bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes
Authors: Liu Shuang , Greenhut Isaac V. , Heist E. Patrick , Heist Melanie R. , Moe Luke A. 
Published: November 2023

ABSTRACT

The popularity and production of whiskey have grown dramatically in recent years. During whiskey fermentation, lactic acid bacteria (LAB) are a major concern since they can outcompete yeast and spoil the fermentation. However, some bacteria present in the fermentation could potentially counter this effect and promote fermentation efficiency. To better understand the possible roles bacteria play in yeast-based whiskey fermentations, we examined bacterial community dynamics across fermentation stages and investigated how variation in the mash recipe affects bacterial community composition and fermentation efficiency. To this end, we collected 193 samples from three distilleries at the beginning (Cook/set), middle (Fermentation), and end (Drop) of whiskey fermentation, with six mash recipes sampled from one distillery. We used high-performance liquid chromatography (HPLC) to quantify the contents of sugars, organic acids, and ethanol, which revealed distinct differences between distilleries and mash recipes. High-throughput Illumina Miseq sequencing of the 16S rRNA gene V4 region revealed that bacterial communities shifted toward Firmicutes during the fermentative conversion of sugar to ethanol, especially Lactobacillales. Mash recipes also influenced sugar composition, fermentation efficiency, and microbial dynamics. Recipe-specific operational taxonomic unit (OTU) biomarkers in Drop samples included
Leuconostoc
for corn,
Lactococcus
for wheat, and
Lactobacillaceae_unclassified
for rye, while
Escherichia/Shigella
was associated with sorghum, suggesting potential suppression of LAB.

IMPORTANCE
Production of ethanol from sugars and yeast is an ancient, ostensibly simple process. The source of sugars varies depending on the desired product and can include fruits, vegetables, molasses, honey, or grains, among other things. The source of yeast can be natural in the case of spontaneous ferments, but dry yeast addition is typical for large-scale fermentations. While the polymicrobial nature of some alcoholic fermentations is appreciated (e.g., for wine), most grain-based ethanol producers view microbes, apart from the added yeast, as “contaminants” meant to be controlled in order to maximize efficiency of ethanol production per unit of sugar. Nonetheless, despite rigorous cleaning-in-place measures and cooking the mash, bacteria are routinely cultured from these fermentations. We now know that bacteria can contribute to fermentation efficiency on an industrial scale, yet nothing is known about the makeup and stability of microbial communities in distilled spirit fermentations. The work here establishes the roles of mash recipes and distillery practices in microbial community assembly and dynamics over the course of fermentation. This represents an important first step in appreciating the myriad roles of bacteria in the production of distilled spirits.
Transcriptional regulation of the fidaxomicin gene cluster and cellular development in
Actinoplanes deccanensis
YP-1 by the pleiotropic regulator MtrA
Authors: Xie Huang , Ruan Jing-Yi , Bu Qing-Ting , Li Yue-Ping , Su Yi-Ting , Zhao Qing-Wei , Du Yi-Ling , Li Yong-Quan 
Published: November 2023

ABSTRACT

Fidaxomicin is an 18-membered glycosidic macrolide polyketide that was clinically used in the treatment of
Clostridium difficile
infection in 2011. Although the biosynthetic mechanism and pathway-specific regulator of fidaxomicin were well elaborated, little is known about the pleiotropic regulators outside the fidaxomicin gene cluster. To further reveal the transcriptional regulatory mechanism of fidaxomicin biosynthesis in
Actinoplanes deccanensis
YP-1, we used the 5′-biotin-labeled
fadR1
promoter (
fadS5R1p
) as a probe to affinity isolate the
fadS5R1p
-interactive protein MtrA, a response regulator of the two-component system MtrAB, from the proteome of mycelia. MtrA is bound directly to
fadS5R1p
to positively regulate gene cluster expression and fidaxomicin production. Fidaxomicin production was improved by 37% in the
mtrA
overexpressed strain. Furthermore, we revealed that MtrA tends to bind GTKAYS motifs and influence genes involved in secondary metabolites, phosphate transport, methionine transport, nitrogen metabolism, drug transport, membrane properties, etc. Overall, for the first time at the transcriptional level, we comprehensively revealed a pleiotropic regulator, MtrA, that not only directly mediates the FadR1-specific pathway to regulate the proper production of fidaxomicin but also participates in bacterial growth and development.

