genomic DNA sequence of MON-21 and MON-22, respectively at both ITS. Isolate Candida boidinii MON-23 was 100% homologous to Candida boidinii 18S rRNA gene sequence. The blast sequence query showed that Kluyveromyces marxianus MON-24 has the maximum identity (99%) with the genomic DNA sequence of Kluyveromyces marxianus at ITS 1 and ITS 4 sequence with that in the Genbank Library Database. Using MEGA 7 software, the phylogenetic trees were constructed to determine the evolutionary relationship of newly identified yeasts from our experiment and previously published yeast species. The sequences of the yeasts were deposited in the National Center for Biotechnology Information (NCBI) database. Ялгаатай эх үүсвэрээс ялгасан хөрөнгөнцрийн шинж чанар Монголчуудын эрт үеэс хэрэглэж ирсэн зарим уламжлалт исгэлэн бүтээгдэхүүн, сүү, сүүн бүтээгдэхүүний дайвар түүхий эд болох шар сүү, жимснээс хөрөнгөнцрийн цэвэр өсгөвөр ялган авч, тэдгээрийн морфологи, биохими, филогенетикийн шинж чанарыг судлав. МОН-21, 22, 23 болон 24 өсгөвөрүүд нь грам эерэг, эсийн урт нь 1.2-10.8 мкм, эсийн өргөн нь 0.5-6.0 мкм хэмжээтэй, пигмент үүсэлт нь цайвар шар өнгөтэй, жигд бөөгнөрсөн, дугуй, товгор хэлбэртэй, МОН-21 өсгөвөр нь нүүрстөрөгчийн эх үүсвэрээр галактоз, декстроз, МОН-22 өсгөвөр нь ксилоз декстроз, МОН-23 өсгөвөр нь сахароз, декстроз, ксилоз, фрюктоз, МОН-24 өсгөвөр нь мальтоз, ксилозыг тус тус ашиглаж чадахгүй байна. Дрожжийн ангилал зүйг ITS ген ашиглан тодорхойлоход, МОН-21 өсгөвөр нь Pichia kudriavzevii DGY49-тай 100%, МОН-22 нь Saccharomyces cerevisiae S5-тай 100%, МОН-23 өсгөвөр нь Candida boidinii NRRL Y-2332-тай 99.88%, МОН-24 өсгөвөр нь Kluyveromyces marxianus CCT 7735-тай 99.88% зүйлд тус тус ижил төсөөтэй байна. Мөн ITS1 болон ITS4 праймеруудыг ашиглан ялгасан өсгөвөрүүдийн зүйлийн генетик хамаарлыг тодорхойлоход, өсгөвөр МОН-23 болон МОН-24 нь бусад өсгөврүүдээс өөр хэмжээтэй буюу жижиг 18S рРНХ-ийн генийн молекултай, МОН-21 болон МОН-22 өсгөвөрүүд нь том 28S рРНХ-ийн генийн молекул хэмжээтэй байна. Эдгээр өсгөвөрүүдийг цаашид нарийвчлан судалж, исгэлтийн үйлдвэрлэлд ашиглах боломжтой хөрөнгө гарган авах, цэвэр өсгөврийн сан байгуулах, бүртгэлжүүлэх, дата мэдээлэл үүсгэх, үндэсний үйлдвэрлэлийг хөрөнгөөр хангах боломжийг нээж өгнө. Түлхүүр үг: хөрөнгөнцөр, kluyveromyces marxianus, рРНХ, pichia kudriavzevii, декстроз

Use of Phyllosphere-associated Lactic Acid Bacteria as Biocontrol Agents to Reduce Salmonella enterica Serovar Poona Growth on Cantaloupe Melons

ABSTRACT Foodborne illness associated with fresh, ready-to-eat produce continues to be a significant challenge to public health. In this study, we created a phyllosphere-associated lactic acid bacteria (PLAB) library and screened it via a high-throughput in vitro fluorescent assay to identify bacteria capable of inhibiting the growth of the pathogenic bacterium Salmonella enterica. One isolate, 14B4, inhibited the growth of S. enterica by >45-fold in vitro; it was able to grow and persist on the surfaces of cantaloupe melons at both ambient (25°C) and refrigerator (5°C) temperatures. Isolate 14B4 inhibited the growth of S. enterica on the surfaces of cantaloupes by >3 log when incubated at 25°C for 24 h and by >4 log when the cantaloupes were stored at 5°C for 3 days and the temperature was shifted to 25°C for 2 days. Genomic DNA sequence analysis of isolate 14B4 revealed that it was Lactococcus lactis and that it did not contain any known antibiotic biosynthesis gene clusters, antibiotic resistance genes, or genes encoding any known virulence factors. Organic acid analysis revealed that L. lactis produces substantial amounts of lactic acid, which is likely the inhibitory substance that reduced the growth of Salmonella on the cantaloupes. HIGHLIGHTS

