bluuebunny/crossref_metadata_2025 huggingface dataset:
Management of Macrocystic Lymphatic Malformation in the Cervicofacial Region
Authors: Han Tao , Chen Haini , Cui Jie , Shen Weimin
Published: February 2022

Purpose

The purpose of our study was to evaluate the efficacy and safety of ultrasound-guided iodine tincture cauterization combined with postoperative intralesional negative pressure in the management of cervicofacial cystic lymphatic malformation (cLM).

Method

From January 2019 to July 2021, indocyanine green lymphography was performed preoperatively to confirm the lymph inflow, and this treatment was administered in 71 patients with cervicofacial cLM in our center. All cases were evaluated by curative effects, treatment frequency, and adverse events. The duration of posttreatment follow-up was from 12 to 14 months.

Results

Indocyanine green lymphography indicated at least one lymphatic inflow in each cLM lesion. Excellent resolution was observed in 87.3% of cases, and good improvement of the treated cLM occurred in 9.9% of cases, and 2 cases with fair outcomes required subsequent treatment. It is noteworthy that no case was treated more than 3 times. Some minor adverse effects, including localized itch and scar, were managed by symptomatic treatment.

Conclusions

Because of satisfactory outcomes and low treatment frequency, ultrasound-guided iodine tincture cauterization combined with intralesional negative pressure represents an efficacious, safe, and feasible method for the management of macro-cLM in the cervicofacial region.
Deciphering the contributions of neuroinflammation to neurodegeneration: lessons from antibody-mediated encephalitis and coronavirus disease 2019
Authors: Shir Dror , Day Gregory S.
Published: February 2022

Purpose of review

Does neuroinflammation promote neurodegeneration? Does neurodegeneration promote neuroinflammation? Or, is the answer to both questions,yes? These questions have proven challenging to answer in patients with typical age-related neurodegenerative diseases in whom the onset of neuroinflammation and neurodegeneration are largely unknown. Patients recovering from diseases associated with abrupt-onset neuroinflammation, including rare forms of antibody-mediated encephalitis (AME) and common complications of novel coronavirus disease 2019 (COVID-19), provide a unique opportunity to untangle the relationship between neuroinflammation and neurodegeneration. This review explores the lessons learned from patients with AME and COVID-19.

Recent findings

Persistent cognitive impairment is increasingly recognized in patients recovering from AME or COVID-19, yet the drivers of impairment remain largely unknown. Clinical observations, neuroimaging and biofluid biomarkers, and pathological studies imply a link between the severity of acute neuroinflammation, subsequent neurodegeneration, and disease-associated morbidity.

Data from patients with AME and COVID-19 inform key hypotheses that may be evaluated through future studies incorporating longitudinal biomarkers of neuroinflammation and neurodegeneration in larger numbers of recovering patients. The results of these studies may inform the contributors to cognitive impairment in patients with AME and COVID-19, with potential diagnostic and therapeutic applications in patients with age-related neurodegenerative diseases.
Social withdrawal and neurocognitive correlates in schizophrenia
Authors: De Donatis Domenico , Porcelli Stefano , De Ronchi Diana , Merlo Pich Emilio , Kas Martien J. , Bilderbeck Amy , Serretti Alessandro
Published: February 2022

Poor neurocognitive performance has been associated with poor functional outcome in schizophrenia (SCZ) in past studies. Nonetheless, the likely association between neurocognition and social withdrawal has never been investigated. The aim of our study was to investigate in a large and heterogeneous sample of SCZ patient cross-sectional associations between neurocognitive domains and social withdrawal. The sample included 761 SCZ patients who completed the baseline visit in the CATIE study. Neurocognition was assessed by a comprehensive battery of tests resulting in five domain scores and a composite score. Social withdrawal was measured by a specific item of the Heinrichs-Carpenter Quality of Life Scale. Social withdrawal was associated with a lower score in the neurocognitive composite score and in ‘Verbal memory,’ ‘Processing speed’ and ‘Working memory’ scores. ‘Verbal memory’ score showed the strongest association with social withdrawal. Eight percent of the total variance of social withdrawal was explained by these three cognitive domains and additional clinical and sociodemographic factors (education years, PANSS positive symptoms score, and employment). Our results confirmed the wide heterogeneity and specificity of the correlation between neurocognitive domains and indicators of functional outcome in SCZ, underlining the role of certain neurocognitive abilities in social withdrawal.
Sneathiella sedimenti sp. nov., isolated from marine sediment
Authors: Lee Yunjeong , Weerawongwiwat Veeraya , Kim Jong-Hwa , Yoon Jung-Hoon , Suh Min Kuk , Kim Han Sol , Lee Jung-Sook , Sukhoom Ampaitip , Kim Wonyong
Published: February 2022

A novel bacterium, designated CAU 1612T, was isolated from coastal sediment sampled in the Republic of Korea. Cells of the strain were Gram-stain-negative, rod-shaped and motile. Optimum growth occurred at 30 °C, at pH 7.0 and with 1.0 % (w/v) NaCl. Based on 16S rRNA gene sequences, phylogenetic analysis revealed that strain CAU 1612T belonged to the genus

Sneathiella

and showed highest similarity to ‘Sneathiella litorea’ JCM 33810T (98.5 %), followed by

