bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extremophile enzyme activity lab: using catalase from
Pyrobaculum calidifontis
to highlight temperature sensitivity and thermostable enzyme activity
Authors: Scott Joseph W. , Steel J. Jordan 
Published: January 2024

ABSTRACT

There are places on earth that are considered to possess extreme physico-chemical characteristics as they relate to life. Surprisingly, there are microbes that have adapted various strategies that enable them to form robust communities in these environments. The microbes that live in these environments, called extremophiles, are described as being thermophilic, psychrophilic, halophilic, acidophilic, alkaliphilic, barophilic, and so on. Given that extremophiles were not discovered until relatively recently due to a view point that the environments in which they inhabited were not conducive to life, it is reasonable to conclude that the concept of extremophiles may be hard to grasp for students. Herein is described a laboratory exercise adapted from laboratory exercises that use mesophilic catalase enzymes to illustrate the influence of physico-chemical parameters on enzyme activity. Catalase is an enzyme that accelerates the degradation of hydrogen peroxide to water and oxygen gas. In addition to mesophilic catalases, the catalase from
Pyrobaculum calidifontis
, a hyperthermophile with an optimal growth temperature of 90°C, is used to highlight the adaptation of an enzyme to an extreme environment. A visual comparison of bubble production by the hyperthermophilic and mesophilic enzymes after heating at high temperatures dramatically illustrates differences in thermostability that will likely reinforce concepts that are given in a pre-laboratory lecture that discusses not only the extremophiles themselves but also their applications in biotechnology and possible role in the field of astrobiology.
Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model
Authors: Huffines Joshua T. , Boone RaNashia L. , Kiedrowski Megan R. 
Published: January 2024

ABSTRACT

Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression.
Staphylococcus aureus
is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where
S. aureus
-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include
S. aureus
and several species belonging to the genus
Corynebacterium
, including
Corynebacterium propinquum
and
Corynebacterium pseudodiphtheriticum
, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and
S. aureus
, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal
C. propinquum and C. pseudodiphtheriticum
, reduce
S. aureus
growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between
Corynebacterium
species and
S. aureus
dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.

IMPORTANCE

Chronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of
S. aureus
and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on
S. aureus
interactions with the nasal epithelium and the dominant genus of the healthy URT,
Corynebacterium
. Interactions between
Corynebacterium
species and
S. aureus
have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of
S. aureus
and clinical isolates of
Corynebacterium
from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.
A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in
Methanosarcina barkeri
Authors: Fausset Hunter , Spietz Rachel L. , Cox Savannah , Cooper Gwendolyn , Spurzem Scott , Tokmina-Lukaszewska Monika , DuBois Jennifer , Broderick Joan B. , Shepard Eric M. , Boyd Eric S. , Bothner Brian 
Published: January 2024

ABSTRACT

Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS
−
). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS
2
). Recently, paradigm-shifting studies indicate that Fe and S in FeS
2
can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS
2
, as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of
Methanosarcina barkeri
MS grown with FeS
2
, Fe(II)/HS
−
, or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that
M. barkeri
adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS
−
, either as a component of the growth medium [Fe(II)/HS
−
] or generated through reduction of FeS
2
, were likely a major factor underpinning these phenotypic differences.

IMPORTANCE

The methanogenic archaeon
Methanosarcina barkeri
holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life’s origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.
A late Eocene lamprophyre-carbonatite association in the SE Tibetan Plateau: Rapid basalt-induced H2O-saturated partial melting of the upper crust
Authors: Yang Tiannan , Xin Di , Xue Chuandong , Dong Mengmeng , Jiang Lili 
Published: January 2024

