bluuebunny/crossref_metadata_2025 huggingface dataset:
Familial hemophagocytic phohistiocytosis induced by PRF1 mutation with neurologic manifestations as the initial clinical presentations: A case report
Authors: You Yang , Wu Wenjuan , Li Baoguang
Published: June 2023

Background:

To investigate the clinical characteristics of familial hemophagocytic phohistiocytosis (FHL) induced by PRF1 gene mutation and with central nervous injury as the initial presentation.

Case presentation:

Herein, we presented 2 cases of a familial hemophagocytic syndrome caused by PRF1 gene mutation in 1 family with central nervous injury as the first symptom and searched relevant literature for clinical analysis of its pathogenic characteristics. Two children from 1 family were included in this study, both of whom had complex heterozygous mutations of C. 1189_1190dupTG (p.H398Afs*23) and C. 394G>A (p.G132R). Literature search further revealed 20 cases of PRF1 gene mutation-induced familial FHL with central nervous injury as the initial presentation. The main neurological symptoms included cranial nerve injury (81.8%), convulsion (77.3%), ataxia (63.6%), encephalopathy (59.1%), and limb paralysis (40.9%). Cranial imaging findings were dominated by the cerebral hemisphere (100%), cerebellar hemisphere (85%), brainstem (55%), and periventricular white matter (40%), and 73.7% of cases had elevated white blood cell count in CSF. Most cases were confirmed by differential diagnosis and gene sequencing, which suggested that C. 673C>T (P.r225W), C. 394G>A (P.G132r), C. 666C>A (p.H222Q), C. 1349C>T (p.T450M), C. 1349C>T (p.T450M), and C. 443C>C (p.A148G) could be focal mutations of this disease.

Conclusion:

Lesions involving the cerebellum and brainstem in children with ataxia and cranial nerve damage could be indicative of primary FHL; thus, the inherent immune test and gene test should be timely performed to help confirm the diagnosis, guide the treatment, and improve the prognosis.
Teratomas from past to the present: A scientometric analysis with global productivity and research trends between 1980 and 2022
Authors: Çalbiyik Murat , Zehir Sinan
Published: June 2023

There is currently no bibliometric study on teratomas in the literature. This study aims to analyze the published articles on teratomas to provide an overview of the subject, determine global productivity, and identify current research trends. Additionally, data on different components of scientific output (countries, journals, institutions, authors) were analyzed. A total of 4209 articles published on teratomas between 1980 and 2022 were analyzed using various bibliometric and statistical methods. Bibliometric network visualization maps were used to determine trending topics, citation analyses, and international collaborations. Spearman correlation coefficient was used for correlation analysis. The top 3 countries that made the most contributions to the literature were the USA (1041, 24.7%), Japan (501, 11.9%), and India (310, 7.3%). The top 3 active institutions were the University of California System (n = 78), University of London (64), and Harvard University (62). The top 3 productive journals were the Journal of Pediatric Surgery (n = 141), Pediatric Surgery International (n = 70), and Journal of Pediatric Surgery Case Reports (69). The most productive author was Ulbright TM. (n = 18). The most studied topics from past to present were ovarian cancer/ovarian teratoma/ovarian torsion, mature cystic teratoma/dermoid cyst, sacrococcygeal teratoma, germ cell tumors, immature teratoma, malignant transformation, mediastinal teratoma/mediastinum, neonate/newborn/infant, prenatal diagnosis, testis/testicular cancer/teratoma, ultrasonography/ultrasound, magnetic resonance imaging, chemotherapy, growing teratoma syndrome, surgery, retroperitoneal teratoma/retroperitoneum, laparoscopic surgery/laparoscopy, children/child, and fetal surgery/fetus. We identified trend research topics in the field of teratomas in recent years, including mature cystic teratoma, ovarian teratoma/neoplasm, ovarian cancer, ovarian torsion, growing teratoma syndrome, recurrence, pediatric, testicular cancer, anti-n-methyl-d-aspartate receptor encephalitis, immature teratoma, retroperitoneal, struma ovarii, and carcinoid. The research leadership in the development of teratoma literature was determined by countries with major economies such as the USA, Japan, India, the UK, China, Turkey, South Korea, and other European countries (France, Germany, Italy).
Application of a selective hospitalization model in the clinical practice of breast surgery
Authors: Chen Ying , Huang Liying , Chen Xia
Published: June 2023

