Biology subjects

Saha, S.

Publications and source records attributed to Saha, S..

9 recordsLinked to original sources

bioRxiv2018

Systematic analysis of the Myxococcus xanthus developmental gene regulatory network supports posttranslational regulation of FruA by C-signaling

Upon starvation Myxococcus xanthus undergoes multicellular development. Rod-shaped cells move into mounds in which some cells differentiate into spores. Cells begin committing to sporulation at 24-30 h poststarvation, but the mechanisms governing commitment are unknown. FruA and MrpC are transcription factors that are necessary for commitment. They bind cooperatively to promoter regions and activate developmental gene transcription, including that of the dev operon. Leading up to and during the commitment period, dev mRNA increased in wild type, but not in a mutant defective in C-signaling, a short-range signaling interaction between cells that is also necessary for commitment. The C-signaling mutant exhibited [~]20-fold less dev mRNA than wild type at 30 h poststarvation, despite a similar level of MrpC and only twofold less FruA. Boosting the FruA level twofold in the C-signaling mutant had little effect on the dev mRNA level, and dev mRNA was not less stable in the C-signaling mutant. Neither did high cooperativity of MrpC and FruA binding upstream of the dev promoter explain the data. Rather, our systematic experimental and computational analyses support a model in which C-signaling activates FruA at least ninefold posttranslationally in order to commit a cell to spore formation.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=169 HEIGHT=200 SRC=\"FIGDIR/small/415331_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@c16410org.highwire.dtl.DTLVardef@909252org.highwire.dtl.DTLVardef@17668a8org.highwire.dtl.DTLVardef@d126c3_HPS_FORMAT_FIGEXP M_FIG C_FIG Abbreviated summaryStarvation promotes MrpC accumulation, whereas nutrients favor proteolysis. MrpC activates transcription of fruA, but FruA protein appears to be activated by short-range C-signaling in a cycle leading to mound formation and lysis of some cells. Activated FruA* and MrpC are proposed to cooperatively stimulate transcription of the dev operon and genes that commit starving rod-shaped cells to form spores, while Dev proteins slow commitment, resulting in a spore-filled fruiting body surrounded by peripheral rods.

molecular biology↗

bioRxiv2018

Isolation, Detection and Characterization of Aerobic Bacteria from Honey Samples of Bangladesh

Honey is a sweet substance made from the nectar of flowers and other chemical secretions from the bees bodies who collect nectar from the flowers and bring it to their hives to transform it to the thick, golden and sweet liquid that we call honey. The benefits of honey are not just limited to its basic use as a natural sweetener, but also its medicinal properties. The purpose of this study was to identify the bacteria that are present in honey commonly found in Bangladesh, which can tolerate the antimicrobial conditions of honey and survive in it. Fortunately, such bacteria could be detected, isolated and characterized by morphological and biochemical tests. The predominant type of bacteria commonly found in both raw and commercial honeys of Bangladesh are gram positive cocci such as streptococci, staphylococci, micrococci, bacilli and lactobacilli. Few gram negative bacteria were also isolated like Escherichia coli (8%) and Klebsiella pneumonia (8%) and some gram negative/gram variable Micrococcus luteus (75%). Hopefully, such knowledge would benefit people in the future as they will know more about the microorganisms present in honey and about the safety and quality of the honey they are about to buy or consume.

microbiology↗

bioRxiv2018

Gene Set Enrichment Analysis (GSEA) of Upregulated Genes in Cocaine Addiction Reveals miRNAs as Potential Therapeutic Agents

Cocaine addiction is a global health problem that causes substantial damage to the health of addicted individuals around the world. Dopamine synthesizing (DA) neurons in the brain play a vital role in the addiction to cocaine. But the underlying molecular mechanisms that help cocaine exert its addictive effect have not been very well understood. Bioinformatics can be a useful tool in the attempt to broaden our understanding in this area. In the present study, Gene Set Enrichment Analysis (GSEA) was carried out on the upregulated genes from a dataset of DA neurons of post-mortem human brain of cocaine addicts. As a result of this analysis, 3 miRNAs have been identified as having significant influence on transcription of the upregulated genes. These 3 miRNAs hold therapeutic potential for the treatment of cocaine addiction.

