Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes

The sulfur-containing amino acid cysteine is abundant in the environment including in freshwater lakes. Biological degradation of cysteine can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments, including freshwater lakes. Here, we investigated the ecological significance of cysteine in oxic freshwater lake environments, using model systems of isolated cultures, controlled growth experiments, and multi-omics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. In total, we identified 29 isolates that produced H2S and belonged to the phylum Proteobacteria Bacteroidetes, and Actinobacteria. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized 3 freshwater isolates using whole-genome sequencing, and quantitatively tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophila, Stenotrophomonas bentonitica (Gammaproteobacteria) and Chryseobacterium piscium (Bacteroidetes). We observed a decrease in cysteine and increase in H2S, and identified genes involved in cysteine degradation in all 3 genomes. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a five-year time series of metagenomic data from the same isolation source at Lake Mendota and identified their presence throughout the time series. Overall, our study shows that sulfur-containing amino acids can drive microbial H2S production in oxic environments. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from degradation of organosulfur compounds.

From Sampling to Analysis: How to Achieve the Best Sample Throughput via Sampling Optimization and Relevant Compound Analysis Using Sum of Ranking Differences Method?

The determination of an optimal volatile sampling procedure is always a key question in analytical chemistry. In this paper, we introduce the application of a novel non-parametric statistical method, the sum of ranking differences (SRD), for the quick and efficient determination of optimal sampling procedures. Different types of adsorbents (Porapak Q, HayeSep Q, and Carbotrap) and sampling times (1, 2, 4, and 6 h) were used for volatile collections of lettuce (Lactuca sativa) samples. SRD identified 6 h samplings as the optimal procedure. However, 1 or 4 h sampling with HayeSep Q and 2 h sampling with Carbotrap are still efficient enough if the aim is to reduce sampling time. Based on our results, SRD provides a novel way to not only highlight an optimal sampling procedure but also decrease evaluation time.

Muscular and Molecular Pathology Associated with SPATA5 Deficiency in a Child with EHLMRS

Mutations in the SPATA5 gene are associated with epilepsy, hearing loss and mental retardation syndrome (EHLMRS). While SPATA5 is ubiquitously expressed and is attributed a role within mitochondrial morphogenesis during spermatogenesis, there is only limited knowledge about the associated muscular and molecular pathology. This study reports on a comprehensive workup of muscular pathology, including proteomic profiling and microscopic studies, performed on an 8-year-old girl with typical clinical presentation of EHLMRS, where exome analysis revealed two clinically relevant, compound-heterozygous variants in SPATA5. Proteomic profiling of a quadriceps biopsy showed the dysregulation of 82 proteins, out of which 15 were localized in the mitochondrion, while 19 were associated with diseases presenting with phenotypical overlap to EHLMRS. Histological staining of our patient’s muscle biopsy hints towards mitochondrial pathology, while the identification of dysregulated proteins attested to the vulnerability of the cell beyond the mitochondria. Through our study we provide insights into the molecular etiology of EHLMRS and provide further evidence for a muscle pathology associated with SPATA5 deficiency, including a pathological histochemical pattern accompanied by dysregulated protein expression.

Authentication of holy basil using markers relating to a toxicology-relevant compound

Holy Basil—Ocimumtenuiflorum—is one of the popular new “superfoods” thought to act as an antioxidant and to reduce stress and anxiety. However, it is often surrogated with other Ocimum species differing in their chemical profiles that may even pose health risks to the consumers. Moreover, even specific chemotypes of Holy Basil itself can be toxicologically relevant, because they sometimes contain the carcinogen compound methyleugenol. Using DNA barcoding based on plastidic markers, O.tenuiflorum can be differentiated from other species of Ocimum. However, this approach is still suboptimal in handling larger sample numbers and in tracing chemotypes that accumulate methyleugenol. We have, therefore, designed a trait-related DNA barcode based on the enzyme eugenol O-methyltransferase (EOMT), responsible for the synthesis of methyleugenol. We show that a multiplex PCR combining trait-related and trait-independent markers can differentiate O.tenuiflorum from other Ocimum species and identify methyleugenol chemotypes of O.tenuiflorum, even in dried material sold as mixtures.

Aptamer-Based Detection of Fumonisin B1: A Systematic Comparison with Conventional and Other Novel Methods

Mycotoxin contamination is a current issue affecting several crops and processed products worldwide. Among the diverse mycotoxin group, fumonisin B1 (FB1) has become a relevant compound because of its adverse effects in the food chain. Conventional analytical methods previously proposed to quantify FB1 comprise LC-MS, HPLC-FLD and ELISA, while novel approaches integrate different sensing platforms and fluorescently labelled agents in combination with antibodies. Nevertheless, such methods could be expensive, time-consuming and require experience. Aptamers (ssDNA) are promising alternatives to overcome some of the drawbacks of conventional analytical methods, their high affinity through specific aptamer-target binding has been exploited in various designs attaining favorable limits of detection (LOD). So far, two aptamers specific to FB1 have been reported, and their modified and shortened sequences have been explored for a successful target quantification. In this critical review spanning the last eight years, we have conducted a systematic comparison based on principal component analysis of the aptamer-based techniques for FB1, compared with chromatographic, immunological and other analytical methods. We have also conducted an <i>in-silico</i> prediction of the folded structure of both aptamers under their reported conditions. The potential of aptasensors for the future development of highly sensitive FB1 testing methods is emphasized.