This study aimed to explore the clinical application of a selective hospitalization model in breast disease specialties and to evaluate its effectiveness. Information of patients registered in the selective hospitalization model and those registered in the direct model between October 1, 2020, and October 31, 2022, were collected. The hospitalization days and expenses of patients admitted through distinct modes and divergent medical categories were examined. After completing relevant examinations during the selected hospitalization period, 708 patients were admitted to our medical group for further treatment during the study period. Furthermore, 401 patients underwent hospitalization procedures immediately after the initial visit and received additional treatment after completing pertinent examinations during hospitalization. For patients who underwent benign surgery after admission, there was a significant difference in the length of hospital stay between patients admitted through selective hospitalization and those admitted directly (P < .001); however, there was no significant difference in total hospital expenses (P = .895). For patients who underwent malignant surgery after admission, there were significant differences in the length of hospital stay (P < .001) and total cost of hospitalization (P = .015). There was no significant difference in the length of hospital stay between the 2 groups of patients initially admitted for neoadjuvant chemotherapy (P = .589); however, the total cost of hospitalization significantly differed (P < .001). The selective hospitalization model can reduce medical expenses and the average length of hospital stay. This new hospitalization model is more flexible and allows for the inclusion of outpatient examination costs in subsequent hospitalization medical insurance reimbursement, greatly reducing the financial burden on patients. It is worthy of further exploration, optimization, and promotion.
Thermal ablative therapies in the gastrointestinal tract
Authors: Manner Hendrik
Published: June 2023

Purpose of review

Thermal ablatives therapies have seen an expanding role in gastrointestinal endoscopy during the last years. The aim of this review is to give an overview of the currently available techniques.

Recent findings

In the upper gastrointestinal tract, mainly in early Barrett's neoplasia, endoscopic ablation strategies ranging from RFA to Hybrid-APC are, together with resection strategies, the main part of the armamentarium. In the small intestine, argon plasma coagulation (APC) can be effectively used for the treatment of angiodysplasias. In the lower gastrointestinal tract, APC and RFA are mainly used. In tumour obstruction, thermal ablation is used to reopen the lumen. The selection of available techniques is still increasing.

The variety of ablation techniques enables the endoscopist to choose the appropriate ablation tool for each individual patient.
Interpretation of serum pancreatic enzymes in pancreatic and nonpancreatic conditions
Authors: Bush Nikhil , Akshintala Venkata S.
Published: June 2023

Purpose of review

Serum levels of amylase and lipase can be elevated in nonpancreatic conditions that may or may not be associated with abdominal pain. This leads to a large proportion of patients being falsely labeled as having acute pancreatitis. In this review, we aim to summarize the existing evidence on pancreatic enzyme elevation in various pancreatic and nonpancreatic conditions and its practical implications in clinical practice and healthcare.

Recent findings

Serum amylase and lipase levels are not specific for pancreatitis. Attempts have been made to validate newer biomarkers including pancreatic elastase, serum trypsin, urinary trypsinogen-activated peptide, phospholipase A2, carboxypeptidase B, activated peptide of carboxypeptidase B, the trypsin 2 alpha 1 activation complex, and circulating cell-free DNA for the diagnosis of acute pancreatitis.

Serum lipase levels can be elevated in many intra-abdominal inflammatory conditions. Although more sensitive and specific than amylase, serum lipase levels are not sufficient to diagnose acute pancreatitis in patients with abdominal pain. There is a need to increase stress on radiological evidence as well increase cut-off levels of enzyme elevation for a more accurate diagnosis of acute pancreatitis.
Management of eagle syndrome
Authors: Sharifi Alireza , Kouhi Ali
Published: June 2023

Purpose of review

Eagle syndrome is a challenging clinical presentation with important potential complications. It can be misdiagnosed due to lack of awareness; this review provides information in terms of diagnosis and management of eagle syndrome.

Recent findings

The importance of early diagnosis of this rare disease is preventing the delay in clinical-surgical treatment. As there is not a universally accepted cut-off for styloid process length, the diagnosis should be confirmed by length of process greater than one-third of the length of mandibular ramus in addition to other clinical symptoms and signs. There are both surgical and pharmacological treatment options for these patients.

Eagle syndrome is a rare clinical condition and its diagnosis is made by physical examination and radiography. When it is suspected by physical examination, definitive diagnosis is confirmed by computed tomography scans of the skull, as the gold standard. Location, degree of elongation of styloid process, and severity and reproducibility of symptoms are important factors in deciding the most appropriate approach. Surgery is frequently the treatment of choice in Eagle syndrome patients. With proper diagnosis and treatment, the prognosis is favourable and recurrence is uncommon.
Emergency Department Volume and Delayed Diagnosis of Pediatric Appendicitis
Authors: Michelson Kenneth A , Bachur Richard G , Rangel Shawn J , Monuteaux Michael C , Mahajan Prashant , Finkelstein Jonathan A
Published: June 2023

Objective:

To determine the association of emergency department (ED) volume of children and delayed diagnosis of appendicitis.

Summary Background Data:

Delayed diagnosis of appendicitis is common in children. The association between ED volume and delayed diagnosis is uncertain, but diagnosis-specific experience might improve diagnostic timeliness.

Methods:

Using Healthcare Cost and Utilization Project 8-state data from 2014-2019, we studied all children with appendicitis <18 years old in all EDs. The main outcome was probable delayed diagnosis: >75% likelihood that a delay occurred based on a previously validated measure. Hierarchical models tested associations between ED volumes and delay, adjusting for age, sex, and chronic conditions. We compared complication rates by delayed diagnosis occurrence.

