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Laboratory-based practical classes are an essential component in teaching molecular biology for undergraduate students. Universidad Regional Amazonica Ikiam is a higher education institution located in the Ecuadorian Amazon rainforest, a high biodiversity place, including amphibians. Based on this, we have established a practical molecular biology program with eight sessions that contextualize the biodiverse surroundings of the University. This program stimulates synchronization of information between theory and practice and improves research skills. During these sessions, students are motivated to identify and characterize antimicrobial peptides from Ecuadorian frog skin secretions, using molecular biology techniques and biochemistry and microbiology knowledge. This practical course was held twice with a total of 56 students from the fifth semester of the biotechnology engineering. The evaluation of the practical program was carried out through a questionnaire applied to students using the Likert scale. Overall, this form of teaching had high receptivity and presented benefits for student learning. Interestingly, 80% of respondents strongly agreed that this course provided tools and knowledge for the development of their undergraduate dissertation. Therefore, practical courses tailored to the student's context can stimulate student learning and interest. Additionally, this experimental methodology is interdisciplinary and can be applied to other research fields and subjects., (© 2022 International Union of Biochemistry and Molecular Biology.)

Molecular cloning is a cornerstone of modern biology laboratories. However, traditional cloning can be time-consuming and problematic. We outline herein a method that utilizes the endogenous gap repair system of yeast cells to clone and assemble DNA constructs. This system is simple, cheap, and requires minimal reagents. It can be used for the assembly of both simple (single DNA fragments) and complex (multiple DNA fragments) constructs into plasmids.

The demand for cloned genes has increased incessantly over the past 32 years, but some who need recombinant plasmids struggle to produce them. While the pitfalls of traditional ligation-dependent cloning are non-trivial, most can be avoided with sufficient effort and attention to detail. Here, the chemical properties of enzymes and reagents used to clone genes into plasmids are reviewed to draw attention to the most pertinent details. In particular, the virtues of agarose gel electrophoresis monitoring, the nature of the interactions between DNA and silica, and challenges associated with thermostable DNA polymerases, restriction endonucleases, and T4 DNA ligase are explored. Common pitfalls associated with Escherichia coli transformation and DNA modifying enzymes are also described. A thorough understanding of established methods is essential for troubleshooting, implementing alternative approaches, and inventing new techniques in response to changes in technology and demand.

Cloning is a key molecular biology procedure for obtaining a genetically homogenous population of organisms or cell lines. It requires the expansion of new cell populations starting from single genetically modified cells. Despite the technical progress, cloning of many cell lines remains difficult. Cloning often fails either due to the strenuous conditions associated with manipulating cells or because many cells don't tolerate a single-cell state. Here we describe a new cloning method utilizing low adhesion microcavity plates. This new technique, named microcavity-assisted cloning (MAC) was developed to clone difficult-to-clone HepG2 cells. The clones were produced following CRISPR/Cas9 knockout of the GSTA1 gene by a random distribution of 200, 400, and 800 cells into 550 microcavities of a 24-well low adhesion plate originally designed for the culture of spheroids. The knockout of GSTA1 was verified at the protein level using Western blotting. The advantages of the MAC method are its low cost, ease of the procedure, and the possibility of scaling up the throughput and automatization. [ABSTRACT FROM AUTHOR]

This study introduces a novel cost-effective technique for cloning of linear DNA plasmid inserts, aiming to address the associated expenses linked with popular in vitro DNA assembly methods. Specifically, we introduce ECOLI (Efficient Cloning Of Linear Inserts), a method utilizing a PCR product-based site-directed mutagenesis. In comparison to other established in vitro DNA assembly methods, our approach is without the need for costly synthesis or specialized kits for recombination or restriction sites. ECOLI offers a fast, efficient, and economical alternative for cloning inserts up to several hundred nucleotides into plasmid constructs, thus enhancing cloning accessibility and efficiency. This method can enhance molecular biology research, as we briefly demonstrated on the Dishevelled gene from the WNT signaling pathway. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to explore the expression of CX3CL1 induced by lipopolysaccharide (LPS) in oral squamous cell carcinoma (OSCC) and its impact on biological characteristics such as invasion and migration, taking the foundation for new targets for the treatment and prognosis of OSCC. Methods: This study utilized a variety of techniques, including bioinformatics, molecular biology, and cell experiments, to investigate the expression of CX3CL1 and its receptor CX3CR1 in OSCC patients' cancer tissues or OSCC cell lines. Extracting, organizing, and analyzing the TCGA database on the expression of CX3CL1 and its receptor CX3CR1 in cancer tissues and corresponding paracancerous normal tissues of OSCC patients by bioinformatics methods. The expression of CX3CL1 in cancerous and normal tissues of OSCC patients was verified by IHC, and the changes inmRNA and protein expression of CX3CL1 and its receptor CX3CR1 in OSCC cell lines were detected before and after lipopolysaccharide LPS stimulation by RT-PCR, ELISA, and WB. Changes in cell biological behavior by overexpression of CX3CL1 in OSCC cell lines were detected by CCK-8, Transwell, scratch healing assay, and cloning assay. The effects of overexpressing cell lines on the AKT pathway and Epithelial-mesenchymal Transition (EMT)-related protein expression before and after LPS stimulation were detected by Western Blot. Results: (1) CX3CL1 and its receptor CX3CR1 were found to be downregulated in OSCC tissues of patients or OSCC cell lines. (2) After LPS stimulation, CX3CL1 gene expression increased in both OSCC cell lines, while CX3CR1 expression remained unchanged. (3) OSCC cell lines overexpressing CX3CL1 showed changes in cell biological characteristics, including decreased proliferation, invasion, migration, and stemness, which were more pronounced after LPS stimulation. (4) Overexpression of CX3CL1 in OSCC cell lines decreased EMT-related protein expression and AKT phosphorylation. On the contrary were promoted by LPS stimulation. Conclusion: CX3CL1 and CX3CR1 are downregulated in OSCC cancer tissues and cell lines compared to adjacent normal tissues and cells. LPS stimulation increases CX3CL1 expression in OSCC cell lines, suggesting that inflammation may induce CX3CL1 expression and that the CX3CL1 gene may play an important role in OSCC progression. Overexpression of CX3CL1 inhibits OSCC cell proliferation, migration, invasion, and stemness, suggesting that CX3CL1 plays a critical role in suppressing OSCC development. CX3CL1 suppresses OSCC invasion and migration by affecting EMT progression and AKT phosphorylation, and partially reverse the process that LPS causes and affects the development of OSCC. [ABSTRACT FROM AUTHOR]