bioinformatics↗

bioRxiv2018

A member of the ferlin calcium sensor family is essential for Toxoplasma gondii rhoptry secretion

Invasion of host cells by apicomplexan parasites such as Toxoplasma gondii is critical for their infectivity and pathogenesis. In Toxoplasma, secretion of essential egress, motility and invasion-related proteins from microneme organelles is regulated by oscillations of intracellular Ca2+. Later stages of invasion are considered Ca2+-independent, including the secretion of proteins required for host cell entry and remodeling from the parasites rhoptries. We identified a family of three Toxoplasma proteins with homology to the ferlin family of double C2 domain-containing Ca2+ sensors. In humans and model organisms such Ca2+ sensors orchestrate Ca2+-dependent exocytic membrane fusion with the plasma membrane. One ferlin that is conserved across the Apicomplexa, TgFER2, localizes to the parasites cortical membrane skeleton, apical end, and rhoptries. Unexpectedly, conditionally TgFER2-depleted parasites secreted their micronemes normally and were completely motile. However, these parasites were unable to invade host cells and were therefore not viable. Specifically, knockdown of TgFER2 prevented rhoptry secretion and these parasites failed to form the moving junction on the parasite-host interface necessary for host cell invasion. Collectively, these data demonstrate that the putative Ca2+ sensor TgFER2 is required for the secretion of rhoptries. These findings provide the first regulatory and mechanistic insights into this critical yet poorly understood aspect of apicomplexan host cell invasion.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC=\"FIGDIR/small/304048_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@505202org.highwire.dtl.DTLVardef@138400aorg.highwire.dtl.DTLVardef@1f468beorg.highwire.dtl.DTLVardef@1089d34_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2018

A novel sialylation site on Neisseria gonorrhoeae lipooligosaccharide links heptose II lactose expression with pathogenicity

Sialylation of lacto-W-neotetraose (LNnT) extending from heptose I (HepI) of gonococcal lipooligosaccharide (LOS) contributes to pathogenesis. Previously, gonococcal LOS sialyltransterase (Lst) was shown to sialylate LOS in Triton X-100 extracts of strain 15253, which expresses lactose from both HepI and HepII, the minimal structure required for mAb 2C7 binding. Ongoing work has shown that growth of 15253 in cytidine monophospho-W-acetylneuraminic acid (CMP-Neu5Ac)-containing media enables binding to CD33/Siglec-3, a cell surface receptor that binds sialic acid, suggesting that lactose termini on LOS of intact gonococci can be sialylated. Neu5Ac was detected on LOSs of strains 15253 and a MS11 mutant with only lactose from HepI and HepII by mass spectrometry; deleting HepII lactose rendered Neu5Ac undetectable. Resistance of HepII lactose Neu5Ac to desialylation by 2-3-specific neuraminidase suggested an 2-6-linkage. Although not associated with increased factor H binding, HepII lactose sialylation inhibited complement C3 deposition on gonococci. 15253 mutants that lacked Lst or HepII lactose were significantly attenuated in mice, confirming the importance of HepII Neu5Ac in virulence. All 75 minimally passaged clinical isolates from Nanjing, China, expressed HepII lactose, evidenced by reactivity with mAb 2C7; mAb 2C7 was bactericidal against the first 62 (of 75) isolates that had been collected sequentially and were sialylated before testing. mAb 2C7 effectively attenuated 15253 vaginal colonization in mice. In conclusion, this novel sialylation site could explain the ubiquity of gonococcal HepII lactose in vivo. Our findings reiterate the candidacy of the 2C7 epitope as a vaccine antigen and mAb 2C7 as an immunotherapeutic antibody.

microbiology↗

bioRxiv2017

Two phosphoglucomutase paralogs regulate triggered secretion of the Toxoplasma micronemes

