bluuebunny/crossref_metadata_2025 huggingface dataset:
In silico design of sgRNA for CRISPR/Cas9-mediated FaRALF33 gene mutagenesis to decrease the infection process to Colletotrichum acutatum in strawberry
Authors: Hernández-Amasifuen Angel David , Yupanqui-Celestino Mao , Jherina Pineda-Lázaro Alexandra , Delgado-Mera Elvin , Ramírez-Viena Linder , Pesantes-Rojas Carlos Roberto , Corazon-Guivin Mike Anderson
Published: February 2024

Rapid alkalinization factors (RALFs) are ubiquitous cysteine-rich peptides present in plants. They exert diverse functions as hormonal signals in various processes, including cell growth, root elongation, and fertilization. RALF peptides can also act as negative regulators of the plant immune response, inhibiting the formation of the signal receptor complex for immune activation. In Fragaria × ananassa, silencing of FaRALF33 gene plays a key role in the defense against the fungal pathogen Colletotrichum acutatum. In this study, single-guide RNA (sgRNAs) were designed in silico for clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) 9-mediated FaRALF33 gene mutagenesis in F. × ananassa for the reduction of C. acutatum infection. FaRALF33 was compared with homologous RALF33 sequences from other plant species, showing that the amino acid sequence of FaRALF33 presents typical sequences of known RALF peptides in RRILA proteolytic site, in addition to tight clustering presented by FaRALF33 with FvRALF33. The online tool CHOPCHOP provided 73 hits for FaRALF33 gene, selecting two sgRNA sequences for mutagenesis, sgRNA 1 (5’-CGACTCTCCCATCTCTTGGACT-3’) and sgRNA 2 (5’-GCAAGCAACGGCAGCGATCA-3’). The predicted secondary structures of the selected sgRNAs presented efficient structures in targeted mutagenesis. The pCas9-TPC-GFP-2XsgRNA vector for CRISPR/Cas9-mediated FaRALF33 gene mutagenesis was designed in silico with two sgRNA sequences (with Arabidopsis thaliana U6-26 promoters) and a green fluorescent protein marker.
Electron collision cross section data in plasma etching modeling
Authors: Chen Jin-Feng , Zhu Lin-Fan ,   Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
Published: February 2024

Semiconductor chips are the cornerstone of the information age, which play a vital role in the rapid development of emerging technologies such as big data, machine learning, and artificial intelligence. Driven by the growing demand for computing power, the chip manufacturing industry has been committed to pursuing higher level of integration and smaller device volumes. As a critical step in the chip manufacturing processes, the etching process therefore faces great challenges. Dry etching (or plasma etching) process based on the low-temperature plasma science and technology is the preferred solution for etching the high-precision circuit pattern. In the low-temperature plasma, electrons obtain energy from the external electromagnetic field and transfer the energy to other particles through collision process. After a series of complex physical and chemical reactions, a large number of active particles such as electrons, ions, atoms and molecules in excited states, and radicals are finally generated, providing the material conditions for etching the substrate. Dry etching chamber is a nonlinear system with multiple space-time dimensions, multiple reaction levels and high complexity. Facing such a complex system, only by fully understanding the basic physical and chemical reaction of the etching process can we optimize the process parameters and improve the etching conditions, so as to achieve precision machining of the semiconductor and meet the growing demand of the chip industry for etching rate and yield. In the early days, the process conditions of dry etching were determined through the trial-and-error method, which is characterized by high cost and low yield. However, with the help of plasma simulation, nowadays people have been able to narrow the scope of experiment to a large extent, and find out efficiently the optimal process conditions in a large number of parameters. In this review, we first introduce the basic theory of the mostly used models for plasma simulation including kinetic, fluid dynamic, hybrid and global models, in which the electron collision cross sections are the key input parameters. Since the formation of the low-temperature plasma is driven by the electron-heavy particle collision processes, and the active species for plasma etching are generated in the reactions induced by electron impact, the accuracy and completeness of the cross-section data greatly affect the reliability of the simulation results. Then, the theoretical and experimental methods of obtaining the cross-section data of etching gases are summarized. Finally, the research status of the electron collision cross sections of etching atoms and molecules is summarized, and the future research prospect is discussed.
Effect of an enhanced public health contact tracing intervention on the secondary transmission of SARS-CoV-2 in educational settings: The four-way decomposition analysis
Authors: Djuric Olivera , Larosa Elisabetta , Cassinadri Mariateresa , Cilloni Silvia , Bisaccia Eufemia , Pepe Davide , Bonvicini Laura , Vicentini Massimo , Venturelli Francesco , Giorgi Rossi Paolo , Pezzotti Patrizio , Mateo Urdiales Alberto , Bedeschi Emanuela ,   The Reggio Emilia Covid-19 Working Group
Published: February 2024

Background:

The aim of our study was to test the hypothesis that the community contact tracing strategy of testing contacts in households immediately instead of at the end of quarantine had an impact on the transmission of SARS-CoV-2 in schools in Reggio Emilia Province.