This article discusses the identification of a novel A allele with a c.421T>C variant on the ABO*A1.02 allele in a Chinese individual. The ABO blood group system is important in transfusion and transplantation medicine, and over 400 ABO alleles have been identified worldwide. The study describes the case of a Chinese pregnant woman with an Aweak phenotype and analyzes her ABO genotype. The findings reveal a compound heterozygous genotype for the ABO*O.01.02 allele and a novel A allele with two variants (c.421T>C and c.467C>T) in exon 7. The c.421T>C variant is predicted to have a damaging effect on the glycosyltransferase A enzyme. The study concludes that this novel allele is responsible for the Aweak phenotype in the Chinese individual. The research was supported by the Guangxi Natural Science Foundation Program. [Extracted from the article]

Bioluminescence is a type of chemiluminescence that arises from a luciferase-catalyzed oxidation reaction of luciferin. Molecular biology and comparative genomics have recently elucidated the genes involved in fungal bioluminescence and the evolutionary history of their clusters. However, most studies on fungal bioluminescence have been limited to observing the changes in light intensity under various conditions. To understand the molecular basis of bioluminescent responses in Omphalotus guepiniiformis under different environmental conditions, we cloned and sequenced the genes of hispidin synthase, hispidin-3-hydroxylase, and luciferase enzymes, which are pivotal in the fungal bioluminescence pathway. Each gene showed high sequence similarity to that of other luminous fungal species. Furthermore, we investigated their transcriptional changes in response to abiotic stresses. Wound stress enhanced the bioluminescence intensity by increasing the expression of bioluminescence pathway genes, while temperature stress suppressed the bioluminescence intensity via the non-transcriptional pathway. Our data suggested that O. guepiniiformis regulates bioluminescence to respond differentially to specific environmental stresses. To our knowledge, this is the first study on fungal bioluminescence at the gene expression level. Further studies are required to address the biological and ecological meaning of different bioluminescence responses in changing environments, and O. quepiniiformis could be a potential model species. [ABSTRACT FROM AUTHOR]

Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements. [ABSTRACT FROM AUTHOR]

Course‐based Undergraduate Research Experiences (CUREs) integrate active, discovery‐based learning into undergraduate curricula, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges. Our CURE focuses on fungal effectors which are proteins secreted by a destructive pathogenic fungus Fusarium oxysporum, one of the top five most devastating plant pathogens. By studying this group of proteins, students are connected to real‐world problems and participate in the search for potential solutions. A 3‐week "standard Boot Camp" is implemented to help students familiarize themselves with all basic techniques and boost their confidence. Next, molecular cloning, a versatile technique with modularity and repeatability, is used as the bedrock of the course. Our past 5 years of experience have confirmed that we have developed a novel and feasible CURE protocol. Measurable progress documented by students who took this course includes stimulated active learning and increased career trajectory to pursue hypothesis‐based research to address societal needs. In addition, data generated through the course advance ongoing lab research. Collectively, we encourage the implementation of CURE among research‐intensive faculty to provide a more inclusive research experience to undergraduate students, an important element in predicting career success. [ABSTRACT FROM AUTHOR]

The search for new drug-producing microorganisms is one of the most promising situations in current world scientific scenarios. The use of molecular biology as well as the cloning of protein and compound genes is already well established as the gold standard method of increasing productivity. Aiming at this increase in productivity, this work aims at the cloning, purification and in silico analysis of l-asparaginase from Fusarium proliferatum in Komagataella phaffii (Pichia pastoris) protein expression systems. The l-asparaginase gene (NCBI OQ439985) has been cloned into Pichia pastoris strains. Enzyme production was analyzed via the quantification of aspartic B-hydroxamate, followed by purification on a DEAE FF ion exchange column. The in silico analysis was proposed based on the combined use of various technological tools. The enzymatic activity found intracellularly was 2.84 IU/g. A purification factor of 1.18 was observed. The in silico analysis revealed the position of five important amino acid residues for enzymatic activity, and likewise, it was possible to predict a monomeric structure with a C-score of 1.59. The production of the enzyme l-asparaginase from F. proliferatum in P. pastoris was demonstrated in this work, being of great importance for the analysis of new methodologies in search of the production of important drugs in therapy. [ABSTRACT FROM AUTHOR]

Students who experience research as undergraduates tend to remain in science, technology, engineering, and mathematics fields. Since course-based undergraduate research experiences (CUREs) are often expensive to implement, we developed a relatively inexpensive first-semester research course for majors entitled "Freshman Research in Biochemistry," in which approximately 100 students participated in an ongoing research project each year. During this course, students conducted laboratory work related to multiple research veins, and graduate teaching assistants (TAs) and the instructor ensured that sufficient data from the laboratory were made available to the students to analyze. During three unique course iterations, students worked on faculty research projects that included connecting contigs of the draft genome of a native Oklahoma bacterial Arhodomonas isolate capable of degrading petroleum hydrocarbons, cloning antibiotic resistance genes from the genus Elizabethkingia, and analyzing RNAseq data from Elizabethkingia anopheles challenged with cell wall-active antibiotics to determine gene function, gene differential expression, and relative gene genome location. During the course, students scored results, analyzed data, maintained laboratory notebooks, and presented posters in a symposium to faculty and graduate TAs. To determine positive impacts of the course on students, they completed the Laboratory Course Assessment Survey in two course sections. Survey data indicated/students agreed that the course included elements of Iteration, Collaboration, and Discovery and Relevance. Students also reported that they gained scientific skills but were ambivalent about whether instructor feedback was harsh. Examination of Student Survey of Instruction responses showed students thought positively about the course, but some considered it too difficult. Biochemistry and Molecular Biology and Biochemistry major cohort tracking revealed no effect of Freshman Research in Biochemistry on student persistence in the major or institution. Nonetheless, we consider the course a cost-conscious model for biochemistry and molecular biology departments for introducing research to first-year students. [ABSTRACT FROM AUTHOR]

The cloning of DNA fragments to plasmid vectors is at the heart of molecular biology. Recent developments have led to various methods utilizing homologous recombination of homology arms. Among them, Seamless Ligation Cloning Extract (SLiCE) is an affordable alternative solution that uses simple Escherichia coli lysates. However, the underlying molecular mechanisms remain unclear and the reconstitution of the extract by defined factors has not yet been reported. We herein show that the key factor in SLiCE is Exonuclease III (ExoIII), a double‐strand (ds) DNA‐dependent 3′‐5′ exonuclease, encoded by XthA. SLiCE prepared from the xthAΔ strain is devoid of recombination activity, whereas purified ExoIII alone is sufficient to assemble two blunt‐ended dsDNA fragments with homology arms. In contrast to SLiCE, ExoIII is unable to digest (or assemble) fragments with 3′ protruding ends; however, the addition of single‐strand DNA‐targeting Exonuclease T overcomes this issue. Through the combination of commercially available enzymes under optimized conditions, we achieved the efficient, reproducible, and affordable cocktail, "XE cocktail," for seamless DNA cloning. By reducing the cost and time required for DNA cloning, researchers will devote more resources to advanced studies and the careful validation of their own findings. [ABSTRACT FROM AUTHOR]