Abstract
The processes by which lamprophyres and associated carbonatites are generated remain subject to debate. The Wase Basin on the SE Tibetan Plateau contains trachytes, rhyolites, and minor carbonatites that were emplaced at 37–36 Ma. Coeval lamprophyre dikes are widespread in the adjacent regions. Geochemically and petrographically, both the extrusive trachytes and dikes can be classified as lamprophyre. The numerous millimete r-sized SiO2-rich and calcite-rich ocelli that occur within the trachytes and dikes are solidified pseudomorphs of felsic and calcic melt drops, respectively. These ocelli combined with inherited granitic zircons suggest magma mixing between the calcic melt or felsic melt and basaltic melt. Petrographic evidence, mineral compositions, and zircon textures and U-Pb ages (827–682 Ma) suggest that the felsic melt and the calcic melt were generated by rapid H2O-saturated partial melting of Neoproterozoic granite and limestone, respectively, at &gt;800 °C and &lt;2 kbar, according to available experimental data. These melts were separated from each other and were stored at upper crustal depths, forming a zone of transient magma lenses or parcels. Melts mixed when an ascending basaltic magma intersected this zone. Reaction between the basaltic melt and the calcic melt occurred when they mixed, which formed clinopyroxene of predominantly diop side-hedenbergite solid solution. The observed heterogeneity of the upper crust combined with the variable degrees of magma mixing account for the great chemical diversity of the lamprophyres of SE Tibet. This model sheds new light on the petrogenesis of other lamprophyre-carbonatite associat ions elsewhere.
Chronostratigraphy of Miocene strata in the Berkeley Hills (California Coast Ranges, USA) and the arrival of the San Andreas transform boundary
Authors: Gerasimov Stacey H. , Hodgin Eben B. , Crowley James L. , Swanson-Hysell Nicholas L. 
Published: January 2024

Abstract
Miocene strata of the Claremont, Orinda, and Moraga formations of the Berkeley Hills (California Coast Ranges, USA) record sedimentation and volcanism during the passage of the Mendocino triple junction and early evolution of the San Andreas fault system. Detrital zircon laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) age spectra indicate a change in sedimentary provenance between the marine Claremont formation (Monterey Group) and the terrestrial Orinda and Moraga Formations associated with uplift of Franciscan Complex lithologies. A sandstone from the Claremont formation produced a detrital zircon chemical abrasion–isotope dilution–thermal ionization mass spectrometry (CA-ID-TIMS) maximum depositional age of 13.298 ± 0.046 Ma, indicating younger Claremont deposition than previously interpreted. A trachydacite tuff clast within the uppermost Orinda Formation yielded a CA-ID-TIMS U-Pb zircon date of 10.094 ± 0.018 Ma, and a dacitic tuff within the Moraga Formation produced a CA-ID-TIMS U-Pb zircon date of 9.974 ± 0.014 Ma. These results indicate rapid progression from subsidence in which deep-water siliceous sediments of the Claremont formation were deposited to uplift that was followed by subsidence during deposition of terrestrial sediments of the Orinda Formation and subsequent eruption of the Moraga Formation volcanics. We associate the Orinda tuff clast and Moraga volcanics with slab-gap volcanism that followed the passage of the Mendocino triple junction. Given the necessary time lag between triple junction passage and the removal of the slab that led to this volcanism, subsidence associated with ca. 13 Ma Claremont sedimentation and subsequent Orinda to Moraga deposition can be attributed to basin formation along the newly arrived transform boundary.
Radiation-Geochemical Characteristics of Cryoconite Sediments on the Witte Glacier (Novaya Zemlya Archipelago)
Authors: Miroshnikov A. Yu. , Asadulin En. E. , Kudikov A. V. , Aliev R. A. , Fedulov V. Yu. , Khvostikov V. A. , Flint M. V. 
Published: January 2024

Abstract
The article presents the results of studying specific organomineral formations—cryoconite sediments—samples of which were taken on the surface of the Witte Glacier (Medvezhiy Bay, Novaya Zemlya) on cruise 76 of the R/V Akademik Mstislav Keldysh. The specific activities of 137Cs, 241Am, 207Bi, 210Pb, and 7Be were measured in 14 samples. Analysis of the materials suggests that cryoconite contains radioactive contamination deposited in the glacier in the period from September 1957 to December 1962 as a result of atmospheric nuclear explosions at the Sukhoy Nos test site, located 100 km from the glacier. Extremely high Bi, Ag, Sb, Mo, Pb, Sn contents and a strong correlation with anthropogenic radionuclides may indicate the technogenic emission of these elements during the destructive impact of nuclear explosions on bedrock, the metallogenic specialization of which corresponds to rich polymetallic mineralization.
Nitidine Chloride Inhibits Proliferation and Induces Mitochondrial-Mediated Apoptosis of Human Melanoma A375 and A2058 Cells In Vitro
Authors: Yexian Li  , Yao Yue , Zeng Linxi , Zhang Jinfang , Zhang Guoqiang 
Published: January 2024

