Publications

@article{noKey,

title = {Secretome of Hypoxia-Preconditioned Mesenchymal Stem Cells Enhance Angiogenesis in Diabetic Rats with Peripheral Artery Disease},

author = {Sazli, Brama Ihsan},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10227841/},

doi = {https://doi.org/10.5455/medarh.2023.77.90-96},

year  = {2023},

date = {2023-01-01},

abstract = {Background:

Lower limb peripheral artery disease (PAD) is the main risk of diabetes mellitus which result to high mortality rate. Approximately, 50% of patients who receive several treatments have passed away or lost limbs at a year’s follow-up. Secretome of hypoxia mesenchymal stem cells (S-MSCs) contains several active soluble molecules from hypoxia MSCs (H-MSCs) that capable inducing anti-inflammatory and vascular regeneration in PAD.



Objective:

In this study, we investigated the therapeutic potential of S-MSCs in improving dynamic function and angiogenesis of PAD diabetic rats.



Methods:

The PAD was established by the incision from the groin to the inner thigh and distal ligation of femoral arteries in rats with diabetes. Rats were administered with 200 µL and 400 µL S-MSCs that successfully filtrated using tangential flow filtration (TFF) system based on various molecular weight cut-off categories intravenously. ELISA assay was used to analyze the cytokines and growth factors contained in S-MSCs. Tarlov score were examined at day 1, 3, 5, 7, 10 and 14. The rats were sacrificed at day 14 and muscle tissues were collected for immunohistochemistry (IHC) and gene expression analysis.



Results:

ELISA assay showed that S-MSCs provides abundant level of VEGF, PDGF, bFGF, IL-10 and TGFβ. In vivo administration of S-MSCs remarkably enhanced the Tarlov score. S-MSCs improved angiogenesis through enhancing VEGF gene expression and significantly increasing CD31 positive area in muscle tissue of PAD diabetic rats.



Conclusion:

Our findings suggest that S-MSCs could improves dynamic function and angiogenesis in PAD diabetic rats.},

keywords = {µPULSE},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural and functional analyses of Pcal_0917, an α-glucosidase from hyperthermophilic archaeon Pyrobaculum calidifontis},

author = {Atta Muhammad, Majida},

url = {https://doi.org/10.1016/j.ijbiomac.2023.125446},

doi = {https://doi.org/10.1016/j.ijbiomac.2023.125446},

year  = {2023},

date = {2023-01-01},

abstract = {Genome analysis of Pyrobaculum calidifontis revealed the presence of α-glucosidase (Pcal_0917) gene. Structural analysis affirmed the presence of signature sequences of Type II α-glucosidases in Pcal_0917. We have heterologously expressed the gene and produced recombinant Pcal_0917 in Escherichia coli. Biochemical characteristics of the recombinant enzyme resembled to that of Type I α-glucosidases, instead of Type II. Recombinant Pcal_0917 existed in a tetrameric form in solution and displayed highest activity at 95 °C and pH 6.0, independent of any metal ions. A short heat-treatment at 90 °C resulted in a 35 % increase in enzyme activity. A slight structural shift was observed by CD spectrometry at this temperature. Half-life of the enzyme was >7 h at 90 °C. Pcal_0917 exhibited apparent Vmax values of 1190 ± 5 and 3.9 ± 0.1 U/mg against p-nitrophenyl α-D-glucopyranoside and maltose, respectively. To the best of our knowledge, Pcal_0917 displayed the highest ever reported p-nitrophenyl α-D-glucopyranosidase activity among the characterized counterparts. Moreover, Pcal_0917 displayed transglycosylation activity in addition to α-glucosidase activity. Furthermore, in combination with α-amylase, Pcal_0917 was capable of producing glucose syrup from starch with >40 % glucose content. These properties make Pcal_0917 a potential candidate for starch hydrolyzing industry.},

keywords = {µPULSE},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {The Role of Mesenchymal Stem Cell Secretome in the Inflammatory Mediators and the Survival Rate of Rat Model of Sepsis},