The term allergy was coined in 1906 by the Austrian scientist and pediatrician Clemens Freiherr von Pirquet. In 1976, Dietrich Kraft became the head of the Allergy and Immunology Research Group at the Department of General and Experimental Pathology of the University of Vienna. In 1983, Kraft proposed to replace natural extracts used in allergy diagnostic tests and vaccines with recombinant allergen molecules and persuaded Michael Breitenbach to contribute his expertise in molecular cloning as one of the mentors of this project. Thus, the foundation for the Vienna School of Molecular Allergology was laid. With the recruitment of Heimo Breiteneder as a young molecular biology researcher, the work began in earnest, resulting in the publication of the cloning of the first plant allergen Bet v 1 in 1989. Bet v 1 has become the subject of a very large number of basic scientific as well as clinical studies. Bet v 1 is also the founding member of the large Bet v 1-like superfamily of proteins with members—based on the ancient conserved Bet v 1 fold—being present in all three domains of life, i.e., archaea, bacteria and eukaryotes. This suggests that the Bet v 1 fold most likely already existed in the last universal common ancestor. The biological function of this protein was probably related to lipid binding. However, during evolution, a functional diversity within the Bet v 1-like superfamily was established. The superfamily comprises 25 families, one of which is the Bet v 1 family, which in turn is composed of 11 subfamilies. One of these, the PR-10-like subfamily of proteins, contains almost all of the Bet v 1 homologous allergens from pollen and plant foods. Structural and functional comparisons of Bet v 1 and its non-allergenic homologs of the superfamily will pave the way for a deeper understanding of the allergic sensitization process. [ABSTRACT FROM AUTHOR]

George Rogers (1927–2021) was elected to Fellowship of the Academy in 1977 for his outstanding contributions to our knowledge of the molecular structure of keratins and the biochemistry of keratinisation. He was a pioneer in the application of electron microscopy to hair and wool ultrastructure and to that of the hair follicle. He discovered citrulline in keratin proteins, and the enzymes, roles, and histochemical localisation of transglutaminase and peptidylarginine deiminase (PAD). He was the first to demonstrate ribosomal-dependent keratin protein synthesis in 1965 followed by detailed studies of the biosynthesis of hair keratin proteins. His research initiated studies on the molecular events in the development of the feather follicle and later led to the cloning and characterisation of the clustered genes of feather and related avian keratins. He also cloned and characterised genes for the three classes of wool keratin proteins and studied the transcription of keratin genes. In 1977, he was awarded a DSc by the University of Adelaide in recognition for his work. In 2013, he was made an Officer in the Order of Australia. George's interest in science began at ten after his mother gave him a chemistry set and he became internationally renowned for the detailed structure and growth of hair and wool. This paper follows his achievements from pioneering electron microscopy work to the advent of gene cloning and DNA sequencing, when he cloned and characterised important genes in this field. Sixty years later, the applications of his discoveries continue whether in scientific research, forensic science, or medicine. [ABSTRACT FROM AUTHOR]

The multicellular green alga Volvox carteri has emerged as a valuable model organism for investigating various aspects of multicellularity and cellular differentiation, photoreception and phototaxis, cell division, biogenesis of the extracellular matrix and morphogenetic movements. While a range of molecular tools and bioinformatics resources have been made available for exploring these topics, the establishment of cell type-specific promoters in V. carteri has not been achieved so far. Therefore, here, we conducted a thorough screening of transcriptome data from RNA sequencing analyses of V. carteri in order to identify potential cell type-specific promoters. Eventually, we chose two putative strong and cell type-specific promoters, with one exhibiting specific expression in reproductive cells (gonidia), the PCY1 promoter, and the other in somatic cells, the PFP promoter. After cloning both promoter regions, they were introduced upstream of a luciferase reporter gene. By using particle bombardment, the DNA constructs were stably integrated into the genome of V. carteri. The results of the expression analyses, which were conducted at both the transcript and protein levels, demonstrated that the two promoters drive cell type-specific expression in their respective target cell types. Transformants with considerably diverse expression levels of the chimeric genes were identifiable. In conclusion, the screening and analysis of transcriptome data from RNA sequencing allowed for the identification of potential cell type-specific promoters in V. carteri. Reporter gene constructs demonstrated the actual usability of two promoters. The investigated PCY1 and PFP promoters were proven to be potent molecular tools for genetic engineering in V. carteri. [ABSTRACT FROM AUTHOR]

But arguably the most important legacy was the canonization of a version of cloning's history shorn of all the contingencies which Crowe has now so meticulously and thoughtfully restored. No biological technique has had a better run in speculative fiction than cloning. [Extracted from the article]

The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to use the cloning-free genome editing (CFGE) approach, proposed by Döhlemann and coworkers (2016), for E. coli genetics, and to deepen the knowledge about the homologous recombination mechanism. The E. coli auxotrophic mutant strains FB182 (hisF892) and FB181 (hisI903) were transformed with the circularized wild-type E. coli (i) hisF gene and hisF gene fragments of decreasing length, and (ii) hisIE gene, respectively. His+ clones were selected based on their ability to grow in the absence of histidine, and their hisF/hisIE gene sequences were characterized. CFGE method allowed the recombination of wild-type his genes (or fragments of them) within the mutated chromosomal copy, with a different recombination frequency based on the fragment length, and the generation of clones with a variable number of in tandem his genes copies. Data obtained pave the way to further evolutionary studies concerning the homologous recombination mechanism and the fate of in tandem duplicated genes. [ABSTRACT FROM AUTHOR]

Avian influenza poses a significant global health threat, with the potential for widespread pandemics and devastating consequences. Hemagglutinin (HA), a critical surface glycoprotein of influenza viruses, plays a pivotal role in viral entry and serves as a primary target for subunit vaccine development. In this study, we successfully cloned, expressed, and purified hemagglutinin from the circulating strain of H5N1 influenza virus using a robust molecular biology approach. The cloning process involved insertion of the synthetic HA gene into the pET21b vector, confirmed through double digestion and sequencing. SDS-PAGE analysis confirmed the presence of the expected 60 kDa protein band post-induction. Following expression, the protein was subjected to purification via Ni-NTA affinity chromatography, yielding pure protein fractions. Native PAGE analysis confirmed the protein's oligomeric forms, essential for optimal antigenicity. Western blot analysis further validated protein identity using anti-His and anti-HA antibodies. MALDI-TOF analysis confirmed the protein's sequence integrity, while hemagglutination assay demonstrated its biological activity in binding to N-acetyl neuraminic acid. These findings underscore the potential of recombinant hemagglutinin as a valuable antigen for diagnosis and biochemical assays as well as for vaccine development against avian influenza. In conclusion, this study represents a critical guide for bacterial production of H5N1 HA, which can be a cost-effective and simpler strategy compared to mammalian protein expression. Further research into optimizing vaccine candidates and production methods will be essential in combating the ongoing threat of avian influenza pandemics. • Avian influenza is a serious global health risk with a potential of leading to widespread pandemics. • Full length hemagglutinin protein from the H5N1 strain was successfully cloned, expressed, and purified in E. coli. • The purified hemagglutinin protein formed oligomers and showed biological activity, making it a promising vaccine target. • This study offers a simple, robust, cost-effective protocol for functional full length hemagglutinin production. [ABSTRACT FROM AUTHOR]

