Predictive stochastic analysis of massive filter-based electrochemical reaction networks

Chemical reaction networks (CRNs) are powerful tools for obtaining mechanistic insight into complex reactive processes. However, they are limited in their applicability where reaction mechanisms are not well understood and products are unknown. Here we report new methods of CRN generation and analysis that overcome these limitations. By constructing CRNs using filters rather than templates, we can capture species and reactions that are unintuitive but fundamentally reasonable. The resulting massive CRNs can then be interrogated via stochastic methods, revealing thermodynamically bounded reaction pathways to species of interest and automatically identifying network products. We apply this methodology to study solid-electrolyte interphase (SEI) formation in Li-ion batteries, generating a CRN with ~86,000,000 reactions. Our methods automatically recover SEI products from the literature and predict previously unknown species. We validate their formation mechanisms using first-principles calculations, discovering novel kinetically accessible molecules. This methodology enables the de novo exploration of vast chemical spaces, with the potential for diverse applications across thermochemistry, electrochemistry, and photochemistry.

Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany

Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.

Liparis inaudita (Orchidaceae, Malaxidinae), a new species from the Bosque de Protección Alto Mayo, San Martín, Peru

Background: During an ongoing inventory of the orchids of the Bosque de Protección Alto Mayo, northern Peru, a population morphologically assignable to Liparis section Decumbentes was found. This is a little-known group restricted to wet montane Andean forests and consists of four species, from which the BPAM populations differs in leaf and labellum morphology. Hypotheses: The features of the plants led us to hypothesize that it represents an unknown species, which can be distinguished morphologically from its congeners. Taxon: Liparis section Decumbentes, Liparis sp. nov. Study site and dates: Peru, department of San Martín, Rioja province, Pardo Miguel Naranjos district, Bosque de Protección Alto Mayo, sector Venceremos. Methods: The unknown entity was studied in detail using fresh, pressed, and alcohol-preserved specimens. We also compared it to type specimens, other specimens of Liparis section Decumbentes housed in herbaria in Peru and abroad, and with descriptions from specialized literature. Results: A leaf feature and the unique labellum morphology of the unknown entity permit it to be distinguished clearly from all other species of Liparis section Decumbentes. Conclusions: The new species shares with L. sessilis the sessile leaf blades and the convex labellum, but differs from it and all other species of the section in its saddle-shaped labellum, which when spread out is narrowly obtrapezoid, with minute basal auricles, laciniate distal margins, and the apex projected into a narrowly triangular lobe.

Introduction.

Given the rich rainforest flora of Papua New Guinea, which includes some 8000 known plant species, it is understandable why this land mass contains such a rich dacine fauna, with the largest number of species of any land mass across the entire Asian/Pacific region. Major collections of Dacini have been obtained, over the past two decades, by male lure trapping and host fruit sampling across large areas of Papua New Guinea. These surveys have provided the specimens for the descriptions of the new species in this book. In particular, the use of vanillylacetone has resulted in the collection of a number of previously unknown species.

Template-free reaction networks enable predictive and automated analysis of complex electrochemical reaction cascades

Chemical reaction networks (CRNs) are powerful tools for obtaining mechanistic insight into complex reactive processes. However, they are limited in their applicability where reaction mechanisms are unintuitive, and products are unknown. Here we report new methods of CRN generation and analysis that overcome these limitations. By constructing CRNs using filters rather than templates, we can capture species and reactions that are unintuitive but fundamentally reasonable. The resulting massive CRNs can then be interrogated via stochastic methods, revealing thermodynamically bounded reaction pathways to species of interest and automatically identifying network products. We apply this methodology to study solid-electrolyte interphase (SEI) formation in Li-ion batteries, generating a CRN with ~86,000,000 reactions. Our methods automatically recover SEI products from the literature and predict previously unknown species. We validate their formation mechanisms using first-principles calculations, discovering multiple novel kinetically accessible molecules. This methodology enables the de novo exploration of vast chemical spaces, with the potential for diverse applications across thermochemistry, electrochemistry, and photochemistry.