author = {Sari et al, Mutiara Indah Sari},

url = {https://www.mdpi.com/2227-9059/11/8/2325},

doi = {https://doi.org/10.3390/biomedicines11082325},

year  = {2023},

date = {2023-01-01},

abstract = {In sepsis, simultaneously elevated levels of pro-inflammatory cytokines and interleukin (IL)-10 indicate immune response dysregulation, increasing the mortality of the host. As mesenchymal stem cell (MSC) secretome is known to have immunomodulatory effects, we aim to assess the role of MSC secretome in the inflammatory mediators (NF-κB p65 and p50, TNF-α, IL-10) and the survival rate of a rat model of sepsis. In this study, forty-eight male Rattus norvegicus rats were divided into one sham group and three groups with sepsis induction: the control group and the sepsis-induced rat groups treated with 150 μL (T1) and 300 μL (T2) of secretome. The survival rate was observed per 6 h for 48 h and plotted using the Kaplan–Meier method. Compared to the control group, T2 showed a significant decrease in the relative expression of NF-κB and the serum TNF-α level, and a significant increase in the serum IL-10 level. Meanwhile, T1 showed a significant decrease in the serum TNF-α level compared to the control group. The Kaplan–Meier Log Rank test did not show significance in the distribution of survival between T1, T2, and the control group. However, from the 18th to the 36th hour, the survival rate of T2 was lower than the survival rate of the control group and T1, with a noticeable difference between T2 and the control group, as well as T1 at the 36th hour. At the 42nd hour, the survival rate of T2 was the same as the control group and remained lower than T1. In conclusion, MSC secretome regulated the inflammatory mediators in rat model of sepsis, with a dose of 150 μL being more effective.},

keywords = {µPULSE},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Combination Effect of Rotator Cuff Repair with Secretome-hypoxia MSCs Ameliorates TNMD, RUNX2, and Healing Histology Score in Rotator Cuff Tear Rats},

author = {Fredianto et al., Meiky},

url = {https://abjs.mums.ac.ir/article_22788_fc78bb4038b5420a87712ecd4c664e9e.pdf},

doi = {10.22038/ABJS.2023.67933.3218},

year  = {2023},

date = {2023-01-01},

abstract = {Objectives: In order to treat a rat model of rotator cuff rupture, this work concentrated on the expression 

of TNMD and RUNX2, followed by rotator cuff repair and secretome-hMSCs.

Methods: A total of thirty 10-weeks-old male Sprague–Dawley rats were separated into five groups randomly, RC 

on week 0, lesion treated with a rotator cuff repair and saline (RC + NaCl group, n = 6) for 2 and 8 weeks, and lesion 

treated with a rotator cuff repair and secretome-hMSCs (RC + secretome-hMSC group, n = 6) for 2 and 8 weeks. 

The supraspinatus and infraspinatus muscle–tendon units were obtained for histological and biomechanical 

investigation at 0, 2 and 8 weeks following injury.

Results: The findings showed that, in comparison with the RC + NaCl group, secretome-hMSCs significantly 

improved tendon repair by upregulating TNMD and RUNX2 expression and histology score.

Conclusion: Combining Secretome-hypoxia MSCs with RC healing may help rats with rotator cuff tears.

 Level of evidence: IV},

keywords = {µPULSE},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {An ependymal cell census identifies heterogeneous and ongoing cell maturation in the adult mouse spinal cord that changes dynamically on injury},

author = {Albors, Aida Rodrigo, et al.},

url = {https://pubmed.ncbi.nlm.nih.gov/36706756/},

doi = {https://doi.org/10.1016/j.devcel.2023.01.003},

year  = {2023},

date = {2023-01-01},

abstract = {The adult spinal cord stem cell potential resides within the ependymal cell population and declines with age. Ependymal cells are, however, heterogeneous, and the biological diversity this represents and how it changes with age remain unknown. Here, we present a single-cell transcriptomic census of spinal cord ependymal cells from adult and aged mice, identifying not only all known ependymal cell subtypes but also immature as well as mature cell states. By comparing transcriptomes of spinal cord and brain ependymal cells, which lack stem cell abilities, we identify immature cells as potential spinal cord stem cells. Following spinal cord injury, these cells re-enter the cell cycle, which is accompanied by a short-lived reversal of ependymal cell maturation. We further analyze ependymal cells in the human spinal cord and identify widespread cell maturation and altered cell identities. This in-depth characterization of spinal cord ependymal cells provides insight into their biology and informs strategies for spinal cord repair.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {BacterAI maps microbial metabolism without prior knowledge},