Auricularia heimuer (A. heimuer F. Wu, B. K. Cui, Y. C. Dai), a well-known gelatinous fungus used for both food and medicine, is a major edible fungus with a more than 1000-year history of cultivation in China. The nutrients of A. heimuer are abundant, including polysaccharides, melanin, mineral elements, etc. The A. heimuer polysaccharides exhibit antioxidant, immunomodulatory, and anticancer properties. A. heimuer is a completely different species grown in China, unlike Auricularia auricula-judae (Bull.) Quel, which was used to characterize it. The cultivated strain varies based on the local climatic factors and cultivation practices. Hardwood chips are the primary material utilized in the cultivation of substitute materials, which is the principal cultivation technique. However, in actual production, straw is frequently replaced for some wood chips to address the issue of a lack of wood. There are three different types of growing techniques: open-air ground cultivation, arch cultivation, and shed-type hanging substitute cultivation of these three, the quality of A. heimuer grown in a shed is superior to that grown in an open-air environment. The A. heimuer genome sequencing project started later than expected, and the entire genome sequencing was not finished until 2019. A. heimuer's molecular biology studies have mostly concentrated on analyzing genetic diversity and identifying cultivars using molecular markers including RAPD, ISSR, and ITS. There have only been a small number of studies on the function of A. heimuer genes, which have only focused on the preliminary cloning and expression study of a few genes, including the laccase gene and the triterpene compound production gene, among others. However, there is still a lack of comprehensive information concerning A. heimuer, necessitating a synopsis. To our knowledge, this is the first published review of A. heimuer, and it summarizes the most recent studies on its molecular biology and cultivation. This review can serve as a guide for future research on the fungus. [ABSTRACT FROM AUTHOR]

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Background: One of the amazing and economical spices is Chilli (Capsicum annum L.) and also called "wonder spice," and it gives great significance to traditional household use and export as well as such a remarkable cash crop in India. However, the important constraints in chilli production are chilli leaf curl disease which has been caused by whitefly (Bemisia tabaci) transmitted by begomoviruses and leads to a major decline in yield. Aim: To explore the stability of the insect resistance gene (tryptophan decarboxylase [TDC]) in resistant genotypes after being challenged with a known number of whiteflies. Since, biotic stress defense allied mechanism regulated during tryptophan biosynthesis. Materials and Methods: The presence of endogenous genes was verified using the polymerase chain reaction (PCR), cloning (T/A vector), and gene expression level (quantitative real-time PCR). Results: Amplification of mitochondrial coxI gene fragment using the primer (C1-J-2195 and L2-N-3014) produced B. tabaci specific ~ 800 bp band. Besides, the whitefly sequence was aligned with the NCBI blast where 92% of identity was observed. TDC gene expression was greater in P2 accession leaves at 48 h post-infestation with 20 number of B. tabaci after feeding and downregulation in less TDC gene expression level at moderately resistant accession ACC 20. Further, all the amplified gene sequences were aligned using NCBI BLAST. The expression of TDC genes in chillies could demoralize the B. tabaci fitness causes mortality. Conclusion: The satisfactory control of viral disease may be achieved with the application of molecular biology, DNA, and RNA-based technologies include the cloning of insect resistance genes. [ABSTRACT FROM AUTHOR]

Molecular cloning is an invaluable research tool in modern molecular biology. However, it is often difficult for students to grasp conceptually without visual aids and even more difficult to understand how to successfully set up a cloning experiment. Here, we describe a flipped classroom activity that simulates cloning using donuts as models of plasmids. Students noted in semistructured interviews that the interactive nature of this activity made it an engaging introduction to molecular cloning. [ABSTRACT FROM AUTHOR]

Bioreporter systems based on detectable enzyme activity, such as that of beta-galactosidase or luciferase, are key in novel bacterial promoter discovery and study. While these systems permit quantification of gene expression, their use is limited by the toxicity of the expressed reporter enzymes in a given host. Indeed, the most potent promoters may be overlooked if their activity causes a lethal overproduction of the reporter genes when screening for transcriptional activity of potential promoter sequences with the luxCDABE cassette. To overcome this limitation, a variation of the mini-CTX- lux plasmid has been designed which allows reduction of promoter activity via the addition of an adjacent fluoride riboswitch. The riboswitch adds a layer of regulation between the promoter and the reporter gene, allowing cloning of stronger promoters by weakening expression, while giving the potential to induce with fluoride to provide a good signal for weaker promoters, thus circumventing limitations associated with reporter toxicity. We noticed the riboswitch potential portability issues between species, suggesting caution when using riboswitches non-native to the species where it is being used. This study introduces a new molecular biology tool which will allow for the identification of previously unverifiable or uncharacterized potent promoters and also provides a cloning vector for translational fusion with luciferase in a plasmid compatible with many species such as from the genera Burkholderia and Pseudomonas. [ABSTRACT FROM AUTHOR]

There is increased interest in strain engineering in the food and industrial yeast Kluyveromyces marxianus and a number of CRISPR/Cas9 systems have been described and used by different groups. The methods that we developed allow for very rapid and efficient inactivation of target genes using the endogenous DNA repair mechanisms of the cell. The strains and plasmids that we use are freely available, and here we provide a set of integrated protocols to easily inactivate genes and to precisely integrate DNA fragments into the genome, for example for promoter replacement, allelic swaps or introduction of point mutations. The protocols use the Cas9/gRNA expression plasmid pUCC001 and Golden Gate assembly for molecular cloning of targeting sequences. A genome-wide set of target sequences is provided. Using these plasmids in wild-type strains or in strains lacking non-homologous end-joining (NHEJ) DNA repair, the first set of protocols explain how to introduce indels (NHEJ-mediated) or precise deletions (homology-dependent repair (HDR)-mediated) at precise targets. The second set of protocols describe how to swap a promoter or coding sequence to yield a reprogrammed gene. The methods do not require the use of dominant or auxotrophic marker genes and thus the strains generated are marker-free. The protocols have been tested in multiple K. marxianus strains, are straightforward and can be carried out in any molecular biology laboratory without specialized equipment. [ABSTRACT FROM AUTHOR]