Sneathiella chungangensis

KCTC 32476T (97.7 %),

Sneathiella aquimaris

KCTC 12842T (96.0 %),

Sneathiella chinensis

LMG 23452T (95.5 %),

Sneathiella limimaris

KCTC 52846T (95.5 %) and

Sneathiella glossodoripedis

KCTC 12842T (95.4 %). The average nucleotide identity and digital DNA–DNA hybridization values of strain CAU 1612T were estimated to be 68.5–81.7 % and ≤23.7 %, respectively, to members of the genus

Sneathiella

. The DNA G+C content was 54.1 mol%. The major cellular fatty acids (>10 %) were C16:0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1
 ω7c and/or C18 : 1
 ω6c). The major menaquinone was Q-10 and the predominant polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. On the basis of taxonomic evidence, strain CAU 1612T represents a novel species, for which the name Sneathiella sedimenti sp. nov. is proposed. The type strain is CAU 1612T (=KCTC 82427T=MCCC 1K06082T).
Efficacy and Safety of a Booster Regimen of Ad26.COV2.S Vaccine against Covid-19
Authors: Hardt Karin , Vandebosch An , Sadoff Jerry , Gars Mathieu Le , Truyers Carla , Lowson David , Van Dromme Ilse , Vingerhoets Johan , Kamphuis Tobias , Scheper Gert , Ruiz-Guiñazú Javier , Faust Saul N. , Spinner Christoph D. , Schuitemaker Hanneke , Van Hoof Johan , Douoguih Macaya , Struyf Frank ,   the ENSEMBLE2 Study Group
Published: February 2022

Background

Despite the availability of effective vaccines against coronavirus disease 2019 (Covid-19), the emergence of variant strains and breakthrough infections pose a challenging new reality. Booster vaccinations are needed to maintain vaccine-induced protection.

Methods

ENSEMBLE2 is an ongoing, randomized, double-blind, placebo-controlled, phase 3 pivotal trial including crossover vaccination after emergency authorization of Covid-19 vaccines. Adults aged ≥18 years were randomized to receive Ad26.COV2.S or placebo as a primary dose plus a booster dose at two months. The primary endpoint was vaccine efficacy against the first occurrence of molecularly-confirmed moderate to severe–critical Covid-19 with onset ≥14 days after booster vaccination in the per-protocol population. Key efficacy, safety, and immunogenicity endpoints were also assessed.

Results

The double-blind phase enrolled 31,300 participants, 14,492 of whom received 2 doses and were evaluable for efficacy (per-protocol set, Ad26.COV2.S n=7484; placebo n=7008). Baseline demographics and characteristics were balanced. Vaccine efficacy was 75.2% (adjusted 95% CI, 54.6-87.3) against moderate to severe–critical Covid-19 and was similar against symptomatic infection (75.6% [55.5-99.9]). Efficacy was consistent across participants with and without comorbidities, and reached 93.7% (58.5-99.9) in the US. Vaccine efficacy against severe–critical Covid-19 was 100% (32.6-100.0; 0 vs 8 cases). The booster vaccine induced robust humoral responses and exhibited an acceptable safety profile.

Conclusions

A homologous Ad26.COV2.S booster administered 2 months after primary single-dose vaccination in adults led to high vaccine efficacy, including against any symptomatic infection and SARS-CoV-2 variants prevalent during the study. (Funding: Janssen Research and Development and others; ENSEMBLE2 ClinicalTrials.gov number, NCT04614948.)
Direct DNA sequencing of ‘Candidatus Liberibacter asiaticus’ from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management
Authors: Higgins Steven Adam , Mann Marina , Heck Michelle
Published: February 2022

The Asian citrus psyllid, Diaphorina citri is an invasive insect 1 and a vector of ’Candidatus Liberibacter asiaticus’ (CLas), a bacterium whose growth in Citrus species results in citrus greening disease 2,3. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification 4 and nevertheless contain significant quantities of host DNA 5,6. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and enabled detection of 156 genetic variants in these strains compared to progenitor strains in Florida, which included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can inform agricultural management strategies related to pathogen evolution 7, insect microbiome surveillance 8, antibiotic resistance screening 9, and gut content analysis 10.
Intraoperative electrical stimulation of the human dorsal spinal cord reveals a map of arm and hand muscle responses
Authors: McIntosh James R. , Joiner Evan. F. , Goldberg Jacob L. , Murray Lynda M. , Yasin Bushra , Mendiratta Anil , Karceski Steven C. , Thuet Earl , Modik Oleg , Shelkov Evgeny , Lombardi Joseph M. , Sardar Zeeshan M. , Lehman Ronald A. , Mandigo Christopher , Riew K. Daniel , Harel Noam Y. , Virk Michael S. , Carmel Jason B.
Published: February 2022