Methods:

We analysed surveillance data on notification of COVID-19 cases in schools between 1 September 2020 and 4 April 2021. We have applied a mediation analysis that allows for interaction between the intervention (before/after period) and the mediator.

Results:

Median tracing delay decreased from 7 to 3.1 days and the percentage of the known infection source increased from 34–54.8% (incident rate ratio-IRR 1.61 1.40–1.86). Implementation of prompt contact tracing was associated with a 10% decrease in the number of secondary cases (excess relative risk –0.1 95% CI –0.35–0.15). Knowing the source of infection of the index case led to a decrease in secondary transmission (IRR 0.75 95% CI 0.63–0.91) while the decrease in tracing delay was associated with decreased risk of secondary cases (1/IRR 0.97 95% CI 0.94–1.01 per one day of delay). The direct effect of the intervention accounted for the 29% decrease in the number of secondary cases (excess relative risk –0.29 95%–0.61 to 0.03).

Conclusions:

Prompt contact testing in the community reduces the time of contact tracing and increases the ability to identify the source of infection in school outbreaks. Although there are strong reasons for thinking it is a causal link, observed differences can be also due to differences in the force of infection and to other control measures put in place.

Funding:

This project was carried out with the technical and financial support of the Italian Ministry of Health – CCM 2020 and Ricerca Corrente Annual Program 2023.
Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster
Authors: Port Julia R , Morris Dylan H , Riopelle Jade C , Yinda Claude Kwe , Avanzato Victoria A , Holbrook Myndi G , Bushmaker Trenton , Schulz Jonathan E , Saturday Taylor A , Barbian Kent , Russell Colin A , Perry-Gottschalk Rose , Shaia Carl , Martens Craig , Lloyd-Smith James O , Fischer Robert J , Munster Vincent J
Published: February 2024

It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24–48 hr), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1–10 µm) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0–100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24–48 hr). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.
Binding to nucleosome poises human SIRT6 for histone H3 deacetylation
Authors: Smirnova Ekaterina , Bignon Emmanuelle , Schultz Patrick , Papai Gabor , Ben Shem Adam
Published: February 2024

Sirtuin 6 (SIRT6) is an NAD+-dependent histone H3 deacetylase that is prominently found associated with chromatin, attenuates transcriptionally active promoters and regulates DNA repair, metabolic homeostasis and lifespan. Unlike other sirtuins, it has low affinity to free histone tails but demonstrates strong binding to nucleosomes. It is poorly understood how SIRT6 docking on nucleosomes stimulates its histone deacetylation activity. Here, we present the structure of human SIRT6 bound to a nucleosome determined by cryogenic electron microscopy. The zinc finger domain of SIRT6 associates tightly with the acidic patch of the nucleosome through multiple arginine anchors. The Rossmann fold domain binds to the terminus of the looser DNA half of the nucleosome, detaching two turns of the DNA from the histone octamer and placing the NAD+ binding pocket close to the DNA exit site. This domain shows flexibility with respect to the fixed zinc finger and moves with, but also relative to, the unwrapped DNA terminus. We apply molecular dynamics simulations of the histone tails in the nucleosome to show that in this mode of interaction, the active site of SIRT6 is perfectly poised to catalyze deacetylation of the H3 histone tail and that the partial unwrapping of the DNA allows even lysines close to the H3 core to reach the enzyme.
Social navigation: distance and grid-like codes support navigation of abstract social space in human brain
Authors: Liang Zilu , Wu Simeng , Wu Jie , Wang Wenxu , Qin Shaozheng , Liu Chao
Published: February 2024

People form impressions about others during daily social encounters and infer personality traits from others’ behaviors. Such trait inference is thought to rely on two universal dimensions, i.e., competence and warmth. These two dimensions can be used to construct a ‘social cognitive map’ organizing massive information obtained from social encounters efficiently. Originated from spatial cognition, the neural codes supporting representation and navigation of spatial cognitive map has been widely studied. Recent studies suggest similar neural mechanism subserves the map-like architecture in social cognition as well. Here we investigated how spatial codes operate beyond physical environment and support the representation and navigation of social cognitive map. We designed a social value space defined by two dimensions of competence and warmth. Behaviorally, participants were able to navigate to a learned location from random starting locations in this abstract social space. At neural level, we identified representation of distance in precuneus, fusiform gyrus and middle occipital gyrus. We also found partial evidence of grid-like representation patterns in medial prefrontal cortex and entorhinal cortex. Moreover, the intensity of grid-like response scaled with performance of navigating in social space and social avoidance trait scores. Our findings suggest a neurocognitive mechanism by which social information can be organized into a structured representation namely cognitive map and its relevance to social well-being.
Temporal transcriptomic dynamics in developing macaque neocortex
Authors: Xu Longjiang , Yuan Zan , Zhou Jiafeng , Zhao Yuan , Liu Wei , Lu Shuaiyao , He Zhanlong , Qiang Boqin , Shu Pengcheng , Chen Yang , Peng Xiaozhong
Published: February 2024