The Management of Cardiovascular Risk through Epigenetic Biomarkers

Epigenetic sciences study heritable changes in gene expression not related to changes in the genomic DNA sequence. The most important epigenetic mechanisms are DNA methylation, posttranslational histone modification, and gene regulation by noncoding RNAs, such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). Cardiovascular diseases (CVD) are responsible for at least one-third of premature deaths worldwide and represent a heavy burden of healthcare expenditure. We will discuss in this review the most recent findings dealing with epigenetic alterations linked to cardiovascular physiopathology in patients. A particular focus will be put on the way these changes can be translated in the clinic, to develop innovative and groundbreaking biomarkers in CVD field.

Complete Genome Sequence of Elephant Endotheliotropic Herpesvirus 4, the First Example of a GC-Rich Branch Proboscivirus

ABSTRACT Multiple species of herpesviruses from three different lineages of the Proboscivirus genus (EEHV1/6, EEHV2/5, and EEHV3/4/7) infect both Asian and African elephants, but lethal hemorrhagic disease is largely confined to Asian elephant calves and is predominantly associated with EEHV1. Milder disease caused by EEHV5 or EEHV4 is being increasingly recognized as well, but little is known about the latter, which is estimated to have diverged at least 35 million years ago from the others within a distinctive GC-rich branch of the Proboscivirus genus. Here, we have determined the complete genomic DNA sequence of a strain of EEHV4 obtained from a trunk wash sample collected from a surviving Asian elephant calf undergoing asymptomatic shedding during convalescence after an acute hemorrhagic disease episode. This represents the first example from among the three known GC-rich branch Proboscivirus species to be assembled and fully annotated. Several distinctive features of EEHV4 compared to AT-rich branch genomes are described A novel group of mammalian DNA viruses called elephant endotheliotropic herpesviruses (EEHVs) belonging to the Proboscivirus genus has been associated with nearly 100 cases of highly lethal acute hemorrhagic disease in young Asian elephants worldwide. The complete 180-kb genomes of prototype strains from three AT-rich branch viruses, EEHV1A, EEHV1B, and EEHV5, have been published. However, less than 6 kb of DNA sequence each from EEHV3, EEHV4, and EEHV7 showed them to be a hugely diverged second major branch with GC-rich characteristics. Here, we determined the complete 206-kb genome of EEHV4(Baylor) directly from trunk wash DNA by next-generation sequencing and de novo assembly procedures. Among a total of 119 genes with an overall colinear organization similar to those of the AT-rich EEHVs, major features of EEHV4 include a family of 26 paralogous 7xTM and vGPCR-like genes plus 25 novel or missing genes. The genome also contains an unusual distribution of tracts of 5 to 11 successive A or T nucleotides in intergenic domains between the mostly much higher GC content protein coding regions. Furthermore, an extremely high GC-rich bias in the third wobble position of codons clearly delineates the coding regions for many but not all proteins. There are also two novel captured cellular genes, including a C-type lectin (vECTL) and an O-linked acetylglucosamine transferase (vOGT), as well as an unusually large and complex Ori-Lyt dyad symmetry domain. Finally, 30 kb from a second strain proved to include three small chimeric domains, indicating the existence of distinct EEHV4A and EEHV4B subtypes. IMPORTANCE Multiple species of herpesviruses from three different lineages of the Proboscivirus genus (EEHV1/6, EEHV2/5, and EEHV3/4/7) infect both Asian and African elephants, but lethal hemorrhagic disease is largely confined to Asian elephant calves and is predominantly associated with EEHV1. Milder disease caused by EEHV5 or EEHV4 is being increasingly recognized as well, but little is known about the latter, which is estimated to have diverged at least 35 million years ago from the others within a distinctive GC-rich branch of the Proboscivirus genus. Here, we have determined the complete genomic DNA sequence of a strain of EEHV4 obtained from a trunk wash sample collected from a surviving Asian elephant calf undergoing asymptomatic shedding during convalescence after an acute hemorrhagic disease episode. This represents the first example from among the three known GC-rich branch Proboscivirus species to be assembled and fully annotated. Several distinctive features of EEHV4 compared to AT-rich branch genomes are described.