Background: The advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology marked the beginning of a new era in the field of molecular biology, allowing the efficient and precise creation of targeted mutations in the genome of every living cell. Since its discovery, different gene editing approaches based on the CRISPR/Cas9 technology have been widely established in mammalian cell lines, while limited knowledge is available on genetic manipulation in fish cell lines. In this work, we developed a strategy to CRISPR/Cas9 gene edit rainbow trout (Oncorhynchus mykiss) cell lines and to generate single cell clone-derived knock-out cell lines, focusing on the phase I biotransformation enzyme encoding gene, cyp1a1, and on the intestinal cell line, RTgutGC, as example. Results: Ribonucleoprotein (RNP) complexes, consisting of the Cas9 protein and a fluorescently labeled crRNA/tracrRNA duplex targeting the cyp1a1 gene, were delivered via electroporation. A T7 endonuclease I (T7EI) assay was performed on flow cytometry enriched transfected cells in order to detect CRISPR-mediated targeted mutations in the cyp1a1 locus, revealing an overall gene editing efficiency of 39%. Sanger sequencing coupled with bioinformatic analysis led to the detection of multiple insertions and deletions of variable lengths in the cyp1a1 region directed by CRISPR/Cas9 machinery. Clonal isolation based on the use of cloning cylinders was applied, allowing to overcome the genetic heterogeneity created by the CRISPR/Cas9 gene editing. Using this method, two monoclonal CRISPR edited rainbow trout cell lines were established for the first time. Sequencing analysis of the mutant clones confirmed the disruption of the cyp1a1 gene open reading frame through the insertion of 101 or 1 base pair, respectively. Conclusions: The designed RNP-based CRISPR/Cas9 approach, starting from overcoming limitations of transfection to achieving a clonal cell line, sets the stage for exploiting permanent gene editing in rainbow trout, and potentially other fish cells, for unprecedented exploration of gene function. [ABSTRACT FROM AUTHOR]

【Objective】The purpose of this study was to obtain a method for extracting high-quality total RNA from the leaves of Paphiopedilum species, which laid a foundation for further molecular biology research.【Method】Four methods were used to extract total RNA from the leaves of three Paphiopedilum species(P.purpuratum, P.dianthum and P.armeniacum).The purity, concentration and integrity of the leaf total RNA of Paphiopediodilum were determined by spectrophotometer and agarose gel electrophoresis.The optimal method was screened and further verified by RT-PCR.【Result】The results showed that the leaf total RNA of Paphiopedilum species extracted by OminiPlant RNA kit method had good purity but general integrity.The leaf total RNA of Paphiopedilum species extracted by modified CTAB method had good purity and integrity, but the extraction efficiency was not high.Although the leaf total RNA of Paphiopedilum species extracted by modified Trizol method(Ⅰ) had good integrity, the purity was very poor, and there were pollutions such as polysaccharides and protein impurities.The fact was that the leaf total RNA of Paphiopedilum species extracted by modified Trizol method(Ⅱ) was intact without degradation, had higher purity and higher yield.The target 252 bp sequences of rbcL gene were cloned by RT-PCR using the leaf total RNA of Paphiopedilum species extracted by modified Trizol method(Ⅱ) as template.【Conclusion】After comprehensive comparison of the above four methods, the modified Trizol method(Ⅱ) in this study was an effective method for high quality total RNA extraction from the leaves of three Paphiopedilum species of P.purpuratum, P.dianthum and P.armeniacum. [ABSTRACT FROM AUTHOR]

Background: The ability to clone DNA sequences quickly and precisely into plasmids is essential for molecular biology studies. The recent development of seamless cloning technologies has made significant improvements in plasmid construction, but simple and reliable tools are always desirable for time- and labor-saving purposes. Results: We developed and standardized a plasmid cloning protocol based on a universal MCS (Multiple Cloning Site) design and bacterial in vivo assembly. With this method, the vector is linearized first by PCR (Polymerase Chain Reaction) or restriction digestion. Then a small amount (10 ~ 20 ng) of this linear vector can be mixed with a PCR-amplified insert (5× molar ratio against vector) and transformed directly into competent E. coli cells to obtain the desired clones through in vivo assembly. Since we used a 36-bp universal MCS as the homologous linker, any PCR-amplified insert with ~ 15 bp compatible termini can be cloned into the vector with high fidelity and efficiency. Thus, the need for redesigning insert-amplifying primers according to various vector sequences and the following PCR procedures was eliminated. Conclusions: Our protocol significantly reduced hands-on time for preparing transformation reactions, had excellent reliability, and was confirmed to be a rapid and versatile plasmid cloning technique. The protocol contains mostly mixing steps, making it an extremely automation-friendly and promising tool in modern biology studies. [ABSTRACT FROM AUTHOR]

The rapid development of molecular biotechnology presents a curricular challenge for educators trying to provide students with relevant coursework. A comprehensive biology education should also include opportunities for students to develop intellectual and technical skills through authentic research experiences. Integrating relevant and interesting research projects into their classes, however, can be a challenging task for instructors. To address these varied demands, we redesigned our existing molecular cloning course to incorporate an independent research project assessing calcium signaling. In the revised course, students use traditional and recombination‐based cloning strategies to generate bacterial and mammalian expression vectors encoding CaMPARI, a novel fluorescent calcium indicator. Bacterially‐expressed CaMPARI is used in protein quantification and purification assays. Students must also design their own research project evaluating the effect of chemotherapeutic agents on calcium signaling in a mammalian system. Revised and novel labs were designed to be modular, facilitating their integration into the course over 2 years. End‐of‐semester student evaluations were compared between years revealing a significant difference in students' perception of the course's difficulty between years. This change in attitude highlights potential pedagogical considerations that must be examined when introducing new material and activities into existing courses. Since calcium signaling is important for cellular process across diverse species, instructors may be able to develop research projects within their respective areas of interest. Integration of authentic research experiences into the curriculum is challenging; however, the framework described here provides a versatile structure that can be adapted to merge diverse instructor interests with evolving educational needs. [ABSTRACT FROM AUTHOR]

Background: Polyploid organisms such as wheat complicate even the simplest of procedures in molecular biology. Whilst knowledge of genomic sequences in crops is increasing rapidly, the scientific community is still a long way from producing a full pan-genome for every species. Polymerase chain reaction and Sanger sequencing therefore remain widely used as methods for characterizing gene sequences in many varieties of crops. High sequence similarity between genomes in polyploids means that if primers are not homeologue-specific via the incorporation of a SNP at the 3' tail, sequences other than the target sequence will also be amplified. Current consensus for gene cloning in wheat is to manually perform many steps in a long bioinformatics pipeline. Results: Here we present AutoCloner (www.autocloner.com), a fully automated pipeline for crop gene cloning that includes a free-to-use web interface for users. AutoCloner takes a sequence of interest from the user and performs a basic local alignment search tool (BLAST) search against the genome assembly for their particular polyploid crop. Homologous sequences are then compiled with the input sequence into a multiple sequence alignment which is mined for single-nucleotide polymorphisms (SNPs). Various combinations of potential primers that cover the entire gene of interest are then created and evaluated by Primer3; the set of primers with the highest score, as well as all possible primers at every SNP location, are then returned to the user for polymerase chain reaction (PCR). We have successfully used AutoCloner to clone various genes of interest in the Apogee wheat variety, which has no current genome sequence. In addition, we have successfully run the pipeline on ~ 80,000 high-confidence gene models from a wheat genome assembly. Conclusion: AutoCloner is the first tool to fully-automate primer design for gene cloning in polyploids, where previously the consensus within the wheat community was to perform this process manually. The web interface for AutoCloner provides a simple and effective polyploid primer-design method for gene cloning, with no need for researchers to download software or input any other details other than their sequence of interest. [ABSTRACT FROM AUTHOR]