While epidural stimulation of the lumbar spinal cord has emerged as a powerful modality for recovery of movement, how it should be targeted to the cervical spinal cord to activate arm and hand muscles is not well-understood, particularly in humans. We sought to map muscle responses to posterior epidural cervical spinal cord stimulation in humans. We hypothesized that lateral stimulation over the dorsal root entry zone would be most effective, and responses would be strongest in the muscles innervated by the stimulated segment. Twenty-five people undergoing clinically indicated cervical spine surgery were consented to map motor responses. During surgery, stimulation was performed in midline and lateral positions at multiple exposed segments; six arm and three leg muscles were recorded on each side of the body. Across all segments and muscles tested, lateral stimulation produced stronger muscle responses than midline despite similar latency and shape of responses. Muscles innervated at a cervical segment had the largest responses from stimulation at that segment, but responses were also observed in muscles innervated at other cervical segments and in leg muscles. The cervical responses were clustered in rostral (C4-C6) and caudal (C7-T1) cervical segments. Strong responses to lateral stimulation are likely due to the proximity of stimulation to afferent axons. Small changes in response sizes to stimulation of adjacent cervical segments argues for local circuit integration, and distant muscle responses suggest activation of long propriospinal connections. This map can help guide cervical stimulation to improve arm and hand function.

New and noteworthy

A map of muscle responses to cervical epidural stimulation during clinically indicated surgery revealed strongest activation when stimulating laterally compared to midline, and differences to be weaker than expected across different segments. In contrast, waveform shapes and latencies were most similar when stimulating midline and laterally indicating activation of overlapping circuitry. Thus, a map of the cervical spinal cord reveals organization and may help guide stimulation to activate arm and hand muscles strongly and selectively.

Graphical abstract
Role of mucin gene for growth in Anas platyrynchos - a novel report
Authors: Murmu Anuj kumar , Pal Aruna , Debnath Manti , Chakraborty Argha , Pal Subhomoy , Banerjee Samiddha , Pal Abantika , Ghosh Nilotpal , Karmakar Utpal , Samanta Rajarshi
Published: February 2022

Mucin gene is expressed at the mucous membrane of the inner layer of the internal organs. Intestinal mucin 2 (MUC2), a major gel-forming mucin, represents a primary barrier component of mucus layers. This is the first report of role of mucin gene in growth traits in animals. In the current study, we had randomly studied Bengal ducks (Anas platyrynchos) reared from day old to 10 weeks of age under organized farm and studied the growth parameters as well as body weight and average daily body weight gain. We had characterized mucin gene for Bengal duck and observed glycosylation and EGF1 (EGF like domain signature) as important domain for growth traits in duck. We observed better expression profile for mucin gene in high growing ducks in comparison to that of lower growing ducks with real time PCR. Hence mucin gene may be employed as a marker for growth traits.
Group-walk, a rigorous approach to group-wise false discovery rate analysis by target-decoy competition
Authors: Freestone Jack , Short Temana , Noble William Stafford , Keich Uri
Published: February 2022

Target-decoy competition (TDC) is a commonly used method for false discovery rate (FDR) control in the analysis of tandem mass spectrometry data. This type of competitionbased FDR control has recently gained significant popularity in other fields after Barber and Candès laid its theoretical foundation in a more general setting that included the feature selection problem. In both cases, the competition is based on a head-to-head comparison between an (observed) target score and a corresponding decoy (knockoff) score. However, the effectiveness of TDC depends on whether the data is homogeneous, which is often not the case: in many settings, the data consists of groups with different score profiles or different proportions of true nulls. In such cases, applying TDC while ignoring the group structure often yields imbalanced lists of discoveries, where some groups might include relatively many false discoveries and other groups include relatively very few. On the other hand, as we show, the alternative approach of applying TDC separately to each group does not rigorously control the FDR.

We developed Group-walk, a procedure that controls the FDR in the target-decoy / knockoff setting while taking into account a given group structure. Group-walk is derived from the recently developed AdaPT — a general framework for controlling the FDR with sideinformation. We show using simulated and real datasets that when the data naturally divides into groups with different characteristics Group-walk can deliver consistent power gains that in some cases are substantial. These groupings include the precursor charge state (4% more discovered peptides at 1% FDR threshold), the peptide length (3.6% increase) and the mass difference due to modifications (26% increase).

Group-walk is available at https://cran.r-project.org/web/packages/groupwalk/index.html
Quantification of phosphonate drugs by 1H-31P HSQC shows that rats are better models of primate drug exposure than mice
Authors: Barekatain Yasaman , Khadka Sunada , Harris Kristen , Delacerda Jorge , Yan Victoria C. , Chen Ko-Chien , Pham Cong-Dat , Uddin Md. Nasir , Avritcher Rony , Eisenberg Eugene J. , Kalluri Raghu , Millward Steven W. , Muller Florian L.
Published: February 2022

The phosphonate group is a key pharmacophore in many anti-viral, anti-microbial, and anti-neoplastic drugs. Due to its high polarity and short retention time, detecting and quantifying such phosphonate-containing drugs with LC/MS-based methods is challenging and requires derivatization with hazardous reagents. Given the emerging importance of phosphonate-containing drugs, developing a practical, accessible, and safe method for their quantitation in pharmacokinetics (PK) studies is desirable. NMR-based methods are often employed in drug discovery but are seldom used for compound quantitation in PK studies. Here, we show that proton-phosphorous (1H-31P) heteronuclear single quantum correlation (HSQC) NMR allows for quantitation of the phosphonate-containing enolase inhibitor HEX in plasma and tissue at micromolar concentrations. Although mice were shown to rapidly clear HEX from circulation (over 95% in <1 hr), the plasma half-life of HEX was more than 1hr in rats and nonhuman primates. This slower clearance rate affords a significantly higher exposure of HEX in rat models compared to mouse models while maintaining a favorable safety profile. Similar results were observed for the phosphonate-containing antibiotic, fosfomycin. Our study demonstrates the applicability of the 1H-31P HSQC method to quantify phosphonate-containing drugs in complex biological samples and illustrates an important limitation of mice as preclinical model species for phosphonate-containing drugs.
Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane
Authors: Lisica Ana , Fouchard Jonathan , Kelkar Manasi , Wyatt Tom P. J. , Duque Julia , Ndiaye Anne-Betty , Bonfanti Alessandra , Baum Buzz , Kabla Alexandre J. , Charras Guillaume T.
Published: February 2022