Despite intense research on mice, the transcriptional regulation of neocortical neurogenesis remains limited in humans and non-human primates. Cortical development in rhesus macaque is known to recapitulate multiple facets of cortical development in humans, including the complex composition of neural stem cells and the thicker supragranular layer. To characterize temporal shifts in transcriptomic programming responsible for differentiation from stem cells to neurons, we sampled parietal lobes of rhesus macaque at E40, E50, E70, E80, and E90, spanning the full period of prenatal neurogenesis. Single-cell RNA sequencing produced a transcriptomic atlas of developing parietal lobe in rhesus macaque neocortex. Identification of distinct cell types and neural stem cells emerging in different developmental stages revealed a terminally bifurcating trajectory from stem cells to neurons. Notably, deep-layer neurons appear in the early stages of neurogenesis, while upper-layer neurons appear later. While these different lineages show overlap in their differentiation program, cell fates are determined post-mitotically. Trajectories analysis from ventricular radial glia (vRGs) to outer radial glia (oRGs) revealed dynamic gene expression profiles and identified differential activation of BMP, FGF, and WNT signaling pathways between vRGs and oRGs. These results provide a comprehensive overview of the temporal patterns of gene expression leading to different fates of radial glial progenitors during neocortex layer formation.
Intermittent fasting promotes ILC3s secreting IL-22 contributing to the beigeing of white adipose tissue
Authors: Chen Hong , Sun Lijun , Feng Lu , Han Xue , Zhang Yunhua , Zhai Wenbo , Zhang Zehe , Mulholland Michael , Zhang Weizhen , Yin Yue
Published: February 2024

Mechanism underlying the metabolic benefit of intermittent fasting remains largely unknown. Here, we reported that intermittent fasting promoted IL-22 production by ILC3s and subsequent beigeing of subcutaneous white adipose tissue. Adoptive transfer of intestinal ILC3s increased beigeing of white adipose tissue in diet-induced-obese mice. Exogenous IL-22 significantly increased the beigeing of subcutaneous white adipose tissue. Deficiency of IL-22 receptor attenuated the beigeing induced by intermittent fasting. Single-cell sequencing of sorted intestinal immune cells revealed that intermittent fasting increased aryl hydrocarbon receptor signaling in ILC3s. Analysis of cell‒cell ligand receptor interactions indicated that intermittent fasting may stimulate the interaction of ILC3s with dendritic cells (DCs) and macrophages. These results establish the role of intestinal ILC3s in beigeing of white adipose tissue, suggesting that ILC3/IL-22/IL-22R axis contributes to the metabolic benefit of intermittent fasting.
FBXO24 modulates mRNA alternative splicing and MIWI degradation and is required for normal sperm formation and piRNA production
Authors: Li Zhiming , Liu Xingping , Zhang Yan , Li Yuanyuan , Zhou Liquan , Yuan Shuiqiao
Published: February 2024

Spermiogenesis is a critical, post-meiotic phase of male gametogenesis, in which the proper gene expression is essential for sperm maturation. However, the underlying molecular mechanism that controls mRNA expression in the round spermatids remains elusive. Here, we identify that FBXO24, an orphan F-box protein, is highly expressed in the testis of humans and mice and interacts with the splicing factors (SRSF2, SRSF3, and SRSF9) to modulate the gene alternative splicing in the round spermatids. Genetic mutation of FBXO24 in mice causes many abnormal splicing events in round spermatids, thus affecting a large number of critical genes related to sperm formation that were dysregulated. Further molecular and phenotypical analyses revealed that FBXO24 deficiency results in aberrant histone retention, incomplete axonemes, oversized chromatoid body (CB), and abnormal mitochondrial coiling along sperm flagella, ultimately leading to male sterility. In addition, we discovered that FBXO24 interacts with MIWI and SCF subunits and mediates the degradation of MIWI via K48-linked polyubiquitination. Furthermore, we show that FBXO24 depletion could lead to aberrant piRNA production in testes, which suggests FBXO24 is required for normal piRNA counts. Collectively, these data demonstrate that FBXO24 is essential for sperm formation and piRNA production by regulating mRNA alternative splicing and MIWI degradation during spermiogenesis.
Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology
Authors: Park Won Yeong , Yun Jieun , Shin Jinho , Oh Byung Ho , Yoon Gilsuk , Hong Seung-Mo , Kim Ki Hean
Published: February 2024

Nondestructive pathology based on three-dimensional (3D) optical microscopy holds promise as a complement to traditional destructive hematoxylin and eosin (H&E) stained slide-based pathology by providing cellular information in high throughput manner. However, conventional techniques provided superficial information only due to shallow imaging depths. Herein, we developed open-top two-photon light sheet microscopy (OT-TP-LSM) for intraoperative 3D pathology. An extended depth of field two-photon excitation light sheet was generated by scanning a nondiffractive Bessel beam, and selective planar imaging was conducted with cameras at 400 frames/s max during the lateral translation of tissue specimens. Intrinsic second harmonic generation was collected for additional extracellular matrix (ECM) visualization. OT-TP-LSM was tested in various human cancer specimens including skin, pancreas, and prostate. High imaging depths were achieved owing to long excitation wavelengths and long wavelength fluorophores. 3D visualization of both cells and ECM enhanced the ability of cancer detection. Furthermore, an unsupervised deep learning network was employed for the style transfer of OT-TP-LSM images to virtual H&E images. The virtual H&E images exhibited comparable histological characteristics to real ones. OT-TP-LSM may have the potential for histopathological examination in surgical and biopsy applications by rapidly providing 3D information.
Glutamate neurotransmission from leptin receptor cells is required for typical puberty and reproductive function in female mice
Authors: Sáenz de Miera Cristina , Bellefontaine Nicole , Allen Susan J , Myers Martin G , Elias Carol F
Published: February 2024