IMPORTANCE

Cascade regulation networks are almost present in various kinds of microorganisms, but locating and systematically elucidating specific pleiotropic regulators related to a certain gene cluster can be a tricky problem. Here, based on the promoter of the fidaxomicin pathway-specific regulator FadR1, we utilized a “DNA to Proteins” affinity purification method and captured a global regulator MtrA, which positively regulates fidaxomicin biosynthesis. In the
mtrA
overexpressed strain, the production of fidaxomicin was improved by 37% compared to the native strain. Then, we combined the “Protein to DNAs” affinity purification method (DAP-seq) with the results of RNA-seq and systematically elucidated the primary and secondary metabolic processes in which MtrA directly or indirectly participates. Thus, our work brought up a new way to improve fidaxomicin production from the perspective of global regulation and analyzed the regulatory mechanism of MtrA. Meanwhile, we provided a novel methodology for the research of cascade regulation networks and vital secondary metabolites.
Acidic pH modulates
Burkholderia cenocepacia
antimicrobial susceptibility in the cystic fibrosis nutritional environment
Authors: Morales L. Daniela , Av-Gay Yossef , Murphy Michael E. P. 
Published: November 2023

ABSTRACT

Burkholderia cenocepacia
is an opportunistic pathogen correlated with increased disease severity and mortality in cystic fibrosis (CF) patients. One major difficulty when treating these infections in CF is the poor relationship between
in vitro
susceptibility and clinical outcome. Previous analysis of CF sputum samples showed elevated levels of zinc and iron ions and an acidic pH (2.9–6.5) compared to healthy individuals. Additionally,
B. cenocepacia
grows at an acidic pH (~3.5)
in vitro
and persists for 24 h in the intracellular acid compartments of amoebas and macrophages. We seek to understand the impact of acidic pH and increased zinc and iron concentrations on antibiotic susceptibility in the CF nutritional environment. The Synthetic Cystic Fibrosis sputum Media (SCFM) was modified to represent the acidic pH and increased zinc and iron concentrations found in CF sputum (SCFM-FeZn). We found that the nutritional environment modulated
B. cenocepacia
susceptibility to antimicrobials, and more strikingly, acidic pH decreased susceptibility to most antimicrobials used clinically to treat these infections. Finally, we assessed susceptibility against a custom compound library of antimicrobials using SCFM-FeZn agar plates. Out of 591 antibiotics, only 18 were active against
B. cenocepacia
at both neutral and acidic pH. Four of these compounds (novobiocin, coumermycin, mitomycin C, and streptonigrin) were selected for susceptibility assays in liquid culture. Here, we show that acidic pH modulates antimicrobial susceptibility in the CF nutritional environment and that susceptibility testing in media that mimic the host nutritional environment could pave the way to finding new therapies against infections in CF.

IMPORTANCE

Burkholderia cenocepacia
causes severe infections in cystic fibrosis (CF) patients. CF patients are prone to reoccurring infections due to the accumulation of mucus in their lungs, where bacteria can adhere and grow. Some of the antibiotics that inhibit
B. cenocepacia
in the laboratory are not effective for CF patients. A major contributor to poor clinical outcomes is that antibiotic testing in laboratories occurs under conditions that are different from those of sputum. CF sputum may be acidic and have increased concentrations of iron and zinc. Here, we used a medium that mimics CF sputum and found that acidic pH decreased the activity of many of the antibiotics used against
B. cenocepacia
. In addition, we assessed susceptibility to more than 500 antibiotics and found four active compounds against
B. cenocepacia
. Our findings give a better understanding of the lack of a relationship between susceptibility testing and the clinical outcome when treating
B. cenocepacia
infections.
Immune targets to stop future SARS-CoV-2 variants
Authors: Silva Souza Milena , Pires Farias Jéssica , Barros Luiz Wilson , Birbrair Alexander , Durães-Carvalho Ricardo , de Souza Ferreira Luís Carlos , Amorim Jaime Henrique 
Published: November 2023