author = {Dama, Adam C.},

url = {https://www.nature.com/articles/s41564-023-01376-0},

doi = {https://doi.org/10.1038/s41564-023-01376-0},

year  = {2023},

date = {2023-01-01},

abstract = {Training artificial intelligence (AI) systems to perform autonomous experiments would vastly increase the throughput of microbiology; however, few microbes have large enough datasets for training such a system. In the present study, we introduce BacterAI, an automated science platform that maps microbial metabolism but requires no prior knowledge. BacterAI learns by converting scientific questions into simple games that it plays with laboratory robots. The agent then distils its findings into logical rules that can be interpreted by human scientists. We use BacterAI to learn the amino acid requirements for two oral streptococci: Streptococcus gordonii and Streptococcus sanguinis. We then show how transfer learning can accelerate BacterAI when investigating new environments or larger media with up to 39 ingredients. Scientific gameplay and BacterAI enable the unbiased, autonomous study of organisms for which no training data exist.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells},

author = {Bouguenina, Habib},

url = {https://www.cell.com/iscience/fulltext/S2589-0042(23)01136-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004223011367%3Fshowall%3Dtrue},

doi = {https://doi.org/10.1016/j.isci.2023.107059},

year  = {2023},

date = {2023-01-01},

abstract = {To address the limitation associated with degron based systems, we have developed iTAG, a synthetic tag based on IMiDs/CELMoDs mechanism of action that improves and addresses the limitations of both PROTAC and previous IMiDs/CeLMoDs based tags. Using structural and sequence analysis, we systematically explored native and chimeric degron containing domains (DCDs) and evaluated their ability to induce degradation. We identified the optimal chimeric iTAG(DCD23 60aa) that elicits robust degradation of targets across cell types and subcellular localizations without exhibiting the well documented “hook effect” of PROTAC-based systems. We showed that iTAG can also induce target degradation by murine CRBN and enabled the exploration of natural neo-substrates that can be degraded by murine CRBN. Hence, the iTAG system constitutes a versatile tool to degrade targets across the human and murine proteome.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Screening for variable drug responses using human iPSC cohorts},

author = {Platani, Melpomeni},

url = {https://www.biorxiv.org/content/10.1101/2023.06.16.545161v1.full},

doi = {https://doi.org/10.1101/2023.06.16.545161},

year  = {2023},

date = {2023-01-01},

abstract = {We have used a cohort of human induced pluripotent stem cell (hiPSC) lines to develop a laboratory-based drug screening platform to predict variable drug responses of potential clinical relevance. Our approach is based on the findings that hiPSC lines reflect the genetic identity of the donor and that pluripotent hiPSC lines express a broad repertoire of gene transcripts and proteins. We demonstrate that a cohort of hiPSC lines from different donors can be screened efficiently in their pluripotent state using high-throughput cell painting assays, allowing detection of variable phenotypic responses to a wide range of clinically approved drugs, across multiple disease areas. Furthermore, we provide information on mechanisms of drug-cell interactions underlying the observed variable responses by using quantitative proteomic analysis to compare sets of hiPSC lines that had been stratified objectively using cell painting data. We propose that information derived from comparative drug screening using curated libraries of hiPSC lines can help to increase the success rate of drug development pipelines and improve the delivery of safe new drugs suitable for a broader ethnic and gender diversity within human populations.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {A Degron Blocking Strategy Towards Improved CRL4CRBN Recruiting PROTAC Selectivity},

author = {Bouguenina, Habib},

url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cbic.202300351},

doi = {https://doi.org/10.1002/cbic.202300351},

year  = {2023},

date = {2023-01-01},

abstract = {Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4CRBN recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4CRBN recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4CRBN neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4CRBN molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Protomer selectivity of type II RAF inhibitors within the RAS/RAF complex},

author = {Vasta, James D.},

url = {https://www.cell.com/cell-chemical-biology/fulltext/S2451-9456(23)00247-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2451945623002477%3Fshowall%3Dtrue},