Abstract
Melanoma is a malignant tumor transforming from normal melanocytes, with strong invasion and low survival rate. Nitidine chloride (NC) is a natural benzophenidine alkaloid extracted from the roots of traditional Chinese medicine zanthoxylum nitidum. In recent years, many studies have found that NC may have strong anti-tumor activity. However, the efficacy of NC against melanoma has rarely been reported, and the potential molecular mechanism remains unknown. Our study explored the effects of NC on the proliferation and apoptosis of human melanoma A375 and A2058 cells. CCK-8 was utilized to detect the effects of different concentrations of NC on the proliferation of A375 and A2058 cells. Within a certain concentration and time range, NC can inhibit the viability of A375 and A2058 cells significantly in a time-dose-dependent manner. In addition, NC-induced apoptosis was confirmed by DAPI staining and flow cytometry analysis of Annexin V-FITC/PI. Moreover, we observed that the ratio of Bax/Bcl-2 in the cytoplasm increases, activating Caspase-3/-9 and ultimately inducing apoptosis via the mitochondrial pathway. Our study indicated that NC has anti-tumor properties against human melanoma cells through inhibiting proliferation and inducing apoptosis. Therefore, the results provide new insights for future work on the utilization of NC in malignant melanoma treatment.
Dichotomic Role of Low-Concentration EGCG in the Oxaliplatin Sensitivity of Colorectal Cancer Cells
Authors: Wang Zhiyong , Wang Min , Huang Jiahao , Lin Mao , Wei Pei 
Published: January 2024

Abstract
Although epigallocatechin-3-gallate (EGCG) can potentiate chemotherapeutic drugs at high concentrations, its clinical translation is hampered by exceeding possible concentration thresholds. This study proposes a dichotomous use of low-concentration EGCG in chemotherapy. During the first cycle of combined treatment with oxaliplatin (OXA), low-concentration EGCG antagonized the cytotoxic effect of OXA on colorectal cancer (CRC) cells. However, when OXA was subsequently administered, the sensitivity of CRC cells markedly increased. Although low-concentration EGCG counteracted OXA, it reduced the OXA-induced secretion of vascular endothelial growth factor by tumor cells, thereby contributing to the increase in the sensitivity of tumor cells to the second round of OXA treatment. Therefore, low-concentration EGCG showed potential as a viable adjunct to modulate chemosensitivity in CRC.
Immunoliposomes As a Promising Antiviral Agent against SARS-CoV-2
Authors: Bobik T. V. , Simonova M. A. , Rushkevich N. U. , Kostin N. N. , Skryabin G. A. , Knorre V. D. , Schulga A. A. , Konovalova E. V. , Proshkina G. M. , Gabibov A. G. , Deev S. M. 
Published: January 2024

Abstract
According to the World Health Organization, as of January 3, 2020 to September 13, 2023, there were approximately 23 million confirmed cases of COVID-19 reported in the Russian Federation, about 400 thousand of which were fatal. Considering the high rate of mutation of the RNA-containing virus genome, which inevitably leads to the emergence of new infectious strains (Eris and Pyrola), the search for medicinal antiviral agents remains an urgent task. Moreover, taking into account the actively mutating receptor-binding domain, this task requires fundamentally new solutions. This study proposes a candidate immunoliposomal drug that targets the S protein of SARS-CoV-2 by the monoclonal neutralizing antibody P4A1 and ensures the penetration of a highly active ribonuclease into the virus-infected cell, which degrades, among cellular RNA, viral RNA too. We demonstrate a more than 40-fold increase in the neutralizing activity of the developed drug compared to the free monoclonal neutralizing antibody.
Neuronal and Muscle Differentiation of Mammalian Cells Is Accompanied by a Change in PHF10 Isoform Expression
Authors: Bayramova D. O. , Azieva A. M. , Feoktistov A. V. , Georgieva S. G. , Soshnikova N. V. 
Published: January 2024