Molecular biologists exploit information conveyed by mechanistic models for experimental purposes. In this article, I make sense of this aspect of biological practice by developing Keller's idea of the distinction between 'models of' and 'models for'. 'Models of (phenomena)' should be understood as models representing phenomena and are valuable if they explain phenomena. 'Models for (manipulating phenomena)' are new types of material manipulations and are important not because of their explanatory force, but because of the interventionist strategies they afford. This is a distinction between aspects of the same model. In molecular biology, models may be treated either as 'models of' or as 'models for'. By analysing the discovery and characterization of restriction–modification systems and their exploitation for DNA cloning and mapping, I identify the differences between treating a model as a 'model of' or as a 'model for'. These lie in the cognitive disposition of the modeller towards the model: a modeller will look at a model as a 'model of' if interested in its explanatory force, or as a 'model for' if interested in the material manipulations it can possibly afford. 1 Introduction 2 'Models of' and 'Models for' in Molecular Biology 2.1 'Models of' in molecular biology 2.2 'Models for': The case of CRISPR–Cas9 2.3 Importance of 'models for' 2.4 'Models for' and philosophy of experimentation in biology 3 'Models for' and the Discovery of Restriction–Modification Systems 3.1 A tale of three Nobel Laureates 3.2 Restriction–modification system model as a 'model of' and a 'model for' 4 Epistemic Disposition and Disposition towards Affordances 4.1 Two cognitive dispositions towards models 4.2 Intentions in philosophy of science and studies of scientific cognition 5 Virtues of 'Models for' 5.1 'Models for', target systems and portability 5.2 How-possibly models and schemas 6 Conclusion [ABSTRACT FROM AUTHOR]

Summary: The foundation of haemophilia A therapy in the last 35 years has been critically dependent on isolation of the Factor VIII (FVIII) protein and discovery of the cDNA sequence of the FVIII gene, published in 1984. Identification of the FVIII sequence resulted in a new era of recombinant concentrates and led to significant improvements in safety, set against the tragedy of widespread HIV and hepatitis infections in haemophilia patients from contaminated plasma‐based products. We chronicle the scientific methods and race leading up to the publication of the FVIII DNA sequence and the legacy that follows through to revolutionary gene therapy treatment in clinical trials today. [ABSTRACT FROM AUTHOR]

Cloning and expression of a desired gene is indispensable in molecular biology studies. Expression vectors, in this regard, should offer much needed flexibility and choice of cloning strategies for both in vivo and in vitro protein expression experiments. Furthermore, availability of option to choose from various reporter tags allows one to be flexible during designing of an experiment in a more relevant manner. Thus, the need of a versatile expression system cannot be ignored. Although several different expression vectors are available for gene expression in mycobacteria, they lack the required versatility of expression and the inclusion of reporter tags. We here present the construction of a set of nine E. coli-Mycobacterium shuttle plasmids, which offer a combination of three mycobacterial promoter systems (heat shock inducible-hsp60, tetracycline-, and acetamide-inducible) along with three polypeptide tags (Green Fluorescent Protein (GFP), Glutathione S-transferase (GST) and hexa-histidine tag). These vectors offer the cloning of a target gene in all the nine given vectors in parallel, thus allowing the generation of recombinant plasmids that will express the target gene from different promoters with different tags. Here, while the hexa-histidine and GST tags can be used for protein purification and pull-down experiments, the GFP-tag can be used for protein localization within the cell. Additionally, the vectors also offer the choice of positioning of the reporter tag either at the N-terminus or at the C-terminus of the expressed protein, which is achieved by cloning of the gene at any of the two blunt-end restriction enzyme sites available in the vector. We believe that these plasmids will be extremely useful in the gene expression studies in mycobacteria by offering the choices of promoters and reporters. Our work also paves the way to developing more such plasmids with other tags and promoters that may find use in mycobacterial biology. [ABSTRACT FROM AUTHOR]

Polymerase chain reaction (PCR)-based technology for clinical HLA typing involves DNA Sanger sequencing of the PCR amplified products of polymorphic loci of HLA, such as HLA-A, -B, -C, -DPB1,- DQB1, and -DRB1, in support of unrelated donor hematopoietic stem cell transplantation. The TA cloning of all the amplicons, followed by Sanger sequencing, provides a primary screening tool of potential organ donors, or to identify individuals who might have potential adverse drug responses. The Class I exon 2 and 3 genes of HLA was amplified as a single fragment and cloned into a TA cloning vector pTZ57R/T, while the Class II exon 2 and 3 amplified fragments were added together in a ligation mix with the vector pTZ57R/T. Positive clones were subjected to Sanger sequencing, and HLA alleles determined using the IMGT database. Results indicate that all the exons of the HLA genes by could be cloned by the strategies described. Furthermore, we were also successful in achieving the amplification of all the desired amplicons as a multiplex PCR, thereby reducing the cost of the modified method further by almost 60%. We present a cost-effective TA cloning strategy for achieving accurate allele typing of HLA at 2- digit resolution. Taken together, an efficient cloning methodology with a significant lower cost for accurate HLA typing presented here is encouraging. The data suggests that it may be employed for routine cloning of variable targets in molecular biology applications. [ABSTRACT FROM AUTHOR]

Introduction: DNA Polymerases, in addition to being indispensable in replication and repair, are also very useful in a number of molecular biology techniques such as DNA amplification, site-directed mutagenesis, DNA sequencing, different kinds of PCR, loopmediated isothermal amplification (LAMP), etc. After the invention of PCR, efforts have been made to focus on the identification and isolation of thermo-tolerant enzymes that amplify DNA efficiently at high temperatures. Materials and methods: In this study, Geobacillus stearothermophilus strain 10 was selected for the cloning of Bst DNA Pol I - encoding gene. Following DNA extraction from the bacterium, PCR was carried out to amplify the pol A gene using designed primers and to clone via pET32a expression vector followed by transfer to the heterologous E.coli BL21 host. The cloned gene was expressed by induction with IPTG and the resultant protein purified by IMAC column. Results: The activity of the functional fragment was assessed by LAMP and showing a relatively high DNA amplification ability in comparison with commercial Bst DNA Polymerase which is usually used in this amplification protocol. Discussion and conclusion: This study found that Klenow fragment of recombinant Bst DNA Pol I can amplify uidA gene in E. coli ATCC25923 during the LAMP reaction. Separation of two fragments of the enzyme can improve the activity of Klenow fragment of enzyme in LAMP. [ABSTRACT FROM AUTHOR]