Results:

Among 93,136 children with appendicitis, 3,293 (3.5%) had delayed diagnosis. Each twofold increase in ED volume was associated with an 6.9% (95% confidence interval [CI] 2.2, 11.3) decreased odds of delayed diagnosis. Each twofold increase in appendicitis volume was associated with a 24.1% (95% CI 21.0, 27.0) decreased odds of delay. Those with delayed diagnosis were more likely to receive intensive care (odds ratio [OR] 1.81, 95% CI 1.48, 2.21), have perforated appendicitis (OR 2.81, 95% CI 2.62, 3.02), undergo abdominal abscess drainage (OR 2.49, 95% CI 2.16, 2.88), have multiple abdominal surgeries (OR 2.56, 95% CI 2.13, 3.07), or develop sepsis (OR 2.02, 95% CI 1.61, 2.54).

Conclusions:

Higher ED volumes were associated with a lower risk of delayed diagnosis of pediatric appendicitis. Delay was associated with complications.
Propranolol Normalizes Metabolomic Signatures Thereby Improving Outcomes After Burn
Authors: Rehou Sarah , de Brito Monteiro Lauar , Auger Christopher , Knuth Carly M. , Abdullahi Abdikarim , Stanojcic Mile , Jeschke Marc G.
Published: June 2023

Objective and Background:

Propranolol, a nonselective beta-receptor blocker, improves outcomes of severely burned patients. While the clinical and physiological benefits of beta-blockade are well characterized, the underlying metabolic mechanisms are less well defined. We hypothesized that propranolol improves outcomes after burn injury by profoundly modulating metabolic pathways.

Methods:

In this phase II randomized controlled trial, patients with burns ≥20% of total body surface area were randomly assigned to control or propranolol (dose given to decrease heart rate <100 bpm). Outcomes included clinical markers, inflammatory and lipidomic profiles, untargeted metabolomics, and molecular pathways.

Results:

Fifty-two severely burned patients were enrolled in this trial (propranolol, n=23 and controls, n=29). There were no significant differences in demographics or injury severity between groups. Metabolomic pathway analyses of the adipose tissue showed that propranolol substantially alters several essential metabolic pathways involved in energy and nucleotide metabolism, as well as catecholamine degradation (P<0.05). Lipidomic analysis revealed that propranolol-treated patients had lower levels of proinflammatory palmitic acid (P<0.05) and saturated fatty acids (P<0.05) with an increased ratio of polyunsaturated fatty acids (P<0.05), thus shifting the lipidomic profile towards an anti-inflammatory phenotype after burn (P<0.05). These metabolic effects were mediated by decreased activation of hormone-sensitive lipase at serine 660 (P<0.05) and significantly reduced endoplasmic reticulum stress by decreasing phospho-JNK (P<0.05).

Conclusion:

Propranolol’s ability to mitigate pathophysiological changes to essential metabolic pathways results in significantly improved stress responses.
Longitudinal Imaging in a Patient With Opioid-associated Amnestic Syndrome
Authors: Barash Jed A. , Schmahmann Jeremy D. , Xie Zhongcong , Lev Michael H. , El Fakhri Georges
Published: June 2023

Since 2012, individuals with a history of opioid misuse have infrequently been observed to develop a sudden-onset amnestic syndrome associated with bilateral hippocampal-restricted diffusion on MRI. Follow-up imaging of this opioid-associated amnestic syndrome (OAS) has revealed persistent hippocampal abnormalities. Given these observations, as well as neuropathological studies demonstrating excessive tau deposition in the hippocampi and other brain regions of individuals with opioid misuse, we describe longitudinal imaging of a patient with a history of OAS from presentation through 53 months later, when tau positron emission tomography (PET) was performed. Our patient was a 21-year-old woman with a history of attention-deficit hyperactivity disorder and substance use disorder, including opioids (intravenous heroin), who was hospitalized for acute-onset, dense anterograde amnesia. Her urine toxicology screen was positive for opiates. On presentation, her brain MRI showed restricted diffusion as well as T2 and fluid-attenuated inversion recovery (FLAIR) hyperintensity of the hippocampi and globi pallidi. On day 3, magnetic resonance spectroscopy of a right hippocampal region of interest showed a mild reduction of N-acetyl aspartate/creatine, slight elevation of choline/creatine, and the appearance of lactate/lipid and glutamate/glutamine peaks. At 4.5 months, there was resolution of restricted diffusion on MRI, although a minimal anterior T2 and FLAIR hyperintense signal in the right hippocampus persisted. However, by 53 months, when mild memory loss was reported, the hippocampi appeared normal on MRI, and [18F]T807 (tau) PET showed no uptake suggestive of tau deposition. This case report supports the investigation into the hypothesis that OAS may follow a trajectory of reversible metabolic injury.
Changing Epidemiology of Haemophilus influenzae carriage among Children in Lombok Island, Indonesia
Authors: Putri Nina Dwi , Salsabila Korrie , Prayitno Ari , Aprianti Shindy Claudya , Paramaiswari Wisiva Tofriska , Krisna Made Ananda , Safari Dodi
Published: June 2023