Aptamer-Based Detection of Fumonisin B1: A Systematic Comparison with Conventional and Other Novel Methods

Mycotoxin contamination is a current issue affecting several crops and processed products worldwide. Among the diverse mycotoxin group, fumonisin B1 (FB1) has become a relevant compound because of its adverse effects in the food chain. Conventional analytical methods previously proposed to quantify FB1 comprise LC-MS, HPLC-FLD and ELISA, while novel approaches integrate different sensing platforms and fluorescently labelled agents in combination with antibodies. Nevertheless, such methods could be expensive, time-consuming and require experience. Aptamers (ssDNA) are promising alternatives to overcome some of the drawbacks of conventional analytical methods, their high affinity through specific aptamer-target binding has been exploited in various designs attaining favorable limits of detection (LOD). So far, two aptamers specific to FB1 have been reported, and their modified and shortened sequences have been explored for a successful target quantification. In this critical review spanning the last eight years, we have conducted a systematic comparison based on principal component analysis of the aptamer-based techniques for FB1, compared with chromatographic, immunological and other analytical methods. We have also conducted an <i>in-silico</i> prediction of the folded structure of both aptamers under their reported conditions. The potential of aptasensors for the future development of highly sensitive FB1 testing methods is emphasized.

Isatin: A Scaffold with Innumerable Biodiversity

: Isatin is an endogenous and a significant category of fused heterocyclic component, widely been a part of several potential biologically useful synthetics. Since its discovery, tons of research work has been conducted with respect to the synthesis, chemical properties, and biological and industrial applications. It contains indole nucleus having both lactam and keto moiety which while being a part of a molecular framework exerted several biological effects, viz.; antimicrobial, antitubercular, anticonvulsant, anticancer etc. Isatin derivatives are synthetically significant substrates, which can be utilized for the synthesis of huge diversified chemical entities of which few members emerged to be a drug. The reason for this review is to provide extensive information pertaining to the chemistry and its significance in altering several pathological states of isatin and its derivatives. A Structure Activity Relationships study thus developed through a gamut of scientific information indicates the importance of mostly electron withdrawing groups, halogens, nitro, alkoxy and to a minor extent groups with positive inductive effects, such as methyl at position 1, 5, 6 and 7 of isatin in alleviating several clinical conditions. It is also observed from the survey that the presence of two oxo groups at position 2 and 3 sometimes become insignificant as fusion with a heterocycle at those position resulted in a biologically relevant compound.

BRAFV600E drives dedifferentiation in small intestinal and colonic organoids and cooperates with mutant p53 and Apc loss in transformation

BRAFV600E confers poor prognosis and is associated with a distinct subtype of colorectal cancer (CRC). Little is known, however, about the genetic events driving the initiation and progression of BRAFV600E mutant CRCs. Recent genetic analyses of CRCs indicate that BRAFV600E often coexists with alterations in the WNT- and p53 pathways, but their cooperation remains ill-defined. Therefore, we systematically compared small and large intestinal organoids from mice harboring conditional BraffloxV600E, Trp53LSL-R172H, and/or Apcflox/flox alleles. Using these isogenic models, we observe tissue-specific differences toward sudden BRAFV600E expression, which can be attributed to different ERK-pathway ground states in small and large intestinal crypts. BRAFV600E alone causes transient proliferation and suppresses epithelial organization, followed by organoid disintegration. Moreover, BRAFV600E induces a fetal-like dedifferentiation transcriptional program in colonic organoids, which resembles human BRAFV600E-driven CRC. Co-expression of p53R172H delays organoid disintegration, confers anchorage-independent growth, and induces invasive properties. Interestingly, p53R172H cooperates with BRAFV600E to modulate the abundance of transcripts linked to carcinogenesis, in particular within colonic organoids. Remarkably, WNT-pathway activation by Apc deletion fully protects organoids against BRAFV600E-induced disintegration and confers growth/niche factor independence. Still, Apc-deficient BRAFV600E-mutant organoids remain sensitive toward the MEK inhibitor trametinib, albeit p53R172H confers partial resistance against this clinically relevant compound. In summary, our systematic comparison of the response of small and large intestinal organoids to oncogenic alterations suggests colonic organoids to be better suited to model the human situation. In addition, our work on BRAF-, p53-, and WNT-pathway mutations provides new insights into their cooperation and for the design of targeted therapies.

Musty and Moldy Taint in Wines: A Review

The literature about musty and moldy taint—the so-called cork taint—in wines is varied because there are many different molecules involved in this wine defect. Chloroanisoles are the most relevant compound responsible for cork taint and of these, 2,4,6-trichloroanisole (TCA) is the most common, but 2,3,4,6-tetrachloroanisole (TeCA) and 2,4,6-tribromoanisole (TBA) can also be responsible of this defect. For other compounds involved in cork taint, geosmin and 2-methylisoborneol (2-MIB) are responsible for earthy off-flavor; pyrazines cause vegetable odors, and guaiacol results in smoked, phenolic and medicinal defects. Off-odors of mushroom in wines are caused by 1-octen-3-ol and 1-octen-3-one coming from grapes contaminated by bunch rot (Botrytis cinerea). The sensory aspects of these molecules are illustrated in this review. Generally, the most important cause of this wine contamination is the natural cork of bottle stoppers, but this is not always true. Different origins of contamination include air pollution of the cellars, wood materials, barrels and chips. A review of the possible prevention or remedial treatments to cork taint is also presented. The best solution for this off-flavor is to prevent the wine contaminations.

Flow Synthesis of Biologically-Relevant Compound Libraries

Flow chemistry is one of the most prominent enabling technologies that has greatly shaped the way chemists’ approach organic synthesis. Specifically, in drug discovery, the advantages of flow techniques over batch procedures allow the rapid and efficient assembly of compound libraries to be tested for biological properties. The aim of the present review is to comment on some representative examples from the last five years of literature that highlight how flow procedures are becoming of increasing importance for the synthesis of biologically-relevant molecules.