ABSTRACT
The SARS-COV-2 variants of concern (VOCs) accumulated mutations that confer to the viral particle a higher infectivity as well as a capacity to escape neutralizing antibodies (NAbs) elicited by vaccines. In this study, we aimed to identify immune determinants that can be targeted to control future SARS-CoV-2 VOC. Using an immunoinformatics pipeline, we constructed a first data set consisting of 215 spike (S) protein amino acid sequences of the wild-type SARS-CoV-2, as well as of the Alpha, Beta, Delta, Gamma, and Omicron variants/subvariants (BA.1, BA.2, BA.4, BA.5, XBB, and BQ.1). A second data set was composed of epitope amino acid sequences for NAb as well as for T-cells involved in anti-viral activity, retrieved from the Immune Epitope Database (IEDB). Epitope conservation and population coverage analyses were carried out using the data sets. The localization of fully conserved epitopes in the S protein was performed using PyMOL. As main results, (i) fully conserved epitopes were identified: 28 for NAbs and 53 and 99 for class-I and class-II human leukocyte antigen, respectively; (ii) the fully conserved epitopes were shown to have high coverage in the world population (99.77% class combined); and (iii) the receptor-binding domain (RBD) of the S protein better balanced numbers of epitopes for NAb and T-cells, while the subunit two concentrated the highest numbers of T-cell epitopes. These results indicate that the RBD region holds different kinds of immune targets that could be used in an escape mutation-proof vaccine antigen to control future SARS-CoV-2 variants.

IMPORTANCE
The emergence of SARS-CoV-2 had a major impact across the world. It is true that the collaboration of scientists from all over the world resulted in a rapid response against COVID-19, mainly with the development of vaccines against the disease. However, many viral genetic variants that threaten vaccines have emerged. Our study reveals highly conserved antigenic regions in the vaccines have emerged. Our study reveals highly conserved antigenic regions in the spike protein in all variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) as well as in the wild-type virus. Such immune targets can be used to fight future SARS-CoV-2 variants.
Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant
Authors: Heidrich Vitor , Knebel Franciele H. , Bruno Julia S. , de Molla Vinícius C. , Miranda-Silva Wanessa , Asprino Paula F. , Tucunduva Luciana , Rocha Vanderson , Novis Yana , Fregnani Eduardo R. , Arrais-Rodrigues Celso , Camargo Anamaria A. 
Published: November 2023

ABSTRACT
Allogeneic hematopoietic stem-cell transplant (allo-HSCT) is potentially curative for several hematological disorders. Before stem-cell infusion, recipients undergo a conditioning regimen with chemo/radiotherapy and immunosuppressants, requiring the use of antibiotics to treat and prevent infections. This regimen promotes drastic alterations in the recipient’s microbiota, including the oral microbiota, which have been associated with allo-HSCT complications and poor outcomes. However, long-term longitudinal studies on the oral microbiota of allo-HSCT recipients are scarce and disregard the existence of distinct microbiota within the oral cavity. Here, we used 16S rRNA gene sequencing to characterize the longitudinal microbiota dynamics in a prospective cohort of 31 allo-HSCT recipients at three oral sites (gingival crevicular fluid, oral mucosa, and supragingival biofilm). We found declines in bacterial diversity and major shifts in microbiota composition in all oral sites during allo-HSCT, including blooms of potentially pathogenic genera. These blooms in some cases preceded respiratory infections caused by the blooming bacteria. We also noticed that differences in microbiota composition between oral sites were lost during allo-HSCT. Overall, after allo-HSCT, the distinct oral microbiota returned to their preconditioning state, although at variable levels of competence per patient. After stratifying patients based on recovery levels, we found that recoverers of the oral mucosa microbiota composition had earlier reconstitution of normal blood leukocyte counts. Most notably, oral mucosa microbiota recovery was an independent biomarker of better allo-HSCT outcomes. This study highlights the potential clinical impact of the oral microbiota in the allo-HSCT setting and the clinical value of tracking oral microbiota changes during allo-HSCT.

IMPORTANCE
The oral cavity is the ultimate doorway for microbes entering the human body. We analyzed oral microbiota dynamics in allogeneic hematopoietic stem-cell transplant recipients and showed that microbiota injury and recovery patterns were highly informative on transplant complications and outcomes. Our results highlight the importance of tracking the recipient’s microbiota changes during allogeneic hematopoietic stem-cell transplant to improve our understanding of its biology, safety, and efficacy.
A 5000 yr record of coastal uplift and subsidence reveals multiple source faults for past earthquakes on the central Hikurangi margin, New Zealand
Authors: Pizer Charlotte , Clark Kate , Howarth Jamie , Howell Andrew , Delano Jaime , Hayward Bruce W. , Litchfield Nicola 
Published: November 2023