The Haemophilus influenzae serotype b conjugate vaccine (Hib vaccine) routine immunization program has been implemented for almost a decade, but there is limited surveillance of H. influenzae carriage in the Indonesian population. H. influenzae was isolated from nasopharyngeal swab specimens from healthy children in Lombok Island, West Nusa Tenggara Province, Indonesia in 2018-2019. Serotyping was performed using a quantitative polymerase chain reaction. Among 96 young children in Lombok Island, we identified H. influenzae from 40 out of 96 NP swab specimens (41.6%). We found 39 non-typeable H. influenzae (NTHi) and 1 serotype b isolate.
Fish-associated Streptococcus agalactiae ST283: first human cases reported from Malaysia
Authors: Zohari Zahira , Barkham Timothy , Mohamad Maswan Norfarhana , Chen Swaine Lin , Muthanna AbdulRahman , Lee Kai Wei , Mohd Desa Mohd Nasir , Azmai Mohammad Noor Amal , Sither Joseph Narcisse Mary , Amin-Nordin Syafinaz
Published: June 2023

In South East Asia,

Streptococcus agalactiae

ST283 causes sepsis in healthy adults. Raw freshwater fish consumption is the only known risk factor. These two case reports are the first from Malaysia. Although they cluster with Singapore ST283, the epidemiology is complicated by the flow of people and fish across borders.
Neuronal wiring diagram of an adult brain
Authors: Dorkenwald Sven , Matsliah Arie , Sterling Amy R , Schlegel Philipp , Yu Szi-chieh , McKellar Claire E. , Lin Albert , Costa Marta , Eichler Katharina , Yin Yijie , Silversmith Will , Schneider-Mizell Casey , Jordan Chris S. , Brittain Derrick , Halageri Akhilesh , Kuehner Kai , Ogedengbe Oluwaseun , Morey Ryan , Gager Jay , Kruk Krzysztof , Perlman Eric , Yang Runzhe , Deutsch David , Bland Doug , Sorek Marissa , Lu Ran , Macrina Thomas , Lee Kisuk , Bae J. Alexander , Mu Shang , Nehoran Barak , Mitchell Eric , Popovych Sergiy , Wu Jingpeng , Jia Zhen , Castro Manuel , Kemnitz Nico , Ih Dodam , Bates Alexander Shakeel , Eckstein Nils , Funke Jan , Collman Forrest , Bock Davi D. , Jefferis Gregory S.X.E. , Seung H. Sebastian , Murthy Mala ,   the FlyWire Consortium
Published: June 2023

Connections between neurons can be mapped by acquiring and analyzing electron microscopic (EM) brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative, yet inadequate for understanding brain function more globally. Here, we present the first neuronal wiring diagram of a whole adult brain, containing 5×107chemical synapses between ∼130,000 neurons reconstructed from a femaleDrosophila melanogaster. The resource also incorporates annotations of cell classes and types, nerves, hemilineages, and predictions of neurotransmitter identities. Data products are available by download, programmatic access, and interactive browsing and made interoperable with other fly data resources. We show how to derive a projectome, a map of projections between regions, from the connectome. We demonstrate the tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine, and descending neurons), across both hemispheres, and between the central brain and the optic lobes. Tracing from a subset of photoreceptors all the way to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviors. The technologies and open ecosystem of the FlyWire Consortium set the stage for future large-scale connectome projects in other species.
Genome-wide analysis of promoter contacts identifies novel regulators of late-stage adipogenesis
Authors: Sandovici Ionel , Mifsud Borbala , Emery Amy , Gulati Pawan , Kentistou Katherine A. , Banu Ayesha , Campbell Niamh , Hardwick Bryn S. , Crooks Alex T. , Fernandez-Twinn Denise S. , Mennitti Lais V. , Srour Luma , Awad Sherine , Chiarugi Davide , Hamilton Russell S. , Wingett Steven W. , Fraser Peter , Ong Ken K. , Schoenfelder Stefan , Mohammad Farhan , O’Rahilly Stephen , Perry John R.B. , Venkitaraman Ashok R. , Ozanne Susan E. , Constância Miguel
Published: June 2023

Adipogenesis is a multi-step process, with epigenetic mechanisms and dynamic 3D chromatin folding thought to play important regulatory roles. However, the kinetics and functional roles of promoter contacts during late-stage adipogenesis are unknown. Here, using multi-omics approaches, we found evidence for promoter switching and widespread 3D rewiring of promoter contacts, as well as changes in the transcriptome and epigenome in late-stage adipogenesis. We identified several clusters of promoter contacts with unique temporal profiles suggesting crucial roles for distal enhancers. By integrating transcriptomics, promoter-capture Hi-C and a siRNA screen of druggable genes, we identified 19 novel regulators of late-stage adipogenesis, over half of which have peptidase or ubiquitin-protein ligase activities. Population-based genetic analyses showed that three of the 19 genes (LAP3,CELA1andGPR157) are involved in regulation of adiposity in humans. These findings shed new light on the epigenetic regulation of late-stage adipogenesis, advancing our understanding of the mechanisms that underpin the formation of functional adipocytes and identifying potential targets for preventing/treating obesity and related disorders.
Anatomy of a mega-radiation: Biogeography and niche evolution inAstragalus
Authors: Folk R.A. , Charboneau J.L.M. , Belitz M. , Singh T. , Kates H.R. , Soltis D.E. , Soltis P.S. , Guralnick R.P. , Siniscalchi C.M.
Published: June 2023

