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Acute myeloid leukemia (AML) represents a heterogeneous disease entity that is continuously moving to a more genetically defined classification. The classification of AML with recurrent chromosomal translocations, including those involving core binding factor subunits, plays a critical role in diagnosis, prognosis, treatment stratification, and residual disease evaluation. Accurate classification of variant cytogenetic rearrangements in AML contributes to effective clinical management. We report here the identification of four variant t(8;V;21) translocations in newly diagnosed AML patients. Two patients showed a t(8;14) and a t(8;10) variation, respectively, with a morphologically normal-appearing chromosome 21 in each initial karyotype. Subsequent fluorescence in situ hybridization (FISH) on metaphase cells revealed cryptic three-way translocations t(8;14;21) and t(8;10;21). Each resulted in RUNX1 :: RUNX1T1 fusion. The other two patients showed karyotypically visible three-way translocations t(8;16;21) and t(8;20;21), respectively. Each resulted in RUNX1 :: RUNX1T1 fusion. Our findings demonstrate the importance of recognizing variant forms of t(8;21) translocations and emphasize the value of applying RUNX1 :: RUNX1T1 FISH for the detection of cryptic and complex rearrangements when abnormalities involving chromosome band 8q22 are observed in patients with AML.

Pneumoconiosis is associated with coal dust particles depositing within the lung causing nodules coalesce to form progressive massive fibrosis (PMF). Cavitary lesions can develop in these PMF areas for concerns of tuberculosis and aspergillosis. We present a 59-year-old patient who had coal workers pneumoconiosis and PMF presenting with chronic dyspnea and hemoptysis with an upper cavitary lesion noted on chest imaging. He notes dyspnea with walking very short distances with associated productive cough. He admits to occasional wheezing, paroxysmal dyspnea, hemoptysis, and orthopnea but denies chest pain. He is an everyday smoker. His physical examination was only remarkable for bronchial breath sounds. On review of his prior imaging, he had a right upper lobe infiltrate as far back as 2012. As the years progressed, a new cavitary lesion developed in the PMF area which progressively got larger with a thick wall and no eccentric region noted inside the cavity. Tuberculosis test was negative. He underwent a transbronchial biopsy with methenamine silver stain which showed acute angle branching and septation suggestive of Aspergillus species. He was diagnosed with pulmonary aspergillosis and treated with voriconazole for 1 year. With pneumoconiosis and evidence confirming aspergillosis, the presence of a new lung infiltration with progression into a cavitary lesion leads to a diagnosis of chronic cavitary pulmonary aspergillosis (CCPA). With follow-up imaging showing extensive lung fibrosis, he had chronic fibrosing pulmonary aspergillosis (CFPA), a late-stage manifestation of CCPA.

We present the case of a 56-year-old woman who was diagnosed with severe coronavirus disease 2019 (COVID-19) pneumonia complicated by severe acute respiratory distress syndrome who was intubated for 19 days. She recovered from COVID-19 after a month. A computed tomography (CT) scan of the chest, after a month, showed improved infiltrates with a small residual cavity within the lingula. A CT angiogram showed a more confluent density in the lingular portion on follow-up 2 months later. She developed intermittent hemoptysis after 3 months in December 2020, which persisted for almost 6 months, and CT of the chest showed the lingular nodular with resolution of the cavitation. She underwent bronchoscopy with bronchoalveolar lavage, confirming Aspergillus fumigatus by galactomannan assay and histology showing branching hyphae. Once she started treatment with itraconazole, her hemoptysis resolved. The follow-up CT of the chest after 2 months of treatment did not show a cavity or a nodule in the lingula. Our patient developed invasive pulmonary aspergillosis (IPA) as a sequela of severe COVID-19 infection. COVID-19-associated invasive pulmonary aspergillosis (CAPA) is an underrecognized complication that needs to be investigated on whether prophylactic treatment is required. Our case also demonstrates that the diagnosis of IPA needs to be considered months after COVID-19 infection when a superimposed fungal infection can occur after a viral infection if the patient continues to have persistent symptoms.

Current guidance in the UK for fertility services on the screening for sexually transmitted infections (STI) is solely directed towards Chlamydia trachomatis . Evidence used to formulate the guidance is based on research undertaken before more sensitive diagnostic methods were available and before testing of some organisms was even possible. This commentary outlines current STI trends, evidence available for STI effect on fertility and new diagnostic methods of screening. It aims to demonstrate that UK guidance should be updated and directed towards areas where further research is required.