doi = {https://doi.org/10.1016/j.chembiol.2023.07.019},

year  = {2023},

date = {2023-01-01},

abstract = {RAF dimer inhibitors offer therapeutic potential in RAF- and RAS-driven cancers. The utility of such drugs is predicated on their capacity to occupy both RAF protomers in the RAS-RAF signaling complex. Here we describe a method to conditionally quantify drug-target occupancy at selected RAF protomers within an active RAS-RAF complex in cells. RAF target engagement can be measured in the presence or absence of any mutant KRAS allele, enabling the high-affinity state of RAF dimer inhibitors to be quantified in the cellular milieu. The intracellular protomer selectivity of clinical-stage type II RAF inhibitors revealed that ARAF protomer engagement, but not engagement of BRAF or CRAF, is commensurate with inhibition of MAPK signaling in various mutant RAS cell lines. Our results support a fundamental role for ARAF in mutant RAS signaling and reveal poor ARAF protomer vulnerability for a cohort of RAF inhibitors undergoing clinical evaluation.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Sperm Cell Painting: A Mechanism Driven Approach for Drug Discovery in Human Spermatozoa},

author = {Johnston, Zoe C},

url = {https://www.biorxiv.org/content/10.1101/2023.09.15.557919v2},

doi = {https://doi.org/10.1101/2023.09.15.557919},

year  = {2023},

date = {2023-01-01},

abstract = {We have adapted the cell painting assay developed by Carpenter and colleagues on cultured U2OS cells to human spermatozoa. In Sperm Cell Painting (SCP) we assemble an image-based quantitative fingerprint of the functional state of sperm. We use this assay to gain insight into the mechanism of action of compounds that modify sperm function and as a platform for contraceptive discovery.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory},

author = {Cook, Michael A},

url = {https://academic.oup.com/jimb/advance-article/doi/10.1093/jimb/kuad042/7459345},

doi = {https://doi.org/10.1093/jimb/kuad042},

year  = {2023},

date = {2023-01-01},

abstract = {Microbial natural products are specialized metabolites that are sources of many bioactive

compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of

biology. The assembly of libraries of producers of natural products has traditionally been the

province of the pharmaceutical industry. This sector has gathered significant historical

collections of bacteria and fungi to identify new drug leads with outstanding outcomes - upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we

report a perspective on our efforts to assemble a library of natural product-producing microbes

and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Overcome the challenge for intratumoral injection of STING agonist for pancreatic cancer by systemic administration},

author = {Li, Keyu},

url = {https://hal.science/hal-04326175/},

doi = {hal-04326175},

year  = {2023},

date = {2023-01-01},

abstract = {Objective: Due to the challenge for intratumoral administration, innate agonists have not made it beyond preclinical studies for efficacy testing in most of tumor types. Pancreatic ductal adenocarcinoma (PDAC) has a T-cell excluded or deserted tumor microenvironment. Innate agonist treatments may serve as a T cell priming mechanism to sensitize PDACs to anti-PD-1 antibody (a-PD-1) treatment. Design: Using a transplant murine model with spontaneously formed liver metastasis and also the genetically engineered KPC mouse model that spontaneously develops PDAC, we compared the antitumor efficacy between intrahepatic/intratumoral and intramuscular systemic administration of BMS-986301, a next-generation STING agonist. Flow cytometry, Nanostring, and cytokine assays were used to evaluate local and systemic immune responses. Results: The study demonstrated that administration of STING agonist systemically via intramuscular injection is equivalent or potentially superior to its intratumoral injection in inducing both effector T cell response and antitumor efficacy. Compared to intratumoral administration, T cell exhaustion and immunosuppressive signals induced by systemic administration were attenuated. Nonetheless, either local or systemic treatment of STING agonist was associated with increased expression of CTLA-4 in the tumors. However, the combination of a-PD-1 and anti-CTLA-4 antibody with systemic STING agonist demonstrated the antitumor efficacy in the KPC mouse spontaneous PDAC model. Our study also demonstrated the feasibility and antitumor efficacy of systemic administration of BMS-986299, a new NLRP3 agonist. Conclusion: For the first time, our study supports the clinical development of innate agonists via systemic administration, instead of local administration, for treating PDAC.},

keywords = {TEMPEST},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors},

author = {Yu, Lei},

url = {https://www.science.org/doi/full/10.1126/sciadv.abp8901},

doi = {https://doi.org/10.1126/sciadv.abp8901},

year  = {2023},

date = {2023-01-01},

abstract = {Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single-cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell suspensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Single-cell transcriptomics unveils xylem cell development and evolution},

author = {Chia-Chun, Tung et, al.},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9830878/},

doi = {https://doi.org/10.1186/s13059-022-02845-1},

year  = {2023},

date = {2023-01-01},

abstract = {Background

Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiosperms, fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed by tracheids in other vascular plants such as gymnosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types.