Description of three new Pipunculus Latreille, 1802 species (Diptera: Pipunculidae) from Central Europe and Turkey

Extensive sampling of Pipunculidae in the frame of faunistic research in former Czechoslovakia as well as several other European countries over the last two decades has resulted in the discovery of several unknown species of this family. In this work, we present descriptions of three new species of the genus Pipunculus Latreille, 1802. Pipunculus adami Kozánek, sp. nov. and P. lindae Kozánek, sp. nov. are described from Slovakia and the Czech Republic, P. anatolicus Kozánek, sp. nov. is described on the basis of specimens from Turkey. The detailed redescription of the male of P. wolfi Kowarz, 1887, including the so far unknown male terminalia, is presented. The key taxonomic characters are visualized as interactive microphotographs provided with browsing software.

Cyanoboletus macroporus (Boletaceae), a new bolete species from Pakistani forests Samina

<em>Cyanoboletus macroporus</em> belonging to <em>C. pulverulentus</em> species complex is designated as a new species from the moist temperate and sub-alpine oak forests of Pakistan after in depth macroscopic, microscopic and phylogenetic analyses using the ITS region of nrDNA as well as comparison with allied taxa. This species belonging to Boletoid group is morphologically distinguished from allied taxa (<em>Cyanoboletus flavosanguineus</em>, <em>C. hymenoglutinosus</em>, <em>C. pulverulentus</em>, <em>C. rainisii</em>, and <em>C. sinopulverulentus</em>) by wider openings of pores. <em>C. macroporus</em> is also phylogenetically distinct from <em>C. sinopulverulentus</em> and <em>C. pulverulentus</em>, the most closely related species. Phylogenetic analysis outlined the existence of previously unknown species of this genus. Field photographs of fresh basidocarps and line drawings of micro-characters are provided along with a phylogenetic tree as well as a comparison table and a key of distinctive features of all the species in this genus. This is the first authentic species belonging to <em>Cyanoboletus</em> from Pakistan. Previously, only <em>C. pulverulentus</em> has been mentioned in literature, but no morphological data is available regarding this report. With the addition of this taxon, species number of <em>Cyanoboletus</em> will increase to eight. From Pakistan, despite of the fact that there is great diversity of mushrooms in moist temperate areas (Yousaf et al. 2012), this is the first study that describes a species belonging to <em>Cyanoboletus</em> genus. Previously only one ambiguous species, <em>Cyanoboletus pulverulentus</em>, has been mentioned in literature (Iqbal & Khalid 1996), but with no available materials that could confirm this finding. In this study, <em>Cyanoboletus macroporus</em> is described as a new to science and increase the current species number of <em>Cyanoboletus</em> to eight.

Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites

The pathogenesis of ulcerative colitis (UC) is unknown, although genetic loci and altered gut microbiota have been implicated. Up to a third of patients with moderate to severe UC require proctocolectomy with ileal pouch ano-anastomosis (IPAA). We aimed to explore the mucosal microbiota of UC patients who underwent IPAA. Methods: For microbiome analysis, mucosal specimens were collected from 34 IPAA individuals. Endoscopic and histological examinations of IPAA were normal in 21 cases, while pouchitis was in 13 patients. 19 specimens from the healthy control (10 from colonic and 9 from ileum) were also analyzed. Data were analyzed using an ensemble of software packages: QIIME2, coda-lasso, clr-lasso, PICRUSt2, and ALDEx2. Results: IPAA specimens had significantly lower bacterial diversity as compared to normal. The microbial composition of the normal pouch was also decreased also when compared to pouchitis. Faecalibacterium prausnitzii, Gemmiger formicilis, Blautia obeum, Ruminococcus torques, Dorea formicigenerans, and an unknown species from Roseburia were the most uncommon in pouch/pouchitis, while an unknown species from Enterobacteriaceae was over-represented. Propionibacterium acnes and Enterobacteriaceae were the species most abundant in the pouchitis and in the normal pouch, respectively. Predicted metabolic pathways among the IPAA bacterial communities revealed an important role of immunometabolites such as SCFA, butyrate, and amino acids. Conclusions: Our findings showed specific bacterial signature hallmarks of dysbiosis and could represent bacterial biomarkers in IPAA patients useful to develop novel treatments in the future by modulating the gut microbiota through the administration of probiotic immunometabolites-producing bacterial strains and the addition of specific prebiotics and the faecal microbiota transplantation.

