Single-Cell Sequencing Demonstrates Complex Resistance Landscape in CLL and MCL Treated with BTK and BCL2 Inhibitors

The genomic landscape of resistance to targeted agents (TAs) used as monotherapy in chronic lymphocytic leukemia (CLL) is complex and often heterogeneous at the patient level. To gain insight into the clonal architecture of acquired genomic resistance to BTK inhibitors and BCL2 inhibitors in CLL, particularly in patients carrying multiple resistance mutations, we performed targeted single-cell DNA sequencing of eight patients who developed progressive disease (PD) on TAs (either class). In all cases, analysis of single-cell architecture revealed mutual exclusivity between multiple resistance mutations to the same TA class, variable clonal co-occurrence of multiple mutations affecting different TAs in patients exposed to both classes, and a phenomenon of multiple independent emergences of identical nucleotide changes leading to canonical resistance mutations. We also report the first observation of established BCL2 resistance mutations in a patient with mantle cell lymphoma (MCL) following PD on sequential monotherapy, implicating BCL2 as a venetoclax resistance mechanism in MCL. Taken together, these data reveal the significant clonal complexity of CLL and MCL progression on TAs at the nucleotide level and confirm the presence of multiple, clonally independent, mechanisms of TA resistance within each individual disease context.

Intraspecific structure of the Coregonus lavaretus complex in water bodies of Siberia: a case of postglacial allopatric origin of Yukagirian whitefish

The results of morphological and genetic analyses of forms/species of the Coregonus lavaretus pidschian (Gmelin, 1789) complex from the Indigirka and Kolyma river basins are presented in the context of there being recent postglacial speciation events. It has been found that the studied whitefishes belong to the sparsely rakered and low lateral-line forms and have previously been described as Coregonus lavaretus pidschian n. jucagiricus Drjagin (Berg), 1932. Based on these characters, this whitefish does not differ from most Arctic whitefish populations (in particular from Coregonus lavaretus glacialis Kirillov, 1972). Analysis of variability of the ND1 gene (mtDNA) showed that whitefishes from the Indigirka and Kolyma basins belong to a distant phylogenetic lineage, which is significantly different from all previously studied whitefish lineages from the Ob, Yenisei, Lena, Anadyr, and Amur river basins. Analysis of variability of the ITS1 fragment (nDNA) showed that all studied forms/species (from Ob River to Amur River basins), including C. l. pidschian n. jucagiricus, have a tandem arrangement of two identical nucleotide fragments and very similar nucleotide composition of the ITS1 region. Based on contemporary data, this phylogenetic lineage of the C. pidschian complex could be considered a young postglacial allopatric species.

The role of biotechnology in the field of biomedical engineering

The modern age is an arena of interdisciplinary research and knowledge domain which involves versatile field of sciences to work cooperatively for the improvement of the mankind. Biotechnology is providing for more personalized healthcare and continued analysis of the human body. As biotechnology advances day by day, we have to uphold the pace to discover future medical applications of it. Biotechnology is a huge and rapidly growing field. Biomedical technology involves the application of engineering and technology principles to the domain of living or biological systems. Generally biomedical denotes larger stress on issues related to human health and diseases. Different kinds of live expression systems like plant or insect cells, transgenic animals, mammals, yeast, Escherichia coli and more are particularly beneficial because biotechnology-derived medicines from them. This type of expressed gene or protein incorporates the identical nucleotide sequence as endogenous form of humans. Application of biotechnology in different domain of biomedical fields has already brought about a substantial difference which denotes the superiority over traditional ways of treatment. It is very easy to understand that how biotechnology can be played a crucial role in medical purposes. This paper will try to highlight the glimpse of multifaceted application of biotechnology in different field as well as from different angle of application.

AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant Achromobacter xylosoxidans in a teaching hospital in Thailand

ABSTRACT This study investigated the genetic basis of multidrug resistance in two strains of Achromobacter xylosoxidans isolated from patients attending a hospital in Thailand in 2012. These isolates were highly resistant to cephalosporins, aminoglycosides, fluoroquinolones, co-trimoxazole and carbapenems. Whole genome sequencing revealed that the two isolates were not clonally related and identified a carbapenem resistance gene-habouring integron (In687), residing in a novel genomic island, AcGI1. This In687 shares 100% identical nucleotide sequence with ones found in Acinetobacter baumannii Aci 16, isolated from the same hospital in 2007. We report the first analysis of multidrug-resistant A. xylosoxidans isolated in Thailand, and the first example of this island in A. xylosoxidans. Our data support the idea that resistance has spread in Thailand via horizontal gene transfer between species and suggest the possibility of A. xylosoxidans may serve as a reservoir of antibiotic resistance, especially in hospital setting.