Parafusin is a phosphoglucomutase (PGM) paralog that acts as a signaling scaffold protein in calcium mediated exocytosis across many eukaryotes. In Toxoplasma gondii the parafusin related protein 1 (PRP1) has been associated in indirect and heterologous studies with the regulated exocytosis of the micronemes, which are required for successful host cell invasion and egress. Here we directly assessed the role of PRP1 by deleting the gene from the parasite. We observed a specific defect in microneme secretion in response to high Ca2+ fluxes, but not to phosphatidic acid fluxes controlling microneme release. We observed no defect in constitutive microneme secretion which was sufficient to support completion of the lytic cycle. Furthermore, deletion of the other PGM in Toxoplasma, PGM2, as well as the double PRP1/PGM2 deletion resulted in a similar phenotype. This suggests a functional interaction between these two genes. Strikingly, tachyzoites without both paralogs are completely viable in vitro and during acute mice infections. This indicates that PGM activity is neither required for glycolysis. In conclusion, the PRP1-PGM2 pair is required for a burst in microneme secretion upon high Ca2+ fluxes, but this burst is not essential to complete the lytic cycle of the parasite.\n\nPlain Language SummaryCalcium mediated control of microneme secretion is essential for host cell invasion and egress of Toxoplasma gondii. Here it is shown that the two phosphoglucomutases in Toxoplasma both function in the translation of a spike in calcium into a burst in microneme secretion.

microbiology↗

bioRxiv2017

The molecular weight of NaYF4:RE photonic up-conversion nanoparticles

Upconversion nanoparticles (UCNPs) are utilized extensively for biomedical imaging, sensing, and therapeutic applications, yet the molecular weight of UCNPs has not previously been reported. We present a theory based upon the crystal structure of UCNPs to estimate the molecular weight of UCNPs: enabling insight into UCNP molecular weight for the first time. We estimate the theoretical molecular weight of various UCNPs reported in the literature, predicting that spherical NaYF4 UCNPs {small tilde} 10 nm in diameter will be {small tilde}1 MDa (i.e. 106 g/mol), whereas UCNPs {small tilde} 45 nm in diameter will be {small tilde}100 MDa (i.e. 108 g/mol). We also predict that hexagonal crystal phase UCNPs will be of greater molecular weight than cubic crystal phase UCNPs. Additionally we find that a Gaussian UCNP diameter distribution will correspond to a lognormal UCNP molecular weight distribution. Our approach could potentially be generalised to predict the molecular weight of other arbitrary crystalline nanoparticles: as such, we provide standalone graphic user interfaces to calculate the molecular weight both UCNPs and arbitrary crystalline nanoparticles. We expect knowledge of UCNP molecular weight to be of wide utility in biomedical applications where reporting UCNP quantity in absolute numbers or molarity will be beneficial for inter-study comparison and repeatability.

biophysics↗

bioRxiv2017

Chemotaxis microsimulation: On the gain in nutrient uptake and bacterial cell division with chemotaxis mechanism

Bacterial swimming alternates between straight runs for several seconds and tumbles into random directions. Chemotactic bacteria remember nutrient sensing history, change tumble frequency to move toward nutrients. A question that has not been addressed is the significance of the nutrition gain and multiplication of bacterial population with chemotaxis mechanism. To quantify these effects, we introduce a microsimulation model, which seamlessly integrates detailed observations and assumptions about single bacterial tumbles, noisy sensing and nutrient uptake for studying up to a few millions of them in a population. We use the model to simulate absorption of nutrients from lysis and agar plates. Contrary to an intuitive feeling that chemotaxis could be useful under nutrient starvation, we see a significant effect only under nutrient rich conditions where bacteria with chemotaxis outgrow their non-chemotactic counterparts by hundreds of times. The model offers the flexibility to study the consequences of newer assumptions, and experimental conditions.\n\nAuthor SummaryChemotaxis is a mechanism that helps bacteria navigate towards nutrients. Several aspects of the mechanism have been well studied over the past 50 years. As most bacterial mechanisms are helpful evolutionarily to survive and to multiply, it would be a natural question to ask how much this swim helps bacteria to gain nutrition and consequently to multiply. However to our knowledge this question has not been asked. We develop a model that integrates bacterial motion, with sensing and nutrient uptake and show that only under nutrient rich conditions this mechanism helps.

biophysics↗

bioRxiv2017

Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. All data are available on https://citrusgreening.org/.

genomics↗