The direction in which a cell divides is set by the orientation of its mitotic spindle and is important for determining cell fate, controlling tissue shape and maintaining tissue architecture. Division perpendicular to the plane of the substrate can promote tissue stratification during development or wound healing, but also metastasis when orientation is aberrant. Much is known about the molecular mechanisms involved in setting the spindle orientation. However, less is known about the contribution of mechanical factors, such as tissue tension, in ensuring spindle orientation in the plane of the epithelium, despite epithelia being continuously subjected to mechanical stresses. Here, we used suspended epithelial monolayers devoid of extracellular matrix and subjected to varying levels of tissue tension to study the orientation of division relative to the tissue plane. We found that decreasing tissue tension by compressing the monolayers or by inhibiting myosin contractility leads to a higher frequency of out-of-plane divisions. Reciprocally, accurate in-plane division can be restored by increasing tissue tension by increasing cell contractility or by tissue stretching. By considering the full three-dimensional geometry of the epithelium, we show that spindles are sensitive to tissue tension, independently of cell shape, through its impact on the tension at subcellular surfaces. Overall, our data suggest that accurate spindle orientation in the plane of the epithelium necessitates the presence of a sufficiently large tension at intercellular junctions.

Significance statement

In growing epithelia, divisions are typically oriented in the plane of the tissue to drive expansion. In some organs, divisions are then re-oriented so that they occur perpendicular to the epithelium plane to drive tissue stratification and cell differentiation. When uncontrolled, this switch in orientation can lead to defects in tissue organisation and, in cancer, likely contribute to metastasis. While much is known about the molecular mechanisms controlling mitotic spindle orientation, less is known about the role of mechanical factors. Here we use mechanical and chemical perturbations to show that mechanics plays a role in controlling the plane of division. Overall, our data suggest that the orientation of spindles in the epithelium plane requires sufficient tension across intercellular junctions.
Expanded Analysis of Pigmentation Genetics in UK Biobank
Authors: Pairo-Castineira Erola , Cornelissen Jaime , Rawlik Konrad , Canela-Xandri Oriol , Loftus Stacie K. , Pavan William J. , Brown Kevin M. , Tenesa Albert , Jackson Ian J.
Published: February 2022

The genetics of pigmentation is an excellent model for understanding gene interactions in a trait almost entirely unaffected by environment. We have analysed pigmentation phenotypes in UK Biobank using DISSECT, a tool which enables genome-wide association studies (GWAS) whilst accounting for relatedness between individuals, and thus allows a much larger cohort to be studied. We have increased the number of candidate genes associated with red and blonde hair colour, basal skin colour and tanning response to UV radiation. As previously described, we find almost all red hair individuals have two variantMC1Ralleles; exome sequence data expands the number of associated coding variants. Rare red-headed individuals with only a singleMC1Rvariant are enriched for an associated eQTL at theASIPgene. We find that females are most likely to self-report red or blonde hair, paler skin and less tanning ability than men, and that variants atKITLG, MC1R, OCA2andIRF4show significant sex differences in effect. After taking sex into account, pigmentation phenotypes are not correlated with sex hormone levels, except for tanning ability, which shows a positive correlation with testosterone in men. Across the UK there is a correlation between place of birth and hair colour; red hair being more common in the north and west, whilst blonde hair is more common in the east. Combining GWAS with transcriptome data to generate a transcriptome wide association study identifies candidate genes whose expression in skin or melanocytes shows association with pigmentation phenotypes. A comparison of candidates associated with different pigmentation phenotypes finds that candidates for blonde hair, but not skin colour, are enriched for skin and hair genes suggesting that it may be hair shape and structure that impacts hair colour, rather than the melanocyte/keratinocyte interaction.
Reproductive strategies in a complex of simultaneously hermaphroditic species, the Allolobophora chlorotica case study
Authors: Dupont L. , Audusseau H. , Porco D. , Butt K. R.
Published: February 2022