Novel Secondary Metabolites from New Zealand Marine Sponges

<p>The isolation and structure elucidation of 12 new compounds from four different genera of marine sponge is described. Continued work with the marine sponge Raspailia topsenti resulted in the isolation of two clerodane diterpenes, raspailodanes F (40) and G (41). Raspailodane F contains a novel tricyclo[5.4.0.0]undecane scaffold including a cyclopropyl ring. A nonadecanoic acid derivative, petrosianoic acid (122), was isolated from an unknown species of the genus Petrosia. It is believed that 122 is only the third nonadecanoic acid derivative reported from the marine environment. The marine sponge Dendrilla rosea was examined for the presence of new spongian diterpenes. While no new diterpenes were discovered, the acetylenic nitrile dendronitrile (158) was isolated along with two known diterpenes and a known steroid. Dendronitrile is the first acetylenic nitrile discovered from the marine environment and only the third ever reported. Seven new lamellarins and one new dictyodendrin were isolated from Dictyodendrilla dendyi alongside one known lamellarin and two known dictyodendrins. Lamellarins Θ (187) and κ (188) are related to known lamellarins. The remaining five lamellarins are sulfated derivatives, lamellarin Θ 4'',4'''-disulfate (190), lamellarin O 4'''-sulfate (191), lamellarin O 4'',4'''-disulfate (192), lamellarin κ 4'''-sulfate (193), and lamellarin κ 4'',4'''- disulfate (194). Dictyodendrin F (195) is a new natural product previously only reported as a semi-synthetic derivative of known dictyodendrins. Lamellarin shows moderate cytotoxic activity. The biological activity of the remaining compounds, particularly the sulfated derivatives, is under investigation. The screening protocol used to analyse crude sponge extracts was refined and a number of advances were made towards the automated analysis of the spectra generated. A method was devised to extract peak data from screen HSQC spectra and by combining these data, to produce a software-based mask of known correlations. The application of this mask was demonstrated in three different ways to three different screen HSQC spectra. To aid in the identification of interesting correlations identified by the mask, a database of HSQC correlations was compiled from literature and in-house sources. A new method of describing the chemical environment of a given position was developed to suit the needs of the database. At present, the database contains 91 compounds and represents over 2500 individual HSQC correlations. Development of both the software screening technique and the HSQC correlation database is ongoing.</p>

Novel Secondary Metabolites from New Zealand Marine Sponges

<p>The isolation and structure elucidation of 12 new compounds from four different genera of marine sponge is described. Continued work with the marine sponge Raspailia topsenti resulted in the isolation of two clerodane diterpenes, raspailodanes F (40) and G (41). Raspailodane F contains a novel tricyclo[5.4.0.0]undecane scaffold including a cyclopropyl ring. A nonadecanoic acid derivative, petrosianoic acid (122), was isolated from an unknown species of the genus Petrosia. It is believed that 122 is only the third nonadecanoic acid derivative reported from the marine environment. The marine sponge Dendrilla rosea was examined for the presence of new spongian diterpenes. While no new diterpenes were discovered, the acetylenic nitrile dendronitrile (158) was isolated along with two known diterpenes and a known steroid. Dendronitrile is the first acetylenic nitrile discovered from the marine environment and only the third ever reported. Seven new lamellarins and one new dictyodendrin were isolated from Dictyodendrilla dendyi alongside one known lamellarin and two known dictyodendrins. Lamellarins Θ (187) and κ (188) are related to known lamellarins. The remaining five lamellarins are sulfated derivatives, lamellarin Θ 4'',4'''-disulfate (190), lamellarin O 4'''-sulfate (191), lamellarin O 4'',4'''-disulfate (192), lamellarin κ 4'''-sulfate (193), and lamellarin κ 4'',4'''- disulfate (194). Dictyodendrin F (195) is a new natural product previously only reported as a semi-synthetic derivative of known dictyodendrins. Lamellarin shows moderate cytotoxic activity. The biological activity of the remaining compounds, particularly the sulfated derivatives, is under investigation. The screening protocol used to analyse crude sponge extracts was refined and a number of advances were made towards the automated analysis of the spectra generated. A method was devised to extract peak data from screen HSQC spectra and by combining these data, to produce a software-based mask of known correlations. The application of this mask was demonstrated in three different ways to three different screen HSQC spectra. To aid in the identification of interesting correlations identified by the mask, a database of HSQC correlations was compiled from literature and in-house sources. A new method of describing the chemical environment of a given position was developed to suit the needs of the database. At present, the database contains 91 compounds and represents over 2500 individual HSQC correlations. Development of both the software screening technique and the HSQC correlation database is ongoing.</p>