Astragalus(Fabaceae), with more than 3,000 species, represents a successful radiation of morphologically highly similar species found across the Northern Hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. Here, for the first time using extensive taxonomic sampling in a phylogenetic analysis, we ask whether (1)Astragalusis uniquely characterized by bursts of radiation or is instead similar to related taxa. Then we test whether the species diversity ofAstragalusis attributable specifically to its predilection for (2) cold and arid habitats or (3) particular soils. Finally, we test (4) whetherAstragalusoriginated in central Asia as proposed and (5) whether niche evolutionary shifts were associated with the colonization of other continents. Our results point to the importance of heterogeneity in the diversification ofAstragalus, with upshifts associated with the earliest divergences but attributable to no abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. We find strong evidence for a central Asian origin and direct dispersals from this region responsible for much of the present-day distribution, highlighting the importance of central Asia as a biogeographic gateway. In contrast to diversification shifts, biogeographic shifts have a strong association with the abiotic environment. Our most important result was a fundamental divide in soil types and diurnal temperature variation between the Eastern and Western Hemisphere species; this divergence does not reflect differences in available habitat among these biogeographic domains but may reflect unique local gains of edaphic and abiotic stress adaptations. While large clades are logistically difficult to tackle, our investigation shows the importance of phylogenetic and evolutionary studies of “mega-radiations.” Our findings reject any simple key innovation behind the dominance and richness ofAstragalusand underline the often nuanced, multifactorial processes leading to species-rich clades.
Disentangling the biotic and abiotic drivers of bird-building collisions in a tropical Asian city using ecological niche modeling
Authors: Tan David J. X. , Freymueller Nicholas A. , Teo Kah Ming , Symes William S. , Lum Shawn K.Y. , Rheindt Frank E.
Published: June 2023

Bird-building collisions are responsible for a large number of bird deaths in cities around the world, yet they remain poorly studied outside of North America. This study presents one of the first city-wide fine-scale and landscape-scale analyses of bird-building collisions from Asia and represents a novel application of maximum entropy modeling (as commonly applied to species distribution modeling) to assess the drivers of bird-building collisions in the tropical city-state of Singapore. Our results show that the drivers of bird-building collisions often vary among taxa, with several migratory taxa having a higher relative collision risk linked to areas with high building densities and high levels of nocturnal blue light pollution. In contrast, non-migratory taxa had a higher collision risk in areas proximate to woodland cover. Projecting these models onto high-fidelity long-term government land-use plans, we demonstrate that our approach can be applied to predict future changes in bird-building collision risk stemming from future increases in blue light pollution and encroachment of buildings into forested areas. Our results suggest that bird-building collision mitigation measures need to account for the differential drivers of collision across both resident and migratory species, and show that combining community science and ecological modeling can be a powerful approach for analyzing bird-building collision data.

Article impact statement

Inferring the drivers and distribution patterns of bird-building collision hotspots in Singapore using community science and maximum entropy modeling
VARIATIONS IN THE ULTRAVIOLET FLORAL PATTERNS AND POLLINATOR PREFERENCE AMONG SELECTED NON-INVASIVE AND INVASIVE PLANTS OF TAMIL NADU, INDIA
Authors: Ravichandran Indhar Saidanyan , Balasingam Parthiban , Rajasekaran Mohan Raj , Ananthapadmanabhan Karthikeyan , Muthuvel Manojkumar , Ramalingam Kottaimuthu , M Vigneshwaran , Nalluchamy Kamaladhasan , Soorangkattan Saravanan , MR Anbarasan , Sivagnanam Chandrasekaran
Published: June 2023