The hypothalamic ventral premammillary nucleus (PMv) is a glutamatergic nucleus essential for the metabolic control of reproduction. However, conditional deletion of leptin receptor long form (LepRb) in vesicular glutamate transporter 2 (Vglut2) expressing neurons results in virtually no reproductive deficits. In this study, we determined the role of glutamatergic neurotransmission from leptin responsive PMv neurons on puberty and fertility. We first assessed if stimulation of PMv neurons induces luteinizing hormone (LH) release in fed adult females. We used the stimulatory form of designer receptor exclusively activated by designer drugs (DREADDs) in LeprCre (LepRb-Cre) mice. We collected blood sequentially before and for 1 hr after intravenous clozapine-N-oxide injection. LH level increased in animals correctly targeted to the PMv, and LH level was correlated to the number of Fos immunoreactive neurons in the PMv. Next, females with deletion of Slc17a6 (Vglut2) in LepRb neurons (LeprΔVGlut2) showed delayed age of puberty, disrupted estrous cycles, increased gonadotropin-releasing hormone (GnRH) concentration in the axon terminals, and disrupted LH secretion, suggesting impaired GnRH release. To assess if glutamate is required for PMv actions in pubertal development, we generated a Cre-induced reexpression of endogenous LepRb (LeprloxTB) with concomitant deletion of Slc17a6 (Vglut2flox) mice. Rescue of Lepr and deletion of Slc17a6 in the PMv was obtained by stereotaxic injection of an adeno-associated virus vector expressing Cre recombinase. Control LeprloxTB mice with PMv LepRb rescue showed vaginal opening, follicle maturation, and became pregnant, while LeprloxTB;Vglut2flox mice showed no pubertal development. Our results indicate that glutamatergic neurotransmission from leptin sensitive neurons regulates the reproductive axis, and that leptin action on pubertal development via PMv neurons requires Vglut2.
Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions
Authors: Little Jordan , Chikina Maria , Clark Nathan L
Published: February 2024

Co-functional proteins tend to have rates of evolution that covary over time. This correlation between evolutionary rates can be measured over the branches of a phylogenetic tree through methods such as evolutionary rate covariation (ERC), and then used to construct gene networks by the identification of proteins with functional interactions. The cause of this correlation has been hypothesized to result from both compensatory coevolution at physical interfaces and nonphysical forces such as shared changes in selective pressure. This study explores whether coevolution due to compensatory mutations has a measurable effect on the ERC signal. We examined the difference in ERC signal between physically interacting protein domains within complexes compared to domains of the same proteins that do not physically interact. We found no generalizable relationship between physical interaction and high ERC, although a few complexes ranked physical interactions higher than nonphysical interactions. Therefore, we conclude that coevolution due to physical interaction is weak, but present in the signal captured by ERC, and we hypothesize that the stronger signal instead comes from selective pressures on the protein as a whole and maintenance of the general function.
Rapid bacterial evaluation beyond the colony forming unit in osteomyelitis
Authors: Sun Qi , Huynh Kimberley , Muratovic Dzenita , Gunn Nicholas J , Zelmer Anja R , Solomon Lucian Bogdan , Atkins Gerald J , Yang Dongqing
Published: February 2024

Examination of bacteria/host cell interactions is important for understanding the aetiology of many infectious diseases. The colony forming unit (CFU) has been the standard for quantifying bacterial burden for the past century, however, this suffers from low sensitivity and is dependent on bacterial culturability in vitro. Our data demonstrate the discrepancy between the CFU and bacterial genome copy number in an osteomyelitis-relevant co-culture system and we confirm diagnosis and quantify bacterial load in clinical bone specimens. This study provides an improved workflow for the quantification of bacterial burden in such cases.
Beyond the Colony-Forming-Unit: Rapid Bacterial Evaluation in Osteomyelitis
Authors: Sun Qi , Huynh Kimberley , Muratovic Dzenita , Gunn Nicholas J. , Zelmer Anja R. , Solomon L. Bogdan , Atkins Gerald J. , Yang Dongqing
Published: February 2024

Examination of bacteria/host cell interactions is important for understanding the aetiology of many infectious diseases. The colony-forming-unit (CFU) has been the standard for quantifying bacterial burden for the past century, however, this suffers from low sensitivity and is dependent on bacterial culturability
in vitro
. Our data demonstrate the discrepancy between the CFU and bacterial genome copy number in an osteomyelitis-relevant co-culture system and we confirm diagnosis and quantify bacterial load in clinical bone specimens. This study provides insight into improving the quantification of bacterial burden in such cases.
Disentangling the relationship between cancer mortality and COVID-19 in the US
Authors: Hansen Chelsea L , Viboud Cécile , Simonsen Lone
Published: February 2024