An in-depth knowledge of reproductive strategies is essential to understand the evolutionary history of species and their resulting patterns of taxonomic diversity. In particular, the study of life history traits related to reproduction could help to resolve the speciation patterns in the cryptic species complexes recently found in earthworms. Here, we carried out a parentage analysis in such a complex, the Allolobophora chlorotica aggregate. Using four nuclear microsatellite markers and a fragment of the cytochrome c oxidase subunit I mitochondrial gene we investigated (i) the mating strategies between individuals belonging to two divergent mitochondrial lineages (L2 and L3) that cannot be distinguished with nuclear markers and (ii) the reproductive isolation between lineages that are differentiated both at the mitochondrial and nuclear level (L2/L3 and L1). Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mitochondrial lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In L2 and L3 crosses, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest between mating partners. In L2/L3 and L1 crosses, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Reproductive strategies are thus likely to contributed to the diversification of this complex of species and we advocate further studies on sexual selection and sex allocation in earthworms.
Evaluation of PRKACA as a Therapeutic Target for Fibrolamellar Carcinoma
Authors: Schalm Stefanie S. , O’Hearn Erin , Wilson Kevin , LaBranche Timothy P. , Silva Grace , Zhang Zhuo , DiPietro Lucian , Bifulco Neil , Woessner Richard , Stransky Nicolas , Sappal Darshan , Campbell Robert , Lobbardi Riadh , Palmer Michael , Kim Joseph , Ye Chaoyang , Dorsch Marion , Lengauer Christoph , Guzi Timothy , Kadambi Vivek , Garner Andrew , Hoeflich Klaus P.
Published: February 2022

Background & Aims

Fibrolamellar carcinoma (FLC) is a rare, difficult-to-treat liver cancer primarily affecting pediatric and adolescent patients, and for which precision medicine approaches have historically not been possible. The DNAJB1-PRKACA gene fusion was identified as a driver of FLC pathogenesis. We aimed to assess whether FLC tumors maintain dependency on this gene fusion and determine if PRKACA is a viable therapeutic target.

Methods

FLC patient-derived xenograft (PDX) shRNA cell lines were implanted subcutaneously into female NOD-SCID mice and tumors were allowed to develop prior to randomization to doxycycline (to induce knockdown) or control groups. Tumor development was assessed every 2 days. To assess the effect of treatment with novel selective PRKACA small molecule kinase inhibitors, BLU0588 and BLU2864, FLC PDX tumor cells were implanted subcutaneously into NOD-SCID mice and tumors allowed to develop. Mice were randomized to treatment (BLU0588 and BLU2864, orally, once daily) or control groups and tumor size determined as above.

Results

Knockdown of DNAJB1-PRKACA reversed a FLC-specific gene signature and reduced PDX tumor growth in mice compared to the control group. Furthermore, FLC PDX tumor growth was significantly reduced with BLU0588 and BLU2864 treatment versus control (P = 0.003 and P = 0.0005, respectively).

Conclusions

We demonstrated, using an inducible knockdown and small molecule approaches, that FLC PDX tumors were dependent upon DNAJB1-PRKACA fusion activity. In addition, this study serves as a proof-of-concept that PRKACA is a viable therapeutic target for FLC and warrants further investigation.
Orally active mGluR2/3 metabotropic antagonist pro-drug mimics the beneficial effects of physical exercise on neurogenesis, behavior, and exercise-related molecular pathways in an Alzheimer’s disease mouse model
Authors: Perez-Garcia Georgina , Bicak Mesude , Buros Jacqueline , Haure-Mirande Jean-Vianney , Perez Gissel M. , Otero-Pagan Alena , Gama Sosa Miguel A. , De Gasperi Rita , Sano Mary , Gage Fred H. , Barlow Carrolee , Dudley Joel T. , Glicksberg Benjamin S. , Wang Yanzhuang , Readhead Benjamin , Ehrlich Michelle E. , Elder Gregory A. , Gandy Sam
Published: February 2022

Modulation of physical activity represents an important intervention that may delay, slow, or prevent mild cognitive impairment (MCI) or dementia due to Alzheimer’s disease (AD). One mechanism proposed to underlie the beneficial effect of physical exercise involves the apparent stimulation of adult hippocampal neurogenesis (AHN). BCI-838 is a pro-drug whose active metabolite BCI-632 is an antagonist at the group II metabotropic glutamate receptor (mGluR2/3). We previously demonstrated that administration of BCI-838 to a mouse model of cerebrovascular accumulation of oligomeric AβE22Q (APPE693Q= “Dutch APP”) reduced learning behavior impairment and anxiety, both of which are associated with the phenotype of the Dutch APP mice. Here we show that (i) administration of BCI-838, physical exercise, or a combination of BCI-838 and physical exercise enhanced AHN in a four-month old mouse model of AD amyloid pathology (APPKM670/671NL/ PSEN1Δexon9 = APP/PS1), (ii) administration of BCI-838 alone or associated with physical exercise led to stimulation of AHN and improvement in both spatial and recognition memory, (iii) significantly, the hippocampal dentate gyrus transcriptome of APP/PS1 mice following BCI-838 treatment up-regulated brain-derived neurotrophic factor (BDNF), PIK3C2A of the PI3K-MTOR pathway, and metabotropic glutamate receptors, and down-regulated EIF5A of ketamine-modulating mTOR activity, and finally (iv) qPCR findings validate a significantly strong association between increased BDNF levels and BCI-838 treatment. Our study points to BCI-838 as a safe and orally active compound capable of mimicking the beneficial effect of exercise on AHN, learning behavior, and anxiety in a mouse model of AD neuropathology.
Three-dimensional analysis and in vivo imaging for sperm release and transport in the murine seminiferous tubule
Authors: Kanazawa Yuta , Omotehara Takuya , Nakata Hiroki , Hirashima Tsuyoshi , Itoh Masahiro
Published: February 2022

Introduction

Spermatozoa released from Sertoli cells must be transported to the epididymis. However, the contribution of the peristaltic motion in the seminiferous tubule to sperm release and transport remains unclear. We, therefore, investigated luminal flow and movements in the seminiferous tubules by three-dimensional analysis and in vivo imaging.