Abstract
Prehistoric records of subduction earthquakes are often distinguished by evidence of synchronous widespread coastal deformation, the extent of which negates the plausibility of alternative source faults. At the Hikurangi subduction margin in New Zealand, untangling the record of subduction interface ruptures is complicated. Large earthquake age uncertainties inhibit unique solutions of along-strike correlations, and complex patterns of coastal deformation caused by upper-plate faulting prevent reliable indication of source faults. In this work, we improved paleoearthquake reconstructions on the central Hikurangi margin with a new, well-constrained 5000 yr earthquake record from Pakuratahi Valley near Napier, North Island, New Zealand. Evidence of laterally extensive paleoenvironmental changes is consistent with coseismic subsidence and coseismic uplift in large earthquakes. Radiocarbon dates on fragile terrestrial macrofossils and tephra isochrons were used to construct robust age models that yielded earthquake ages of 4839–4601 calibrated (cal.) yr B.P., 3630–3564 cal. yr B.P., 2687–2439 cal. yr B.P., and 1228–823 cal. yr B.P. Integration of these ages with refined earthquake chronology from nearby Ahuriri Lagoon indicated that the next large earthquake impacting the Napier area is more likely to cause coastal subsidence than uplift. Drawing on correlations with cotemporal evidence elsewhere on the central margin, we infer that the overall patterns of coseismic deformation could be generated by either rupture of the subduction interface or upper-plate faults, or both. This inability to separate source faults for past earthquakes limits the efficiency of forecasting future earthquakes. Similar problems of intertwined paleoearthquake signatures likely apply to other plate boundaries, where we recommend cautious interpretation of coastal deformation to accurately address the hazard from both types of source faults.
New biogeochemical insights into Mesozoic terrestrial paleoecology and evidence for omnivory in troodontid dinosaurs
Authors: Cullen Thomas M. , Cousens Brian L. 
Published: November 2023

Abstract
The Cretaceous paleocommunities of North America preserve a rich record of biodiversity that suggests many species occupied narrow biogeographic ranges in comparison to their ecological equivalents in extant systems. How taxa in these systems partitioned their niches and structured their communities can be difficult to determine from fossils alone, which has led to a variety of hypotheses concerning diets and habitat use. Here, we examine element ratios (Sr/Ca, Ba/Ca) in the enamel of a suite of co-occurring vertebrate taxa sampled from a spatiotemporally constrained interval in the Oldman Formation of Alberta, Canada, to reconstruct trophic structure, and use δ13C, δ18O, and 87Sr/86Sr compositions to test for niche partitioning and habitat use among hadrosaurids, ceratopsids, and ankylosaurs. We also test previously proposed dietary hypotheses of troodontid theropods.
In large ornithischians, we find Ba/Ca and Sr/Ca ratios that are consistent with herbivory, with hadrosaurs distinct from ceratopsids and ankylosaurids in their 87Sr/86Sr ranges, a pattern that is indicative of differences in habitat use/breadth, dietary plant sources, and feeding height. The sampled mammals, varanoid lizards, dromaeosaurids, and tyrannosaurids preserve a gradient of lower Sr/Ca and Ba/Ca ratios that is consistent with animal-dominant omnivorous to faunivorous diets. Troodontids, which have been variably hypothesized as either faunivorous, omnivorous, or herbivorous due to their distinct and unusual dentition, preserve Sr/Ca and Ba/Ca ratios that fall between those of the ornithischians and the dromaeosaurids. From these multi-proxy data, we interpret troodontids as mixed-feeding to plant-dominant omnivores. These proxies represent a valuable tool for understanding the trophic and community ecology of Cretaceous ecosystems and hold enormous potential for future research in paleobiology.
Expanding the metamorphic devolatilization model: Komatiites as a source for orogenic gold deposits in high-grade metamorphic rocks
Authors: Yu Chang , Zhong Richen , Tomkins Andrew G. , Cui Hao , Chen Yanjing 
Published: November 2023