Locusta migratoria is one of the global destructive migratory agricultural pests. The species serves as a model insect for the study of morphology, physiology, developmental biology, and neurosciences and so on. In recent years, there has been growing interest in the research of the cell and molecular biology of L. migratoria, and a lot of genes of signalling pathways have been cloned. The Hedgehog (Hh) signalling pathway is essential for cellular proliferation and differentiation during embryonic development. Fused (Fu) is a conserved component of the Hh signalling pathway, and it plays a central role in embryonic development. The Fu gene was cloned from the grasshopper L. migratoria. The gene encodes a 717 amino acid protein. Then, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect the expression pattern of the Lm-Fu gene at different development stages and tissues. The result showed that the gene was upregulated at the embryonic period and second instar, and the expression level was the highest in the head at the different tissues. Western blotting was used to assess the abundance of the Lm-Fu protein, which was expressed at different development stages. The embryogenesis of L. migratoria was examined by immunohistochemical staining, and the Lm-Fu protein was detected in the head, prothorax and legs. The results showed that the Lm-Fu gene plays an important role during embryonic development. [ABSTRACT FROM AUTHOR]

Molecular cloning is a cornerstone of biomedical, biotechnological, and synthetic biology research. As such, improved cloning methodologies can significantly advance the speed and cost of research projects. Whereas current popular cloning approaches use in vitro assembly of DNA fragments, in vivo cloning offers potential for greater simplification. It is generally assumed that bacterial in vivo cloning requires Escherichia coli strains with enhanced recombination ability; however, this is incorrect. A widely present, bacterial RecA-independent recombination pathway is re-emerging as a powerful tool for molecular cloning and DNA assembly. This poorly understood pathway offers optimal cloning properties (i.e. seamless, directional, and sequence-independent) without requiring in vitro DNAassembly or specialized bacteria, therefore vastly simplifying cloning procedures. Although the use of this pathway to performDNAassembly was first reported over 25 years ago, it failed to gain popularity, possibly due to both technical and circumstantial reasons. Technical limitations have now been overcome, and recent reports have demonstrated its versatility for DNA manipulation. Here, we summarize the historical trajectory of this approach and collate recent reports to provide a roadmap for its optimal use. Given the simplified protocols and minimal requirements, cloning using in vivo DNA assembly in E. coli has the potential to become widely employed across the molecular biology community. [ABSTRACT FROM AUTHOR]

Undergraduate research experiences are excellent opportunities to engage students in science alongside experienced scientists, but at large institutions, it is challenging to accommodate all students. To address and engage a larger number of students, we developed a modular laboratory course based on the course‐based undergraduate research experiences model. This new course was integrated with the scientific aims of a research laboratory studying the cellular and molecular mechanisms underlying tissue regeneration in planarians. In this course, students were asked to identify genes with roles in planarian biology. Students analyzed and cloned an assigned gene, determined its expression pattern in situ and examined its function in regeneration. Additionally, we developed critical thinking and scientific communication skills by incorporating activities focused on critical concepts. Students obtained high quality primary data and were successful in completing and mastering the course learning outcomes. They benefitted by developing basic research skills, learning to perform, trouble‐shooting experiments, reading and critically analyzing primary literature, and using the information to defend and explain their experimental results. Through this course, students also increased their confidence and ability to perform independent scientific research. The course was designed to make it accessible to the community to implement and adapt as appropriate in diverse institutions. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):547–559, 2019. [ABSTRACT FROM AUTHOR]

Knock-in (KI) gene targeting can be employed for a wide range of applications in stem cell research. However, vectors for KI require multiple complicated processes for construction, including multiple times of digestion/ligation steps and extensive restriction mapping, which has imposed limitations for the robust applicability of KI gene targeting. To circumvent this issue, here we introduce versatile and systematic methods for generating KI vectors by molecular cloning. In this approach, we employed the Multisite Gateway technology, an efficient in vitro DNA recombination system using proprietary sequences and enzymes. KI vector construction exploiting these methods requires only efficient steps, such as PCR and recombination, enabling robust KI gene targeting. We show that combinatorial usage of the KI vectors generated using this method and site-specific nucleases enabled the precise integration of fluorescent protein genes in multiple loci of human and common marmoset (marmoset; Callithrix jacchus) pluripotent stem cells. The methods described here will facilitate the usage of KI technology and ultimately help to accelerate stem cell research. [ABSTRACT FROM AUTHOR]

Circadian clock genes holds tremendous potential for breeding crops better adapted to environmental fluctuations inherent to climate change. Endogenous TOC1 promoter and CCA1 gene from rice were isolated, cloned and mobilized into pCAMBIA1300 vectors and RNAi constructs A, B and C. Embryogenic calli of varying ages derived from mature seeds of Taipei 309 were employed for Agrobacterium-mediated genetic transformation generating T0, T1 and T2 independent transgenic lines were analyzed for over-expression and repression of CCA1 gene along with various morphological traits. Six hundred and thirty two T0 transgenic plants were generated from rice calli using constructs A, B and C. T0 progeny plants derived from constructs A, B and C did not show any considerable difference in morphological traits. T1and T2 progeny plants derived from construct A exhibited over-expression of CCA1 gene, on the contrary, progeny plants derived from RNAi constructs B and C exhibited repression of CCA1 gene in qRT-PCR analysis at different time points and showed rhythmicity peaking at dawn (6:00 AM) and lowest expression at 12:00 Noon. T1 and T2 progeny plants derived from construct A, namely, A-17 and A-45 exhibited reduced number of tillers/panicles (6–8), reduced thousand seed weight (10.1–16.6g), decreased seed length (4.98 to 6.58mm), decreased seed width (1.1–1.8mm) as compared to wild type plants. T1 and T2 progeny plants of construct B and C showed increased number of tillers/panicles (8–19), better seed yield (4.98–28.9g), increased thousand seed weight (15.6–29.03g), slightly increased seed length (5.7–7.43mm) and slightly increased seed width (1.7–2.98mm) as compared to wild type plants. Chlorophyll content in T1 and T2 progeny plants did not show any significant difference among the three constructs, however, rhythmicity was observed over the period of time in conjunction to CCA1 gene expression. Evidence has been presented which demonstrates that endogenous repression of CCA1 gene resulted in improved morphological traits: increased number of tillers/panicle, thousand seed weight, seed size; whereas, over-expression leads to diminution in morphological traits: decreased number of tillers/panicle, thousand seed weight, seed size as compared to the wild type in T1 and T2 progeny plants. This is first report of successful regulation of endogenous CCA1 gene under control of TOC1 promoter and its effect on improved growth vigor in Japonica rice. [ABSTRACT FROM AUTHOR]