Cancer is considered a risk factor for COVID-19 mortality, yet several countries have reported that deaths with a primary code of cancer remained within historic levels during the COVID-19 pandemic. Here, we further elucidate the relationship between cancer mortality and COVID-19 on a population level in the US. We compared pandemic-related mortality patterns from underlying and multiple cause (MC) death data for six types of cancer, diabetes, and Alzheimer’s. Any pandemic-related changes in coding practices should be eliminated by study of MC data. Nationally in 2020, MC cancer mortality rose by only 3% over a pre-pandemic baseline, corresponding to ~13,600 excess deaths. Mortality elevation was measurably higher for less deadly cancers (breast, colorectal, and hematological, 2–7%) than cancers with a poor survival rate (lung and pancreatic, 0–1%). In comparison, there was substantial elevation in MC deaths from diabetes (37%) and Alzheimer’s (19%). To understand these differences, we simulated the expected excess mortality for each condition using COVID-19 attack rates, life expectancy, population size, and mean age of individuals living with each condition. We find that the observed mortality differences are primarily explained by differences in life expectancy, with the risk of death from deadly cancers outcompeting the risk of death from COVID-19.
A seven-sex species recognizes self and non-self mating-type via a novel protein complex
Authors: Yan Guanxiong , Ma Yang , Wang Yanfang , Zhang Jing , Cheng Haoming , Tan Fanjie , Wang Su , Zhang Delin , Xiong Jie , Yin Ping , Miao Wei
Published: February 2024

Although most species have two sexes, multisexual (or multi-mating type) species are also widespread. However, it is unclear how mating-type recognition is achieved at the molecular level in multisexual species. The unicellular ciliate Tetrahymena thermophila has seven mating types, which are determined by the MTA and MTB proteins. In this study, we found that both proteins are essential for cells to send or receive complete mating-type information, and transmission of the mating-type signal requires both proteins to be expressed in the same cell. We found that MTA and MTB form a mating-type recognition complex that localizes to the plasma membrane, but not to the cilia. Stimulation experiments showed that the mating-type-specific regions of MTA and MTB mediate both self- and non-self-recognition, indicating that T. thermophila uses a dual approach to achieve mating-type recognition. Our results suggest that MTA and MTB form an elaborate multifunctional protein complex that can identify cells of both self and non-self mating types in order to inhibit or activate mating, respectively.
Enhancing bone regeneration and osseointegration using rhPTH(1-34) and dimeric R25CPTH(1-34) in an osteoporotic beagle model
Authors: Shin Jeong-Oh , Lee Jong-Bin , Lee Sihoon , Kim Jin-Woo
Published: February 2024

This study investigates the effects of two parathyroid hormone (PTH) analogs, rhPTH(1-34) and dimeric R25CPTH(1-34), on bone regeneration and osseointegration in a postmenopausal osteoporosis model using beagle dogs. Twelve osteoporotic female beagles were subjected to implant surgeries and assigned to one of three groups: control, rhPTH(1-34), or dimeric R25CPTH(1-34). Bone regeneration and osseointegration were evaluated after 10 weeks using micro-computed tomographic (micro-CT), histological analyses, and serum biochemical assays. Results showed that the rhPTH(1-34) group demonstrated superior improvements in bone mineral density, trabecular architecture, and osseointegration compared to controls, while the dimeric R25CPTH(1-34) group exhibited similar, though slightly less pronounced, anabolic effects. Histological and TRAP assays indicated both PTH analogs significantly enhanced bone regeneration, especially in artificially created bone defects. The findings suggest that both rhPTH(1-34) and dimeric R25CPTH(1-34) hold potential as therapeutic agents for promoting bone regeneration and improving osseointegration around implants in osteoporotic conditions, with implications for their use in bone-related pathologies and reconstructive surgeries.
Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancer
Authors: Kim Tackhoon , Park Byung-Sun , Heo Soobeen , Jeon Heeju , Kim Jaeyeal , Kim Donghwa , Lee Sang Kook , Jung So-Youn , Kong Sun-Young , Lu Timothy K
Published: February 2024