Fossil evidence shows that pollinator-mediated plant reproduction evolved ∼140 million years ago and bee facilitated pollination evolved ∼70 million years ago. Human vision is limited to the visible color range of 400 to 750 nanometres, whereas most pollinators can perceive the ultraviolet (UV) range in addition to visible colors. Bees have been reported to have highest spectral sensitivity in the ultraviolet spectrum. The main objectives of the study were (1) to assess the prevalence of ultraviolet floral patterns, (2) to analyse floral patterns in relation to plant-pollinator interaction among invasive and non-invasive plants, and (3) to test for intraspecific floral pattern variations among plants with different flower color morphs. A study was conducted on 188 plant species (80 invasive and 108 non-invasive) from parts of Western and Eastern Ghats region of Tamil Nadu, India. The flowers of the studied plant species were imaged in ultraviolet (320-380 nm) and visible spectrums. The mode of pollination for the selected species were documented and confirmed with existing literature. The intraspecific variations in the floral patterns among flower color polymorphic plant species (N=10) were documented in ultraviolet and visible spectrums. Among the studied plant species, around 58% had discernible floral patterns when observed in the UV spectrum, whereas the rest were observed to completely absorb or reflect UV radiation. Whereas 46% of the studied plants exhibited no pattern in the visible spectrum. A significant difference was observed in the pollinator relationship among the ultraviolet floral patterns in invasive plants (χ2= 63.98,df= 32,P< 0.001), whereas no significant variation was evidenced in the pollinator relationship among the ultraviolet floral patterns in non-invasive plants (χ2= 19.50,df= 24,P= 0.724). Analysis of pollinator preference revealed that invasive species were mostly pollinated by bee and butterfly mediated pollination, whereas non-invasive species were mostly pollinated by bees and generalist insects. Intraspecific variations in the floral ultraviolet signal were observed among different morphs in a few flower color polymorphic species, especially inLantana camara. The multispectral analysis of floral patterns revealed that plants utilize both the visible and ultraviolet spectrums to effectively communicate with pollinators. The results from the present study strongly suggest that the variation in the floral ultraviolet signature among invasive species might play a vital role in plant-pollinator interaction and invasion success.
Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection
Authors: Böhne Astrid , Fernández Rosa , Leonard Jennifer A. , McCartney Ann M. , McTaggart Seanna , Melo-Ferreira José , Monteiro Rita , Oomen Rebekah A. , Vinnere Pettersson Olga , Struck Torsten H.
Published: June 2023

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe’s eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA’s pan- European network. To demonstrate the community’s capability and capacity to realise ERGA’s ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA’s member base. SSP aims to aid participating researchers through i) establishing standards for and collecting of sample/ specimen metadata; ii) prioritisation of species for genome sequencing; and iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA’s high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.
Fungal phylogeny reconstructed using heterogeneous models reveals new placement of Microsporidia
Authors: Riquelme-Medina Ignacio , McInerney James O.
Published: June 2023

Fungi have significant impacts on global ecosystems, playing roles in organic matter decomposition, as disease agents, as well as having both positive and negative economic effects. Fungal evolutionary history remains partly unresolved with the presence on manyincertae sedisclades, lacking a robust placement on the fungal phylogenetic tree. Some of the more problematic groups whose placement remains unclear are the intracellular parasitesMicrosporidiaand Cryptomycota, both of whom have accelerated rates of nucleotide substitution and reduced genomes, which makes the resolution of these groups hard. In this project we used tree and data heterogeneous models, that can account for different substitution rates between different protein families as well as different parts of the phylogenetic tree, to reconstruct the phylogeny. We recovered a well-supported topology for much of the fungal phylogeny as well as a robust placement for bothMicrosporidiaand Cryptomycota, the former being rooted deeply within the fungi and the latter a placement on a sister branch to the fungi.
Comparable analysis of multiple DNA double-strand break repair pathways in CRISPR-mediated endogenous tagging
Authors: Tei Chiharu , Hata Shoji , Mabuchi Akira , Okuda Shotaro , Ito Kei K , Genova Mariya , Fukuyama Masamitsu , Yamamoto Shohei , Chinen Takumi , Toyoda Atsushi , Kitagawa Daiju
Published: June 2023

CRISPR-mediated endogenous tagging, utilizing the homology-directed repair (HDR) of DNA double-strand breaks (DSBs) with exogenously incorporated donor DNA, is a powerful tool in biological research. Inhibition of the non-homologous end joining (NHEJ) pathway has been proposed as a promising strategy for improving the low efficiency of accurate knock-in via the HDR pathway. However, the influence of alternative DSB repair pathways on gene knock-in remains to be fully explored. In this study, our long-read amplicon sequencing analysis reveals various patterns of imprecise repair in CRISPR/Cas-mediated knock-in, even under conditions where NHEJ is inhibited. Suppression of the microhomology-mediated end joining (MMEJ) or the single strand annealing (SSA) repair mechanisms leads to a reduction in distinct patterns of imprecise repair, thereby elevating the efficiency of accurate knock-in. Furthermore, a novel reporter system shows that the SSA pathway contributes to a specific pattern of imprecise repair, known as asymmetric HDR. Collectively, our study uncovers the involvement of multiple DSB repair pathways in CRISPR/Cas-mediated gene knock-in and proposes alternative approaches to enhance the efficiency of precise gene knock-in.
High-Intensity Interval Training Attenuates Impairment in Regulatory Protein Machinery of Mitochondrial Quality Control in Skeletal Muscle of Diet-Induced Obese Mice
Authors: Tincknell James B. , Kugler Benjamin , Spicuzza Haley , Yan Huimin , You Tongjian , Zou Kai
Published: June 2023