Results

Through both single-cell and laser capture microdissection transcriptomic profiling, we determine the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Based on cross-species analyses of single-cell clusters and overlapping trajectories, we reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages, whereas the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed trait, exhibit strong transcriptomic similarity to vessel elements rather than libriform fibers.



Conclusions

This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format},

author = {Chen, Yan, et al.},

url = {https://www.protocols.io/view/alkaline-sds-cell-lysis-of-microbes-with-acetone-p-b2raqd2e.html},

doi = {dx.doi.org/10.17504/protocols.io.6qpvr6xjpvmk/v1},

year  = {2023},

date = {2023-01-01},

abstract = {This high-throughput protocol details the steps to extract protein from Gram-negative bacteria, Gram-positive bacteria, or non-filamentous fungi in 96-well plate format for quantitative proteomic workflows. This protocol uses a bench-top automated liquid dispenser but the volumes and times also apply to manual and multi-channel pipetter use. This protocol is designed for lab-based, culture conditions and synthetic community experiments where complex sample matrices are minimized. Additional sample preservation and/or protein extraction methods may be required for environmental samples (e.g., feces, soil) to minimize protein degradation and maintain sample integrity.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study},

author = {Leech, Sophie Meghan, et al.},

url = {https://www.mdpi.com/2072-6643/15/3/696},

doi = {https://doi.org/10.3390/nu15030696},

year  = {2023},

date = {2023-01-01},

abstract = {Breastmilk is thought to influence the infant gut by supplying prebiotics in the form of human milk oligosaccharides and potentially seeding the gut with breastmilk microbes. However, the presence of a breastmilk microbiota and origins of these microbes are still debated. As a pilot study, we assessed the microbes present in expressed breastmilk at six-weeks postpartum using shotgun metagenomic sequencing in a heterogenous cohort of women who delivered by vaginal (n = 8) and caesarean delivery (n = 8). In addition, we estimated the microbial load of breastmilk at six-weeks post-partum with quantitative PCR targeting the 16S rRNA gene. Breastmilk at six-weeks postpartum had a low microbial mass, comparable with PCR no-template and extraction controls. Microbes identified through metagenomic sequencing were largely consistent with skin and oral microbes, with four samples returning no identifiable bacterial sequences. Our results do not provide convincing evidence for the existence of a breastmilk microbiota at six-weeks postpartum. It is more likely that microbes present in breastmilk are sourced by ejection from the infant’s mouth and from surrounding skin, as well as contamination during sampling and processing.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {High-Throughput Exonuclease Assay Based on the Fluorescent Base Analogue 2-Aminopurine},

author = {Botto, Margherita M.},

url = {https://pubs.acs.org/doi/full/10.1021/acsomega.2c06577},

doi = {https://doi.org/10.1021/acsomega.2c06577},

year  = {2023},

date = {2023-01-01},

abstract = {Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair, and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited. Here, we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3′ and 5′ DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high-throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {High-throughput microbial culturomics using automation and machine learning},

author = {Huang, Yiming},

url = {https://www.nature.com/articles/s41587-023-01674-2},

doi = {https://doi.org/10.1038/s41587-023-01674-2},

year  = {2023},

date = {2023-01-01},

abstract = {Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype–genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments},

author = {Gatto, Laurent},

url = {https://www.nature.com/articles/s41592-023-01785-3#Ack1},

doi = {https://doi.org/10.1038/s41592-023-01785-3},

year  = {2023},

date = {2023-01-01},

abstract = {Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition and data analysis. We expect that broadly accepted community guidelines and standardized metrics will enhance rigor, data quality and alignment between laboratories. Here we propose best practices, quality controls and data-reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics.},

keywords = {MANTIS},

pubstate = {published},

tppubtype = {article}

}