Homogeneity of Mycoplasma agalctiae vaccine strains in an agalaxy- high-burden environment

Background and Objectives: Interrogation of the genomic relations between Iranian Mycoplasma agalactiae vaccine strains of Taliqan, Lorestan and Shiraz. Materials and Methods: Two MLVA (covering VNTR loci of 5, 9, 17 and 19) and MLST (comprising dnaA, gltX, gyrB, C, tufA genes) genotyping systems plus nucleotide structure analysis of P80 gene, was conducted. Results: The shared MLVA pattern represented by the three strains differed to that of the Mag PG2 laboratory strain, only at locus VNTR19 where the PG2 genome hold a 3 bp longer stretch. In MLST analysis, at dnaA, gltX, gyrB, metS and tufA loci, the three strains displayed alleles 1, 21, 2, 2 and 1, respectively. At, gltX locus a new allele (21) was detected where a new sequence type (ST33) was identified. Besides, the trio strains hold an identical nucleotide structure in their ma-mp81 gene. Conclusion: In explanation, lack of efficient disease control measures, has possibly contributed in evolution of a clone or a few clones that gradually overwhelmed the population over the time. Besides, the similarity between the Iranian and the PG2 strains, might be due to homoplasy or farming exercises such as animal importation. Inclusion of further local isolates in next studies will help to assess these assumptions.

A Key For Hypoxia Genetic Adaptation In Alpaca Could Be A HIF1A Truncated bHLH Protein Domain

Animals exposed to hypoxia, triggers a physiological response via Hypoxia Inducible Factors (HIF1). In this study, we have evidenced the existence of genetic events that caused the loss of most of the bHLH domain in HIF1A proteins borne by Alpaca and other members of the Cetartiodactyla superorder. In these truncate domains, some stop codons are found at identical nucleotide positions in both, Artiodactyls and Cetaceans, indicating that mutations originating the truncated domains occurs before their divergence about 55 million years ago. The relevance of this findings for adaptation of Alpacas to hypoxia of high altitude conditions are discussed.

Characterization of Klebsiella sp. strain S1: a bacterial producer of secoisolariciresinol through biotransformation

Secoisolariciresinol (SECO) is a lignan of potential therapeutic value for diseases such as cancer, but its use has been limited by the lack of ideal production methods, even though its precursors are abundant in plants, such as flaxseeds. Here, we report the characterization of a bacterial strain, S1, isolated from the human intestinal flora, which could produce secoisolariciresinol by biotransformation of precursors in defatted flaxseeds. This bacterium was a Gram-negative and facultatively anaerobic straight rod without capsules. Biochemical assays showed that it was negative for production of oxidase, lysine decarboxylase, ornithine decarboxylase, arginine dihydrolase, and β-glucolase. The G + C content of genomic DNA was 57.37 mol%. Phylogenetic analysis by 16S rRNA and rpoB gene sequences demonstrated S1’s close relatedness to Klebsiella. No homologues were found for wzb or wzc (capsular genes), which may explain why Klebsiella sp. strain S1 does not have the capsule and was isolated from a healthy human individual. Based on the percentages of homologous genes with identical nucleotide sequences between the bacteria in comparison, we found that clear-cut genetic boundaries had been formed between S1 and any other Klebsiella strains compared, dividing them into distinct phylogenetic lineages. This work demonstrates that the intestinal Klebsiella, well known as important opportunistic pathogens prevalent in potentially fatal nosocomial infections, may contain lineages that are particularly beneficial to the human health.

Novel Organization of the Arginine Catabolic Mobile Element and Staphylococcal Cassette ChromosomemecComposite Island and Its Horizontal Transfer between Distinct Staphylococcus aureus Genotypes

ABSTRACTIn this study, 425 methicillin-resistantStaphylococcus aureus(MRSA) isolates recovered in the Dutch-German Euregio were investigated for the presence of the arginine catabolic mobile element (ACME). Sequence analysis by whole-genome sequencing revealed an entirely new organization of the ACME-staphylococcal cassette chromosomemeccomposite island (SCCmec-CI), with truncated ACME type II located downstream of SCCmec. An identical nucleotide sequence of ACME-SCCmec-CI was found in two distinct MRSA lineages (t064-ST8 and t002-ST5), which has not been reported previously inS. aureus.

Continuous Presence of Noroviruses and Sapoviruses in Raw Sewage Reflects Infections among Inhabitants of Toyama, Japan (2006 to 2008)

ABSTRACT Various genotypes of norovirus (NoV) (genogroup I genotype 1 [GI.1], -2, -4, -5, -8, -11, -12, and -14; GII.3, -4, -6, -7, -10, -13, -14, and -15), and sapovirus (SaV) (GI.1 and GI.2, GII.1, and GIV.1) were detected from raw sewage from April 2006 to March 2008, while limited numbers of genotypes of NoV (GI.8, GII.4, GII.6, and GII.13) and SaV (GII.3 and GIV.1) and of NoV (GII.4, GII.7, and GII.13) were detected from clinical cases and healthy children, respectively. During the winter 2006 to 2008, a large number of sporadic gastroenteritis outbreaks and many outbreaks caused by NoV GII.4 occurred among inhabitants in Toyama, Japan. The copy number of genomes of NoV GII detected from raw sewage changed in relation to the number of outbreaks. NoV strains of the same genotypes observed in both raw sewage and human specimens belonged to the same cluster by phylogenetic analysis and had almost identical nucleotide sequences among each genotype. These data suggest that NoVs and SaVs detected from raw sewage reflect the viruses circulating in the community, irrespective of symptoms, and that subclinical infections of NoV are common in Japan. Combined surveys of raw sewage with those of clinical cases help us to understand the relationship between infection of these viruses and gastroenteritis.