Abstract
The PBAF chromatin remodeling complex of the SWI/SNF family plays a critical role in the regulation of gene expression during tissue differentiation and organism development. The subunits of the PBAF complex have domains responsible for binding to N-terminal histone sequences. It determines the specificity of binding of the complex to chromatin. PHF10, a specific subunit of the PBAF complex, contains a DPF domain, which is a unique chromatin interaction domain. A PHF10 isoform that lacks the DPF domain is also present in vertebrate cells. This work shows that during neuronal and muscle differentiation of human and mouse cells, the expression of PHF10 isoforms changes: the form that does not have DPF replaces the form in which it is present. Replacement of PHF10 isoforms in the PBAF complex may affect its selectivity in the regulation of genes in differentiating cells.
Effects of anisotropy on the electronic structure and nonlinear optical rectification in a quantum dot with hydrogen molecular ion
Authors: Sari H. 
Published: January 2024

AbstractIn this study, the effects of anisotropy and quantum dot size on energy levels and nonlinear optical rectification of a $$D_{2}^{ + }$$

D

2

+

molecular complex confined to a two-dimensional quantum dot are investigated. The energy eigenvalues and corresponding eigenfunctions of the resulting eigenvalue equation are obtained using the adiabatic approach and the two-dimensional diagonalization method. We conclude that the evolution of the energy spectrum depends predominantly on the anisotropy-induced change of geometric confinement size. In addition, it has been determined that the peak position of the nonlinear optical rectification shifts to lower or higher energies as the asymmetry of the system increases, depending on whether the QD is in the oblate or prolate case. This feature can be considered an advantage in tuning the nonlinear optical properties of systems based on two-dimensional semiconductor heterostructures.
Persistent homotopy groups of metric spaces
Authors: Mémoli Facundo , Zhou Ling 
Published: January 2024

In this paper, we study notions of persistent homotopy groups of compact metric spaces. We pay particular attention to the case of fundamental groups, for which we obtain a more precise description via a persistent version of the notion of discrete fundamental groups due to Berestovskii–Plaut and Barcelo et al. Under fairly mild assumptions on the spaces, we prove that the persistent fundamental group admits a tree structure which encodes more information than its persistent homology counterpart. We also consider the rationalization of the persistent homotopy groups and by invoking results of Adamaszek–Adams and Serre, we completely characterize them in the case of the circle. Finally, we establish that persistent homotopy groups enjoy stability in the Gromov–Hausdorff sense. We then discuss several implications of this result including that the critical spectrum of Plaut et al. is also stable under this notion of distance.
Automatic Parallelism Management
Authors: Westrick Sam , Fluet Matthew , Rainey Mike , Acar Umut A. 
Published: January 2024

On any modern computer architecture today, parallelism comes with a modest cost,
born from the creation and management of threads or tasks. Today, programmers
battle this cost by manually optimizing/tuning their codes to minimize the cost
of parallelism without harming its benefit, performance. This is a difficult
battle: programmers must reason about architectural constant factors hidden
behind layers of software abstractions, including thread schedulers and memory
managers, and their impact on performance, also at scale. In languages that
support higher-order functions, the battle hardens: higher order functions can
make it difficult, if not impossible, to reason about the cost and benefits of
parallelism.
Motivated by these challenges and the numerous advantages of high-level
languages, we believe that it has become essential to manage parallelism
automatically so as to minimize its cost and maximize its benefit. This is a
challenging problem, even when considered on a case-by-case,
application-specific basis. But if a solution were possible, then it could
combine the many correctness benefits of high-level languages with performance
by managing parallelism without the programmer effort needed to ensure
performance. This paper proposes techniques for such automatic management of
parallelism by combining static (compilation) and run-time techniques.
Specifically, we consider the Parallel ML language with task parallelism, and
describe a compiler pipeline that embeds "potential parallelism" directly into
the call-stack and avoids the cost of task creation by default. We then pair
this compilation pipeline with a run-time system that dynamically converts
potential parallelism into actual parallel tasks. Together, the compiler and
run-time system guarantee that the cost of parallelism remains low without
losing its benefit. We prove that our techniques have no asymptotic impact on
the work and span of parallel programs and thus preserve their asymptotic
properties. We implement the proposed techniques by extending the MPL compiler
for Parallel ML and show that it can eliminate the burden of manual optimization
while delivering good practical performance.