Materials and Methods

Serial testicular sections were cut in 5-μm-thick and 50-μm-interval and stained by PAS-hematoxylin. After the three-dimensional reconstruction of the seminiferous tubules, the localization of the flowing spermatozoa and stages observed in the sections were recorded in each reconstructed tubule. The luminal movements in the seminiferous tubule were observed by in vivo imaging using a fluorescent-reporter mouse and two-photon excitation microscopy system.

Results

Flowing spermatozoa were mainly scattered in the lumina at stage VII/VIII, and clustered spermatozoa were also found in some regions. The clustered spermatozoa were observed at zero to two regions in each seminiferous tubule. Flowing spermatozoa were also found in the opposite direction to the rete testis. The flagellum direction of the spermatozoa attached to the seminiferous epithelium was reversed within a few seconds to a few tens of seconds when observed by in vivo imaging. The epithelium at the inner curve of the seminiferous tubule moved more actively and attached fewer spermatozoa compared to that at the outer curve.

Discussion

This study revealed the presence of repeatedly reversed luminal flow in the seminiferous tubule. Such movements are suggested to help the sperm release from the Sertoli cells and the following aggregation of the released spermatozoa.
Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP
Authors: Imaizumi Yuki , Takanuki Kazunori , Miyake Takuya , Takemoto Mizuki , Hirata Kunio , Hirose Mika , Oi Rika , Kobayashi Tatsuya , Miyoshi Kenichi , Aruga Rie , Yokoyama Tatsuhiko , Katagiri Shizuka , Matsuura Hiroaki , Iwasaki Kenji , Kato Takayuki , Kaneko Mika K. , Kato Yukinari , Tajiri Michiko , Akashi Satoko , Nureki Osamu , Hizukuri Yohei , Akiyama Yoshinori , Nogi Terukazu
Published: February 2022

Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including E. coli RseP. Our observations are consistent with a rearrangement of the RseP domains surrounding the active center to expose the substrate-binding site where a conserved electrostatic linkage between the transmembrane and membrane-associated domains mediates the conformational changes, suggesting that RseP has a gating mechanism to regulate substrate entry. Mutational analysis also supports that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet and is clamped at the active center for efficient cleavage. Furthermore, this substrate accommodation mechanism appears to be common across distinct intramembrane proteases.
Domain expansion and functional diversification in vertebrate reproductive proteins
Authors: Rivera Alberto M. , Wilburn Damien B. , Swanson Willie J.
Published: February 2022

The rapid evolution of fertilization proteins can result in remarkable diversity in their structure and function. Many of the proteins in vertebrate egg coats contain copies (1-6) of the ZP-N domain. These ZP-N domains can facilitate multiple reproduction functions, including species-specific sperm recognition. We integrated phylogenetics and machine learning to investigate how ZP-N domains diversified in structure and function. The most C-terminal ZP-N domain of each paralog is associated with another domain type (ZP-C) which together form a “ZP module.” All modular ZP-N domains were phylogenetically distinct from non-modular or free ZP-N domains. Machine learning-based classification identified 8 residues that form a stabilizing network in modular ZP-N domains that is absent in free domains. Positive selection was identified in some free ZP-N domains. Our findings suggest that purifying selection has conserved an essential structural core in modular ZP-N domains, while free N-terminal domains have been able to experience functionally diversify.
Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution
Authors: Morales-Briones Diego F. , Kadereit Gudrun
Published: February 2022

Flaveria (Asteraceae) is the prime model for the study of C4 photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C3-C4 intermediate phenotypes, still existing in Flaveria today. Molecular phylogenies of Flaveria based on concatenated data matrices are currently used to reconstruct the complex sequence of trait shifts during C4 evolution. To assess the possible role of hybridization in C4 evolution in Flaveria, we re-analyzed transcriptome data of 17 Flaveria species to infer the extent of gene tree discordance and possible reticulation events. We found massive gene tree discordance as well as reticulation along the backbone and within clades containing C3-C4 intermediate and C4-like species. An early hybridization event between two C3 species might have triggered C4 evolution in the genus. The clade containing all C4 species plus the C4-like species F. vaginata and F. palmeri is robust but of hybrid origin involving F. angustifolia and F. sonorensis (both C3-C4 intermediate) as parental lineages. Hybridization seems to be a driver of C4 evolution in Flaveria and likely promoted the fast acquisition of C4 traits. This new insight can be used in further exploring C4 evolution and can inform C4 bioengineering efforts.
Selective inhibition of protein secretion by abrogating receptor-coat interactions during ER export
Authors: Gomez-Navarro Natalia , Maldutyte Julija , Poljak Kristina , Peak-Chew Sew-Yeu , Orme Jonathon , Bisnett Brittany J. , Lamb Caitlin H. , Boyce Michael , Gianni Davide , Miller Elizabeth A.
Published: February 2022