Tyrosine kinases play a crucial role in cell proliferation and survival and are extensively investigated as targets for cancer treatment. However, the efficacy of most tyrosine kinase inhibitors (TKIs) in cancer therapy is limited due to resistance. In this study, we identify a synergistic combination therapy involving TKIs for the treatment of triple negative breast cancer. By employing pairwise tyrosine kinase knockout CRISPR screens, we identify
FYN
and
KDM4
as critical targets whose inhibition enhances the effectiveness of TKIs, such as NVP-ADW742 (IGF-1R inhibitor), gefitinib (EGFR inhibitor), and imatinib (ABL inhibitor) both
in vitro
and
in vivo
. Mechanistically, treatment with TKIs upregulates the transcription of
KDM4
, which in turn demethylates H3K9me3 at
FYN
enhancer for
FYN
transcription. This compensatory activation of
FYN
and
KDM4
contributes to the resistance against TKIs.
FYN
expression is associated with therapy resistance and persistence by demonstrating its upregulation in various experimental models of drug-tolerant persisters and residual disease following targeted therapy, chemotherapy, and radiotherapy. Collectively, our study provides novel targets and mechanistic insights that can guide the development of effective combinatorial targeted therapies, thus maximizing the therapeutic benefits of TKIs.
Sperm motility in mice with Oligo-astheno-teratozoospermia restored by in vivo injection and electroporation of naked mRNA
Authors: Vilpreux Charline , Martinez Guillaume , Court Magali , Appaix Florence , Duteyrat Jean-Luc , Henry Maxime , Vollaire Julien , Ayad Camille , Yavz Altan , De Macedo Lisa , Chevalier Geneviève , Lambert Emeline , Conte Sekou Ahmed , Giordani Elsa , Josserand Véronique , Brocard Jacques , Charles Coutton , Verrier Bernard , Ray Pierre F. , Loeuillet Corinne , Arnoult Christophe , Escoffier Jessica
Published: February 2024

Oligo-astheno-teratozoospermia (OAT), a recurent cause of male infertility, is the most frequent disorder of spermatogenesis with a probable genetic cause. Patients and mice bearing mutations in the ARMC2 gene have a decreased sperm concentration, and individual sperm show multiple morphological defects and a lack of motility – a canonical OAT phenotype. Intra Cellular Sperm Injection (ICSI) is required to treat such a condition but it has limited efficacy and was associated with a small increase in birth defects. Consequently, new targeted treatments are needed to restore spermatogenesis. Here, a combination of in vivo injection and electroporation of capped and poly-A-tailed naked mRNA is tested as a strategy to treat ARMC2 -related infertility in mouse. mRNAs coding for several reporter genes are tested and the efficiency and the kinetic of expression are assessed using in vivo and in vitro 2D and 3D imaging experiments. We show that mRNA-coded reporter proteins are detected for up to 3 weeks mostly in germ cells, making the use of mRNA possible to treat infertility. We compare these results with those obtained with a more conventional DNA plasmid vector. In contrast, the use of the non-integrative plasmid Enhanced Episomal Vector (EEV) shows low and transient expression in spermatogenic cells. Consequently, injection and electroporation of naked mRNA- Armc2 into the testes of Armc2 -deficient males were performed and we show the presence of normal and motile sperm in the epididymis. This study shows for the first time that mRNA- Armc2 efficiently restores spermatogenesis and opens new paths for male infertility treatment.All procedures involving animals were performed in line with the French guidelines for the use of live animals in scientific investigations. The study protocol was approved by the local ethics committee (ComEth Grenoble #318) and received governmental authorization (ministerial agreement #38109-2022072716142778).
Taste triggers a homeostatic temperature control in hungry flies
Authors: Umezaki Yujiro , Hidalgo Sergio , Nguyen Erika , Nguyen Tiffany , Suh Jay , Uchino Sheena S , Chiu Joanna , Hamada Fumika
Published: February 2024

Hungry animals consistently show a desire to obtain food. Even a brief sensory detection of food can trigger bursts of physiological and behavioral changes. However, the underlying mechanisms by which the sensation of food triggers the acute behavioral response remain elusive. We have previously shown in Drosophila that hunger drives a preference for low temperature. Because Drosophila is a small ectotherm, a preference for low temperature implies a low body temperature and a low metabolic rate. Here, we show that taste-sensing triggers a switch from a low to a high temperature preference in hungry flies. We show that taste stimulation by artificial sweeteners or optogenetics triggers an acute warm preference, but is not sufficient to reach the fed state. Instead, nutrient intake is required to reach the fed state. The data suggest that starvation recovery is controlled by two components: taste-evoked and nutrient-induced warm preferences, and that taste and nutrient quality play distinct roles in starvation recovery. Animals are motivated to eat based on time of day or hunger. We found that clock genes and hunger signals profoundly control the taste-evoked warm preferences. Thus, our data suggest that the taste-evoked response is one of the critical layers of regulatory mechanisms representing internal energy homeostasis and metabolism.
Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C
Authors: Baier Alexander S , Gioacchini Nathan , Eek Priit , Leith Erik M , Tan Song , Peterson Craig L
Published: February 2024

The yeast SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a ‘pincer-like’ conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5–nucleosome complex suggests that promoter proximal, histone H2B ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.
RNA polymerase III is involved in regulating Plasmodium falciparum virulence
Authors: Diffendall Gretchen , Claes Aurelie , Barcons-Simon Anna , Nyarko Prince , Dingli Florent , Santos Miguel M , Loew Damarys , Claessens Antoine , Scherf Artur
Published: February 2024