Mitochondrial quality control processes are essential in governing mitochondrial integrity and function. The purpose of the study was to examine the effects of 10 weeks of HIIT on the regulatory protein machinery of skeletal muscle mitochondrial quality control and whole-body glucose homeostasis in diet-induced obese mice. Male C57BL/6 mice were randomly assigned to a low-fat diet (LFD) or high-fat diet (HFD) group. After 10 weeks, HFD-fed mice were divided into sedentary and HIIT (HFD+HIIT) groups and remained on HFD for another 10 weeks (n=9/group). Graded exercise test, glucose and insulin tolerance tests, mitochondrial respiration and regulatory protein markers of mitochondrial quality control processes were determined by immunoblots. Ten weeks of HIIT enhanced ADP-stimulated mitochondrial respiration in diet-induced obese mice (P < 0.05) but did not improve whole-body insulin sensitivity. Importantly, the ratio of Drp1(Ser616) over Drp1(Ser637) phosphorylation, an indicator of mitochondrial fission, was attenuated in HFD-HIIT compared to HFD (−35.7%, P < 0.05). Regarding autophagy, skeletal muscle p62 content was lower in HFD group than LFD group (−35.1%, P < 0.05), however, such reduction was disappeared in HFD+HIIT group. In addition, LC3B II/I ratio was higher in HFD than LFD group (15.5%, P < 0.05) but was ameliorated in HFD+HIIT group (−29.9%, P < 0.05). Overall, our study demonstrated that 10 weeks of HIIT was effective in improving skeletal muscle mitochondrial respiration and the regulatory protein machinery of mitochondrial quality control in diet-induced obese mice through the alterations of mitochondrial fission protein Drp1 activity and p62/LC3B-mediated regulatory machinery of autophagy.
Chromatin compaction and spatial organization in rice interphase nuclei
Authors: Doležalová Alžběta , Beránková Denisa , Koláčková Veronika , Hřibová Eva
Published: June 2023

Chromatin organization and its interactions are essential for biological processes such as DNA repair, transcription, and DNA replication. Detailed cytogenetics data on chromatin conformation, and the arrangement and mutual positioning of chromosome territories in interphase nuclei are still widely missing in plants. In this study, level of chromatin condensation in interphase nuclei of rice (Oryza sativa) and the distribution of chromosome territories (CTs) were analyzed. Super-resolution, stimulated emission depletion (STED), microscopy showed different level of chromatin condensation in leaf and root interphase nuclei. 3D immuno-FISH experiments with painting probes specific to chromosomes 9 and 2 were conducted to investigate their spatial distribution in root and leaf nuclei. Six different configurations of chromosome territories, including their complete association, weak association, and complete separation, were observed in root meristematic nuclei, and four configurations were observed in leaf nuclei. The volume of CTs and frequency of their association varied between the tissue types. The frequency of association of CTs specific to chromosome 9, containing NOR region, is also affected by the activity of the 45S rDNA locus. Our data suggested that the arrangement of chromosomes in the nucleus is connected to the position and the size of the nucleolus.

Highlight

Super-resolution STED microscopy uncovered detailed chromatin ultrastructure; high level of differences in chromatin condensation and mutual positioning of chromosome territories between and within leaf and root meristem G1 were observed.
Discovering Matrix Adducts for Enhanced Metabolite Profiling with Stable Isotope-Labeled MALDI-MSI
Authors: Baquer Gerard , Bernús Miguel , Sementé Lluc , van Zeijl René , García-Altares Maria , Heijs Bram , Boutureira Omar , Correig Xavier , Ràfols Pere
Published: June 2023

Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) is a widely used technique for spatial metabolomics analysis, but the matrix introduces spectral interferences that impede data processing. In this study, we present an experimental and computational workflow utilizing isotopic labeling to discover and annotate matrix adducts in MALDI-MSI. Our approach enables the removal of matrix-related signals, improving metabolite annotation accuracy, extending metabolome coverage, and facilitating the interpretation of tissue morphology.
AMF-SporeChipprovides new insights into arbuscular mycorrhizal fungal pre-symbiotic hyphal growth dynamics at the cellular level
Authors: Richter Felix , Calonne-Salmon Maryline , van der Heijden Marcel G. A. , Declerck Stéphane , Stanley Claire E.
Published: June 2023

Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants and deliver a wide range of soil-based ecosystem services. Due to their conspicuous belowground lifestyle in a dark environment surrounded by soil particles, much is still to be learned about the influence of environmental (i.e., physical) cues on spore germination, hyphal morphogenesis and hyphopodium formation in AMF.

To fill existing gaps in AMF knowledge, we developed a new microfluidic platform – termed theAMF-SporeChip– to immobiliseRhizophagusandGigasporaspores and confront pre-symbiotic hyphae with physical obstacles. In combination with timelapse microscopy, the fungi could be examined at the cellular level and in real-time.

TheAMF-SporeChipallowed us to acquire movies with unprecedented visual clarity and therefore identify various exploration strategies of AMF pre-symbiotic hyphae. We witnessed anastomosis formation involving directed hyphal growth in a “stop-and-go” manner, yielding visual evidence of pre-anastomosis signalling and decision-making. Remarkably, we also revealed a so-far undescribed reversible cytoplasmic retraction as part of a highly dynamic space navigation.