Abstract
Orogenic gold deposits contribute the largest proportion of the world’s gold reserves, and the source of their ore-forming components has been recognized as the metamorphic devolatilization of metapelites or metabasites across the greenschist- to amphibolite-facies transition. However, hypozonal orogenic gold deposits represent an enigma in this context. Some of these apparently formed in higher-grade metamorphic rocks when temperatures were beyond the wet solidus of quartz-feldspar–bearing rocks; it is therefore puzzling how these fluids were generated in the source and migrated through the crust without causing partial melting. Here, we show that devolatilization of hydrated komatiites, a volumetrically significant lithological unit in Precambrian greenstone belts, is a viable model that can plausibly lead to gold mineralization at amphibolite-facies conditions. Our thermodynamic simulations indicate that subsolidus metamorphic devolatilization of komatiites at ~700 °C (upper amphibolite facies) can unlock significant amounts of gold via dehydration of talc and chlorite. This genetic model is supported by the geochemical characteristics of, and estimated pressure-temperature (P-T) formation conditions of, hypozonal gold deposits and the intimate spatiotemporal association between hypozonal deposits and komatiites in greenstone belts. This work expands the P-T range of the metamorphic devolatilization model and enhances its robustness in explaining gold mineralization in metamorphic terranes.
Sustained deformation across the Sub-Himalayas since 200 ka
Authors: Bouscary Chloé , King Georgina E. , Grujic Djordje , Lavé Jérôme , Almeida Rafael , Hetényi György , Herman Frédéric 
Published: November 2023

Abstract
The Himalayan Main Frontal Thrust (MFT) currently accommodates approximately half, i.e., 12–23 mm/yr, of the convergence between the Indian and Eurasian tectonic plates by uplift and deformation of the Sub-Himalayas. While deformation is well documented at modern and million-year time scales, almost no quantitative data are available that constrain Quaternary time scale deformation rates along and within this key tectonic unit. Filling this knowledge gap is crucial to better understanding tectonics and the seismic cycle in this densely populated Himalayan region. We quantify exhumation rates in the Sub-Himalayas using the recently established luminescence thermochronometry technique over time scales of 105 yr, which documents exhumation over the final few kilometers of Earth’s crust. The ultra-low closure temperature of luminescence thermochronometry enables us to resolve thermal histories from the Siwalik Group (Nepal) rocks, which have experienced maximum burial temperatures of ~120 °C. An extensive set of 33 samples was collected from western Nepal to eastern Bhutan, from which 22 yield exhumation rates of ~3–11 mm/yr over the past ~200 k.y. We converted these values to minimum cumulative thrust slip rates of ~6–22 mm/yr, assuming a thrust dip angle of 30°. Our luminescence thermochronometry results show that the Sub-Himalayan fold-and-thrust belt, particularly the MFT, accommodates at least 62% of Himalayan convergence since at least 200 ka. Our data also show activity of some intra-Siwalik thrusts throughout this period, implying that internal deformation of the orogenic wedge and strain partitioning may have occurred.
Source and Generation Parameters of the Granitoid Melts of the Archean Charnockite–Enderbite Complex in Karelia, with Reference to the Pon’goma-Navolok Massif
Authors: Kozlovskii V. M. , Kurdyukov E. B. , Yakushik M. A. , Travin V. V. , Zinger T. F. , Yakushev A. I. , Fugzan M. M. , Kirnozova T. I. , Ushakova S. A. 
Published: November 2023

Abstract—
The paper presents authors’ original detailed data on rocks of the Archean Pon’goma-Navolok charnockite−enderbite complex in northern Karelia. The rocks practically have not been modified and are preserved within a rigid block among Paleoproterozoic zones of ductile deformations and metamorphism. The geochemistry of the rocks and their isotope−geochemical features indicate that the protolith from which the enderbite melts of the main phase of the massif were derived may have been amphibolites. The enderbite melts were derived from these amphibolites under the effect of K2O-, Na2O-, and SiO2-bearing fluids; and the enderbites were subsequently charnockitized with the involvement of fluids enriched in K2O and SiO2. Physicochemical modeling indicates that the enderbite melt was derived from the amphibolite protolith at a depth of about 45 km (P = 14.8 kbar, T = 1030−1080°C) under the effect of saline H2O−CO2 fluid. Comparison of the P−T parameters of the granulite-facies metamorphism of the metabasites and the parameters under which the enderbite melts were derived indicates that Archean granulite-facies metamorphism in the Belomorian belt in northern Karelia was of contact but not regional nature and was induced by the high-temperature field of an emplaced enderbite massif. The orthogneisses hosting the Pan’goma-Navolok massif inherit geochemical features of the unsheared, ungneissose, and unmetamorphosed enderbites. This means that enderbites analogous to those of the Pan’goma-Navolok massif may have served as the protolith of some of the orthogneisses, and that enderbites may have been spread more widely in the Archean than the currently preserved single enderbite massifs.