While often undetected and untreated, persistent seasonal asymptomatic malaria infections remain a global public health problem. Despite the presence of parasites in the peripheral blood, no symptoms develop. Disease severity is correlated with the levels of infected red blood cells (iRBCs) adhering within blood vessels. Changes in iRBC adhesion capacity have been linked to seasonal asymptomatic malaria infections, however how this is occurring is still unknown. Here, we present evidence that RNA polymerase III (RNA Pol III) transcription in Plasmodium falciparum is downregulated in field isolates obtained from asymptomatic individuals during the dry season. Through experiments with in vitro cultured parasites, we have uncovered an RNA Pol III-dependent mechanism that controls pathogen proliferation and expression of a major virulence factor in response to external stimuli. Our findings establish a connection between P. falciparum cytoadhesion and a non-coding RNA family transcribed by Pol III. Additionally, we have identified P. falciparum Maf1 as a pivotal regulator of Pol III transcription, both for maintaining cellular homeostasis and for responding adaptively to external signals. These results introduce a novel perspective that contributes to our understanding of P. falciparum virulence. Furthermore, they establish a connection between this regulatory process and the occurrence of seasonal asymptomatic malaria infections.
exKidneyBERT: a language model for kidney transplant pathology reports and the crucial role of extended vocabularies
Authors: Yang Tiancheng , Sucholutsky Ilia , Jen Kuang-Yu , Schonlau Matthias
Published: February 2024

Background

Pathology reports contain key information about the patient’s diagnosis as well as important gross and microscopic findings. These information-rich clinical reports offer an invaluable resource for clinical studies, but data extraction and analysis from such unstructured texts is often manual and tedious. While neural information retrieval systems (typically implemented as deep learning methods for natural language processing) are automatic and flexible, they typically require a large domain-specific text corpus for training, making them infeasible for many medical subdomains. Thus, an automated data extraction method for pathology reports that does not require a large training corpus would be of significant value and utility.

Objective

To develop a language model-based neural information retrieval system that can be trained on small datasets and validate it by training it on renal transplant-pathology reports to extract relevant information for two predefined questions: (1) “What kind of rejection does the patient show?”; (2) “What is the grade of interstitial fibrosis and tubular atrophy (IFTA)?”

Methods

Kidney BERT was developed by pre-training Clinical BERT on 3.4K renal transplant pathology reports and 1.5M words. Then, exKidneyBERT was developed by extending Clinical BERT’s tokenizer with six technical keywords and repeating the pre-training procedure. This extended the model’s vocabulary. All three models were fine-tuned with information retrieval heads.

Results

The model with extended vocabulary, exKidneyBERT, outperformed Clinical BERT and Kidney BERT in both questions. For rejection, exKidneyBERT achieved an 83.3% overlap ratio for antibody-mediated rejection (ABMR) and 79.2% for T-cell mediated rejection (TCMR). For IFTA, exKidneyBERT had a 95.8% exact match rate.

Conclusion

ExKidneyBERT is a high-performing model for extracting information from renal pathology reports. Additional pre-training of BERT language models on specialized small domains does not necessarily improve performance. Extending the BERT tokenizer’s vocabulary library is essential for specialized domains to improve performance, especially when pre-training on small corpora.
Effect of lag screw on stability of first metatarsophalangeal joint arthrodesis with medial plate
Authors: Daszkiewicz Karol , Rucka Magdalena , Czuraj Krzysztof , Andrzejewska Angela , Łuczkiewicz Piotr
Published: February 2024

Background

First metatarsophalangeal joint (MTP-1) arthrodesis is a commonly performed procedure in the treatment of disorders of the great toe. Since the incidence of revision after MTP-1 joint arthrodesis is not insignificant, a medial approach with a medially positioned locking plate has been proposed as a new technique. The aim of the study was to investigate the effect of the application of a lag screw on the stability and strength of first metatarsophalangeal joint arthrodesis with medial plate.

Methods

The bending tests in a testing machine were performed for models of the first metatarsal bone and the proximal phalanx printed on a 3D printer from polylactide material. The bones were joined using the locking titanium plate and six locking screws. The specimens were divided into three groups of seven each: medial plate and no lag screw, medial plate with a lag screw, dorsal plate with a lag screw. The tests were carried out quasi-static until the samples failure.

Results

The addition of the lag screw to the medial plate significantly increased flexural stiffness (41.45 N/mm vs 23.84 N/mm, p = 0.002), which was lower than that of the dorsal plate with a lag screw (81.29 N/mm, p < 0.001). The similar maximum force greater than 700 N (p > 0.50) and the relative bone displacements lower than 0.5 mm for a force of 50 N were obtained for all fixation techniques.