Our findings demonstrated how AMF employ an intricate mechanism of space searching, involving reversible cytoplasmic retraction, branching and directional changes. In turn, theAMF-SporeChipis expected to open many future frontiers for AMF research.
Global Diversity in Mammalian Life Histories: Environmental Realms and Evolutionary Adaptations
Authors: Beccari E. , Capdevila Lanzaco P. , Salguero-Gómez R. , Pérez Carmona C.
Published: June 2023

Mammalian life history strategies can be characterized by a few axes of variation, which conform a space where species are positioned according to which life history strategies are favoured in the environment they exploit. Yet, we still lack global descriptions of the diversity of realized mammalian life history and of how this diversity is shaped by the environment. We used six life history traits to build a global life history space and explored how major environmental realms (land, air, water) influence mammalian life history strategies. We demonstrate that realms are tightly linked to distinct life history strategies. Predominantly, aquatic and aerial species adhere to slower life history strategies, while terrestrial species tend to exhibit faster life histories. Highly encephalized terrestrial species are a notable exception to these patterns. In addition, species transitioning between the terrestrial and aquatic realms, such as seals, show intermediate life history strategies. Further, different mode-of-life may play a significant role in allowing to expand the set of strategies exploitable in the terrestrial realm. Our results provide compelling evidence of the link between environmental realms and the diversity of life history strategies among mammals.

Statement of authorship

P.C.L., R.S-G., and C.P.C. conceived the core ideas behind this paper, all authors provided fundamental inputs for its final development. E.B collected all data and performed the literature search needed to sort species in environmental realms. E.B. analysed the data with fundamental inputs from C.P.C., P.C.L, and R.G-S. All authors contributed to interpretation of the results. E.B. and C.P.C. led the writing of the manuscript which was edited by all authors.
Standing genetic variation andde novomutations underlie parallel evolution of island bird phenotypes
Authors: Estandía Andrea , Sendell-Price Ashley T. , Robertson Bruce C. , Clegg Sonya M.
Published: June 2023

Parallel evolution occurs when the same trait evolves in closely related lineages in response to similar ecological contexts and provides some of the best examples of determinism in evolutionary biology. However, from a genetic standpoint, this process can be driven by either new mutations that appear independently in each diverging population or by selection on existing genetic variation common to both lineages. Small-bodied birds, for example, tend to increase in size after they colonise a new island, following what is known as the ‘island rule’. Such is the case of the silvereye (Zosterops lateralis), a prolific natural coloniser of southwest Pacific islands. Island forms of this bird species increase in body size after they establish, with the pattern and pace of change consistent with directional natural selection and evident even in the most recent colonisations within the last 200 years. The system provides an exceptional opportunity to explore the genomic basis of repeated body size evolution. We sequenced 377 whole genomes from 31 different silvereye populations, which revealed that both mechanisms are at play: in some lineages, new mutations are highly associated with body and bill size, but there are also highly associated polymorphisms present across all populations. Our research sheds light on the genomic basis of repeated body size evolution and emphasises that multiple molecular mechanisms can underlie similar evolutionary trajectories even within a single taxon.
Theoretical validation of growth curves for quantifying phage-bacteria interactions
Authors: Blazanin Michael , Vasen Emma , Jolis Cèlia Vilaró , An William , Turner Paul E.
Published: June 2023

Bacteria-infecting viruses, bacteriophages, are the most abundant biological entities on the planet, frequently serving as model systems in basic research and increasingly relevant for medical applications such as phage therapy. A common need is to quantify the infectivity of a phage to a given bacterial host (or the resistance of a host to a phage). However, current methods to quantify infectivity suffer from low-throughput or low-precision. One method that has the potential for high-throughput and high-precision quantification of phage-bacteria interactions is growth curves, where bacterial density is measured over time in the presence and absence of phages. Recent work has proposed several approaches to quantify these curves into a metric of phage infectivity. However, little is known about how these metrics relate to one another or to underlying phage and bacterial traits. To address this gap, we apply ecological modeling of phage and bacterial populations to simulate growth curves across a wide range of trait values. Our findings show that many growth curve metrics provide parallel measures of phage infectivity. Informative metrics include the peak and decline portions of bacterial growth curves, are driven by the interactions between underlying phage and bacterial traits, and correlate with conventional measures of phage fitness. Moreover, we show how intrapopulation trait variation can alter growth curve dynamics. Finally, we test the sensitivity of growth curve metrics to inoculum densities, and assess techniques to compare growth curves across different bacterial hosts. In all, our findings support the use of growth curves for precise high-throughput quantification of phage-bacteria interactions across the microbial sciences.

Significance

Bacteriophages are viruses that infect bacteria. Phages have long been laboratory models and are increasingly being explored as antimicrobials. Commonly, we need to quantify how well a phage infects a bacterial strain. Unfortunately, current methods are either laborious or imprecise. One method that could be better is growth curves, where bacterial growth is measured over time in the presence or absence of phages. However, it has remained unclear how to use such data to produce a single metric of phage infectivity. Here, we used simulations to show that many different metrics provide parallel measures of phage infectivity that match conventional measures across a range of conditions. Our work suggests that growth curves can provide rapid, precise measurement of phage infectivity.