Anti-α4β7 therapy with vedolizumab (VDZ) has been suggested as possible immune intervention in HIV. Relatively little is known about the α4β7-integrin (α4β7) expression of different T-cell subsets in different anatomical compartments of healthy individuals, patients with HIV or inflammatory bowel disease (IBD). Surface expression of α4β7 as well as the frequency of activation, homing and exhaustion markers of T cells were assessed by multicolour flow cytometry in healthy volunteers (n = 15) compared to HIV infected patients (n = 52) or patients diagnosed with ulcerative colitis (UC) (n = 14), 6 of whom treated with vedolizumab. In addition, lymph nodal cells (n = 6), gut-derived cells of healthy volunteers (n = 5) and patients with UC (n = 6) were analysed. Additionally, we studied longitudinal PBMC samples of an HIV patient who was treated with vedolizumab for concomitant UC. Overall, only minor variations of the frequency of α4β7 on total CD4+ T cells were detectable regardless of the disease status or (VDZ) treatment status in peripheral blood and the studied tissues. Peripheral α4β7+ CD4+ T cells of healthy individuals and patients with UC showed a higher activation status and were more frequently CCR5+ than their α4β7- counterparts. Also, the frequency of α4β7+ cells was significantly lower in peripheral blood CD4+ effector memory T cells of HIV-infected compared to healthy individuals and this reduced frequency did not recover in HIV patients on ART. Conversely, the frequency of peripheral blood naïve α4β7+ CD4+ T cells was significantly reduced under VDZ treatment. The results of the current study will contribute to the understanding of the dynamics of α4β7 expression pattern on T cells in HIV and UC and will be useful for future studies investigating VDZ as possible HIV cure strategy. [ABSTRACT FROM AUTHOR]

Introduction: HIV misdiagnosis leads to severe individual and public health consequences. Retesting for verification of all HIV-positive cases prior to antiretroviral therapy initiation can reduce HIV misdiagnosis, yet this practice has not been not widely implemented. Methods: We evaluated and compared the cost of retesting for verification of HIV seropositivity (retesting) to the cost of antiretroviral treatment (ART) for misdiagnosed cases in the absence of retesting (no retesting), from the perspective of the health care system. We estimated the number of misdiagnosed cases based on a review of misdiagnosis rates, and the number of positives persons needing ART initiation by 2020. We presented the total and per person costs of retesting as compared to no retesting, over a ten-year horizon, across 50 countries in Africa grouped by income level. We conducted univariate sensitivity analysis on all model input parameters, and threshold analysis to evaluate the parameter values where the total costs of retesting and the costs no retesting are equivalent. Cost data were adjusted to 2017 United States Dollars. Results and discussion: The estimated number of misdiagnoses, in the absence of retesting was 156,117, 52,720 and 29,884 for lower-income countries (LICs), lower-middle income countries (LMICs), and upper middle-income countries (UMICs), respectively, totaling 240,463 for Africa. Under the retesting scenario, costs per person initially diagnosed were: $40, $21, and $42, for LICs, LMICs, and UMICs, respectively. When retesting for verification is implemented, the savings in unnecessary ART were $125, $43, and $75 per person initially diagnosed, for LICs, LMICs, and UMICs, respectively. Over the ten-year horizon, the total costs under the retesting scenario, over all country income levels, was $475 million, and was $1.192 billion under the no retesting scenario, representing total estimated savings of $717 million in HIV treatment costs averted. Conclusions: Results show that to reduce HIV misdiagnosis, countries in Africa should implement the WHO’s recommendation of retesting for verification prior to ART initiation, as part of a comprehensive quality assurance program for HIV testing services. [ABSTRACT FROM AUTHOR]

Background: The Joint United Nations Programme on HIV/AIDS (UNAIDS) Fast-Track initiative seeks to eliminate AIDS as a health threat by 2030, with its focus on UNAIDS 90-90-90 targets. Effective policies and programs, if scaled nationally, have the potential to generate a greater impact on HIV control, yet a synthesis of successful HIV policies/programs aligned to the targets is currently unavailable. To fill this gap, we conducted a systematic review to evaluate successful HIV policies and programs to direct future interventions. Methods: For the period 2007–2018, we searched 8 databases and classified eligible studies by country income level, UNAIDS targets, intervention type, and reported outcomes. Study outcomes were classified as per UNAIDS targets; proportionally: 90% target 1, 81% target 2, and 73% target 3. Results: We retrieved 5201 citations and a final set of eight studies on policies. Break up by income: three (38%) from high income, one (12%) from middle income and four (50%) from low income. Break up by outcomes reported: 36% (4/11) focused on HIV testing, 46% (5/11) on antiretroviral therapy initiation, and 18% (2/11) on viral suppression. Across studies, UNAIDS targets were met in high-income countries, where policies and guidelines were adhered to, whereas in low and middle-income countries, non-adherence led to failure to reach the targets. Targets were also met when country infrastructure supported a targeted program and stakeholders were actively engaged. Conclusions: From the studies identified, we deduced a clear, positive correlation between implementation of policies and programs that resulted in an increase in patient awareness and an increase in partner notification with services that encouraged them, and together these resulted in increasing testing rates, and deployment of linkage/retention programs that improved retention in care. An analysis of these studies also suggests that policies, combined with the scale-up incentives, are needed to change the status quo. Incentives to improve the targets must exist; performance incentives at the health care worker level and country level incentives that could transform the nature of care. Given the complexity in reporting of targets, a one size fits all model is not a feasible option. However, the policies created a strong framework to shape future interventions. [ABSTRACT FROM AUTHOR]

There is still no safe and effective vaccine against dengue virus infection. Epidemics of dengue virus infection are increasingly a threat to human health around the world. Antibodies generated in response to dengue infection have been shown to impact disease development and effectiveness of dengue vaccine. In this study, we investigated monoclonal antibody responses to an experimental dengue vaccine in rhesus macaques. Variable regions of both heavy chain (VH) and light chain (VL) were cloned from single antibody-secreting B cells. A total of 780 monoclonal antibodies (mAbs) composed of paired VH and VL were characterized. Results show that the vaccination induces mAbs with diverse germline sequences and a wide range of binding affinities. Six potent neutralizing mAbs were identified among 130 dengue envelope protein binders. Critical amino acids for each neutralizing antibody binding to the dengue envelope protein were identified by alanine scanning of mutant libraries. Diverse epitopes were identified, including epitopes on the lateral ridge of DIII, the I-III hinge, the bc loop adjacent to the fusion loop of DII, and the β-strands and loops of DI. Significantly, one of the neutralizing mAbs has a previously unknown epitope in DII at the interface of the envelope and membrane protein and is capable of neutralizing all four dengue serotypes. Taken together, the results of this study not only provide preclinical validation for the tested experimental vaccine, but also shed light on a potential application of the rhesus macaque model for better dengue vaccine evaluation and design of vaccines and immunization strategies. [ABSTRACT FROM AUTHOR]