Conclusions

The lag screw significantly increased the shear stiffness in particular and reduced relative transverse displacements to the level that should not delay the healing process for the full load of the MTP-1 joint arthrodesis with the medial plate. It is recommended to use the locking screws with a larger cross-sectional area of the head to minimize rotation of the medial plate relative to the metatarsal bone.
Revisiting the type material of two African Diplozoinae (Diplozoidae: Monogenea), with remarks on morphology, systematics and diplozoid specificity
Authors: Dos Santos Quinton Marco , Avenant-Oldewage Annemariè
Published: February 2024

The morphological characterisation of Diplozoidae spp. is highly reliant on the details of the sclerotised components of the hooks and clamps in the haptor. Only six species of Paradiplozoon (Diplozoinae) have been described from Africa, four of which have adequate morphological and even comparative ITS2 rDNA data available. However, the descriptions of Paradiplozoon ghanense (Thomas, 1957) and Paradiplozoon aegyptense (Fischthal & Kuntz, 1963) lack essential taxonomic information, specifically the details for their haptoral sclerites. As such, all available material from museum collections for these two species were studied using light microscopy to supplement the original morphometric descriptions. The holotype and paratypes of P. aegyptense were studied, but only voucher material for P. ghanense could be sourced. However, this voucher material for P. ghanense was deposited by the species authority and bore a striking resemblance to the illustrations and collection details from the original description. They were thus identified as the type series for the taxon, with a lectotype and paralectotype designated. Both P. ghanense and P. aegyptense could be readily distinguished from other taxa based on the supplementary data generated here, supporting their distinctness. The haptoral sclerites of P. aegyptense were most similar to those of Paradiplozoon krugerense Dos Santos & Avenant-Oldewage, 2016, also described from Labeo spp., while the sclerites of P. ghanense were most similar to Paradiplozoon bingolense Civáňová, Koyun & Koubková, 2013 and Paradiplozoon iraqense Al-Nasiri & Balbuena, 2016. Additionally, a voucher of P. aegyptense collected from the alestid type host of P. ghanense was reidentified as the latter species here. This greatly simplified the known host specificity for Paradiplozoon spp. in Africa, with P. aegyptense now exclusively reported from Cypriniformes (Cyprinidae and Danionidae), and P. ghanense restricted to Characiformes (Alestidae). The occurrence of all diplozoids from non-cyprinoid hosts was also investigated and several records of diplozoids occurring on non-cyprinoid hosts were collated and scrutinised. Excluding the two instances of diplozoids described and exclusively occurring on Characiformes fishes (P. ghanense and Paradiplozoon tetragonopterini (Sterba, 1957)), most other non-cyprinoid collections appear sporadic and unsubstantiated, but warrant further investigation supported by diligent taxonomic data. Even though the morphometric descriptions of both P. ghanense and P. aegyptense were fully reported on here, additional material will be needed to study their genetic profiles and phylogeny.
Wood identification based on macroscopic images using deep and transfer learning approaches
Authors: Ergun Halime
Published: February 2024

Identifying forest types is vital for evaluating the ecological, economic, and social benefits provided by forests, and for protecting, managing, and sustaining them. Although traditionally based on expert observation, recent developments have increased the use of technologies such as artificial intelligence (AI). The use of advanced methods such as deep learning will make forest species recognition faster and easier. In this study, the deep network models RestNet18, GoogLeNet, VGG19, Inceptionv3, MobileNetv2, DenseNet201, InceptionResNetv2, EfficientNet and ShuffleNet, which were pre-trained with ImageNet dataset, were adapted to a new dataset. In this adaptation, transfer learning method is used. These models have different architectures that allow a wide range of performance evaluation. The performance of the model was evaluated by accuracy, recall, precision, F1-score, specificity and Matthews correlation coefficient. ShuffleNet was proposed as a lightweight network model that achieves high performance with low computational power and resource requirements. This model was an efficient model with an accuracy close to other models with customisation. This study reveals that deep network models are an effective tool in the field of forest species recognition. This study makes an important contribution to the conservation and management of forests.
The toxicity assessment of phosmet on development, reproduction, and gene expression in Daphnia magna
Authors: Ataş Mustafa , Bereketoglu Ceyhun
Published: February 2024

The use of pesticides to control pests, weeds, and diseases or to regulate plant growth is indispensable in agricultural production. However, the excessive use of these chemicals has led to significant concern about their potential negative impacts on health and the environment. Phosmet is one such pesticide that is commonly used on plants and animals against cold moth, aphids, mites, suckers, and fruit flies. Here, we investigated the effects of phosmet on a model organism, Daphnia magna using acute and chronic toxicity endpoints such as lethality, mobility, genotoxicity, reproduction, and gene expression. We performed survival experiments in six-well plates at seven different concentrations (0.01, 0.1, 1, 10, 25, 50, 100 μM) as well as the control in three replicates. We observed statistically significant mortality rates at 25 µM and above upon 24 h of exposure, and at 1 µM and above following 48 h of exposure. Genotoxicity analysis, reproduction assay and qPCR analysis were carried out at concentrations of 0.01 and 0.1 μM phosmet as these concentrations did not show any lethality. Comet assay showed that exposure to phosmet resulted in significant DNA damage in the cells. Interestingly, 0.1 μM phosmet produced more offspring per adult compared to the control group indicating a hormetic response. Gene expression profiles demonstrated several genes involved in different physiological pathways, including oxidative stress, detoxification, immune system, hypoxia and iron homeostasis. Taken together, our results indicate that phosmet has negative effects on Daphnia magna in a dose- and time-dependent manner and could also induce lethal and physiological toxicities to other aquatic organisms.