Green gram, rich in dietary fiber is known to enhance the function of immune system. However information pertaining to the immunomodulatory potential of its non starch polysaccharides (NSPs) is scanty. Hence, five different NSPs were extracted successively using water (WSP), hot water (55 o C, HWSP), EDTA (0.5%, Pectins) and alkali (10%, Hemicellulose A and B) which varied in their arabinose to galactose ratio, sugar, protein, uronic acid contents, molecular weight distribution and immunomodulatory activity. Hemicellulose B was relatively rich in carbohydrate content (~95%) and also possessed potent immunomodulatory activity among the various NSPs. Hemicellulose B was further fractionated on DEAE-cellulose column into six different fractions by eluting step-wise with water, ammonium carbonate (0.1, 0.2, 0.3 M AC) and sodium hydroxide (0.1 and 0.2 M NaOH). 0.1 M AC eluted fraction was found to be the major one amounting to ~ 50% yield and showed relatively significant (p < 0.001) activity towards splenocyte proliferation and macrophage activation as compared with rest of the DEAE eluted fractions., (Copyright © 2018. Published by Elsevier Ltd.)

Resistant starch is not digestible in the small intestine and is fermented by lactic acid bacteria in the large intestine into short chain fatty acids, such as acetate, propionate and butyrate, which result in several health benefits in analogy with dietary fibre components. The mode and mechanism of resistant starch degradation by lactic acid bacteria is still not understood. In the present study, we have purified α-D-glucosidase from Lactobacillus fermentum NCDC 156 by employing three sequential steps i.e. ultra filtration, DEAE-cellulose and Sephadex G-100 chromatographies. It was found to be a monomeric protein (~50 kDa). The optimum pH and temperature of this enzyme were found to be 5.5 and 37°C, respectively. Under optimised conditions with p-nitrophenyl-D-glucopyranoside as the substrate, the enzyme exhibited a K m of 0.97 mM. Its activity was inhibited by Hg 2+ and oxalic acid. N-terminal blocked purified enzyme was subjected to lysyl endopeptidase digestion and the resultant peptides were subjected to BLAST analysis to understand their homology with other α-D-glucosidases from lactobacillus species.

Wheat bran water unextractable portion (WB-WUP) was subjected to xylanase treatment to obtain a mixture of xylo-oligosaccharides (XOS). XOS mixture was purified on charcoal-celite column and the individual oligosaccharides were separated on a Bio-Gel P-2 column. The sugar composition of the purified oligosaccharides was determined by GLC and their structure was deduced by ESI-MS and (1)H and (13)C NMR. The major oligosaccharides identified were xylobiose and xylotriose (consisting of arabinose). Five strains of lactobacilli (probiotics), XOS (prebiotics) and a combination of both (synbiotics) in milk (as medium) were monitored for antioxidant activity. DPPH radical scavenging activity (~70 %) as well as ferric reducing power (~80 mg/100 ml FeSO4eq) were significantly higher (p < 0.05) in all the synbiotic preparations compared to that of control. The present study indicated that the synbiotic preparations consisting of XOS and lactobacilli can be effectively used as dietary supplement.

In the recent years there has been a growing interest in the use of oligosaccharides as prebiotics to modulate gut microbiota with an aim to improve the gut health. Though xylo-oligosaccharides (XOS) have been increasingly used as prebiotics, information pertaining to the enzymes used by lactobacilli to degrade these substrates is scanty. Present investigation reports the purification and characterization of β-D-xylosidase from Lactobacillus brevis NCDC01 grown on XOS. Three sequential steps consisting of ultra-filtration, DEAE cellulose ion-exchange and Sephacryl S-100 gel filtration chromatographies were employed to purify the enzyme to apparent homogeneity and it was found to be monomeric on SDS-PAGE with an apparent molecular mass of ~58.0 kDa. The pH and temperature optima were 6.0 and 40 °C respectively. The enzyme remained stable over a pH range of 5.5-7.5 and up to 50 °C for 30 min. Under optimum pH and temperature with p-nitrophenyl β-D-xylopyranoside as a substrate, the enzyme exhibited a K(m) of 0.87 mM. The enzyme does not require any metal ion for activity or stability but is completely inhibited by Hg(2+), Pb(2+), p-chloromercuribenzoate (PCMB), oxalic acid and citric acid. This is perhaps the first report on the purification and characterization of β-D-xylosidase from Lactobacillus brevis NCDC01., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

The role of prebiotics in improving human health has attracted global attention and the research is mostly focused on the strains belonging to the genera Bifidobacterium and Lactobacillus. Non-digestible oligosaccharides hold significant role in recent research due to their prebiotic nature. Soluble polysaccharides (SP, 14.4%), isolated from ragi bran consisted mainly of arabinose and xylose with minor quantities of rhamnose, mannose, galactose and glucose. Ragi bran SP subjected to purified endoxylanase (from 96 h ragi malt) treatment to obtain xylo-oligosaccharides which were further purified on Biogel P-2 followed by HPLC. The purified oligosaccharide yielded (RO-1; 17.9%) was identified as xylobiose by electrospray ionization mass spectrometry (282 + 23 = 305) and (1)HNMR. In vitro studies carried out using Bifidobacterium and Lactobacillus sp. proved the prebiotic nature of the crude xylo-oligosaccharides (XOs) and RO-1. Acetate was found to be the chief short chain fatty acid released during fermentation of both crude XOs and purified xylobiose and 24 h bacterial culture showed high xylanase activity (1020-1690 μU min(-1)).

Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and quantitative PCR to allow for a robust determination of the level of nearly any cellular RNA in the background of ~5,500 different mutants. As an initial test of this approach, we sought to identify the full complement of factors that impact pre-mRNA splicing. Increasing lines of evidence suggest a relationship between pre-mRNA splicing and other cellular pathways including chromatin remodeling, transcription, and 3' end processing, yet in many cases the specific proteins responsible for functionally connecting these pathways remain unclear. Moreover, it is unclear whether all pathways that are coupled to splicing have been identified. As expected, our approach sensitively detects pre-mRNA accumulation in the vast majority of strains containing mutations in known splicing factors. Remarkably, however, several additional candidates were found to cause increases in pre-mRNA levels similar to that seen for canonical splicing mutants, none of which had previously been implicated in the splicing pathway. Instead, several of these factors have been previously implicated to play roles in chromatin remodeling, 3' end processing, and other novel categories. Further analysis of these factors using splicing-sensitive microarrays confirms that deletion of Bdf1, a factor that links transcription initiation and chromatin remodeling, leads to a global splicing defect, providing evidence for a novel connection between pre-mRNA splicing and this component of the SWR1 complex. By contrast, mutations in 3' end processing factors such as Cft2 and Yth1 also result in pre-mRNA splicing defects, although only for a subset of transcripts, suggesting that spliceosome assembly in S. cerevisiae may more closely resemble mammalian models of exon-definition. More broadly, our work demonstrates the capacity of this approach to identify novel regulators of various cellular RNAs., Competing Interests: The authors have declared that no competing interests exist.

Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 gene deletion mutants, on induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We followed up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during multiple stresses, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the "activating" mark H3K4me3 in gene repression., Competing Interests: The authors have declared that no competing interests exist.

Despite the large number of software tools developed to address different areas of microarray data analysis, very few offer an all-in-one solution with little learning curve. For microarray core labs, there are even fewer software packages available to help with their routine but critical tasks, such as data quality control (QC) and inventory management. We have developed a simple-to-use web portal to allow bench biologists to analyze and query complicated microarray data and related biological pathways without prior training. Both experiment-based and gene-based analysis can be easily performed, even for the first-time user, through the intuitive multi-layer design and interactive graphic links. While being friendly to inexperienced users, most parameters in Goober can be easily adjusted via drop-down menus to allow advanced users to tailor their needs and perform more complicated analysis. Moreover, we have integrated graphic pathway analysis into the website to help users examine microarray data within the relevant biological content. Goober also contains features that cover most of the common tasks in microarray core labs, such as real time array QC, data loading, array usage and inventory tracking. Overall, Goober is a complete microarray solution to help biologists instantly discover valuable information from a microarray experiment and enhance the quality and productivity of microarray core labs. The whole package is freely available at http://sourceforge.net/projects/goober. A demo web server is available at http://www.goober-array.org.

Optically trapped single cells of the biflagellated, green alga, Chlamydomonas reinhardtii, rotate. The rotational dynamics of trapped wild-type and mutant cells show that functional flagella play a decisive role: the entire flagellar apparatus (central microtubules, radial spokes, and dynein arms) is involved. Any aberration in this apparatus leads to non-functionality, indicating a gear-type mechanism. The translational and rotational motions of the wild-type and mutant cells do not differ significantly. Optical forces alone do not play a vital role in the rotational dynamics of this cellular motor, making them useful as probes of the internal dynamics without external influence.

We demonstrate rotation of live Chlamydomonas reinhardtii cells in an optical trap; the speed and direction of rotation are amenable to control by varying the optical trapping force. Cells rotate with a frequency of 60-100 rpm; functional flagella are shown to play a decisive role in rotation. The rotating cells generate torque (typically ~7500-12000 pN nm) that is much larger than that generated chemically by a dynein head in vitro (40 pN nm). The total force associated with a rotating live cell (~10 pN) suggests that activity of only a small fraction (~5%) of dynein molecules per beat cycle is sufficient to generate flagellar motion.

Gene expression studies require high quality messenger RNA (mRNA) in addition to other factors such as efficient primers and labeling reagents. To prevent RNA degradation and to improve the quality of gene array expression data, several commercial reagents have become available. We examined a conventional hot-phenol lysis method and RNA stabilization reagents, and generated comparative gene expression profiles from Escherichia coli cells grown on minimal medium. Our data indicate that certain RNA stabilization reagents induce stress responses and proper caution must be exercised during their use. We observed that the laboratory reagent (phenol/EtOH, 5:95, v/v) worked efficiently in isolating high quality mRNA and reproducibility was such that reliable gene expression profiles were generated. To assist in the analysis of gene expression data, we wrote a number of macros that use the most recent gene annotation and process data in accordance with gene function. Scripts were also written to examine the occurrence of artifacts, based on GC content, length of the individual open reading frame (ORF), its distribution on plus and minus DNA strands, and the distance from the replication origin.