Protein secretion is an essential cellular process that permits cell growth, movement and communication. Traffic of proteins within the eukaryotic secretory pathway is mediated by transport intermediates that bud from one compartment, populated with appropriate cargo proteins, and fuse with a downstream compartment to deliver their contents. Here, we explore the possibility that protein secretion can be selectively inhibited by perturbing protein-protein interactions that drive capture into transport vesicles. Human PCSK9 is a major determinant of cholesterol metabolism, whose secretion is mediated by a specific cargo adaptor of the ER export machinery, SEC24A. We map a series of protein-protein interactions between PCSK9, its ER export receptor, SURF4, and SEC24A, that mediate secretion of PCSK9. We show that the interaction between SURF4 and SEC24A can be inhibited by 4-PBA, a small molecule that occludes a cargo-binding domain of SEC24. This inhibition reduces secretion of PCSK9 and additional SURF4 clients that we identify by mass spectrometry, leaving other secreted cargoes unaffected. We propose that selective small molecule inhibition of cargo recognition by SEC24 is a potential therapeutic intervention for atherosclerosis and other diseases that are modulated by secreted proteins.
G protein-coupled estrogen receptor activation by Bisphenol-A disrupts protection from apoptosis conferred by estrogen receptors ERα and ERβ in pancreatic beta cells
Authors: Babiloni-Chust Ignacio , dos Santos Reinaldo S. , Medina-Gali Regla M. , Perez-Serna Atenea A. , Encinar José-Antonio , Martinez-Pinna Juan , Gustafsson Jan-Ake , Marroqui Laura , Nadal Angel
Published: February 2022

17β-estradiol protects pancreatic β-cells from apoptosis via the estrogen receptors ERα, ERβ and GPER. Conversely, the endocrine disruptor Bisphenol-A (BPA), which exerts multiple effects in this cell type via the same estrogen receptors, increased basal apoptosis. The molecular initiated events that trigger these opposite actions have yet to be identified. We demonstrated that combined genetic downregulation and pharmacological blockade of each estrogen receptor increased apoptosis to a different extent. The increase in apoptosis induced by BPA was diminished by the pharmacological blockade or the genetic silencing of GPER, and it was partially reproduced by the GPER agonist G1. BPA and G1-induced apoptosis were abolished upon pharmacological inhibition, silencing of ERα and ERβ, or in dispersed islet cells from ERβ knockout (BERKO) mice. Yet, the ERα and ERβ agonists, PPT and DPN, respectively, had no effect on beta cell viability. To exert their biological actions, ERα and ERβ form homodimers and heterodimers. Molecular dynamic simulations together with proximity ligand assay and coimmunoprecipitation experiments indicated that the interaction of BPA with ERα and ERβ as well as the GPER activation by G1 decreased ERαβ heterodimers. We propose that ERαβ heterodimers play an antiapoptotic role in beta cells and that BPA- and G1-induced decrease in ERαβ heterodimers leads to beta cell apoptosis. Unveiling how different estrogenic chemicals affect the crosstalk among estrogen receptors should help to identify diabetogenic endocrine disruptors.

Highlights

Pharmacological blockade and gene silencing of estrogen receptors ERα, ERβ and GPER indicate that they are antiapoptotic in basal conditions.

GPER activation by G1 and BPA triggered apoptosis via a crosstalk with ERα and ERβ.

BPA interaction with ERα and ERβ as well as GPER activation decreased ERαβ heterodimers, which was associated to increased apoptosis.

This pathway represents a novel molecular initiating event underlying the pro-apoptotic effect of BPA

The EndoC-βH1 cell line may be a valid model of human β-cells for identifying diabetogenic pollutants.
A subset of gut leukocytes have telomerase-dependent “hyper-long” telomeres and require telomerase for function in zebrafish
Authors: Ellis Pam S. , Martins Raquel R. , Thompson Emily J. , Farhat Asma , Renshaw Stephen A. , Henriques Catarina M.
Published: February 2022

Telomerase, the enzyme capable of elongating telomeres, is usually restricted in human somatic cells, which contributes to progressive telomere shortening with cell-division and ageing. Using the zebrafish model, we show that subsets gut immune cells have telomerase-dependent “hyper-long” telomeres, which we identified as being predominantly macrophages and dendritics (mpeg1.1+ and cd45+mhcII+). Notably, mpeg+ macrophages have much longer telomeres in the gut than in their haematopoietic tissue of origin, suggesting that there is a gut-specific modulation of telomerase in these cells.

Moreover, we show that a subset of gut mpeg+ cells express telomerase (tert) in young WT zebrafish, but that the relative proportion of these cells decreases with ageing. Importantly, this is accompanied by telomere shortening and DNA damage responses with ageing and a telomerase-dependent decrease in expression of autophagy and immune activation markers. Finally, these telomerase-dependent molecular alterations are accompanied by impaired phagocytosis of E.coli and increased gut permeability in vivo. Together, our data show that limiting levels of telomerase lead to changes in gut immunity and gut permeability, which, together, are likely contributors to local and systemic tissue degeneration and increased susceptibility to infection with ageing.

GRAPHICAL ABSTRACT

Our data show that limiting levels of telomerase contribute to alterations in gut immunity, namely increased apoptosis, decreased autophagy and immune activation of mpeg+ macrophages in the gut. This is accompanied by a decreased ability to clear pathogens and increased gut permeability. Together, these are likely contributors to local and systemic tissue degeneration and susceptibility to infection with ageing.
Lipid-mediated nuclear moonlighting of cytosolic glyceraldehyde-3-phosphate dehydrogenase in plant heat response
Authors: Kim Sang-Chul , Yao Shuaibing , Zhang Qun , Wang Xuemin
Published: February 2022

Cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) is a glycolytic enzyme, but it undergoes stress-induced nuclear translocation for moonlighting and regulating gene expression. To elucidate how the cytosolic enzyme moves into the nuclei under stress, we show that the plasma membrane-associated phospholipase Dδ(PLDδ) and its product phosphatidic acid (PA) promote heat-induced nuclear translocation of GAPC. The GAPC nuclear accumulation and Arabidopsis seedling tolerance to heat stress were reduced in pldδ, which was restored by genetic complementation with intact PLDδ, but not with catalytically inactive enzyme. GAPC overexpression enhanced the seedling thermotolerance and the expression of heat-inducible genes, but this was not observed when GAPC was overexpressed in the pldδ background. The GAPC nuclear accumulation and seedling thermotolerance were also decreased by application with a vesicle trafficking inhibitor brefeldin A (BFA) or zinc that inhibited the PA-GAPC interaction. Heat stress elevated PA levels in nuclei from wild-type, but not from pldδ and BFA-treated plants. Lipid labeling and fluorescence resonance energy transfer analyses demonstrated heat-induced nuclear co-localization of PA and GAPC, which was impaired by BFA or zinc treatment. Taken together, our data suggest that PLDδ-produced PA mediates nuclear translocation of GAPC via lipid-protein interaction and vesicle trafficking for plants to cope with heat.

One sentence summary

The lipid mediator phosphatidic acid produced by a plasma membrane-associated phospholipase D mediates the nuclear moonlighting of cytosolic glyceraldehyde-3-phosphate dehydrogenase under heat.
Active site center redesign increases protein stability preserving catalysis
Authors: Romero-Romero Maria Luisa , Garcia-Seisdedos Hector , Ibarra-Molero Beatriz
Published: February 2022

The stabilization of natural proteins is a long-standing desired goal in protein engineering. Optimizing the hydrophobicity of the protein core often results in extensive stability enhancements. However, the presence of totally or partially buried catalytic charged residues, essential for protein function, has limited the applicability of this strategy. Here, focusing on the thioredoxin, we aimed to augment protein stability by removing buried charged residues in the active site without loss of catalytic activity. To this end, we performed a charged-to-hydrophobic substitution of a buried and functional group, resulting in a significant stability increase yet abolishing catalytic activity. Then, to simulate the catalytic role of the buried ionizable group, we designed a combinatorial library of variants targeting a set of seven surface residues adjacent to the active site. Notably, more than 50% of the library variants restored, to some extent, the catalytic activity. The combination of experimental study of 2% of the library with the prediction of the whole mutational space by Partial Least-squares regression revealed that a single point mutation at the protein surface is sufficient to fully restore the catalytic activity without thermostability cost. As a result, we engineered one of the highest thermal stability reported for a protein with a natural occurring fold (138 °C). Further, our hyperstable variant preserves the catalytic activity both in vitro and in vivo.

SIGNIFICANCE

The major driving force of protein folding is the hydrophobic effect, and increasing the protein core hydrophobicity essentially increases protein stability. Active sites often contain buried ionizable groups, which can be essential for function but dramatically reduce protein stability. Thus, increasing the protein core hydrophobicity cannot be applied to enzyme active sites without a functional cost. We propose a method to enhance protein stability by overcoming this obstacle. We show that catalytic properties of buried charges can be mimicked with surface mutations, thus paving the way to unlock the optimization of the hydrophobic core to stabilize enzymes.
Modifications of lipoic arm by reactive nitrogen species regulate α-ketoacid dehydrogenases
Authors: Seim Gretchen L. , Fang Zixiang , Pagliarini David J. , Fan Jing
Published: February 2022

Mitochondrial α-ketoacid dehydrogenases, including the pyruvate dehydrogenase complex (PDHC) and the oxoglutarate dehydrogenase complex (OGDC), are a family of multi-subunit enzyme complexes that use a lipoic arm to transfer an acyl group to coenzyme A (CoA). The regulation of α-ketoacid dehydrogenases plays crucial roles in mitochondrial metabolism and cellular energy homeostasis. We previously found that PDHC and OGDC become profoundly inhibited in macrophages upon classical activation, causing substantial remodeling of the TCA cycle. This inhibition was driven by the loss of the catalytically active lipoic moiety; however, the molecular mechanism causing this loss was not clear. Here we show that reactive nitrogen species (RNS), which are produced by activated macrophages, can cause a series of thiol-modifications to the lipoic arm that inactivate PDHC and OGDC. CoA-SNO, the non-enzymatic product between RNS and the E2 subunit’s natural substrate CoA, plays a key role in efficiently delivering RNS mediated modifications onto the lipoic arm. This work reveals a new biochemical mechanism capable of substantially regulating mitochondrial α-ketoacid dehydrogenases, which has potential relevance for a range of physiological and pathological conditions.